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All Classes All Packages

A

a() - Static method in class org.biojava.bio.seq.DNATools
 
a() - Static method in class org.biojava.bio.seq.NucleotideTools
 
a() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Alanine
a() - Static method in class org.biojava.bio.seq.RNATools
 
A_THALIANA - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
AA indicates that a sequence contains AA (amino acid) symbols.
AAindex - Class in org.biojava.bio.proteomics.aaindex
Symbol property table based on the Amino Acid Index Database.
AAindex(String) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindex
Initializes the AAindex symbol property table.
AAindexStreamReader - Class in org.biojava.bio.proteomics.aaindex
Iterator over AAindex objects that are stored in a stream in the AAindex1 file format.
AAindexStreamReader(BufferedReader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
Initializes the iterator.
AAindexStreamReader(Reader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
Initializes the iterator.
ABBREV_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
abbreviation - Variable in class org.biojava.bibliography.BiblioJournal
An abbreviation of the journal title.
ABI_MAGIC - Static variable in class org.biojava.bio.chromatogram.ChromatogramFactory
The magic number for ABIF files.
ABIFChromatogram - Class in org.biojava.bio.program.abi
An implementation of Chromatogram to encapulsulate chromatogram data extracted from the files produced by ABI sequencers, such as the the 377 and the 3700.
ABIFChromatogram() - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram
 
ABIFChromatogram.Parser - Class in org.biojava.bio.program.abi
An extension of ABIFParser that reads the particular fields from the ABIF that contain the chromatogram data and initializes the fields in its enclosing ABIFChromatogram instance.
ABIFParser - Class in org.biojava.bio.program.abi
A general base parser for files produced by ABI software.
ABIFParser(File) - Constructor for class org.biojava.bio.program.abi.ABIFParser
Creates a new ABIFParser for a file.
ABIFParser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFParser
Creates a new ABIFParser for an input stream.
ABIFParser(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser
Creates a new ABIFParser for the specified ABIFParser.DataAccess object.
ABIFParser.DataAccess - Interface in org.biojava.bio.program.abi
Concatenation of the Seekable and DataInput interfaces.
ABIFParser.TaggedDataRecord - Class in org.biojava.bio.program.abi
An aggregate immutable type for an ABIF tagged data record.
ABITools - Class in org.biojava.bio.program.abi
Useful functionality for working with fasta files where the quality of the DNA is encoded as upper and lower case DNA characters.
ABITools() - Constructor for class org.biojava.bio.program.abi.ABITools
 
ABITrace - Class in org.biojava.bio.program.abi
Title: ABITrace

ABITrace is a class for managing ABI file information, it is capable of opening an ABI file and storing the most important fields, which can be recalled as simple java types.
ABITrace(byte[]) - Constructor for class org.biojava.bio.program.abi.ABITrace
The byte[] constructor parses an ABI file represented as a byte array.
ABITrace(File) - Constructor for class org.biojava.bio.program.abi.ABITrace
The File constructor opens a local ABI file and parses the content.
ABITrace(URL) - Constructor for class org.biojava.bio.program.abi.ABITrace
The URL constructor opens an ABI file from any URL.
AbiTraceRenderer - Class in org.biojava.bio.gui.sequence
Renders an ABI trace file as a chromatogram graph.
AbiTraceRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
ABORT_PARSING - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
 
AbortErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
Abstract() - Constructor for class org.biojava.bio.AnnotationType.Abstract
 
Abstract() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
 
Abstract() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
Abstract(String) - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
Construct a block with a given name.
Abstract(NexusBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
AbstractAlignmentStyler - Class in org.biojava.bio.program.blast2html
Abstract implementation of AlignmentStyler, contains utility methods for generating a set of HTML styles from a list of RGB colours.
AbstractAlignmentStyler() - Constructor for class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
 
AbstractAlphabet - Class in org.biojava.bio.symbol
An abstract implementation of Alphabet.
AbstractAlphabet() - Constructor for class org.biojava.bio.symbol.AbstractAlphabet
 
AbstractAnnotation - Class in org.biojava.bio
A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
AbstractAnnotation() - Constructor for class org.biojava.bio.AbstractAnnotation
Protected no-args constructor intended for sub-classes.
AbstractAnnotation(Map) - Constructor for class org.biojava.bio.AbstractAnnotation
Create a new Annotation by copying the key-value pairs from a map.
AbstractAnnotation(Annotation) - Constructor for class org.biojava.bio.AbstractAnnotation
Copy-constructor.
AbstractBeadRenderer - Class in org.biojava.bio.gui.sequence
AbstractBeadRenderer is a an abstract base class for the creation of FeatureRenderers which use a 'string of beads' metaphor for displaying features.
AbstractBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Creates a new AbstractBeadRenderer with no delegates.
AbstractBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Creates a new AbstractBeadRenderer object.
AbstractBioEntryDB - Class in org.biojavax.bio.db
An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.
AbstractBioEntryDB() - Constructor for class org.biojavax.bio.db.AbstractBioEntryDB
 
AbstractChangeable - Class in org.biojava.utils
Useful base-class for objects implementing Changeable
AbstractChangeable() - Constructor for class org.biojava.utils.AbstractChangeable
 
AbstractChromatogram - Class in org.biojava.bio.chromatogram
A basic, abstract implementation of Chromatogram.
AbstractChromatogram() - Constructor for class org.biojava.bio.chromatogram.AbstractChromatogram
Create a new AbstractChromatogram.
AbstractCrossOverFunction - Class in org.biojavax.ga.functions
Abstract implementation of CrossOverFunction.
AbstractCrossOverFunction() - Constructor for class org.biojavax.ga.functions.AbstractCrossOverFunction
 
AbstractDistribution - Class in org.biojava.bio.dist
An abstract implementation of Distribution.
AbstractDistribution() - Constructor for class org.biojava.bio.dist.AbstractDistribution
 
AbstractFeatureHolder - Class in org.biojava.bio.seq
An abstract implementation of FeatureHolder.
AbstractFeatureHolder() - Constructor for class org.biojava.bio.seq.AbstractFeatureHolder
 
AbstractGeneticAlgorithm - Class in org.biojavax.ga.impl
Base class from which most implementations of GeneticAlgorithm will inherit.
AbstractGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
AbstractLocation - Class in org.biojava.bio.symbol
An abstract implementation of Location.
AbstractLocation() - Constructor for class org.biojava.bio.symbol.AbstractLocation
 
AbstractLocationDecorator - Class in org.biojava.bio.symbol
Abstract Location decorator (wrapper).
AbstractLocationDecorator(Location) - Constructor for class org.biojava.bio.symbol.AbstractLocationDecorator
Construct a new decorator wrapping the specified Location.
AbstractManyToOneTranslationTable - Class in org.biojava.bio.symbol
an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractManyToOneTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
 
AbstractMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
 
AbstractMatrixPairDPCursor(SymbolList, SymbolList, int, int, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
AbstractMutationFunction - Class in org.biojavax.ga.functions
Abstract implementation of MutationFunction all custom implementations should inherit from here.
AbstractMutationFunction() - Constructor for class org.biojavax.ga.functions.AbstractMutationFunction
 
AbstractOrderNDistribution - Class in org.biojava.bio.dist
Simple base class for OrderNDistributions.
AbstractOrderNDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.AbstractOrderNDistribution
Construct a new NthOrderDistribution.
AbstractOrganism - Class in org.biojavax.ga.impl
Abstract implementation of Organism.
AbstractOrganism() - Constructor for class org.biojavax.ga.impl.AbstractOrganism
 
AbstractOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.AbstractOrganism
 
AbstractOrthologueSet - Class in org.biojava.bio.program.homologene
 
AbstractOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthologueSet
 
AbstractOrthoPairCollection - Class in org.biojava.bio.program.homologene
An abstract implementation of the OrthoPairCollection interface.
AbstractOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
 
AbstractOrthoPairSet - Class in org.biojava.bio.program.homologene
represents the Homologene Group.
AbstractOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairSet
 
AbstractPeptideDigestRenderer - Class in org.biojava.bio.gui.sequence
A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.
AbstractPeptideDigestRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
AbstractPeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
AbstractPopulation - Class in org.biojavax.ga.impl
Most Population implementations will want to inherit from here.
AbstractPopulation() - Constructor for class org.biojavax.ga.impl.AbstractPopulation
 
AbstractPopulation(String) - Constructor for class org.biojavax.ga.impl.AbstractPopulation
 
AbstractRangeLocation - Class in org.biojava.bio.symbol
Base class for simple contiguous Location implementations.
AbstractRangeLocation() - Constructor for class org.biojava.bio.symbol.AbstractRangeLocation
 
AbstractReversibleTranslationTable - Class in org.biojava.bio.symbol
an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractReversibleTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractReversibleTranslationTable
 
AbstractRichSequenceDB - Class in org.biojavax.bio.db
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
AbstractRichSequenceDB() - Constructor for class org.biojavax.bio.db.AbstractRichSequenceDB
 
AbstractSequenceDB - Class in org.biojava.bio.seq.db
An abstract implementation of SequenceDB that provides the sequenceIterator method.
AbstractSequenceDB() - Constructor for class org.biojava.bio.seq.db.AbstractSequenceDB
 
AbstractSVMClassifierModel - Class in org.biojava.stats.svm
Abstract implementation of SVMClassifierModel.
AbstractSVMClassifierModel() - Constructor for class org.biojava.stats.svm.AbstractSVMClassifierModel
 
AbstractSVMTarget - Class in org.biojava.stats.svm
An abstract implementation of an SVMModel.
AbstractSVMTarget() - Constructor for class org.biojava.stats.svm.AbstractSVMTarget
 
AbstractSymbol - Class in org.biojava.bio.symbol
The base-class for Symbol implementations.
AbstractSymbol() - Constructor for class org.biojava.bio.symbol.AbstractSymbol
 
AbstractSymbolList - Class in org.biojava.bio.symbol
Abstract helper implementation of the SymbolList core interface.
AbstractSymbolList() - Constructor for class org.biojava.bio.symbol.AbstractSymbolList
 
AbstractSymbolList.EditScreener - Class in org.biojava.bio.symbol
This adapter screens all edit events to see if they overlap with a window of interest.
AbstractSymbolList.EditTranslater - Class in org.biojava.bio.symbol
This translates edit events that fall within a window into window co-ordinates.
AbstractTaxon - Class in org.biojava.bio.taxa
Deprecated.
replaced by classes in org.biojavax.bio.taxa
AbstractTaxon() - Constructor for class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
AbstractTaxon(String, String) - Constructor for class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
AbstractTerm - Class in org.biojava.ontology
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
AbstractTerm() - Constructor for class org.biojava.ontology.AbstractTerm
 
AbstractTrainer - Class in org.biojava.bio.dp
An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.
AbstractTrainer() - Constructor for class org.biojava.bio.dp.AbstractTrainer
 
AbstractTrainer(DP) - Constructor for class org.biojava.bio.dp.AbstractTrainer
 
abstractType - Variable in class org.biojava.bibliography.BiblioDescription
It specifies how BiblioDescription.theAbstract is coded.
AbstractULAlignment - Class in org.biojava.bio.alignment
 
AbstractULAlignment() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment
 
AbstractULAlignment.LeftRightLocationComparator<T> - Class in org.biojava.bio.alignment
Orders by location left to right.
AbstractULAlignment.SubULAlignment - Class in org.biojava.bio.alignment
 
AbstractWrapper - Class in org.biojava.bio.program.tagvalue
An abstract TagValueWrapper that does nothing!
AbstractWrapper() - Constructor for class org.biojava.bio.program.tagvalue.AbstractWrapper
 
ACC_ABSTRACT - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_FINAL - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_INTERFACE - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_NATIVE - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_PRIVATE - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_PROTECTED - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_PUBLIC - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_STATIC - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_STRICT - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_SUPER - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_SYNCHRONIZED - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_TRANSIENT - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
ACC_VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
ACC_VOLATILE - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
 
accept() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter
returns a TriState indicating the current outcome of evaluating this filter.
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.And
 
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
 
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Or
 
accept(Object) - Method in interface org.biojava.bio.CollectionConstraint
accept returns true if the value fulfills the constraint.
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.And
 
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
 
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Or
 
accept(Object) - Method in interface org.biojava.bio.PropertyConstraint
accept returns true if the value fulfills the constraint.
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.And
 
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
 
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByClass
 
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
 
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
 
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Or
 
accept(Object) - Method in interface org.biojava.bio.search.FilterTest
 
accept(Object) - Method in class org.biojava.bio.search.FilterTest.Equals
 
accept(Object) - Method in class org.biojava.bio.search.FilterTest.FindRegex
 
accept(Object) - Method in class org.biojava.bio.search.FilterTest.GreaterThan
 
accept(Object) - Method in class org.biojava.bio.search.FilterTest.LessThan
 
accept(Object) - Method in class org.biojava.bio.search.FilterTest.MatchRegex
 
accept(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFRecordFilter
Return whether or not to accept record.
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
 
accept(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueFilter
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.And
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Not
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Or
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Xor
 
accept(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairFilter
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.And
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Not
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Or
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Xor
 
accept(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairSetFilter
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor
 
accept(Feature) - Method in interface org.biojava.bio.seq.FeatureFilter
This method determines whether a feature is to be accepted.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.And
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
Accept a Feature if it is an instance of SimilarityPairFeature and its score is <= filter's minimum score and >= filter's maximum score.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
Accept the Feature if it is an instance of FramedFeature and matches the value of getFrame().
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Not
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
Accept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
Returns true if the feature has a matching source property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
Returns true if the feature has a matching source property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
Returns true if the feature overlaps this filter's location.
ACCEPT_ALL - Static variable in interface org.biojava.bio.program.gff.GFFRecordFilter
A GFFRecordFilter that accepts everything.
AcceptAll() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
 
AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
 
AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
 
AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
 
AcceptAll() - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
 
ACCESSION - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
accessionNumber() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Gets the accession number of the AAindex entry.
AcnumHitReader - Class in org.biojava.bio.seq.db.emblcd
AcnumHitReader reads the "acnum.hit" file of an EMBL CD-ROM format binary index.
AcnumHitReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumHitReader
Creates a new AcnumHitReader.
AcnumTrgReader - Class in org.biojava.bio.seq.db.emblcd
AcnumTrgReader reads the "acnum.trg" file of an EMBL CD-ROM format binary index.
AcnumTrgReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumTrgReader
Creates a new AcnumTrgReader.
ACRONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
Use this to define acronyms for things.
ACRONYM - Static variable in interface org.biojavax.Namespace
 
activityFailed(Object, Exception) - Method in interface org.biojava.utils.ActivityListener
Notification of errors behind the scenes.
ActivityListener - Interface in org.biojava.utils
Interface for object which monitor long-running activities.
activityProgress(Object, int, int) - Method in interface org.biojava.utils.ActivityListener
Estimated progress of an activity.
add(int, CodeGenerator) - Method in class org.biojava.utils.bytecode.InstructionVector
 
add(Object) - Method in class org.biojava.utils.FileAsList
 
add(Object) - Method in class org.biojava.utils.MergingSet
 
add(Object) - Method in class org.biojava.utils.SmallSet
 
add(Object) - Method in class org.biojavax.ga.util.WeightedSet
Adds a new Object with a weight of zero.
add(String) - Method in class org.biojava.bio.program.gff.GFFEntrySet
Add a comment to the end of this set.
add(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFEntrySet
Add a GFFRecord to the end of this set.
add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
 
add(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
 
add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
 
add(CodeGenerator) - Method in class org.biojava.utils.bytecode.InstructionVector
 
ADD_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
 
addAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
 
addAllFeatures(Sequence, FeatureHolder) - Static method in class org.biojava.bio.seq.SequenceTools
Add features to a sequence that contain the same information as all those in a feature holder.
addAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation
Add a new Annotation to to the end of the list to be merged.
addAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
Add a DB to be merged in this view.
addBioEntry(String, BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
 
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
 
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
addBioEntry(BioEntry) - Method in interface org.biojavax.bio.db.BioEntryDBLite
Adds a sequence to the database.
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
 
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
Add a BioEntry, the name of the BioEntry will be used as the ID
addBottomConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
Add a configuration as the most default place to look.
addChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Add a ChangeListener to a projected feature.
addChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addChangeListener adds a listener for all types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
addChangeListener adds a listener for all types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
addChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
 
addChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable
Deprecated.
use addChangeListener(cl, ChangeType.UNKNOWN)
addChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport
Add a listener that will be informed of all changes.
addChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
 
addChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Add a listener that will be informed of all changes.
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addChangeListener adds a listener for specific types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
addChangeListener adds a listener for specific types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
 
addChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable
Add a listener that will be informed of changes of a given type.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport
Add a listener that will be informed of changes of a given type (and it's subtypes)
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Add a listener that will be informed of changes of a given type.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
addCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addCharLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addCharState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addCharState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addCharState(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addCharStateKeyword(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addCharStateKeyword(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addCharStateKeyword(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
Deprecated.
 
addChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
Deprecated.
Add a taxon as a child to a parent.
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
Deprecated.
 
addCluster(UnigeneCluster) - Method in interface org.biojava.bio.program.unigene.UnigeneDB
Add a cluster to a database.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
Tell the builder to add the given comment at the current location.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
 
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
 
addComment(Comment) - Method in interface org.biojavax.bio.BioEntry
Adds a comment instance to this bioentry.
addComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry
Adds a comment instance to this bioentry.
addCommentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
 
addComponentSequence(ComponentFeature.Template) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
 
addCount(Distribution, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Registers that sym was counted in this state.
addCount(Distribution, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
Registers that sym was counted in this state.
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
 
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
 
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
Deprecated.
 
addCount(State, State, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
Add 'count' to the transition from->to.
addDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
Add a distributed data source.
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
 
addDbId(AGAVEDbId) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf
 
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
 
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
 
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
 
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
 
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
 
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
add @param id
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
 
addDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple
Adds a descriptor.
addDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple
Adds a descriptor.
addDetailHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
Extend this FeatureSetHandler to delegate certain detail elements to the specified handler type.
addDigestFeatures() - Method in class org.biojava.bio.proteomics.Digest
Adds peptides as features to the Sequence in this class.
addElementId(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf
 
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
 
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
 
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
 
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
 
addEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper
addEnzyme adds an enzyme to be searched for in the Sequence.
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
Add a silent optimisable transition to instance.
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
 
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
 
addEquate(String, List) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addEquate(String, List) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addEquate(String, List) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addExceptionTableEntry(Label, Label, CodeClass, Label) - Method in interface org.biojava.utils.bytecode.CodeContext
Add an exception table entry.
addFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
Add a feature to the featureholder
addFeatureHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
Extend this FeatureSetHandler to delegate certain feature elements to the specified handler type.
addFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder
Add an extra FeatureHolder to the set of FeatureHolders which are merged.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
addFeatureProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener
Notify the listener of a feature property.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
Add an annotation-bundle entry to the feature.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Null implementation
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Notify the listener of a feature property.
addFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
Adds a relationship to this feature holder.
addFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Adds a relationship to this feature holder.
addFeatureToSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
addFile(File) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
Add sequences from a file to the sequence database.
addFile(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
 
addFilterAndGlyph(FeatureFilter, Glyph) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
 
addForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
 
addGapInSource(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
Add a gap at pos within the source coordinates.
addGapInSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
addGapInView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
Add a single gap at pos within the view coordintates.
addGapInView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
addGapsInSource(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
Add length gaps at pos within the source coordinates.
addGapsInSource(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
addGapsInView(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
Add length gaps at pos within the view coordinates.
addGapsInView(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
 
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
 
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
 
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
Adds a feature to the Handler attribute of the StAXFeatureHandler object
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
 
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
 
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
 
addHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
The addHitProperty method adds a key/value pair containing some property of a particular hit.
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
addHotSpot(ImageMap.HotSpot) - Method in interface org.biojava.bio.gui.sequence.ImageMap
addHotSpot adds a hotspot to the map.
addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide
 
addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide
 
addIdAlias(AGAVEIdAlias) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
 
addIdAlias(AGAVEIdAlias) - Method in interface org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf
 
addImplementation(Class, Class) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer
Install a new mapping from a class of Feature.Template to a class of Feature implementations.
addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
addItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
addItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
 
addItem(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addItem(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addItem(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
addItemAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
addItemTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
 
addKey(String, int) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
addKey adds a new identifier namespace.
addKeyPath(String, Object[]) - Method in class org.biojava.bio.program.tagvalue.Index2Model
Add a key and a path to that key in the tag-value hierachy.
addLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
Add a piece of text to this renderer's label
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
Add a silent persistent transition to instance.
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
 
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
 
addListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub
add a ChangeListener associated with given key.
addListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub
 
addMapPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
 
addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addMatrixEntry(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
addMatrixEntry(String) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
 
addName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
Adds the name to this taxon in the given name class.
addName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Adds the name to this taxon in the given name class.
addName(Connection, Taxon, String, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Adds a new name of the given nameClass to the taxon.
addNeg(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
 
addNode(boolean) - Method in class org.biojava.utils.automata.FiniteAutomaton
Add a node to the FA.
addNode(boolean) - Method in interface org.biojava.utils.automata.NfaBuilder
 
addNode(boolean) - Method in class org.biojava.utils.automata.NfaSubModel
 
addNote(Note) - Method in class org.biojavax.EmptyRichAnnotation
Adds a note to this annotation.
addNote(Note) - Method in interface org.biojavax.RichAnnotation
Adds a note to this annotation.
addNote(Note) - Method in class org.biojavax.SimpleRichAnnotation
Adds a note to this annotation.
addObject(NexusObject) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
Appends an object to the end of the file.
addOboFileEventListener(OboFileEventListener) - Method in class org.biojava.ontology.obo.OboFileParser
 
addOntology(Ontology) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
addOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
addOrganism(Organism) - Method in interface org.biojavax.ga.Population
Adds an Organism to the Population
addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation
 
addOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
addOrganisms(Set) - Method in interface org.biojavax.ga.Population
Adds several organisms to the population
addOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
addOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population
Adds several organisms to the population
addOrganisms(Population) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
addOrganisms(Population) - Method in interface org.biojavax.ga.Population
Adds the residents of one population to this one
addOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
Add an orthologue to the set.
addOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
 
addOrthologueProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
add a property to the current Orthologue
addOrthologueProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
addOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
adds a specified OrthoPair relationship to this group.
addOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
addOrthoPairProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
add a property to the current OrthoPair
addOrthoPairProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat
Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource
Adds a parse error listener to the list of listeners.
addPattern(String) - Method in class org.biojava.utils.automata.PatternBlitz
add the specified regex to the patterns used for searching.
addPattern(String, boolean) - Method in class org.biojava.utils.regex.Search
add a search pattern to the searches to be conducted by this object.
addPattern(String, String, boolean) - Method in class org.biojava.utils.regex.Search
add a search pattern to the searches to be conducted by this object.
addPos(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
 
addPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
 
addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
 
addProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType
Add a value to the specified property slot.
addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
 
addProperty(AGAVEProperty) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf
 
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
 
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
 
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
 
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
Deprecated.
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
 
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry
Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm
Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable
Adds a ranked cross reference to the existing set.
addRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry
Adds a ranked docref instance to this bioentry.
addRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry
Adds a ranked docref instance to this bioentry.
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
 
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
 
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
 
addRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry
Adds a relation instance to this bioentry.
addRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry
Adds a relation instance to this bioentry.
addRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR
 
addRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
 
addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
addRenderer adds a renderer.
addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
addRenderer adds a renderer as a new track.
addRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes
Add a repository to FeatureTypes.
addRequest(Runnable) - Method in class org.biojava.utils.SimpleThreadPool
 
addRequest(Runnable) - Method in interface org.biojava.utils.ThreadPool
addRequest requests that a Runnable be scheduled to be run by one of the threads in the pool.
addRichSequence(String, RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
 
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
Add a sequence.
addRichSequence(RichSequence) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
Adds a sequence to the database.
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
 
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
 
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
 
addSearchProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
The addSearchProperty method adds a key/value pair containing some property of the overall search result.
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
addSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
Add a secondary key.
addSequence(String, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
Add a sequence into the tree.
addSequence(String, Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
Add a sequence under a particular id.
addSequence(AlignmentElement) - Method in interface org.biojava.bio.alignment.ARAlignment
 
addSequence(AlignmentElement) - Method in class org.biojava.bio.alignment.FlexibleAlignment
add a new a alignment usings a location to the reference sequence.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
 
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
 
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.DummySequenceDB
 
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
addSequence always throws a ChangeVetoException as this implementation is immutable.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
addSequence(Sequence) - Method in interface org.biojava.bio.seq.db.SequenceDBLite
Adds a sequence to the database.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.WebSequenceDB
Not supported, You can't add sequences to a WebDB!
addSequence(Sequence) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
addSequence(Sequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
addSequenceDB(String, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
This method creates a new (and empty) HashSequenceDB with the given name that will be accessible through this sequence db installation through this name and all given other identifiers.
addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
As this is a dummy implementation adding a sequenceDB doesn't do anything
addSequenceDB(SequenceDBLite, Set) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
addSequenceDB adds a new SequenceDB under its own identifier which will additionally be recognised by the set of other identifiers.
addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
addSequenceDB adds a new SequenceDB which will be accessible via the name returned by its getName() method and via all other given identifiers.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblProcessor
Deprecated.
 
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser
Deprecated.
 
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankProcessor
Deprecated.
 
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.OrganismParser
Deprecated.
 
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
addSequenceProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener
Notify the listener of a sequence-wide property.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
Add an annotation-bundle entry to the sequence.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Notify the listener of a sequence-wide property.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
Deprecated.
 
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Notify the listener of a sequence-wide property.
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addSequenceViewerListener adds a listener for mouse click SequenceViewerEvents.
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
 
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
addSequenceViewerListener adds a listener for mouse click SequenceViewerEvents.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addSequenceViewerMotionListener adds a listener for mouse motion SequenceViewerEvents.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
 
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
addSequenceViewerMotionListener adds a listener for mouse motion SequenceViewerEvents.
addSet(Set) - Method in class org.biojava.utils.MergingSet
 
addState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addState(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addState(State) - Method in interface org.biojava.bio.dp.MarkovModel
Adds a state to the model.
addState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
addState(State) - Method in class org.biojava.bio.dp.WMAsMM
 
addStateLabel(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addStateLabel(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addStateLabel(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addStyle(String, String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
Add a colour style to this Styler.
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
 
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
 
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
 
addSubHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
addSymbol(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addSymbol(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addSymbol(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
addSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet
Adds a symbol to this alphabet.
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolList
Add a new Symbol to the end of this list.
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
SoftMaskedAlphabets cannot add new Symbols.
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
addSymbolList(SymbolList, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
tool to construct the SymbolList by adding Symbols.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
Deprecated.
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
addSymbols(Alphabet, Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SeqIOListener
Notify the listener of symbol data.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
does nothing for now.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleSequenceBuilder
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SmartSequenceBuilder
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Prints out the sequences properties in order.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Notify the listener of symbol data.
addSymbols(SymbolList, int) - Method in class org.biojava.bio.symbol.SuffixTree
Add a count for all motifs with length of up to window to this tree.
addSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
addSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl
 
addSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl
 
addSynonym(Object) - Method in interface org.biojava.ontology.Term
Add a synonym for this term.
addSynonym(Object) - Method in class org.biojava.ontology.Term.Impl
 
addSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl
 
addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
Add a synonym for this term.
addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
Add a synonym for this term.
addTable(SymbolPropertyTable) - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
Adds a symbol property table to the database.
addTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
Add a tag to retain.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Add a TAXLABEL.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addTaxLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
Add a TAXLABEL.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Add a TAXLABEL.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
addTaxLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
Add a TAXLABEL.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Add a TAXLABEL.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
 
addTaxLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.TaxaBlockListener
Add another value after the TAXLABEL tag.
addThrownException(CodeClass) - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
Adds a feature to the ThrownException attribute of the GeneratedCodeMethod object
addTitle(int, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
add title information to an Orthologue (this is not in enclosed in the Orthologue element because it comes completely separate in the Homologene data files.
addTitle(int, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
addToCache(String, File) - Static method in class org.biojava.utils.io.FlatFileCache
 
addToEnvironment(String, Object) - Method in class org.biojava.naming.ObdaContext
 
addTopConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
Add a configuration as the most authoritative place to look.
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
 
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in interface org.biojava.utils.automata.NfaBuilder
 
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.NfaSubModel
 
addTranslation(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Add a translation.
addTranslation(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
 
addTranslation(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.TreesBlockListener
Add a translation.
addTree(String, TreesBlock.NewickTreeString) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Adds a tree.
addTree(String, TreesBlock.NewickTreeString) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
 
addTree(String, TreesBlock.NewickTreeString) - Method in interface org.biojavax.bio.phylo.io.nexus.TreesBlockListener
Adds a tree.
addTree(String, WeightedGraph<String, DefaultWeightedEdge>) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Deprecated. 
addTree(String, WeightedGraph<String, DefaultWeightedEdge>, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Add a tree, converting weighted graph (JGraphT) to NewickString.
addTypeWithParent(Class) - Method in class org.biojava.utils.walker.WalkerFactory
Register a type as being a 'container' class.
addVariableModification(char, double[]) - Method in class org.biojava.bio.proteomics.MassCalc
Add Variable modifications.
addVariableModification(Symbol, double[]) - Method in class org.biojava.bio.proteomics.MassCalc
Add Variable modifications.
addVector(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
addVector(Object, double, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
addXMLCollectionConstraintWriter(Class, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
Register a writer for the specified class of collection constraint
addXMLCollectionConstraintWriter(CollectionConstraint, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
Register a writer for a singleton property constraint.
addXMLFilterWriter(Class, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
Add a writer for the specified class of filters
addXMLFilterWriter(FeatureFilter, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
Add a writer for a singleton filter.
addXMLPropertyConstraintWriter(Class, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
Register a writer for the specified class of property constraint
addXMLPropertyConstraintWriter(PropertyConstraint, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
Register a writer for a singleton property constraint.
addXref(AGAVEXref) - Method in interface org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf
 
addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
add @param xref
addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
 
advance() - Method in interface org.biojava.bio.dp.MarkovModel
The maximum advance for this model.
advance() - Method in interface org.biojava.bio.dp.onehead.DPCursor
Advance.
advance() - Method in class org.biojava.bio.dp.onehead.SmallCursor
 
advance() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
advance() - Method in class org.biojava.bio.dp.WMAsMM
 
ADVANCE - Static variable in interface org.biojava.bio.dp.EmissionState
This signals that the advance array has been altered.
affiliation - Variable in class org.biojava.bibliography.BiblioPerson
Their affiliation.
AGAVE_AGAVE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
AGAVE_ALT_IDS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
 
AGAVE_ANNOTATIONS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler
 
AGAVE_ASSEMBLY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler
 
AGAVE_BIO_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
AGAVE_BIO_SEQUENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
 
AGAVE_CDS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECdsHandler
 
AGAVE_CHROMOSOME_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
 
AGAVE_CLASSIFICATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
 
AGAVE_COMP_RESULT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
 
AGAVE_COMPUTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
 
AGAVE_CONTIG_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
 
AGAVE_DBID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
 
AGAVE_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
 
AGAVE_ELEMENT_ID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
 
AGAVE_EVIDENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
 
AGAVE_EXONS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler
 
AGAVE_FRAGMENT_ORDER_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
 
AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
 
AGAVE_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
 
AGAVE_ID_ALIAS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
 
AGAVE_KEYWORD_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
 
AGAVE_MAP_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
 
AGAVE_MAP_POSITION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
 
AGAVE_MATCH_ALIGN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
 
AGAVE_MATCH_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
 
AGAVE_MATCH_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
 
AGAVE_MRNA_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
 
AGAVE_NOTE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
 
AGAVE_PREDICTED_PROTEIN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
 
AGAVE_QUALIFIER_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
 
AGAVE_QUERY_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
 
AGAVE_RELATED_ANNOT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
 
AGAVE_RESULT_GROUP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
 
AGAVE_RESULT_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
 
AGAVE_SCI_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
 
AGAVE_SEQ_FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
 
AGAVE_SEQ_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
 
AGAVE_SEQ_MAP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
 
AGAVE_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
 
AGAVE_TRANSCRIPT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
 
AGAVE_UNORDERED_FRAGMENTS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler
 
AGAVE_VIEW_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
 
AGAVE_XREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
 
AGAVE_XREF_PROP_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
 
AGAVE_XREFS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
 
Agave2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave
Dumping the data from biojava with source of agave into agave format
AGAVEAltIdsPropHandler - Class in org.biojava.bio.seq.io.agave
Deals with alternate sequence IDs
AGAVEAnnotationsHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEAnnotFilter - Interface in org.biojava.bio.seq.io.agave
This interface defines mapping from BioJava into AGAVE format.
AGAVEAnnotFilterFactory - Interface in org.biojava.bio.seq.io.agave
 
AGAVEAssemblyHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEBioSeqCallbackItf - Interface in org.biojava.bio.seq.io.agave
An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEBioSeqHandler - Class in org.biojava.bio.seq.io.agave
Handles the AGAVE <bio_sequence> element
AGAVEBioSequenceHandler - Class in org.biojava.bio.seq.io.agave
Handles the AGAVE <bio_sequence> element
AGAVECallbackItf - Interface in org.biojava.bio.seq.io.agave
An interface that can be tested for by nested handlers when trying to do a callback.
AGAVECdsHandler - Class in org.biojava.bio.seq.io.agave
Handles the AGAVE <cds> element
AGAVEChromosomeCallbackItf - Interface in org.biojava.bio.seq.io.agave
An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEChromosomeHandler - Class in org.biojava.bio.seq.io.agave
Handles the AGAVE <chromosome> element
AGAVEClassificationHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVECompResultHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEComputationHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEContigCallbackItf - Interface in org.biojava.bio.seq.io.agave
An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEContigHandler - Class in org.biojava.bio.seq.io.agave
Handles the AGAVE <contig> element
AGAVEDbId - Class in org.biojava.bio.seq.io.agave
 
AGAVEDbId() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEDbId
 
AGAVEDbIdCallbackItf - Interface in org.biojava.bio.seq.io.agave
this is the interface implemented by several classes
AGAVEDbIdPropCallbackItf - Interface in org.biojava.bio.seq.io.agave
 
AGAVEDbIdPropHandler - Class in org.biojava.bio.seq.io.agave
Deals with database crossreferences
AGAVEDescPropHandler - Class in org.biojava.bio.seq.io.agave
Deals with database crossreferences
AGAVEElementIdPropHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEEvidenceCallbackItf - Interface in org.biojava.bio.seq.io.agave
 
AGAVEEvidenceHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEExonsPropHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.agave
An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEFragmentOrderHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEFragmentOrientationHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEGeneHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEHandler - Class in org.biojava.bio.seq.io.agave
Handles the root AGAVE element modified for agave format
AGAVEHandler() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEHandler
 
AGAVEIdAlias - Class in org.biojava.bio.seq.io.agave
 
AGAVEIdAliasCallbackItf - Interface in org.biojava.bio.seq.io.agave
 
AGAVEIdAliasPropHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEKeywordPropHandler - Class in org.biojava.bio.seq.io.agave
Deals with AGAVE keywords
AGAVEMapLocation - Class in org.biojava.bio.seq.io.agave
 
AGAVEMapLocation() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
AGAVEMapLocationPropHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEMapPosition - Class in org.biojava.bio.seq.io.agave
 
AGAVEMapPosition() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapPosition
 
AGAVEMapPositionPropHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEMatchAlignPropHandler - Class in org.biojava.bio.seq.io.agave
Deals with match_align
AGAVEMatchDescPropHandler - Class in org.biojava.bio.seq.io.agave
Deals with match_desc
AGAVEMatchRegion - Class in org.biojava.bio.seq.io.agave
match_region
AGAVEMatchRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
AGAVEMatchRegionPropHandler - Class in org.biojava.bio.seq.io.agave
Deals with match_region
AGAVEMrnaHandler - Class in org.biojava.bio.seq.io.agave
Handles the AGAVE <mrna> element
AGAVENotePropHandler - Class in org.biojava.bio.seq.io.agave
Deals with note
AGAVEPredictedProteinHandler - Class in org.biojava.bio.seq.io.agave
Handles the AGAVE <predicted_protein> element
AGAVEProperty - Class in org.biojava.bio.seq.io.agave
 
AGAVEProperty(String, String, String, String) - Constructor for class org.biojava.bio.seq.io.agave.AGAVEProperty
 
AGAVEQualifierPropHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEQueryRegion - Class in org.biojava.bio.seq.io.agave
 
AGAVEQueryRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
AGAVEQueryRegionPropHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVERelatedAnnot - Class in org.biojava.bio.seq.io.agave
 
AGAVERelatedAnnot() - Constructor for class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
construct..
AGAVERelatedAnnotPropHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEResultGroupHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVEResultPropertyPropHandler - Class in org.biojava.bio.seq.io.agave
 
AGAVESciPropertyPropHandler - Class in org.biojava.bio.seq.io.agave
sci_property
AGAVESeqFeatureHandler - Class in org.biojava.bio.seq.io.agave
seq_feature
AGAVESeqLocationPropHandler - Class in org.biojava.bio.seq.io.agave
seq_location
AGAVESeqMapHandler - Class in org.biojava.bio.seq.io.agave
sequence_map
AGAVESeqPropHandler - Class in org.biojava.bio.seq.io.agave
Deals with sequence code
AGAVETranscriptHandler - Class in org.biojava.bio.seq.io.agave
transcript
AGAVEUnorderedFragmentsHandler - Class in org.biojava.bio.seq.io.agave
unordered_fragments
AGAVEViewPropHandler - Class in org.biojava.bio.seq.io.agave
Moves view attributes into annotation properties.
AgaveWriter - Class in org.biojava.bio.seq.io.agave
Writes Sequence into AGAVE XML document.
AgaveWriter() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter
Default constructor uses generic annotation to attribute mapping.
AgaveWriter(AGAVEAnnotFilter) - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter
Construct with data source specific annotation to attribute mapping.
AgaveWriter.Indent - Class in org.biojava.bio.seq.io.agave
Implements indenting for elements.
AGAVEXref - Class in org.biojava.bio.seq.io.agave
xref
AGAVEXref() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXref
 
AGAVEXrefCallbackItf - Interface in org.biojava.bio.seq.io.agave
 
AGAVEXrefPropHandler - Class in org.biojava.bio.seq.io.agave
handle AGAVE xref
AGAVEXrefPropPropHandler - Class in org.biojava.bio.seq.io.agave
xref_property
AGAVEXrefs - Class in org.biojava.bio.seq.io.agave
xrefs
AGAVEXrefs() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXrefs
 
AGAVEXrefsPropHandler - Class in org.biojava.bio.seq.io.agave
Deals with database crossreferences (xrefs)
Aggregator - Class in org.biojava.bio.program.tagvalue
Joins multipel values into single values.
Aggregator(TagValueListener, BoundaryFinder, String) - Constructor for class org.biojava.bio.program.tagvalue.Aggregator
 
ala() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Alanine (A)
align(Sequence, Sequence, AlignmentAlgorithm) - Static method in class org.biojava.bio.alignment.AlignmentPair
 
alignAll(SequenceIterator, SequenceDB) - Method in class org.biojava.bio.alignment.AlignmentAlgorithm
 
AlignIOConstants - Class in org.biojava.bio.seq.io
AlignIOConstants contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing alignments.
AlignIOConstants() - Constructor for class org.biojava.bio.seq.io.AlignIOConstants
 
alignment - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
alignment Alignment field.
alignment(List, SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews
View a SymbolList over a cross-product Alphabet as an Alignment.
alignment(Map) - Static method in class org.biojava.bio.symbol.SymbolListViews
Construct an alignment of the SymbolLists contained in the values collection of labelToSymList.
Alignment - Interface in org.biojava.bio.alignment
An alignment containing multiple SymbolLists.
ALIGNMENT - Static variable in interface org.biojava.bio.seq.homol.Homology
Signals that the alignment describing the homologous sequences has changed.
ALIGNMENT_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.AlignmentStAXHandler
 
Alignment.SymbolListIterator - Class in org.biojava.bio.alignment
Iterator implementation looping over symbol lists in an alignment using the labels.
AlignmentAlgorithm - Class in org.biojava.bio.alignment
This Interface provides methods for the alignment of bio-sequences.
AlignmentAlgorithm() - Constructor for class org.biojava.bio.alignment.AlignmentAlgorithm
 
AlignmentElement - Interface in org.biojava.bio.alignment
AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.
AlignmentFormat - Interface in org.biojava.bio.seq.io
 
AlignmentMarker - Class in org.biojava.bio.program.blast2html
Class to do simple HTML colouring of sequence alignments.
AlignmentMarker(ColourCommand, AlignmentStyler) - Constructor for class org.biojava.bio.program.blast2html.AlignmentMarker
Creates a new AlignmentMarker instance.
AlignmentPair - Class in org.biojava.bio.alignment
This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.
AlignmentPair(Sequence, Sequence, int, int, int, int, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.AlignmentPair
 
AlignmentPair(Sequence, Sequence, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.AlignmentPair
 
alignmentRange - Variable in class org.biojava.bio.alignment.FlexibleAlignment
 
AlignmentRenderer - Class in org.biojava.bio.gui.sequence
 
AlignmentRenderer() - Constructor for class org.biojava.bio.gui.sequence.AlignmentRenderer
 
AlignmentStAXHandler - Class in org.biojava.bio.program.ssbind
AlignmentStAXHandler handles the BlastLikeAlignment element of BioJava BlastLike XML.
all - Static variable in interface org.biojava.bio.seq.FeatureFilter
All features are selected by this filter.
all - Static variable in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
All features are selected by this filter.
all() - Static method in class org.biojava.bio.seq.FilterUtils
Return a filter which matches all features.
ALL - Static variable in interface org.biojava.bio.program.xff.ElementRecognizer
 
ALL - Static variable in interface org.biojava.bio.seq.io.agave.ElementRecognizer
 
ALL - Static variable in interface org.biojava.bio.seq.io.game.ElementRecognizer
 
AllElementRecognizer() - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
 
AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
 
AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
 
allGaps(SymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
make sure that all Symbols in this range are gaps
allIn(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
Destructive down-cast an annotation to a type.
allOut(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
allOut returns a new Annotation containing only those values in the Annotation argument which are not of a type specified by the AnnotationType.
AllPairsInCollection(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
 
AllValuesIn(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.AllValuesIn
Create an AllValuesIn based upon a PropertyConstraint and a cardinality.
alph - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
alphabet - Variable in class org.biojava.bio.alignment.AbstractULAlignment
 
Alphabet - Interface in org.biojava.bio.symbol
The set of AtomicSymbols which can be concatenated together to make a SymbolList.
alphabetForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Retrieve the alphabet for a specific name.
AlphabetIndex - Interface in org.biojava.bio.symbol
Map between Symbols and index numbers.
AlphabetManager - Class in org.biojava.bio.symbol
Utility methods for working with Alphabets.
AlphabetManager() - Constructor for class org.biojava.bio.symbol.AlphabetManager
 
AlphabetResolver - Class in org.biojava.bio.program.ssbind
AlphabetResolvers are helpers which determine which type of sequence Alphabet to expect from a search result.
AlphabetResolver() - Constructor for class org.biojava.bio.program.ssbind.AlphabetResolver
 
alphabets() - Static method in class org.biojava.bio.symbol.AlphabetManager
Get an iterator over all alphabets known.
alphaIndex(Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
 
alphaIndex(Symbol) - Method in class org.biojava.utils.automata.Nfa
 
AlreadyExistsException - Exception in org.biojava.ontology
Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
AlreadyExistsException() - Constructor for exception org.biojava.ontology.AlreadyExistsException
 
AlreadyExistsException(String) - Constructor for exception org.biojava.ontology.AlreadyExistsException
 
ALT_ID - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
ALT_YEAST_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the alternative yeast nuclear genetic code.
AlternateTokenization - Class in org.biojava.bio.seq.io
Implementation of SymbolTokenization which binds symbols to strings of characters.
AlternateTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.AlternateTokenization
 
ALTERNATIVE_PRODUCTS - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
A name for a comment type.
ALWAYS_VETO - Static variable in interface org.biojava.utils.ChangeListener
Convenience implementation which vetoes every change of which it is notified.
AlwaysVetoListener() - Constructor for class org.biojava.utils.ChangeListener.AlwaysVetoListener
Private constructor.
AMBIGUOUS - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
AMBIGUOUS indicates that a sequence contains ambiguity symbols.
aminoAcids - Static variable in class org.biojavax.bio.seq.io.FastaFormat
 
and - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
and(FeatureFilter.And, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
and(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils
Constructs a new filter which matches the intersection of a set of filters.
and(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a new filter which matches the intersection of two other filters.
And(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.And
Create a new And from two child constraints.
And(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.And
 
And(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.And
 
And(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
 
And(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.And
Create a new And from two child constraints.
And(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.And
 
And(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.And
 
And(BioSQLFeatureFilter, BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
annot - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
Annotatable - Interface in org.biojava.bio
Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder - Class in org.biojava.bio
Deprecated.
use new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY) instead
annotate(Sequence) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
 
annotate(Sequence) - Method in class org.biojava.bio.molbio.RestrictionMapper
annotate adds Features which represent restriction sites.
annotate(Sequence) - Method in interface org.biojava.bio.seq.SequenceAnnotator
Return an annotated version of a sequence.
ANNOTATE_EXISTING - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
 
AnnotatedSequenceDB - Class in org.biojava.bio.seq.db
SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
AnnotatedSequenceDB(SequenceDB, SequenceAnnotator) - Constructor for class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
annotateSequence(Sequence, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
annotateSequence(Sequence, GFFEntrySet, boolean) - Static method in class org.biojava.bio.program.gff.GFFTools
Annotates a sequence with the features from a GFF entry set.
annotateSequences(SequenceDB, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
Annotates all sequences in a sequence DB with features from a GFF entry set.
annotateXFF(File, Sequence) - Static method in class org.biojava.bio.program.xff.XFFTools
 
annotateXFF(File, Sequence, Annotation) - Static method in class org.biojava.bio.program.xff.XFFTools
 
annotation - Variable in class org.biojava.bio.seq.Feature.Template
 
annotation - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
 
Annotation - Interface in org.biojava.bio
Arbitrary annotation associated with one or more objects.
ANNOTATION - Static variable in interface org.biojava.bio.Annotatable
Signals that the associated Annotation has altered in some way.
ANNOTATION_ADD - Static variable in class org.biojava.bio.MergeAnnotation
ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
ANNOTATION_CHANGED - Static variable in class org.biojava.bio.MergeAnnotation
ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
ANNOTATION_REMOVE - Static variable in class org.biojava.bio.MergeAnnotation
ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
AnnotationBuilder - Class in org.biojava.bio.program.tagvalue
Builds an Annotation tree from TagValue events using an AnnotationType to work out which fields are of what type.
AnnotationBuilder(AnnotationType) - Constructor for class org.biojava.bio.program.tagvalue.AnnotationBuilder
Make a new AnnotationBuilder that will build Annotation instances of a given type.
AnnotationChanger - Class in org.biojava.bio
AnnotationChanger remaps the values of an Annotation to new values specified by a ValueChanger.
AnnotationChanger(Annotation, ChangeTable) - Constructor for class org.biojava.bio.AnnotationChanger
Creates a new AnnotationChanger using the specified ValueChanger to remap its values.
AnnotationContains(Object, Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.AnnotationContains
Make a new AnnotationContains that will accept features with an annotation bundle where the value-set assosiated with the property key contains a member equal to value.
AnnotationDB - Interface in org.biojava.bio.annodb
A database of Annotation instances.
AnnotationFactory - Class in org.biojava.bio.program.ssbind
AnnotationFactory is a utility class for making Annotations from Maps.
AnnotationFactory() - Constructor for class org.biojava.bio.program.ssbind.AnnotationFactory
 
annotationForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
 
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
 
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
annotationForwarder - Variable in class org.biojava.bio.seq.impl.SubSequence
 
annotationForwarder - Variable in class org.biojava.bio.seq.NewSimpleAssembly
 
annotationForwarder - Variable in class org.biojava.bio.seq.SimpleAssembly
 
annotationForwarder - Variable in class org.biojava.bio.symbol.AbstractSymbol
 
annotationForwarder - Variable in class org.biojava.bio.symbol.SimpleAlphabet
 
AnnotationForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.Annotatable.AnnotationForwarder
Deprecated.
Create a new AnnotationForwarder that will forward events for a source using a change support.
AnnotationLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
 
AnnotationLabelMaker(Object) - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
 
AnnotationRenamer - Class in org.biojava.bio
AnnotationRenamer remaps the keys of an Annotation to new keys specified by a TagMapper.
AnnotationRenamer(Annotation, PropertyChanger) - Constructor for class org.biojava.bio.AnnotationRenamer
Creates a new AnnotationRenamer using the specified TagMapper to remap its keys.
AnnotationTools - Class in org.biojava.bio
AnnotationTools is a set of static utility methods for manipulating Annotations and AnnotationTypes.
AnnotationTools() - Constructor for class org.biojava.bio.AnnotationTools
 
AnnotationType - Interface in org.biojava.bio
A set of constraints on the data contained in an Annotation.
AnnotationType.Abstract - Class in org.biojava.bio
An abstract base class useful for implementing AnnotationType instances.
AnnotationType.Impl - Class in org.biojava.bio
An implementation of AnnotationType.
ANY - Static variable in interface org.biojava.bio.AnnotationType
The type that accepts all annotations and is the supertype of all other annotations.
ANY - Static variable in class org.biojava.bio.CardinalityConstraint
The property can have any number of values, including none.
ANY - Static variable in interface org.biojava.bio.CollectionConstraint
ANY is a constraint which accepts a property for addition under all conditions.
ANY - Static variable in interface org.biojava.bio.PropertyConstraint
ANY is a constraint which accepts a property for addition under all conditions.
ANY - Static variable in class org.biojava.ontology.OntoTools
 
App - Class in org.biojava
Hello world!
App() - Constructor for class org.biojava.App
 
AppBeanRunner - Class in org.biojava.utils.xml
Create a bean from an XML file, then attempt to enter it.
AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner
 
append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel
 
append(T, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
Append the specified FASTQ formatted sequences to the specified appendable.
append(T, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
Append the specified FASTQ formatted sequences to the specified appendable.
appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
appendMatrixData(String, Object) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
appendMatrixData(String, Object) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
 
appendQuality(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.
appendQuality(String) - Method in interface org.biojava.bio.program.fastq.ParseListener
Notify this listener of a quality line.
appendSequence(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.
appendSequence(String) - Method in interface org.biojava.bio.program.fastq.ParseListener
Notify this parse listener of an additional sequence line.
AppEntry - Interface in org.biojava.utils.xml
 
AppException - Exception in org.biojava.utils.xml
 
AppException(String) - Constructor for exception org.biojava.utils.xml.AppException
 
applicants - Variable in class org.biojava.bibliography.BiblioPatent
Array of applicants.
ARAlignment - Interface in org.biojava.bio.alignment
ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
arcHeight - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
 
ARCHITECTURE - Static variable in interface org.biojava.bio.dp.MarkovModel
Signals that the architecture of the model is changing.
arcWidth - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
 
areDisjoint(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Determines if two queries can be proven to be disjoint.
areEmissionSpectraEqual(Distribution[], Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
Compares the emission spectra of two distribution arrays.
areEmissionSpectraEqual(Distribution, Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
Compares the emission spectra of two distributions.
areEqual(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Decide if two feature filters accept exactly the same set of features.
areEqual(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
Return whether two locations are equal.
areProperSubset(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Determines if the set of features matched by sub can be proven to be a proper subset of the features matched by sup.
arg() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Arginine (R)
ARG_C - Static variable in class org.biojava.bio.proteomics.Protease
 
ARG_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager
 
ArrayStateMachineToolkit - Class in org.biojava.utils.automata
 
ArrowedFeatureRenderer - Class in org.biojava.bio.gui.sequence
A Feature Renderer that paints the Feature as a right facing arrow Based heavily on BasicFeatureRenderer
ArrowedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
ArrowGlyph - Class in org.biojava.bio.gui.glyph
A Glyph that paints an arrow shape within the bounds.
ArrowGlyph() - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
Creates a new ArrowGlyph, which is filled with the color blue by default.
ArrowGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
This constructs an arrow in the given bounds, which is colored blue.
ArrowGlyph(Rectangle2D.Float, Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
Constructor which sets both the size of this arrow and its color.
ArrowGlyph(Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
Creates a new ArrowGlyph, which is filled with the given color.
ASCID_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the ascidian mitochondrial genetic code.
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
asCriterion() - Method in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
This method returns a Hibernate Criterion object that can be used to query the database.
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
 
asMap() - Method in class org.biojava.bio.AbstractAnnotation
 
asMap() - Method in interface org.biojava.bio.Annotation
Return a map that contains the same key/values as this Annotation.
asMap() - Method in class org.biojava.bio.MergeAnnotation
 
asMap() - Method in class org.biojava.bio.OverlayAnnotation
Return a Map view onto this annotation.
asMap() - Method in class org.biojavax.EmptyRichAnnotation
Return a map that contains the same key/values as this Annotation.
asMap() - Method in class org.biojavax.ga.util.WeightedSet
Converts the Set to a map from key Objects to Double weights.
asMap() - Method in class org.biojavax.SimpleRichAnnotation
Return a map that contains the same key/values as this Annotation.
asn() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Asparagine (N)
asp() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Aspartic Acid (D)
ASP_N - Static variable in class org.biojava.bio.proteomics.Protease
 
ASP_N - Static variable in class org.biojava.bio.proteomics.ProteaseManager
 
AssembledSymbolList - Class in org.biojava.bio.seq.impl
Support class for applications which need to patch together sections of sequence into a single SymbolList.
AssembledSymbolList() - Constructor for class org.biojava.bio.seq.impl.AssembledSymbolList
 
AssertionFailure - Error in org.biojava.utils
An unchecked exception representing an Assertion failure.
AssertionFailure(String) - Constructor for error org.biojava.utils.AssertionFailure
 
AssertionFailure(String, Throwable) - Constructor for error org.biojava.utils.AssertionFailure
 
AssertionFailure(Throwable) - Constructor for error org.biojava.utils.AssertionFailure
 
AtomicSymbol - Interface in org.biojava.bio.symbol
A symbol that is not ambiguous.
attemptClose(ResultSet) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Attempt to close the ResultSet.
attemptClose(Statement) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Attempt to close the Statement.
ATTR_FORMAT - Static variable in interface org.biojava.bibliography.BibRefSupport
A vocabulary name, or a part of a vocabulary name.
ATTR_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport
A part of a vocabulary name.
ATTR_SCOPE - Static variable in interface org.biojava.bibliography.BibRefSupport
A vocabulary name, or a part of a vocabulary name.
attribute(String, String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
attribute(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
attribute(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
Add an un-qualified attribute to an element.
attribute(String, String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
attribute(String, String, String) - Method in interface org.biojava.utils.xml.XMLWriter
Add an attribute to an element.
AUTHOR_LIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
AUTHORITY - Static variable in interface org.biojavax.Namespace
 
authors - Variable in class org.biojava.bibliography.BibRef
The authors and contributors are responsible for creating the contents of the cited resource.
AUTHORS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
automaticUpdate(Connection, DBHelper, TaxonFactory, File, File) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
This method tries to perform a complete update according to the given TaxonFactory, which already contains the newes taxa and the files available at the NCBI-FTP-Site.
AutomatonException - Exception in org.biojava.utils.automata
An exception thrown by classes of this package.
AutomatonException(String) - Constructor for exception org.biojava.utils.automata.AutomatonException
 
AutomatonException(Throwable) - Constructor for exception org.biojava.utils.automata.AutomatonException
 
AutomatonException(Throwable, String) - Constructor for exception org.biojava.utils.automata.AutomatonException
 
available() - Method in class org.biojava.utils.io.UncompressInputStream
 
average(Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
Averages two or more distributions.
AverageResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.AverageResolver
 
AVG_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 

B

b() - Static method in class org.biojava.bio.seq.DNATools
 
b() - Static method in class org.biojava.bio.seq.NucleotideTools
 
B_TAURUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
back - Variable in class org.biojava.bio.dp.BackPointer
The previous backpointer (towards origin of DP matrix) in traceback.
BackMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
 
BackMatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
 
BackPointer - Class in org.biojava.bio.dp
A backpointer.
BackPointer(State) - Constructor for class org.biojava.bio.dp.BackPointer
 
BackPointer(State, BackPointer, double) - Constructor for class org.biojava.bio.dp.BackPointer
 
backPointers - Variable in class org.biojava.bio.dp.twohead.Cell
 
backward(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
 
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
backward_initialize(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
backward_recurse(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
backward_termination(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
 
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
 
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
backwards(ScoreType) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
 
backwards(ScoreType) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
 
backwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
 
backwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP
 
BACTERIAL - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the bacterial and plant plastid genetic code.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.program.phred.PhredFormat
This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.StreamReader
This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in interface org.biojava.utils.ParseErrorListener
Method called when the parser encounters a bad line.
BarLogoPainter - Class in org.biojava.bio.gui
A logo painter that paints in bars.
BarLogoPainter() - Constructor for class org.biojava.bio.gui.BarLogoPainter
 
BASE_COUNT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
BASE_COUNT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
BASE_COUNT_TAG_FULL - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
BASEPOSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
BASEPOSITION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
BaseXMLWriter - Class in org.biojava.bio.program.xml
Base XMLWriter class for writing XML representations of Java Value Objects with bespoke architectures.
BaseXMLWriter() - Constructor for class org.biojava.bio.program.xml.BaseXMLWriter
 
BasicFeatureRenderer - Class in org.biojava.bio.gui.sequence
 
BasicFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
BasicFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
 
BasicImapRenderer - Class in org.biojava.bio.gui.sequence
BasicImapRenderer is a decorator for BasicFeatureRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the BasicFeatureRenderer.
BasicImapRenderer(BasicFeatureRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.BasicImapRenderer
Creates a new BasicImapRenderer.
BasicState(String) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState
This is the default constructor
BasicState(String, TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState
when this constructor is used, a fixed listener is used with this state.
BasicXFFHelper - Class in org.biojava.bio.program.xff
 
BasicXFFHelper() - Constructor for class org.biojava.bio.program.xff.BasicXFFHelper
 
BasisSymbol - Interface in org.biojava.bio.symbol
A symbol that can be represented as a string of Symbols.
BaumWelchSampler - Class in org.biojava.bio.dp
Train a hidden markov model using a sampling algorithm.
BaumWelchSampler(DP) - Constructor for class org.biojava.bio.dp.BaumWelchSampler
 
BaumWelchTrainer - Class in org.biojava.bio.dp
Train a hidden markov model using maximum likelihood.
BaumWelchTrainer(DP) - Constructor for class org.biojava.bio.dp.BaumWelchTrainer
 
beadDepth - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
 
beadDisplacement - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
 
BeadFeatureRenderer - Interface in org.biojava.bio.gui.sequence
BeadFeatureRenderers use a 'string of beads' metaphor for displaying features.
beadFill - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
 
beadOutline - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
 
beadStroke - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
 
BeanAsAnnotation - Class in org.biojava.bio
Create an Annotation with properties matching those of a JavaBean instance.
BeanAsAnnotation(Object) - Constructor for class org.biojava.bio.BeanAsAnnotation
Create a new BeanAsAnnotation for a bean.
BeanAsMap - Class in org.biojava.utils
 
BeanAsMap(Object) - Constructor for class org.biojava.utils.BeanAsMap
 
beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
 
beginComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
Opening a comment tag.
beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
beginComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
Opening a comment tag.
beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
beginComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Opening a comment tag.
beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
 
beginFileComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
 
beginFileComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
This method will get called when a comment is started on the file, and not any block within it.
beginWriting() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.INSDseqFormat
Informs the writer that we want to start writing.
beginWriting() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
Informs the writer that we want to start writing.
BETWEEN_BASES - Static variable in interface org.biojavax.bio.seq.Position
A symbol representing a position that falls in between two bases, eg. 2^3 falls somewhere in the gap between 2 and 3.
BetweenLocation - Class in org.biojava.bio.symbol
Between view onto an underlying Location instance.
BetweenLocation(Location) - Constructor for class org.biojava.bio.symbol.BetweenLocation
 
BiblioArticle - Class in org.biojava.bibliography
It represents an article.
BiblioArticle() - Constructor for class org.biojava.bibliography.BiblioArticle
 
BiblioBook - Class in org.biojava.bibliography
It represents a book.
BiblioBook() - Constructor for class org.biojava.bibliography.BiblioBook
 
BiblioBookArticle - Class in org.biojava.bibliography
It represents a book article.
BiblioBookArticle() - Constructor for class org.biojava.bibliography.BiblioBookArticle
 
BiblioCriterion - Class in org.biojava.bibliography
The criteria define how the matching or ordering should be done during queries.
BiblioCriterion() - Constructor for class org.biojava.bibliography.BiblioCriterion
 
BiblioDescription - Class in org.biojava.bibliography
It represents an account of the content of the cited resource.
BiblioDescription() - Constructor for class org.biojava.bibliography.BiblioDescription
 
BiblioEntryStatus - Class in org.biojava.bibliography
It defines information related to the citation itself rather than to the cited resource.
BiblioEntryStatus() - Constructor for class org.biojava.bibliography.BiblioEntryStatus
 
BiblioJournal - Class in org.biojava.bibliography
A class describing journals.
BiblioJournal() - Constructor for class org.biojava.bibliography.BiblioJournal
 
BiblioJournalArticle - Class in org.biojava.bibliography
It represents a journal article.
BiblioJournalArticle() - Constructor for class org.biojava.bibliography.BiblioJournalArticle
 
BiblioOrganisation - Class in org.biojava.bibliography
It represents an organisation dealing with the bibliographic resources.
BiblioOrganisation() - Constructor for class org.biojava.bibliography.BiblioOrganisation
 
BiblioPatent - Class in org.biojava.bibliography
It represents a patent.
BiblioPatent() - Constructor for class org.biojava.bibliography.BiblioPatent
 
BiblioPerson - Class in org.biojava.bibliography
It represents a person dealing with the bibliographic resources.
BiblioPerson() - Constructor for class org.biojava.bibliography.BiblioPerson
 
BiblioProceeding - Class in org.biojava.bibliography
It represents a conference proceeding.
BiblioProceeding() - Constructor for class org.biojava.bibliography.BiblioProceeding
 
BiblioProvider - Class in org.biojava.bibliography
This class and its sub-classes define active participants of the process of creation and dissemination of the bibliographic resources.
BiblioProvider() - Constructor for class org.biojava.bibliography.BiblioProvider
 
BiblioScope - Class in org.biojava.bibliography
It represent an extent or scope of the content of the cited resource.
BiblioScope() - Constructor for class org.biojava.bibliography.BiblioScope
 
BiblioService - Class in org.biojava.bibliography
It represents a service dealing with the bibliographic resources.
BiblioService() - Constructor for class org.biojava.bibliography.BiblioService
 
BiblioSubject - Class in org.biojava.bibliography
It represents the topic of the content of the cited resource.
BiblioSubject() - Constructor for class org.biojava.bibliography.BiblioSubject
 
BiblioTechReport - Class in org.biojava.bibliography
It represents a technical report.
BiblioTechReport() - Constructor for class org.biojava.bibliography.BiblioTechReport
 
BiblioThesis - Class in org.biojava.bibliography
It represents a thesis.
BiblioThesis() - Constructor for class org.biojava.bibliography.BiblioThesis
 
BiblioWebResource - Class in org.biojava.bibliography
It represents a WWW resource.
BiblioWebResource() - Constructor for class org.biojava.bibliography.BiblioWebResource
 
BibRef - Class in org.biojava.bibliography
This class is a core class of the bibliographic data model - it represents a bibliographic reference, a citation.
BibRef() - Constructor for class org.biojava.bibliography.BibRef
 
BibRefException - Exception in org.biojava.bibliography
An exception raised when communciation with the BibRef APIs fails.
BibRefException(String) - Constructor for exception org.biojava.bibliography.BibRefException
Create a new BibRefException with a message.
BibRefException(String, Throwable) - Constructor for exception org.biojava.bibliography.BibRefException
Create a nw BibRefException with a message and a root cause.
BibRefException(Throwable) - Constructor for exception org.biojava.bibliography.BibRefException
Create a new BibRefException with a root cause.
BibRefQuery - Interface in org.biojava.bibliography
The interface BibRefQuery is a fundamental part of the Bibliographic Query Service.
BibRefSupport - Interface in org.biojava.bibliography
This interface defines supporting utilities for working with bibliographic repositories.
binary(int) - Static method in class org.biojava.bio.symbol.PackingFactory
 
binary(long) - Static method in class org.biojava.bio.symbol.PackingFactory
 
BinarySearch - Class in org.biojava.utils.math
solves y = f(x) = 0 by binary search.
BinarySearch() - Constructor for class org.biojava.utils.math.BinarySearch
 
bind(String, Object) - Method in class org.biojava.naming.ObdaContext
 
bind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
 
bind(Name, Object) - Method in class org.biojava.naming.ObdaContext
 
bind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
 
bindSymbol(Symbol, char) - Method in class org.biojava.bio.seq.io.CharacterTokenization
Bind a Symbol to a character.
bindSymbol(Symbol, String) - Method in class org.biojava.bio.seq.io.AlternateTokenization
Bind a Symbol to a string.
BioEntry - Interface in org.biojavax.bio
This class relates to the bioentry table in BioSQL.
BioEntryDB - Interface in org.biojavax.bio.db
.
BioEntryDBLite - Interface in org.biojavax.bio.db
A database of BioEntrys.
BioEntryIterator - Interface in org.biojavax.bio
Essentially the same as SequenceIterator.
BioEntryRelationship - Interface in org.biojavax.bio
Represents the relation between two bioentries.
BIOENTRYS - Static variable in interface org.biojavax.bio.db.BioEntryDBLite
Signals that sequences are being added to or remove from the database.
BioError - Error in org.biojava.bio
A nestable biological error.
BioError() - Constructor for error org.biojava.bio.BioError
Create a new BioError.
BioError(String) - Constructor for error org.biojava.bio.BioError
Create a new BioError with a message.
BioError(String, Throwable) - Constructor for error org.biojava.bio.BioError
Create a new BioError with a cause and a message.
BioError(Throwable) - Constructor for error org.biojava.bio.BioError
Create a new BioError with a cause.
BioError(Throwable, String) - Constructor for error org.biojava.bio.BioError
Deprecated.
Use BioError(message, ex) instead.
BioException - Exception in org.biojava.bio
A nestable biological exception.
BioException() - Constructor for exception org.biojava.bio.BioException
Create a new BioException.
BioException(String) - Constructor for exception org.biojava.bio.BioException
Create a new BioException with a message.
BioException(String, Throwable) - Constructor for exception org.biojava.bio.BioException
Create a new BioException with a cause and a message.
BioException(Throwable) - Constructor for exception org.biojava.bio.BioException
Create a new BioException with a cause.
BioException(Throwable, String) - Constructor for exception org.biojava.bio.BioException
Deprecated.
use new BioException(message, ex) instead
BioFetchSequenceDB - Class in org.biojava.bio.seq.db.biofetch
Simple SequenceDB implementation backed by a BioFetch (HTTP) server.
BioFetchSequenceDB(String, String) - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
Construct a BioFetchSequenceDB which connects to the specified BioFetch server.
BioFetchSequenceDBProvider - Class in org.biojava.bio.seq.db.biofetch
Directory-services plugin for biofetch databases.
BioFetchSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
 
BioIndex - Class in org.biojava.bio.seq.db
The original object for indexing sequence files.
BioIndex(File) - Constructor for class org.biojava.bio.seq.db.BioIndex
Load an existing index file.
BioIndex(File, String, int) - Constructor for class org.biojava.bio.seq.db.BioIndex
 
biojavaToFile(int, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Converts a Biojava object to the given filetype.
biojavaToFile(String, String, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes a Biojava SequenceIterator, SequenceDB, Sequence or Aligment to an OutputStream
BioMatcher - Interface in org.biojava.bio.search
Interface for things that perform matches.
BioPattern - Interface in org.biojava.bio.search
 
BIOPHYSICOCHEMICAL_PROPERTIES - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
A name for a comment type.
BioRuntimeException - Exception in org.biojava.bio
A nestable biological exception.
BioRuntimeException() - Constructor for exception org.biojava.bio.BioRuntimeException
Create a new BioRuntimeException.
BioRuntimeException(String) - Constructor for exception org.biojava.bio.BioRuntimeException
Create a new BioRuntimeException with a message.
BioRuntimeException(String, Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException
Create a new BioRuntimeException with a cause and a message.
BioRuntimeException(Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException
Create a new BioRuntimeException with a cause.
BioRuntimeException(Throwable, String) - Constructor for exception org.biojava.bio.BioRuntimeException
Deprecated.
use new BioRuntimeException(message, ex) instead
BIOSEQUENCE_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
 
BIOSEQUENCE_ORACLECLOB - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
 
BioSQLAcceptAllFilter - Class in org.biojavax.bio.db.biosql
The class that accepts all features.
BioSQLAcceptAllFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
 
BioSQLAcceptNoneFilter - Class in org.biojavax.bio.db.biosql
The class that accepts no features.
BioSQLAcceptNoneFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
 
BioSQLBioEntryDB - Class in org.biojavax.bio.db.biosql
 
BioSQLBioEntryDB(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
Creates a new instance of BioSQLBioEntryDB
BioSQLBioEntryDB(String, Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
Creates a new instance of BioSQLBioEntryDB
BioSQLCrossReferenceResolver - Class in org.biojavax.bio.db.biosql
A simple implementation of CrossReferenceResolver
BioSQLCrossReferenceResolver(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
Requires a Hibernate session to work correctly.
BioSQLFeatureFilter - Interface in org.biojavax.bio.db.biosql
A filter for accepting or rejecting a feature.
BioSQLFeatureFilter.And - Class in org.biojavax.bio.db.biosql
A filter that returns all features accepted by both child filter.
BioSQLFeatureFilter.ByName - Class in org.biojavax.bio.db.biosql
Construct one of these to filter features by display name.
BioSQLFeatureFilter.ByNote - Class in org.biojavax.bio.db.biosql
A filter that returns all features that have the given note, and the value and rank is checked as well.
BioSQLFeatureFilter.ByNoteTermOnly - Class in org.biojavax.bio.db.biosql
A filter that returns all features that have a note with the given term.
BioSQLFeatureFilter.ByRank - Class in org.biojavax.bio.db.biosql
Construct one of these to filter features by rank.
BioSQLFeatureFilter.BySequenceName - Class in org.biojavax.bio.db.biosql
Accept features that reside on a sequence with a particular name.
BioSQLFeatureFilter.BySourceTerm - Class in org.biojavax.bio.db.biosql
Construct one of these to filter features by source.
BioSQLFeatureFilter.BySourceTermName - Class in org.biojavax.bio.db.biosql
Construct one of these to filter features by source (name only - parent ontology is ignored).
BioSQLFeatureFilter.ByStrand - Class in org.biojavax.bio.db.biosql
A filter that returns all features having locations on a given strand.
BioSQLFeatureFilter.ByTypeTerm - Class in org.biojavax.bio.db.biosql
Construct one of these to filter features by type.
BioSQLFeatureFilter.ByTypeTermName - Class in org.biojavax.bio.db.biosql
Construct one of these to filter features by type (name only - parent ontology is ignored).
BioSQLFeatureFilter.ContainedByRichLocation - Class in org.biojavax.bio.db.biosql
A filter that returns all features contained within a location.
BioSQLFeatureFilter.HibernateFeatureFilter - Class in org.biojavax.bio.db.biosql
A filter for Hibernate-BioSQL filters to extend.
BioSQLFeatureFilter.Not - Class in org.biojavax.bio.db.biosql
A filter that returns all features not accepted by a child filter.
BioSQLFeatureFilter.Or - Class in org.biojavax.bio.db.biosql
A filter that returns all features accepted by at least one child filter.
BioSQLFeatureFilter.OverlapsRichLocation - Class in org.biojavax.bio.db.biosql
A filter that returns all features overlapping a location.
BioSQLFeatureFilter.Tools - Class in org.biojavax.bio.db.biosql
A class representing some useful stuff you can do with BioSQLFeatureFilters, for instance converting plain FeatureFilters into a their BioSQLFeatureFilter equivalents (where possible).
BioSQLRichObjectBuilder - Class in org.biojavax.bio.db.biosql
Takes requests for RichObjects and sees if it can load them from a Hibernate database.
BioSQLRichObjectBuilder(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder
Creates a new instance of SimpleRichObjectBuilder.
BioSQLRichSequenceDB - Class in org.biojavax.bio.db.biosql
 
BioSQLRichSequenceDB(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
Creates a new instance of BioSQLRichSequenceDB
BioSQLRichSequenceDB(String, Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
Creates a new instance of BioSQLRichSequenceDB
BioSQLRichSequenceHandler - Class in org.biojavax.bio.db.biosql
A handler which loads sequence data from a BioSQL database, caching it where possible.
BioSQLRichSequenceHandler(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
Requires a Hibernate session to work correctly.
BioSQLSequenceDB - Class in org.biojava.bio.seq.db.biosql
Deprecated.
Use hibernate and org.biojavax.bio.db.*
BioSQLSequenceDB(String, String, String, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
Connect to a BioSQL database.
BioSQLSequenceDB(String, String, String, String, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
Connect to a BioSQL database.
BioSQLSequenceDB(DataSource, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
BioSQLSequenceDBProvider - Class in org.biojava.bio.seq.db.biosql
Deprecated.
Use hibernate and org.biojavax.bio.db.*
BioSQLSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
Deprecated.
 
BioStore - Class in org.biojava.bio.program.indexdb
BioStores represent directory and file structures which index flat files according to the OBDA specification.
BioStore(File, boolean) - Constructor for class org.biojava.bio.program.indexdb.BioStore
Creates a new BioStore flatfile index at the specified location with the specified caching behaviour.
BioStoreFactory - Class in org.biojava.bio.program.indexdb
BioStoreFactory creates BioStore instances.
BioStoreFactory() - Constructor for class org.biojava.bio.program.indexdb.BioStoreFactory
Creates a new BioStoreFactory.
BIT_PACKED - Static variable in class org.biojava.bio.seq.io.SmartSequenceBuilder
 
bitsOfInformation(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
Calculates the total bits of information for a distribution.
Blast2HTMLHandler - Class in org.biojava.bio.program.blast2html
Takes a SAX event stream and a HTMLRenderer to produce a HTML Blast like program report.
Blast2HTMLHandler(HTMLRenderer) - Constructor for class org.biojava.bio.program.blast2html.Blast2HTMLHandler
A content handler for rendering blast like outputs into HTML.
BlastLikeHomologyBuilder - Class in org.biojava.bio.program.ssbind
BlastLikeHomologyBuilder populates a List with Homology instances created from SAX events supplied via a SeqSimilarityAdapter.
BlastLikeHomologyBuilder(List) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
Creates a new BlastLikeHomologyBuilder which will instantiate Homology objects into the List target.
BlastLikeSAXParser - Class in org.biojava.bio.program.sax
A facade class allowing for direct SAX2-like parsing of the native output from Blast-like bioinformatics software.
BlastLikeSAXParser() - Constructor for class org.biojava.bio.program.sax.BlastLikeSAXParser
Initialises SAXParser, and sets default namespace prefix to "biojava".
BlastLikeSearchBuilder - Class in org.biojava.bio.program.ssbind
BlastLikeSearchBuilder will create SeqSimilaritySearchResults from SAX events via a SeqSimilarityAdapter.
BlastLikeSearchBuilder(List) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
Creates a new BlastLikeSearchBuilder which will instantiate results into the List target.
BlastLikeSearchBuilder(List, SequenceDB, SequenceDBInstallation) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
Creates a new BlastLikeSearchBuilder which will instantiate results into the List target.
BlastLikeSearchFilter - Interface in org.biojava.bio.search
A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter - Class in org.biojava.bio.search
 
BlastLikeSearchFilter.And - Class in org.biojava.bio.search
 
BlastLikeSearchFilter.ByHitProperty - Class in org.biojava.bio.search
Applies test to the value specified by the key in hit properties.
BlastLikeSearchFilter.BySearchProperty - Class in org.biojava.bio.search
Applies test to the value specified by the key in search properties.
BlastLikeSearchFilter.BySubHitProperty - Class in org.biojava.bio.search
Applies test to the value specified by the key in subhit properties.
BlastLikeSearchFilter.Node - Interface in org.biojava.bio.search
 
BlastLikeSearchFilter.Not - Class in org.biojava.bio.search
 
BlastLikeSearchFilter.Or - Class in org.biojava.bio.search
 
BlastLikeToXMLConverter - Class in org.biojava.bio.program
A class that converts the raw output from a variety of bioinformatics software and converts it to XML that will validate against the biojava:BlastLikeDataSetCollection DTD.
BlastLikeToXMLConverter(String) - Constructor for class org.biojava.bio.program.BlastLikeToXMLConverter
Creates a new BlastToXMLConverter instance.
BlastXMLParser - Class in org.biojava.bio.program.sax.blastxml
This class parses NCBI Blast XML output.
BlastXMLParser() - Constructor for class org.biojava.bio.program.sax.blastxml.BlastXMLParser
 
BlastXMLParserFacade - Class in org.biojava.bio.program.sax.blastxml
A facade class that wraps the NCBI Blast XML parsing framework in a more user-friendly form.
BlastXMLParserFacade() - Constructor for class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
 
BLEPH_MNUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the blepharisma macronuclear genetic code.
Block(int, int, int, int) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
Block(SimpleGappedSymbolList.Block) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
blockCount(Location) - Static method in class org.biojava.bio.symbol.LocationTools
Return the number of contiguous blocks in a location.
blockEnded(NexusBlockParser) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
 
blockEnded(NexusBlockParser) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
This method gets called when the block parser is expected to have finished parsing a block.
blockIterator() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
blockIterator() - Method in class org.biojava.bio.symbol.AbstractRangeLocation
 
blockIterator() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
blockIterator() - Method in interface org.biojava.bio.symbol.Location
Return an Iterator over the set of maximal contiguous sub-locations.
blockIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
Iterate over all blocks in the file in order.
blockIterator() - Method in class org.biojavax.bio.seq.CompoundRichLocation
Return an Iterator over the set of maximal contiguous sub-locations.
blockIterator() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Return an Iterator over the set of maximal contiguous sub-locations.
blockIterator() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Return an Iterator over the set of maximal contiguous sub-locations.
BlockIterator() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Get list of the un-gapped region of the SymbolList.
BlockPainter - Interface in org.biojava.bio.gui
 
BLUNT - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
BLUNT the end type created by enzymes which leave a blunt end.
BooleanElementHandlerBase - Class in org.biojava.utils.stax
StAX handler for any element which just contains a string representation of an boolean.
BooleanElementHandlerBase() - Constructor for class org.biojava.utils.stax.BooleanElementHandlerBase
 
Border() - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
 
BOTH_FORWARD_COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
BoundaryFinder - Interface in org.biojava.bio.program.tagvalue
 
bPointers - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
bPointers - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
Description of the Field
breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
Deprecated.
Converts the symbol list passed in into an array of strings.
breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Converts the symbol list passed in into an array of strings.
BROAD_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
BROAD_SYNONYM - Static variable in class org.biojava.ontology.Synonym
 
build() - Method in class org.biojava.bio.program.fastq.FastqBuilder
Build and return a new FASTQ formatted sequence configured from the properties of this builder.
buildDataParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener.
buildDataStore(File, SequenceStreamer, Packing, int, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
 
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
 
buildDataStore(File, SequenceDB, Packing, int, int) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory
Build a new DataStore.
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory
 
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory
 
builder() - Static method in class org.biojava.bio.program.fastq.Fastq
Create and return a new FastqBuilder.
builder(Fastq) - Static method in class org.biojava.bio.program.fastq.Fastq
Create and return a new FastqBuilder configured from the specified FASTQ formatted sequence.
buildLibInfoParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
Generate a tag-value parser for the library info unigene files.
buildObject(Class, List) - Method in class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder
This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
buildObject(Class, List) - Method in interface org.biojavax.RichObjectBuilder
This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
buildObject(Class, List) - Method in class org.biojavax.SimpleRichObjectBuilder
This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
BumpedRenderer - Class in org.biojava.bio.gui.sequence
 
BumpedRenderer() - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
 
BumpedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
 
BumpedRenderer(SequenceRenderer, int, int) - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
 
ByAccession(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
 
byAncestor(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where at least one of the ancestors matches the specified filter.
byAncestor(FeatureFilter.ByAncestor, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
ByAncestor(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
byAnnotation(Object, Object) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where the annotation property named key is equal to value.
ByAnnotation(Object, Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotation
Make a new ByAnnotation that will accept features with an annotation bundle containing 'value' associated with 'key'.
byAnnotationType(Object, Class) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where the annotation property named key is an instance of valClass.
byAnnotationType(AnnotationType) - Static method in class org.biojava.bio.seq.FilterUtils
Match features with annotations matching the specified AnnotationType
ByAnnotationType() - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.PropertyConstraint.ByAnnotationType
Create a new constraint by type.
ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
byChild(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where at least one child feature matches the supplied filter.
byChild(FeatureFilter.ByChild, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
ByChild(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByChild
 
byClass(Class) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features which are assignable to the specified class or interface.
ByClass(Class) - Constructor for class org.biojava.bio.PropertyConstraint.ByClass
Create a new ByClass instance.
ByClass(Class) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByClass
 
byComponentName(String) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches all features which implement the ComponentFeature interface and have a componentName property equal to the specified value
ByComponentName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
byDescendant(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where at least one decendant feature -- possibly but not necessarily an immediate child -- matches the specified filter.
byDescendant(FeatureFilter.ByDescendant, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
ByDescendant(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
ByFeature(Feature) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByFeature
 
byFrame(FramedFeature.ReadingFrame) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches FramedFeatures with the specified reading frame.
byHitProperty(BlastLikeSearchFilter.ByHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
 
ByHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
 
ByHomologeneID(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
 
ByLocalName(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
 
ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
 
ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
 
ByLocationComparator() - Constructor for class org.biojava.bio.seq.Feature.ByLocationComparator
 
ByLocationMinMaxComparator - Class in org.biojava.bio.seq
A Comparator similar to Feature.ByLocationComparator except that the min and max positions of the location are both compared
ByLocationMinMaxComparator() - Constructor for class org.biojava.bio.seq.ByLocationMinMaxComparator
 
ByLocationMinMaxFeatureComparator - Class in org.biojava.bio.seq
Comparator that compares the min and max positions of Features Required by org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer instances.
ByLocationMinMaxFeatureComparator() - Constructor for class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
 
byLocationOrder - Static variable in interface org.biojava.bio.seq.Feature
byLocationOrder contains a Feature comparator which compares by the minimum base position of their Location.
ByLocusID(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
 
ByMaxIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
 
ByMinIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
 
ByMinIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
 
byName - Static variable in interface org.biojava.bio.seq.db.IDMaker
A simple implementation of IDMaker that hashes by sequence name.
ByName() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByName
 
ByName(String) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.ByName
 
ByName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
Create a ByType filter that filters in all features with type fields equal to type.
ByNote(Note) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
 
ByNoteTermOnly(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
 
ByNSName(String, String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
 
ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
 
ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
 
byPairwiseScore(double, double) - Static method in class org.biojava.bio.seq.FilterUtils
Match SeqSimilaritiy features with scores in the specified range.
ByPairwiseScore(double, double) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
Creates a new ByPairwiseScore.
byParent(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where the parent feature matches the specified filter.
byParent(FeatureFilter.ByParent, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
ByParent(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByParent
 
ByRank(int) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
Create a Rank filter that filters in all features with rank fields equal to rank.
ByRef(String) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
 
byScore - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit
byScore contains a SeqSimilaritySearchHit comparator which compares by their score.
byScore - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
byScore contains a SeqSimilaritySearchSubHit comparator which compares by the score of the sub-hit.
ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
 
ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
 
bySearchProperty(BlastLikeSearchFilter.BySearchProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
 
BySearchProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
 
bySequenceName(String) - Static method in class org.biojava.bio.seq.FilterUtils
Match features attached to sequences with a specified name.
BySequenceName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
BySequenceName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
 
BySimilarityType(SimilarityType) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
 
bySource(String) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features with a specific source value.
BySource(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySource
Create a BySource filter that filters in all features which have sources equal to source.
BySourceTerm(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
Create a BySourceTerm filter that filters in all features with sourceTerm fields equal to source.
BySourceTermName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
Create a BySourceTerm filter that filters in all features with sourceTerm fields having name equal to sourceTermName.
byStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.FilterUtils
Match StrandedFeatures on the specified strand.
ByStrand(RichLocation.Strand) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
Creates a filter that returns everything on strand str.
bySubHitCount - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit
bySubHitCount contains a SeqSimilaritySearchHit comparator which compares by their number of sub-hits.
BySubHitCountComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
 
bySubHitProperty(BlastLikeSearchFilter.BySubHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
 
BySubHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
 
bySubjectStart - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
bySubjectStart contains a SeqSimilaritySearchSubHit comparator which compares by the start position of the sub-hit on the subject sequence.
BySubjectStartComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
 
ByTaxon(Taxon) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
 
ByTaxon(Taxon) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
 
ByTaxonID(int) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
 
BYTE_MAX_VALUE - Static variable in class org.biojava.bio.program.scf.SCF
Represents the maximum unsigned value of a byte for wrapping purposes
ByteCode - Class in org.biojava.utils.bytecode
Factory for objects which encapsulate individual Java bytecode instructions.
ByteCode() - Constructor for class org.biojava.utils.bytecode.ByteCode
 
ByteElementHandlerBase - Class in org.biojava.utils.stax
StAX handler for any element which just contains a string representation of a byte.
ByteElementHandlerBase() - Constructor for class org.biojava.utils.stax.ByteElementHandlerBase
 
BYTES_IN_BYTE - Static variable in class org.biojava.utils.Constants
 
BYTES_IN_CHAR - Static variable in class org.biojava.utils.Constants
 
BYTES_IN_DOUBLE - Static variable in class org.biojava.utils.Constants
 
BYTES_IN_FLOAT - Static variable in class org.biojava.utils.Constants
 
BYTES_IN_INT - Static variable in class org.biojava.utils.Constants
 
BYTES_IN_LONG - Static variable in class org.biojava.utils.Constants
 
BYTES_IN_SHORT - Static variable in class org.biojava.utils.Constants
 
bytesRead - Variable in class org.biojava.ontology.obo.OboFileParser
 
ByTitle(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
 
byType(String) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features with a specific type value.
ByType(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByType
Create a ByType filter that filters in all features with type fields equal to type.
ByTypeTerm(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
Create a ByTypeTerm filter that filters in all features with typeTerm fields equal to typeTerm.
ByTypeTermName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
Create a ByTypeTermName filter that filters in all features with typeTerm fields having name equal to typeTermName.
byURN - Static variable in interface org.biojava.bio.seq.db.IDMaker
A simple implementation of IDMaker that hashes by URN.
ByURN() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByURN
 

C

c() - Static method in class org.biojava.bio.seq.DNATools
 
c() - Static method in class org.biojava.bio.seq.NucleotideTools
 
c() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Cysteine
c() - Static method in class org.biojava.bio.seq.RNATools
 
C_ELEGANS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
cache - Variable in class org.biojava.utils.io.CachingInputStream
The byte cache itself.
Cache - Interface in org.biojava.utils.cache
Interface for managing caches of objects.
CACHE_PROPERTY - Static variable in class org.biojava.utils.io.InputStreamProvider
 
cachedOutcome - Variable in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
 
CacheMap - Interface in org.biojava.utils.cache
Interface for managing caches of objects fetchable by key.
CacheReference - Interface in org.biojava.utils.cache
Interface for a reference to an object, analogous to java.lang.ref.Referencce, but more flexible.
CachingInputStream - Class in org.biojava.utils.io
A wrapper around InputStream that provides in-memory caching of the input data.
CachingInputStream(InputStream) - Constructor for class org.biojava.utils.io.CachingInputStream
 
CachingKernel - Class in org.biojava.stats.svm
Caches the results of a nested kernel so that k(a, b) need only be calculated once.
CachingKernel() - Constructor for class org.biojava.stats.svm.CachingKernel
 
CachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.CachingKernel
 
CachingSequenceDB - Class in org.biojava.bio.seq.db
SequenceDB implementation that caches the results of another SequenceDB.
CachingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.CachingSequenceDB
Create a new CachingSequenceDB that caches the sequences in parent.
calcCell(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator
Calculate the 'scores' array in the cell at cells[0][0].
calcDist() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByName
 
calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByURN
 
calcID(Sequence) - Method in interface org.biojava.bio.seq.db.IDMaker
Calculate the id for a sequence.
calcKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
 
calcLineExtent(MouseEvent) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
calculatePrimRecLen(int) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
calculatePrimRecLen calculates the byte length of primary namespace records.
calculateScore(Distribution, Symbol) - Method in interface org.biojava.bio.dp.ScoreType
Calculates the score associated with a distribution and a symbol.
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.NullModel
 
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Odds
 
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Probability
 
calculateSecRecLen(int, String, Map) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
calculateSecRecLen calculates the byte length of secondary namespace records.
callbackStack - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
this is the stack of handler objects for the current feature.
callbackStack - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
this is the stack of handler objects for the current feature.
callboxesValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Flag for call boxes.
canAccept(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
Accepts all URLs that are of the file protocol.
canAccept(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
Accepts all URLs that are of the jdbc protocol.
canAccept(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
 
canAccept(CodeClass) - Method in class org.biojava.utils.bytecode.ParametricType
 
canAdvance() - Method in interface org.biojava.bio.dp.onehead.DPCursor
Can we advance?
CANDIES_NOT_SORTED - Static variable in interface org.biojava.utils.candy.CandyVocabulary
A property name.
CandyEntry - Class in org.biojava.utils.candy
This is a basic container for a vocabulary entry.
CandyEntry() - Constructor for class org.biojava.utils.candy.CandyEntry
An empty constructor.
CandyEntry(String) - Constructor for class org.biojava.utils.candy.CandyEntry
It creates an entry instance with given name and empty value.
CandyEntry(String, String) - Constructor for class org.biojava.utils.candy.CandyEntry
It creates an entry instance with given name and value.
CandyEntry(String, String, Hashtable) - Constructor for class org.biojava.utils.candy.CandyEntry
It creates an entry instance with given name, value and additional properties.
CandyException - Exception in org.biojava.utils.candy
 
CandyException(String) - Constructor for exception org.biojava.utils.candy.CandyException
 
CandyException(String, Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
 
CandyException(Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
 
CandyFinder - Interface in org.biojava.utils.candy
This interface is a main entry point to a set of controlled vocabularies.
CandyVocabulary - Interface in org.biojava.utils.candy
This interface defines functionality of a controlled vocabulary.
canMerge(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
Determines whether the locations are touching or not (if they could be merged in a single Location.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
Check to see if a given stream is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat
Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.FastaFormat
Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat
Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Check to see if a given file is in our format.
canRead(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat
Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
Check to see if a given file is in our format.
CardinalityConstraint - Class in org.biojava.bio
A constraint on the number of values a property can have.
Cavg - Static variable in class org.biojava.bio.proteomics.MassCalc
Constant value of Carbon average mass
Cell - Class in org.biojava.bio.dp.twohead
A single cell in the DP matrix.
Cell() - Constructor for class org.biojava.bio.dp.twohead.Cell
 
CellCalculator - Interface in org.biojava.bio.dp.twohead
The interface for all functions that can calculate the 'scores' array for a given cell.
CellCalculatorFactory - Interface in org.biojava.bio.dp.twohead
 
CellCalculatorFactoryMaker - Interface in org.biojava.bio.dp.twohead
The interface for all functions that can calculate the 'scores' array for a given cell.
CEREVISIAE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
Saccharomyces cerevisiae codon preferences
ChainedChanger(ChangeTable.Changer[]) - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
 
change(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
 
change(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Changer
Produce a modified value from an old value.
change(Object) - Method in class org.biojava.bio.program.tagvalue.RegexChanger
 
change(Object, Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
 
CHANGE_COMMON_NAME - Static variable in interface org.biojava.bio.taxa.Taxon
Deprecated.
Change type to indicate that the common name of this Taxon is changing.
CHANGE_SCIENTIFIC_NAME - Static variable in interface org.biojava.bio.taxa.Taxon
Deprecated.
Change type to indicate that the scientific name of this Taxon is changing.
Changeable - Interface in org.biojava.utils
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeableCache - Class in org.biojava.utils.cache
A cache that clears values as the keys fire ChangeEvents of a given type.
ChangeableCache(ChangeType) - Constructor for class org.biojava.utils.cache.ChangeableCache
 
ChangeAdapter - Class in org.biojava.utils
This is a ChangeListener that ignores everything.
ChangeAdapter() - Constructor for class org.biojava.utils.ChangeAdapter
 
ChangeEvent - Class in org.biojava.utils
Event which encapsulates a change in any mutable BioJava object.
ChangeEvent(Object, ChangeType) - Constructor for class org.biojava.utils.ChangeEvent
Construct a ChangeEvent with no change details.
ChangeEvent(Object, ChangeType, Object) - Constructor for class org.biojava.utils.ChangeEvent
Construct a ChangeEvent specifying a new value for a property, or an object to be added to a collection.
ChangeEvent(Object, ChangeType, Object, Object) - Constructor for class org.biojava.utils.ChangeEvent
Construct a ChangeEvent specifying a new value for a property, and giving the previous value.
ChangeEvent(Object, ChangeType, Object, Object, ChangeEvent) - Constructor for class org.biojava.utils.ChangeEvent
Construct a ChangeEvent to be fired because another ChangeEvent has been received from a property object.
ChangeEventRecorder() - Constructor for class org.biojava.utils.ChangeListener.ChangeEventRecorder
 
ChangeForwarder - Class in org.biojava.utils
This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeForwarder(Object, ChangeSupport) - Constructor for class org.biojava.utils.ChangeForwarder
Create a new ChangeForwarder for forwarding events.
ChangeForwarder.Retyper - Class in org.biojava.utils
A ChangeForwarder that systematically uses a given type and wraps the old event.
ChangeHub - Interface in org.biojava.utils
Interface implemented by ChangeHubs, i.e.
ChangeListener - Interface in org.biojava.utils
Interface for objects which listen to ChangeEvents.
ChangeListener.AlwaysVetoListener - Class in org.biojava.utils
An implementation that always vetoes everything.
ChangeListener.ChangeEventRecorder - Class in org.biojava.utils
A listener that remembers the ChangeEvent of the last change.
ChangeListener.LoggingListener - Class in org.biojava.utils
A listener that writes information about the event stream to a PrintStream.
changeSupport() - Method in class org.biojava.utils.ChangeForwarder
Return the underlying ChangeSupport instance that can be used to fire ChangeEvents and mannage listeners.
ChangeSupport - Class in org.biojava.utils
A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeSupport() - Constructor for class org.biojava.utils.ChangeSupport
Generate a new ChangeSupport instance.
ChangeSupport(int) - Constructor for class org.biojava.utils.ChangeSupport
Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources.
ChangeSupport(int, int) - Constructor for class org.biojava.utils.ChangeSupport
Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources, and which will grow by delta each time.
ChangeSupport(Set) - Constructor for class org.biojava.utils.ChangeSupport
 
ChangeSupport(Set, int, int) - Constructor for class org.biojava.utils.ChangeSupport
Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources, and which will grow by delta each time.
ChangeTable - Class in org.biojava.bio.program.tagvalue
A mapping between keys and actions to turn old values into new values.
ChangeTable() - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable
 
ChangeTable.ChainedChanger - Class in org.biojava.bio.program.tagvalue
An implementation of Changer that applies a list of Changer instances to the value in turn.
ChangeTable.Changer - Interface in org.biojava.bio.program.tagvalue
Callback used to produce a new value from an old one.
ChangeTable.Splitter - Interface in org.biojava.bio.program.tagvalue
Callback used to produce a list of values from a single old one.
ChangeType - Class in org.biojava.utils
Class for all constants which are used to indicate change types.
ChangeType(String, Class, String) - Constructor for class org.biojava.utils.ChangeType
Construct a new ChangeType with supertype UNKNOWN.
ChangeType(String, Class, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
Construct a new ChangeType.
ChangeType(String, Field) - Constructor for class org.biojava.utils.ChangeType
Construct a new ChangeType with superType UNKNOWN.
ChangeType(String, Field, ChangeType) - Constructor for class org.biojava.utils.ChangeType
Construct a new ChangeType.
ChangeType(String, String, String) - Constructor for class org.biojava.utils.ChangeType
 
ChangeType(String, String, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
 
ChangeVetoException - Exception in org.biojava.utils
Exception which is thrown when a ChangeListener does not wish a change to take place.
ChangeVetoException() - Constructor for exception org.biojava.utils.ChangeVetoException
 
ChangeVetoException(String) - Constructor for exception org.biojava.utils.ChangeVetoException
Create an exception with a detail message
ChangeVetoException(String, Throwable) - Constructor for exception org.biojava.utils.ChangeVetoException
 
ChangeVetoException(Throwable, String) - Constructor for exception org.biojava.utils.ChangeVetoException
Deprecated.
use new ChangeVetoException(reason, ex);
ChangeVetoException(Throwable, ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException
Propogate an exception without (additional) explanation.
ChangeVetoException(Throwable, ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException
Propogate an exception, giving a detail message
ChangeVetoException(ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException
Construct an exception to veto a change without explanation.
ChangeVetoException(ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException
Construct an exception to veto a change for a specified reason.
CHARACTER - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
 
characters(char[], int, int) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler
Describe characters method here.
characters(char[], int, int) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
characters(char[], int, int) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
Signal a span of character data in the XML input.
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
 
characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.StreamParser
 
characters(char[], int, int) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
 
characters(char[], int, int) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
 
characters(char[], int, int) - Method in class org.biojava.utils.stax.CharElementHandlerBase
 
characters(char[], int, int) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
 
characters(char[], int, int) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
 
characters(char[], int, int) - Method in class org.biojava.utils.stax.IntElementHandlerBase
 
characters(char[], int, int) - Method in class org.biojava.utils.stax.LongElementHandlerBase
 
characters(char[], int, int) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
characters(char[], int, int) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
characters(char[], int, int) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
Signal a span of character data in the XML input.
characters(char[], int, int) - Method in class org.biojava.utils.stax.StringElementHandlerBase
 
CHARACTERS_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
A constant representing the name of Characters blocks.
CharactersBlock - Class in org.biojavax.bio.phylo.io.nexus
Represents Nexus characters blocks.
CharactersBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Delegates to NexusBlock.Abstract constructor using CharactersBlock.CHARACTERS_BLOCK as the name.
CharactersBlock(String) - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlock
For the DATA block subclass.
CharactersBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus
Builds Nexus characters blocks.
CharactersBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
CharactersBlockListener - Interface in org.biojavax.bio.phylo.io.nexus
Listens to events that represent Nexus characters blocks.
CharactersBlockParser - Class in org.biojavax.bio.phylo.io.nexus
Parses Nexus characters blocks.
CharactersBlockParser(CharactersBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser
Delegates to NexusBlockParser.Abstract.
CharacterTokenization - Class in org.biojava.bio.seq.io
Implementation of SymbolTokenization which binds symbols to single unicode characters.
CharacterTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.CharacterTokenization
 
charAt(int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
 
charAt(int) - Method in class org.biojava.utils.RepeatedCharSequence
 
CharElementHandlerBase - Class in org.biojava.utils.stax
StAX handler for any element which just contains a string representation of a char.
CharElementHandlerBase() - Constructor for class org.biojava.utils.stax.CharElementHandlerBase
 
charValue(Symbol) - Method in class org.biojava.utils.regex.PatternFactory
Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for.
charValue(Symbol) - Method in class org.biojava.utils.regex.Search
 
checkException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
 
checkException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
 
checkIOException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
 
checkIOException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
 
checkIOException() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
 
children - Variable in class org.biojava.bio.taxa.SimpleTaxon
Deprecated.
 
CHLORO_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the chlorophycean mitochondrial genetic code.
Chromatogram - Interface in org.biojava.bio.chromatogram
Encapsulates the basic information you would want from a chromatogram.
ChromatogramFactory - Class in org.biojava.bio.chromatogram
A factory that creates Chromatogram objects from files or streams.
ChromatogramFactory() - Constructor for class org.biojava.bio.chromatogram.ChromatogramFactory
 
ChromatogramGraphic - Class in org.biojava.bio.chromatogram.graphic
Encapsulates a configurable method for drawing a Chromatogram into a graphics context.
ChromatogramGraphic() - Constructor for class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Default constructor with no Chromatogram.
ChromatogramGraphic(Chromatogram) - Constructor for class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Creates a new ChromatogramGraphic, initially displaying the given chromatogram.
ChromatogramGraphic.Option - Class in org.biojava.bio.chromatogram.graphic
A typesafe enumeration of the options available for configuring the behavior of a ChromatogramGraphic instance.
ChromatogramNonlinearScaler - Interface in org.biojava.bio.chromatogram.graphic
Provides the mechanism whereby a ChromatogramGraphic can display a Chromatogram with a non-linear horizontal scale.
ChromatogramNonlinearScaler.Identity - Class in org.biojava.bio.chromatogram.graphic
The default scaler that displays the chromatogram 1:1.
ChromatogramTools - Class in org.biojava.bio.chromatogram
Utility class for dealing with Chromatograms.
chromosomes - Variable in class org.biojavax.ga.impl.AbstractOrganism
 
CHROMOSOMES - Static variable in interface org.biojavax.ga.Organism
 
ChunkedSymbolList - Class in org.biojava.bio.symbol
SymbolList implementation using constant-size chunks.
ChunkedSymbolList(SymbolList[], int, int, Alphabet) - Constructor for class org.biojava.bio.symbol.ChunkedSymbolList
 
ChunkedSymbolListFactory - Class in org.biojava.bio.seq.io
class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves.
ChunkedSymbolListFactory(SymbolListFactory) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
 
ChunkedSymbolListFactory(SymbolListFactory, int) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
 
CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.Protease
 
CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.ProteaseManager
 
CILIATE_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the ciliate nuclear genetic code.
CIRCLE - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
CIRCLE indicates a circular image map hotspot.
CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichLocation
 
CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichSequence
 
CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
CircularFeatureFilteringRenderer - Class in org.biojava.bio.gui.sequence
 
CircularFeatureFilteringRenderer(CircularRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
 
CircularFeatureRenderer - Interface in org.biojava.bio.gui.sequence
 
CircularFeaturesRenderer - Class in org.biojava.bio.gui.sequence
 
CircularFeaturesRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
 
CircularFeaturesRenderer(CircularFeatureRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
 
circularLength - Variable in class org.biojavax.bio.seq.SimpleRichLocation
 
CircularLocation - Class in org.biojava.bio.symbol
Circular view onto an underlying Location instance.
CircularLocation(Location, int) - Constructor for class org.biojava.bio.symbol.CircularLocation
Constructs a CircularLocation by wrapping another Location It is preferable to use LocationTools to make CircularLocations
CircularLocation(Location, int, int) - Constructor for class org.biojava.bio.symbol.CircularLocation
Makes a CircularLocation where the 5' end of the Location is specified.
CircularMLR - Class in org.biojava.bio.gui.sequence
Renders multiple renderers, each in their own concentric rings.
CircularMLR() - Constructor for class org.biojava.bio.gui.sequence.CircularMLR
 
CircularPaddedRenderer - Class in org.biojava.bio.gui.sequence
 
CircularPaddedRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
 
CircularPaddedRenderer(double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
 
CircularPaddedRenderer(CircularRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
 
CircularPaddedRenderer(CircularRenderer, double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
 
CircularReferenceException - Exception in org.biojava.bio.taxa
Deprecated.
replaced by classes in org.biojavax.bio.taxa
CircularReferenceException() - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
Deprecated.
 
CircularReferenceException(String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
Deprecated.
 
CircularReferenceException(Throwable) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
Deprecated.
 
CircularReferenceException(Throwable, String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
Deprecated.
 
CircularRenderer - Interface in org.biojava.bio.gui.sequence
Render information from a CircularRendererContext onto a graphics context.
CircularRendererContext - Interface in org.biojava.bio.gui.sequence
A context providing information for rendering sequences into circular coordinate systems.
CircularRendererPanel - Class in org.biojava.bio.gui.sequence
Renders a sequence as a circle using a CircularRenderer.
CircularRendererPanel() - Constructor for class org.biojava.bio.gui.sequence.CircularRendererPanel
 
CircularView - Class in org.biojava.bio.seq
A circular view onto another Sequence object.
CircularView(Sequence) - Constructor for class org.biojava.bio.seq.CircularView
 
CircularView(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.CircularView
 
CITATION_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_FIRST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_ID_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_INSTITUTE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_ISSUE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_LAST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_PATENT_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_PUB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
CITATION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_VOL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CITATION_YEAR_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ClassifierExample - Class in org.biojava.stats.svm.tools
A simple toy example that allows you to put points on a canvas, and find a polynomial hyperplane to seperate them.
ClassifierExample() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample
 
ClassifierExample.PointClassifier - Class in org.biojava.stats.svm.tools
An extention of JComponent that contains the points & encapsulates the classifier.
classify() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Learn a model from the current points.
classify(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
classify(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
classify(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
Classify - Class in org.biojava.stats.svm.tools
 
Classify() - Constructor for class org.biojava.stats.svm.tools.Classify
 
classListToString(CodeClass[]) - Static method in class org.biojava.utils.bytecode.CodeUtils
Format an array of classes as a comma-seperated list.
ClassTools - Class in org.biojava.utils
Utility methods for manipulating class objects and resources.
clear() - Method in class org.biojava.bio.dp.twohead.EmissionCache
 
clear() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
clear() - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
clear() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
clear() - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
clear() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
clear() - Method in interface org.biojava.stats.svm.SVMTarget
 
clear() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Remove all points from the canvas, and discard any model.
clear() - Method in interface org.biojava.utils.cache.CacheReference
 
clear() - Method in class org.biojava.utils.FileAsList
 
clear() - Method in class org.biojava.utils.io.FlatFileCache
 
clear() - Method in class org.biojava.utils.io.SoftHashMap
 
clear() - Method in class org.biojavax.EmptyRichAnnotation
Removes all notes from this annotation object.
clear() - Method in class org.biojavax.ga.util.WeightedSet
 
clear() - Method in interface org.biojavax.RichAnnotation
Removes all notes from this annotation object.
clear() - Method in class org.biojavax.SimpleRichAnnotation
Removes all notes from this annotation object.
clearCounts() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Clears all of the counts to zero.
clearCounts() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
clearCounts() - Method in interface org.biojava.bio.dp.TransitionTrainer
Clears all of the counts to zero.
clearCounts(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.DistributionTrainer
Clears all of the counts to zero.
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
 
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
 
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
Deprecated.
 
clearEnzymes() - Method in class org.biojava.bio.molbio.RestrictionMapper
clearEnzymes removes all enzymes from those to be searched for in the Sequence.
clearLRUCache() - Static method in class org.biojavax.RichObjectFactory
Removes all objects from the LRU cache.
clearLRUCache(Class) - Static method in class org.biojavax.RichObjectFactory
Removes all objects of the specified class from the LRU cache.
clearPatterns() - Method in class org.biojava.utils.regex.Search
remove all patterns from the pattern cache.
clearRenderers() - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
clearRenderers removes all renderers from this renderer.
clearRenderers() - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
clearRenderers removes all the renderers.
clearTraces() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
Sets the trace data structures to null.
clearTraceValues() - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
Sets all the traces to null.
ClientSide(String) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ClientSide
Creates a new ClientSide image map.
clobToString(Connection, ResultSet, int) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
Deprecated.
 
clone() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Performs a partial deep copy and invalidates regenerable structures.
clone() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
 
clone() - Method in class org.biojava.bio.seq.Feature.Template
 
clone() - Method in class org.biojava.bio.seq.impl.RevCompSequence
clone() should make a complete copy of the Sequence with all features (and children) and return a SimpleSequence that is unconnected from the original sequence.
clone() - Method in class org.biojava.utils.ExecRunner
We override the clone method here to prevent cloning of our class.
clone() - Method in class org.biojava.utils.TypedProperties
 
close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
close closes the underlying InputStream.
close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
close closes the underlying RandomAccessFile.
close() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
close closes the underlying EntryNamRandomAccess which in turn closes the lower level RandomAccessFile.
close() - Method in interface org.biojava.bio.seq.io.StreamParser
 
close() - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
 
close() - Method in class org.biojava.naming.ObdaContext
 
close() - Method in interface org.biojava.utils.bytecode.CodeContext
Close the context for writing.
close() - Method in class org.biojava.utils.io.CountedBufferedReader
 
close() - Method in class org.biojava.utils.io.RandomAccessReader
close closes the underlying RandomAccessFile.
close() - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
close() - Method in interface org.biojava.utils.xml.XMLWriter
Close this XMLWriter, and it's underlying stream.
closeSubComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
 
closeTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
closeTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
closeTag(String) - Method in interface org.biojava.utils.xml.XMLWriter
Closes an un-qualified element.
closeTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
closeTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
Closes an element
CLUSTAL - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
CLUSTAL indicates that the alignment format is Clustal.
CLUSTAL_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
CLUSTAL_AA premade CLUSTAL | AA;
CLUSTAL_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
CLUSTAL_DNA premade CLUSTAL | DNA;
CLUSTAL_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
CLUSTAL_RNA premade CLUSTAL | RNA;
ClustalWAlignmentSAXParser - Class in org.biojava.bio.program.sax
A SAX2 parser for dealing with a multiple sequence alignment as produced by ClustalW outputing .aln format.
ClustalWAlignmentSAXParser() - Constructor for class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser
Initialises internal state Sets namespace prefix to "biojava"
Cmono - Static variable in class org.biojava.bio.proteomics.MassCalc
Constant value of Carbon monoisotopic mass
CNBr - Static variable in class org.biojava.bio.proteomics.Protease
 
CNBr - Static variable in class org.biojava.bio.proteomics.ProteaseManager
 
CodeClass - Interface in org.biojava.utils.bytecode
Interface for Java classes within the bytecode generation framework.
CodeContext - Interface in org.biojava.utils.bytecode
Interface which encapsulates the stream to which Java bytecode can be written.
CodeException - Exception in org.biojava.utils.bytecode
An exception indicating that something went wrong generating byte code.
CodeException() - Constructor for exception org.biojava.utils.bytecode.CodeException
 
CodeException(String) - Constructor for exception org.biojava.utils.bytecode.CodeException
 
CodeField - Class in org.biojava.utils.bytecode
Wrap up details about a field in a Java class file.
CodeGenerator - Interface in org.biojava.utils.bytecode
Interface for an object which can produce Java bytecode.
CodeMethod - Interface in org.biojava.utils.bytecode
Wrap up details about a method in a Java class file
codes - Variable in class org.biojava.bibliography.BiblioSubject
Classification code (call number) is usually either Dewey decimal or Congress classification.
CodeUtils - Class in org.biojava.utils.bytecode
Utility code for things you will frequently need.
CodeUtils() - Constructor for class org.biojava.utils.bytecode.CodeUtils
 
CodonPref - Interface in org.biojava.bio.symbol
 
CodonPrefFilter - Interface in org.biojava.bio.symbol
 
CodonPrefFilter.AcceptAll - Class in org.biojava.bio.symbol
 
CodonPrefFilter.ByName - Class in org.biojava.bio.symbol
 
CodonPrefFilter.EverythingToXML - Class in org.biojava.bio.symbol
 
CodonPrefTools - Class in org.biojava.bio.symbol
An utility class for codon preferences
CodonPrefTools() - Constructor for class org.biojava.bio.symbol.CodonPrefTools
 
CollectionConstraint - Interface in org.biojava.bio
Used by AnnotationType to represent the constraint on the collection of values in a property-slot.
CollectionConstraint.AllValuesIn - Class in org.biojava.bio
CollectionConstraint which validates all members of a Collection.
CollectionConstraint.And - Class in org.biojava.bio
A collection constraint that accpepts collections iff they are accepted by both child constraints.
CollectionConstraint.Contains - Class in org.biojava.bio
CollectionConstraint which validates a portion of a Collection.
CollectionConstraint.Or - Class in org.biojava.bio
A collection constraint that accepts items iff they are accepted by either child constraints.
colors - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
The map containing the colors for drawing traces.
ColourCommand - Interface in org.biojava.bio.program.blast2html
Interface for specifying whether a particular pair of residues/bases should be coloured.
columns - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
columns() - Method in class org.biojava.bio.dp.ProfileHMM
Retrieve the number of columns in the model.
columns() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
 
columns() - Method in interface org.biojava.bio.dp.WeightMatrix
The number of columns modeled by the weight matrix.
Comment - Interface in org.biojavax
A simple ranked comment designed to be used for BioEntry comments in BioSQL.
COMMENT - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
COMMENT - Static variable in interface org.biojavax.bio.BioEntry
 
COMMENT_ABS_MAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_ABSORPTION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_ERROR_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_EVENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_EXPERIMENTS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_INTERACT_INTACT_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_INTERACT_LABEL_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_INTERACTANT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_ISOFORM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_KIN_KM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_KIN_VMAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_KINETICS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_LINK_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_LINK_URI_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_LOCTYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_METHOD_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_ORGANISMS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_PH_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_REDOX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
COMMENT_TEMPERATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
commentIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
This iterator iterates over all parts of the comment.
commentIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
Iterate over all comments in the file in order.
commentLine(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
A comment line has been encountered.
commentLine(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
 
commentLine(String) - Method in class org.biojava.bio.program.gff.GFFWriter
Prints the comment directly to the PrintWriter after adding a leading '#'.
commentLine(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
A comment line has been encountered.
commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
 
commentText(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
Receiving free text inside a comment tag.
commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
commentText(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
Receiving free text inside a comment tag.
commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
commentText(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Receiving free text inside a comment tag.
commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
 
commit() - Method in class org.biojava.bio.program.indexdb.BioStore
commit writes an index to disk.
commit() - Method in class org.biojava.bio.seq.db.BioIndex
 
commit() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
commit commits changes.
commit() - Method in interface org.biojava.bio.seq.db.IndexStore
Commit the stored indices to permanent storage.
commit() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
commit() - Method in interface org.biojava.utils.Commitable
commit commits pending changes.
commit() - Method in class org.biojava.utils.FileAsList
 
Commitable - Interface in org.biojava.utils
Implementations of Commitable support atomic changes from one known state to another via commit/rollback semantics.
CommitFailure - Exception in org.biojava.utils
 
CommitFailure(String) - Constructor for exception org.biojava.utils.CommitFailure
 
CommitFailure(String, Throwable) - Constructor for exception org.biojava.utils.CommitFailure
 
CommitFailure(Throwable) - Constructor for exception org.biojava.utils.CommitFailure
 
commitStore() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
COMMON - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
Use this to define common names for things.
COMMON_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
COMNAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CompactedDataStore - Class in org.biojava.bio.program.ssaha
An implementation of DataStore that will map onto a file using the NIO constructs.
CompactedDataStoreFactory - Class in org.biojava.bio.program.ssaha
Builder for a data store that is backed by a java.nio.MappedByteBuffer.
CompactedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
 
ComparableOntology - Interface in org.biojavax.ontology
An Ontology that can be compared to another.
ComparableTerm - Interface in org.biojavax.ontology
Makes Term objects comparable properly and adds some extra features to them.
ComparableTriple - Interface in org.biojavax.ontology
Comparable triples, obviously.
comparator() - Static method in class org.biojava.bio.seq.ByLocationMinMaxComparator
 
COMPARATOR - Static variable in class org.biojava.ontology.Synonym
 
compare(Object, Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
 
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
 
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
 
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
 
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
 
compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxComparator
 
compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
 
compare(Object, Object) - Method in class org.biojava.bio.seq.Feature.ByLocationComparator
 
compare(Object, Object) - Method in class org.biojava.bio.seq.io.EmblReferenceComparator
 
compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblFeatureComparator
Deprecated.
 
compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblPropertyComparator
Deprecated.
 
compareTo(Object) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
compareTo(Object) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Empty Rich Locations return 0 when compared to other Empty ones, or -1 otherwise.
compareTo(Object) - Method in class org.biojavax.bio.seq.RichLocation.Strand
Strands are compared first by symbol, then by number.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Features are sorted first by rank, then parent, type, and source.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Relations are compared first by rank, then object, subject, then finally term.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntry
Bioentries are ordered first by namespace, then name, accession, and finally version.
compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
A relationship is compared first by rank, then object, subject, and term.
compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
NCBITaxon objects are compared only by their NCBITaxID fields.
compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
Taxon names are sorted by class first, then name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableOntology
Ontologies are compared only by name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
Terms are sorted by ontology first, then name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
Triples are sorted in order of ontology, subject, object, and finally predicate.
compareTo(Object) - Method in class org.biojavax.SimpleComment
Comments are ordered first by their rank, then by a string comparison of their text values.
compareTo(Object) - Method in class org.biojavax.SimpleCrossRef
Compares cross references first by database name, then by accession, then by version.
compareTo(Object) - Method in class org.biojavax.SimpleDocRef
Document references are compared first by author, then by location, then by title.
compareTo(Object) - Method in class org.biojavax.SimpleDocRefAuthor
Document authors are compared first by name, then consortium status, then editor status.
compareTo(Object) - Method in class org.biojavax.SimpleNamespace
Namespaces are compared only by name.
compareTo(Object) - Method in class org.biojavax.SimpleNote
Notes are compared first by rank, then by the term.
compareTo(Object) - Method in class org.biojavax.SimpleRankedCrossRef
Ranked cross references are sorted first by rank, then by cross reference.
compareTo(Object) - Method in class org.biojavax.SimpleRankedDocRef
Ranked document references are sorted first by rank then location then by actual document reference.
compareTo(Synonym) - Method in class org.biojava.ontology.Synonym
 
compile(String) - Method in class org.biojava.utils.regex.PatternFactory
Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
compile(String, String) - Method in class org.biojava.utils.regex.PatternFactory
Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
complement(Symbol) - Static method in class org.biojava.bio.seq.DNATools
Complement the symbol.
complement(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
Complement the symbol.
complement(Symbol) - Static method in class org.biojava.bio.seq.RNATools
Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
Retrieve a complement view of list.
complement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools
Retrieve a complement view of list.
complement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
Retrieve a complement view of list.
COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
complementTable() - Static method in class org.biojava.bio.seq.DNATools
Get a translation table for complementing DNA symbols.
complementTable() - Static method in class org.biojava.bio.seq.NucleotideTools
Get a translation table for complementing Nucleotide symbols.
complementTable() - Static method in class org.biojava.bio.seq.RNATools
Get a translation table for complementing DNA symbols.
complete() - Method in interface org.biojava.bio.program.fastq.ParseListener
Notify this listener the FASTQ formatted sequence is complete.
completeCycle() - Method in interface org.biojava.bio.dp.HMMTrainer
indicate that a cycle of training is completed and the emission/transition matrices should be updated.
completeCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer
 
completedActivity(Object) - Method in interface org.biojava.utils.ActivityListener
Notification that an activity is complete.
COMPONENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ComponentFeature - Interface in org.biojava.bio.seq
Feature which represents a component in an assembly (contig).
ComponentFeature.Template - Class in org.biojava.bio.seq
Template for constructing a new ComponentFeature.
componentLocation - Variable in class org.biojava.bio.seq.ComponentFeature.Template
 
componentLocationIterator() - Method in class org.biojava.bio.symbol.MergeLocation
 
componentSequence - Variable in class org.biojava.bio.seq.ComponentFeature.Template
 
componentSequenceName - Variable in class org.biojava.bio.seq.ComponentFeature.Template
 
composeName(String, String) - Method in class org.biojava.naming.ObdaContext
 
composeName(Name, Name) - Method in class org.biojava.naming.ObdaContext
 
Composite() - Constructor for class org.biojava.directory.RegistryConfiguration.Composite
 
Composition - Class in org.biojava.bio.molbio
Computes composition statistics about a SymbolList.
Composition() - Constructor for class org.biojava.bio.molbio.Composition
 
Compound() - Constructor for class org.biojava.bio.program.formats.Ligand.Compound
 
CompoundRichLocation - Class in org.biojavax.bio.seq
An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
CompoundRichLocation() - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
 
CompoundRichLocation(Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
Constructs a CompoundRichLocation from the given set of members, with the default term of "join".
CompoundRichLocation(ComparableTerm, Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
Constructs a CompoundRichLocation from the given set of members.
compute(double) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc.ChargeCalculator
computes charge at given pH
compute(double) - Method in interface org.biojava.utils.math.ComputeObject
workhorse method for this class.
ComputeObject - Interface in org.biojava.utils.math
interface for classes that return a single double precision value for a single double precision argument.
conditionedDistributions() - Method in interface org.biojava.bio.dist.OrderNDistribution
Get the conditioned distributions.
CONFIG_FILE - Static variable in class org.biojava.directory.SystemRegistry
 
CONFIG_LOCATOR - Static variable in class org.biojava.directory.SystemRegistry
 
conjunctAdd - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
conjunction - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
connect() - Method in interface org.biojava.bibliography.BibRefQuery
It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication.
connect() - Method in interface org.biojava.bibliography.BibRefSupport
It creates a connection to an object providing the supporting utilities, or/and it makes all necessary initialization steps needed for further communication.
connect() - Method in interface org.biojava.utils.candy.CandyFinder
It creates a connection to an object representing a vocabulary finder, or/and it makes all necessary initialization steps needed for further communication.
connect(byte[]) - Method in interface org.biojava.bibliography.BibRefQuery
It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication, and it makes the collection described by collectionId the current collection.
connectModel() - Method in class org.biojava.bio.dp.ProfileHMM
This is called by constructor in setting up the allowed transitions in the model
connectModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
This is called by constructor in setting up the allowed transitions in the model
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ConstantPool - Class in org.biojava.utils.bytecode
Build a Java class file constant pool.
ConstantPool() - Constructor for class org.biojava.utils.bytecode.ConstantPool
 
constantPoolSize() - Method in class org.biojava.utils.bytecode.ConstantPool
 
Constants - Class in org.biojava.utils
Some usefull constants for working with binary files.
Constants() - Constructor for class org.biojava.utils.Constants
 
constrain(double) - Method in enum org.biojava.bio.program.fastq.FastqVariant
Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.
construct(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
Constructs a RichLocation object based on the given collection of members.
constructSubsets() - Method in class org.biojava.utils.automata.DfaBuilder
 
containedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features with locations wholly contained by the specified Location.
ContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
Creates a filter that returns everything contained within loc.
ContainedByRichLocation(RichLocation) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
Creates a filter that returns everything contained within loc.
contains(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
contains(int) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
 
contains(int) - Method in class org.biojava.bio.symbol.CircularLocation
 
contains(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
contains(int) - Method in interface org.biojava.bio.symbol.Location
Checks if this location contains a point.
contains(int) - Method in class org.biojava.bio.symbol.PointLocation
 
contains(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Checks if this location contains a point.
contains(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Checks if this location contains a point.
contains(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Checks if this location contains a point.
contains(Object) - Method in class org.biojava.utils.MergingSet
 
contains(Object) - Method in class org.biojava.utils.SmallSet
 
contains(Object) - Method in class org.biojavax.ga.util.WeightedSet
 
contains(String) - Method in interface org.biojava.utils.candy.CandyVocabulary
It checks if a given entry exists in this vocabulary.
contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
 
contains(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
 
contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
 
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
 
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
contains(Location) - Method in class org.biojava.bio.symbol.CircularLocation
 
contains(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
contains(Location) - Method in interface org.biojava.bio.symbol.Location
Checks if this location contains the other.
contains(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Checks if this location contains the other.
contains(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Checks if this location contains the other.
contains(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Checks if this location contains the other.
contains(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
Return true iff all indices in locB are also contained by locA.
contains(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
contains(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet
Returns whether or not this Alphabet contains the symbol.
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
contains(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
contains(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
 
contains(Note) - Method in class org.biojavax.EmptyRichAnnotation
Returns true if the given note exists in this annotation.
contains(Note) - Method in interface org.biojavax.RichAnnotation
Returns true if the given note exists in this annotation.
contains(Note) - Method in class org.biojavax.SimpleRichAnnotation
Returns true if the given note exists in this annotation.
Contains(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.Contains
Create a Contains based upon a PropertyConstraint and a cardinality.
CONTAINS_PREFIX - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
containsAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
 
containsCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
containsFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder
Check if the feature is present in this holder.
containsFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
containsFeature() will return true if this seq contains the feature in question, or if if the original (non reverse complement) sequence contains the feature;
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.MergeFeatureHolder
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly
 
containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
 
containsFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Check if the feature is present in this holder.
containsFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence
Check if the feature is present in this holder.
containsFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
Returns true if the given FeatureFilter is already contained in this renderer.
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
containsKey(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
 
containsKey(Object) - Method in class org.biojava.utils.OverlayMap
 
containsKey(Object) - Method in class org.biojava.utils.SmallMap
 
containsName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
Tests for the presence of a name in a given class.
containsName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Tests for the presence of a name in a given class.
containsNode(FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
 
containsObject(NexusObject) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
Checks to see if we contain an object.
containsProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
 
containsProperty(Object) - Method in interface org.biojava.bio.Annotation
Returns whether there the property is defined.
containsProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
 
containsProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
 
containsProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation
Returns whether there the property is defined.
containsProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation
Deprecated. 
containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
Detects whether a particular table is present in the database.
containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.HypersonicDBHelper
Deprecated.
 
containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
Deprecated.
 
containsTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Checks to see if we contain the given TAXLABEL.
containsTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Checks to see if we contain the given TAXLABEL.
containsTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Checks to see if we contain the given TAXLABEL.
containsTerm(String) - Method in class org.biojava.ontology.IntegerOntology
 
containsTerm(String) - Method in interface org.biojava.ontology.Ontology
Determines if this ontology currently contains a term named name
containsTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
 
containsTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
Determines if this ontology currently contains a term named name
containsTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
Returns wether a transition exists or not.
containsTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
containsTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
 
containsTranslation(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Checks to see if we contain the given translation.
containsTree(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Checks to see if we contain the given tree.
containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology
 
containsTriple(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology
See if a triple exists in this ontology
containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl
 
containsTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
See if a triple exists in this ontology
CONTENT - Static variable in interface org.biojava.bio.alignment.Alignment
Signals that SymbolLists will be added to or removed from an alignment.
contextForLabel(SequenceRenderContext, String) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
 
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
contributors - Variable in class org.biojava.bibliography.BibRef
The authors and contributors are responsible for creating the contents of the cited resource.
convert() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
 
convert() - Method in class org.biojava.bio.program.PdbToXMLConverter
 
convert(Fastq) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
 
convert(Fastq) - Method in class org.biojava.bio.program.fastq.SangerFastqWriter
 
convert(Fastq) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter
 
convert(Fastq, FastqVariant) - Static method in class org.biojava.bio.program.fastq.FastqTools
Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
convert(FeatureFilter) - Static method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools
Convert a non-BioSQL FeatureFilter into a BioSQL one.
convertTo(FastqVariant) - Method in class org.biojava.bio.program.fastq.Fastq
Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.
convertValueToText(Object, boolean, boolean, boolean, int, boolean) - Method in class org.biojava.bio.gui.FeatureTree
Labels Sequence objects with their name, Annotations with the tag Annotations, Features with the tag Features and other objects with the toString value.
COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
coordinateDisplayOn(boolean) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
coordinateDisplayOn toggles the display of sequence coordinates.
COPYRIGHT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
cost - Variable in class org.biojava.bibliography.BiblioWebResource
The cost of accessing the resource.
CostMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch
A matrix with the size length(sequence1) times length(sequence2)
Count - Interface in org.biojava.bio.dist
An encapsulation of a count over the Symbols within an alphabet.
CountedBufferedReader - Class in org.biojava.utils.io
 
CountedBufferedReader(Reader) - Constructor for class org.biojava.utils.io.CountedBufferedReader
 
countFeatures() - Method in interface org.biojava.bio.seq.FeatureHolder
Count how many features are contained.
countFeatures() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
countFeatures() - Method in class org.biojava.bio.seq.impl.DummySequence
 
countFeatures() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
countFeatures() - Method in class org.biojava.bio.seq.impl.RevCompSequence
 
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
countFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
 
countFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
countFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
countFeatures() - Method in class org.biojava.bio.seq.MergeFeatureHolder
 
countFeatures() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
countFeatures() - Method in class org.biojava.bio.seq.SimpleAssembly
 
countFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
 
countFeatures() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Count how many features are contained.
countFeatures() - Method in class org.biojavax.bio.seq.ThinRichSequence
Count how many features are contained.
COUNTS - Static variable in interface org.biojava.bio.dist.Count
Whenever a component count changes the values that would be returned by getCount, they should fire a ChangeEvent with this object as the type.
countToDistribution(Count) - Static method in class org.biojava.bio.dist.DistributionTools
Make a distribution from a count.
coverage - Variable in class org.biojava.bibliography.BibRef
It defines an extent or scope of the content of the cited resource.
coverage(Location) - Static method in class org.biojava.bio.symbol.LocationTools
Return the number of positions which are covered by a Location
CRC64Checksum - Class in org.biojavax.utils
Utility class that calculates a CRC64 checksum on a stream of bytes.
CRC64Checksum() - Constructor for class org.biojavax.utils.CRC64Checksum
 
create(File) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
Creates a new Chromatogram object from the named file.
create(File) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
Create a new ABIF object from a file.
create(File) - Static method in class org.biojava.bio.program.scf.SCF
 
create(InputStream) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
Creates a new Chromatogram object from the supplied stream.
create(InputStream) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
Create a new ABIF object from a stream of bytes.
create(InputStream, long) - Static method in class org.biojava.bio.program.scf.SCF
 
CREATE_DATE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
CREATE_DUMMYSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
 
CREATE_REALSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
 
CREATE_REL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
createArrayType(String) - Static method in class org.biojava.utils.bytecode.ParametricType
Create a new ParametricType that claims to resolve to an array type.
createBinary(String) - Static method in class org.biojavax.ga.util.GATools
Creates a SymbolList in the GABinary Alphabet
createBioStore() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
createBioStore creates a BioStore reflecting the current state of the factory and returns a reference to it.
createCode(OutputStream) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
createDistribution(Alphabet) - Method in interface org.biojava.bio.dist.DistributionFactory
Generate a new Distribution as requested.
createDistribution(Alphabet) - Method in class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
 
createDistribution(Alphabet) - Method in class org.biojava.bio.dist.OrderNDistributionFactory
Creates an OrderNDistribution of the appropriate type.
createDNA(String) - Static method in class org.biojava.bio.seq.DNATools
Return a new DNA SymbolList for dna.
createDNA(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
Create and return a new DNA SymbolList from the specified FASTQ formatted sequence.
createDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools
Return a new DNA Sequence for dna.
createDNASequence(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
Create and return a new DNA Sequence from the specified FASTQ formatted sequence.
createDP(MarkovModel) - Method in interface org.biojava.bio.dp.DPFactory
 
createDP(MarkovModel) - Method in class org.biojava.bio.dp.DPFactory.DefaultFactory
 
createDummy(String, String) - Static method in class org.biojava.bio.seq.SequenceTools
Create a new Sequence that has no annotation, no features and a zero-length symbol list.
createDummy(Alphabet, int, Symbol, String, String) - Static method in class org.biojava.bio.seq.SequenceTools
Create a new Sequence that contains a single symbol repeated over and over.
createDummySequence(String, Alphabet, int) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
createEmblParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.CircularView
Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.FeatureHolder
Create a new Feature, and add it to this FeatureHolder.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.DummySequence
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.RevCompSequence
createFeature() will call createFeature() on the underlying Sequence.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SubSequence
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Create a projected feature with properties matching the template.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
 
createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Create a new Feature, and add it to this FeatureHolder.
createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.ThinRichSequence
Create a new Feature, and add it to this FeatureHolder.
createFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
Deprecated.
Please use new 1-arg createFeature instead.
createFeature(Feature, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Create a new projected feature.
createFeature(Feature, Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
createFeatureHolder() - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
createFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler
Create a new template of the appropriate type.
createFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
 
createField(String, CodeClass, int) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
createGappedDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools
Get a new dna as a GappedSequence
createGappedProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools
Get a new protein as a GappedSequence
createGFFRecord(Feature, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Internal method to create a GFFRecord from an individual Feature.
createImmutableAlignment(Map) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
A factory method for creating new immutable alignments, particularly for use as base call alignments.
createImmutableSymbolList(Alphabet, List) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
A factory method for creating new symbol lists with a given alphabet.
createInnerBounds(CircularRendererContext) - Static method in class org.biojava.bio.gui.sequence.GUITools
 
createList(Object[]) - Static method in class org.biojava.utils.ListTools
 
createList(List) - Static method in class org.biojava.utils.ListTools
 
createMatches() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
 
createMethod(String, CodeClass, CodeClass[], int) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
Create a new method.
createMethod(String, CodeClass, CodeClass[], String[], int) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
Create a new method.
createNodeSet() - Method in class org.biojava.utils.automata.FiniteAutomaton
 
createNodeSet() - Method in interface org.biojava.utils.automata.NfaBuilder
 
createNodeSet() - Method in class org.biojava.utils.automata.NfaSubModel
 
createNucleotide(String) - Static method in class org.biojava.bio.seq.NucleotideTools
Return a new Nucleotide SymbolList for nucleotide.
createNucleotideSequence(String, String) - Static method in class org.biojava.bio.seq.NucleotideTools
Return a new Nucleotide Sequence for nucleotide.
createObjectType(String) - Static method in class org.biojava.utils.bytecode.ParametricType
Create a new ParametricType that claims to resolve to an object type.
createOntology(String, String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
createOntology(String, String) - Method in interface org.biojava.ontology.OntologyFactory
Creates a new Ontology
createOntologyTerm(Ontology) - Method in class org.biojava.ontology.Ontology.Impl
 
createOrthologue(int, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
Create an orthologue.
createOrthologue(int, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
 
createOrthologue(Taxon, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
Create an orthologue.
createOrthologue(Taxon, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
 
createOrthoPair(Orthologue, Orthologue, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
Create a curated orthology entry.
createOrthoPair(Orthologue, Orthologue, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
 
createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
Create a computed orthology entry.
createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
 
createOrthoPairSet() - Method in interface org.biojava.bio.program.homologene.HomologeneDB
Create a Homologene Group.
createOrthoPairSet() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
 
createOuterBounds(CircularRendererContext, double) - Static method in class org.biojava.bio.gui.sequence.GUITools
 
createPhred(SymbolList, SymbolList) - Static method in class org.biojava.bio.program.phred.PhredTools
Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.
createPhredSequence(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
Create and return a new PhredSequence from the specified FASTQ formatted sequence.
createPrimitiveType(String) - Static method in class org.biojava.utils.bytecode.ParametricType
Create a new ParametricType that claims to resolve to a primative type.
createProtease(String, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
createProtease(String, boolean, String, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
createProtease(SymbolList, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
createProtease(SymbolList, boolean, SymbolList, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
Creates and registers a new Protease.
createProtein(String) - Static method in class org.biojava.bio.seq.ProteinTools
Return a new Protein SymbolList for protein.
createProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools
Return a new PROTEIN Sequence for protein.
createQualityScores(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
Create and return a new SymbolList of quality scores from the specified FASTQ formatted sequence.
createRecord(GFFDocumentHandler, List, String, String) - Method in class org.biojava.bio.program.gff.GFFParser
Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
createRecord(GFF3DocumentHandler, List, String, String, Ontology, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser
Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.
createRegex(SymbolList) - Static method in class org.biojava.bio.symbol.MotifTools
createRegex creates a regular expression which matches the SymbolList.
createRenderer(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
createRenderer(int) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
 
createRichSequence(String, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
Create a new RichSequence in the specified namespace.
createRichSequence(String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
Create a new RichSequence in the default namespace.
createRichSequence(String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
Create a new RichSequence in the default namespace.
createRichSequence(Namespace, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
Create a new RichSequence in the specified namespace.
createRichSequence(Namespace, String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
Create a new RichSequence in the specified namespace.
createRNA(String) - Static method in class org.biojava.bio.seq.RNATools
Return a new RNA SymbolList for rna.
createRNASequence(String, String) - Static method in class org.biojava.bio.seq.RNATools
Return a new RNA Sequence for rna.
createSequence(SymbolList, String, String, Annotation) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
 
createSequence(SymbolList, String, String, Annotation) - Method in interface org.biojava.bio.seq.SequenceFactory
Deprecated.
Creates a sequence using these parameters.
createSequence(SymbolList, String, String, Annotation) - Static method in class org.biojava.bio.seq.SequenceTools
 
createSeriesList(String, String, int) - Static method in class org.biojava.utils.ListTools
Create a new SeriesList with the given leader, trailer and size.
createState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
createSubcontext(String) - Method in class org.biojava.naming.ObdaContext
 
createSubcontext(String, Attributes) - Method in class org.biojava.naming.ObdaContext
 
createSubcontext(Name) - Method in class org.biojava.naming.ObdaContext
 
createSubcontext(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
 
createSwissprotParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
 
createSymbol(char, String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager
Deprecated.
Use the two-arg version of this method instead.
createSymbol(char, Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Deprecated.
use the new version, without the token argument
createSymbol(char, Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Deprecated.
use the three-arg version of this method instead.
createSymbol(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generate a new AtomicSymbol instance with a name and an Empty Annotation.
createSymbol(String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generate a new AtomicSymbol instance with a name and Annotation.
createSymbol(Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generates a new Symbol instance that represents the tuple of Symbols in symList.
createSymbol(Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generates a new Symbol instance that represents the tuple of Symbols in symList.
createSymbolDistribution(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
Create and return a new array of symbol Distributions from the specified FASTQ formatted sequence.
createTaxon(int, String) - Static method in class org.biojava.bio.program.homologene.HomologeneTools
add a Taxon
createTaxon(String, String) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
Deprecated.
 
createTaxon(String, String) - Method in interface org.biojava.bio.taxa.TaxonFactory
Deprecated.
Create a new orphan Taxon with a given scientific and common name.
createTaxon(String, String) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
Deprecated.
 
createTemplate() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
generates a very basic Template for the feature with SmallAnnotation in the annotation field.
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
 
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
 
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
 
createTemplate() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
generates a very basic Template for the feature with SmallAnnotation in the annotation field.
createTerm(String) - Method in class org.biojava.ontology.IntegerOntology
 
createTerm(String) - Method in interface org.biojava.ontology.Ontology
Create a new term in this ontology.
createTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
 
createTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
Create a new term in this ontology.
createTerm(String, String) - Method in class org.biojava.ontology.IntegerOntology
 
createTerm(String, String) - Method in interface org.biojava.ontology.Ontology
Create a new term in this ontology.
createTerm(String, String) - Method in class org.biojava.ontology.Ontology.Impl
 
createTerm(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in class org.biojava.ontology.IntegerOntology
 
createTerm(String, String, Object[]) - Method in interface org.biojava.ontology.Ontology
Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in class org.biojava.ontology.Ontology.Impl
 
createTerm(String, String, Object[]) - Method in class org.biojavax.ontology.SimpleComparableOntology
Create a new term in this ontology.
createTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
Makes a transition between two states legal.
createTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
createTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
 
createTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.IntegerOntology
 
createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.ontology.Ontology
Creates a new Triple.
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.Ontology.Impl
 
createTriple(Term, Term, Term, String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
Creates a new Triple.
createType(String) - Static method in class org.biojava.utils.bytecode.ParametricType
Create a new ParametricType that claims nothing.
createType(String, FeatureFilter, Set) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
Create a new type in this repository.
createType(String, CodeClass[]) - Static method in class org.biojava.utils.bytecode.ParametricType
Create a new ParametricType that claims to be castable to all the classes in a list.
createUnigene(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
 
createUnigene(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
 
createUnigene(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
 
createUnigene(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
Create a new UnigeneDB instance referred to by a URL.
createURL(Object) - Method in interface org.biojava.utils.net.URLFactory
createURL returns a URL which is relevant to the object in a way specified by the implementation.
createVariable(String, String) - Method in class org.biojava.ontology.IntegerOntology
 
createVariable(String, String) - Method in interface org.biojava.ontology.Ontology
Create a new term in this ontology that is used as a variable.
createVariable(String, String) - Method in class org.biojava.ontology.Ontology.Impl
 
createVariable(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
Create a new term in this ontology that is used as a variable.
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
 
criterionAliasMap() - Method in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
Returns a map of property names (keys) to aliases (values), if the criterion returned by asCriterion() uses aliases at all.
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
 
CROSS_OVER_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
 
CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
 
CrosshairRenderer - Class in org.biojava.bio.gui.sequence
CrosshairRenderer draws a crosshair, optionally with coordinates.
CrosshairRenderer() - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer
Creates a new CrosshairRenderer in light grey with coordinates displayed.
CrosshairRenderer(Paint) - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer
Creates a new CrosshairRenderer of the specified colour, with coordinates displayed.
CrossOverFunction - Interface in org.biojavax.ga.functions
Crosses two chromosomes.
CrossOverFunction.NoCross - Class in org.biojavax.ga.functions
A place holder CrossOverFunction that doesn't perform cross overs
CrossProductTokenization - Class in org.biojava.bio.seq.io
Tokenization for cross-product alphabets.
CrossProductTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
 
CrossProductTokenization(Alphabet, List) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
 
CrossRef - Interface in org.biojavax
Represents a cross reference to another database.
CROSSREF - Static variable in interface org.biojavax.bio.seq.RichFeature
 
CROSSREF - Static variable in interface org.biojavax.DocRef
 
CrossReferenceResolutionException - Exception in org.biojavax
An exception that indicates that an attempt to resolve a CrossRef has failed.
CrossReferenceResolutionException() - Constructor for exception org.biojavax.CrossReferenceResolutionException
Creates a new instance of CrossReferenceResolutionException
CrossReferenceResolutionException(String) - Constructor for exception org.biojavax.CrossReferenceResolutionException
Creates a new instance of CrossReferenceResolutionException with a message.
CrossReferenceResolutionException(String, Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException
Creates a new instance of CrossReferenceResolutionException with a message and a cause.
CrossReferenceResolutionException(Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException
Creates a new instance of CrossReferenceResolutionException with a cause.
CrossReferenceResolver - Interface in org.biojavax
This interface returns symbols or sequence for a given cross-reference.
crossReferences - Variable in class org.biojava.bibliography.BibRef
It is an array of identifiers, all of them pointing to the same cited source but usually stored in different bibliographic repositories.
crypticVariable - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
cState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
Gets the c loop state
CURATED - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
CURATED - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
 
currentCol() - Method in interface org.biojava.bio.dp.onehead.DPCursor
The current column of the matrix.
currentCol() - Method in class org.biojava.bio.dp.onehead.SmallCursor
 
currentRes() - Method in interface org.biojava.bio.dp.onehead.DPCursor
The current symbol.
CUT_COMPOUND - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
CUT_COMPOUND a cut type where the enzyme cuts in two positions relative to the recognition site.
CUT_SIMPLE - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
CUT_SIMPLE a cut type where the enzyme cuts in one position relative to the recognition site.
cutType - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
cys() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Cysteine (C)

D

d() - Static method in class org.biojava.bio.seq.DNATools
 
d() - Static method in class org.biojava.bio.seq.NucleotideTools
 
d() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Aspartic Acid
D_MELANOGASTER - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
D_RERIO - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
data - Variable in class org.biojava.bio.alignment.FlexibleAlignment
 
DATA_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.DataBlock
A constant representing the name of Data blocks.
DATA_TYPE_ASCII_ARRAY - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
DATA_TYPE_DATE - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
DATA_TYPE_FLOAT - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
DATA_TYPE_INTEGER - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
DATA_TYPE_PSTRING - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
DATA_TYPE_TIME - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
DATABASE - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
A name for a comment type.
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
databaseID - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
 
DatabaseURLGenerator - Interface in org.biojava.bio.program.blast2html
Takes a database ID and some configuration properties ( such as base URL ) and returns either a URL or a full anchor tag.
DataBlock - Class in org.biojavax.bio.phylo.io.nexus
Represents Nexus data blocks.
DataBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.DataBlock
Delegates to NexusBlock.Abstract constructor using DataBlock.DATA_BLOCK as the name.
DataBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus
Builds Nexus characters blocks.
DataBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.DataBlockBuilder
 
DataBlockListener - Interface in org.biojavax.bio.phylo.io.nexus
Listens to events that represent Nexus data blocks.
DataBlockParser - Class in org.biojavax.bio.phylo.io.nexus
Parses Nexus data blocks.
DataBlockParser(DataBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.DataBlockParser
Delegates to CharactersBlockParser.
dataRecord - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
DATASOURCE - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
DATASOURCE_SELECTION - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
DataStore - Interface in org.biojava.bio.program.ssaha
A repository that can be searched with a sequence.
DataStoreFactory - Interface in org.biojava.bio.program.ssaha
Builder for a data store.
dataType - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
date - Variable in class org.biojava.bibliography.BibRef
Defines a date associated with an event in the life cycle of the cited resource when this resource became available.
DATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
DATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
DATE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
DATE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
dateFormat - Variable in class org.biojava.ontology.obo.OboFileParser
 
DB_NUCLEOTIDE - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
 
DB_PROTEIN - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
 
DBHelper - Class in org.biojava.bio.seq.db.biosql
Deprecated.
Use hibernate and org.biojavax.bio.db.*
DBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
 
DBHelper.BioSequenceStyle - Class in org.biojava.bio.seq.db.biosql
Deprecated.
 
DBHelper.DeleteStyle - Class in org.biojava.bio.seq.db.biosql
Deprecated.
 
DBHelper.JoinStyle - Class in org.biojava.bio.seq.db.biosql
Deprecated.
 
DBREF_DB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
DBREF_PRIMARY_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
DBREF_SEC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
DBREFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
DBResolver(SequenceDB) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
 
dbxp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
dbxp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
dbxp - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
DBXREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
debug(String) - Method in class org.biojava.bio.alignment.AbstractULAlignment
 
DEBUG - Static variable in class org.biojava.utils.io.SoftHashMap
 
DebuggingRichSeqIOListener - Class in org.biojavax.bio.seq.io
This is purely for debugging purposes.
DebuggingRichSeqIOListener(InputStream) - Constructor for class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
declareNamespace(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
declareNamespace(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
Hints that a namespace is going to be used in a sub-tree.
decodeDNAToken(char) - Static method in class org.biojava.bio.program.abi.ABIFParser
Decodes a character into a Symbol in the DNA alphabet.
decorate(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
decorate(Location) - Method in class org.biojava.bio.symbol.BetweenLocation
 
decorate(Location) - Method in class org.biojava.bio.symbol.CircularLocation
 
DEF - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
DEFAULT - Static variable in interface org.biojava.bio.dist.DistributionFactory
The default DistributionFactory object.
DEFAULT - Static variable in class org.biojava.bio.dist.OrderNDistributionFactory
Factory which used DistributionFactory.DEFAULT to create conditioned distributions.
DEFAULT - Static variable in interface org.biojava.bio.dp.DPFactory
 
DEFAULT - Static variable in class org.biojava.bio.program.phred.PhredFormat
 
DEFAULT - Static variable in class org.biojava.bio.seq.impl.FeatureImpl
Default implementation of FeatureRealizer, which wraps simple implementations of Feature and StrandedFeature.
DEFAULT - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
DEFAULT - Static variable in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
 
DEFAULT - Static variable in class org.biojava.bio.seq.io.GAMEFormat
 
DEFAULT - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
DEFAULT - Static variable in class org.biojava.bio.seq.projection.ProjectionEngine
The standard projection engine object.
DEFAULT - Static variable in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
 
DEFAULT - Static variable in interface org.biojavax.ga.functions.SelectionFunction
Selects all members of a population for replication
DEFAULT_CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
 
DEFAULT_DELIMITERS - Static variable in class org.biojava.utils.TypedProperties
the default string of delimiter characters used by getAsStringList()
DEFAULT_FINDER_NAME - Static variable in interface org.biojava.utils.candy.CandyFinder
A default name of this (and any) finder.
DEFAULT_LIMIT - Static variable in class org.biojava.utils.io.SoftHashMap
 
DEFAULT_MAX_CROSS - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
 
DEFAULT_MUTATION_PROBS - Static variable in interface org.biojavax.ga.functions.MutationFunction
 
DEFAULT_TERM_CHAR - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree
 
DEFAULT_VARIANT - Static variable in class org.biojava.bio.program.fastq.FastqBuilder
Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER.
DefaultDistributionFactory() - Constructor for class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
 
DefaultFactory(CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.DPFactory.DefaultFactory
 
DefaultMaskingDetector() - Constructor for class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
 
DefaultOps - Class in org.biojava.ontology
Default implementation of OntologyOps.
DefaultOps() - Constructor for class org.biojava.ontology.DefaultOps
 
DefaultURLGeneratorFactory - Class in org.biojava.bio.program.blast2html
A simple default URLGeneratorFactory which returns a single NcbiDatabaseURLGenerator instance.
DefaultURLGeneratorFactory() - Constructor for class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
 
defineClass(GeneratedCodeClass) - Method in class org.biojava.utils.bytecode.GeneratedClassLoader
Define a class based upon a GeneratedCodeClass.
DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
delegate - Variable in class org.biojava.bio.program.tagvalue.StateMachine
 
delegate(StAXContentHandler) - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
 
delegate(StAXContentHandler) - Method in interface org.biojava.utils.stax.DelegationManager
 
delegates - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
 
DelegatingTransformer(FilterUtils.FilterTransformer, FilterUtils.FilterTransformer) - Constructor for class org.biojava.bio.seq.FilterUtils.DelegatingTransformer
Create a new DelegatingTransformer that will apply t1 and then t2 if t1 fails.
delegationCache - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
 
DelegationManager - Interface in org.biojava.bio.seq.io.agave
Interface which exposes delegation services offered by a StAX event source.
DelegationManager - Interface in org.biojava.utils.stax
Interface which exposes delegation services offered by a StAX event source.
DELETE_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
 
DELETE_MYSQL4 - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
 
DELETE_POSTGRESQL - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
 
deleteTerm(Term) - Method in class org.biojava.ontology.IntegerOntology
 
deleteTerm(Term) - Method in interface org.biojava.ontology.Ontology
Remove a term from an ontology, together with all triples which refer to it.
deleteTerm(Term) - Method in class org.biojava.ontology.Ontology.Impl
 
deleteTerm(Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
Remove a term from an ontology, together with all triples which refer to it.
DELIMITER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
depth - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
depth - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
Description of the Field
DEPTH - Static variable in class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
DEPTH - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Constant DEPTH indicating a change to the depth of the renderer.
DEPTH - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
DESC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
describeSequence(Sequence) - Method in class org.biojava.bio.program.phred.PhredFormat
Return a suitable description line for a Sequence.
describeSequence(Sequence) - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
Return a suitable description line for a Sequence.
description - Variable in class org.biojava.bibliography.BibRef
An account of the content of the cited resource.
description - Variable in class org.biojava.ontology.AbstractTerm
 
description - Variable in class org.biojava.utils.candy.CandyEntry
A value of this entry.
description(String) - Method in interface org.biojava.bio.program.fastq.ParseListener
Notify this parse listener of a description line.
DESCRIPTION - Static variable in interface org.biojavax.bio.BioEntry
 
DESCRIPTION - Static variable in interface org.biojavax.Namespace
 
DESCRIPTION - Static variable in interface org.biojavax.ontology.ComparableOntology
 
DESCRIPTION - Static variable in interface org.biojavax.ontology.ComparableTerm
 
DESCRIPTOR - Static variable in interface org.biojavax.ontology.ComparableTriple
 
destination - Variable in class org.biojava.bio.program.tagvalue.StateMachine.Transition
the terminus of this Transition
destroy() - Method in interface org.biojava.bibliography.BibRefQuery
It frees all resources related to this query collection.
destroy() - Method in interface org.biojava.utils.candy.CandyVocabulary
It frees all resources related to this vocabulary.
destroy() - Static method in class org.biojava.utils.io.FlatFileCache
 
destroySubcontext(String) - Method in class org.biojava.naming.ObdaContext
 
destroySubcontext(Name) - Method in class org.biojava.naming.ObdaContext
 
destroyTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
Breaks a transition between two states legal.
destroyTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
destroyTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
 
DfaBuilder - Class in org.biojava.utils.automata
 
DiagonalAddKernel - Class in org.biojava.stats.svm
Adds a class specific constant to k(x, x).
DiagonalAddKernel() - Constructor for class org.biojava.stats.svm.DiagonalAddKernel
 
DiagonalCachingKernel - Class in org.biojava.stats.svm
Caches the leading diagonal of a kernel matrix.
DiagonalCachingKernel() - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel
Create a new CachingKernel.
DiagonalCachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel
Creates a new DiagonalCachingKernel that nests k.
diddleQueue() - Method in class org.biojava.utils.IndexedChangeHub
 
Digest - Class in org.biojava.bio.proteomics
This class contains methods for calculating the results of proteolytic digestion of a protein sequence this class is not designed to be thread safe
Digest() - Constructor for class org.biojava.bio.proteomics.Digest
Creates a new Digest Bean
DIGEST - Static variable in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
DIGEST - Static variable in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
 
dimensionRatio - Variable in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
 
disconnect() - Method in interface org.biojava.bibliography.BibRefQuery
It disconnects from the repository.
disconnect() - Method in interface org.biojava.bibliography.BibRefSupport
It closes connection with a utility object.
disconnect() - Method in interface org.biojava.utils.candy.CandyFinder
It closes connection with the finder object.
DISJOINT_FROM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
disjunctAdd - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
disjunction - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
DISPLACEMENT - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Constant DISPLACEMENT indicating a change to the Y-axis displacement of the features.
displayString() - Method in class org.biojava.utils.ChangeSupport
 
DistanceBasedTreeMethod - Class in org.biojavax.bio.phylo
 
DistanceBasedTreeMethod() - Constructor for class org.biojavax.bio.phylo.DistanceBasedTreeMethod
 
DISTANCES_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
A constant representing the name of Distances blocks.
DistancesBlock - Class in org.biojavax.bio.phylo.io.nexus
Represents Nexus distances blocks.
DistancesBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Delegates to NexusBlock.Abstract constructor using DistancesBlock.DISTANCES_BLOCK as the name.
DistancesBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus
Builds Nexus distances blocks.
DistancesBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
DistancesBlockListener - Interface in org.biojavax.bio.phylo.io.nexus
Listens to events that represent Nexus distances blocks.
DistancesBlockParser - Class in org.biojavax.bio.phylo.io.nexus
Parses Nexus distances blocks.
DistancesBlockParser(DistancesBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser
Delegates to NexusBlockParser.Abstract.
DistDataSource - Interface in org.biojava.bio.seq.distributed
Object which contributes data to a DistributedSequenceDB.
distForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
 
distOverAlignment(Alignment) - Static method in class org.biojava.bio.dist.DistributionTools
Equivalent to distOverAlignment(a, false, 0.0).
distOverAlignment(Alignment, boolean) - Static method in class org.biojava.bio.dist.DistributionTools
Creates an array of distributions, one for each column of the alignment.
distOverAlignment(Alignment, boolean, double) - Static method in class org.biojava.bio.dist.DistributionTools
Creates an array of distributions, one for each column of the alignment.
DistributedSequenceDB - Class in org.biojava.bio.seq.distributed
Sequence database from the meta-DAS system.
DistributedSequenceDB() - Constructor for class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
Distribution - Interface in org.biojava.bio.dist
An encapsulation of a probability distribution over the Symbols within an alphabet.
DISTRIBUTION - Static variable in interface org.biojava.bio.dp.EmissionState
This signals that the distribution associate with an EmissionState has been altered.
Distribution.NullModelForwarder - Class in org.biojava.bio.dist
Deprecated.
use new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY) instead
DistributionFactory - Interface in org.biojava.bio.dist
A thing that can make Distributions.
DistributionFactory.DefaultDistributionFactory - Class in org.biojava.bio.dist
The default DistributionFactory implementation.
DistributionLogo - Class in org.biojava.bio.gui
The GUI component for rendering a DistributionLogo.
DistributionLogo() - Constructor for class org.biojava.bio.gui.DistributionLogo
Create a new DistributionLogo object.
DistributionTools - Class in org.biojava.bio.dist
A class to hold static methods for calculations and manipulations using Distributions.
DistributionTrainer - Interface in org.biojava.bio.dist
An object that can be used to train a distribution up.
DistributionTrainerContext - Interface in org.biojava.bio.dist
A context within a group of DistributionTrainers can be trained together.
DIVISION - Static variable in interface org.biojavax.bio.BioEntry
 
DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
DIVISION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
DivisionLkpReader - Class in org.biojava.bio.seq.db.emblcd
DivisionLkpReader reads the "division.lkp" file of an EMBL CD-ROM format binary index.
DivisionLkpReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.DivisionLkpReader
Creates a new DivisionLkpReader.
DNA - Static variable in interface org.biojava.bio.chromatogram.Chromatogram
The sequence label for the list of called bases.
DNA - Static variable in class org.biojava.bio.seq.io.FastaAlignmentFormat
 
DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
DNA indicates that a sequence contains DNA (deoxyribonucleic acid) symbols.
DNAAmbPack - Class in org.biojava.bio.symbol
Packing utility class for DNA.
DNAAmbPack() - Constructor for class org.biojava.bio.symbol.DNAAmbPack
 
DNAComposition - Class in org.biojava.bio.molbio
Computes composition statistics about a DNA SymbolList.
DNAComposition() - Constructor for class org.biojava.bio.molbio.DNAComposition
 
DNANoAmbPack - Class in org.biojava.bio.symbol
A Packing implementation which handles the DNA alphabet, without any support for ambiguity symbols.
DNANoAmbPack(byte) - Constructor for class org.biojava.bio.symbol.DNANoAmbPack
Construct a new packing which returns the specified byte value for unknown Symbols (such as ambiguity symbols).
DNANoAmbPack(Symbol) - Constructor for class org.biojava.bio.symbol.DNANoAmbPack
Construct a new packing which translates unknown symbols into the specified symbol.
DNAStyle - Class in org.biojava.bio.gui
A simple implementation of SymbolStyle optimized for DNA.
DNAStyle() - Constructor for class org.biojava.bio.gui.DNAStyle
 
dnaSymbolFromPhred(Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools
Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
dnaToken(Symbol) - Static method in class org.biojava.bio.seq.DNATools
Get a single-character token for a DNA symbol
DNATools - Class in org.biojava.bio.seq
Useful functionality for processing DNA sequences.
DO_NOTHING - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
doAnnotation(Sequence) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
Apply the annotation to a sequence.
docNumber - Variable in class org.biojava.bibliography.BiblioPatent
The document number.
docOffice - Variable in class org.biojava.bibliography.BiblioPatent
Document office.
DocRef - Interface in org.biojavax
Represents a documentary reference.
DocRefAuthor - Interface in org.biojavax
Represents an author of a documentary reference.
DocRefAuthor.Tools - Class in org.biojavax
Useful tools for working with authors.
docType - Variable in class org.biojava.bibliography.BiblioPatent
Document type.
documentEnd() - Method in interface org.biojava.ontology.obo.OboFileEventListener
end of parsing a new OBO file
documentEnd() - Method in class org.biojava.ontology.obo.OboFileHandler
 
documentStart() - Method in interface org.biojava.ontology.obo.OboFileEventListener
starting to parse a new OBO file
documentStart() - Method in class org.biojava.ontology.obo.OboFileHandler
 
DOI_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
Holds a reference to the key that must be used to store DOI references.
doLayer(SequenceRenderContext, FeatureFilter) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
DOMAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
domain1 - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
doPreProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Emit any per-sequence header information.
doProcessFeature(Feature, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Internal method to process an individual Feature.
doProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Internal method to process an individual Sequence.
doRefreshRenderers() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
doRetain() - Method in class org.biojava.bio.program.tagvalue.TagDropper
Find out if known tags are retained or dropped.
doSortPeptides() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
 
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
 
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
 
DotState - Interface in org.biojava.bio.dp
A Dot state.
DoubleAlphabet - Class in org.biojava.bio.symbol
An efficient implementation of an Alphabet over the infinite set of double values.
DoubleAlphabet.DoubleRange - Class in org.biojava.bio.symbol
A range of double values.
DoubleAlphabet.DoubleSymbol - Class in org.biojava.bio.symbol
A single double value.
DoubleAlphabet.SubDoubleAlphabet - Class in org.biojava.bio.symbol
A class to represent a contiguous range of double symbols.
DoubleElementHandlerBase - Class in org.biojava.utils.stax
StAX handler for any element which just contains a string representation of a double.
DoubleElementHandlerBase() - Constructor for class org.biojava.utils.stax.DoubleElementHandlerBase
 
DoubleRange(double, double) - Constructor for class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
 
Doublet() - Constructor for class org.biojava.utils.ListTools.Doublet
 
Doublet(Object, Object) - Constructor for class org.biojava.utils.ListTools.Doublet
 
DoubleTokenization - Class in org.biojava.bio.seq.io
 
DoubleTokenization() - Constructor for class org.biojava.bio.seq.io.DoubleTokenization
 
doubleValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
this method is expected to reverse-translate any symbol in the source alphabet.
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
this method is expected to reverse-translate any symbol in the source alphabet.
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
 
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
 
dp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
dp - Static variable in class org.biojavax.bio.seq.io.FastaFormat
 
DP - Class in org.biojava.bio.dp
Objects that can perform dymamic programming operations upon sequences with HMMs.
DP() - Constructor for class org.biojava.bio.dp.DP
This method will result in a DP with no model.
DP(MarkovModel) - Constructor for class org.biojava.bio.dp.DP
 
dp_ipi - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
dp_uniprot - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
DP.ReverseIterator - Class in org.biojava.bio.dp
 
DPCompiler - Class in org.biojava.bio.dp.twohead
This is an implementation of CellCalculatorFactoryMaker that compiles the HMM object down to Java byte-code that is equivalent in behaviour to the interpreter.
DPCompiler(boolean) - Constructor for class org.biojava.bio.dp.twohead.DPCompiler
 
DPCursor - Interface in org.biojava.bio.dp.onehead
Encapsulates the dynamic programmming matrix, and the context within algorithms work.
DPFactory - Interface in org.biojava.bio.dp
The interface for objects that can generate a DP object for a MarkovModel.
DPFactory.DefaultFactory - Class in org.biojava.bio.dp
 
DPInterpreter - Class in org.biojava.bio.dp.twohead
 
DPInterpreter(DP) - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter
 
DPInterpreter.Maker - Class in org.biojava.bio.dp.twohead
 
DPMatrix - Interface in org.biojava.bio.dp
 
DR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
DRAW_CALL_A - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to fill in the callboxes for calls of nucleotide A.
DRAW_CALL_C - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to fill in the callboxes for calls of nucleotide C.
DRAW_CALL_G - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to fill in the callboxes for calls of nucleotide G.
DRAW_CALL_OTHER - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to fill in the callboxes for non-base calls (gaps, ambiguities).
DRAW_CALL_SEPARATORS - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to draw vertical lines separating the calls.
DRAW_CALL_T - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to fill in the callboxes for calls of nucleotide T.
DRAW_TRACE_A - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to draw the chromatogram trace for nucleotide A.
DRAW_TRACE_C - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to draw the chromatogram trace for nucleotide C.
DRAW_TRACE_G - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to draw the chromatogram trace for nucleotide G.
DRAW_TRACE_T - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to draw the chromatogram trace for nucleotide T.
drawableCallboxesValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Flag for drawable call boxes.
drawLine(Graphics2D, SequenceRenderContext, int, StrandedFeature.Strand) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
draws required bar in correct translation frame.
drawTo(Graphics2D) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Draws the chromatogram onto the provided graphics context.
dropBoundaryValues() - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
 
DROSOPHILA_MELANOGASTER_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
Drosophila melanogaster codon preferences
dsCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
DummyCrossReferenceResolver - Class in org.biojavax
A simple implementation of CrossReferenceResolver.
DummyCrossReferenceResolver() - Constructor for class org.biojavax.DummyCrossReferenceResolver
 
DummyRichSequenceHandler - Class in org.biojavax.bio.seq
 
DummyRichSequenceHandler() - Constructor for class org.biojavax.bio.seq.DummyRichSequenceHandler
 
DummySequence - Class in org.biojava.bio.seq.impl
A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
DummySequence(String, String) - Constructor for class org.biojava.bio.seq.impl.DummySequence
 
DummySequenceDB - Class in org.biojava.bio.seq.db
DummySequenceDB is an implementation which contains only a DummySequence.
DummySequenceDB(String) - Constructor for class org.biojava.bio.seq.db.DummySequenceDB
 
DummySequenceDBInstallation - Class in org.biojava.bio.seq.db
DummySequenceDBInstallation is an implementation which returns the same DummySequenceDB instance regardless of the identifier used to retrieve a database.
DummySequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.DummySequenceDBInstallation
 
DummySymbolList - Class in org.biojava.bio.symbol
Symbol list which just consists of non-informative symbols.
DummySymbolList(Alphabet, int, Symbol) - Constructor for class org.biojava.bio.symbol.DummySymbolList
 
DummySymbolList(FiniteAlphabet, int) - Constructor for class org.biojava.bio.symbol.DummySymbolList
 
dumpBlocks() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Debugging method
duplicate() - Method in class org.biojava.utils.automata.NfaSubModel
Makes a deep clone of this instance.
DuplicateTaxonException - Exception in org.biojava.bio.program.homologene
 
DuplicateTaxonException() - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
 
DuplicateTaxonException(String) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
 
DuplicateTaxonException(Throwable) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
 
DuplicateTaxonException(Throwable, String) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
 

E

e() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Glutamic Acid
EbiDatabaseURLGenerator - Class in org.biojava.bio.program.blast2html
Simple URL generator for EMBL at the EBI.
EbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
 
EbiFormat - Class in org.biojava.bio.taxa
Deprecated.
replaced by classes in org.biojavax.bio.taxa
EbiFormat() - Constructor for class org.biojava.bio.taxa.EbiFormat
Deprecated.
 
EC_FROM_STRING - Static variable in class org.biojava.bio.program.formats.FormatTools
 
EC_PATTERN - Static variable in interface org.biojava.bio.EcNumber
A Pattern that can be used to parse EC strings into the indiidual numbers.
eCache - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
eCache - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
Description of the Field
ECHIN_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the echinoderm mitochondrial genetic code.
Echo - Class in org.biojava.bio.program.tagvalue
A simple listener that just echoes events back to the console.
Echo() - Constructor for class org.biojava.bio.program.tagvalue.Echo
 
Echo(PrintStream) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Echo
 
EcNumber - Interface in org.biojava.bio
An ec (enzyme classification) number.
EcNumber.Impl - Class in org.biojava.bio
A simple implementation of EcNumber.
ECOLI - Static variable in class org.biojava.bio.symbol.CodonPrefTools
Escherichia coli codon preferences
edit(Object, Edit) - Method in interface org.biojava.bio.alignment.EditableAlignment
edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
edit(Object, Edit) - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
edit(Edit) - Method in class org.biojava.bio.dp.SimpleStatePath
 
edit(Edit) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
edit(Edit) - Method in class org.biojava.bio.seq.impl.DummySequence
 
edit(Edit) - Method in class org.biojava.bio.seq.impl.RevCompSequence
edit() will try to edit the underlying Sequence.
edit(Edit) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
edit(Edit) - Method in class org.biojava.bio.seq.impl.SubSequence
 
edit(Edit) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
edit(Edit) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
edit(Edit) - Method in class org.biojava.bio.seq.SimpleAssembly
 
edit(Edit) - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
edit(Edit) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
 
edit(Edit) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
edit(Edit) - Method in class org.biojava.bio.symbol.SimpleSymbolList
Apply and edit to the SymbolList as specified by Edit.
edit(Edit) - Method in interface org.biojava.bio.symbol.SymbolList
Apply an edit to the SymbolList as specified by the edit object.
edit(Edit) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Apply an edit to the SymbolList as specified by the edit object.
edit(Edit) - Method in class org.biojavax.bio.seq.ThinRichSequence
Apply an edit to the SymbolList as specified by the edit object.
edit(RichSequence, Edit) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
Apply an edit to the Sequence as specified by the edit object.
edit(RichSequence, Edit) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
Apply an edit to the Sequence as specified by the edit object.
edit(RichSequence, Edit) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
Apply an edit to the Sequence as specified by the edit object.
Edit - Class in org.biojava.bio.symbol
Encapsulates an edit operation on a SymbolList.
Edit(int, int, SymbolList) - Constructor for class org.biojava.bio.symbol.Edit
Create a new Edit.
Edit(int, int, SymbolList, Map<String, Object>) - Constructor for class org.biojava.bio.symbol.Edit
Create a new Edit with some properties.
Edit(int, Alphabet, Symbol) - Constructor for class org.biojava.bio.symbol.Edit
Convenience construtor for making single residue changes
EDIT - Static variable in interface org.biojava.bio.symbol.SymbolList
Signals that the SymbolList is being edited.
EditableAlignment - Interface in org.biojava.bio.alignment
EditableAlignment is an interface that defines methods for shifting bases within an Alignment.
edition - Variable in class org.biojava.bibliography.BiblioBook
Edition.
editor - Variable in class org.biojava.bibliography.BiblioBook
Editor.
EDITOR_LIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
EDITOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
EditScreener(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
 
EditTranslater(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
 
elementLength - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
ElementRecognizer - Interface in org.biojava.bio.program.xff
Simple interface for filtering SAX/StAX startElement events.
ElementRecognizer - Interface in org.biojava.bio.seq.io.agave
This class is copied to agave package Simple interface for filtering SAX/StAX startElement events
ElementRecognizer - Interface in org.biojava.bio.seq.io.game
Simple interface for filtering SAX/StAX startElement events
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.program.xff
 
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.seq.io.agave
 
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.seq.io.game
 
ElementRecognizer.ByLocalName - Class in org.biojava.bio.program.xff
Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName - Class in org.biojava.bio.seq.io.agave
Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName - Class in org.biojava.bio.seq.io.game
Filter elements by local name (not recommended).
ElementRecognizer.ByNSName - Class in org.biojava.bio.program.xff
Filter elements by name and namespace.
ElementRecognizer.ByNSName - Class in org.biojava.bio.seq.io.agave
Filter elements by name and namespace.
ElementRecognizer.ByNSName - Class in org.biojava.bio.seq.io.game
Filter elements by name and namespace.
ElementRecognizer.HasAttribute - Class in org.biojava.bio.program.xff
Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute - Class in org.biojava.bio.seq.io.agave
Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute - Class in org.biojava.bio.seq.io.game
Filter elements on the existence of a specified attribute.
EllipticalBeadRenderer - Class in org.biojava.bio.gui.sequence
EllipticalBeadRenderer renders features as simple ellipses.
EllipticalBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
Creates a new EllipticalBeadRenderer object with the default settings.
EllipticalBeadRenderer(double, double, Paint, Paint, Stroke, double) - Constructor for class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
Creates a new EllipticalBeadRenderer.
email - Variable in class org.biojava.bibliography.BiblioPerson
Their e-mail address.
Embl - Class in org.biojava.bio.program.formats
 
Embl() - Constructor for class org.biojava.bio.program.formats.Embl
 
EMBL - Static variable in class org.biojava.bio.program.tagvalue.LineSplitParser
A LineSplitParser pre-configured to process EMBL-style flat files.
EMBL - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
EMBL indicates that the sequence format is EMBL.
EMBL_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
EMBL_AA premade EMBL | AA.
EMBL_AGAVE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
 
EMBL_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
EMBL_DNA premade EMBL | DNA.
EMBL_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
The name of the current format
EMBL_GENBANK_FEATURE_TABLE_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
 
EMBL_PRE87_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
The name of the Pre-87 format
EMBL_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
EMBL_RNA premade EMBL | RNA.
EMBL_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
 
Embl2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave
Map EMBL data into AGAVE format
EmblCDROMIndexReader - Class in org.biojava.bio.seq.db.emblcd
EmblCDROMIndexReader is an abstract class whose concrete subclasses read EMBL CD-ROM format indices from an underlying InputStream.
EmblCDROMIndexReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
Creates a new EmblCDROMIndexReader instance.
EmblCDROMIndexStore - Class in org.biojava.bio.seq.db
EmblCDROMIndexStores implement a read-only IndexStore backed by EMBL CD-ROM format binary indices.
EmblCDROMIndexStore(File, File, File, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.EmblCDROMIndexStore
Creates a new EmblCDROMIndexStore backed by a random access binary index.
EmblCDROMIndexStore(File, File, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.EmblCDROMIndexStore
Creates a new EmblCDROMIndexStore backed by a random access binary index.
EmblCDROMRandomAccess - Class in org.biojava.bio.seq.db.emblcd
EmblCDROMRandomAccess is an abstract class whose concrete subclasses can perform fast lookups in EMBL CD-ROM format index files.
EmblCDROMRandomAccess(File, int, int, long) - Constructor for class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
Creates a new EmblCDROMRandomAccess object.
EmblFileFormer - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
EmblFileFormer() - Constructor for class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
Creates a new EmblFileFormer using System.out stream.
EmblFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
Creates a new EmblFileFormer using the specified stream.
EMBLFormat - Class in org.biojavax.bio.seq.io
Format reader for EMBL files.
EMBLFormat() - Constructor for class org.biojavax.bio.seq.io.EMBLFormat
 
EMBLFormat.Terms - Class in org.biojavax.bio.seq.io
Implements some EMBL-specific terms.
EmblLikeFormat - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io.EMBLFormat instead
EmblLikeFormat() - Constructor for class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
EmblLikeLocationParser - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
EmblProcessor - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
EmblProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.EmblProcessor
Deprecated.
 
EmblProcessor.Factory - Class in org.biojava.bio.seq.io
Deprecated.
Factory which wraps SequenceBuilders in an EmblProcessor
EmblReferenceComparator - Class in org.biojava.bio.seq.io
 
EmblReferenceComparator() - Constructor for class org.biojava.bio.seq.io.EmblReferenceComparator
 
EMBLXML_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
The name of this format
EMBLxmlFormat - Class in org.biojavax.bio.seq.io
Format reader for EMBLxml files.
EMBLxmlFormat() - Constructor for class org.biojavax.bio.seq.io.EMBLxmlFormat
 
EMBLxmlFormat.Terms - Class in org.biojavax.bio.seq.io
Implements some EMBLxml-specific terms.
emissionAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel
Alphabet that is emitted by the emission states.
emissionAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
emissionAlphabet() - Method in class org.biojava.bio.dp.WMAsMM
 
EmissionCache - Class in org.biojava.bio.dp.twohead
Cache for columns of emission probabilities in pair-wise alignment algorithms.
EmissionCache(Alphabet, State[], int, ScoreType) - Constructor for class org.biojava.bio.dp.twohead.EmissionCache
 
emissions - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
emissions - Variable in class org.biojava.bio.dp.twohead.Cell
 
emissionsNull - Variable in class org.biojava.bio.dp.onehead.SingleDP
 
emissionsOdds - Variable in class org.biojava.bio.dp.onehead.SingleDP
 
emissionsProb - Variable in class org.biojava.bio.dp.onehead.SingleDP
 
EmissionState - Interface in org.biojava.bio.dp
A state in a markov process that has an emission spectrum.
empty - Static variable in interface org.biojava.bio.symbol.Location
The Location which contains no points.
EMPTY - Static variable in interface org.biojava.bio.annodb.AnnotationDB
An AnnotationDB that is always empty.
EMPTY - Static variable in interface org.biojava.bio.CollectionConstraint
EMPTY is a constraint which only accepts the empty set.
EMPTY_ALPHABET - Static variable in interface org.biojava.bio.symbol.Alphabet
A really useful static alphabet that is always empty.
EMPTY_ANNOTATION - Static variable in interface org.biojava.bio.Annotation
A really useful empty and immutable annotation object.
EMPTY_ANNOTATION - Static variable in interface org.biojavax.RichAnnotation
 
EMPTY_FEATURE_HOLDER - Static variable in interface org.biojava.bio.seq.FeatureHolder
 
EMPTY_LINE_EOR - Static variable in interface org.biojava.bio.program.tagvalue.TagValueParser
EMPTY_LINE_EOR is a special EOR value which allows an empty line to be used as a record separator.
EMPTY_LIST - Static variable in interface org.biojava.bio.symbol.SymbolList
A useful object that represents an empty symbol list, to avoid returning null.
EMPTY_LIST - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
EMPTY_LOCATION - Static variable in interface org.biojavax.bio.seq.RichLocation
The empty location matches nothing.
EMPTY_PAIRWISE - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
Constant EMPTY_PAIRWISE is an empty alignment for situations where there is no available alignment data or the implementation does not want to create one.
EMPTY_POSITION - Static variable in interface org.biojavax.bio.seq.Position
The empty position lies nowhere.
emptyBP - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
emptyBP - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
Description of the Field
emptyFeature - Variable in class org.biojavax.bio.seq.io.RichSeqIOAdapter
This is a dummy feature.
EmptyFeatureHolder() - Constructor for class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
emptyList(Alphabet) - Static method in class org.biojava.bio.symbol.SymbolListViews
Get a new immutable, empty symbol list with the given alphabet.
EmptyRichAnnotation - Class in org.biojavax
A place holder for a RichAnnotation that prevents null having to be used
EmptyRichAnnotation() - Constructor for class org.biojavax.EmptyRichAnnotation
 
EmptyRichLocation - Class in org.biojavax.bio.seq
An Empty implementation of RichLocation.
EmptyRichLocation() - Constructor for class org.biojavax.bio.seq.EmptyRichLocation
 
end - Variable in class org.biojava.utils.automata.FiniteAutomaton
 
end() - Method in interface org.biojava.bio.search.BioMatcher
Get the last symbol index that matches the pattern.
end() - Method in class org.biojava.bio.search.MaxMismatchMatcher
 
end() - Method in class org.biojava.utils.regex.Matcher
Returns the index of the last character matched, plus one.
end(int) - Method in class org.biojava.utils.regex.Matcher
Returns the index of the last Symbol, plus one, of the subsequence captured by the given group during the previous match operation.
END_RECORD_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
 
END_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
END_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
END_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
 
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
endBlock() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
Notifies the parser that a block is ending.
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
endBlock() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
Notifies the parser that a block is ending.
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
endBlock() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Finished reading a block.
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
 
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
 
endComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
 
endComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
Closing a comment tag.
endComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
endComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
Closing a comment tag.
endComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
endComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Closing a comment tag.
endComment() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
 
endDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
end of data for DB
endDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
endDocument() - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
Indicates that the current GFF document has now ended.
endDocument() - Method in class org.biojava.bio.program.gff.GFFFilterer
 
endDocument() - Method in class org.biojava.bio.program.gff.GFFWriter
Flushes the PrintWriter to make sure that everything is written.
endDocument() - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
Indicates that the current GFF document has now ended.
endDocument() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
endDocument() - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
endDocument() - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
endElement() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
endElement(String, String, String) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler
Called when the end of an element is reached.
endElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
endElement(String, String, String) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
 
endElement(String, String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
endElement(String, String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
endElement(String, String, String, StAXContentHandler) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.FeatureHandler
StAX callback for element ends.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.CharElementHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.IntElementHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.LongElementHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.StringElementHandlerBase
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler
when exiting, put the DbXrefElement into the annotation bundle
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMESpanPropHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEAspectHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler.SeqRelHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEPropertyHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESpanHandler
 
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
Element specific exit handler Subclass to do anything useful.
endFeature() - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
endFeature() - Method in class org.biojava.bio.seq.io.FeatureTableParser
Deprecated.
 
endFeature() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
endFeature() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
endFeature() - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
endFeature() - Method in interface org.biojava.bio.seq.io.SeqIOListener
Mark the end of data associated with one specific feature.
endFeature() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
endFeature() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
endFeature() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Null implementation.
endFeature() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
endFeature() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
endFeature() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Mark the end of data associated with one specific feature.
endFile() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
 
endFile() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Finished reading a file.
endFile() - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
 
endFile() - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
Finished reading a file.
endFileComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
 
endFileComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
This method will get called when a comment is ended on the file, and not any block within it.
endGroup() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
end of data for group
endGroup() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
endHeader() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
endHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
endHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
endHeader() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
endHeader() - Method in class org.biojava.bio.search.FilteringContentHandler
 
endHeader() - Method in class org.biojava.bio.search.SearchContentAdapter
 
endHeader() - Method in class org.biojava.bio.search.SearchContentFilter
 
endHeader() - Method in interface org.biojava.bio.search.SearchContentHandler
The endHeader method indicates the end of a formatted header.
endHeader() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
endHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
endHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
endHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
endHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
endHit() - Method in class org.biojava.bio.search.FilteringContentHandler
 
endHit() - Method in class org.biojava.bio.search.SearchContentAdapter
 
endHit() - Method in class org.biojava.bio.search.SearchContentFilter
 
endHit() - Method in interface org.biojava.bio.search.SearchContentHandler
The endHit method indicates the end of a formatted hit.
endHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
endIndex - Variable in class org.biojava.ontology.obo.OboFileParser.SOPair
 
endLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
endLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
endOrthologue() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
end of data for this Orthologue
endOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
endOrthoPair() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
end of data for this OrthoPair
endOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
endPrefixMapping(String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
endPrefixMapping(String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
endPrefixMapping(String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
endPrefixMapping(String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
endPrefixMapping(String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
endPrefixMapping(String) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
endPrefixMapping(String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
endRecord() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
endRecord() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
 
endRecord() - Method in class org.biojava.bio.program.tagvalue.Echo
 
endRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer
 
endRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer2
 
endRecord() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
endRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
endRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
 
endRecord() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
The current record has ended.
endSearch() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
endSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
endSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
endSearch() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
endSearch() - Method in class org.biojava.bio.search.FilteringContentHandler
 
endSearch() - Method in class org.biojava.bio.search.SearchContentAdapter
 
endSearch() - Method in class org.biojava.bio.search.SearchContentFilter
 
endSearch() - Method in interface org.biojava.bio.search.SearchContentHandler
The endSearch method indicates the end of useful search information.
endSearch() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
endSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger
 
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
 
endSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener
Indicates that a sequence has been searched against a DataStore.
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
 
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
 
endSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
endSequence() - Method in class org.biojava.bio.seq.io.EmblProcessor
Deprecated.
 
endSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
endSequence() - Method in class org.biojava.bio.seq.io.GenbankProcessor
Deprecated.
 
endSequence() - Method in class org.biojava.bio.seq.io.OrganismParser
Deprecated.
 
endSequence() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
endSequence() - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
endSequence() - Method in interface org.biojava.bio.seq.io.SeqIOListener
Notify the listener that processing of the sequence is complete.
endSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
endSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
endSequence() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Notify the listener that processing of the sequence is complete.
endSequence() - Method in class org.biojava.bio.seq.io.SwissprotProcessor
Deprecated.
 
endSequence() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
endSequence() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
endSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Notify the listener that processing of the sequence is complete.
endSubHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
endSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
endSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
endSubHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
endSubHit() - Method in class org.biojava.bio.search.FilteringContentHandler
 
endSubHit() - Method in class org.biojava.bio.search.SearchContentAdapter
 
endSubHit() - Method in class org.biojava.bio.search.SearchContentFilter
 
endSubHit() - Method in interface org.biojava.bio.search.SearchContentHandler
The endSubHit method indicates the end of a formatted subhit.
endSubHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
endTag() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
endTag() - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
endTag() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
 
endTag() - Method in class org.biojava.bio.program.tagvalue.Echo
 
endTag() - Method in class org.biojava.bio.program.tagvalue.Indexer
 
endTag() - Method in class org.biojava.bio.program.tagvalue.Indexer2
 
endTag() - Method in class org.biojava.bio.program.tagvalue.MultiTagger
 
endTag() - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
 
endTag() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
endTag() - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
endTag() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
 
endTag() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
endTag() - Method in class org.biojava.bio.program.tagvalue.TagDropper
 
endTag() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
End the current tag.
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
endTokenGroup() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
Closing a line (semi-colon encountered).
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
endTokenGroup() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
Closing a line (semi-colon encountered).
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
endTokenGroup() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Closing a line (semi-colon encountered).
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
 
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
 
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
 
endTree() - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
endTree() - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
endTree() - Method in interface org.biojava.utils.stax.StAXContentHandler
 
endTree() - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
enrich(Feature) - Static method in class org.biojavax.bio.seq.RichFeature.Tools
Takes a normal Feature and attempts to convert it into a RichFeature.
enrich(Sequence) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
Boldly attempts to convert a Sequence into a RichSequence.
enrich(Location) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
Attempts to convert a plain Location into a RichLocation.
entropy(Distribution, Symbol) - Static method in class org.biojava.bio.gui.DistributionLogo
Calculate the information content of a symbol in bits.
entry - Variable in class org.biojava.utils.candy.CandyEntry
A unique identifier of this entry.
ENTRY_ACCESSION_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_CREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_CREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ENTRY_DATACLASS_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ENTRY_NAMESPACE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ENTRY_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport
A vocabulary name.
ENTRY_RELCREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_RELUPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_STATUS_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_STATUS_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_SUBACC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_SUBVER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_SUBWGSVER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ENTRY_TAX_DIVISION_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_UPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_UPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ENTRY_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ENTRY_VERSION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
EntryNamIdxReader - Class in org.biojava.bio.seq.db.emblcd
EntryNamIdxReader reads the "entrynam.idx" file of an EMBL CD-ROM format binary index.
EntryNamIdxReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader
Creates a new EntryNamIdxReader.
EntryNamRandomAccess - Class in org.biojava.bio.seq.db.emblcd
EntryNamRandomAccess objects provide random access to records within the "entrynam.idx" file of an EMBL CD-ROM format binary index.
EntryNamRandomAccess(File, int, int, long) - Constructor for class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
 
entrySet() - Method in class org.biojava.utils.BeanAsMap
 
entrySet() - Method in class org.biojava.utils.cache.WeakValueHashMap
 
entrySet() - Method in class org.biojava.utils.io.SoftHashMap
 
entrySet() - Method in class org.biojava.utils.OverlayMap
 
entrySet() - Method in class org.biojava.utils.SmallMap
 
entryStatus - Variable in class org.biojava.bibliography.BibRef
It defines information related to the citation itself rather than to the cited resource.
Enumeration(Object[]) - Constructor for class org.biojava.bio.PropertyConstraint.Enumeration
Creates a new Enumeration using the elements of the specified array as a constraint.
Enumeration(Set) - Constructor for class org.biojava.bio.PropertyConstraint.Enumeration
Creates a new Enumeration using the members of the specified set as a constraint.
enzyme - Variable in class org.biojava.bio.molbio.RestrictionSite.Template
enzyme RestrictionEnzyme field.
Enzyme - Class in org.biojava.bio.program.formats
 
Enzyme() - Constructor for class org.biojava.bio.program.formats.Enzyme
 
Enzyme() - Constructor for class org.biojava.bio.program.formats.Ligand.Enzyme
 
eof() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
Checks if the end of the file or stream is reached.
eq - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
equals(boolean[], boolean[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(boolean, boolean) - Static method in class org.biojava.utils.ObjectUtil
 
equals(double[], double[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(double, double) - Static method in class org.biojava.utils.ObjectUtil
 
equals(float[], float[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(float, float) - Static method in class org.biojava.utils.ObjectUtil
 
equals(int[], int[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(int, int) - Static method in class org.biojava.utils.ObjectUtil
 
equals(long[], long[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(long, long) - Static method in class org.biojava.utils.ObjectUtil
 
equals(Object) - Method in class org.biojava.bio.AbstractAnnotation
 
equals(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
equals(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
 
equals(Object) - Method in class org.biojava.bio.dist.AbstractDistribution
 
equals(Object) - Method in class org.biojava.bio.dp.SimpleWeightMatrix
 
equals(Object) - Method in class org.biojava.bio.dp.TrainerTransition
Two transitions are equal if they have the same trainer, from and to states.
equals(Object) - Method in class org.biojava.bio.dp.Transition
Two transitions are equal if they have the same from and to states.
equals(Object) - Method in class org.biojava.bio.EcNumber.Impl
 
equals(Object) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
equals(Object) - Method in class org.biojava.bio.molbio.RestrictionEnzyme
 
equals(Object) - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
 
equals(Object) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
 
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
 
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
equals(Object) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
 
equals(Object) - Method in class org.biojava.bio.seq.Feature.Template
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.And
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.Not
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
 
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
 
equals(Object) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
equals(Object) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
equals(Object) - Method in class org.biojava.bio.symbol.AbstractLocation
 
equals(Object) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
equals(Object) - Method in class org.biojava.bio.symbol.AbstractSymbolList
Provides logical equality for two SymbolLists that share the same list of canonical symbols
equals(Object) - Method in class org.biojava.bio.symbol.CircularLocation
 
equals(Object) - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
equals(Object) - Method in interface org.biojava.bio.symbol.Location
Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
equals(Object) - Method in interface org.biojava.bio.taxa.Taxon
Deprecated.
Two taxa are equal if they have equivalent children, common and scientific names.
equals(Object) - Method in class org.biojava.ontology.Term.Impl
 
equals(Object) - Method in interface org.biojava.ontology.Triple
Check to see if an object is an equivalent Triple.
equals(Object) - Method in class org.biojava.ontology.Triple.Impl
Two triples are equal if all their fields are identical.
equals(Object) - Method in class org.biojava.utils.ListTools.Doublet
 
equals(Object) - Method in class org.biojava.utils.ListTools.Triplet
 
equals(Object) - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
 
equals(Object) - Method in class org.biojava.utils.TypedProperties
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
 
equals(Object) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojavax.bio.seq.RichLocation.Strand
Strands are equal if their numbers and symbols match.
equals(Object) - Method in class org.biojavax.bio.seq.SimplePosition
Two positions are equal if they share all parameters in common, eg. fuzzy start+end, start, end, type.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Features are equal when they have the same rank, parent, type, and source.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Relations are equal if their objects, subjects and terms are equal.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojavax.bio.SimpleBioEntry
Two bioentries are equal if they share the same namespace, name, accession and version.
equals(Object) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
Relationships are equal if they share the same rank, object, subject and term.
equals(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
NCBITaxon objects are equal if their NCBITaxID fields match.
equals(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
Two taxon names are equal if their name and class match.
equals(Object) - Method in class org.biojavax.EmptyRichAnnotation
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableOntology
Ontologies are equal if their names are equal.
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
Two terms are equal if they are in the same ontology and share the same name.
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
Check to see if an object is an equivalent Triple.
equals(Object) - Method in class org.biojavax.SimpleComment
Two comments are defined as equal if their text values and rankings are identical.
equals(Object) - Method in class org.biojavax.SimpleCrossRef
Equality is defined as having the same database name, accession and version.
equals(Object) - Method in class org.biojavax.SimpleDocRef
Document references are equal if they have the same author and location and title.
equals(Object) - Method in class org.biojavax.SimpleDocRefAuthor
Document references are equal if they have all fields the same.
equals(Object) - Method in class org.biojavax.SimpleNamespace
Namespaces are equal only by name.
equals(Object) - Method in class org.biojavax.SimpleNote
Notes are equal if they have the same rank and term.
equals(Object) - Method in class org.biojavax.SimpleRankedCrossRef
Ranked cross references are the same if they have the same rank and refer to the same cross reference (cross references are equal).
equals(Object) - Method in class org.biojavax.SimpleRankedDocRef
Two ranked document references are equal if they have the same rank and refer to the same location and same document reference.
equals(Object[], Object[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(Object, Object) - Static method in class org.biojava.utils.ObjectUtil
 
equals(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
Equals(Object) - Constructor for class org.biojava.bio.search.FilterTest.Equals
 
EQUIVALENCE - Static variable in class org.biojava.ontology.OntoTools
 
EQUIVALENT - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
Use this to define equivalent names for things.
ERROR_FEATURES_PROPERTY - Static variable in class org.biojava.bio.seq.io.SequenceBuilderBase
 
errorProbabilities(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
Return the error probabilities from the specified FASTQ formatted sequence.
errorProbabilities(Fastq, double[]) - Static method in class org.biojava.bio.program.fastq.FastqTools
Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.
errorProbability(char) - Method in enum org.biojava.bio.program.fastq.FastqVariant
Convert the specified quality in ASCII format to an error probability.
errorProbability(int) - Method in enum org.biojava.bio.program.fastq.FastqVariant
Calculate the error probability given the specified quality score.
escape(String, boolean) - Static method in class org.biojava.ontology.obo.OboFileParser
 
escapeChars - Static variable in class org.biojava.ontology.obo.OboFileParser
 
estimatedSize - Variable in class org.biojava.bibliography.BiblioWebResource
An estomated size in kilobytes.
EUPL_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the euplotid nuclear genetic code.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.CachingKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
Return the dot product of a, b.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.DiagonalCachingKernel
Returns the kernel product of two Objects.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.LinearKernel
Deprecated.
The linear kernel is equal to the dot product of a and b.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.ListSumKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.NormalizingKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.PolynomialKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.RadialBaseKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.SigmoidKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
Evaluate the kernel function between two SparseVectors.
evaluate(Object, Object) - Method in interface org.biojava.stats.svm.SVMKernel
Return the dot product of two vectors in an arbitrary feature space.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
Calculate the dot product between the SuffixTrees a and b.
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
 
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
 
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
 
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
 
evaluate(BlastLikeSearchFilter.Node) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter
computes the outcome of this filter on the specified node and stores it.
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
 
Event() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Event
 
EverythingToXML(PrintWriter) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
 
EVIDENCE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
EVIDENCE_ATTRIBUTE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
EVIDENCE_CATEGORY_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
EVIDENCE_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
EVIDENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
EXACT_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
EXACT_SYNONYM - Static variable in class org.biojava.ontology.Synonym
 
ExactValue(Object) - Constructor for class org.biojava.bio.PropertyConstraint.ExactValue
Get a PropertyConstraint that matches this object and all those that are equal to it (by the Object.equals() method).
ExceptionFound - Variable in class org.biojava.bio.seq.db.GenbankSequenceDB
 
exec(String) - Method in class org.biojava.utils.ExecRunner
The exec(String) method runs a process inside of a watched thread.
exec(String[], Reader, Writer, Writer) - Static method in class org.biojava.utils.ProcessTools
Deprecated.
Execute the specified command and wait for it to return.
exec(String[], String[], File, Reader, Writer, Writer, long) - Static method in class org.biojava.utils.ProcessTools
Deprecated.
Execute the specified command and wait for it to return, or kill it if the specified timeout expires first.
exec(String, OutputStream, OutputStream) - Method in class org.biojava.utils.ExecRunner
Convenience method for calling exec with OutputStreams.
exec(String, PrintWriter, PrintWriter) - Method in class org.biojava.utils.ExecRunner
The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread.
exec(String, Reader, Writer, Writer) - Static method in class org.biojava.utils.ProcessTools
Deprecated.
Execute the specified command and wait for it to return.
exec(String, String[]) - Method in class org.biojava.utils.ExecRunner
Sometimes special cases may occur that the arguments of an external program are Strings containing white spaces.
exec(String, String[], File, Reader, Writer, Writer, long) - Static method in class org.biojava.utils.ProcessTools
Deprecated.
Execute the specified command and wait for it to return.
exec(String, String[], OutputStream, OutputStream) - Method in class org.biojava.utils.ExecRunner
Convenience method for calling exec with OutputStreams.
exec(String, String[], PrintWriter, PrintWriter) - Method in class org.biojava.utils.ExecRunner
The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread.
ExecRunner - Class in org.biojava.utils
Makes running external executables easier, optionally under a watched thread.
ExecRunner() - Constructor for class org.biojava.utils.ExecRunner
Basic ExecRunner constructor.
ExecRunner(String) - Constructor for class org.biojava.utils.ExecRunner
ExecRunner constructor which also conveniently runs exec(String).
ExecRunner(String, String[]) - Constructor for class org.biojava.utils.ExecRunner
ExecRunner constructor which also conveniently runs exec(String).
execute() - Method in class org.biojava.utils.process.ExternalProcess
Executes the external process and waits for its termination.
execute(String) - Static method in class org.biojava.utils.process.ExternalProcess
Executes an external program.
execute(String, String, StringWriter, StringWriter) - Static method in class org.biojava.utils.process.ExternalProcess
Executes an external program.
execute(Properties) - Method in class org.biojava.utils.process.ExternalProcess
Executes the external process and waits for its termination.
expandCache(int) - Method in class org.biojava.utils.io.CachingInputStream
Expands the cache to hold some number of additionalBytes.
ExternalProcess - Class in org.biojava.utils.process
Utility class to execute an external process and to handle the STDOUT, STDERR and STDIN streams in multiple threads managed by a thread pool.
ExternalProcess() - Constructor for class org.biojava.utils.process.ExternalProcess
Initializes the external process.
ExternalProcess(ThreadPool) - Constructor for class org.biojava.utils.process.ExternalProcess
Initializes the external process.
extractOverlappingLocation(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Try to determine the minimal location which all features matching a given filter must overlap.
extras - Variable in class org.biojava.utils.candy.CandyEntry
A container for the additional properties represented by this entry.

F

f() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Phenylalanine
factorize(Alphabet, Set) - Static method in class org.biojava.bio.symbol.AlphabetManager
Return a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.EmblProcessor.Factory
Deprecated.
 
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory
Deprecated.
 
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor.Factory
Deprecated.
 
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory
Deprecated.
 
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor.Factory
Deprecated.
 
Factory(SequenceBuilderFactory, TaxonFactory, TaxonParser, String, String, String) - Constructor for class org.biojava.bio.seq.io.OrganismParser.Factory
Deprecated.
 
FACTORY - Static variable in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
 
FACTORY - Static variable in class org.biojava.bio.seq.io.SimpleSequenceBuilder
 
FACTORY - Static variable in class org.biojava.bio.seq.io.SmartSequenceBuilder
 
FACTORY - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory
Accessor for the default factory.
FALSE - Static variable in class org.biojava.utils.TriState
 
FASTA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
FASTA indicates that the alignment format is Fasta.
FASTA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
FASTA indicates that the sequence format is Fasta.
FASTA_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
FASTA_AA premade FASTA | AA;
FASTA_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
FASTA_AA premade FASTA | AA.
FASTA_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
FASTA_DNA premade FASTA | DNA;
FASTA_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
FASTA_DNA premade FASTA | DNA.
FASTA_FORMAT - Static variable in class org.biojavax.bio.seq.io.FastaFormat
The name of this format
FASTA_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
FASTA_RNA premade FASTA | RNA;
FASTA_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
FASTA_RNA premade FASTA | RNA.
FastaAlignmentFormat - Class in org.biojava.bio.seq.io
This class implements the AlignmentFormat interface to read FASTA alignments.
FastaAlignmentFormat() - Constructor for class org.biojava.bio.seq.io.FastaAlignmentFormat
 
FastaDescriptionLineParser - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io.FastaFormat
FastaDescriptionLineParser(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.FastaDescriptionLineParser
Deprecated.
 
FastaDescriptionLineParser.Factory - Class in org.biojava.bio.seq.io
Deprecated.
Factory which wraps SequenceBuilders in a FastaDescriptionLineParser
FastaFormat - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io.FastaFormat
FastaFormat - Class in org.biojavax.bio.seq.io
Format object representing FASTA files.
FastaFormat() - Constructor for class org.biojava.bio.seq.io.FastaFormat
Deprecated.
 
FastaFormat() - Constructor for class org.biojavax.bio.seq.io.FastaFormat
 
FastaHeader - Class in org.biojavax.bio.seq.io
This class is used by FastaFormat to determine which fields are in the fasta header.
FastaHeader() - Constructor for class org.biojavax.bio.seq.io.FastaHeader
 
FastaSearchSAXParser - Class in org.biojava.bio.program.sax
FastaSearchSAXParser is a SAX2 compliant parser for '-m 10' format output from the the Fasta search program (see the Fasta documentation for details of this format).
FastaSearchSAXParser() - Constructor for class org.biojava.bio.program.sax.FastaSearchSAXParser
Creates a new FastaSearchSAXParser instance.
FastaSequenceSAXParser - Class in org.biojava.bio.program.sax
A SAX2 parser for dealing with multiple sequences in FASTA format.
FastaSequenceSAXParser() - Constructor for class org.biojava.bio.program.sax.FastaSequenceSAXParser
Initialises internal state Sets namespace prefix to "biojava"
fastq(Fastq) - Method in interface org.biojava.bio.program.fastq.StreamListener
Notify this listener of a FASTQ formatted sequence.
Fastq - Class in org.biojava.bio.program.fastq
FASTQ formatted sequence.
FASTQ_ILLUMINA - org.biojava.bio.program.fastq.FastqVariant
Illumina FASTQ sequence format variant.
FASTQ_SANGER - org.biojava.bio.program.fastq.FastqVariant
Sanger FASTQ sequence format variant.
FASTQ_SOLEXA - org.biojava.bio.program.fastq.FastqVariant
Solexa FASTQ sequence format variant.
FastqBuilder - Class in org.biojava.bio.program.fastq
Fluent builder API for creating FASTQ formatted sequences.
FastqBuilder() - Constructor for class org.biojava.bio.program.fastq.FastqBuilder
Create a new FASTQ formatted sequence builder.
FastqBuilder(Fastq) - Constructor for class org.biojava.bio.program.fastq.FastqBuilder
Create a new FASTQ formatted sequence builder configured from the specified FASTQ formatted sequence.
FastqReader - Interface in org.biojava.bio.program.fastq
Reader for FASTQ formatted sequences.
FastqTools - Class in org.biojava.bio.program.fastq
Utility methods for FASTQ formatted sequences.
FastqVariant - Enum in org.biojava.bio.program.fastq
FASTQ sequence format variant.
FastqWriter - Interface in org.biojava.bio.program.fastq
Writer for FASTQ formatted sequences.
FastXMLWriter - Class in org.biojava.utils.xml
Simple implementation of XMLWriter, optimized for speed.
FastXMLWriter(PrintWriter) - Constructor for class org.biojava.utils.xml.FastXMLWriter
 
Feature - Interface in org.biojava.bio.seq
A feature within a sequence, or nested within another feature.
FEATURE - Static variable in interface org.biojavax.bio.seq.RichLocation
 
FEATURE_ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_COLLAPSING - Static variable in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
FEATURE_DESC_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
FEATURE_FLAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
FEATURE_FROM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.FeatureHandler
 
FEATURE_HEADER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
FEATURE_INTERBP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_INTERVAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_INTERVALS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_ISCOMP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_KEY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_LINE_PREFIX - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
FEATURE_LOC_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
FEATURE_OPERATOR_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_ORIGINAL_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
FEATURE_PARTIAL3_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_PARTIAL5_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_POINT_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_RENDERER - Static variable in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
FEATURE_TABLE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
FEATURE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
FEATURE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
FEATURE_TO_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATURE_VARIATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
Feature.ByLocationComparator - Class in org.biojava.bio.seq
ByLocationComparator compares Features by the minimum base position of their Location.
Feature.Template - Class in org.biojava.bio.seq
Template class for a plain feature.
FeatureBlockSequenceRenderer - Class in org.biojava.bio.gui.sequence
FeatureBlockSequenceRenderer forms a bridge between Sequence rendering and Feature rendering.
FeatureBlockSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
Creates a new FeatureBlockSequenceRenderer which uses a BasicFeatureRenderer as its renderer.
FeatureBlockSequenceRenderer(FeatureRenderer) - Constructor for class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
Creates a new FeatureBlockSequenceRenderer which uses the specified FeatureRenderer.
featureData(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
Deprecated.
 
featureFilter(FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
FeatureFilter - Interface in org.biojava.bio.seq
A filter for accepting or rejecting a feature.
FeatureFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
 
FeatureFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
 
FeatureFilter.And - Class in org.biojava.bio.seq
A filter that returns all features accepted by both child filter.
FeatureFilter.AnnotationContains - Class in org.biojava.bio.seq
Retrieve features that contain a given annotation, and that the set of values contains the value given.
FeatureFilter.ByAncestor - Class in org.biojava.bio.seq
Filter by applying a nested FeatureFilter to all ancestor features.
FeatureFilter.ByAnnotation - Class in org.biojava.bio.seq
Retrieve features that contain a given annotation with a given value.
FeatureFilter.ByAnnotationType - Class in org.biojava.bio.seq
A filter that returns all features that have an annotation bundle that is of a given annotation type.
FeatureFilter.ByChild - Class in org.biojava.bio.seq
Filter by applying a nested FeatureFilter to the child features.
FeatureFilter.ByClass - Class in org.biojava.bio.seq
Filter which accepts only those filters which are an instance of a specific Java class
FeatureFilter.ByComponentName - Class in org.biojava.bio.seq
Accepts features which are ComponentFeatures and have a componentSequenceName property of the specified value.
FeatureFilter.ByDescendant - Class in org.biojava.bio.seq
Filter by applying a nested FeatureFilter to all descendant features.
FeatureFilter.ByFeature - Class in org.biojava.bio.seq
Accept only features which are equal to the specified feature
FeatureFilter.ByPairwiseScore - Class in org.biojava.bio.seq
ByPairwiseScore is used to filter SimilarityPairFeatures by their score.
FeatureFilter.ByParent - Class in org.biojava.bio.seq
Filter by applying a nested FeatureFilter to the parent feature.
FeatureFilter.BySequenceName - Class in org.biojava.bio.seq
Accept features that reside on a sequence with a particular name.
FeatureFilter.BySource - Class in org.biojava.bio.seq
Construct one of these to filter features by source.
FeatureFilter.ByType - Class in org.biojava.bio.seq
Construct one of these to filter features by type.
FeatureFilter.ContainedByLocation - Class in org.biojava.bio.seq
A filter that returns all features contained within a location.
FeatureFilter.FrameFilter - Class in org.biojava.bio.seq
Accept features with a given reading frame.
FeatureFilter.HasAnnotation - Class in org.biojava.bio.seq
Retrieve features that contain a given annotation with any value.
FeatureFilter.Not - Class in org.biojava.bio.seq
A filter that returns all features not accepted by a child filter.
FeatureFilter.OnlyChildren - Class in org.biojava.bio.seq
Accepts features where all immediate children meet the supplied filter.
FeatureFilter.OnlyDescendants - Class in org.biojava.bio.seq
Accepts features where all descendants meet the supplied filter.
FeatureFilter.Or - Class in org.biojava.bio.seq
A filter that returns all features accepted by at least one child filter.
FeatureFilter.OverlapsLocation - Class in org.biojava.bio.seq
A filter that returns all features overlapping a location.
FeatureFilter.ShadowContainedByLocation - Class in org.biojava.bio.seq
A filter that accepts all features whose shadow is contained by a specified Location.
FeatureFilter.ShadowOverlapsLocation - Class in org.biojava.bio.seq
A filter that accepts all features whose shadow overlaps a specified Location.
FeatureFilter.StrandFilter - Class in org.biojava.bio.seq
Accept features with a given strandedness.
FeatureHandler - Class in org.biojava.bio.program.xff
StAX handler for the basic feature type of XFF.
FeatureHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.FeatureHandler
Construct a new Feature handler, passing in an XFF-parsing environment.
FeatureHolder - Interface in org.biojava.bio.seq
The interface for objects that contain features.
FeatureHolder.EmptyFeatureHolder - Class in org.biojava.bio.seq
 
featureHolderAllocated() - Method in class org.biojava.bio.seq.impl.SimpleFeature
A utility function to find out if the feature holder delegate has been instantiated yet.
featureHolderAllocated() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
featureHolderAsSet(FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils
Returns a FeatureHolder as a Set of Features
FeatureHolderUtils - Class in org.biojava.bio.seq
This class intendes to provide some FeatureHolder utilities.
FeatureHolderUtils() - Constructor for class org.biojava.bio.seq.FeatureHolderUtils
 
FeatureImpl - Class in org.biojava.bio.seq.impl
Wrap up default sets of Feature implementations.
FeatureImpl() - Constructor for class org.biojava.bio.seq.impl.FeatureImpl
 
FeatureLabelRenderer - Class in org.biojava.bio.gui.sequence
 
FeatureLabelRenderer() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer
 
FeatureLabelRenderer(FeatureLabelRenderer.LabelMaker) - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer
 
FeatureLabelRenderer.AnnotationLabelMaker - Class in org.biojava.bio.gui.sequence
 
FeatureLabelRenderer.LabelMaker - Interface in org.biojava.bio.gui.sequence
 
FeatureLabelRenderer.SourceLabelMaker - Class in org.biojava.bio.gui.sequence
 
FeatureLabelRenderer.TypeLabelMaker - Class in org.biojava.bio.gui.sequence
 
featureListener - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
featureListener - Variable in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
 
featureListener - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
featureListener - Variable in class org.biojava.bio.seq.io.game.StAXPropertyHandler
 
FEATUREQUAL_NAME_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATUREQUAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATUREQUAL_VALUE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FEATUREQUALS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FeatureRealizer - Interface in org.biojava.bio.seq
Interface for translators which map from Feature.Template instances to real Feature objects.
featureRelationshipSet - Variable in class org.biojavax.bio.seq.RichFeature.Template
 
FeatureRenderer - Interface in org.biojava.bio.gui.sequence
 
features - Variable in class org.biojava.bio.seq.io.GenbankProcessor
Deprecated.
 
features() - Method in interface org.biojava.bio.seq.Feature
Iterate over any child features which are held by this feature.
features() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
features() - Method in interface org.biojava.bio.seq.FeatureHolder
Iterate over the features in no well defined order.
features() - Method in class org.biojava.bio.seq.impl.DummySequence
 
features() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
features() - Method in class org.biojava.bio.seq.impl.RevCompSequence
 
features() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
features() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
features() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
features() - Method in class org.biojava.bio.seq.impl.SubSequence
 
features() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
features() - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
features() - Method in class org.biojava.bio.seq.MergeFeatureHolder
Iterate over all the features in all child FeatureHolders.
features() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
features() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
features() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
features() - Method in class org.biojava.bio.seq.SimpleAssembly
 
features() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
 
features() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Iterate over any child features which are held by this feature.
features() - Method in class org.biojavax.bio.seq.ThinRichSequence
Iterate over the features in no well defined order.
FEATURES - Static variable in interface org.biojava.bio.seq.FeatureHolder
Signals that features have been added or removed directly within this FeatureHolder.
FEATURES_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
FeatureSource - Interface in org.biojava.bio.gui.sequence
A closure that allows AbstractPeptideDigestRenderer implementations to obtain the features of the rendered sequence.
FeatureTableParser - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
featureTemplate - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
featureTemplate - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
FeatureTree - Class in org.biojava.bio.gui
FeatureTree is GUI tree to display the features and annotations of the sequences in a SequenceDB Nested Features are displayed as expandable leaves.
FeatureTree() - Constructor for class org.biojava.bio.gui.FeatureTree
Create a new FeatureTree
FeatureTypes - Class in org.biojava.bio.seq
Registry of known types of features.
FeatureTypes() - Constructor for class org.biojava.bio.seq.FeatureTypes
 
FeatureTypes.Repository - Interface in org.biojava.bio.seq
A named collection of Types.
FeatureTypes.RepositoryImpl - Class in org.biojava.bio.seq
A simple implementation of a Repository.
FeatureTypes.Type - Interface in org.biojava.bio.seq
A type of feature.
fetch(String) - Method in class org.biojava.bio.seq.db.BioIndex
 
fetch(String) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
 
fetch(String) - Method in interface org.biojava.bio.seq.db.IndexStore
Fetch an Index based upon an ID.
fetch(String) - Method in class org.biojava.bio.seq.db.TabIndexStore
 
FetchURL - Class in org.biojava.bio.seq.db
 
FetchURL(String, String) - Constructor for class org.biojava.bio.seq.db.FetchURL
Constructs a fetchURL object based on the database name and specified return format of sequence.
FileAsList - Class in org.biojava.utils
FileAsList creates a writable List implementation backed by a random access file.
FileAsList(File, boolean) - Constructor for class org.biojava.utils.FileAsList
Creates a new FileAsList instance from an existing backing file.
FileAsList(File, int) - Constructor for class org.biojava.utils.FileAsList
Creates a new FileAsList and corresponding backing file.
fileCommentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
 
fileCommentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
This method will get called when comment text is found on the file, and not any block within it.
FileStreamer(SequenceFormat, SymbolTokenization, File) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
 
FileStreamer(SequenceFormat, SymbolTokenization, List) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
 
fileToBiojava(int, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Reads a file and returns the corresponding Biojava object.
fileToBiojava(String, String, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Reads a file with the specified format and alphabet
FILL - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Constant FILL indicating a change to the fill of the features.
FILL - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
FILL - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
fillBuffer(StringBuffer, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Simple method that adds spaces onto the buffer passed in.
fillColors - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
The map containing the fill colors for callboxes.
fillPaint(Symbol) - Method in class org.biojava.bio.gui.DNAStyle
 
fillPaint(Symbol) - Method in class org.biojava.bio.gui.PlainStyle
 
fillPaint(Symbol) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
 
fillPaint(Symbol) - Method in interface org.biojava.bio.gui.SymbolStyle
Return the fill paint for a symbol.
fillTemplate(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
fillTemplate(FramedFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
 
fillTemplate(HomologyFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
 
fillTemplate(SimilarityPairFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
 
fillTemplate(RemoteFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
 
fillTemplate(StrandedFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
filter - Variable in class org.biojava.bio.gui.sequence.FilteringRenderer
 
filter - Variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
filter is the filter applied to both FeatureHolders.
filter(AnnotationType) - Method in interface org.biojava.bio.annodb.AnnotationDB
Find all Annotation instances in this DB that are of a particular type.
filter(AnnotationType) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
 
filter(AnnotationType) - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
 
filter(AnnotationType) - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
 
filter(AnnotationType) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
 
filter(AnnotationType) - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
 
filter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFEntrySet
Filter this entry set into another set.
filter(OrthologueFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthologueSet
 
filter(OrthologueFilter) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
Filter the contents of a set.
filter(OrthoPairFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairSet
 
filter(OrthoPairFilter) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
filter an OrthoPairSet
filter(OrthoPairSetFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
 
filter(OrthoPairSetFilter) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
Filter the database for a specified group.
filter(OrthoPairSetFilter) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
filter(FeatureFilter) - Method in interface org.biojava.bio.seq.db.SequenceDB
Query features attached to all sequences in this database.
filter(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
filter(FeatureFilter) - Method in interface org.biojava.bio.seq.FeatureHolder
Query this set of features using a supplied FeatureFilter.
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.DummySequence
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.RevCompSequence
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SubSequence
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
filter(FeatureFilter) - Method in class org.biojava.bio.seq.SimpleAssembly
 
filter(FeatureFilter) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
filter(FeatureFilter) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
filter(FeatureFilter) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Query this set of features using a supplied FeatureFilter.
filter(FeatureFilter) - Method in class org.biojavax.bio.seq.ThinRichSequence
Query this set of features using a supplied FeatureFilter.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
filter(FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.FeatureHolder
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.DummySequence
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.RevCompSequence
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SubSequence
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.MergeFeatureHolder
When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.SimpleAssembly
 
filter(FeatureFilter, boolean) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
filter(FeatureFilter, boolean) - Method in class org.biojavax.bio.seq.ThinRichSequence
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
FILTER - Static variable in class org.biojava.bio.gui.sequence.FilteringRenderer
 
FILTER - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
Constant FILTER indicating a change to the renderer's filter.
FilterByLength(SearchListener, int) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.FilterByLength
 
FilteringContentHandler - Class in org.biojava.bio.search
 
FilteringContentHandler(BlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.FilteringContentHandler
 
FilteringContentHandler(BlastLikeSearchFilter, SearchContentHandler) - Constructor for class org.biojava.bio.search.FilteringContentHandler
 
FilteringContentHandler.FilterVisitor - Class in org.biojava.bio.search
Visitor class that parses the filter tree
FilteringRenderer - Class in org.biojava.bio.gui.sequence
 
FilteringRenderer() - Constructor for class org.biojava.bio.gui.sequence.FilteringRenderer
 
FilteringRenderer(SequenceRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.FilteringRenderer
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
 
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.program.xff.ElementRecognizer
Recognize an element based upon the start element parameters.
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
 
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.seq.io.agave.ElementRecognizer
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
 
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.seq.io.game.ElementRecognizer
 
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute
 
FilterTest - Interface in org.biojava.bio.search
Class for implementing tests with BlastLikeSearchFilter objects.
FilterTest.Equals - Class in org.biojava.bio.search
Tests that the value associated with the specified key is equal to the value supplied here by whatever criterion of equality appropriate to those objects.
FilterTest.FindRegex - Class in org.biojava.bio.search
Tests that the value associated with the specified key contains a part matched by the supplied regex.
FilterTest.GreaterThan - Class in org.biojava.bio.search
Tests that the value associated with the specified key is greater than the specified threshold.
FilterTest.LessThan - Class in org.biojava.bio.search
Tests that the value associated with the specified key is less than the specified threshold.
FilterTest.MatchRegex - Class in org.biojava.bio.search
Tests that the value associated with the specified key is matched in its entirety by the supplied regex.
FilterTransformer - Class in org.biojava.bio.seq.filter
Base-class for visitors that re-write a filter tree.
FilterTransformer() - Constructor for class org.biojava.bio.seq.filter.FilterTransformer
 
FilterUtils - Class in org.biojava.bio.seq
A set of FeatureFilter algebraic operations.
FilterUtils.DelegatingTransformer - Class in org.biojava.bio.seq
An implementation of FilterTransformer that attempts to transform by one transformer, and if that fails, by another.
FilterUtils.FilterTransformer - Interface in org.biojava.bio.seq
An object able to transform some FeatureFilter instances sytematically into others.
FilterVisitor() - Constructor for class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
 
finalize() - Method in class org.biojava.bio.alignment.SimpleAlignment
 
finalize() - Method in class org.biojava.bio.seq.io.NameTokenization
 
finalize() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
 
finalize() - Method in class org.biojava.bio.symbol.SimpleSymbolList
 
finalize() - Method in class org.biojava.utils.process.ExternalProcess
find() - Method in interface org.biojava.bio.search.BioMatcher
Attempt to find the next match.
find() - Method in class org.biojava.bio.search.MaxMismatchMatcher
 
find() - Method in class org.biojava.utils.regex.Matcher
Attempts to find the next subsequence of the input sequence that matches the pattern.
find(int) - Method in class org.biojava.utils.regex.Matcher
Resets this matcher and then attempts to find the next subsequence of the input sequence that matches the pattern, starting at the specified index.
find(String[], String[], Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery
The easiest direct method for querying a repository.
findByAuthor(BiblioProvider, Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery
This is a convenient method for a common query.
findById(String) - Method in interface org.biojava.bibliography.BibRefQuery
This is a convenient method returning just one citation.
findById(String, String[]) - Method in interface org.biojava.bibliography.BibRefQuery
This is a convenient method returning just one citation, perhaps with a limited number of attributes.
findFactory(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
Find the UnigeneFactory that can accept a URL.
findMatches(SymbolList) - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
This will return an int[] giving the offsets of the matches in text (ie the location of the first symbol of each match in the text).
findRecord(String) - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
findRecord performs a binary search within the file for a record specified by an identifier String.
FindRegex(String) - Constructor for class org.biojava.bio.search.FilterTest.FindRegex
 
findSourceBlock(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Finds the index of the block containing the source coordinate indx.
findSourceGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Finds the index of the Block before the gap at indx within the following gap.
findTaxon(Object[]) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
 
findUnescaped(String, char) - Static method in class org.biojava.ontology.obo.OboFileParser
 
findUnescaped(String, char, int, int) - Static method in class org.biojava.ontology.obo.OboFileParser
 
findUnescaped(String, char, int, int, boolean) - Static method in class org.biojava.ontology.obo.OboFileParser
 
findViewBlock(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Finds the index of the Block containing indx within the view ranges.
findViewGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Finds the index of the Block before the gap at indx within the view range.
finishedReading() - Method in interface org.biojava.bio.program.abi.ABIFParser.DataAccess
Called when the parser has finished reading.
finishWriting() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.INSDseqFormat
Informs the writer that are done writing.
finishWriting() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
Informs the writer that are done writing.
FiniteAlphabet - Interface in org.biojava.bio.symbol
An alphabet over a finite set of Symbols.
FiniteAutomaton - Class in org.biojava.utils.automata
Class for modelling finite automata.
fireEndFeature() - Method in class org.biojava.bio.program.xff.FeatureHandler
Fire the endFeature event.
fireHits(int, int, SearchListener) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
 
fireMouseClicked(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
 
fireMouseDragged(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
 
fireMouseMoved(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
 
fireMousePressed(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
 
fireMouseReleased(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
 
firePostChange(Object, ChangeEvent) - Method in interface org.biojava.utils.ChangeHub
invoke the firePostChangeEvent on all ChangeListeners associated with a specific key.
firePostChange(Object, ChangeEvent) - Method in class org.biojava.utils.IndexedChangeHub
 
firePostChangeEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeSupport
Inform the listeners that a change has taken place using their firePostChangeEvent methods.
firePreChange(Object, ChangeEvent) - Method in interface org.biojava.utils.ChangeHub
invoke the firePreChangeEvent on all ChangeListeners associated with a specific key.
firePreChange(Object, ChangeEvent) - Method in class org.biojava.utils.IndexedChangeHub
 
firePreChangeEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeSupport
Inform the listeners that a change is about to take place using their firePreChangeEvent methods.
firePropertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.StackedLogoPainter
 
firePropertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.TextLogoPainter
 
firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.StackedLogoPainter
 
firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.TextLogoPainter
 
firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.StackedLogoPainter
 
firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.TextLogoPainter
 
firePropertyChange(String, Object, Object) - Method in class org.biojava.bio.gui.StackedLogoPainter
 
firePropertyChange(String, Object, Object) - Method in class org.biojava.bio.gui.TextLogoPainter
 
fireStartFeature() - Method in class org.biojava.bio.program.xff.FeatureHandler
Fire the startFeature event.
firstName - Variable in class org.biojava.bibliography.BiblioPerson
The person's christian name (first name).
firstNonGap() - Method in interface org.biojava.bio.symbol.GappedSymbolList
Return the index of the first Symbol that is not a Gap character.
firstNonGap() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
firstPage - Variable in class org.biojava.bibliography.BiblioArticle
First page of the article.
firstToken(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
fitness(Organism, Population, GeneticAlgorithm) - Method in interface org.biojavax.ga.functions.FitnessFunction
Calculates the fitness of org.
FITNESS_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
 
FitnessFunction - Interface in org.biojavax.ga.functions
Calculates the fitness of an Organism in a Population of Organisms
fivePrimeBlockIterator() - Method in class org.biojava.bio.symbol.CircularLocation
Iterates over the location blocks in order starting with the most 5'
FixedBaseWidthScaler - Class in org.biojava.bio.chromatogram.graphic
A ChromatogramNonlinearScaler that scales all the base calls in a chromatogram to the same width in pixels, optionally biasing the peak of the call to the center.
FixedBaseWidthScaler(float) - Constructor for class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler
Creates a new scaler that will scale bases to the specified width without attempting to center their peaks.
FixedBaseWidthScaler(float, boolean) - Constructor for class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler
Creates a new scaler that will scale bases to the specified width and may or may not bias the peaks to the center.
FixedSizeCache - Class in org.biojava.utils.cache
Cache which stores up to limit Objects.
FixedSizeCache(int) - Constructor for class org.biojava.utils.cache.FixedSizeCache
 
FixedSizeMap - Class in org.biojava.utils.cache
A cache that only remembers a given number of keys.
FixedSizeMap(int) - Constructor for class org.biojava.utils.cache.FixedSizeMap
 
FIXEDWIDTH - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
 
FLAT_QUERY_ANCHORED - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
FLAT_QUERY_ANCHORED_NO_IDENTITIES - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
FlatFileCache - Class in org.biojava.utils.io
Provides a cache for storing multiple small files in memory.
FlatFileUnigeneFactory - Class in org.biojava.bio.program.unigene
A UnigeneFactory that will use flat-file indexing of the unigene ascii-art files.
FlatFileUnigeneFactory() - Constructor for class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
 
FlatSequenceDB - Class in org.biojava.bio.seq.db.flat
FlatSequenceDB is an OBDA flatfile sequence databank implementation.
FlatSequenceDB(String, String) - Constructor for class org.biojava.bio.seq.db.flat.FlatSequenceDB
 
FlatSequenceDBProvider - Class in org.biojava.bio.seq.db.flat
FlatSequenceDBProvider directory-services plugin for flatfile databases.
FlatSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
 
flatten(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
Takes a set of locations and returns the set of all members.
flatten(RichLocation) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
Takes a location and returns the set of all members.
flatView(MarkovModel) - Static method in class org.biojava.bio.dp.DP
 
FlexibleAlignment - Class in org.biojava.bio.alignment
FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment.
FlexibleAlignment(List<AlignmentElement>) - Constructor for class org.biojava.bio.alignment.FlexibleAlignment
construct this object with the reference sequence which can either be a gappedSymbolList or not label in all cases refers to an object that holds the display name (generally just a String). since more than one sequence in an alignment could have the same name this works as long as the labels are different objects even though they may hold the same name.
flip() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
Return a strand that represents flipping this onto the opposite strand.
flip(Location, int) - Static method in class org.biojava.bio.symbol.LocationTools
Flips a location relative to a length.
flip(SymbolList, StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.DNATools
Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
flipLocation(Location, int) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
Flip a location.
flipStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
 
fList - Variable in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
 
FloatElementHandlerBase - Class in org.biojava.utils.stax
StAX handler for any element which just contains a string representation of a float.
FloatElementHandlerBase() - Constructor for class org.biojava.utils.stax.FloatElementHandlerBase
 
flush() - Method in class org.biojava.utils.RepeatedCharSequence
 
flushFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
force() - Method in class org.biojava.utils.io.LargeBuffer
 
forClass(Class) - Static method in class org.biojava.utils.bytecode.IntrospectedCodeClass
Get the CodeClass for a Java Class.
forClass(String) - Static method in class org.biojava.utils.bytecode.IntrospectedCodeClass
Get the CodeClass for a Java class name.
forIndex(int) - Static method in class org.biojava.bio.seq.DNATools
Return the symbol for an index - compatible with index.
forIndex(int) - Static method in class org.biojava.bio.seq.NucleotideTools
Return the symbol for an index - compatible with index.
forIndex(int) - Static method in class org.biojava.bio.seq.RNATools
Return the symbol for an index - compatible with index.
format - Variable in class org.biojava.bibliography.BibRef
It describes the physical or digital manifestation of the cited resource.
Format - Interface in org.biojava.bio.program.formats
A file format supported by the tag-value event-based parsing system.
formatLocation(StringBuffer, Location) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
formatLocation creates a String representation of a Location.
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
Deprecated.
formatLocation creates a String representation of a Location.
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
formatLocation creates a String representation of a Location.
formatLocation(Feature) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
Deprecated.
Formats the location of a feature.
formatLocation(Feature) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Creates a string representation of the location of a feature
formatOutput() - Method in class org.biojava.bio.alignment.AlignmentPair
 
formatOutput(int) - Method in class org.biojava.bio.alignment.AlignmentPair
This method provides a BLAST-like formated alignment from the given Strings, in which the sequence coordinates and the information "Query" or "Sbjct", respectively is added to each line.
formatPoint(int, int, boolean) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Formats the points from fuzzy locations.
Formats - Class in org.biojava.bio.program.tagvalue
This is intended as a repository for tag-value and AnnotationType information about common file formats.
Formats() - Constructor for class org.biojava.bio.program.tagvalue.Formats
 
formatToFactory(SequenceFormat, Alphabet) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
as this essentially duplicates the operation available in the method identifyBuilderFactory.
FormatTools - Class in org.biojava.bio.program.formats
 
forMethod(Method) - Static method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
forName(String) - Static method in class org.biojavax.bio.seq.RichLocation.Strand
Returns the strand object that matches the symbol given.
forSubset - Variable in class org.biojava.bibliography.BiblioCriterion
A name of a repository subset which this criterion is valid/used for.
forSymbol(char) - Static method in class org.biojava.bio.seq.DNATools
Retrieve the symbol for a symbol.
forSymbol(char) - Static method in class org.biojava.bio.seq.NucleotideTools
Retrieve the symbol for a symbol.
forSymbol(char) - Static method in class org.biojava.bio.seq.RNATools
Retrieve the symbol for a symbol.
forValue(int) - Static method in class org.biojavax.bio.seq.RichLocation.Strand
Returns the strand object that matches the number given.
forward(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
 
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
FORWARD - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
forward_initialize(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
forwardChangeEvent(ChangeEvent) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolder
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
 
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
 
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
forwardRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
forwards(ScoreType) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
 
forwards(ScoreType) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
 
forwardsBackwards(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
 
forwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
Returns a matrix for the specified States describing all valid Transitions between those States.
forwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP
Compute the log(score) of all transitions between the specified States.
fp - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
Frame - Interface in org.biojava.bio.seq
Title: Frame.
FRAME_0 - Static variable in interface org.biojava.bio.seq.Frame
 
FRAME_0 - Static variable in interface org.biojava.bio.seq.FramedFeature
 
FRAME_1 - Static variable in interface org.biojava.bio.seq.Frame
 
FRAME_1 - Static variable in interface org.biojava.bio.seq.FramedFeature
 
FRAME_2 - Static variable in interface org.biojava.bio.seq.Frame
 
FRAME_2 - Static variable in interface org.biojava.bio.seq.FramedFeature
 
FramedFeature - Interface in org.biojava.bio.seq
Title: FramedFeature.
FramedFeature.ReadingFrame - Class in org.biojava.bio.seq
A singleton to hold the frame information
FramedFeature.Template - Class in org.biojava.bio.seq
 
FrameFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
 
FrameFilter(int) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
 
FrameFilter(FramedFeature.ReadingFrame) - Constructor for class org.biojava.bio.seq.FeatureFilter.FrameFilter
Build a new filter that matches all features of a reading frame.
frequency(int) - Method in class org.biojava.bio.symbol.SuffixTree
Return the number of motifs of a given length encoded in this SuffixTree.
from - Variable in class org.biojava.bio.dp.TrainerTransition
 
from - Variable in class org.biojava.bio.dp.Transition
 
FROM_TRACE_SAMPLE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating the lowest (leftmost) trace sample that should be drawn.
fromArray(double[]) - Static method in class org.biojava.bio.symbol.DoubleAlphabet
Retrieve a SymbolList view of an array of doubles.
fromArray(int[]) - Static method in class org.biojava.bio.symbol.IntegerAlphabet
Retrieve a SymbolList view of an array of integers.
fromBook - Variable in class org.biojava.bibliography.BiblioBookArticle
Book this is from.
fromJournal - Variable in class org.biojava.bibliography.BiblioJournalArticle
The journal that this article is in.
FUGU_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
Takifugu rubripes codon preferences
full - Static variable in interface org.biojava.bio.symbol.Location
The Location which contains all points.
FULL_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
FullHmmerProfileHMM - Class in org.biojava.bio.program.hmmer
This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
fullyLoadRichSequence(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
 
FundamentalAtomicSymbol - Class in org.biojava.bio.symbol
An atomic symbol consisting only of itself.
FundamentalAtomicSymbol(String, Annotation) - Constructor for class org.biojava.bio.symbol.FundamentalAtomicSymbol
 
FuzzyLocation - Class in org.biojava.bio.symbol
A 'fuzzy' location a-la Embl fuzzy locations.
FuzzyLocation(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver) - Constructor for class org.biojava.bio.symbol.FuzzyLocation
Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).
FuzzyLocation(int, int, int, int, FuzzyLocation.RangeResolver) - Constructor for class org.biojava.bio.symbol.FuzzyLocation
Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).
FuzzyLocation.RangeResolver - Interface in org.biojava.bio.symbol
Determines how a FuzzyLocation should be treated when used as a normal Location.
FuzzyPointLocation - Class in org.biojava.bio.symbol
FuzzyPointLocation represents two types of EMBL-style partially-defined locations.
FuzzyPointLocation(int, int, FuzzyPointLocation.PointResolver) - Constructor for class org.biojava.bio.symbol.FuzzyPointLocation
Creates a new FuzzyPointLocation object.
FuzzyPointLocation.PointResolver - Interface in org.biojava.bio.symbol
Determines how a FuzzyPointLocation should be treated when used as a normal Location.
FWORM_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the flatworm mitochondrial genetic code.

G

g() - Static method in class org.biojava.bio.seq.DNATools
 
g() - Static method in class org.biojava.bio.seq.NucleotideTools
 
g() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Glycine
g() - Static method in class org.biojava.bio.seq.RNATools
 
GACross - Interface in org.biojavax.ga.functions
Holds the results of a CrossOver event, objects of this type are made by CrossOverFunctions
GACrossResult - Interface in org.biojavax.ga.functions
Holds the results of a CrossOver event, objects of this type are made by CrossOverFunctions
GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
 
GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
Description of the Field
GAME_ASPECT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAspectHandler
 
GAME_ASPECT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler
 
GAME_DBXREF_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler
Description of the Field
GAME_DBXREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler
 
GAME_DESCRIPTION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
 
GAME_FEATURE_SET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
Description of the Field
GAME_FEATURE_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
Description of the Field
GAME_FEATURESET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
 
GAME_FEATURESET_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler
 
GAME_FEATURESPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
 
GAME_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
Description of the Field
GAME_GENE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
 
GAME_MAP_POS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
 
GAME_NAME_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMENamePropHandler
 
GAME_PROPERTY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEPropertyHandler
Description of the Field
GAME_RESIDUES_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
 
GAME_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqHandler
Description of the Field
GAME_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
 
GAME_SEQ_REL_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
Description of the Field
GAME_SEQREL_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler
 
GAME_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESpanHandler
Description of the Field
GAME_SPAN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESpanPropHandler
 
GAME_TYPE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMETypePropHandler
 
GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game
Handles the GAME <annotation> element
GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game12
Handles the GAME <annotation> element
GAMEAspectHandler - Class in org.biojava.bio.seq.io.game12
Handles the GAME <aspect> element
GAMEAspectPropHandler - Class in org.biojava.bio.seq.io.game
Handles the GAME <aspect> element
GAMEDbxrefHandler - Class in org.biojava.bio.seq.io.game12
Handles the GAME <dbxref> element
GAMEDbxrefPropHandler - Class in org.biojava.bio.seq.io.game
Deals with database crossreferences
GAMEDbxrefPropHandler.DbXrefElement - Class in org.biojava.bio.seq.io.game
 
GAMEDescriptionPropHandler - Class in org.biojava.bio.seq.io.game
StAX handler for GAME <description> elements.
GAMEDescriptionPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
 
GAMEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.game
An interface that can be tested for by nested handlers when trying to do a callback.
GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game
Handles the <feature_set> element
GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game12
Handles the GAME <feature_set> element this element is used to represent transcripts.
GAMEFeatureSetPropHandler - Class in org.biojava.bio.seq.io.game
Handles the GAME element
GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game
Handles the <feature_span> element
GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game12
Handles the GAME <feature_span> element
GAMEFeatureSpanHandler.SeqRelHandler - Class in org.biojava.bio.seq.io.game12
 
GAMEFormat - Class in org.biojava.bio.seq.io
A rudimentary read-only GAME 1.2 Format object.
GAMEFormat() - Constructor for class org.biojava.bio.seq.io.GAMEFormat
 
GAMEGeneHandler - Class in org.biojava.bio.seq.io.game12
Handles the GAME <annotation> element
GAMEGenePropHandler - Class in org.biojava.bio.seq.io.game
Handles the GAME <gene> element
GAMEHandler - Class in org.biojava.bio.seq.io.game
Handles the root GAME element
GAMEHandler - Class in org.biojava.bio.seq.io.game12
Handles the root GAME element
GAMEHandler() - Constructor for class org.biojava.bio.seq.io.game.GAMEHandler
 
GAMEHandler(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.game12.GAMEHandler
Constructor for the GAMEHandler object
GAMEMapPosPropHandler - Class in org.biojava.bio.seq.io.game
Handles the GAME <map_position> element Currently, it just ignores it!
GAMENameCallbackItf - Interface in org.biojava.bio.seq.io.game
An interface that can be tested for by nested handlers when trying to do a callback.
GAMENamePropHandler - Class in org.biojava.bio.seq.io.game
StAX handler for the GAME <name> element.
GAMENamePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMENamePropHandler
 
GAMEPropertyHandler - Class in org.biojava.bio.seq.io.game12
Handles the GAME <dbxref> element
GAMEResiduesPropHandler - Class in org.biojava.bio.seq.io.game
StAX handler for GAME <residues> elements.
GAMEResiduesPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
 
GAMESeqHandler - Class in org.biojava.bio.seq.io.game12
Handles the GAME <seq> element
GAMESeqPropHandler - Class in org.biojava.bio.seq.io.game
Handles the GAME <seq> element
GAMESeqRelHandler - Class in org.biojava.bio.seq.io.game12
Handles the GAME <> element
GAMESeqRelPropHandler - Class in org.biojava.bio.seq.io.game
Handles the GAME <aspect> element
GAMESpanHandler - Class in org.biojava.bio.seq.io.game12
Handles the GAME <> element.
GAMESpanPropHandler - Class in org.biojava.bio.seq.io.game
Handles the GAME <span> element Currently, it just ignores it!
GAMETranscriptCallbackItf - Interface in org.biojava.bio.seq.io.game
An interface that can be tested for by nested handlers when trying to do a callback.
GAMETypePropHandler - Class in org.biojava.bio.seq.io.game
StAX handler for GAME <type> elements.
GAMETypePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMETypePropHandler
 
GapDistribution - Class in org.biojava.bio.dist
This distribution emits gap symbols.
GapDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.GapDistribution
Get a GapDistribution for an alphabet.
GappedContext() - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
 
GappedRenderer - Class in org.biojava.bio.gui.sequence
A renderer that will display a gapped sequence as a discontinuous series of regions.
GappedRenderer() - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer
 
GappedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer
 
GappedSequence - Interface in org.biojava.bio.seq
Extension of GappedSymbolList which also projects features into the gapped coordinate system.
GappedSymbolList - Interface in org.biojava.bio.symbol
This extends SymbolList with API for manipulating, inserting and deleting gaps.
gappedToLocation(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Translates a Location from the gapped view into the underlying sequence.
gappedView(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools
Create a new gapped sequence for a sequence.
GAPS - Static variable in interface org.biojava.bio.alignment.EditableAlignment
 
GAStoppingCriteria - Interface in org.biojavax.ga
Used by a GeneticAlgorithm.run() method to determine when the algorithm should stop
GAStoppingCriteria.MaximumGeneration - Class in org.biojavax.ga
Simple Implementation of GAStoppingCriteria, signals a GeneticAlgorithm to stop after n generations
GATools - Class in org.biojavax.ga.util
Utility methods for the GA library
GATools() - Constructor for class org.biojavax.ga.util.GATools
 
GCG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
GCG indicates that the sequence format is GCG.
ge - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
GENBANK - Static variable in class org.biojava.bio.program.tagvalue.LineSplitParser
A LineSplitParser pre-configured to process GENBANK-style flat files.
GENBANK - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
GENBANK indicates that the sequence format is GENBANK.
GENBANK_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
GENBANK_DNA premade GENBANK | AA.
GENBANK_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
GENBANK_DNA premade GENBANK | DNA.
GENBANK_FORMAT - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
The name of this format
GENBANK_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
GENBANK_DNA premade GENBANK | RNA.
GenbankFileFormer - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenbankFileFormer() - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
Creates a new GenbankFileFormer using System.out stream.
GenbankFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
Creates a new GenbankFileFormer using the specified stream.
GenbankFormat - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io.GenbankFormat
GenbankFormat - Class in org.biojavax.bio.seq.io
Format reader for GenBank files.
GenbankFormat() - Constructor for class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
GenbankFormat() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat
 
GenbankFormat.Terms - Class in org.biojavax.bio.seq.io
Implements some GenBank-specific terms.
GenbankLocationParser - Class in org.biojavax.bio.seq.io
Parses Genbank location strings into RichLocation objects.
GenbankProcessor - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenbankProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor
Deprecated.
 
GenbankProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor
Deprecated.
 
GenbankProcessor.Factory - Class in org.biojava.bio.seq.io
Deprecated.
Factory which wraps sequence builders in a GenbankProcessor
GenbankRichSequenceDB - Class in org.biojavax.bio.db.ncbi
This class contains functions accessing DNA sequences in Genbank format.
GenbankRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
The default constructor delegates to the parent class.
GenbankSequenceDB - Class in org.biojava.bio.seq.db
This class contains functions accessing DNA sequences in Genbank format.
GenbankSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenbankSequenceDB
 
GenbankXmlFormat - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io.INSDseqFormat
GenbankXmlFormat() - Constructor for class org.biojava.bio.seq.io.GenbankXmlFormat
Deprecated.
 
GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
GENELOCATION_NAME_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
GENELOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
GenEmblFeatureComparator - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenEmblPropertyComparator - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
GENENAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
generate() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Generates a comment string based on the current values of the internal fields.
generate(int) - Method in class org.biojava.bio.dp.DP
Generates an alignment from a model.
generateAuthorString(List<DocRefAuthor>, boolean) - Static method in class org.biojavax.DocRefAuthor.Tools
Takes a set of authors and creates a comma-separated string.
generateBackwardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
 
generateCallboxes() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Precomputes the Rectangle2Ds that are the in-memory representation of the callboxes.
generateChangeSupport() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
generateChangeSupport() - Method in class org.biojava.utils.AbstractChangeable
Called the first time a ChangeSupport object is needed.
generateCrossProductAlphaFromName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generates a new CrossProductAlphabet from the give name.
GeneratedClassLoader - Class in org.biojava.utils.bytecode
A class loader that actually produces real Java classes from GeneratedCodeClass instances.
GeneratedClassLoader() - Constructor for class org.biojava.utils.bytecode.GeneratedClassLoader
Create a new loader with the default parent.
GeneratedClassLoader(ClassLoader) - Constructor for class org.biojava.utils.bytecode.GeneratedClassLoader
Create a new loader with an explicitly set parent class loader.
GeneratedCodeClass - Class in org.biojava.utils.bytecode
A CodeClass implementation that is used to generate new classes.
GeneratedCodeClass(String, Class, Class[], int) - Constructor for class org.biojava.utils.bytecode.GeneratedCodeClass
 
GeneratedCodeClass(String, CodeClass, CodeClass[], int) - Constructor for class org.biojava.utils.bytecode.GeneratedCodeClass
 
GeneratedCodeMethod - Class in org.biojava.utils.bytecode
A method that will be generated.
generateDrawableCallboxes(AffineTransform) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Precomputes the callboxes in screen coordinates.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.Annotatable.AnnotationForwarder
Deprecated.
 
generateEvent(ChangeEvent) - Method in class org.biojava.bio.dist.Distribution.NullModelForwarder
Deprecated.
 
generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder
generateEvent generates events in response to layout change and repaint requests.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder
 
generateEvent(ChangeEvent) - Method in class org.biojava.bio.MergeAnnotation.PropertyForwarder
 
generateEvent(ChangeEvent) - Method in class org.biojava.bio.OverlayAnnotation.PropertyForwarder
 
generateEvent(ChangeEvent) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
 
generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
 
generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
 
generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder
Return the new event to represent the originating event ce.
generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder.Retyper
 
generateForardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
 
generateOrderNSequence(String, OrderNDistribution, int) - Static method in class org.biojava.bio.dist.DistributionTools
Deprecated.
use generateSequence() or generateSymbolList() instead.
generateRecord(byte[], Object) - Method in class org.biojava.utils.FileAsList
 
generateSequence(String, Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools
Produces a sequence by randomly sampling the Distribution.
generateSubpaths() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Precomputes the GeneralPaths used to draw the traces.
generateSymbolList(Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools
Produces a SymbolList by randomly sampling a Distribution.
generateViterbiClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
 
generatorAt(int) - Method in class org.biojava.utils.bytecode.InstructionVector
 
GENERIC_PROVIDER - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a provider type.
GENESYNONYM_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
GeneticAlgorithm - Interface in org.biojavax.ga
The class that runs the cycles of reproduction, evolution and selection, potentially on multiple Populations
GENETICCODE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
GeneticCodes - Class in org.biojava.bio.seq
Collects the references to translation methods in one place.
GENPEPT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
GENPEPT indicates that the sequence format is GENPEPT.
GenpeptFormat - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenpeptFormat() - Constructor for class org.biojava.bio.seq.io.GenpeptFormat
Deprecated.
 
GenpeptRichSequenceDB - Class in org.biojavax.bio.db.ncbi
This class contains functions accessing Peptide sequences in Genpept format.
GenpeptRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
The default constructor delegates to the parent class.
GenpeptSequenceDB - Class in org.biojava.bio.seq.db
 
GenpeptSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenpeptSequenceDB
 
get() - Method in interface org.biojava.utils.cache.CacheReference
 
get() - Method in class org.biojava.utils.io.LargeBuffer
 
get(int) - Method in class org.biojava.stats.svm.SparseVector
Retrieve the value at dimension dim.
get(int) - Method in class org.biojava.utils.FileAsList
 
get(int) - Method in class org.biojava.utils.ListTools.Doublet
 
get(int) - Method in class org.biojava.utils.ListTools.SeriesList
 
get(int) - Method in class org.biojava.utils.ListTools.Triplet
 
get(int) - Method in class org.biojava.utils.SingletonList
 
get(long) - Method in class org.biojava.utils.io.LargeBuffer
 
get(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
get the Transition associated with the specified tag.
get(Object) - Method in interface org.biojava.utils.cache.CacheMap
Retrieve the Object associated with the key, or null if either no value has been associated or if the key's value has been cleared by the cache.
get(Object) - Method in class org.biojava.utils.cache.ChangeableCache
 
get(Object) - Method in class org.biojava.utils.cache.FixedSizeMap
 
get(Object) - Method in class org.biojava.utils.cache.WeakCacheMap
 
get(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
 
get(Object) - Method in class org.biojava.utils.io.SoftHashMap
 
get(Object) - Method in class org.biojava.utils.OverlayMap
 
get(Object) - Method in class org.biojava.utils.SmallMap
 
get(String) - Method in class org.biojava.bio.program.indexdb.BioStore
 
get(String) - Method in interface org.biojava.bio.program.indexdb.IndexStore
get returns a record specified by a primary identifier.
get(String, String) - Method in class org.biojava.bio.program.indexdb.BioStore
 
get(String, String) - Method in interface org.biojava.bio.program.indexdb.IndexStore
get returns a list of Records by searching against the primary identifiers if the namespace argument is equal to the primary namespace or otherwise by searching the secondary namespaces.
get_() - Method in class org.biojava.bio.proteomics.StructureTools
 
get3PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation
 
get5PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation
The point at which indicates the 5' end of the Location.
getA() - Method in class org.biojava.bio.molbio.DNAComposition
Get the relative compositon of 'A'.
getA() - Method in class org.biojava.utils.ListTools.Doublet
 
getA() - Method in class org.biojava.utils.ListTools.Triplet
 
getAbsorptionMax() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property absorptionMax.
getAbsorptionNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property absorptionNote.
getAccession() - Method in interface org.biojava.bio.program.homologene.Orthologue
get the Accession ID associated with this orthologue.
getAccession() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
 
getAccession() - Method in interface org.biojavax.bio.BioEntry
Returns the accession of this bioentry.
getAccession() - Method in class org.biojavax.bio.SimpleBioEntry
Returns the accession of this bioentry.
getAccession() - Method in interface org.biojavax.CrossRef
Returns the accession of the object that the crossref refers to.
getAccession() - Method in class org.biojavax.SimpleCrossRef
Returns the accession of the object that the crossref refers to.
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getAccession(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
 
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getAcronym() - Method in interface org.biojavax.Namespace
If the namespace has an acronym, this will return it.
getAcronym() - Method in class org.biojavax.SimpleNamespace
If the namespace has an acronym, this will return it.
getAddedFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
getAddHandler() - Method in class org.biojava.bio.program.gff.GFFEntrySet
Get the GFFDocumentHandler for adding to this set.
getAdditionalAccessionTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the secondary/tertiary/additional accession term
getAddPos() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Retrieve the current value of addPos.
getAddress(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
Get the URL object for locating sequence object using eutils.
getAddress(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
 
getAddress(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
 
getAddress(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
 
getAddress(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
 
getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Get the URL object for locating sequence object using eutils.
getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
Get the URL object for locating sequence object using eutils.
getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
Get the URL object for locating sequence object using eutils.
getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
 
getAdvance() - Method in interface org.biojava.bio.dp.EmissionState
Determine the number of symbols this state advances along one or more symbol lists.
getAdvance() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getAE(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
getAlignLength(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getAlignLength(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
 
getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
Deprecated.
 
getAlignment() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
Gets the Alignment - one of LEADING, TRAILING or CENTER.
getAlignment() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.
getAlignment() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getAlignment() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getAlignment() - Method in interface org.biojava.bio.seq.homol.Homology
Retrieve the Alignment that specifies how the homologous regions are aligned.
getAlignment() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
getAlignment returns the Alignment of two similar features.
getAlignment() - Method in class org.biojava.bio.seq.homol.SimpleHomology
getAlignment returns the alignment, which uses the HomologyFeatures as keys.
getAlignment() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
getAlignment returns the alignment between the two features.
getAlignment() - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
 
getAlignment(SymbolList) - Static method in class org.biojava.bio.program.abi.ABITools
View a symbol list over the QUALITY alphabet as an alignment.
getAlignmentNumber() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
A method that simply returns the number of alignments fetched with this RemoteQBlastOutputProperties object.
getAlignmentOption(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
 
getAlignmentOption(String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties
Method that returns the value associated with the key given in parameter.
getAlignmentOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
 
getAlignmentOptions() - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties
Method to get all keys to the information stored in this object.
getAlignmentOutputFormat() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
Method that returns the alignment output format for this actual RemoteQBlastOutputProperties object
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService
This method extracts the actual Blast report for this request ID.
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService
Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.
getAlignmentStyles() - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
Returns a fragment of HTML that defines the FONT styles to be used in the alignment markup.
getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getAlignUnits(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getAll() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
All sequences that map to this cluster.
getAllAmbiguitySymbol(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Return the ambiguity symbol which matches all symbols in a given alphabet.
getAllBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery
It returns all citations from the current collection as a (possibly big) array.
getAllBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery
It returns all citations from the current collection as a (possibly big) array, perhaps with a limited number of attributes.
getAllBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery
It returns all citations from the current collection as an XML stream.
getAllCharStates() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getAllDataRecords() - Method in class org.biojava.bio.program.abi.ABIFParser
Obtain all data records.
getAllEntries() - Method in interface org.biojava.utils.candy.CandyVocabulary
It returns all available vocabulary entries.
getAllEnzymes() - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getAllEnzymes returns an unmodifable set of all available enzymes.
getAllIDs() - Method in interface org.biojava.bibliography.BibRefQuery
A convenient method returning just identifiers of all current citations.
getAllNames() - Method in interface org.biojava.utils.candy.CandyVocabulary
It return all names (entry identifiers) available in this vocabulary.
getAllNodes(UkkonenSuffixTree.SuffixNode, ArrayList, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
getAllProteases() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getAllScientificNames(Connection) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Returns all the scientific names, which are currently stored in the database.
getAllSymbols(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Return a set containing all possible symbols which can be considered members of a given alphabet, including ambiguous symbols.
getAllVocabularies() - Method in interface org.biojava.utils.candy.CandyFinder
It returns all available vocabularies.
getAllVocabularyNames() - Method in interface org.biojava.utils.candy.CandyFinder
It returns names of all vocabularies known to this vocabulary finder.
getAlpha(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getAlpha(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
getAlpha(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
getAlphabet() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
getAlphabet() - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
getAlphabet() - Method in class org.biojava.bio.alignment.SimpleAlignment
 
getAlphabet() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
Gives the alphabet used by this matrix.
getAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
 
getAlphabet() - Method in interface org.biojava.bio.dist.Count
The alphabet from which this Count is over.
getAlphabet() - Method in interface org.biojava.bio.dist.Distribution
The alphabet from which this spectrum emits symbols.
getAlphabet() - Method in class org.biojava.bio.dist.GapDistribution
 
getAlphabet() - Method in class org.biojava.bio.dist.IndexedCount
 
getAlphabet() - Method in class org.biojava.bio.dist.PairDistribution
 
getAlphabet() - Method in class org.biojava.bio.dist.SimpleDistribution
 
getAlphabet() - Method in class org.biojava.bio.dist.TranslatedDistribution
 
getAlphabet() - Method in class org.biojava.bio.dist.UniformDistribution
 
getAlphabet() - Method in class org.biojava.bio.dp.SimpleStatePath
 
getAlphabet() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
 
getAlphabet() - Method in interface org.biojava.bio.dp.WeightMatrix
The alphabet for the sequences that this weight matrix models.
getAlphabet() - Method in class org.biojava.bio.gui.SimpleSymbolStyle
 
getAlphabet() - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
 
getAlphabet() - Method in interface org.biojava.bio.program.ssaha.DataStore
The alphabet of symbol lists that can be searched against this DataStore.
getAlphabet() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
 
getAlphabet() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
 
getAlphabet() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
 
getAlphabet() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
 
getAlphabet() - Method in class org.biojava.bio.seq.db.WebSequenceDB
 
getAlphabet() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
getAlphabet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
getAlphabet() - Method in class org.biojava.bio.seq.impl.DummySequence
 
getAlphabet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
getAlphabet() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
getAlphabet() - Method in class org.biojava.bio.seq.impl.SubSequence
 
getAlphabet() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
getAlphabet() - Method in class org.biojava.bio.seq.io.AlternateTokenization
 
getAlphabet() - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolReader
Find the alphabet of all symbols which may be returned by this SymbolReader.
getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolTokenization
The alphabet to which this tokenization applies.
getAlphabet() - Method in class org.biojava.bio.seq.io.WordTokenization
 
getAlphabet() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
getAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools
Gets the protein alphabet
getAlphabet() - Method in class org.biojava.bio.seq.SimpleAssembly
 
getAlphabet() - Method in interface org.biojava.bio.symbol.AlphabetIndex
Retrieve the alphabet that this indexes.
getAlphabet() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
 
getAlphabet() - Method in class org.biojava.bio.symbol.DNAAmbPack
 
getAlphabet() - Method in class org.biojava.bio.symbol.DNANoAmbPack
 
getAlphabet() - Method in class org.biojava.bio.symbol.DummySymbolList
 
getAlphabet() - Method in class org.biojava.bio.symbol.PackedSymbolList
 
getAlphabet() - Method in interface org.biojava.bio.symbol.Packing
The FiniteAlphabet this packing is for.
getAlphabet() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolList
Get the alphabet of this SymbolList.
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
 
getAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
 
getAlphabet() - Method in class org.biojava.bio.symbol.SuffixTree
Return the Alphabet containing all Symbols which might be found in this SuffixTree.
getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolList
The alphabet that this SymbolList is over.
getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
 
getAlphabet() - Method in class org.biojava.utils.regex.Pattern
 
getAlphabet() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
The alphabet that this SymbolList is over.
getAlphabet() - Method in class org.biojavax.bio.seq.ThinRichSequence
The alphabet that this SymbolList is over.
getAlphabet(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
getAlphabet accepts a value which represents a sequence format and returns the relevant FiniteAlphabet object.
getAlphabetIndex(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Get an indexer for a specified alphabet.
getAlphabetIndex(Symbol[]) - Static method in class org.biojava.bio.symbol.AlphabetManager
Get an indexer for an array of symbols.
getAlphabetName() - Method in class org.biojavax.bio.seq.ThinRichSequence
 
getAlphabets() - Method in interface org.biojava.bio.symbol.Alphabet
Return an ordered List of the alphabets which make up a compound alphabet.
getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
getAlphabets() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
getAlphabets() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
getAlphabets() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
Gets the components of the Alphabet.
getAlphaStar(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getAltIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
This is not supported.
getAmbiguity(Set<Symbol>) - Method in interface org.biojava.bio.symbol.Alphabet
Get a symbol that represents the set of symbols in syms.
getAmbiguityImpl(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet
Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
getAngle(int) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
Return the angle for an index into a sequence.
getAngle(int) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
 
getAnnotatedQuerySeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
getAnnotatedSubjectSeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
getAnnotation() - Method in interface org.biojava.bio.Annotatable
Should return the associated annotation object.
getAnnotation() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getAnnotation() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getAnnotation returns the Annotation associated with this sub-hit.
getAnnotation() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
 
getAnnotation() - Method in class org.biojava.bio.seq.impl.DummySequence
 
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
getAnnotation() - Method in class org.biojava.bio.seq.impl.SubSequence
 
getAnnotation() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
getAnnotation() - Method in class org.biojava.bio.seq.io.AlternateTokenization
 
getAnnotation() - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
getAnnotation() - Method in class org.biojava.bio.seq.io.WordTokenization
 
getAnnotation() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
getAnnotation() - Method in class org.biojava.bio.seq.SimpleAssembly
 
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
 
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
 
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
 
getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
The SoftMaskedAlphabet has no annotation
getAnnotation() - Method in class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
getAnnotation() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
getAnnotation() - Method in class org.biojava.ontology.OntologyTerm.Impl
 
getAnnotation() - Method in class org.biojava.ontology.RemoteTerm.Impl
 
getAnnotation() - Method in class org.biojava.ontology.Term.Impl
 
getAnnotation() - Method in class org.biojava.ontology.Triple.Impl
 
getAnnotation() - Method in class org.biojavax.bio.seq.CompoundRichLocation
Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.SimpleBioEntry
Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTerm
Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTriple
Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.SimpleCrossRef
Should return the associated annotation object.
getAnnotation(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getAnnotation returns an immutable, static annotation describing the enzyme.
getAnnotations() - Method in class org.biojava.bio.MergeAnnotation
Gets an unmodifiable view of the list of Annotations that are part of the MergeAnnotation.
getAnnotationType() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
Get the AnnotationType used as a constraint.
getAnnotationType() - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
Return the AnnotationType built by this handler
getAnnotator() - Method in class org.biojava.bio.program.gff.GFFEntrySet
Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.
getAnnotator(boolean) - Method in class org.biojava.bio.program.gff.GFFEntrySet
Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.
getArg_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getArrowHeadSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
getArrowScoop() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
getArrowScoop() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
getArrowSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
getArrowSize() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
getArticleAuthors() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Gets the names of the authors which first published an article about the AAindex entry.
getArticleTitle() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Gets the title of the article which describes the AAindex entry.
getAsp_N() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getAttributes(String) - Method in class org.biojava.naming.ObdaContext
 
getAttributes(String, String[]) - Method in class org.biojava.naming.ObdaContext
 
getAttributes(Name) - Method in class org.biojava.naming.ObdaContext
 
getAttributes(Name, String[]) - Method in class org.biojava.naming.ObdaContext
 
getAuthority() - Method in interface org.biojavax.Namespace
This method will return the authority that governs the namespace.
getAuthority() - Method in class org.biojavax.SimpleNamespace
This method will return the authority that governs the namespace.
getAuthorityId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
Return the authority id for this identifier.
getAuthorList() - Method in interface org.biojavax.DocRef
Returns the authors of the document reference as a set of DocRefAuthor implementation instances.
getAuthorList() - Method in class org.biojavax.SimpleDocRef
Returns the authors of the document reference as a set of DocRefAuthor implementation instances.
getAuthors() - Method in interface org.biojavax.DocRef
Returns the authors of the document reference.
getAuthors() - Method in class org.biojavax.SimpleDocRef
Returns the authors of the document reference.
getAutomaton() - Method in class org.biojava.utils.automata.FiniteAutomaton
 
getAutomaton() - Method in interface org.biojava.utils.automata.NfaBuilder
 
getAutomaton() - Method in class org.biojava.utils.automata.NfaSubModel
 
getB() - Method in class org.biojava.bio.proteomics.StructureTools
 
getB() - Method in class org.biojava.utils.ListTools.Doublet
 
getB() - Method in class org.biojava.utils.ListTools.Triplet
 
getBackwardTransitions() - Method in class org.biojava.bio.dp.DP
 
getBackwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
 
getBasecalls() - Method in class org.biojava.bio.program.abi.ABITrace
Returns an int[] array that represents the basecalls - each int in the array corresponds to an x-coordinate point in the graph that is a peak (a base location).
getBaseCalls() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
Return the total number of base calls.
getBaseCalls() - Method in interface org.biojava.bio.chromatogram.Chromatogram
Returns an alignment that describes the base calls for this chromatogram.
getBaseColor(Symbol) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the color that will be used to draw the trace for the given DNA symbol.
getBaseFillColor(Symbol) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the color that will be used to fill in the callboxes for calls with the given symbol.
getBases() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getBases() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
getBases() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
getbaseURL() - Method in class org.biojava.bio.seq.db.FetchURL
 
getBeadDepth() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
getBeadDepth returns the depth of a single bead produced by this renderer.
getBeadDepth() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
getBeadDepth returns the depth of a single bead produced by the renderer.
getBeadDepth() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
 
getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
getBeadDisplacement returns the displacement of beads from the centre line of the renderer.
getBeadDisplacement() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
getBeadDisplacement returns the displacement of beads from the centre line of the renderer.
getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
 
getBeadFill() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
getBeadFill returns the bead fill paint.
getBeadOutline() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
getBeadOutline returns the bead outline paint.
getBeadStroke() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
getBeadStroke returns the bead outline stroke.
getBibRefAsXML(BibRef) - Method in interface org.biojava.bibliography.BibRefQuery
A convenient utility method converting a given citation to its XML representation.
getBibRefCount() - Method in interface org.biojava.bibliography.BibRefQuery
It returns the number of citations in the current collection.
getBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery
It returns an enumeration of all citations from the current collection.
getBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery
It returns an enumeration of all citations from the current collection, perhaps with a limited number of attributes.
getBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery
It returns an enumeration of all citations from the current collection.
getBinaryAlphabet() - Static method in class org.biojavax.ga.util.GATools
Gets a Reference to the FlyWeight GA_Binary Alphabet.
getBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
getBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite
Retrieve a single BioEntry by its id.
getBioEntry(String) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
 
getBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB
 
getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractBioEntryDB
 
getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
getBioEntryIterator() - Method in interface org.biojavax.bio.db.BioEntryDB
Returns a BioEntryIterator over all BioEntrys in the database.
getBioEntrys(Set) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
getBioEntrys(Set) - Method in interface org.biojavax.bio.db.BioEntryDBLite
Retrieve multiple BioEntry by their ids.
getBioEntrys(Set) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
 
getBioEntrys(Set) - Method in class org.biojavax.bio.db.HashBioEntryDB
 
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
getBioEntrys(Set, BioEntryDB) - Method in interface org.biojavax.bio.db.BioEntryDBLite
Retrieve multiple BioEntry into a specific sequence database.
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
 
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.HashBioEntryDB
 
getBioSequenceStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
Returns the an object indicating the style of biosequence storage that this database should employ.
getBioSequenceStyle() - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
Deprecated.
 
getBlastAdvancedOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
Simply return the string given as argument via setBlastAdvancedOptions
getBlastDatabase() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
This method returns the value of the database used for this particular blast run.
getBlastProgram() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
This method returns the value of the program used for this particular blast run.
getBlockDepth() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
 
getBlockDepth() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
 
getBlockListener() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
getBlockListener() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
Obtain the listener for this parser.
getBlockName() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
 
getBlockName() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlock
Get the block name.
getBlockName() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
Obtains the name of this block.
getBlockName() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
getBlockPainter() - Method in class org.biojava.bio.gui.DistributionLogo
 
getBlockPainter() - Method in interface org.biojava.bio.gui.LogoContext
 
getBlockParser(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
getBlockParser(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Gets the parser to use for a given block.
getBlockWidth() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
getBlosum100() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM100 amino acid substitution matrix.
getBlosum100_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM100.50 amino acid substitution matrix.
getBlosum30() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM30 amino acid substitution matrix.
getBlosum30_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM30.50 amino acid substitution matrix.
getBlosum35() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM35 amino acid substitution matrix.
getBlosum35_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM35.50 amino acid substitution matrix.
getBlosum40() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM40 amino acid substitution matrix.
getBlosum40_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM40.50 amino acid substitution matrix.
getBlosum45() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM45 amino acid substitution matrix.
getBlosum45_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM45.50 amino acid substitution matrix.
getBlosum50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM50 amino acid substitution matrix.
getBlosum50_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM50.50 amino acid substitution matrix.
getBlosum55() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM55 amino acid substitution matrix.
getBlosum55_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM55.50 amino acid substitution matrix.
getBlosum60() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM60 amino acid substitution matrix.
getBlosum60_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM60.50 amino acid substitution matrix.
getBlosum62() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM62 amino acid substitution matrix.
getBlosum62_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM62.50 amino acid substitution matrix.
getBlosum65() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM65 amino acid substitution matrix.
getBlosum65_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM65.50 amino acid substitution matrix.
getBlosum70() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM70 amino acid substitution matrix.
getBlosum70_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM70.50 amino acid substitution matrix.
getBlosum75() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM75 amino acid substitution matrix.
getBlosum75_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM75.50 amino acid substitution matrix.
getBlosum80() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM80 amino acid substitution matrix.
getBlosum80_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM80.50 amino acid substitution matrix.
getBlosum85() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM85 amino acid substitution matrix.
getBlosum85_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM85.50 amino acid substitution matrix.
getBlosum90() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM90 amino acid substitution matrix.
getBlosum90_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUM90.50 amino acid substitution matrix.
getBlosumn() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUMN amino acid substitution matrix.
getBlosumn_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the BLOSUMN.50 amino acid substitution matrix.
getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.MultiTagger
 
getBounds() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
 
getBounds() - Method in interface org.biojava.bio.gui.glyph.Glyph
 
getBounds() - Method in class org.biojava.bio.gui.glyph.HelixGlyph
 
getBounds() - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
 
getBounds() - Method in class org.biojava.bio.gui.glyph.TurnGlyph
 
getBounds() - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
 
getBounds() - Method in interface org.biojava.bio.gui.LogoContext
 
getBuilderFactory(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
getBuilderFactory accepts a value which represents a sequence format and returns the relevant SequenceBuilderFactory object.
getC() - Method in class org.biojava.bio.molbio.DNAComposition
Get the relative compositon of 'C'.
getC() - Method in class org.biojava.bio.proteomics.StructureTools
 
getC() - Method in class org.biojava.stats.svm.SMOTrainer
 
getC() - Method in class org.biojava.utils.ListTools.Triplet
 
getCallboxBounds(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the screen-coordinate bounds of the callbox for a given call.
getCallboxBounds(int, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the bounds of the callbox for a given call.
getCallboxCount() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the number of callboxes, regenerating them if necessary.
getCallContaining(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Synonym for ChromatogramGraphic.getCallContaining(float, boolean) with pointOnScreen=true.
getCallContaining(float, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Same as ChromatogramGraphic.getCallContaining(Point2D, boolean), except that only the x-coordinate of the point is specified.
getCallContaining(Point2D) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Synonym for ChromatogramGraphic.getCallContaining(Point2D, boolean) with pointOnScreen=true.
getCallContaining(Point2D, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the 0-based index of the call containing a given point.
getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
Get the cardinality constraint used to validate the number of property values.
getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains
Get the cardinality constraint used to validate the number of property values.
getCategory() - Method in class org.biojava.ontology.Synonym
 
getCell(int[]) - Method in interface org.biojava.bio.dp.DPMatrix
 
getCell(int[]) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
getCell(int[]) - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
 
getChainedEvent() - Method in class org.biojava.utils.ChangeEvent
Return the event which caused this to be fired, or null if this change was not caused by another event.
getChange() - Method in class org.biojava.utils.ChangeEvent
Return an object which is to be the new value of some property, or is to be added to a collection.
getChangeEvent() - Method in exception org.biojava.utils.ChangeVetoException
Return the ChangeEvent which is being vetoed.
getChanger() - Method in class org.biojava.bio.AnnotationChanger
getMapper returns the ValueChanger being used to remap the Annotation.
getChanger(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
Get the Changer currently registered to handle a tag.
getChangeSupport() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
getChangeSupport() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractDistribution
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.TranslatedDistribution
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getChangeSupport lazily instantiates a helper for change listeners.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getChangeSupport lazily instantiates a helper for change listeners.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.MergeAnnotation
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.OverlayAnnotation
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.SimpleAssembly
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.AbstractSymbol
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
getChangeSupport(ChangeType) - Method in class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
getChangeSupport(ChangeType) - Method in class org.biojava.ontology.AbstractTerm
 
getChangeSupport(ChangeType) - Method in class org.biojava.ontology.OntologyTerm.Impl
 
getChangeSupport(ChangeType) - Method in class org.biojava.utils.AbstractChangeable
Called to retrieve the ChangeSupport for this object.
getChangeTable() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
 
getChangeTypes(Class) - Static method in class org.biojava.utils.ChangeType
Get all ChangeType objects defined within a class.
getChar() - Method in class org.biojava.utils.io.LargeBuffer
 
getChar(long) - Method in class org.biojava.utils.io.LargeBuffer
 
getCharacter() - Method in class org.biojava.utils.RepeatedCharSequence
 
getCharacterOffset() - Method in exception org.biojava.utils.ParserException
Get the character offset in the line where an error was detected.
getCharLabels() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getCharStateLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getCharStateLabelKeywords(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getChild() - Method in class org.biojava.bio.seq.FeatureFilter.Not
 
getChild() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
 
getChild(SuffixTree.SuffixNode, int) - Method in class org.biojava.bio.symbol.SuffixTree
Get the n'th child of a node.
getChild(SuffixTree.SuffixNode, Symbol) - Method in class org.biojava.bio.symbol.SuffixTree
Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
getChild1() - Method in class org.biojava.bio.CollectionConstraint.And
Get the first child CollectionConstraint.
getChild1() - Method in class org.biojava.bio.CollectionConstraint.Or
Get the first child CollectionConstraint.
getChild1() - Method in class org.biojava.bio.PropertyConstraint.And
Get the first child PropertyConstraint.
getChild1() - Method in class org.biojava.bio.PropertyConstraint.Or
Get the first child PropertyConstraint.
getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.And
 
getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
getChild1() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
getChild1() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
getChild2() - Method in class org.biojava.bio.CollectionConstraint.And
Get the seccond child CollectionConstraint.
getChild2() - Method in class org.biojava.bio.CollectionConstraint.Or
Get the seccond child CollectionConstraint.
getChild2() - Method in class org.biojava.bio.PropertyConstraint.And
Get the seccond child PropertyConstraint.
getChild2() - Method in class org.biojava.bio.PropertyConstraint.Or
Get the seccond child PropertyConstraint.
getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.And
 
getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
getChild2() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
getChild2() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
getChildren() - Method in class org.biojava.bio.taxa.SimpleTaxon
Deprecated.
 
getChildren() - Method in interface org.biojava.bio.taxa.Taxon
Deprecated.
The children of this Taxon.
getChildren() - Method in class org.biojava.bio.taxa.WeakTaxon
Deprecated.
 
getChildrenOf(Connection, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Returns all children of the specified taxon.
getChildrenOf(Connection, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Returns the children as a Stack of this given taxon.
getChildrenRaw() - Method in class org.biojava.bio.taxa.WeakTaxon
Deprecated.
 
getChromatogram() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Accessor for the in-use chromatogram.
getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getChromNum(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getChromosome() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getChromosome(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getChromosomes() - Method in interface org.biojavax.ga.functions.GACross
Gets the chromosomes after the cross
getChromosomes() - Method in interface org.biojavax.ga.functions.GACrossResult
Gets the chromosomes after the cross
getChromosomes() - Method in class org.biojavax.ga.functions.SimpleGACrossResult
 
getChromosomes() - Method in class org.biojavax.ga.impl.AbstractOrganism
 
getChromosomes() - Method in interface org.biojavax.ga.Organism
Gets the organisms 'chromosome' sequences
getChymotrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getCircular() - Method in interface org.biojavax.bio.seq.RichSequence
Is the sequence circular?
getCircular() - Method in class org.biojavax.bio.seq.ThinRichSequence
Is the sequence circular?
getCircularLength() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Retrieves the circular length of this location.
getCircularLength() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
Retrieves the circular length of this location.
getCircularLength() - Method in interface org.biojavax.bio.seq.RichLocation
Retrieves the circular length of this location.
getCircularLength() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Retrieves the circular length of this location.
getClasses() - Method in class org.biojava.utils.bytecode.ParametricType
 
getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getClassifyId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getClassifySystem(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getClassifyType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getClassLoader(Class) - Static method in class org.biojava.utils.ClassTools
Get the classloader which loaded clazz.
getClassLoader(Object) - Static method in class org.biojava.utils.ClassTools
Get the classloader which loaded the class of obj.
getClassNumber(int) - Method in interface org.biojava.bio.EcNumber
Get the class number associated with the particular level of the ec number.
getClassNumber(int) - Method in class org.biojava.bio.EcNumber.Impl
 
getCleaveageResidues() - Method in class org.biojava.bio.proteomics.Protease
The list of residues that the protease will cleave at.
getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getCloneId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getCloneLibrary(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getCluster(String) - Method in interface org.biojava.bio.program.unigene.UnigeneDB
Fetch a cluster by its cluster id.
getCNBr() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getCodeClass() - Method in interface org.biojava.utils.bytecode.CodeContext
Get the class for which a method is being generated.
getCodeMethod() - Method in interface org.biojava.utils.bytecode.CodeContext
Get the method which is being generated.
getCodonAlphabet() - Static method in class org.biojava.bio.seq.DNATools
Gets the (DNA x DNA x DNA) Alphabet
getCodonAlphabet() - Static method in class org.biojava.bio.seq.RNATools
Gets the (RNA x RNA x RNA) Alphabet
getCodonPref() - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
 
getCodonPreference(String) - Static method in class org.biojava.bio.symbol.CodonPrefTools
get the specified codon preference.
getCodonPrefs() - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
 
getCollapsing() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
Returns true if this class collapses to zero depth when there are no visible features.
getCollectionConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandler
 
getCollectionId() - Method in interface org.biojava.bibliography.BibRefQuery
It returns an identification of the current query collection.
getColourClass(String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
Returns the colour class for the specified colour (in hex).
getColumn(int) - Method in class org.biojava.bio.dp.SimpleWeightMatrix
 
getColumn(int) - Method in interface org.biojava.bio.dp.WeightMatrix
Retrieve a column as an EmissionState.
getCommands() - Method in class org.biojava.utils.process.ExternalProcess
Gets the command line including the path or name of the external program and its command line arguments.
getComment() - Method in interface org.biojava.bio.AnnotationType
Get the comment for the whole AnnotationType.
getComment() - Method in class org.biojava.bio.AnnotationType.Impl
 
getComment() - Method in interface org.biojava.bio.program.gff.GFFRecord
The feature comment.
getComment() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getComment() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Gets the user comment for the AAindex entry.
getComment() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
getComment() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
Getter for property comment.
getComment() - Method in interface org.biojavax.Comment
Returns the comment part of this comment.
getComment() - Method in class org.biojavax.SimpleComment
Returns the comment part of this comment.
getComment(Object) - Method in interface org.biojava.bio.AnnotationType
Get the comment for a particular property.
getComment(Object) - Method in class org.biojava.bio.AnnotationType.Impl
 
getComments() - Method in class org.biojava.bio.program.scf.SCF
Returns the comments fields as a Properties mapping.
getComments() - Method in interface org.biojavax.bio.BioEntry
Returns a set of all comments associated with this bioentry.
getComments() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Returns all comments.
getComments() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Returns all comments.
getComments() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Returns all comments.
getComments() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Returns all comments.
getComments() - Method in class org.biojavax.bio.SimpleBioEntry
Returns a set of all comments associated with this bioentry.
getCommentType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property commentType.
getCommonName() - Method in class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
getCommonName() - Method in interface org.biojava.bio.taxa.Taxon
Deprecated.
The common name of the Taxon.
getComparator() - Method in class org.biojava.utils.FileAsList
 
getComponentList(boolean) - Method in class org.biojava.bio.symbol.MergeLocation
Gets the component locations that make up this one
getComponentLocation() - Method in interface org.biojava.bio.seq.ComponentFeature
Return a location which identifies a portion of the component sequence which is to be included in the assembly.
getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
getComponentName() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
getComponentSequence() - Method in interface org.biojava.bio.seq.ComponentFeature
Get the sequence object which provides a component of this feature's parent sequence.
getComponentSequenceName() - Method in interface org.biojava.bio.seq.ComponentFeature
Get the name of the component sequence.
getComputationTime() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getConditionedAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
Get the conditioned alphabet.
getConditionedAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution
Get the conditioned alphabet.
getConditioningAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
Get the conditioning alphabet of this distribution.
getConditioningAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution
Get the conditioning alphabet of this distribution.
getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getConfidence(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Composite
 
getConfigLocator() - Method in interface org.biojava.directory.RegistryConfiguration
getConfigLocator returns a locator for the configuration.
getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Impl
 
getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Composite
 
getConfiguration() - Method in interface org.biojava.directory.RegistryConfiguration
getConfiguration returns a mapping of registry database names to collections of tag-value pairs.
getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Impl
 
getConstant() - Method in class org.biojava.stats.svm.PolynomialKernel
 
getConstant() - Method in class org.biojava.stats.svm.SigmoidKernel
 
getConstants() - Method in interface org.biojava.utils.bytecode.CodeContext
Get the constants pool for this context.
getConstraint(Object) - Method in interface org.biojava.bio.AnnotationType
Retrieve the constraint that will be applied to all properties with a given key.
getConstraint(Object) - Method in class org.biojava.bio.AnnotationType.Impl
 
getConstructor(CodeClass[]) - Method in interface org.biojava.utils.bytecode.CodeClass
Get a constructor by argument list.
getConstructor(CodeClass[]) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getConstructor(CodeClass[]) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getContainingClass() - Method in class org.biojava.utils.bytecode.CodeField
Get the class that contains this field.
getContainingClass() - Method in interface org.biojava.utils.bytecode.CodeMethod
The class that contains this method
getContainingClass() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
 
getContainsTerm() - Static method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Gets the default CONTAINS term used for defining the relationship between features.
getContentHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
correct this later
getContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
getContext() - Method in class org.biojava.stats.svm.TrainingEvent
 
getContext(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
See if empty tags are treated as a continuation of previous tags or as a new tag with the value of the empty string.
getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser
Report whether empty tags will be treated as continuations of the last non -empty tag.
getCoordinates() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
getCoordinates returns the hotspot coordinates.
getCopyrightTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the copyright term
getCoreOntology() - Static method in class org.biojava.ontology.OntoTools
Get the Ontology that defines our core "central dogma".
getCount() - Method in interface org.biojava.utils.candy.CandyVocabulary
It returns a number of entries contained in this vocabulary.
getCount(Distribution, Symbol) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Return the number of counts of a particular symbol which will be used to train the specified distribution.
getCount(Distribution, Symbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
getCount(DistributionTrainerContext, AtomicSymbol) - Method in interface org.biojava.bio.dist.DistributionTrainer
Get the current count for this state.
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
 
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
 
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
Deprecated.
 
getCount(AtomicSymbol) - Method in interface org.biojava.bio.dist.Count
Return the counts for a given Symbol.
getCount(AtomicSymbol) - Method in class org.biojava.bio.dist.IndexedCount
 
getCRC() - Method in interface org.biojavax.DocRef
Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references.
getCRC() - Method in class org.biojavax.SimpleDocRef
Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references.
getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getCreateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getCreateOnUnderlyingSequence() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
getCrossOverFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
 
getCrossOverFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACross
Returns the collection of cross over locations from the last cross
getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACrossResult
Returns the collection of cross over locations from the last cross
getCrossOverPositions() - Method in class org.biojavax.ga.functions.SimpleGACrossResult
 
getCrossOverProbs() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
 
getCrossOverProbs() - Method in interface org.biojavax.ga.functions.CrossOverFunction
 
getCrossOverProbs() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
getCrossProductAlphabet(List) - Static method in class org.biojava.bio.symbol.AlphabetManager
Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCrossProductAlphabet(List, String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Attempts to create a cross product alphabet and register it under a name.
getCrossProductAlphabet(List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCrossref() - Method in interface org.biojavax.DocRef
The document reference may refer to an object in another database.
getCrossref() - Method in class org.biojavax.SimpleDocRef
The document reference may refer to an object in another database.
getCrossRef() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Retrieves the crossref associated with this location.
getCrossRef() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
Retrieves the crossref associated with this location.
getCrossRef() - Method in interface org.biojavax.bio.seq.RichLocation
Retrieves the crossref associated with this location.
getCrossRef() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Retrieves the crossref associated with this location.
getCrossRef() - Method in interface org.biojavax.RankedCrossRef
Return the cross reference associated with this object.
getCrossRef() - Method in class org.biojavax.SimpleRankedCrossRef
Return the cross reference associated with this object.
getCrossResults() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm
Get a List containing details of all the cross over events during the run.
getCurrentCycle() - Method in interface org.biojava.stats.svm.TrainingContext
 
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
getCurrentFeature() - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Gets the feature currently being created.
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Gets the feature currently being created.
getCurrentScore() - Method in class org.biojava.bio.dp.AbstractTrainer
 
getCurrentScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
 
getCutoff() - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold
 
getCuttingSize() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
The cutting size of a restriction enzyme is defined has the number of nucleotides that are directly involved in the recognition sequence.
getCutType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
getCutType returns the type of cut produced by the enzyme.
getCycle() - Method in class org.biojava.bio.dp.AbstractTrainer
 
getCycle() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
 
getDataAccess() - Method in class org.biojava.bio.program.abi.ABIFParser
Returns the accessor for the raw data being parsed by this parser.
getDatabase(String) - Method in class org.biojava.directory.Registry
getDatabase retrieves a database instance known by a name String.
getDataBase() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
 
getDatabaseName() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property databaseName.
getDatabaseURLGenerators() - Method in class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
 
getDatabaseURLGenerators() - Method in interface org.biojava.bio.program.blast2html.URLGeneratorFactory
Returns a list of 0, 1 or more DatabaseURLGenerator The first is used to link from the id in the summary table, all are used as a list of links in the detail section.
getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
Getter for the Ensembl-specific 'dataClass' term
getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
Getter for the Ensembl-specific 'dataClass' term
getDataClassTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the DataClass term
getDataRecord(String, int) - Method in class org.biojava.bio.program.abi.ABIFParser
Get the entry from the file TOC with the given name and tag number.
getDataSource(String, String, String, String) - Static method in class org.biojava.utils.JDBCPooledDataSource
 
getDataSources() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
Get the current set of all currently registered data sources.
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
 
getDataStore(File) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory
Get a pre-built data store associated with a file.
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory
 
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory
 
getDataType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
getDataType() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getDateAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the date annotated term
getDateCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the date created term
getDateUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the date updated term
getDayhoff() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the DAYHOFF amino acid substitution matrix.
getDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
retrieve the DB that has just been built
getDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
getDB() - Method in class org.biojava.bio.seq.db.FetchURL
 
getDbCode() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
getDBHelper(Connection) - Static method in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
Returns a DBHelper implementation suitable for a particular database.
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
 
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getDbId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
 
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
 
getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
return a set of DbId
getDbname() - Method in interface org.biojavax.CrossRef
Returns the name of the database the cross reference refers to.
getDbname() - Method in class org.biojavax.SimpleCrossRef
Returns the name of the database the cross reference refers to.
getDBTaxon(Connection, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Attempts to get a Taxon object corresponding to the specified taxon_id (i.e. the database's internal id for the taxon).
getDbXrefId() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
 
getDbxrefList(String, int, int) - Method in class org.biojava.ontology.obo.OboFileParser
 
getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocation
 
getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
getDecorator(Class) - Method in interface org.biojava.bio.symbol.Location
Checks the decorator chain for an instance of decoratorClass and return it if found.
getDecorator(Class) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Checks the decorator chain for an instance of decoratorClass and return it if found.
getDecorator(Class) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Checks the decorator chain for an instance of decoratorClass and return it if found.
getDecorator(Class) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Checks the decorator chain for an instance of decoratorClass and return it if found.
getDefaultChanger() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
Get the changer that will be applied to values of tags with no specific handler registered.
getDefaultConstraint() - Method in interface org.biojava.bio.AnnotationType
Get the CollectionConstraint that will be applied to all properties without an explicit binding.
getDefaultConstraint() - Method in class org.biojava.bio.AnnotationType.Impl
 
getDefaultCrossReferenceResolver() - Static method in class org.biojavax.RichObjectFactory
Returns the default cross ref resolver object.
getDefaultFactory() - Static method in class org.biojava.ontology.OntoTools
 
getDefaultFormat() - Method in class org.biojava.bio.program.phred.PhredFormat
Deprecated. 
getDefaultFormat() - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated. 
getDefaultFormat() - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated. 
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GAMEFormat
Deprecated. 
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankFormat
Deprecated. 
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankXmlFormat
Deprecated.
 
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenpeptFormat
Deprecated.
 
getDefaultFormat() - Method in interface org.biojava.bio.seq.io.SequenceFormat
Deprecated.
new implementations should only write a single format.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLFormat
getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.FastaFormat
getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.GenbankFormat
getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.INSDseqFormat
getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtFormat
getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultNamespace() - Static method in class org.biojavax.RichObjectFactory
Returns the default namespace object.
getDefaultOntology() - Static method in class org.biojavax.RichObjectFactory
Returns the default ontology object.
getDefaultPaint() - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
 
getDefaultPositionResolver() - Static method in class org.biojavax.RichObjectFactory
Returns the default position resolver object.
getDefaultRichSequenceHandler() - Static method in class org.biojavax.RichObjectFactory
Returns the default sequence resolver object.
getDefaultSplitter() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
Get the splitter that will be applied to values of tags with no specific handler registered.
getDelegate() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
getDelegate() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
getDelegate() - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
getDelegate() - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper
get listener to which all calls will be delegated
getDelegate() - Method in class org.biojava.bio.seq.io.SeqIOFilter
Retrieve the delegate that is wrapped.
getDelegate() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
Retrieve the delegate that is wrapped.
getDelegate() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
The compound alpha that holds the symbols used by this wrapper
getDelegateParser() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
getDelete() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Returns the current expenses of a single delete operation.
getDelete() - Method in class org.biojava.bio.alignment.SmithWaterman
 
getDelete(int) - Method in class org.biojava.bio.dp.ProfileHMM
Retrieves the delete state for column indx.
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
Returns the an object indicating the style of deletion that this database should employ.
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper
Deprecated.
 
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
 
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper
Deprecated.
 
getDepth() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
getDepth() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
Gets the Depth attribute of the LightPairDPCursor object
getDepth() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor
retrieve the depth of this cursor
getDepth() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
getDepth(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
getDepth returns the total depth of a list of SequenceRenderers.
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
 
getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer
 
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
 
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularMLR
 
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularPaddedRenderer
 
getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularRenderer
Get the depth needed for this renderer.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
getDepth calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
getDepth calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
 
getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
Returns the depth property of this class.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
getDepth calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
getDepth calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
 
getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
Retrieve the depth of this renderer when rendering src.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
 
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
 
getDepth(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LineInfo
 
getDepthScaler() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
Retrieve the current DepthScaler.
getDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
This gives you the description of this matrix if there is one.
getDescription() - Method in class org.biojava.bio.program.fastq.Fastq
Return the description of this FASTQ formatted sequence.
getDescription() - Method in class org.biojava.bio.program.fastq.FastqBuilder
Return the description for this FASTQ formatted sequence builder.
getDescription() - Method in enum org.biojava.bio.program.fastq.FastqVariant
Return the description of this FASTQ sequence format variant.
getDescription() - Method in class org.biojava.bio.program.homologene.SimilarityType.PlaceHolder
 
getDescription() - Method in interface org.biojava.bio.program.homologene.Taxon
returns the name of the Taxon
getDescription() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
 
getDescription() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Gets the description for the AAindex entry.
getDescription() - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
 
getDescription() - Method in class org.biojava.ontology.IntegerOntology
 
getDescription() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
getDescription() - Method in interface org.biojava.ontology.Ontology
Return a human-readable description of this ontology, or the empty string if none is available
getDescription() - Method in class org.biojava.ontology.Ontology.Impl
 
getDescription() - Method in class org.biojava.ontology.OntologyTerm.Impl
 
getDescription() - Method in class org.biojava.ontology.RemoteTerm.Impl
 
getDescription() - Method in interface org.biojava.ontology.Term
Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojava.ontology.Term.Impl
 
getDescription() - Method in class org.biojava.ontology.Triple.Impl
 
getDescription() - Method in interface org.biojava.utils.candy.CandyVocabulary
It returns a description of this vocabulary.
getDescription() - Method in interface org.biojavax.bio.BioEntry
Returns a description of this sequence.
getDescription() - Method in class org.biojavax.bio.SimpleBioEntry
Returns a description of this sequence.
getDescription() - Method in interface org.biojavax.Namespace
Returns a description of this namespace.
getDescription() - Method in interface org.biojavax.ontology.ComparableOntology
Return a human-readable description of this ontology.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableOntology
Return a human-readable description of this ontology.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableTerm
Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableTriple
Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojavax.SimpleNamespace
Returns a description of this namespace.
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getDescription(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
 
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getDescriptionNumber() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
A method that simply returns the number of descriptions fetched with this RemoteQBlastOutputProperties object.
getDescriptor() - Method in interface org.biojava.utils.bytecode.CodeClass
 
getDescriptor() - Method in interface org.biojava.utils.bytecode.CodeMethod
A human-readable description of the class
getDescriptor() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getDescriptor() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
 
getDescriptor() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getDescriptors() - Method in interface org.biojavax.ontology.ComparableTriple
Returns all descriptors.
getDescriptors() - Method in class org.biojavax.ontology.SimpleComparableTriple
Returns all descriptors.
getDetailsHandler() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
Return a handler for the XFF details element.
getDFA() - Method in class org.biojava.utils.automata.DfaBuilder
 
getDimAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector
Retrieve the dimension at a specific index.
getDimensionRatio() - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
getDimensionRatio returns the maximum ratio of long dimension to short dimension of the bead.
getDimensionsNChar() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Get the NCHAR value.
getDimensionsNChar() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Get the NCHAR value.
getDimensionsNTax() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Get the NTAX value.
getDimensionsNTax() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Get the NTAX value.
getDimensionsNTax() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Get the NTAX value.
getDinucleotideAlphabet() - Static method in class org.biojava.bio.symbol.CodonPrefTools
returns an RNA dinucleotide alphabet.
getDirection() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
getDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getDirection returns the direction in which this context expects the sequence to be rendered - HORIZONTAL or VERTICAL.
getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanel
Retrieve the current rendering direction.
getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Retrieve the current rendering direction.
getDirection() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
Gets the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.
getDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getDirection() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
getDirection() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getDirection returns the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.
getDisplayName() - Method in interface org.biojavax.bio.taxa.NCBITaxon
Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific
getDisplayName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific or if there are no scientific names at all, the empty string.
getDistanceBetweenFeatures() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
getDistribution() - Method in interface org.biojava.bio.dp.EmissionState
Get the Distribution associated with this state.
getDistribution() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getDistribution() - Method in class org.biojava.bio.gui.DistributionLogo
Retrieve the currently rendered dist.
getDistribution() - Method in interface org.biojava.bio.gui.LogoContext
 
getDistribution() - Method in class org.biojava.bio.molbio.Composition
Returns the distribution backing this class.
getDistribution(Symbol) - Method in interface org.biojava.bio.dist.OrderNDistribution
 
getDivision() - Method in interface org.biojavax.bio.BioEntry
Returns the division of this bioentry.
getDivision() - Method in class org.biojavax.bio.SimpleBioEntry
Returns the division of this bioentry.
getDNA() - Method in class org.biojava.bio.program.phred.PhredSequence
Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
getDNA() - Static method in class org.biojava.bio.seq.DNATools
Return the DNA alphabet.
getDNAAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence
 
getDNADistribution(double) - Static method in class org.biojava.bio.seq.DNATools
return a SimpleDistribution of specified GC content.
getDNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Creates a DNA symbol tokenizer.
getDNASequence(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
Get the called DNA sequence from a chromatogram.
getDNAxDNA() - Static method in class org.biojava.bio.seq.DNATools
Gets the (DNA x DNA) Alphabet
getDNAxDNADistribution(double, double) - Static method in class org.biojava.bio.seq.DNATools
return a (DNA x DNA) cross-product Distribution with specified DNA contents in each component Alphabet.
getDocumentReference() - Method in interface org.biojavax.RankedDocRef
Represents a reference to a document.
getDocumentReference() - Method in class org.biojavax.SimpleRankedDocRef
Represents a reference to a document.
getDotStatesIndex() - Method in class org.biojava.bio.dp.DP
 
getDouble() - Method in class org.biojava.utils.io.LargeBuffer
 
getDouble(long) - Method in class org.biojava.utils.io.LargeBuffer
 
getDoubleValue(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
 
getDoubleValue(Symbol) - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
 
getDownstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
getDownstreamCut returns the cut site within or downstream of the recognition site.
getDownstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
getDownstreamEndType returns the double-stranded end type produced by the primary (intra-site or downstream) cut.
getDP() - Method in class org.biojava.bio.dp.AbstractTrainer
 
getDP() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
 
getDTDHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
 
getE() - Method in class org.biojava.bio.proteomics.StructureTools
 
getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getEcNumber(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getEdgeLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
getEdgeLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
Tree navigation methods
getEditDistance() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
This gives the edit distance according to the given parameters of this certain object.
getElementId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getElementId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getElementIds() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getElementIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getElideComments() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Is the format going to emit events when comments data or remarks from bibliographic references are read?
getElideComments() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Is the format going to emit events when comments data or remarks from bibliographic references are read?
getElideFeatures() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Is the format going to emit events when feature data is read?
getElideFeatures() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Is the format going to emit events when feature data is read?
getElideReferences() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Is the format going to emit events when bibliographic reference data is read?
getElideReferences() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Is the format going to emit events when bibliographic reference data is read?
getElideSymbols() - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
Return a flag indicating if symbol data will be skipped when parsing streams.
getElideSymbols() - Method in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
getElideSymbols() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Is the format going to emit events when sequence data is read?
getElideSymbols() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Is the format going to emit events when sequence data is read?
getEliminateEnd() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getEliminateStart() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getEmail() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService
Get the email for QBlast.
getEmail() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Get the email for Entrez.
getEmblBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Get a default SequenceBuilderFactory for handling EMBL files.
getEMBLTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
Getter for the EMBL term
getEMBLxmlTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
Getter for the EMBLxml term
getEmission(Symbol, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache.
getEmissions(List) - Method in class org.biojava.bio.dp.twohead.EmissionCache
 
getEmissions(List, boolean) - Method in class org.biojava.bio.dp.twohead.EmissionCache
Retrieve the emission scores from the cache for every EmissionState for the specified symbols.
getEnd() - Method in interface org.biojava.bio.program.gff.GFFRecord
The end of this feature within the source sequence.
getEnd() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getEnd() - Method in interface org.biojava.bio.program.gff3.GFF3Record
 
getEnd() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
getEnd() - Method in class org.biojava.bio.seq.impl.SubSequence
 
getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
getEnd() - Method in class org.biojava.utils.automata.FiniteAutomaton
 
getEnd() - Method in interface org.biojava.utils.automata.NfaBuilder
 
getEnd() - Method in class org.biojava.utils.automata.NfaSubModel
 
getEnd() - Method in interface org.biojavax.bio.seq.Position
Returns the end of the range of bases this base could lie in.
getEnd() - Method in class org.biojavax.bio.seq.SimplePosition
Returns the end of the range of bases this base could lie in.
getEnd() - Method in interface org.biojavax.RankedDocRef
The end position in the sequence that this reference is referred to from.
getEnd() - Method in class org.biojavax.SimpleRankedDocRef
The end position in the sequence that this reference is referred to from.
getEndLabel() - Method in class org.biojava.utils.bytecode.InstructionVector
 
getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
Get the current string indicating that a record has ended.
getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.RegexParser
Get the explicit end-of-record string.
getEntityResolver() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries.
getEntryByName(String) - Method in interface org.biojava.utils.candy.CandyVocabulary
It returns a selected vocabulary entry.
getEnvironment() - Method in class org.biojava.naming.ObdaContext
 
getEnvironmentProperties() - Method in class org.biojava.utils.process.ExternalProcess
Gets environment variables for the external process.
getEnzyme() - Method in interface org.biojava.bio.molbio.RestrictionSite
getEnzyme returns the enzyme which cuts at this site.
getEnzyme() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
 
getEnzyme(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getEnzyme returns an enzyme by name.
getEpsilon() - Method in class org.biojava.stats.svm.SMOTrainer
 
getEquates() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getErrorHandler() - Method in class org.biojava.bio.program.gff.GFFParser
Find the error handler used by this parser.
getErrorHandler() - Method in class org.biojava.bio.program.gff3.GFF3Parser
Find the error handler used by this parser.
getErrorHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
 
getErrorHandler() - Method in class org.biojava.utils.process.ExternalProcess
Gets the output error handler which is responsible for the standard error output of the external process.
getErrString() - Method in class org.biojava.utils.ExecRunner
Returns the error string if exec(String) was invoked.
getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
Return the overall E-value of this hit.
getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
Return the E-value of this sub-hit.
getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getEvent() - Method in class org.biojava.utils.ChangeListener.ChangeEventRecorder
 
getEvents() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property events.
getEvidenceAttrTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the evidence attr term
getEvidenceCategoryTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the evidence category term
getEvidenceDateTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the evidence date term
getEvidenceTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the evidence type term
getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getExonIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getExtendedName() - Method in interface org.biojavax.DocRefAuthor
Returns the extended version of the authors name.
getExtendedName() - Method in class org.biojavax.SimpleDocRefAuthor
Returns the extended version of the authors name.
getFactory() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Getter for property factory.
getFactory() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
Getter for property factory.
getFactory(String, FiniteAutomaton) - Method in class org.biojava.utils.automata.ArrayStateMachineToolkit
 
getFastaBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Get a default SequenceBuilderFactory for handling FASTA files.
getFeature() - Method in interface org.biojava.bio.program.gff.GFFRecord
The feature type filed.
getFeature() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
Retrieve the current feature.
getFeature() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getFeature() - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
 
getFeature() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Retrieves the feature this location is associated with.
getFeature() - Method in interface org.biojavax.bio.seq.RichLocation
Retrieves the feature this location is associated with.
getFeature() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Retrieves the feature this location is associated with.
getFeature(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
 
getFeatureDescTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the FeatureDesc term
getFeatureFilter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Return the current FeatureFilter.
getFeatureFilter() - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandler
 
getFeatureFilter(int) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
Returns the ith FeatureFilter in this renderer.
getFeatureFromOriginal(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am including this method so that you can get the corresponding feature from the original sequence.
getFeatureHolder() - Method in interface org.biojava.bio.gui.sequence.FeatureSource
 
getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleFeature
A utility function to retrieve the feature holder delegate, creating it if necessary.
getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
getFeatureID(Feature) - Method in class org.biojava.bio.program.xff.BasicXFFHelper
 
getFeatureID(Feature) - Method in interface org.biojava.bio.program.xff.XFFHelper
 
getFeatureListener() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
Return the object which receives startFeature/endFeature notifications.
getFeatureListener() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
Return current feature listener
getFeatureListener() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
Return current feature listener
getFeatureOriginalTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the feature original term
getFeatureRealizer() - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
Returns the FeatureRealizer set by "setFeatureRealizer".
getFeatureRefTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the feature ref term
getFeatureRelationshipSet() - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
Returns the set of relationships held in this feature holder.
getFeatureRelationshipSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Returns the set of relationships held in this feature holder.
getFeatureRenderer() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
getFeatureRenderer returns the currently active renderer.
getFeatures() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
The features to render.
getFeatures() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
getFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getFeatures returns all of the Features belonging to the currently rendered Sequence.
getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
getFeatures() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
The features to render.
getFeatures() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
 
getFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getFeatures() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
getFeatures() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getFeatures returns all of the Features belonging to the currently rendered Sequence.
getFeatures() - Method in interface org.biojava.bio.seq.homol.Homology
Retrieve the set of features that mark homologous regions.
getFeatures() - Method in class org.biojava.bio.seq.homol.SimpleHomology
getFeatures returns the constituent HomologyFeatures which are also used as the keys in the alignment.
getFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
 
getFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
Returns the list of features in this featureholder.
getFeatures(String, FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
 
getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
getFeatures(FeatureFilter) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
Get all features matching a FeatureFilter provided by this DistDataSource.
getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
 
getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
getFeatureSet() - Method in interface org.biojavax.bio.seq.RichSequence
The features for this sequence.
getFeatureSet() - Method in class org.biojavax.bio.seq.ThinRichSequence
The features for this sequence.
getFeatureSource() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
getFeatureStatusTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the feature status term
getFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler
Get the template for the feature being constructed.
getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getFeatureType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getFeatureVariationTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the feature variation term
getField() - Method in class org.biojava.utils.ChangeType
Return a Field object where this change type is declared.
getFieldByName(String) - Method in interface org.biojava.utils.bytecode.CodeClass
Get a field by its name.
getFieldByName(String) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getFieldByName(String) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getFields() - Method in interface org.biojava.utils.bytecode.CodeClass
Get all fields accessible through this class.
getFields() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getFields() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getFile() - Method in interface org.biojava.bio.program.indexdb.Record
getFile returns the random access file in which the record belongs.
getFile() - Method in class org.biojava.bio.program.indexdb.Record.Impl
 
getFile() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
getFile returns the File wrapped.
getFile() - Method in interface org.biojava.bio.seq.db.Index
The file to retrieve from.
getFile() - Method in class org.biojava.bio.seq.db.SimpleIndex
 
getFile() - Method in class org.biojava.utils.io.RAF
 
getFileIndex(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
 
getFilePointer() - Method in class org.biojava.utils.io.CountedBufferedReader
 
getFilePointer() - Method in class org.biojava.utils.io.RandomAccessReader
getFilePointer returns the effective position of the pointer in the underlying RandomAccessFile.
getFiles() - Method in class org.biojava.bio.seq.db.BioIndex
 
getFiles() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
 
getFiles() - Method in interface org.biojava.bio.seq.db.IndexStore
Retrieve the Set of files that are currently indexed.
getFiles() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
getFill() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
getFill() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
 
getFill() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
getFill() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
 
getFillColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
Get the background color of the label area.
getFillPaint() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
Returns the paint properties of this glyph.
getFilter() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
getFilter() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
getFilter() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
getFilter returns the current filter.
getFilter() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
 
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
 
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
 
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
getFinderName() - Method in interface org.biojava.utils.candy.CandyFinder
It returns a name of this vocabulary finder.
getFirstIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Getter for property firstIntActID.
getFirstOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair
gets the first orthologue in the orthology relationship.
getFirstOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
 
getFitness() - Method in class org.biojavax.ga.impl.AbstractOrganism
 
getFitness() - Method in interface org.biojavax.ga.Organism
Returns the current fitness of this organism.
getFitnessFunction() - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
 
getFitnessFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
Returns the fitness function, i.e. the class that computes the fitness of each organism in a population.
getFitnessFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
getFloat() - Method in class org.biojava.utils.io.LargeBuffer
 
getFloat(long) - Method in class org.biojava.utils.io.LargeBuffer
 
getFloatOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Helper method for converting a Number-valued option into a float primitive.
getFont() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
getFont() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
Gets the Font attribute of the SequenceRenderContext object
getFont() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getFont() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
getFormat() - Method in class org.biojava.bio.seq.db.BioIndex
 
getFormat() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
 
getFormat() - Method in interface org.biojava.bio.seq.db.IndexStore
Retrieve the format of the index file.
getFormat() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
getFormat(String) - Static method in class org.biojava.bio.program.formats.FormatTools
Attempt to find aformat for a format identifer string.
getForwarders(ChangeType) - Method in class org.biojava.utils.Unchangeable
 
getForwardRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
getForwardRegex returns a regular expression which matches the forward strand of the recognition site.
getForwardTransitions() - Method in class org.biojava.bio.dp.DP
 
getForwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
 
getFrame() - Method in interface org.biojava.bio.program.gff.GFFRecord
The frame of the feature.
getFrame() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
 
getFrame() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getFrame() - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
Retrieve the reading frame this filter matches.
getFrame() - Method in interface org.biojava.bio.seq.Frame
A method to get the frame information of the implementing object
getFrame() - Method in class org.biojava.bio.seq.FramedFeature.ReadingFrame
 
getFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
 
getFrequency() - Method in interface org.biojava.bio.symbol.CodonPref
returns a Distribution giving the frequency of codons (sums to one over the totality of codons).
getFrequency() - Method in class org.biojava.bio.symbol.SimpleCodonPref
 
getFrequencyForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref
returns a Distribution giving the frequency of synonymous codons.
getFrequencyForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref
 
getFrequencyOfNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution
returns the frequency with which synonymous codons start with a specified pair of bases.
getFrom() - Method in exception org.biojava.bio.dp.IllegalTransitionException
 
getFTIdTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the FTId term
getFullName() - Method in class org.biojava.utils.bytecode.CodeField
Get the fully qualified name of the field.
getFullName() - Method in interface org.biojava.utils.bytecode.CodeMethod
The fully qualified name for this class
getFullName() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
 
getFuzzyEnd() - Method in interface org.biojavax.bio.seq.Position
Returns true if the position has a fuzzy end.
getFuzzyEnd() - Method in class org.biojavax.bio.seq.SimplePosition
Returns true if the position has a fuzzy end.
getFuzzyStart() - Method in interface org.biojavax.bio.seq.Position
Returns true if the position has a fuzzy start.
getFuzzyStart() - Method in class org.biojavax.bio.seq.SimplePosition
Returns true if the position has a fuzzy start.
getG() - Method in class org.biojava.bio.molbio.DNAComposition
Get the relative compositon of 'G'.
getG() - Method in class org.biojava.bio.proteomics.StructureTools
 
getGap() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getGapExt() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Returns the current expenses of any extension of a gap operation.
getGapExt() - Method in class org.biojava.bio.alignment.SmithWaterman
 
getGapSymbol() - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
getGapSymbol() - Method in interface org.biojava.bio.symbol.Alphabet
Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
getGapSymbol() - Static method in class org.biojava.bio.symbol.AlphabetManager
Get the special `gap' Symbol.
getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
getGapSymbol() - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
getGapSymbol() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
 
getGapSymbol(List) - Static method in class org.biojava.bio.symbol.AlphabetManager
Get the gap symbol appropriate to this list of alphabets.
getGenbankBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Get a default SequenceBuilderFactory for handling GenBank files.
getGenBankTerm() - Static method in class org.biojavax.bio.seq.io.GenbankFormat.Terms
Getter for the Genbank term
getGeneNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the GeneName term
getGenerateSequenceHeader() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Discover if per-sequence header lines will be generated.
getGeneration() - Method in interface org.biojavax.ga.GeneticAlgorithm
 
getGeneration() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm
The current generation
getGeneSynonymTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the GeneSynonym term
getGeneticCode() - Method in interface org.biojava.bio.symbol.CodonPref
the genetic code that this codon preference is based on.
getGeneticCode() - Method in class org.biojava.bio.symbol.SimpleCodonPref
 
getGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon
Returns the genetic code of this taxon, which may be null if not known.
getGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Returns the genetic code of this taxon, which may be null if not known.
getGeneticCode(int) - Static method in class org.biojava.bio.seq.RNATools
Retrieve a TranslationTable by number.
getGeneticCode(String) - Static method in class org.biojava.bio.seq.RNATools
Retrieve a TranslationTable by name.
getGeneticCodeName() - Method in interface org.biojava.bio.symbol.CodonPref
get the name of the genetic code
getGeneticCodeName() - Method in class org.biojava.bio.symbol.SimpleCodonPref
 
getGeneticCodeNames() - Static method in class org.biojava.bio.seq.RNATools
Retrieve a Set containing the name of each genetic code.
getGenomicTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
Getter for the Ensembl-specific 'genomic' term
getGenpeptBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Get a default SequenceBuilderFactory for handling Genpept files.
getGlu_C_bicarbonate() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getGlu_C_phosphate() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getGlyphForFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
Returns the Glyph object which is assigned to the given feature filter.
getGonnet() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the GONNET amino acid substitution matrix.
getGraphics() - Method in interface org.biojava.bio.gui.LogoContext
 
getGroupAttributes() - Method in interface org.biojava.bio.program.gff.GFFRecord
A Map containing the group / attribute information.
getGroupAttributes() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getGroupOrder(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getH() - Method in class org.biojava.bio.proteomics.StructureTools
 
getHandler(String, String) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
Retrieve a FilterHandler for the specified tag name.
getHandler(SeqSimilarityStAXAdapter) - Method in interface org.biojava.bio.program.ssbind.StAXHandlerFactory
getHandler returns an appropriate StAXContentHandler implementation containing a reference to a parent context.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.agave.StAXHandlerFactory
Return a suitable StAX content handler.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game.StAXHandlerFactory
Return a suitable StAX content handler.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game12.StAXHandlerFactory
Return a suitable StAX content handler.
getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
get iterator for current stack starting at the position below mine.
getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
get iterator for current stack starting at the position below mine.
getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
return iterator to callbackStack
getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
return iterator to callbackStack
getHeader() - Method in class org.biojavax.bio.seq.io.FastaFormat
 
getHeaderDefinitions() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer
Returns the appropriate style and javascript definitions for this renderer.
getHeight() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the height of the whole graphic (in pixels).
getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
getHeightScaling returns the state of the height scaling policy.
getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
getHeightScaling returns the state of the height scaling policy.
getHibernateSession() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
 
getHibernateSession() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
getHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
 
getHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
 
getHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
Return all hits in this sequence similarity search result.
getHits() - Method in class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
 
getHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
getHomologeneID() - Method in interface org.biojava.bio.program.homologene.Orthologue
get the Homologene ID.
getHomologeneID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
 
getHomology() - Method in interface org.biojava.bio.seq.homol.HomologyFeature
 
getHomology() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
 
getHorizontalScale() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the in-use horizontal scale factor.
getI() - Method in class org.biojava.bio.proteomics.StructureTools
 
getId() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
getId() - Method in class org.biojavax.bio.seq.SimplePosition
Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.SimpleBioEntry
Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Gets the Hibernate ID.
getId() - Method in class org.biojavax.ontology.SimpleComparableOntology
Gets the Hibernate ID.
getId() - Method in class org.biojavax.ontology.SimpleComparableTerm
Gets the Hibernate ID.
getId() - Method in class org.biojavax.ontology.SimpleComparableTriple
Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleComment
Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleCrossRef
Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleDocRef
Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleNamespace
Gets the Hibernate ID.
getID() - Method in interface org.biojava.bio.program.indexdb.Record
getID returns the primary identifier of the record.
getID() - Method in class org.biojava.bio.program.indexdb.Record.Impl
 
getID() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
The public unigene ID.
getID() - Method in interface org.biojava.bio.seq.db.Index
The ID of the sequence at this position in this file.
getID() - Method in class org.biojava.bio.seq.db.SimpleIndex
 
getID() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
 
getID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Getter for property ID.
getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getIdAlias(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getIdentifier() - Method in interface org.biojava.utils.lsid.Identifiable
Return the identifier of this object.
getIdentifier() - Method in interface org.biojavax.bio.BioEntry
Returns the identifier of this bioentry.
getIdentifier() - Method in class org.biojavax.bio.SimpleBioEntry
Returns the identifier of this bioentry.
getIdentifier() - Method in interface org.biojavax.ontology.ComparableTerm
Returns the (optional) identifier associated with this term.
getIdentifier() - Method in class org.biojavax.ontology.SimpleComparableTerm
Returns the (optional) identifier associated with this term.
getIdentity() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the IDENTITY amino acid substitution matrix.
getIDMaker() - Method in class org.biojava.bio.seq.db.HashSequenceDB
Retrieve the IDMaker associated with this database.
getIDMaker() - Method in class org.biojavax.bio.db.HashRichSequenceDB
Retrieve the IDMaker associated with this database.
getIDs() - Method in class org.biojava.bio.seq.db.BioIndex
 
getIDs() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
 
getIDs() - Method in interface org.biojava.bio.seq.db.IndexStore
Retrieve the set of all current IDs.
getIDs() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
getIfFalse() - Method in class org.biojava.utils.bytecode.IfExpression
 
getIfInstruction() - Method in class org.biojava.utils.bytecode.IfExpression
 
getIfTrue() - Method in class org.biojava.utils.bytecode.IfExpression
 
getImage(int, int) - Method in class org.biojava.bio.program.abi.ABITrace
Returns a BufferedImage that represents the entire trace.
getImageMap() - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
getImageMap returns the current image map.
getImageMap() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
getImageMap returns the current image map.
getImageMap() - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
getImageMap returns the current image map.
getImplementationNames(Class) - Static method in class org.biojava.utils.Services
Return a Set of names of implementations of the given service interface in the classloader from which BioJava was loaded.
getImplementationNames(Class, ClassLoader) - Static method in class org.biojava.utils.Services
Return a List of names of implementations of the given service interface available in a given classloader.
getIndex(double) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
Calculate the position in the sequence relating to the angle.
getIndex(double) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
 
getIndexStore() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
Retrieve the IndexStore.
getInitialContext(Hashtable) - Method in class org.biojava.naming.ObdaInitialContextFactory
 
getInnerMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
getInnerMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
getInput() - Method in interface org.biojava.utils.process.OutputHandler
Gets the input stream.
getInput() - Method in class org.biojava.utils.process.StreamPipe
Gets the input stream
getInput() - Method in class org.biojava.utils.process.WriterOutputHandler
Gets the input stream.
getInputHandler() - Method in class org.biojava.utils.process.ExternalProcess
Gets the input handler which is responsible for the standard input of the external process.
getInputStream(File) - Method in class org.biojava.utils.io.InputStreamProvider
get an InputStream for the file
getInputStream(String) - Static method in class org.biojava.utils.io.FlatFileCache
 
getInputStream(String) - Method in class org.biojava.utils.io.InputStreamProvider
get an InputStream for this file
getInputStream(URL) - Method in class org.biojava.utils.io.InputStreamProvider
 
getINSDseqTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms
Getter for the INSDseq term
getInsert() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Returns the current expenses of a single insert operation.
getInsert() - Method in class org.biojava.bio.alignment.SmithWaterman
 
getInsert(int) - Method in class org.biojava.bio.dp.ProfileHMM
Retrieves the insert state at column indx.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
Returns the id value created during the last insert command.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.HypersonicDBHelper
Deprecated.
 
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper
Deprecated.
 
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
Deprecated.
 
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
 
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper
Deprecated.
 
getInstance() - Static method in class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity
Retrieve the singleton instance of this class.
getInstance() - Static method in class org.biojava.bio.dist.IgnoreCountsTrainer
Returns the global singleton instance of the IgnoreCountsTrainer.
getInstance() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getInstance() - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory
 
getInstance() - Static method in class org.biojava.bio.symbol.DoubleAlphabet
Retrieve the single DoubleAlphabet instance.
getInstance() - Static method in class org.biojava.bio.symbol.IntegerAlphabet
Retrieve the single IntegerAlphabet instance.
getInstance() - Static method in class org.biojava.bio.taxa.EbiFormat
Deprecated.
 
getInstance() - Static method in class org.biojava.naming.ObdaUriParser
 
getInstance() - Static method in class org.biojava.utils.io.FlatFileCache
 
getInstance() - Static method in class org.biojava.utils.walker.WalkerFactory
 
getInstance(Class) - Static method in class org.biojava.utils.walker.WalkerFactory
Make a WalkerFactory that handles a Visitor for a class of type typeClazz.
getInstance(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet
Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.
getInstance(FiniteAlphabet, SoftMaskedAlphabet.MaskingDetector) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet
Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any Symbol is soft masked or not.
getInt() - Method in class org.biojava.utils.io.LargeBuffer
 
getInt(long) - Method in class org.biojava.utils.io.LargeBuffer
 
getIntegerOntology() - Static method in class org.biojava.ontology.OntoTools
Get the Ontology that defines integers.
getInteractions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property interactions.
getInterfaces() - Method in interface org.biojava.utils.bytecode.CodeClass
 
getInterfaces() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getInterfaces() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getInternalSymbolList() - Method in interface org.biojavax.bio.seq.RichSequence
A special function that returns the SymbolList that this RichSequence is based around.
getInternalSymbolList() - Method in class org.biojavax.bio.seq.SimpleRichSequence
A special function that returns the SymbolList that this RichSequence is based around.
getInternalSymbolList() - Method in class org.biojavax.bio.seq.ThinRichSequence
A special function that returns the SymbolList that this RichSequence is based around.
getIntFromSymbolList(SymbolList, int) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
Retrieves, unwraps, and returns an int from a SymbolList containing IntegerAlphabet.IntegerSymbols.
getIntOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Helper method for converting a Number-valued option into an int primitive.
getInvTransform() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns a new AffineTransform describing the transformation from output space to chromatogram space.
getIsoelectricPoint(SymbolList) - Static method in class org.biojava.bio.proteomics.IsoelectricPointCalc
Static public method to compute the pI for a polypeptide in denaturating and reduced conditions with both free ends.
getIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property isoforms.
getIsoIDs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Getter for property isoIDs.
getIsoschizomers(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getIsoschizomers returns an unmodifable set of the isoschizomers of this enzyme.
getItem() - Method in interface org.biojava.stats.svm.ItemValue
 
getItem() - Method in class org.biojava.stats.svm.SimpleItemValue
 
getItems() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getIterator() - Method in class org.biojava.utils.ListTools.Doublet
 
getIterator() - Method in class org.biojava.utils.ListTools.Triplet
 
getJName() - Method in interface org.biojava.utils.bytecode.CodeClass
 
getJName() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getJName() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getJoiner() - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
getJoinStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
Returns the an object indicating the style of table joining that this database should employ.
getJoinStyle() - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
Deprecated.
 
getJoinTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation
Getter for the "join" term
getJournalReference() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Gets a reference to the journal which published the article about the AAindex entry.
getKernel() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
getKernel() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
getKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getKernel() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Retrieve the currently used kernel
getKernelValue(int, int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getKey() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
 
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains
 
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation
 
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.HasAnnotation
 
getKey() - Method in class org.biojava.utils.cache.KeyedWeakReference
 
getKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
 
getKeys() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
 
getKeys() - Method in class org.biojava.bio.program.tagvalue.Index2Model
 
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getKeyword(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
 
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getKeywordTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the keyword term
getKineticsNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property kineticsNote.
getKmpNextTable() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
Returns the table of border lengths
getKMs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property KMs.
getLabel() - Method in interface org.biojava.bio.alignment.AlignmentElement
 
getLabel() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
 
getLabel() - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
 
getLabel() - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
 
getLabel() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
return the label of this class.
getLabel() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
 
getLabel() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
getLabel() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Getter for property label.
getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getLabel(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
getLabelGlyph(SequenceRenderContext, FontRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
 
getLabelMaker() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
 
getLabels() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
getLabels() - Method in interface org.biojava.bio.alignment.Alignment
The list of SymbolLists in the alignment.
getLabels() - Method in class org.biojava.bio.alignment.FlexibleAlignment
getLabels will return a list of labels in left to right order
getLabels() - Method in class org.biojava.bio.alignment.SimpleAlignment
 
getLabels() - Method in class org.biojava.bio.dp.SimpleStatePath
 
getLabels() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
getLabels() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
getLabelsAt(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
getLambda() - Method in class org.biojava.stats.svm.DiagonalAddKernel
Retrieve the scale factor.
getLast() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
Get the last complete annotation built.
getLastScore() - Method in class org.biojava.bio.dp.AbstractTrainer
 
getLastScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
 
getLeader() - Method in class org.biojava.utils.ListTools.SeriesList
 
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getLeadingBorder returns the leading border of the primary sequence.
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel
Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.
getLeadingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
Gets the LeadingBorder attribute of the SequenceRenderContext object.
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getLeadingBorder returns the leading border.
getLeadingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
getLeftValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon
Gets the left value.
getLeftValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Gets the left value.
getLength() - Method in interface org.biojava.bio.program.indexdb.Record
getLength returns the length of the record in bytes.
getLength() - Method in class org.biojava.bio.program.indexdb.Record.Impl
 
getLength() - Method in class org.biojava.bio.search.SeqContentPattern
Get the current length.
getLength() - Method in interface org.biojava.bio.seq.db.Index
The entry can be slurped out of the file by grabbing length bytes from start.
getLength() - Method in class org.biojava.bio.seq.db.SimpleIndex
 
getLength() - Method in class org.biojava.bio.symbol.CircularLocation
 
getLength() - Method in class org.biojava.utils.RepeatedCharSequence
 
getLevel() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
return current stack level.
getLevel() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
return current stack level.
getLimit() - Method in class org.biojava.utils.cache.FixedSizeCache
 
getLine() - Method in exception org.biojava.utils.ParserException
Get the text of the line where the exception occured.
getLineNumber() - Method in exception org.biojava.utils.ParserException
Get the line number in the stream where this exception occured.
getLines() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Retrieve the number of lines that the sequence will be rendered over.
getLineWidth() - Method in class org.biojava.bio.program.phred.PhredFormat
Retrive the current line width.
getLineWidth() - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
Retrive the current line width.
getLineWidth() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Retrive the current line width.
getLineWidth() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Retrive the current line width.
getListener() - Method in class org.biojava.bio.program.tagvalue.ParserListener
getListener returns the listener of the pair.
getListener() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
return the TagValueListener assigned to this State.
getListener() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
 
getListener(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
getListeners(ChangeType) - Method in class org.biojava.utils.Unchangeable
 
getLITDBEntryNumbers() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Gets the list of literature database identifiers for the AAindex entry.
getLoc() - Method in interface org.biojava.bio.alignment.AlignmentElement
 
getLoc() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
 
getLocation() - Method in class org.biojava.bio.program.indexdb.BioStore
getLocation returns the directory where the index is located.
getLocation() - Method in interface org.biojava.bio.seq.Feature
The location of this feature.
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
 
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
 
getLocation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getLocation() - Method in class org.biojava.bio.seq.RemoteFeature.Region
Retrieve the Location of the Region.
getLocation() - Method in class org.biojavax.bio.seq.SimpleRichFeature
The location of this feature.
getLocation() - Method in interface org.biojavax.DocRef
Returns a textual description of the document reference.
getLocation() - Method in interface org.biojavax.RankedDocRef
If this object was constructed using a location instead of two integers, then this method will return that location.
getLocation() - Method in class org.biojavax.SimpleDocRef
Returns a textual description of the document reference.
getLocation() - Method in class org.biojavax.SimpleRankedDocRef
 
getLocationHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
 
getLocationSequenceTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the location seq term
getLocator() - Method in exception org.biojava.utils.ParserException
Get a locator for the stream which caused this exception.
getLocusID() - Method in interface org.biojava.bio.program.homologene.Orthologue
get the locus ID associated with this orthologue.
getLocusID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
 
getLogoFont() - Method in class org.biojava.bio.gui.TextBlock
Retrieve the current font.
getLogoFont() - Method in class org.biojava.bio.gui.TextLogoPainter
Retrieve the current font.
getLogoPainter() - Method in class org.biojava.bio.gui.DistributionLogo
Retrieve the current logo painter.
getLong() - Method in class org.biojava.utils.io.LargeBuffer
 
getLong(long) - Method in class org.biojava.utils.io.LargeBuffer
 
getLSID() - Method in class org.biojava.bio.program.formats.Embl
 
getLSID() - Method in class org.biojava.bio.program.formats.Enzyme
 
getLSID() - Method in interface org.biojava.bio.program.formats.Format
Retrieve the LSID associated with this format.
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Compound
 
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
 
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Reaction
 
getLSID() - Method in class org.biojava.bio.program.formats.Swissprot
 
getLys_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getMagicalState() - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
getMagicalState(Alphabet, int) - Static method in class org.biojava.bio.dp.MagicalState
 
getMapAll() - Method in class org.biojava.bio.molbio.RestrictionMapper
getMapAll returns whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it.
getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getMapLocation(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getMapper() - Method in class org.biojava.bio.AnnotationRenamer
getMapper returns the TagMapper being used to remap the Annotation.
getMapper() - Method in class org.biojava.bio.program.tagvalue.TagRenamer
Retrieve the mapper used to rename tags
getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getMapPosition(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getMapType() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
getMaskedAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
Gets the Alphabet upon which masking is being applied
getMaskingDetector() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
Getter for the MaskingDetector
getMass(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc
Get the Mass of this peptide.
getMass(SymbolList, String, boolean) - Static method in class org.biojava.bio.proteomics.MassCalc
getMass calculates the mass of this peptide.
getMatch() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Returns the current expenses of a single match operation.
getMatch() - Method in class org.biojava.bio.alignment.SmithWaterman
 
getMatch() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the MATCH amino acid substitution matrix.
getMatch(int) - Method in class org.biojava.bio.dp.ProfileHMM
Retrieve the match state at column indx.
getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getMatchAlign(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getMatchChar() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getMatchDesc(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getMatches() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
 
getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
getMatches() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
 
getMatches() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
getMatches() - Method in interface org.biojava.bio.symbol.Symbol
The alphabet containing the symbols matched by this ambiguity symbol.
getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getMatchRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getMatrixData(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getMatrixData(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
getMatrixLabels() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getMatrixLabels() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
getMax() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
The maximum score in this matrix.
getMax() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
 
getMax() - Method in interface org.biojava.bio.chromatogram.Chromatogram
Gets the max intensity from all the traces.
getMax() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
getMax() - Method in class org.biojava.bio.symbol.CircularLocation
This will give you the coordinate of the maximum point contained by this Location.
getMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
getMax() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
getMax() - Method in interface org.biojava.bio.symbol.Location
The maximum position contained.
getMax() - Method in class org.biojava.bio.symbol.PointLocation
 
getMax() - Method in class org.biojava.bio.symbol.RangeLocation
 
getMax() - Method in class org.biojavax.bio.seq.EmptyRichLocation
The maximum position contained.
getMax() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
The maximum position contained.
getMax() - Method in class org.biojavax.bio.seq.SimpleRichLocation
The maximum position contained.
getMax(AtomicSymbol) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
 
getMax(AtomicSymbol) - Method in interface org.biojava.bio.chromatogram.Chromatogram
Gets the max intensity on the trace for the specified nucleotide.
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver
Resolves the maximum possible base for this position.
getMax(Position) - Method in interface org.biojavax.bio.seq.PositionResolver
Resolves the maximum possible base for this position.
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver
Resolves the maximum possible base for this position.
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver
Resolves the maximum possible base for this position.
getMaxCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern
Get the maximum counts required for a symbol.
getMaxCrossOvers() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
 
getMaxCrossOvers() - Method in interface org.biojavax.ga.functions.CrossOverFunction
 
getMaxCrossOvers() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
getMaxGenerations() - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
 
getMaxPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Retrieves the end position of this location.
getMaxPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
Retrieves the end position of this location.
getMaxPosition() - Method in interface org.biojavax.bio.seq.RichLocation
Retrieves the end position of this location.
getMaxPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Retrieves the end position of this location.
getMaxRunTimeExceeded() - Method in class org.biojava.utils.ExecRunner
Returns whether the maximum runtime was exceeded or not.
getMaxRunTimeSecs() - Method in class org.biojava.utils.ExecRunner
Returns the maximum run time in seconds for this object.
getMaxScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
getMaxScore returns the maximum score accepted.
getMaxSize() - Method in class org.biojava.utils.cache.FixedSizeMap
 
getMaxValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
 
getMergeAnnotation() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
 
getMerged() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
Return a list of merged DBs.
getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
See if tags are being merged.
getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser
Report whether empty tags will be treated as continuations of the last non -empty tag.
getMessage() - Method in class org.biojava.utils.ParseErrorEvent
Find the message about this event
getMetaData() - Method in class org.biojava.bio.program.indexdb.BioStore
 
getMetaData() - Method in interface org.biojava.bio.program.indexdb.IndexStore
getMetaData returns a data structure which represents an OBDA "config.dat" flatfile indexing configuration file.
getMethod() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
Get the Method used.
getMethod(String, CodeClass[]) - Method in interface org.biojava.utils.bytecode.CodeClass
Get a method by name and argument list.
getMethod(String, CodeClass[]) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getMethod(String, CodeClass[]) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getMethods() - Method in interface org.biojava.utils.bytecode.CodeClass
Get all methods declared by this class and its super classes, removing all super class methods that are over ridden.
getMethods() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getMethods() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getMethodsByName(String) - Method in interface org.biojava.utils.bytecode.CodeClass
Get the name of all methods that could be invoked through this class with a given name.
getMethodsByName(String) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getMethodsByName(String) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getMin() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
The minimum score of this matrix.
getMin() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
getMin() - Method in class org.biojava.bio.symbol.CircularLocation
This will give you the coordinate of the minimum point contained by this Location.
getMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
getMin() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
getMin() - Method in interface org.biojava.bio.symbol.Location
The minimum position contained.
getMin() - Method in class org.biojava.bio.symbol.PointLocation
 
getMin() - Method in class org.biojava.bio.symbol.RangeLocation
 
getMin() - Method in class org.biojavax.bio.seq.EmptyRichLocation
The minimum position contained.
getMin() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
The minimum position contained.
getMin() - Method in class org.biojavax.bio.seq.SimpleRichLocation
The minimum position contained.
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver
Resolves the minimum possible base for this position.
getMin(Position) - Method in interface org.biojavax.bio.seq.PositionResolver
Resolves the minimum possible base for this position.
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver
Resolves the minimum possible base for this position.
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver
Resolves the minimum possible base for this position.
getMinCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern
Get the minimum counts required for a symbol.
getMinIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
get the lowest level of identity observed in this Group
getMinIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
getMinimumLeader(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
getMinimumLeader returns the maximum value of getMinimumLeader() for a list of SequenceRenderers.
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
Retrieve the minimum leading distance for this renderer when rendering src.
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
 
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
getMinimumTrailer(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
getMinimumTrailer returns the maximum value of getMinimumTrailer() for a list of SequenceRenderers.
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
Retrieve the minimum trailing distance for this renderer when rendering src.
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
 
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
getMinimumWidth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.LabelRenderer
Retrieve the minimum space required to render the label.
getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
 
getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
 
getMinPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Retrieves the start position of this location.
getMinPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
Retrieves the start position of this location.
getMinPosition() - Method in interface org.biojavax.bio.seq.RichLocation
Retrieves the start position of this location.
getMinPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Retrieves the start position of this location.
getMinScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
getMinScore returns the minimum score accepted.
getMinValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
 
getMismatches() - Method in class org.biojava.bio.search.MaxMismatchPattern
 
getMissing() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getMissing() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
getMitoGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon
Returns the mitochondrial genetic code of this taxon, which may be null if not known.
getMitoGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Getter for property mitoGeneticCode.
getModel() - Method in class org.biojava.bio.dp.DP
 
getModel() - Method in interface org.biojava.bio.dp.ModelInState
The model that is inside this state.
getModel() - Method in class org.biojava.bio.dp.SimpleModelInState
 
getModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
getModifiable() - Method in class org.biojava.utils.MergingSet
 
getModifiers() - Method in interface org.biojava.utils.bytecode.CodeClass
Get the modifiers associated with the class.
getModifiers() - Method in class org.biojava.utils.bytecode.CodeField
Get the moddifiers applied to this field.
getModifiers() - Method in interface org.biojava.utils.bytecode.CodeMethod
Get the modifiers, such as PUBLIC, ABSTRACT and so on
getModifiers() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getModifiers() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
 
getModifiers() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getMolecularWeight() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property molecularWeight.
getMolecularWeight(SymbolList) - Static method in class org.biojava.bio.proteomics.MassCalc
Calculate the molecular weight of a protein, making estimates whenever it is possible like averaging mass values for ambiguity symbols or counting zero when gaps are encountered.
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getMolType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
 
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getMolTypeTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
getter for the MolType term
getMolWeightError() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property molWeightError.
getMolWeightMethod() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property molWeightMethod.
getMolWeightRangeEnd() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property molWeightRangeEnd.
getMolWeightRangeStart() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property molWeightRangeStart.
getMoreSearches() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
getMoreSearches() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
getMoreSearches() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
getMoreSearches() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
getMoreSearches() - Method in class org.biojava.bio.search.SearchContentAdapter
 
getMoreSearches() - Method in class org.biojava.bio.search.SearchContentFilter
 
getMoreSearches() - Method in interface org.biojava.bio.search.SearchContentHandler
getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source.
getMoreSearches() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
getMotifs() - Method in class org.biojava.bio.program.Meme
 
getMouseEvent() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
Get the mouse event that caused this.
getMultiplier() - Method in class org.biojava.stats.svm.PolynomialKernel
 
getMultiplier() - Method in class org.biojava.stats.svm.SigmoidKernel
 
getMutationFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
 
getMutationFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
getMutationProbs() - Method in class org.biojavax.ga.functions.AbstractMutationFunction
 
getMutationProbs() - Method in interface org.biojavax.ga.functions.MutationFunction
 
getMutationProbs() - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
getMutationSpectrum() - Method in class org.biojavax.ga.functions.AbstractMutationFunction
 
getMutationSpectrum() - Method in interface org.biojavax.ga.functions.MutationFunction
 
getMutationSpectrum() - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
getMyComponents(Name) - Method in class org.biojava.naming.ObdaContext
 
getName() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
Every substitution matrix has a name like "BLOSUM30" or "PAM160".
getName() - Method in interface org.biojava.bio.annodb.AnnotationDB
The name of this AnnotationDB.
getName() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
 
getName() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
 
getName() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
 
getName() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
 
getName() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
 
getName() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getName() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
getName returns the enzyme name.
getName() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
retrieves name of this group.
getName() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
getName() - Method in class org.biojava.bio.program.indexdb.BioStore
The name of this store or null if the name has not been set.
getName() - Method in class org.biojava.bio.proteomics.Protease
Gets the name of this Protease
getName() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
 
getName() - Method in class org.biojava.bio.seq.db.BioIndex
 
getName() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
getName() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
Deprecated.
 
getName() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.DummySequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getName returns the database name as defined within the EMBL CD-ROM index.
getName() - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
 
getName() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
Get the name of this sequence database.
getName() - Method in interface org.biojava.bio.seq.db.IndexStore
Retrieve the name of this store.
getName() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
 
getName() - Method in interface org.biojava.bio.seq.db.SequenceDBLite
Get the name of this sequence database.
getName() - Method in class org.biojava.bio.seq.db.SubSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
getName() - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
 
getName() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
getName() - Method in interface org.biojava.bio.seq.FeatureTypes.Repository
The name of this repository.
getName() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
 
getName() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
Get the name of this type.
getName() - Method in class org.biojava.bio.seq.impl.DummySequence
 
getName() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
getName() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
getName() - Method in class org.biojava.bio.seq.impl.SubSequence
 
getName() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
getName() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
getName() - Method in interface org.biojava.bio.seq.Sequence
The name of this sequence.
getName() - Method in class org.biojava.bio.seq.SimpleAssembly
 
getName() - Method in interface org.biojava.bio.symbol.Alphabet
Get the name of the alphabet.
getName() - Method in interface org.biojava.bio.symbol.CodonPref
get name of object
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
 
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
getName() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
 
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
getName() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
getName() - Method in class org.biojava.bio.symbol.SimpleCodonPref
 
getName() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
 
getName() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
getName() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
The name of the Alphabet
getName() - Method in interface org.biojava.bio.symbol.Symbol
The long name for the symbol.
getName() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
 
getName() - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
Deprecated.
 
getName() - Method in interface org.biojava.bio.taxa.TaxonFactory
Deprecated.
Name for this TaxonFactory.
getName() - Method in class org.biojava.bio.taxa.WeakTaxonFactory
Deprecated.
 
getName() - Method in interface org.biojava.directory.SequenceDBProvider
The name of this provider.
getName() - Method in class org.biojava.ontology.IntegerOntology
 
getName() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
getName() - Method in interface org.biojava.ontology.Ontology
Return the name of this ontology
getName() - Method in class org.biojava.ontology.Ontology.Impl
 
getName() - Method in class org.biojava.ontology.OntologyTerm.Impl
 
getName() - Method in class org.biojava.ontology.RemoteTerm.Impl
 
getName() - Method in class org.biojava.ontology.Synonym
 
getName() - Method in interface org.biojava.ontology.Term
Return the name of this term.
getName() - Method in class org.biojava.ontology.Term.Impl
 
getName() - Method in class org.biojava.ontology.Triple.Impl
 
getName() - Method in interface org.biojava.utils.bytecode.CodeClass
 
getName() - Method in class org.biojava.utils.bytecode.CodeField
Get the name of the field.
getName() - Method in interface org.biojava.utils.bytecode.CodeMethod
The name of the method.
getName() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getName() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
 
getName() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getName() - Method in class org.biojava.utils.bytecode.LocalVariable
 
getName() - Method in class org.biojava.utils.bytecode.ParametricType
Get the name of this type.
getName() - Method in interface org.biojava.utils.candy.CandyVocabulary
It returns a name of this vocabulary.
getName() - Method in class org.biojava.utils.ChangeType
Return the name of this change.
getName() - Method in class org.biojava.utils.regex.Pattern
return the String label associated with this pattern.
getName() - Method in interface org.biojavax.bio.BioEntry
Returns the name of this bioentry.
getName() - Method in interface org.biojavax.bio.db.BioEntryDBLite
Get the name of this sequence database.
getName() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
 
getName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
 
getName() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
getName() - Method in class org.biojavax.bio.db.HashBioEntryDB
 
getName() - Method in class org.biojavax.bio.db.HashRichSequenceDB
 
getName() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
 
getName() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
 
getName() - Method in interface org.biojavax.bio.seq.RichFeature
Returns the name of this feature.
getName() - Method in class org.biojavax.bio.seq.RichLocation.Strand
Returns the string symbol of this strand.
getName() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Returns the name of this feature.
getName() - Method in class org.biojavax.bio.SimpleBioEntry
Returns the name of this bioentry.
getName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
Returns this name.
getName() - Method in interface org.biojavax.DocRefAuthor
Returns a textual description of the authors name.
getName() - Method in class org.biojavax.ga.impl.AbstractOrganism
 
getName() - Method in class org.biojavax.ga.impl.AbstractPopulation
 
getName() - Method in interface org.biojavax.ga.Organism
Gets the organisms name
getName() - Method in interface org.biojavax.ga.Population
 
getName() - Method in interface org.biojavax.Namespace
The name of the namespace is immutable and must be set by the constructor of the instantiating class.
getName() - Method in class org.biojavax.ontology.SimpleComparableOntology
Return the name of this ontology
getName() - Method in class org.biojavax.ontology.SimpleComparableTerm
Return the name of this term.
getName() - Method in class org.biojavax.ontology.SimpleComparableTriple
Return the name of this term.
getName() - Method in class org.biojavax.SimpleDocRefAuthor
Returns a textual description of the authors name.
getName() - Method in class org.biojavax.SimpleNamespace
The name of the namespace is immutable and must be set by the constructor of the instantiating class.
getNameClass() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
Returns the class of this name.
getNameClasses() - Method in interface org.biojavax.bio.taxa.NCBITaxon
Returns all the name classes available for a taxon.
getNameClasses() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Returns all the name classes available for a taxon.
getNamedIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
Getter for property namedIsoforms.
getNameHierarchy() - Method in interface org.biojavax.bio.taxa.NCBITaxon
Returns the taxonomy hierarchy of this taxon entry in the form: least specific; more specific; ...; most specific.
getNameHierarchy() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific.
getNameInNamespace() - Method in class org.biojava.naming.ObdaContext
 
getNameParser(String) - Method in class org.biojava.naming.ObdaContext
 
getNameParser(Name) - Method in class org.biojava.naming.ObdaContext
 
getNames() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getNames() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Getter for property names.
getNames(String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
Returns all the names available for a taxon in a given class.
getNames(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Returns all the names available for a taxon in a given class.
getNameSet() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
 
getNamesMap() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
 
getNamespace() - Method in interface org.biojavax.bio.BioEntry
Returns the namespace of this bioentry.
getNamespace() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Getter for property namespace.
getNamespace() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
Getter for property namespace.
getNamespace() - Method in class org.biojavax.bio.SimpleBioEntry
Returns the namespace of this bioentry.
getNamespaceId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
Return the namespace id for this identifier within the authority.
getNameToSymbol() - Method in class org.biojava.bio.seq.io.NameTokenization
 
getNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon
Gets the NCBI taxon ID.
getNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Gets the NCBI taxon ID.
getNCutters(int) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getNCutters returns an unmodifable set of all enzymes with a cut site of size n.
getNegShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Retrieve the shape used to represent negative points.
getNestedKernel() - Method in class org.biojava.stats.svm.NestedKernel
Retrieve the currently nested SVMKernel.
getNestedValue(NestedValue, String, int) - Method in class org.biojava.ontology.obo.OboFileParser
 
getNewTag(Object) - Method in interface org.biojava.bio.program.tagvalue.PropertyChanger
getNewTag returns the tag which substitutes the specified value.
getNewTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper
 
getNexusBlock() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
 
getNexusBlock() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder
Obtain the constructed block.
getNexusFile() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
Obtain the constructed file.
getNodePrefix() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Returns the node prefix.
getNodeRank() - Method in interface org.biojavax.bio.taxa.NCBITaxon
Gets the node rank of this taxon.
getNodeRank() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Gets the node rank of this taxon.
getNodes() - Method in class org.biojava.utils.automata.FiniteAutomaton
get all Nodes within this instance.
getNodes() - Method in interface org.biojava.utils.automata.NfaBuilder
 
getNodes() - Method in class org.biojava.utils.automata.NfaSubModel
 
getNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution
returns Set containing the nonWobbleBases that occur in codons that encode this residue
getNormalizingVector() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
Retrive the current normalizing vector.
getNotCleaveResidues() - Method in class org.biojava.bio.proteomics.Protease
The list of residues that will prevent cleavage if they follow the cleavage residue.
getNote() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
 
getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property note.
getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Getter for property note.
getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getNote(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
 
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getNote(Note) - Method in class org.biojavax.EmptyRichAnnotation
Uses the term and rank to lookup a note in this annotation.
getNote(Note) - Method in interface org.biojavax.RichAnnotation
Uses the term and rank to lookup a note in this annotation.
getNote(Note) - Method in class org.biojavax.SimpleRichAnnotation
Uses the term and rank to lookup a note in this annotation.
getNoteSet() - Method in class org.biojavax.bio.seq.CompoundRichLocation
Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.bio.SimpleBioEntry
Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.EmptyRichAnnotation
Returns an immutable set of all notes in this annotation.
getNoteSet() - Method in interface org.biojavax.RichAnnotatable
Returns the set of notes associated with this object.
getNoteSet() - Method in interface org.biojavax.RichAnnotation
Returns an immutable set of all notes in this annotation.
getNoteSet() - Method in class org.biojavax.SimpleCrossRef
Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.SimpleRichAnnotation
Returns an immutable set of all notes in this annotation.
getNuc4_2() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the NUC.4.2 nucleotide substitution matrix.
getNuc4_4() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the NUC.4.4 nucleotide substitution matrix.
getNucleotide() - Static method in class org.biojava.bio.seq.NucleotideTools
Return the Nucleotide alphabet.
getNucleotideParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Creates a nucleotide symbol tokenizer.
getNullModel() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
 
getNullModel() - Method in interface org.biojava.bio.dist.Distribution
Retrieve the null model Distribution that this Distribution recognizes.
getNullModel() - Method in class org.biojava.bio.dist.GapDistribution
 
getNullModel() - Method in class org.biojava.bio.dist.PairDistribution
 
getNullModel() - Method in class org.biojava.bio.dist.SimpleDistribution
 
getNullModel() - Method in class org.biojava.bio.dist.TranslatedDistribution
 
getNullModel() - Method in class org.biojava.bio.dist.UniformDistribution
 
getNullModel(Distribution, Distribution) - Static method in class org.biojava.bio.dist.PairDistribution
Get a uniform null model over a PairDistribution over [first,second].
getNullModelWeight() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Return the number of pseudocounts added to the distribution when training.
getNullModelWeight() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
getNumber() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
Return a number (usually, but not always, a motif count) associated with this node of the tree.
getNumberExperiments() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Getter for property numberExperiments.
getNumCount() - Method in interface org.biojava.utils.candy.CandyFinder
It returns the number of available vocabularies.
getNumGapsInQuery() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getNumGapsInSubject() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getNumIdenticals() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getNumSimilars() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getObject() - Method in interface org.biojava.ontology.Triple
Return the object term of this triple.
getObject() - Method in class org.biojava.ontology.Triple.Impl
 
getObject() - Method in interface org.biojavax.bio.BioEntryRelationship
Returns the object of this relationship (ie. the BioEntry which this relationship starts from).
getObject() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
Returns the object of this relationship (ie. the feature which this relationship starts from).
getObject() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Returns the object of this relationship (ie. the feature which this relationship starts from).
getObject() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
Returns the object of this relationship (ie. the BioEntry which this relationship starts from).
getObject() - Method in class org.biojavax.ontology.SimpleComparableTriple
Return the object term of this triple.
getObject(Class, Object[]) - Static method in class org.biojavax.RichObjectFactory
Delegates to a RichObjectBuilder to construct/retrieve the object, and returns it.
getObjectId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
Return the object id of this identifier.
getOboFileEventListener() - Method in class org.biojava.ontology.obo.OboFileParser
 
getObsolete() - Method in interface org.biojavax.ontology.ComparableTerm
Checks to see if this term is obsolete.
getObsolete() - Method in class org.biojavax.ontology.SimpleComparableTerm
Checks to see if this term is obsolete.
getOffset() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
Get the angle through which the origin of the sequence is rotated through.
getOffset() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
 
getOffset() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
 
getOffset() - Method in interface org.biojava.bio.program.indexdb.Record
getOffset returns the byte offset in the file at which the record begins.
getOffset() - Method in class org.biojava.bio.program.indexdb.Record.Impl
 
getOldIDHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
 
getOntology() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
getOntology() - Method in interface org.biojava.ontology.OntologyTerm
Get the remote ontology referenced by this term
getOntology() - Method in class org.biojava.ontology.OntologyTerm.Impl
 
getOntology() - Method in class org.biojava.ontology.RemoteTerm.Impl
 
getOntology() - Method in interface org.biojava.ontology.Term
Return the ontology in which this term exists.
getOntology() - Method in class org.biojava.ontology.Term.Impl
 
getOntology() - Method in class org.biojava.ontology.Triple.Impl
 
getOntology() - Method in class org.biojavax.ontology.SimpleComparableTerm
Return the ontology in which this term exists.
getOntology() - Method in class org.biojavax.ontology.SimpleComparableTriple
Return the ontology in which this term exists.
getOntology(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
getOps() - Method in class org.biojava.ontology.IntegerOntology
 
getOps() - Method in interface org.biojava.ontology.Ontology
Return the associated OntologyOps.
getOps() - Method in class org.biojava.ontology.Ontology.Impl
 
getOps() - Method in class org.biojavax.ontology.SimpleComparableOntology
Return the associated OntologyOps.
getOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the current value for the specified option.
getOrCreateTerm(String) - Method in interface org.biojavax.ontology.ComparableOntology
Looks for a term with the given name and returns it.
getOrCreateTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
Looks for a term with the given name and returns it.
getOrCreateTriple(Term, Term, Term) - Method in interface org.biojavax.ontology.ComparableOntology
Looks for a triple with the given subject object and predicate and returns it.
getOrCreateTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
Looks for a triple with the given subject object and predicate and returns it.
getOrder() - Method in class org.biojava.stats.svm.PolynomialKernel
 
getOrderedLocusNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the OrderedLocusName term
getOrderTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation
Getter for the "order" term
getORFNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the ORFName term
getOrganelleTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the Organelle term
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getOrganism(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
 
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getOrganismByName(String) - Method in class org.biojavax.ga.impl.SimplePopulation
 
getOrganismByName(String) - Method in interface org.biojavax.ga.Population
Gets the specified organism
getOrganisms() - Method in class org.biojavax.ga.impl.SimplePopulation
 
getOrganisms() - Method in interface org.biojavax.ga.Population
Gets the Set of Organisms
getOrientation() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
getOrImportTerm(Term) - Method in interface org.biojavax.ontology.ComparableOntology
Looks for a term with the same name as the given term and returns it.
getOrImportTerm(Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
Looks for a term with the same name as the given term and returns it.
getOrthologue(String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
Returns an orthologue of specified ID.
getOrthologue(String) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
 
getOrthologue(String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
 
getOrthologue(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
 
getOrthoPairSets() - Method in interface org.biojava.bio.program.homologene.HomologeneDB
Get the HomologeneGroups in this database.
getOrthoPairSets() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
 
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getOS(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
 
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getOtherSeqIdTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms
Getter for the INSDseq term
getOuterMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
getOuterMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
getOuterPaint() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
Returns the paint properties of the outer line of this glyph.
getOutline() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
getOutline() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
getOutline() - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
getOutline returns the colour used to draw the lines.
getOutline() - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
getOutline returns the colour used to draw the lines.
getOutline() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
getOutline() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
 
getOutline() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
getOutline() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
 
getOutput() - Method in interface org.biojava.utils.process.InputHandler
Gets the output stream.
getOutput() - Method in class org.biojava.utils.process.ReaderInputHandler
Gets the output stream.
getOutput() - Method in class org.biojava.utils.process.StreamPipe
Gets the output stream.
getOutputFormat() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
Simply returns stream output format for the actual RemoteQBlastOutputProperties object
getOutputHandler() - Method in class org.biojava.utils.process.ExternalProcess
Gets the output handler which is responsible for the standard output of the external process.
getOutputOption(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
Method that returns any value associated to any key for this RemoteQBlastOutputProperties object.
getOutputOption(String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties
Method that returns the value associated with the key given in parameter.
getOutputOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
 
getOutputOptions() - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties
Method to get all keys to the information stored in this object.
getOutString() - Method in class org.biojava.utils.ExecRunner
Returns the output string if exec(String) was invoked.
getOverlay() - Method in class org.biojava.bio.OverlayAnnotation
Get the map used for the overlay.
getOverlayMap() - Method in class org.biojava.utils.OverlayMap
Return the object containing the overlay mappings.
getPacking(FiniteAlphabet, boolean) - Static method in class org.biojava.bio.symbol.PackingFactory
Get the default packing for an alphabet.
getPadding() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
Retrieve the current padding.
getPaint() - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
 
getPaint() - Method in class org.biojava.bio.gui.glyph.TurnGlyph
 
getPam10() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM10 amino acid substitution matrix.
getPam100() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM100 amino acid substitution matrix.
getPam110() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM110 amino acid substitution matrix.
getPam120() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM120 amino acid substitution matrix.
getPam130() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM130 amino acid substitution matrix.
getPam140() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM140 amino acid substitution matrix.
getPam150() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM150 amino acid substitution matrix.
getPam160() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM160 amino acid substitution matrix.
getPam170() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM170 amino acid substitution matrix.
getPam180() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM180 amino acid substitution matrix.
getPam190() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM190 amino acid substitution matrix.
getPam20() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM20 amino acid substitution matrix.
getPam200() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM200 amino acid substitution matrix.
getPam210() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM210 amino acid substitution matrix.
getPam220() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM220 amino acid substitution matrix.
getPam230() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM230 amino acid substitution matrix.
getPam240() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM240 amino acid substitution matrix.
getPam250() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM250 amino acid substitution matrix.
getPam260() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM260 amino acid substitution matrix.
getPam270() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM270 amino acid substitution matrix.
getPam280() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM280 amino acid substitution matrix.
getPam290() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM290 amino acid substitution matrix.
getPam30() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM30 amino acid substitution matrix.
getPam300() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM300 amino acid substitution matrix.
getPam310() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM310 amino acid substitution matrix.
getPam320() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM320 amino acid substitution matrix.
getPam330() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM330 amino acid substitution matrix.
getPam340() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM340 amino acid substitution matrix.
getPam350() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM350 amino acid substitution matrix.
getPam360() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM360 amino acid substitution matrix.
getPam370() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM370 amino acid substitution matrix.
getPam380() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM380 amino acid substitution matrix.
getPam390() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM390 amino acid substitution matrix.
getPam40() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM40 amino acid substitution matrix.
getPam400() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM400 amino acid substitution matrix.
getPam410() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM410 amino acid substitution matrix.
getPam420() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM420 amino acid substitution matrix.
getPam430() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM430 amino acid substitution matrix.
getPam440() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM440 amino acid substitution matrix.
getPam450() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM450 amino acid substitution matrix.
getPam460() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM460 amino acid substitution matrix.
getPam470() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM470 amino acid substitution matrix.
getPam480() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM480 amino acid substitution matrix.
getPam490() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM490 amino acid substitution matrix.
getPam50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM50 amino acid substitution matrix.
getPam500() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM500 amino acid substitution matrix.
getPam60() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM60 amino acid substitution matrix.
getPam70() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM70 amino acid substitution matrix.
getPam80() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM80 amino acid substitution matrix.
getPam90() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return the PAM90 amino acid substitution matrix.
getParameterType(int) - Method in interface org.biojava.utils.bytecode.CodeMethod
Get the type of the parameter at a given position
getParameterType(int) - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
 
getParent() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
Get the original sequenceDB from this annotated sequenceDB.
getParent() - Method in class org.biojava.bio.seq.db.SequenceDBWrapper
Return the parent SequenceDB.
getParent() - Method in interface org.biojava.bio.seq.Feature
Return the FeatureHolder to which this feature has been attached.
getParent() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getParent() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
getParent() - Method in class org.biojava.bio.seq.projection.ReparentContext
 
getParent() - Method in class org.biojava.bio.taxa.SimpleTaxon
Deprecated.
 
getParent() - Method in interface org.biojava.bio.taxa.Taxon
Deprecated.
The parent of this Taxon.
getParent() - Method in class org.biojava.bio.taxa.WeakTaxon
Deprecated.
 
getParent() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Return the FeatureHolder to which this feature has been attached.
getParent(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
 
getParent(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
getParentMap() - Method in class org.biojava.utils.OverlayMap
Return the object containing the fallback mappings.
getParentNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon
Returns the parent NCBI taxon ID, if known.
getParentNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Returns the parent NCBI taxon ID, if known.
getParents() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
Get a set of URIs for parent types.
getParser() - Method in class org.biojava.bio.program.tagvalue.ParserListener
getParser returns the parser of the pair.
getParser(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
getParserListener(TagValueListener) - Method in interface org.biojava.bio.annodb.IndexedAnnotationDB.ParserListenerFactory
Get the ParserListener for a TagValueListener.
getParserListener(TagValueListener) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
 
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Embl
 
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Enzyme
 
getParserListener(TagValueListener) - Method in interface org.biojava.bio.program.formats.Format
Retrieve a ParserListener pair for the format that will pass all events on to a listener.
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Compound
 
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
 
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Reaction
 
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Swissprot
 
getParserListenerFactory() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
Get the ParserListenerFactory used by this IndexedAnnotationDB.
getPartHandler(XFFFeatureSetHandler) - Method in interface org.biojava.bio.program.xff.XFFPartHandlerFactory
Return a suitable StAX content handler.
getPath() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
Get the list of SequenceRenderer instances that were passed through to produce this event
getPathEnd(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
getPathLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
getPathPrefix() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getPathPrefix returns the abstract path currently being appended to the raw sequence database filenames extracted from the binary index.
getPattern() - Method in class org.biojava.bio.program.tagvalue.RegexParser
Get the Pattern currently used to split lines.
getPattern() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
 
getPattern() - Method in class org.biojava.bio.search.MaxMismatchPattern
 
getPatterns(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getPatterns returns two Pattern objects for an enzyme, one matches the forward strand and one the reverse.
getPercentGapsQuery() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getPercentGapsTarget() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getPercentIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPair
get percentage identity.
getPercentIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
 
getPercentIdentityQuery() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getPercentIdentitySubject() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getPercentSimilarityQuery() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getPercentSimilaritySubject() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getPhase() - Method in interface org.biojava.bio.program.gff3.GFF3Record
 
getPhase() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
getPHDependence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property PHDependence.
getPhredAlphabet() - Static method in class org.biojava.bio.program.phred.PhredTools
Retrieves the PHRED alphabet from the AlphabetManager.
getPhredSymbol(Symbol, Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools
Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
getPI(SymbolList, boolean, boolean) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc
Computes isoelectric point of specified peptide.
getPlasmidTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the Plasmid term
getPopulation() - Method in interface org.biojavax.ga.GeneticAlgorithm
The registered Population
getPopulation() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
getPos() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
Get the offset within the sequence - the symbol index.
getPos() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
 
getPosition() - Method in interface org.biojava.bio.molbio.RestrictionSite
getPosition returns the common, forward strand cut site.
getPosition() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
 
getPosition1() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
getPosition2() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
getPositions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
getPosShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Retrieve the shape used to represent positive points.
getPredicate() - Method in interface org.biojava.ontology.Triple
Return a Term which defines the type of relationship between the subject and object terms.
getPredicate() - Method in class org.biojava.ontology.Triple.Impl
 
getPredicate() - Method in class org.biojavax.ontology.SimpleComparableTriple
Return a Term which defines the type of relationship between the subject and object terms.
getPrevious() - Method in class org.biojava.utils.ChangeEvent
Return the old value of a property being changed.
getPrimaryKey() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getPrimaryKey returns the primary identifier namespace.
getPrimaryKeyName() - Method in class org.biojava.bio.program.tagvalue.Index2Model
Retrieve the tag currently used as primary key.
getPrimaryKeyName() - Method in class org.biojava.bio.program.tagvalue.Indexer
Retrieve the tag currently used as primary key.
getPrintStream() - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
getPrintStream() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
getPrintStream() - Method in interface org.biojava.bio.seq.io.SeqFileFormer
Deprecated.
getPrintStream returns the PrintStream to which an instance will write the formatted data.
getPrintStream() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
getPrintStream returns the PrintStream to which an instance of SwissprotFileFormer will write the formatted data.
getPrintStream() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Gets the print stream currently being written to.
getPrintStream() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Gets the print stream currently being written to.
getProbabilityAlphabet() - Static method in class org.biojava.bio.program.scf.SCF
 
getProjectAccessionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
Getter for the ProjectAccession term
getProjectedFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
getProjectionContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
getProjectionContext() - Method in interface org.biojava.bio.seq.projection.Projection
 
getPropClass() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
getProperties() - Method in class org.biojava.bio.AbstractAnnotation
Implement this to return the Map delegate.
getProperties() - Method in class org.biojava.bio.AnnotationChanger
getProperties returns the mapped contents of the underlying Annotation as a Map.
getProperties() - Method in class org.biojava.bio.AnnotationRenamer
getProperties returns the mapped contents of the underlying Annotation as a Map.
getProperties() - Method in interface org.biojava.bio.AnnotationType
Retrieve the set of properties for which constraints have been explicity specified.
getProperties() - Method in class org.biojava.bio.AnnotationType.Impl
 
getProperties() - Method in class org.biojava.bio.BeanAsAnnotation
 
getProperties() - Method in class org.biojava.bio.seq.io.ReferenceAnnotation
Deprecated.
 
getProperties() - Method in class org.biojava.bio.SimpleAnnotation
Get the property value pairs in this annotation
getProperties() - Method in class org.biojava.bio.SmallAnnotation
 
getProperties(Object) - Method in class org.biojavax.EmptyRichAnnotation
Find all the Notes with any rank that match the key.
getProperties(Object) - Method in interface org.biojavax.RichAnnotation
Find all the Notes with any rank that match the key.
getProperties(Object) - Method in class org.biojavax.SimpleRichAnnotation
Deprecated. 
getProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
 
getProperty(Object) - Method in interface org.biojava.bio.Annotation
Retrieve the value of a property by key.
getProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
 
getProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
 
getProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation
Retrieve the value of a property by key.
getProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation
Deprecated. 
getProperty(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
 
getProperty(Annotation, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
 
getProperty(Annotation, Object) - Method in interface org.biojava.bio.AnnotationType
Get the Collection of values associated with an Annotation bundle according to the type we believe it to be.
getProperty(Annotation, String) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getProperty(Annotation, String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getProperty(Annotation, String) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
ThomasD made this a bit safer...
getProperty(Annotation, String) - Static method in class org.biojava.bio.seq.io.agave.UtilHelper
inhibit the getProperty(key) of Annotation from throw exception when key does not exist.
getPropertyAsBoolean(String) - Method in class org.biojava.utils.TypedProperties
Searches for the property with the specified key in this property list.
getPropertyAsDouble(String) - Method in class org.biojava.utils.TypedProperties
Searches for the property with the specified key in this property list.
getPropertyAsInteger(String) - Method in class org.biojava.utils.TypedProperties
Searches for the property with the specified key in this property list.
getPropertyAsLong(String) - Method in class org.biojava.utils.TypedProperties
Searches for the property with the specified key in this property list.
getPropertyAsStringList(String) - Method in class org.biojava.utils.TypedProperties
just like getPropertyAsStringList(String key, String delims) but uses ',' (comma), ';' (semicolon) and '\t' (tab) as the possible delimiters.
getPropertyAsStringList(String, String) - Method in class org.biojava.utils.TypedProperties
Searches for the property with the specified key in this property list.
getPropertyClass() - Method in class org.biojava.bio.PropertyConstraint.ByClass
Get the Class used as the constraint.
getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
Get the PropertyConstraint used to validate each property value.
getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains
Get the PropertyConstraint used to validate each property value.
getPropertyConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandler
 
getProps() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
getPropType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
getProteaseByName(String) - Static method in class org.biojava.bio.proteomics.Protease
Retrieves a reference to the named Protease.
getProteaseByName(String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
Gets a Protease instance by name.
getProteaseList() - Static method in class org.biojava.bio.proteomics.Protease
Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager.
getProteinExistsTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
Getter for the protein exists term
getProteinExistsTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the protein exists term
getProteinParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Creates a protein symbol tokenizer.
getProteinTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the protein type term
getPrototype() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
The prototype is a RestrictionEnzyme that represents a set of isoshizomers.
getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
Return the overall P-value of this hit.
getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
Return the P-value of this sub-hit.
getPValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getPValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getQcalls() - Method in class org.biojava.bio.program.abi.ABITrace
Returns an int[] array that represents the quality - each int in the array corresponds to an quality value 90-255) in the graph at a base location).
getQuality() - Method in class org.biojava.bio.program.fastq.Fastq
Return the quality scores for this FASTQ formatted sequence.
getQuality() - Method in class org.biojava.bio.program.phred.PhredSequence
Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.
getQuality() - Method in interface org.biojava.bio.program.phred.Qualitative
Retreives the list of quality symbols from the underlying object.
getQualityAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence
 
getQualityAt(int) - Method in interface org.biojava.bio.program.phred.Qualitative
Retreives the quality symbol for the specified index.
getQuery() - Method in class org.biojava.bio.alignment.AlignmentPair
Return the query sequence as a gapped sequence.
getQueryEnd() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getQueryEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
Return the end position of the last sub-hit in the query sequence.
getQueryEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
Return the end position of the sub-hit in the query sequence.
getQueryEnd() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getQueryEnd() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getQueryEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getQueryEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getQueryLength() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getQueryRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getQuerySeqHolder() - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
getQuerySeqHolder returns the database of query sequences used to retrieve sequences for creation of the various result objects.
getQuerySequence() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
Returns the query sequence which was used to perform the search.
getQuerySequence() - Method in class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
 
getQuerySequence() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
getQueryStart() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getQueryStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
Return the start position of the first sub-hit in the query sequence.
getQueryStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
Return the start position of the sub-hit in the query sequence.
getQueryStart() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getQueryStart() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getQueryStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getQueryStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getQueryStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
Return the strand of the hit with respect to the query sequence.
getQueryStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
Return the strand of the sub-hit with respect to the query sequence.
getQueryStrand() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getQueryStrand() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getQueryStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getQueryStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getRadius() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
Get the current radius at which data should be rendered.
getRadius() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
 
getRadius() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
 
getRange() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
getRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getRange returns a RangeLocation representing the region of the sequence currently being rendered.
getRange() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
getRange() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
getRange() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
getRange() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
The range of the SymbolList to render.
getRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getRange() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
getRange() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getRange returns a RangeLocation representing the region of the sequence currently being rendered.
getRanges() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
 
getRanges() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
 
getRanges() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
 
getRank() - Method in interface org.biojavax.bio.BioEntryRelationship
Returns the rank of this relationship.
getRank() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
 
getRank() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Retrieves the rank associated with this location.
getRank() - Method in interface org.biojavax.bio.seq.RichFeature
Returns the rank of this feature.
getRank() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
Gets the rank of this relationship.
getRank() - Method in interface org.biojavax.bio.seq.RichLocation
Retrieves the rank associated with this location.
getRank() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Returns the rank of this feature.
getRank() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Gets the rank of this relationship.
getRank() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Retrieves the rank associated with this location.
getRank() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
Returns the rank of this relationship.
getRank() - Method in interface org.biojavax.Comment
Returns the rank of this comment.
getRank() - Method in interface org.biojavax.Note
Gets the rank that defines this note.
getRank() - Method in interface org.biojavax.RankedCrossRef
Return the rank associated with the cross reference.
getRank() - Method in interface org.biojavax.RankedDocRef
The rank of this reference.
getRank() - Method in class org.biojavax.SimpleComment
Returns the rank of this comment.
getRank() - Method in class org.biojavax.SimpleNote
Gets the rank that defines this note.
getRank() - Method in class org.biojavax.SimpleRankedCrossRef
Return the rank associated with the cross reference.
getRank() - Method in class org.biojavax.SimpleRankedDocRef
The rank of this reference.
getRankedCrossRefs() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Returns the set of all ranked cross references associated with an object.
getRankedCrossRefs() - Method in class org.biojavax.bio.SimpleBioEntry
Returns the set of all ranked cross references associated with an object.
getRankedCrossRefs() - Method in class org.biojavax.ontology.SimpleComparableTerm
Returns the set of all ranked cross references associated with an object.
getRankedCrossRefs() - Method in interface org.biojavax.RankedCrossRefable
Returns the set of all ranked cross references associated with an object.
getRankedDocRefs() - Method in interface org.biojavax.bio.BioEntry
Returns a set of all bioentrydocrefs associated with this bioentry.
getRankedDocRefs() - Method in class org.biojavax.bio.SimpleBioEntry
Returns a set of all bioentrydocrefs associated with this bioentry.
getReader() - Method in class org.biojava.bio.program.tagvalue.Indexer
Retrieve the reader that can be safely used to index this file.
getReader() - Method in class org.biojava.bio.program.tagvalue.Indexer2
Retrieve the reader that can be safely used to index this file.
getReader() - Method in class org.biojava.utils.process.ReaderWriterPipe
Gets the reader.
getReadingFrame() - Method in interface org.biojava.bio.seq.FramedFeature
return the reading frame of the feature.
getReadingFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
 
getRealScientificName(Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
This returns the true scientific name of a given taxon, if there is one.
getRecognitionSequence(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getRecognitionSequence returns a string that describes the recognition site of this enzyme.
getRecognitionSite() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
getRecognitionSite returns the forward strand of the recognition site.
getRecordKey(Object[]) - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
getRecordKey returns the field from the record on which the records were sorted in the index.
getRecordKey(Object[]) - Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
getRecordKey returns the field from the record on which the records were sorted in the index.
getRecordList() - Method in class org.biojava.bio.program.indexdb.BioStore
getRecordList returns all the Records in the index.
getRecurse() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
getRecurse() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
getRecurse returns the recursion flag of the filter.
getRecurse() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Return whether features will be filtered recursively or not.
getRecursive() - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
 
getRedoxPotential() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property redoxPotential.
getRef() - Method in interface org.biojava.bio.program.homologene.OrthoPair
get reference to evidence for orthology.
getRef() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
 
getRegions() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
 
getRegions() - Method in interface org.biojava.bio.seq.RemoteFeature
Retrieve the list of Regions that locate this feature both localy and remotely.
getRegistryConfiguration() - Method in class org.biojava.directory.Registry
getRegistryConfiguration returns the configuration of the registry.
getRegistryPath() - Static method in class org.biojava.directory.SystemRegistry
Get the list of places that will be searched for registry files.
getRel() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
getRel() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
 
getRelAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the release annotated term
getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getRelatedAnnot(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getRelationships() - Method in interface org.biojavax.bio.BioEntry
Returns a set of all relationships associated with this bioentry.
getRelationships() - Method in class org.biojavax.bio.SimpleBioEntry
Returns a set of all relationships associated with this bioentry.
getRelCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the release created term
getRelUpdatedRecordVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
Getter for the RelUpdatedRecordVersion term
getRelUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the release updated term
getRemark() - Method in interface org.biojavax.DocRef
If remarks have been made about this document reference, this method will return them.
getRemark() - Method in class org.biojavax.SimpleDocRef
If remarks have been made about this document reference, this method will return them.
getRemoteBioEntry(CrossRef) - Method in class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
Given the CrossRef return the corresponding BioEntry
getRemoteBioEntry(CrossRef) - Method in interface org.biojavax.CrossReferenceResolver
Given the CrossRef return the corresponding BioEntry
getRemoteBioEntry(CrossRef) - Method in class org.biojavax.DummyCrossReferenceResolver
Given the CrossRef return the corresponding BioEntry
getRemoteFeature() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
 
getRemoteFeature() - Method in interface org.biojava.bio.seq.RemoteFeature
Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.
getRemoteSymbolList(CrossRef, Alphabet) - Method in class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
Given a cross reference, return the corresponding symbol list.
getRemoteSymbolList(CrossRef, Alphabet) - Method in interface org.biojavax.CrossReferenceResolver
Given a cross reference, return the corresponding symbol list.
getRemoteSymbolList(CrossRef, Alphabet) - Method in class org.biojavax.DummyCrossReferenceResolver
Given a cross reference, return the corresponding symbol list.
getRemoteTerm() - Method in interface org.biojava.ontology.RemoteTerm
Return the imported term
getRemoteTerm() - Method in class org.biojava.ontology.RemoteTerm.Impl
 
getRemoteTerms() - Method in interface org.biojava.ontology.OntologyOps
Get the set of all remote terms.
getRenderedWidth() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the width of the graphic as it will be rendered.
getRenderedWidth(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the width of the graphic as it would be rendered with the specified horizontal scale.
getRenderer() - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
 
getRenderer() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
 
getRenderer() - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 
getRenderer() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
getRenderer return the current renderer.
getRenderer() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getRenderer returns the current PairwiseSequenceRenderer.
getRenderer() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
getRenderer() - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
 
getRenderer() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getRenderer returns the current SequenceRenderer.
getRenderingHints() - Method in class org.biojava.bio.gui.DistributionLogo
 
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getRenderingHints returns the RenderingHints currently being used by the Graphics2D instances of delegate renderers.
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getRenderingHints returns the RenderingHints currently being used by the Graphics2D instances of delegate renderers.
getReplace() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Returns the current expenses of a single replace operation.
getReplace() - Method in class org.biojava.bio.alignment.SmithWaterman
 
getRepository(String) - Static method in class org.biojava.bio.seq.FeatureTypes
Fetch a repository by name.
getRepositoryNames() - Static method in class org.biojava.bio.seq.FeatureTypes
Find the names of all known repositories.
getResidue() - Method in interface org.biojava.bio.symbol.WobbleDistribution
returns the residue encoded by this WobbleDistribution
getResolver() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
 
getResolver() - Method in interface org.biojava.bio.seq.RemoteFeature
 
getResolver() - Method in class org.biojava.bio.symbol.FuzzyLocation
Retrieve the Location that this decorates.
getResolver() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getResultType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getRetrievalMode() - Method in class org.biojava.bio.seq.db.FetchURL
Get the retrieval mode
getRetrievalType() - Method in class org.biojava.bio.seq.db.FetchURL
Get the retrieval type
getReturnCode() - Method in exception org.biojava.utils.ProcessTimeoutException
Get the return code from the dying child process.
getReturnFormat() - Method in class org.biojava.bio.seq.db.FetchURL
 
getReturnType() - Method in interface org.biojava.utils.bytecode.CodeMethod
Get the return type
getReturnType() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
 
getReverseRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
getReverseRegex returns a regular expression which matches the reverse strand of the recognition site.
getReverter() - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
 
getReverter() - Method in class org.biojava.bio.seq.projection.ReparentContext
 
getReverter() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
getRevisionId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
Return the revision id of this identifier.
getRichAnnotation() - Method in class org.biojavax.bio.seq.CompoundRichLocation
Return the associated annotation object.
getRichAnnotation() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Return the associated annotation object.
getRichAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Return the associated annotation object.
getRichAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Return the associated annotation object.
getRichAnnotation() - Method in class org.biojavax.bio.SimpleBioEntry
Return the associated annotation object.
getRichAnnotation() - Method in interface org.biojavax.RichAnnotatable
Return the associated annotation object.
getRichAnnotation() - Method in class org.biojavax.SimpleCrossRef
Return the associated annotation object.
getRichLocation() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
 
getRichLocation() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
 
getRichSequence(String) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
getRichSequence(String) - Method in class org.biojavax.bio.db.HashRichSequenceDB
 
getRichSequence(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Given the appropriate Genbank ID, return the matching RichSequence object.
getRichSequence(String) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
Given the appropriate Genbank ID, return the matching RichSequence object.
getRichSequence(String) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
Retrieve a single RichSequence by its id.
getRichSequence(String, Namespace) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Given the appropriate Genbank ID, return the matching RichSequence object.
getRichSequence(String, Namespace) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
Given the appropriate Genbank ID, return the matching RichSequence object.
getRichSequenceIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
getRichSequenceIterator() - Method in interface org.biojavax.bio.db.RichSequenceDB
Returns a RichSequenceIterator over all sequences in the database.
getRichSequences(Set) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
getRichSequences(Set) - Method in class org.biojavax.bio.db.HashRichSequenceDB
 
getRichSequences(Set) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Retrieve rich sequences from a Genbank
getRichSequences(Set) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
Retrieve rich sequences from a Genbank
getRichSequences(Set) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
Retrieve multiple RichSequence by its id.
getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.HashRichSequenceDB
 
getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Retrieve rich sequences from a Genbank
getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
Retrieve rich sequences from a Genbank
getRichSequences(Set, RichSequenceDB) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
Retrieve multiple RichSequence into a specific sequence database.
getRightValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon
Gets the right value.
getRightValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Gets the right value.
getRNA() - Static method in class org.biojava.bio.seq.RNATools
Return the RNA alphabet.
getRNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Creates a RNA symbol tokenizer.
getRoot() - Method in class org.biojava.bio.symbol.SuffixTree
Return the node object which is the root of this suffix tree.
getRoot() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
getRoot() - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
Deprecated.
 
getRoot() - Method in interface org.biojava.bio.taxa.TaxonFactory
Deprecated.
Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.
getRoot() - Method in class org.biojava.bio.taxa.WeakTaxonFactory
Deprecated.
 
getRootType() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString
See if the tree is rooted.
getS() - Method in class org.biojava.bio.proteomics.StructureTools
 
getSBFactory() - Method in class org.biojava.bio.seq.db.BioIndex
 
getSBFactory() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
 
getSBFactory() - Method in interface org.biojava.bio.seq.db.IndexStore
Retrieve the SequenceBuilderFactory used to build Sequence instances.
getSBFactory() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
getScale() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
getScale() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getScale returns the scale in pixels per Symbol.
getScale() - Method in class org.biojava.bio.gui.sequence.SequencePanel
Retrieve the current scale.
getScale() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
getScale() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Retrieve the current scale.
getScale() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
Gets the scale as pixels per Symbol
getScale() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getScale() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
getScale() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getScale returns the scale in pixels per Symbol.
getScale(int) - Method in interface org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler
Retrieve the scaling factor at a given depth
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
 
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
 
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
 
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
 
getSchema() - Method in interface org.biojava.bio.annodb.AnnotationDB
Get an AnnotationType that accepts all Annotation instances in this DB.
getSchema() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
 
getSchema() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
 
getSchema() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
 
getSchema() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
 
getSchema() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
 
getSchema() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
getSchema() - Method in interface org.biojava.bio.seq.FeatureHolder
Return a schema-filter for this FeatureHolder.
getSchema() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
Get the schema for this type.
getSchema() - Method in class org.biojava.bio.seq.impl.DummySequence
 
getSchema() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
getSchema() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getSchema() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
getSchema() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
getSchema() - Method in class org.biojava.bio.seq.impl.SubSequence
 
getSchema() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
getSchema() - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
getSchema() - Method in class org.biojava.bio.seq.MergeFeatureHolder
 
getSchema() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
getSchema() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
getSchema() - Method in class org.biojava.bio.seq.SimpleAssembly
 
getSchema() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
 
getSchema() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Return a schema-filter for this FeatureHolder.
getSchema() - Method in class org.biojavax.bio.seq.ThinRichSequence
Return a schema-filter for this FeatureHolder.
getSchema(String) - Method in class org.biojava.naming.ObdaContext
 
getSchema(Name) - Method in class org.biojava.naming.ObdaContext
 
getSchema(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
getSchemaClassDefinition(String) - Method in class org.biojava.naming.ObdaContext
 
getSchemaClassDefinition(Name) - Method in class org.biojava.naming.ObdaContext
 
getScientificName() - Method in class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
getScientificName() - Method in interface org.biojava.bio.taxa.Taxon
Deprecated.
The scientific name of this taxon.
getScope() - Method in class org.biojava.ontology.Synonym
 
getScore() - Method in class org.biojava.bio.alignment.SimpleAlignment
 
getScore() - Method in interface org.biojava.bio.dp.DPMatrix
 
getScore() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
getScore() - Method in class org.biojava.bio.dp.SimpleStatePath
 
getScore() - Method in interface org.biojava.bio.dp.StatePath
Return the overall score for this state-path and it's emissions.
getScore() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
 
getScore() - Method in interface org.biojava.bio.program.gff.GFFRecord
The score of the feature.
getScore() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getScore() - Method in interface org.biojava.bio.program.gff3.GFF3Record
 
getScore() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
Return the overall score of this hit in the units defined by the search algorithm.
getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
Return the score of this sub-hit in the units defined by the search algorithm.
getScore() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getScore() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getScore() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
getScore returns the alignment score.
getScore() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
getScore returns the alignment score.
getScore() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
getSearchableDBs() - Method in interface org.biojava.bio.search.SeqSimilaritySearcher
Return a set of all databases that can be searched with this sequence similarity searcher.
getSearchContentHandler() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
getSearchContentHandler gets the handler which will recieve the method calls generated by the adapter.
getSearchContentHandler() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
getSearchContentHandler gets the handler which will receive the method calls generated by the adapter.
getSearchParameters() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
Returns the search parameters used in the search that produced this search result.
getSearchParameters() - Method in class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
 
getSearchParameters() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
getSearchProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
 
getSearchProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
 
getSecondaryDirection() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
getSecondaryDirection returns the direction in which the secondary sequence is rendered.
getSecondaryDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondaryDirection returns the direction in which this context expects the secondary sequence to be rendered - HORIZONTAL or VERTICAL.
getSecondaryDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getSecondaryFeatures() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
getSecondaryFeatures returns the features on the secondary sequence.
getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondaryFeatures returns all of the Features belonging to the currently rendered secondary Sequence.
getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getSecondaryRange() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
getSecondaryRange returns the range of the secondary sequence currently rendered.
getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondaryRange returns a RangeLocation representing the region of the secondary sequence currently being rendered.
getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getSecondarySequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondarySequence returns the entire secondary Sequence currently being rendered.
getSecondarySymbols() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
getSecondarySymbols returns the symbols of the secondary sequence.
getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondarySymbols returns all of the Symbols belonging to the currently rendered secondary Sequence.
getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getSecondarySymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondarySymbolTranslation returns the current translation in Symbols which will be applied when rendering.
getSecondIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Getter for property secondIntActID.
getSecondOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair
gets the first orthologue in the orthology relationship.
getSecondOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
 
getSelectionFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
 
getSelectionFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
getSeqCautions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property seqCautions.
getSeqDB() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
 
getSeqDBs() - Method in interface org.biojava.bio.seq.homol.HomologyDB
Retrieve the SeqDBs that have been searched against each other.
getSeqID() - Method in class org.biojava.bio.seq.RemoteFeature.Region
Return the remote Sequence ID if this Region is on another Sequence (isRemote will return true), null otherwise.
getSeqIDs() - Method in class org.biojava.bio.program.Meme
 
getSeqIOEvents(Sequence, SeqIOListener) - Method in class org.biojava.bio.seq.io.SeqIOEventEmitter
Deprecated.
getSeqIOEvents scans a Sequence object and sends events describing its data to the SeqIOListener.
getSeqName() - Method in interface org.biojava.bio.program.gff.GFFRecord
The sequence name field.
getSeqName() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
Retrieve the current sequence name.
getSeqName() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getSequence() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
 
getSequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSequence returns the entire Sequence currently being rendered.
getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
getSequence() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getSequence returns the entire Sequence currently being rendered.
getSequence() - Method in class org.biojava.bio.program.abi.ABITrace
Returns the original programatically determined (unedited) sequence as a SymbolList.
getSequence() - Method in class org.biojava.bio.program.fastq.Fastq
Return the sequence for this FASTQ formatted sequence.
getSequence() - Method in class org.biojava.bio.proteomics.Digest
 
getSequence() - Method in interface org.biojava.bio.seq.Feature
Return the Sequence object to which this feature is (ultimately) attached.
getSequence() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getSequence() - Method in class org.biojava.bio.seq.impl.SubSequence
Return the parent sequence of which this is a partial view
getSequence() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
getSequence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
getSequence() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Return the Sequence object to which this feature is (ultimately) attached.
getSequence(int) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
getSequence(String) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
getSequence(String) - Method in class org.biojava.bio.seq.db.CachingSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
 
getSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDBLite
Retrieve a single sequence by its id.
getSequence(String) - Method in class org.biojava.bio.seq.db.SubSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
getSequence(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
Get a Sequence object for an ID.
getSequence(String) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
 
getSequence(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
getSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
getSequence(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Get the sequence for a feature.
getSequence(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
getSequenceDB() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
Returns the sequence database against which the search was performed.
getSequenceDB() - Method in class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
 
getSequenceDB() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
getSequenceDB(String) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
 
getSequenceDB(String) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
Return the SequenceDB for the given identifier.
getSequenceDB(String) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
If the given identifier is known to this sequence db installation because it has been used in a call to addSequenceDB(), then this method returns the SequenceDB associated with this identifier.
getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
 
getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
Deprecated.
 
getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
 
getSequenceDB(Map) - Method in interface org.biojava.directory.SequenceDBProvider
Get a sequence database.
getSequenceDBs() - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
 
getSequenceDBs() - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
Return all sequence dbs available in this sequence db installation.
getSequenceDBs() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
Return a newly created set of the SequenceDB objects that were already created through method addSequenceDB().
getSequenceFormat() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getSequenceFormat returns the current sequence format name.
getSequenceFormat() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
 
getSequenceFormat() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
 
getSequenceFormat() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
 
getSequenceFormat() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
 
getSequenceFormat() - Method in class org.biojava.bio.seq.db.WebSequenceDB
 
getSequenceFormat(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
getSequenceFormat accepts a value which represents a sequence format and returns the relevant SequenceFormat object.
getSequenceId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getSequenceId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getSequenceID() - Method in interface org.biojava.bio.program.gff3.GFF3Record
 
getSequenceID() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
getSequenceLength() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
Return the sequence length.
getSequenceLength() - Method in interface org.biojava.bio.chromatogram.Chromatogram
Returns the number of bases called by whatever base-calling software analyzed the chromatogram as loaded.
getSequenceLength() - Method in class org.biojava.bio.program.abi.ABITrace
Returns the length of the sequence (number of bases) in this trace.
getSequenceLength() - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
Gets the sequenceLength attribute of the GAMESeqHandler object
getSequenceLength() - Method in class org.biojavax.bio.seq.SimpleRichSequence
 
getSequenceLength() - Method in class org.biojavax.bio.seq.ThinRichSequence
 
getSequenceName() - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
getSequenceName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
 
getSequenceOffset() - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
getSequenceRef() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Getter for property sequenceRef.
getSequences() - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
 
getSequences() - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
get all the top level sequences bio_sequence --> SimpleSequence contig --> SimpleAssembly --> SimpleSequence( if only one sequence ) chromosome -> SimpleAssembly -> SimpleSequence( if only one sequence)
getSequences(Set) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
Retrieve sequences from a Genbank
getSequences(Set, SequenceDB) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
Retrieve sequences from a Genbank
getSequenceType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Getter for property sequenceType.
getSeqVersion() - Method in interface org.biojavax.bio.seq.RichSequence
The version of the associated symbol list.
getSeqVersion() - Method in class org.biojavax.bio.seq.ThinRichSequence
The version of the associated symbol list.
getShape(int[], int[]) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils
 
getShape(List) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils
 
getShape(List, List) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils
 
getShatter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Determine if features with non-contiguous locations will be broken into multiple GFF records.
getShort() - Method in class org.biojava.utils.io.LargeBuffer
 
getShort(long) - Method in class org.biojava.utils.io.LargeBuffer
 
getSibling() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
getSibling returns the sibling Feature, query for subject and vice versa.
getSibling() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
getSibling returns the sibling feature of the pair.
getSignificantBits() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
Return the number of significant bits.
getSignificantBits() - Method in interface org.biojava.bio.chromatogram.Chromatogram
Returns the number of bits of the traces which are significant.
getSimilarity() - Method in interface org.biojava.bio.program.homologene.OrthoPair
gets the second orthologue in the orthology relationship.
getSimilarity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
 
getSize() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
 
getSize() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
Deprecated.
 
getSize() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
Gets the current size of the border in pixels.
getSleepTime() - Method in class org.biojava.utils.process.ExternalProcess
Gets the number of milliseconds the ExternalProcess.execute(Properties) method should pauses after the external process is terminated.
getSource() - Method in interface org.biojava.bio.program.gff.GFFRecord
The source, or creator of this feature.
getSource() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
Retrieve the current source.
getSource() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getSource() - Method in interface org.biojava.bio.program.gff3.GFF3Record
 
getSource() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
getSource() - Method in interface org.biojava.bio.seq.Feature
The source of the feature.
getSource() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
getSource() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getSource() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
getSource() - Method in class org.biojava.utils.ChangeForwarder
Retrieve the 'source' object for ChangeEvents fired by this forwarder.
getSource() - Method in class org.biojavax.bio.seq.SimpleRichFeature
The source of the feature.
getSourceAlphabet() - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
 
getSourceAlphabet() - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
 
getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
 
getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
 
getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable
 
getSourceAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable
The alphabet of Symbols that can be translated.
getSourceFile() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
Get the source file associated with this code class.
getSourceHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
 
getSourceSymbolList() - Method in interface org.biojava.bio.symbol.GappedSymbolList
Return the underlying (ungapped) SymbolList.
getSourceSymbolList() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
getSourceTerm() - Method in interface org.biojava.bio.seq.Feature
An ontology term defining the source of this feature.
getSourceTerm() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getSourceTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
 
getSourceTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeature
An ontology term defining the source of this feature.
getSourceTermName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
 
getSpacer() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Retrieve the current spacer value
getSpeciesForShortName(String) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
Converts short species names (like Hs) to long species names (like Homo Sapiens).
getSpeciesTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the Species term
getSplitOffset() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
Get the current offset at which lines are split.
getSplitter(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
Get the Splitter currently registered to handle a tag.
getStandardFillPaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle
 
getStandardOutlinePaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle
 
getStart() - Method in interface org.biojava.bio.program.gff.GFFRecord
The start of this feature within the source sequence.
getStart() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getStart() - Method in interface org.biojava.bio.program.gff3.GFF3Record
 
getStart() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
getStart() - Method in interface org.biojava.bio.seq.db.Index
Skipping this number of bytes through the file should put the file pointer to the first byte of the sequence.
getStart() - Method in class org.biojava.bio.seq.db.SimpleIndex
 
getStart() - Method in class org.biojava.bio.seq.impl.SubSequence
 
getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
getStart() - Method in class org.biojava.utils.automata.FiniteAutomaton
 
getStart() - Method in interface org.biojava.utils.automata.NfaBuilder
 
getStart() - Method in class org.biojava.utils.automata.NfaSubModel
 
getStart() - Method in interface org.biojava.utils.automata.StateMachineInstance
 
getStart() - Method in interface org.biojavax.bio.seq.Position
Returns the beginning of the range of bases this base could lie in.
getStart() - Method in class org.biojavax.bio.seq.SimplePosition
Returns the beginning of the range of bases this base could lie in.
getStart() - Method in interface org.biojavax.RankedDocRef
The start position in the sequence that this reference is referred to from.
getStart() - Method in class org.biojavax.SimpleRankedDocRef
The start position in the sequence that this reference is referred to from.
getStartLabel() - Method in class org.biojava.utils.bytecode.InstructionVector
 
getState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
getStateLabels(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getStates() - Method in class org.biojava.bio.dp.DP
 
getStatesFormat() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getStatusDateTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
Getter for the StatusDate term
getStatusTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
Getter for the Status term
getStAXContentHandler() - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
Return a StAXContentHandler which can deal with any FilterXML construct known to this class.
getStoreLocation() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getStoreLocation returns the directory of the bew index.
getStoreName() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getStoreName returns the name to be given to the new index.
getStrainTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the Strain term
getStrand() - Method in interface org.biojava.bio.program.gff.GFFRecord
The strand of the feature.
getStrand() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
 
getStrand() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getStrand() - Method in interface org.biojava.bio.program.gff3.GFF3Record
 
getStrand() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
getStrand() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
Retrieve the strand this matches.
getStrand() - Method in interface org.biojava.bio.seq.FramedFeature
 
getStrand() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
getStrand() - Method in interface org.biojava.bio.seq.StrandedFeature
Retrieve the strand that this feature lies upon.
getStrand() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
 
getStrand() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Retrieves the strand associated with this location.
getStrand() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
Retrieves the strand associated with this location.
getStrand() - Method in interface org.biojavax.bio.seq.RichLocation
Retrieves the strand associated with this location.
getStrand() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Retrieve the strand that this feature lies upon.
getStrand() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Retrieves the strand associated with this location.
getStrandedFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
 
getStrandedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the Strand term; legal values are "single", "double", and "mixed".
getStringSequence() - Method in class org.biojavax.bio.seq.SimpleRichSequence
 
getStructure() - Method in class org.biojava.bio.proteomics.StructureTools
 
getStyle() - Method in class org.biojava.bio.gui.DistributionLogo
Retrieve the current style.
getStyle() - Method in interface org.biojava.bio.gui.LogoContext
 
getStyle(String, String, String[]) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
Return the styles for the two aligned characters.
getStyle(String, String, String[]) - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
Returns the styles for the two aligned characters in the form of predefined font classes.
getSubAlphabet(double, double) - Static method in class org.biojava.bio.symbol.DoubleAlphabet
 
getSubAlphabet(int, int) - Static method in class org.biojava.bio.symbol.IntegerAlphabet
Construct a finite contiguous subset of the IntegerAlphabet.
getSubContext(PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
getSubContext creates a new context which has FeatureHolders filtered using the current filter.
getSubHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
 
getSubHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
 
getSubHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
Return all sub-hits for this sequence similarity search hit.
getSubHits() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getSubHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getSubject() - Method in class org.biojava.bio.alignment.AlignmentPair
Return the subject sequence as a gapped sequence.
getSubject() - Method in interface org.biojava.ontology.Triple
Return the subject term of this triple
getSubject() - Method in class org.biojava.ontology.Triple.Impl
 
getSubject() - Method in interface org.biojavax.bio.BioEntryRelationship
Returns the subject of this relationship (ie. the BioEntry which this relationship targets).
getSubject() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
Gets the feature that this relationship refers to.
getSubject() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Gets the feature that this relationship refers to.
getSubject() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
Returns the subject of this relationship (ie. the BioEntry which this relationship targets).
getSubject() - Method in class org.biojavax.ontology.SimpleComparableTriple
Return the subject term of this triple
getSubjectDBInstallation() - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
getSubjectDBInstallation returns the installation in which all the databases searched may be found.
getSubjectEnd() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getSubjectEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
Return the end position of the last sub-hit in the subject sequence.
getSubjectEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
Return the start position of the sub-hit in the subject sequence.
getSubjectEnd() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getSubjectEnd() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getSubjectEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getSubjectEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getSubjectID() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
The sequence identifier of this hit within the sequence database against which the search was performed.
getSubjectID() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getSubjectID() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getSubjectLength() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getSubjectStart() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getSubjectStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
Return the start position of the first sub-hit in the subject sequence.
getSubjectStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
Return the start position of the sub-hit in the subject sequence.
getSubjectStart() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getSubjectStart() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getSubjectStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getSubjectStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getSubjectStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
Return the strand of the sub-hit with respect to the subject sequence.
getSubjectStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
Return the strand of the sub-hit with respect to the subject sequence.
getSubjectStrand() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
getSubjectStrand() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
getSubjectStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getSubjectStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getSubMatrix() - Method in class org.biojava.bio.alignment.SmithWaterman
 
getSubmitterAccessionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
Getter for the SubmitterAccession term
getSubmitterVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
Getter for the SubmitterVersion term
getSubmitterWgsVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
Getter for the SubmitterWgsVersion term
getSubSeqStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
getSubstitutionMatrix() - Method in class org.biojava.bio.alignment.AlignmentPair
 
getSubstitutionMatrix(BufferedReader) - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
This constructor can be used to guess the alphabet of this substitution matrix.
getSubstitutionMatrix(FiniteAlphabet, BufferedReader) - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return a new substitution matrix with the specified alphabet.
getSubstitutionMatrix(FiniteAlphabet, BufferedReader, String) - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
Return a new substitution matrix with the specified alphabet and name.
getSuperClass() - Method in interface org.biojava.utils.bytecode.CodeClass
 
getSuperClass() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
getSuperClass() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
getSuppliers(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getSuppliers returns a string describing the suppliers of this enzyme according to REBASE encoding for commercial sources or an empty String if the enzyme is not commecially available.
getSupportedCriteria() - Method in interface org.biojava.bibliography.BibRefSupport
It returns all supported searching and sorting criteria for the whole bibliographic repository.
getSupportedCriteria(String) - Method in interface org.biojava.bibliography.BibRefSupport
It returns all supported searching and sorting criteria in the given repository subset.
getSupportedValues(String, String) - Method in interface org.biojava.bibliography.BibRefSupport
It returns a controlled vocabulary containing all possible values of the attribute given in attrName in the context given in resourceType.
getSwissprotBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Get a default SequenceBuilderFactory for handling Swissprot files.
getSymbol() - Method in exception org.biojava.bio.symbol.IllegalSymbolException
Retrieve the symbol that caused this exception, or null.
getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet
Retrieve the Symbol for a double.
getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
getSymbol(double, double) - Method in class org.biojava.bio.symbol.DoubleAlphabet
Retrieve the symbol for a range of doubles.
getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet
Retrieve the Symbol for an int.
getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
getSymbol(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
getSymbol(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
getSymbol(List) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
Gets the compound symbol composed of the Symbols in the List.
getSymbol(List<Symbol>) - Method in interface org.biojava.bio.symbol.Alphabet
Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
getSymbolArray() - Method in class org.biojava.bio.symbol.SimpleSymbolList
Return the Java Symbol[] array that backs this object.
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
getSymbolList() - Method in interface org.biojava.bio.alignment.AlignmentElement
 
getSymbolList() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
 
getSymbolParser() - Method in class org.biojava.bio.seq.db.BioIndex
 
getSymbolParser() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
 
getSymbolParser() - Method in interface org.biojava.bio.seq.db.IndexStore
Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
getSymbolParser() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
getSymbolPropertyTable(String) - Static method in class org.biojava.bio.seq.ProteinTools
 
getSymbols() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getSymbols() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
The SymbolList that is currently rendered by this context.
getSymbols() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
getSymbols() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSymbols returns all of the Symbols belonging to the currently rendered Sequence.
getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePanel
Retrieve the currently rendered SymbolList
getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Retrieve the currently rendered SymbolList
getSymbols() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
The SymbolList that is currently rendered by this SequenceRenderContext.
getSymbols() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
 
getSymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getSymbols() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
getSymbols() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getSymbols returns all of the Symbols belonging to the currently rendered Sequence.
getSymbols() - Method in interface org.biojava.bio.seq.Feature
Return a list of symbols that are contained in this feature.
getSymbols() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getSymbols() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
getSymbols() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
getSymbols() - Method in interface org.biojava.bio.seq.StrandedFeature
Return a list of symbols that are contained in this feature.
getSymbols() - Method in interface org.biojava.bio.symbol.BasisSymbol
The list of symbols that this symbol is composed from.
getSymbols() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
 
getSymbols() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
getSymbols() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
 
getSymbols() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
getSymbols() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
getSymbols() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Return a list of symbols that are contained in this feature.
getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSymbolTranslation returns the current translation in Symbols which will be applied when rendering.
getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getSymbolTranslation returns the current translation in Symbols which will be applied when rendering.
getSyms() - Method in class org.biojava.bio.symbol.PackedSymbolList
Return the long array within which the symbols are bit-packed.
getSynonyms() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
getSynonyms() - Method in class org.biojava.ontology.OntologyTerm.Impl
 
getSynonyms() - Method in class org.biojava.ontology.RemoteTerm.Impl
 
getSynonyms() - Method in interface org.biojava.ontology.Term
Return the synonyms for this term.
getSynonyms() - Method in class org.biojava.ontology.Term.Impl
 
getSynonyms() - Method in class org.biojava.ontology.Triple.Impl
 
getSynonyms() - Method in class org.biojavax.ontology.SimpleComparableTerm
Return the synonyms for this term.
getSynonyms() - Method in class org.biojavax.ontology.SimpleComparableTriple
Return the synonyms for this term.
getT() - Method in class org.biojava.bio.molbio.DNAComposition
Get the relative compositon of 'T'.
getT() - Method in class org.biojava.bio.proteomics.StructureTools
 
getTable() - Method in class org.biojava.bio.dist.TranslatedDistribution
Retrieve the translation table encapsulating the map from this emission spectrum to the underlying one.
getTableNumber() - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
 
getTag() - Method in class org.biojava.bio.program.tagvalue.TagValue
 
getTagGroup() - Method in class org.biojava.bio.program.tagvalue.RegexParser
Get the group number that matches the tag.
getTags() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
getTags() - Method in class org.biojava.bio.program.tagvalue.TagDropper
Get the complete set of tags that are currently recognized.
getTAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools
Gets the protein alphabet including the translation termination symbols
getTarget() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
Get the Object that was the target of the mouse gesture or null if the mouse is not gesturing over any recognizable rendered object.
getTarget(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
getTarget(Object) - Method in interface org.biojava.stats.svm.SVMTarget
 
getTargetAlphabet() - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
 
getTargetAlphabet() - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
 
getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
 
getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
 
getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable
 
getTargetAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable
The alphabet of Symbols that will be produced.
getTargetOntology() - Method in class org.biojava.ontology.OntologyTerm.Impl
 
getTaxa() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
get the taxa represented in this group
getTaxa() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
getTaxLabels() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Get the TAXLABEL values added so far.
getTaxLabels() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Get the TAXLABEL values added so far.
getTaxLabels() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Get the TAXLABEL values added so far.
getTaxon() - Method in interface org.biojava.bio.program.homologene.Orthologue
return the Taxon associated with this orthologue
getTaxon() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
 
getTaxon() - Method in interface org.biojavax.bio.BioEntry
Gets the taxon associated with this bioentry.
getTaxon() - Method in class org.biojavax.bio.SimpleBioEntry
Gets the taxon associated with this bioentry.
getTaxon(int) - Static method in class org.biojava.bio.program.homologene.HomologeneTools
get the Taxon corresponding to this Taxon ID
getTaxon(Connection, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Attempts to get a Taxon object corresponding to the specified NCBI taxon ID.
getTaxon(Connection, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Attempts to get a Taxon object corresponding to the specified name.
getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getTaxonId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getTaxonID() - Method in interface org.biojava.bio.program.homologene.Orthologue
a convenience method to return the TaxonID for thsi orhtologue.
getTaxonID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
 
getTaxonID() - Method in interface org.biojava.bio.program.homologene.Taxon
returns the taxon ID
getTaxonID() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
 
getTempBuffer() - Method in class org.biojava.ontology.obo.OboFileParser
 
getTemperatureDependence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property temperatureDependence.
getTerm() - Method in interface org.biojavax.bio.BioEntryRelationship
Returns the term describing the relationship.
getTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
 
getTerm() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Retrieves the term associated with this location.
getTerm() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
Gets the term that describes this relationship.
getTerm() - Method in interface org.biojavax.bio.seq.RichLocation
Retrieves the term associated with this location.
getTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Gets the term that describes this relationship.
getTerm() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Retrieves the term associated with this location.
getTerm() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
Returns the term describing the relationship.
getTerm() - Method in interface org.biojavax.Note
Gets the term that defines this note.
getTerm() - Method in class org.biojavax.SimpleNote
Gets the term that defines this note.
getTerm(String) - Method in class org.biojava.ontology.IntegerOntology
 
getTerm(String) - Method in interface org.biojava.ontology.Ontology
Fetch the term with the specified name.
getTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
 
getTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
Fetch the term with the specified name.
getTermMass() - Method in class org.biojava.bio.proteomics.MassCalc
getTermMass returns the terminal mass being used by the instance methods.
getTerms() - Method in class org.biojava.ontology.IntegerOntology
 
getTerms() - Method in interface org.biojava.ontology.Ontology
Return all the terms in this ontology
getTerms() - Method in class org.biojava.ontology.Ontology.Impl
 
getTerms() - Method in class org.biojavax.ontology.SimpleComparableOntology
Return all the terms in this ontology
getTermSet() - Method in interface org.biojavax.ontology.ComparableOntology
Returns the set of terms in this ontology.
getTermSet() - Method in class org.biojavax.ontology.SimpleComparableOntology
Returns the set of terms in this ontology.
getTestClass() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
getText() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property text.
getTextColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
Get the color of the label text
getThis() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
Gets the This attribute of the GeneratedCodeMethod object
getThreshold() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
getThreshold() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
getThreshold() - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getThrownExceptions() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
Gets the ThrownExceptions attribute of the GeneratedCodeMethod object
getTickDirection() - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
getTissueTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the Tissue term
getTitle() - Method in interface org.biojava.bio.program.homologene.Orthologue
return the title used by Genbank for this protein
getTitle() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
 
getTitle() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
The cluster title.
getTitle() - Method in interface org.biojavax.DocRef
Returns the title of the document reference.
getTitle() - Method in class org.biojavax.SimpleDocRef
Returns the title of the document reference.
getTo() - Method in exception org.biojava.bio.dp.IllegalTransitionException
 
getToken() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getToken() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
Returns the token for strandedness.
getTokenization(String) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
getTokenization(String) - Method in interface org.biojava.bio.symbol.Alphabet
Get a SymbolTokenization by name.
getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet
Creates a new parser (Mark Schreiber 3 May 2001).
getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
getTokenization(String) - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
getTokenization(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
 
getTokenTable() - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
getTokenType() - Method in class org.biojava.bio.seq.io.AlternateTokenization
Tokens have fixed size.
getTokenType() - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
getTokenType() - Method in interface org.biojava.bio.seq.io.SymbolTokenization
Determine the style of tokenization represented by this object.
getTokenType() - Method in class org.biojava.bio.seq.io.WordTokenization
 
getTokenType() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
 
getTool() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService
Get the tool identifier for QBlast.
getTool() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Get the tool identifier for Entrez.
getTopNode() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Returns the top node of the previously requested graph.
getTotalDepth() - Method in class org.biojava.bio.gui.sequence.LineInfo
 
getTotalWeight() - Method in class org.biojavax.ga.util.WeightedSet
The total weight that has been added to this Set.
getTrace() - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
getTrace(AtomicSymbol) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
 
getTrace(AtomicSymbol) - Method in interface org.biojava.bio.chromatogram.Chromatogram
Returns an array containing the intensities of the sampled waveform representing the chromatogram trace for base nucleotide.
getTrace(AtomicSymbol) - Method in class org.biojava.bio.program.abi.ABITrace
Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point.
getTraceLength() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
 
getTraceLength() - Method in interface org.biojava.bio.chromatogram.Chromatogram
Returns the length of the trace of the Chromatogram.
getTraceLength() - Method in class org.biojava.bio.program.abi.ABITrace
Returns the length of the trace (number of x-coordinate points in the graph).
getTraceOffset(Chromatogram, int) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
Get a specific value from the trace offset sequence in the given chromatogram and extract its int value.
getTraceOffsetArray(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
Converts the peak offsets list of the given chromatogram into a new int array.
getTraceOffsets(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
Get the peak offsets for the called bases of a chromatogram.
getTrackLayout() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
getTrailer() - Method in class org.biojava.utils.ListTools.SeriesList
 
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getTrailingBorder returns the trailing border of the primary sequence.
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel
Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.
getTrailingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
Gets the TrailingBorder attribute of the SequenceRenderContext object.
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getTrailingBorder returns the trailing border.
getTrailingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
getTrainer(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Return the Distribution trainer object from the current context.
getTrainer(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
getTransform() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns a new AffineTransform describing the transformation from chromatogram coordinates to output coordinates.
getTransformAndConcat(AffineTransform) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Concatenates the chromatogram-to-output transform to the provided given AffineTransform.
getTransformer() - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
 
getTransformer() - Method in class org.biojava.bio.seq.projection.ReparentContext
 
getTransformer() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
getTransitions() - Method in class org.biojava.utils.automata.FiniteAutomaton
retrieve Set of all transitions in instance.
getTransitions() - Method in interface org.biojava.utils.automata.NfaBuilder
 
getTransitions() - Method in class org.biojava.utils.automata.NfaSubModel
 
getTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
retrieve the TransitionTable for this State.
getTranslation() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
getTranslations() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Get the translations added so far.
getTransposonTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
Getter for the Transposon term
getTree(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Returns a tree for given label
getTreeAsWeightedJGraphT(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Get given (NewickString) tree by label, converts it to weighted graph (JGraphT).
getTrees() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Returns all trees.
getTreeString() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString
Get the Newick string describing the tree.
getTreeText(UndirectedGraph<String, DefaultEdge>, String, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
 
getTreeText(WeightedGraph<String, DefaultWeightedEdge>, String, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
 
getTrimTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
See if tag trimming is enabled.
getTrimTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser
See if trimming of tags is enabled.
getTrimValue() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
See if value trimming is enabled.
getTrimValue() - Method in class org.biojava.bio.program.tagvalue.RegexParser
See if trimming of values is enabled.
getTriples(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology
 
getTriples(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology
Return all triples from this ontology which match the supplied pattern.
getTriples(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl
 
getTriples(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
Return all triples from this ontology which match the supplied pattern.
getTripleSet() - Method in interface org.biojavax.ontology.ComparableOntology
Returns the set of triples in this ontology.
getTripleSet() - Method in class org.biojavax.ontology.SimpleComparableOntology
Returns the set of triples in this ontology.
getTrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
getType() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
getType returns the type of hotspot.
getType() - Method in class org.biojava.bio.program.formats.Embl
 
getType() - Method in class org.biojava.bio.program.formats.Enzyme
 
getType() - Method in interface org.biojava.bio.program.formats.Format
Get the AnnotationType that constrains the events that will be fired.
getType() - Method in class org.biojava.bio.program.formats.Ligand.Compound
 
getType() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
 
getType() - Method in class org.biojava.bio.program.formats.Ligand.Reaction
 
getType() - Method in class org.biojava.bio.program.formats.Swissprot
 
getType() - Method in interface org.biojava.bio.program.gff3.GFF3Record
 
getType() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
getType() - Method in interface org.biojava.bio.seq.Feature
The type of the feature.
getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
getType() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getType() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
 
getType() - Method in class org.biojava.utils.bytecode.CodeField
Get the type of the field.
getType() - Method in class org.biojava.utils.bytecode.LocalVariable
 
getType() - Method in interface org.biojava.utils.bytecode.ParametricCodeGenerator
 
getType() - Method in class org.biojava.utils.ChangeEvent
Find the type of this event.
getType() - Method in class org.biojava.utils.ChangeForwarder.Retyper
 
getType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
Getter for property type.
getType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
getType() - Method in interface org.biojavax.bio.seq.Position
Returns the type of this position if it is not a point/single position.
getType() - Method in class org.biojavax.bio.seq.SimplePosition
Returns the type of this position if it is not a point/single position.
getType() - Method in class org.biojavax.bio.seq.SimpleRichFeature
The type of the feature.
getType(String) - Static method in class org.biojava.bio.seq.FeatureTypes
Get a Type by URI.
getType(String) - Method in interface org.biojava.bio.seq.FeatureTypes.Repository
Find the type for a name.
getType(String) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
 
getType1() - Method in interface org.biojava.utils.bytecode.PParametricCodeGenerator
 
getType2() - Method in interface org.biojava.utils.bytecode.PParametricCodeGenerator
 
getTypeClass() - Method in class org.biojava.utils.walker.WalkerFactory
 
getTypeHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
 
getTypes() - Method in interface org.biojava.bio.seq.FeatureTypes.Repository
Get a set of all type names defined in this repository.
getTypes() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
 
getTypeTerm() - Method in interface org.biojava.bio.seq.Feature
An ontology term defining the type of feature.
getTypeTerm() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
getTypeTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
 
getTypeTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeature
An ontology term defining the type of feature.
getTypeTermName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
 
getUngappedLocation() - Method in interface org.biojava.bio.symbol.GappedSymbolList
Get a Location that contains exactly those positions that are not gaps.
getUngappedLocation() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
getUniProtDBNameTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
Getter for the UniProt combined database term
getUniprotKWOnto() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the private uniprot ontology.
getUniProtTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
Getter for the UniProt term
getUniProtXMLTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Getter for the UniProtXML term
getUnique() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
The unique sequence that is used as a representative for this cluster.
getUnits() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
getUnprojectedFeatures() - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Get the features before projection.
getUnprojectedFeatures() - Method in class org.biojava.bio.seq.projection.ReparentContext
 
getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getUpdateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getUpstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
getUpstreamCut returns the cut site upstream of the recognition site.
getUpstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
getUpstreamEndType returns the double-stranded end type produced by the secondary (upstream) cut.
getUri() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property uri.
getURI() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
Get the URI for this type.
getURI() - Method in interface org.biojavax.Namespace
If the namespace has a URI, this will return it.
getURI() - Method in class org.biojavax.SimpleNamespace
If the namespace has a URI, this will return it.
getURL() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
getURL returns the hotspot URL.
getURN() - Method in class org.biojava.bio.seq.impl.DummySequence
 
getURN() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
getURN() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
getURN() - Method in class org.biojava.bio.seq.impl.SubSequence
 
getURN() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
getURN() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
getURN() - Method in interface org.biojava.bio.seq.Sequence
A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.
getURN() - Method in class org.biojava.bio.seq.SimpleAssembly
 
getURN() - Method in class org.biojavax.bio.seq.ThinRichSequence
A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.
getUserObject() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
getUserObject returns the current user object (or null).
getValue() - Method in class org.biojava.bio.program.tagvalue.TagValue
 
getValue() - Method in class org.biojava.bio.PropertyConstraint.ExactValue
Get the value that all properties must match.
getValue() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains
 
getValue() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation
 
getValue() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
getValue() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
Returns the integer label for strandedness.
getValue() - Method in interface org.biojava.stats.svm.ItemValue
 
getValue() - Method in class org.biojava.stats.svm.SimpleItemValue
 
getValue() - Method in interface org.biojava.utils.walker.Walker
If the visitor has a return value, then the result of applying the visitor to the tree can be obtained using this method, otherwise the result will be null.
getValue() - Method in interface org.biojavax.Note
Gets the value that defines this note.
getValue() - Method in class org.biojavax.SimpleNote
Gets the value that defines this note.
getValue() - Method in class org.biojavax.utils.CRC64Checksum
 
getValueAt(Symbol, Symbol) - Method in class org.biojava.bio.alignment.SubstitutionMatrix
There are some substitution matrices containing more columns than lines.
getValueAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector
Retrieve the value at a specific index.
getValueGroup() - Method in class org.biojava.bio.program.tagvalue.RegexParser
Get the group number that matches the value.
getValues() - Method in class org.biojava.bio.PropertyConstraint.Enumeration
getValues returns the set of values which constrain the property.
getVariable(int) - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
Gets the Variable attribute of the GeneratedCodeMethod object.
getVariable(String) - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
Gets the Variable attribute of the GenerateCodeMethod object by name.
getVariableMasses(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc
Get all masses including the variable mass.
getVariant() - Method in class org.biojava.bio.program.fastq.Fastq
Return the FASTQ sequence format variant for this FASTQ formatted sequence.
getVariant() - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
 
getVariant() - Method in class org.biojava.bio.program.fastq.SangerFastqReader
 
getVariant() - Method in class org.biojava.bio.program.fastq.SolexaFastqReader
 
getVector() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
getVector(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getVectorNTISupport() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
Is VectorNTI compatable output being produced?
getVersion() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
getVersion() - Method in interface org.biojava.utils.candy.CandyVocabulary
It returns a vesrion of this vocabulary.
getVersion() - Method in interface org.biojavax.bio.BioEntry
Gets the version of this bioentry.
getVersion() - Method in class org.biojavax.bio.SimpleBioEntry
Gets the version of this bioentry.
getVersion() - Method in interface org.biojavax.CrossRef
Returns the version of the object that the crossref refers to.
getVersion() - Method in class org.biojavax.SimpleCrossRef
Returns the version of the object that the crossref refers to.
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getVersion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
 
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
getVersionLineTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
Getter for the Ensembl-specific 'versionLine' term
getVerticalScale() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the in use vertical scale factor.
getViewedFeature() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
getViewedFeature() - Method in interface org.biojava.bio.seq.projection.Projection
 
getVisibleRange() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
getVisibleRange(SequenceRenderContext, Graphics2D) - Static method in class org.biojava.bio.gui.sequence.GUITools
 
getVisibleSecondarySymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getVisibleSecondarySymbolCount returns the maximum number of secondary Symbols which can be rendered in the visible area (excluding all borders) of the PairwiseSequencePanel at the current scale.
getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the PairwiseSequencePanel at the current scale.
getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the TranslatedSequencePanel at the current scale.
getVMaxes() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Getter for property VMaxes.
getVocabularyByName(String) - Method in interface org.biojava.utils.candy.CandyFinder
It returns a selected vocabulary.
getVocabularyFinder() - Method in interface org.biojava.bibliography.BibRefSupport
It returns an object representing a central place where all controlled vocabularies can be received from and shared by all users.
getWalker(Visitor) - Method in class org.biojava.utils.walker.WalkerFactory
Get a Walker that is customosed to a particular visitor.
getWeight(Object) - Method in class org.biojavax.ga.util.WeightedSet
Determines the normalized weight for o
getWeight(Symbol) - Method in class org.biojava.bio.dist.AbstractDistribution
Retrieve the weight for this distribution.
getWeight(Symbol) - Method in interface org.biojava.bio.dist.Distribution
Return the probability that Symbol s is emitted by this spectrum.
getWeight(Symbol) - Method in class org.biojava.bio.dist.GapDistribution
 
getWeight(Symbol) - Method in class org.biojava.bio.dist.PairDistribution
 
getWeight(Symbol) - Method in class org.biojava.bio.dist.TranslatedDistribution
 
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.AbstractDistribution
Override this method to implement getting the weight for an atomic symbol.
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution
 
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.UniformDistribution
 
getWeightMatrixID() - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
Get the value of the weight matrix id.
getWeights() - Method in class org.biojava.bio.dist.SimpleDistribution
Get the underlying array that stores the weights.
getWeights(State) - Method in interface org.biojava.bio.dp.MarkovModel
Get a probability Distribution over the transition from 'source'.
getWeights(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
getWeights(State) - Method in class org.biojava.bio.dp.WMAsMM
 
getWidth() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns the width of the whole graphic (in pixels).
getWidth() - Method in class org.biojava.bio.seq.io.AlternateTokenization
Get the width of the tokens.
getWidth() - Method in class org.biojava.stats.svm.RadialBaseKernel
 
getWobbleDistributionForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref
returns a WobbleDistribution for a specified residue.
getWobbleDistributionForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref
 
getWobbleFrequency(Symbol) - Method in interface org.biojava.bio.symbol.WobbleDistribution
returns the frequency of a specific wobble base in a set of synonymous codons that start with the same two bases.
getWorkingDirectory() - Method in class org.biojava.utils.process.ExternalProcess
Gets the working directory for the external process.
getWrap() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
getWrap() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
 
getWrap() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
 
getWrap() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
 
getWrapIncrement() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
 
getWrapIncrement() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
 
getWrapIncrement() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
 
getWrapped() - Method in class org.biojava.bio.AnnotationChanger
getWrapped returns the Annotation being remapped.
getWrapped() - Method in class org.biojava.bio.AnnotationRenamer
getWrapped returns the Annotation being remapped.
getWrapped() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
getWrappedKernel() - Method in class org.biojava.stats.svm.SigmoidKernel
 
getWriter() - Method in class org.biojava.utils.process.ReaderWriterPipe
Gets the writer.
getXFFEnvironment() - Method in class org.biojava.bio.program.xff.FeatureHandler
Return the XFF processing environment passed in when this handler was created.
getXrefDb() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
 
getXrefProps() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
 
getXrefs() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
return a set of AGAVEXref
getXrefs(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
 
getXrefs(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
getXrefs(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
GFF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
GFF indicates that the sequence format is GFF.
GFF3DocumentHandler - Interface in org.biojava.bio.program.gff3
The interface for things that listen to GFF event streams.
GFF3Parser - Class in org.biojava.bio.program.gff3
Parse a stream of GFF text into a stream of records and comments.
GFF3Parser() - Constructor for class org.biojava.bio.program.gff3.GFF3Parser
 
GFF3Record - Interface in org.biojava.bio.program.gff3
A record in a GFF3 formatted file.
GFF3Record.Impl - Class in org.biojava.bio.program.gff3
 
GFFDataSource - Class in org.biojava.bio.seq.distributed
Use a GFFEntrySet as a DataSource for adding annotation to sequences.
GFFDataSource(GFFEntrySet) - Constructor for class org.biojava.bio.seq.distributed.GFFDataSource
 
GFFDocumentHandler - Interface in org.biojava.bio.program.gff
The interface for things that listen to GFF event streams.
GFFEntrySet - Class in org.biojava.bio.program.gff
A set of entries and comments as a representation of a GFF file.
GFFEntrySet() - Constructor for class org.biojava.bio.program.gff.GFFEntrySet
Make an empty GFFEntrySet.
GFFErrorHandler - Interface in org.biojava.bio.program.gff
Interface which captures any errors which occur when parsing a GFF stream.
GFFErrorHandler.AbortErrorHandler - Class in org.biojava.bio.program.gff
 
GFFErrorHandler.SkipRecordErrorHandler - Class in org.biojava.bio.program.gff
 
GFFFilterer - Class in org.biojava.bio.program.gff
An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others.
GFFFilterer(GFFDocumentHandler, GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFFilterer
Create a new GFFFilterer that will forward to handler everything that filter accepts.
gffFromSeqDB(SequenceDB) - Static method in class org.biojava.bio.program.gff.GFFTools
Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.
gffFromSequence(Sequence) - Static method in class org.biojava.bio.program.gff.GFFTools
Creates a GFFEntrySet containing one entry for each feature on a sequence.
GFFParser - Class in org.biojava.bio.program.gff
Parse a stream of GFF text into a stream of records and comments.
GFFParser() - Constructor for class org.biojava.bio.program.gff.GFFParser
 
GFFRecord - Interface in org.biojava.bio.program.gff
A single GFF record.
GFFRecordFilter - Interface in org.biojava.bio.program.gff
A filter that will accept or reject a GFFEntry.
GFFRecordFilter.AcceptAll - Class in org.biojava.bio.program.gff
Implementation of GFFRecordFilter that accepts everything.
GFFRecordFilter.FeatureFilter - Class in org.biojava.bio.program.gff
Implementation of GFFRecordFilter that accepts records based upon the feature field.
GFFRecordFilter.FrameFilter - Class in org.biojava.bio.program.gff
 
GFFRecordFilter.NotFilter - Class in org.biojava.bio.program.gff
 
GFFRecordFilter.SequenceFilter - Class in org.biojava.bio.program.gff
Implementation of GFFRecordFilter that accepts records based upon the sequence name.
GFFRecordFilter.SourceFilter - Class in org.biojava.bio.program.gff
Implementation of GFFRecordFilter that accepts records based upon the source field.
GFFRecordFilter.StrandFilter - Class in org.biojava.bio.program.gff
 
GFFTools - Class in org.biojava.bio.program.gff
 
GFFTools() - Constructor for class org.biojava.bio.program.gff.GFFTools
 
GFFWriter - Class in org.biojava.bio.program.gff
Listens to a stream of GFF events and writes the lines to a PrintWriter.
GFFWriter(PrintWriter) - Constructor for class org.biojava.bio.program.gff.GFFWriter
Create a new GFFWriter that will write to out.
GI_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
gList - Variable in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
 
gln() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Glutamine (Q)
GLOBAL - Static variable in class org.biojava.bio.taxa.SimpleTaxonFactory
Deprecated.
The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.
GLOBAL - Static variable in class org.biojava.bio.taxa.WeakTaxonFactory
Deprecated.
The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.
glu() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Glutamic Acid (E)
GLU_C_BICARB - Static variable in class org.biojava.bio.proteomics.Protease
 
GLU_C_BICARB - Static variable in class org.biojava.bio.proteomics.ProteaseManager
 
GLU_C_PHOS - Static variable in class org.biojava.bio.proteomics.Protease
 
GLU_C_PHOS - Static variable in class org.biojava.bio.proteomics.ProteaseManager
 
gly() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Glycine (G)
Glyph - Interface in org.biojava.bio.gui.glyph
The Glyph interface for painting a shape within bounds
GlyphFeatureRenderer - Class in org.biojava.bio.gui.sequence
A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilter
GlyphFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
 
GlyphUtils - Class in org.biojava.bio.gui.glyph
Utils class used by Glyph implementors.
GOParser - Class in org.biojava.ontology.io
Simple parser for the Gene Ontology (GO) flatfile format.
GOParser() - Constructor for class org.biojava.ontology.io.GOParser
 
graphicsToSecondarySequence(double) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
graphicsToSecondarySequence converts a graphical position to a sequence coordinate on the secondary sequence.
graphicsToSecondarySequence(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
graphicsToSecondarySequence converts a graphical position to a secondary sequence index.
graphicsToSecondarySequence(double) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
graphicsToSecondarySequence(Point) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
graphicsToSecondarySequence converts a graphical position to a secondary sequence index.
graphicsToSecondarySequence(Point) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
graphicsToSecondarySequence converts a graphical position to a secondary sequence index.
graphicsToSecondarySequence(Point) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
graphicsToSequence converts a graphical position to a sequence index.
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
graphicsToSequence(double) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
Converts a graphical position into a sequence coordinate.
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
graphicsToSequence converts a graphical position to a sequence index.
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
graphicsToSequence converts a graphical position to a sequence index.
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
graphicsToSequence(Point2D) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
Converts a graphical position into a sequence coordinate.
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
graphicsToSequence converts a graphical position to a sequence index.
greater(int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
GreaterThan(double) - Constructor for class org.biojava.bio.search.FilterTest.GreaterThan
 
group() - Method in interface org.biojava.bio.search.BioMatcher
Get the matching region as a SymbolList.
group() - Method in class org.biojava.bio.search.MaxMismatchMatcher
 
group() - Method in class org.biojava.utils.regex.Matcher
Returns the input subsequence matched by the previous match.
group(int) - Method in class org.biojava.utils.regex.Matcher
Returns the input subsequence captured by the given group during the previous match operation.
groupCount() - Method in class org.biojava.utils.regex.Matcher
Returns the number of capturing groups in this matcher's pattern.
groups - Variable in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
 
growIfNecessary() - Method in class org.biojava.utils.ChangeSupport
Grows the internal resources if by adding one more listener they would be full.
guessFileType(File) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
because there is no standard file naming convention and guessing by file name is inherantly error prone and bad.
guessRecLen(RandomAccessFile) - Method in class org.biojava.bio.seq.db.BioIndex
 
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.FastaFormat
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
GUITools - Class in org.biojava.bio.gui.sequence
 
GZIP_MAGIC - Static variable in class org.biojava.utils.io.InputStreamProvider
The magic number found at the start of a GZIP stream.

H

h() - Static method in class org.biojava.bio.seq.DNATools
 
h() - Static method in class org.biojava.bio.seq.NucleotideTools
 
h() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Histidine
H_SAPIENS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
H_VULGARE - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
handleEndElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.HitStAXHandler
 
handleEndElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.HSPStAXHandler
 
handleEndElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
 
handlesAmbiguity() - Method in class org.biojava.bio.symbol.DNAAmbPack
 
handlesAmbiguity() - Method in class org.biojava.bio.symbol.DNANoAmbPack
 
handlesAmbiguity() - Method in interface org.biojava.bio.symbol.Packing
Flag to state if ambiguities are stored.
handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.HitStAXHandler
 
handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.HSPStAXHandler
 
handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler
 
handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
 
hasAnnotation(Object) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where the property key has been defined as having some value, regardless of the exact value.
HasAnnotation(Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.HasAnnotation
Make a new ByAnnotation that will accept features with an annotation bundle containing any value associated with 'key'.
HasAttribute(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
 
HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute
 
HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute
 
hasBoundedMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
hasBoundedMax() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
hasBoundedMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
hasBoundedMin() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
hasChangeListeners() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
hasChangeListeners() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
hasChangeSupport() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
hasChild(int) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
Determine if this node has a child corresponding to a given index number.
hasChild(Character) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode
Determine if this node has a child corresponding to a given character
hasFeatures(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
Find out if this DistDataSource can provide features on a sequence with a particular ID.
hasFeatures(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
 
hasFeatures(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
hasGeneratedClass(String) - Method in class org.biojava.utils.bytecode.GeneratedClassLoader
Discover if a class for this name has already been defined by this class loader.
HashBioEntryDB - Class in org.biojavax.bio.db
An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.
HashBioEntryDB() - Constructor for class org.biojavax.bio.db.HashBioEntryDB
Generate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name.
HashBioEntryDB(String) - Constructor for class org.biojavax.bio.db.HashBioEntryDB
Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name.
hashCode() - Method in class org.biojava.bio.AbstractAnnotation
 
hashCode() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
hashCode() - Method in class org.biojava.bio.CollectionConstraint.Contains
 
hashCode() - Method in class org.biojava.bio.dist.AbstractDistribution
 
hashCode() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
 
hashCode() - Method in class org.biojava.bio.dp.TrainerTransition
The hash code is model.hashCode() ^ from.hashCode() ^ to.hashCode()
hashCode() - Method in class org.biojava.bio.dp.Transition
The hash code is from.hashCode() ^ to.hashCode()
hashCode() - Method in class org.biojava.bio.EcNumber.Impl
 
hashCode() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
hashCode() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
 
hashCode() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
 
hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
 
hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
hashCode() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
 
hashCode() - Method in class org.biojava.bio.seq.Feature.Template
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.And
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.Not
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
 
hashCode() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
hashCode() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
hashCode() - Method in class org.biojava.bio.symbol.AbstractLocation
 
hashCode() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
hashCode() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
hashCode() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
hashCode() - Method in class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
hashCode() - Method in interface org.biojava.bio.taxa.Taxon
Deprecated.
The hash-code of a Taxon is equal to the hash-code of it's scientific name.
hashCode() - Method in class org.biojava.ontology.Term.Impl
 
hashCode() - Method in interface org.biojava.ontology.Triple
The hashcode for a Triple.
hashCode() - Method in class org.biojava.ontology.Triple.Impl
 
hashCode() - Method in class org.biojava.utils.ListTools.Doublet
 
hashCode() - Method in class org.biojava.utils.ListTools.Triplet
 
hashCode() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
 
hashCode() - Method in class org.biojava.utils.TypedProperties
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
 
hashCode() - Method in class org.biojavax.bio.seq.CompoundRichLocation
hashCode() - Method in class org.biojavax.bio.seq.EmptyRichLocation
ALWAYS RETURNS 17
hashCode() - Method in class org.biojavax.bio.seq.RichLocation.Strand
hashCode() - Method in class org.biojavax.bio.seq.SimpleRichFeature
hashCode() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
hashCode() - Method in class org.biojavax.bio.seq.SimpleRichLocation
hashCode() - Method in class org.biojavax.bio.SimpleBioEntry
hashCode() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
hashCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
hashCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
hashCode() - Method in class org.biojavax.EmptyRichAnnotation
hashCode() - Method in class org.biojavax.ontology.SimpleComparableOntology
hashCode() - Method in class org.biojavax.ontology.SimpleComparableTerm
hashCode() - Method in class org.biojavax.ontology.SimpleComparableTriple
The hashcode for a Triple.
hashCode() - Method in class org.biojavax.SimpleComment
hashCode() - Method in class org.biojavax.SimpleCrossRef
hashCode() - Method in class org.biojavax.SimpleDocRef
hashCode() - Method in class org.biojavax.SimpleDocRefAuthor
hashCode() - Method in class org.biojavax.SimpleNamespace
hashCode() - Method in class org.biojavax.SimpleNote
hashCode() - Method in class org.biojavax.SimpleRankedCrossRef
hashCode() - Method in class org.biojavax.SimpleRankedDocRef
hashCode(int, boolean) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, boolean[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, double) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, double[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, float) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, float[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, int) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, int[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, long) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, long[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, Object) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, Object[]) - Static method in class org.biojava.utils.ObjectUtil
 
HashedFastaIterator - Class in org.biojavax.bio.seq.io
Iterates over a Fasta file that is kept in memory for optimized access.
HashedFastaIterator(BufferedInputStream, Alphabet, Namespace) - Constructor for class org.biojavax.bio.seq.io.HashedFastaIterator
 
HashRichSequenceDB - Class in org.biojavax.bio.db
An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.
HashRichSequenceDB() - Constructor for class org.biojavax.bio.db.HashRichSequenceDB
Generate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name.
HashRichSequenceDB(String) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB
Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name.
HashRichSequenceDB(IDMaker) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB
Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have a null name.
HashRichSequenceDB(IDMaker, String) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB
Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have the requested name.
HashSequenceDB - Class in org.biojava.bio.seq.db
An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
HashSequenceDB() - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
Generate a HashSequenceDB object that will use byName to generate ids for sequences and have a null name.
HashSequenceDB(String) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
Generate a HashSequenceDB object that will use byName to generate ids and will have the requested name.
HashSequenceDB(IDMaker) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have a null name.
HashSequenceDB(IDMaker, String) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have the requested name.
hasListeners() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
hasListeners() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
hasListeners() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
 
hasListeners() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
hasListeners returns true if there are active listeners for BioJava events.
hasListeners() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
hasListeners() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
hasListeners returns true if there are active listeners for BioJava events.
hasListeners() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
hasListeners() - Method in class org.biojava.utils.AbstractChangeable
Discover if we have any listeners registered.
hasListeners() - Method in class org.biojava.utils.ChangeSupport
Return true if we have any listeners registered at all.
hasListeners(String) - Method in class org.biojava.bio.gui.StackedLogoPainter
 
hasListeners(String) - Method in class org.biojava.bio.gui.TextLogoPainter
 
hasListeners(ChangeType) - Method in class org.biojava.utils.AbstractChangeable
Discover if we have listeners registered for a particular change type.
hasListeners(ChangeType) - Method in class org.biojava.utils.ChangeSupport
Return true if we have listeners registered for a particular change type.
hasMoreSymbols() - Method in interface org.biojava.bio.seq.io.SymbolReader
Determine if there are more symbols left to read in this stream.
hasNext() - Method in class org.biojava.bio.alignment.Alignment.SymbolListIterator
 
hasNext() - Method in class org.biojava.bio.dp.DP.ReverseIterator
 
hasNext() - Method in class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
 
hasNext() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
Are there further Cells to be computed?
hasNext() - Method in class org.biojava.bio.dp.twohead.MatrixPairDPCursor
 
hasNext() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor
test wether the cursor can be advanced further
hasNext() - Method in interface org.biojava.bio.program.homologene.OrthologueSet.Iterator
 
hasNext() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection.Iterator
are more OrthoPairSets available?
hasNext() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet.Iterator
 
hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet.Iterator
 
hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection.Iterator
 
hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet.Iterator
 
hasNext() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
 
hasNext() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
 
hasNext() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
 
hasNext() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
Checks if there is a further SymbolPropertyTable object.
hasNext() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator
Checks if there is a further SymbolPropertyTable object.
hasNext() - Method in class org.biojava.bio.seq.io.StreamReader
 
hasNext() - Method in interface org.biojava.bio.seq.SequenceIterator
Returns whether there are more sequences to iterate over.
hasNext() - Method in class org.biojava.utils.MergingIterator
 
hasNext() - Method in interface org.biojavax.bio.BioEntryIterator
Returns whether there are more sequences to iterate over.
hasNext() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator
 
hasNext() - Method in class org.biojavax.bio.seq.io.RichStreamReader
Returns whether there are more sequences to iterate over.
hasNext() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
Returns whether there are more sequences to iterate over.
hasOffsetData - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
hasOpenSubComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
 
hasSequence(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
Find out if this DistDataSource provides the sequence information for a sequence ID.
hasSequence(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
 
hasSequence(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
hasWeights() - Method in class org.biojava.bio.dist.SimpleDistribution
Indicate whether the weights array has been allocated yet.
Havg - Static variable in class org.biojava.bio.proteomics.MassCalc
Constant value of Hydrogen average mass
HEADER_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HeaderStAXHandler
 
HeaderlessFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
 
headerLine - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
headerLine - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
headerLine - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
HeaderStAXHandler - Class in org.biojava.bio.program.ssbind
HeaderStAXHandler handles the Header element of BioJava BlastLike XML.
HeadlessRenderContext - Class in org.biojava.bio.gui.sequence
A stand-alone SequenceRenderContext to make it easy to render to an image.
HeadlessRenderContext(Sequence, RangeLocation, int) - Constructor for class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
heads() - Method in interface org.biojava.bio.dp.MarkovModel
Deprecated.
use advance().length
heads() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
heads() - Method in class org.biojava.bio.dp.WMAsMM
 
HEIGHT_IS_AUTHORITATIVE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether height or vertical scale is the authoritative measure.
HEIGHTSCALING - Static variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
Constant HEIGHTSCALING indicating a change to the feature height scaling policy.
HelixGlyph - Class in org.biojava.bio.gui.glyph
A Glyph that paints a Helix within the bounds
HelixGlyph() - Constructor for class org.biojava.bio.gui.glyph.HelixGlyph
 
HelixGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.HelixGlyph
 
HibernateFeatureFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
HIDDEN - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
his() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Histidine (H)
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.HitMerger
 
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
 
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.FilterByLength
 
hit(int, int, int, int) - Method in interface org.biojava.bio.program.ssaha.SearchListener
There has been a hit between the query sequence and a database sequence.
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
 
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
 
HIT_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HitStAXHandler
 
HitMerger - Class in org.biojava.bio.program.ssaha
A listener that merges overlapping hits and culls all hits under a given length.
HitMerger(SearchListener, int) - Constructor for class org.biojava.bio.program.ssaha.HitMerger
Build a new HitMerger that will pass events on to a delegate.
HitStAXHandler - Class in org.biojava.bio.program.ssbind
AlignmentStAXHandler handles the Hit element of BioJava BlastLike XML.
hmm - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
hmm() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
Gets the inner HmmerProfileHMM state
HmmerProfileHMM - Class in org.biojava.bio.program.hmmer
This is a class for representing HMMER generated Profile HMM.
HmmerProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory, String) - Constructor for class org.biojava.bio.program.hmmer.HmmerProfileHMM
 
HmmerProfileParser - Class in org.biojava.bio.program.hmmer
A class for parsing in Hmmer markov models from HMM_ls files generated by HMMER training note that this class is still currently experimental.
HmmerProfileParser(String) - Constructor for class org.biojava.bio.program.hmmer.HmmerProfileParser
 
HMMTrainer - Interface in org.biojava.bio.dp
interface implemented by objects that train HMMs.
Hmono - Static variable in class org.biojava.bio.proteomics.MassCalc
Constant value of Hydrogen monoisotopic mass
HOMOID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
HomologeneBuilder - Interface in org.biojava.bio.program.homologene
an interface for Homologene dataset Builders
HomologeneDB - Interface in org.biojava.bio.program.homologene
Homologene is a NCBI dataset that curates sets of orthologues from the reference model organisms.
HomologeneTools - Class in org.biojava.bio.program.homologene
Homologene is a NCBI dataset that curates sets of orthologues from the reference model ogranisms.
HomologeneTools() - Constructor for class org.biojava.bio.program.homologene.HomologeneTools
 
homology - Variable in class org.biojava.bio.seq.homol.HomologyFeature.Template
 
Homology - Interface in org.biojava.bio.seq.homol
Signifies that two or more features are homologous.
HOMOLOGY_FEATURE_TYPE - Static variable in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
HOMOLOGY_FEATURE_TYPE is the type String used by BlastLikeHomologyBuilder when creating HomologyFeatures.
HomologyDB - Interface in org.biojava.bio.seq.homol
 
HomologyFeature - Interface in org.biojava.bio.seq.homol
 
HomologyFeature.Template - Class in org.biojava.bio.seq.homol
 
HORIZONTAL_NONLINEAR_SCALER - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option specifying the non-linear scaling function to apply, as embodied in a ChromatogramNonlinearScaler object.
HotSpot(String, URL, Integer[]) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.HotSpot
Creates a new HotSpot with a null user object.
HotSpot(String, URL, Integer[], Object) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.HotSpot
Creates a new HotSpot.
hotSpots() - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide
 
hotSpots() - Method in interface org.biojava.bio.gui.sequence.ImageMap
hotSpots iterates over the hotspots in the map
hotSpots() - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide
 
hp - Static variable in class org.biojavax.bio.seq.io.FastaFormat
 
HSP_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HSPStAXHandler
 
HSPStAXHandler - Class in org.biojava.bio.program.ssbind
HSPStAXHandler handles the HSP element of BioJava BlastLike XML.
HSPSUMMARY_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler
 
HSPSummaryStAXHandler - Class in org.biojava.bio.program.ssbind
HSPSummaryStAXHandler handles the HSPSummary element of BioJava BlastLike XML.
HTML - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
HTMLRenderer - Class in org.biojava.bio.program.blast2html
Renders HTML version of blast-like output.
HTMLRenderer(PrintWriter, String, int, URLGeneratorFactory, AlignmentMarker, Properties) - Constructor for class org.biojava.bio.program.blast2html.HTMLRenderer
Creates an HTMLRenderer, that outputs the HTML to the specified PrintWriter.
HYDROPATHICITY - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 
HypersonicDBHelper - Class in org.biojava.bio.seq.db.biosql
Deprecated.
Use hibernate and org.biojavax.bio.db.*
HypersonicDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.HypersonicDBHelper
Deprecated.
 

I

i() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Isoleucine
ID_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ID_KEY - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
ID_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
ID_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
Identifiable - Interface in org.biojava.utils.lsid
Marks an implementor as having a LifeScienceIdentifier.
identifier - Variable in class org.biojava.bibliography.BibRef
It is an unambiguous reference to this citation "within the world".
IDENTIFIER - Static variable in interface org.biojavax.bio.BioEntry
 
IDENTIFIER - Static variable in interface org.biojavax.ontology.ComparableTerm
 
identifyFormat(String, String) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
identifyFormat performs a case-insensitive mapping of a pair of common sequence format name (such as 'embl', 'genbank' or 'fasta') and alphabet name (such as 'dna', 'rna', 'protein', 'aa') to an integer.
IDMaker - Interface in org.biojava.bio.seq.db
Interface for objects that define how to make an ID for a sequence.
IDMaker.ByName - Class in org.biojava.bio.seq.db
 
IDMaker.ByURN - Class in org.biojava.bio.seq.db
 
ids() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
ids() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.DummySequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
 
ids() - Method in interface org.biojava.bio.seq.db.SequenceDB
Get an immutable set of all of the IDs in the database.
ids() - Method in class org.biojava.bio.seq.db.SubSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
 
ids() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
ids() - Method in interface org.biojavax.bio.db.BioEntryDB
Get an immutable set of all of the IDs in the database.
ids() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
 
ids() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
ids() - Method in class org.biojavax.bio.db.HashBioEntryDB
 
ids() - Method in class org.biojavax.bio.db.HashRichSequenceDB
 
ids() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
 
ids() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
 
ids(boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
Get the complete set of sequence IDs provided by this DistDataSource.
ids(boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
 
ids(boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
IfExpression - Class in org.biojava.utils.bytecode
A CodeGenerator that provides something semanticaly identical to if.
IfExpression(byte, CodeGenerator, CodeGenerator) - Constructor for class org.biojava.utils.bytecode.IfExpression
 
IG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
IG indicates that the sequence format is IG.
ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
ignorableWhitespace(char[], int, int) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
ignorableWhitespace(char[], int, int) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
ignorableWhitespace(char[], int, int) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
ignorableWhitespace(char[], int, int) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
IgnoreCountsTrainer - Class in org.biojava.bio.dist
A distribution trainer that just ignores all counts.
IgnoreCountsTrainer() - Constructor for class org.biojava.bio.dist.IgnoreCountsTrainer
Constructor intended for sub-classes.
IgnoreRecordException - Exception in org.biojava.bio.program.gff
Ignore this record in the stream.
IgnoreRecordException() - Constructor for exception org.biojava.bio.program.gff.IgnoreRecordException
 
ile() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Isoleucine (I)
IllegalAlignmentEditException - Exception in org.biojava.bio.alignment
The usual reason for throwing an IllegalAlignmentEditException is that you are trying to shift a group of bases in such a way that it would require deleting bases.
IllegalAlignmentEditException() - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException
Just make the exception.
IllegalAlignmentEditException(String) - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException
Make the exception with a message.
IllegalAlignmentEditException(Throwable) - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException
 
IllegalAlignmentEditException(Throwable, String) - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException
 
IllegalAlphabetException - Exception in org.biojava.bio.symbol
The exception to indicate that an invalid alphabet has been used.
IllegalAlphabetException() - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException
Just make the exception.
IllegalAlphabetException(String) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException
Make the exception with a message.
IllegalAlphabetException(Throwable) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException
 
IllegalAlphabetException(Throwable, String) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException
 
IllegalIDException - Exception in org.biojava.bio.seq.db
 
IllegalIDException() - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
 
IllegalIDException(String) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
 
IllegalIDException(Throwable) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
 
IllegalIDException(Throwable, String) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
 
IllegalOrganismException - Exception in org.biojavax.ga.exception
Indicates an invalid organism
IllegalOrganismException() - Constructor for exception org.biojavax.ga.exception.IllegalOrganismException
 
IllegalOrganismException(String) - Constructor for exception org.biojavax.ga.exception.IllegalOrganismException
 
IllegalSymbolException - Exception in org.biojava.bio.symbol
The exception to indicate that a symbol is not valid within a context.
IllegalSymbolException(String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException
Make the exception with a message.
IllegalSymbolException(Throwable, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException
 
IllegalSymbolException(Throwable, Symbol, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException
 
IllegalSymbolException(Symbol, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException
Make the exception with a message and a symbol.
IllegalTransitionException - Exception in org.biojava.bio.dp
This exception indicates that there is no transition between two states.
IllegalTransitionException() - Constructor for exception org.biojava.bio.dp.IllegalTransitionException
 
IllegalTransitionException(State, State) - Constructor for exception org.biojava.bio.dp.IllegalTransitionException
 
IllegalTransitionException(State, State, String) - Constructor for exception org.biojava.bio.dp.IllegalTransitionException
 
IlluminaFastqReader - Class in org.biojava.bio.program.fastq
Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqReader() - Constructor for class org.biojava.bio.program.fastq.IlluminaFastqReader
 
IlluminaFastqWriter - Class in org.biojava.bio.program.fastq
Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqWriter() - Constructor for class org.biojava.bio.program.fastq.IlluminaFastqWriter
 
ImageMap - Interface in org.biojava.bio.gui.sequence
ImageMap represents a collection of image map hotspots.
ImageMap.ClientSide - Class in org.biojava.bio.gui.sequence
ClientSide represents a client-side style image map.
ImageMap.HotSpot - Class in org.biojava.bio.gui.sequence
HotSpots represent an image map hotspot.
ImageMap.ServerSide - Class in org.biojava.bio.gui.sequence
ServerSide represents a server-side style image map.
ImageMapRenderer - Interface in org.biojava.bio.gui.sequence
ImageMapRenderers create strings representing Features suitable for use in HTML image maps.
Impl() - Constructor for class org.biojava.bio.AnnotationType.Impl
Create a new Impl with no constraints.
Impl() - Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl
 
Impl(int, int, int, int) - Constructor for class org.biojava.bio.EcNumber.Impl
Make a new EcNumber.Impl with the data provided.
Impl(String, String) - Constructor for class org.biojava.ontology.Ontology.Impl
 
Impl(String, Map) - Constructor for class org.biojava.directory.RegistryConfiguration.Impl
 
Impl(String, RAF, long, int) - Constructor for class org.biojava.bio.program.indexdb.Record.Impl
Creates a new Impl record.
Impl(CollectionConstraint) - Constructor for class org.biojava.bio.AnnotationType.Impl
Create a new Impl with a default collection constraint.
Impl(GFF3Record) - Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl
 
Impl(PropertyConstraint, Location) - Constructor for class org.biojava.bio.AnnotationType.Impl
Create a new Impl with a default property and cardinality constraint.
Impl(Ontology, String) - Constructor for class org.biojava.ontology.Term.Impl
 
Impl(Ontology, String, String) - Constructor for class org.biojava.ontology.Term.Impl
 
Impl(Ontology, String, String) - Constructor for class org.biojava.ontology.Variable.Impl
 
Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.ontology.Term.Impl
 
Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.ontology.Variable.Impl
 
Impl(Ontology, Ontology) - Constructor for class org.biojava.ontology.OntologyTerm.Impl
 
Impl(Ontology, Ontology, Object[]) - Constructor for class org.biojava.ontology.OntologyTerm.Impl
 
Impl(Ontology, Term, String) - Constructor for class org.biojava.ontology.RemoteTerm.Impl
 
Impl(Ontology, Term, String, Object[]) - Constructor for class org.biojava.ontology.RemoteTerm.Impl
 
Impl(Term, Term, Term) - Constructor for class org.biojava.ontology.Triple.Impl
 
Impl(Term, Term, Term, Object[]) - Constructor for class org.biojava.ontology.Triple.Impl
 
Impl(Term, Term, Term, String, String) - Constructor for class org.biojava.ontology.Triple.Impl
 
Impl(Term, Term, Term, String, String, Object[]) - Constructor for class org.biojava.ontology.Triple.Impl
 
importTaxon(Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
Deprecated.
 
importTaxon(Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
Deprecated.
Import a Taxon and all its children into the implementation provided by this factory.
importTaxon(Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
Deprecated.
 
importTerm(Term, String) - Method in class org.biojava.ontology.IntegerOntology
 
importTerm(Term, String) - Method in class org.biojava.ontology.Ontology.Impl
 
importTerm(Term, String) - Method in interface org.biojava.ontology.Ontology
Create a view of a term from another ontology.
importTerm(Term, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
Create a view of a term from another ontology.
in - Variable in class org.biojava.utils.io.CachingInputStream
The underlying input stream whose data we're caching
IN_RANGE - Static variable in interface org.biojavax.bio.seq.Position
A symbol representing a position that occupies a single base somewhere in a range, eg. 5.10 falls on some base between 5 and 10.
incCounts(int, int) - Method in class org.biojava.bio.symbol.SuffixTree
 
INCLUDES_PREFIX - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
increaseCount(AtomicSymbol, double) - Method in interface org.biojava.bio.dist.Count
Set the probability or odds that Symbol s is emitted by this state.
increaseCount(AtomicSymbol, double) - Method in class org.biojava.bio.dist.IndexedCount
 
indent() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
indent() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
Add a level of indentation
Indent() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
 
INDENT - Static variable in class org.biojava.bio.seq.io.agave.AgaveWriter
use a two space indent
INDETERMINATE - Static variable in class org.biojava.utils.TriState
 
index - Variable in class org.biojava.ontology.obo.OboFileParser.SOPair
 
index(State) - Method in class org.biojava.bio.dp.WMAsMM
 
index(Symbol) - Static method in class org.biojava.bio.seq.DNATools
Return an integer index for a symbol - compatible with forIndex.
index(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
Return an integer index for a symbol - compatible with forIndex.
index(Symbol) - Static method in class org.biojava.bio.seq.RNATools
Return an integer index for a symbol - compatible with forIndex.
Index - Interface in org.biojava.bio.seq.db
This defines an index entry for an individual sequence within a set of indexed files.
INDEX - Static variable in interface org.biojava.bio.symbol.AlphabetIndex
Indicates that the index is changing, probably due to the underlying alphabet changing.
Index2Model - Class in org.biojava.bio.program.tagvalue
 
Index2Model() - Constructor for class org.biojava.bio.program.tagvalue.Index2Model
 
IndexedAnnotationDB - Class in org.biojava.bio.annodb
A database of Annotation instances backed by an indexed file set.
IndexedAnnotationDB(String, File, Index2Model, List, int, AnnotationType, IndexedAnnotationDB.ParserListenerFactory) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB
Create a new IndexedAnnotationDB.
IndexedAnnotationDB(BioStore) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB
Initialise the db from a store.
IndexedAnnotationDB.ParserListenerFactory - Interface in org.biojava.bio.annodb
A factory for retrieving parsers and listeners.
IndexedAnnotationDB.StaticMethodRPFactory - Class in org.biojava.bio.annodb
An implementation of ParserListenerFactory that uses a static method.
IndexedChangeHub - Class in org.biojava.utils
implements Changeable support with a ChangeHub that stores ChangeListener by key.
IndexedChangeHub() - Constructor for class org.biojava.utils.IndexedChangeHub
 
IndexedChangeHub.ListenerMemento - Class in org.biojava.utils
 
IndexedCount - Class in org.biojava.bio.dist
An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.
IndexedCount(AlphabetIndex) - Constructor for class org.biojava.bio.dist.IndexedCount
Get a new InexedCount for an alphabet indexer.
IndexedCount(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.IndexedCount
Get a new IdexedCount for an alphabet using the default indexer.
IndexedSequenceDB - Class in org.biojava.bio.seq.db
This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.
IndexedSequenceDB(IDMaker, IndexStore) - Constructor for class org.biojava.bio.seq.db.IndexedSequenceDB
Create an IndexedSequenceDB by specifying both the IDMaker and IndexStore used.
IndexedSequenceDB(IndexStore) - Constructor for class org.biojava.bio.seq.db.IndexedSequenceDB
Create an IndexedSequenceDB by specifying IndexStore used.
indexEmbl(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools
indexEmbl indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.
Indexer - Class in org.biojava.bio.program.tagvalue
Listens to tag-value events and passes on indexing events to an IndexStore.
Indexer(File, IndexStore) - Constructor for class org.biojava.bio.program.tagvalue.Indexer
Build a new Indexer.
Indexer2 - Class in org.biojava.bio.program.tagvalue
Listens to tag-value events and passes on indexing events to an IndexStore.
Indexer2(File, IndexStore, Index2Model) - Constructor for class org.biojava.bio.program.tagvalue.Indexer2
Build a new Indexer.
indexFasta(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools
indexFasta indexes DNA, RNA or protein Fasta format sequence files on primary identifier.
indexForSymbol(Symbol) - Method in interface org.biojava.bio.symbol.AlphabetIndex
Return the unique index for a symbol.
indexGenbank(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools
indexGenbank indexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary.
IndexStore - Interface in org.biojava.bio.program.indexdb
IndexStore is an interface for indexing flatfiles according to the OBDA specification.
IndexStore - Interface in org.biojava.bio.seq.db
This defines the objects that IndexedSequenceDB uses to store all of the database state, such as name, format, sequence builder and the actual file offsets.
indexSwissprot(String, File, File[]) - Static method in class org.biojava.bio.program.indexdb.IndexTools
indexSwissprot indexes Swissprot format protein sequence files on ID as primary identifier.
IndexTools - Class in org.biojava.bio.program.indexdb
IndexTools contains static utility methods for creating flatfile indices according to the OBDA standard.
inFeature() - Method in class org.biojava.bio.seq.io.FeatureTableParser
Deprecated.
 
InfinitelyAmbiguousSymbolList - Class in org.biojavax.bio.seq
A symbol list that is Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.
InfinitelyAmbiguousSymbolList(FiniteAlphabet) - Constructor for class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Creates a new instance of InfinitelyAmbiguousSymbolList
init() - Method in interface org.biojava.utils.xml.Initializable
 
INIT_PROP_LOG - Static variable in interface org.biojava.bibliography.BibRefSupport
A property name ("log").
INIT_PROP_SUPPORT - Static variable in interface org.biojava.bibliography.BibRefSupport
A property name ("bibrefsupport").
initComponents() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
initialiseProfileHMM(int) - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
Initializable - Interface in org.biojava.utils.xml
 
initialize() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
initialize(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator
Initialize the cell at [0][0] to the recursion initial parameters.
initializeVariables(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver) - Method in class org.biojava.bio.symbol.FuzzyLocation
Refactored initialization code from the constructors.
initPopulation() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
Assigns a fitness value to each organism within the population according to the currently set fitness function.
input - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
 
InputHandler - Interface in org.biojava.utils.process
Interface to a threadable input handler for an external process.
InputStreamProvider - Class in org.biojava.utils.io
A class that provides an InputStream from a File.
InputStreamProvider() - Constructor for class org.biojava.utils.io.InputStreamProvider
 
INSDSEQ_FORMAT - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
The name of this format
INSDSEQ_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
INSDseqFormat - Class in org.biojavax.bio.seq.io
Format reader for INSDseq files.
INSDseqFormat() - Constructor for class org.biojavax.bio.seq.io.INSDseqFormat
 
INSDseqFormat.Terms - Class in org.biojavax.bio.seq.io
Implements some INSDseq-specific terms.
INSDSEQS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
insertObject(NexusObject, int) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
Inserts an object at the given position.
instance() - Static method in class org.biojava.bio.symbol.AlphabetManager
Deprecated.
all AlphabetManager methods have become static
instance() - Static method in class org.biojava.directory.SystemRegistry
Get the singleton Registry instance representing the system-wide default registry.
INSTANCE - Static variable in class org.biojava.bio.gui.sequence.LayeredRenderer
Static LayeredRenderer INSTANCE used by MultiLineRenderers.
INSTANCE - Static variable in class org.biojava.bio.seq.io.GenEmblFeatureComparator
Deprecated.
 
INSTANCE - Static variable in class org.biojava.bio.seq.io.GenEmblPropertyComparator
Deprecated.
 
INSTANCE - Static variable in class org.biojava.bio.symbol.DoubleAlphabet
 
INSTANCE - Static variable in class org.biojava.bio.symbol.IntegerAlphabet
The singleton instance of the IntegerAlphabet class.
INSTANCE - Static variable in class org.biojava.utils.xml.XMLBeans
 
instanceOf(Annotation) - Method in class org.biojava.bio.AnnotationType.Abstract
 
instanceOf(Annotation) - Method in interface org.biojava.bio.AnnotationType
Validate an Annotation against this AnnotationType.
instantiateBean(Element) - Method in class org.biojava.utils.xml.XMLBeans
 
instantiateBean(Element, ClassLoader, Map) - Method in class org.biojava.utils.xml.XMLBeans
 
instantiateDB(URL, HomologeneBuilder) - Static method in class org.biojava.bio.program.homologene.HomologeneTools
instantiate a HomologeneDB.
instantiateTemplate(Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils
This attempts to divine the 'best' template class for a feature and return a new instance readly for pupulating.
Instruction - Interface in org.biojava.utils.bytecode
Base class for java bytecode instructions.
InstructionVector - Class in org.biojava.utils.bytecode
A list of Instructions and/or other CodeGenerator objects.
InstructionVector() - Constructor for class org.biojava.utils.bytecode.InstructionVector
 
INTEGER - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
INTEGER indicates that a sequence contains integer alphabet symbols, such as used to describe sequence quality data.
IntegerAlphabet - Class in org.biojava.bio.symbol
An efficient implementation of an Alphabet over the infinite set of integer values.
IntegerAlphabet.IntegerSymbol - Class in org.biojava.bio.symbol
A single int value.
IntegerAlphabet.SubIntegerAlphabet - Class in org.biojava.bio.symbol
A class to represent a finite contiguous subset of the infinite IntegerAlphabet
IntegerOntology - Class in org.biojava.ontology
 
IntegerOntology.IntTerm - Class in org.biojava.ontology
 
IntegerSymbol(int) - Constructor for class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
integerSymbolFromPhred(Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools
Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.
IntegerTokenization - Class in org.biojava.bio.seq.io
 
IntegerTokenization() - Constructor for class org.biojava.bio.seq.io.IntegerTokenization
 
IntElementHandlerBase - Class in org.biojava.utils.stax
StAX handler for any element which just contains a string representation of an integer.
IntElementHandlerBase() - Constructor for class org.biojava.utils.stax.IntElementHandlerBase
 
Interaction() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
 
INTERACTION - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
A name for a comment type.
internalClassify(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
intersect(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils
Operator: Intersect FeatureHolder1 with FeatureHolder2
intersection(AnnotationType, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
Calculate an AnnotationType that matches all Annotation instances matched by both types.
intersection(CollectionConstraint, CollectionConstraint) - Static method in class org.biojava.bio.AnnotationTools
Return the CollectionConstraint which accept only collections accepted by both of those specified.
intersection(PropertyConstraint, PropertyConstraint) - Static method in class org.biojava.bio.AnnotationTools
Calculate the intersection of two PropertyConstraint instances.
intersection(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
 
intersection(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
intersection(Location) - Method in class org.biojava.bio.symbol.CircularLocation
 
intersection(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
intersection(Location) - Method in interface org.biojava.bio.symbol.Location
Returns a Location that contains all points common to both ranges.
intersection(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Returns a Location that contains all points common to both ranges.
intersection(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Returns a Location that contains all points common to both ranges.
intersection(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Returns a Location that contains all points common to both ranges.
intersection(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
Return the intersection of two locations.
INTERSECTION_OF - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
IntrospectedCodeClass - Class in org.biojava.utils.bytecode
CodeClass instances that represent normal Java Class objects.
IntTerm(int) - Constructor for class org.biojava.ontology.IntegerOntology.IntTerm
 
IntTerm(int, Object[]) - Constructor for class org.biojava.ontology.IntegerOntology.IntTerm
 
intValue() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
intValue() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
intValue() - Method in class org.biojavax.bio.seq.RichLocation.Strand
Returns the numeric value of this strand.
iNumberOfColours - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
The number of unique colours.
invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidEnd(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
The `end' field of the GFF entry was not a valid value.
invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidEnd(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidFrame(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidFrame(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
The `frame' field of the GFF entry was not a valid value.
invalidFrame(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidFrame(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidScore(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidScore(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
The `score' field of the GFF entry was not a valid value.
invalidScore(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidScore(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidStart(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidStart(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
The `start' field of the GFF entry was not a valid value.
invalidStart(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidStart(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidStrand(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
The `strand' field of the GFF entry was not a valid value.
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFWriter
 
InvalidTermException - Exception in org.biojava.ontology
Thrown to indicate that an ontology term is not acceptable or appropriate in a given context
InvalidTermException() - Constructor for exception org.biojava.ontology.InvalidTermException
 
InvalidTermException(String) - Constructor for exception org.biojava.ontology.InvalidTermException
 
InvalidTermException(String, Throwable) - Constructor for exception org.biojava.ontology.InvalidTermException
 
InvalidTermException(Throwable) - Constructor for exception org.biojava.ontology.InvalidTermException
 
INVERT_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the invertebrate mitochondrial genetic code.
IOExceptionFound - Variable in class org.biojava.bio.seq.db.GenbankSequenceDB
 
IS_A - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
IS_A - Static variable in class org.biojava.ontology.OntoTools
 
IS_OBSOLETE - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
isActive() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
isActive returns true if both the Sequences to be rendered and the PairwiseHomologyRenderer are not null.
isActive() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
isActive() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
isActive() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
isActive() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
isActive returns true if both the Sequence to be rendered and the SequenceRenderer are not null.
isArray() - Method in interface org.biojava.utils.bytecode.CodeClass
Discover if the class is an array type.
isArray() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
isArray() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
isArray() - Method in class org.biojava.utils.bytecode.ParametricType
 
isbn - Variable in class org.biojava.bibliography.BiblioBook
ISBN number.
isBoundaryEnd(Object) - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
 
isBoundaryStart(Object) - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
 
isCaseSensitive() - Method in interface org.biojava.utils.candy.CandyVocabulary
It returns true if the vocabulary entries should be considered as case-sensitive.
isColoured(String, String) - Method in interface org.biojava.bio.program.blast2html.ColourCommand
Returns true if the alignment pair should be coloured else false.
isComponentResolvable() - Method in interface org.biojava.bio.seq.ComponentFeature
Determine if the sequence references by this ComponentFeature is available in this context.
isConsortium() - Method in interface org.biojavax.DocRefAuthor
Is this author actually a consortium?
isConsortium() - Method in class org.biojavax.SimpleDocRefAuthor
Is this author actually a consortium?
isContiguous() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
isContiguous() - Method in class org.biojava.bio.symbol.AbstractRangeLocation
 
isContiguous() - Method in class org.biojava.bio.symbol.CircularLocation
Delegates to the wrapped location.
isContiguous() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
isContiguous() - Method in interface org.biojava.bio.symbol.Location
Determine if a Location is contiguous.
isContiguous() - Method in class org.biojavax.bio.seq.CompoundRichLocation
Determine if a Location is contiguous.
isContiguous() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Determine if a Location is contiguous.
isContiguous() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Determine if a Location is contiguous.
isDeprecated() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
Get the deprecation flag.
isDiagonal() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
 
isDisjoint(FeatureFilter) - Method in interface org.biojava.bio.seq.OptimizableFilter
Returns true if this filter is disjoint from filt - that is, there is no Feature that is accepted by both filters.
isEditor() - Method in interface org.biojavax.DocRefAuthor
Is this author actually an editor?
isEditor() - Method in class org.biojavax.SimpleDocRefAuthor
Is this author actually an editor?
isEmpty() - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
 
isEmpty() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
 
isEmpty() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
 
isEmpty() - Method in class org.biojavax.ga.util.WeightedSet
 
isEndoProtease() - Method in class org.biojava.bio.proteomics.Protease
 
isEscapeStarter(char) - Static method in class org.biojava.ontology.obo.OboFileParser
 
isFloatType(CodeClass) - Static method in class org.biojava.utils.bytecode.CodeUtils
Returns true if the class is a floating point number.
isHaploid() - Method in class org.biojavax.ga.impl.AbstractOrganism
 
isHaploid() - Method in class org.biojavax.ga.impl.SimpleOrganism
Simple Organisms are Halpoid
isHaploid() - Method in interface org.biojavax.ga.Organism
Is the organism Haploid?
isIllumina() - Method in enum org.biojava.bio.program.fastq.FastqVariant
Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_ILLUMINA.
isIntegerType(CodeClass) - Static method in class org.biojava.utils.bytecode.CodeUtils
Returns true if the class is an integer number.
isInterleaved() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
isInterleaved() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
isLabels() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
isLabels() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
isMasked(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
Default Behaivour is that if the whole token is lower case it is masked.
isMasked(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
 
isMasked(BasisSymbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
Determines if a Symbol is masked.
isMatchingType(ChangeType) - Method in class org.biojava.utils.ChangeType
Return true iff ct is equal to this type or any of it's supertypes (including ChangeType.UNKNOWN).
isMaxFuzzy() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
isMinFuzzy() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
isMultiSource(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
Returns false if all the locations in the set are from the same strand of the same sequence.
isMyChangeEvent(ChangeEvent, IndexedChangeHub.ListenerMemento) - Method in class org.biojava.utils.IndexedChangeHub
 
isNewTag() - Method in class org.biojava.bio.program.tagvalue.TagValue
 
isObject() - Method in class org.biojava.utils.bytecode.ParametricType
 
IsoelectricPointCalc - Class in org.biojava.bio.proteomics
Class that computes isoelectric point for denaturated proteins.
IsoelectricPointCalc() - Constructor for class org.biojava.bio.proteomics.IsoelectricPointCalc
 
IsoelectricPointCalc.ChargeCalculator - Class in org.biojava.bio.proteomics
 
Isoform() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Creates a new instance.
isOppositeStrand() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
isOrganismsDiffer() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Getter for property organismsDiffer.
isPalindromic() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
isPalindromic returns true if the recognition site is palindromic.
isParseable(String) - Static method in class org.biojavax.bio.seq.io.UniProtCommentParser
Returns true if the comment may be parseable (starts with -!
isParseable(Comment) - Static method in class org.biojavax.bio.seq.io.UniProtCommentParser
Returns true if the comment may be parseable (starts with -!
isPrimitive() - Method in interface org.biojava.utils.bytecode.CodeClass
Discover if the class represents a primitive type.
isPrimitive() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
isPrimitive() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
isPrimitive() - Method in class org.biojava.utils.bytecode.ParametricType
Discover if this type must resolve to a primative.
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
 
isProperSubset(FeatureFilter) - Method in interface org.biojava.bio.seq.OptimizableFilter
Returns true if this filter is a proper subset of sup - that is, for every feature that matches this, it also matches sup.
isPrototype() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
 
isQuote(char) - Static method in class org.biojava.ontology.obo.OboFileParser
 
isReady() - Method in interface org.biojava.bibliography.BibRefQuery
It checks if the repository is available.
isReady() - Method in interface org.biojava.bibliography.BibRefSupport
It checks if a utility object is available.
isReady() - Method in interface org.biojava.utils.candy.CandyFinder
It checks if a vocabulary finder object is available.
isReady(String, long) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService
This method is used only for the executeBlastSearch method to check for completion of request using the NCBI specified RTOE variable
isReady(String, long) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService
Simple method to check if the specified request has been completed by the service used.
isRemote() - Method in class org.biojava.bio.seq.RemoteFeature.Region
Return whether this Region is remote or local.
isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
 
isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
 
isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
 
isRequired(String) - Method in interface org.biojava.bio.symbol.CodonPrefFilter
indicates if the current CodonPref is to be accepted
isRespectCase() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
isSane() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
isSane() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
isSanger() - Method in enum org.biojava.bio.program.fastq.FastqVariant
Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SANGER.
isScaleByInformation() - Method in class org.biojava.bio.gui.DistributionLogo
 
isShowAccession() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
isShowDescription() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
isShowIdentifier() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
isShowName() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
isShowNamespace() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
isShowVersion() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
issn - Variable in class org.biojava.bibliography.BiblioJournal
A standard number for journals.
isSolexa() - Method in enum org.biojava.bio.program.fastq.FastqVariant
Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SOLEXA.
isStarred() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString
Tests whether this tree has a star before it's name.
isStrict() - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
Determine if this writer is in strict mode.
isStrict() - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
Determine if this writer is in strict mode.
isSubTypeOf(FeatureTypes.Type, FeatureTypes.Type) - Static method in class org.biojava.bio.seq.FeatureTypes
Work out if one type is a sub-type of another.
issue - Variable in class org.biojava.bibliography.BiblioJournalArticle
The issue of the journal.
issueSupplement - Variable in class org.biojava.bibliography.BiblioJournalArticle
Suplement.
isTaxonHidden() - Method in interface org.biojavax.bio.taxa.NCBITaxon
used in getNameHierarchy() to determine whether this taxonomy level is displayed
isTaxonHidden() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific.
isTerminal() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
Determine is this node is terminal (has no children).
isTerminal() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode
Determine is this node is terminal (has no children).
isTokens() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
isTrainingComplete(TrainingAlgorithm) - Method in interface org.biojava.bio.dp.StoppingCriteria
Decide if the training has completed.
isTransposed() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
 
isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
 
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
 
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
isUnchanging(ChangeType) - Method in class org.biojava.utils.AbstractChangeable
 
isUnchanging(ChangeType) - Method in interface org.biojava.utils.Changeable
A particular ChangeType can never be raised by this Changeable.
isUnchanging(ChangeType) - Method in class org.biojava.utils.ChangeSupport
 
isUnchanging(ChangeType) - Method in class org.biojava.utils.Unchangeable
 
isUnchanging(ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
A particular ChangeType can never be raised by this Changeable.
isUnchanging(ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
isUnchanging(ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
itemAlphas() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
itemAlphas() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
items() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
items() - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
items() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
items() - Method in interface org.biojava.stats.svm.SVMTarget
 
itemTargets() - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
itemTargets() - Method in interface org.biojava.stats.svm.SVMTarget
 
ItemValue - Interface in org.biojava.stats.svm
A simple Object-double tuple.
iterator() - Method in interface org.biojava.bio.annodb.AnnotationDB
Loop over each Annotation in this db.
iterator() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
 
iterator() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
 
iterator() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
 
iterator() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
 
iterator() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
 
iterator() - Method in class org.biojava.bio.dp.SimpleStatePath
 
iterator() - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
 
iterator() - Method in interface org.biojava.bio.program.homologene.OrthologueSet
Return an iterator to the contents of the set.
iterator() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
 
iterator() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
returns an iterator to the members of this set
iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
 
iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
 
iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
iterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
iterator() - Method in class org.biojava.bio.seq.impl.DummySequence
 
iterator() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
iterator() - Method in class org.biojava.bio.seq.impl.SubSequence
 
iterator() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
iterator() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
iterator() - Method in class org.biojava.bio.seq.SimpleAssembly
 
iterator() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
iterator() - Method in interface org.biojava.bio.symbol.FiniteAlphabet
Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.
iterator() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
iterator() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
iterator() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
iterator() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
iterator() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
 
iterator() - Method in interface org.biojava.bio.symbol.SymbolList
An Iterator over all Symbols in this SymbolList.
iterator() - Method in class org.biojava.utils.FileAsList
 
iterator() - Method in class org.biojava.utils.MergingSet
 
iterator() - Method in class org.biojava.utils.SmallSet
 
iterator() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
An Iterator over all Symbols in this SymbolList.
iterator() - Method in class org.biojavax.bio.seq.ThinRichSequence
An Iterator over all Symbols in this SymbolList.
iterator() - Method in class org.biojavax.ga.util.WeightedSet
Returns an unmodifiable iterator over the keys of the set.
iterator(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
An Iterator over all Symbols in this SymbolList.
iterator(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
An Iterator over all Symbols in this SymbolList.
iterator(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
An Iterator over all Symbols in this SymbolList.

J

JDBCConnectionPool - Class in org.biojava.utils
Really simple connection pool for JDBC databases.
JDBCConnectionPool(String) - Constructor for class org.biojava.utils.JDBCConnectionPool
 
JDBCConnectionPool(String, String, String) - Constructor for class org.biojava.utils.JDBCConnectionPool
 
JDBCPooledDataSource - Class in org.biojava.utils
Returns a DataSource that implements connection pooling Uses Jakarta Commons DBCP and Pool packages.
JDBCPooledDataSource() - Constructor for class org.biojava.utils.JDBCPooledDataSource
 
JOIN_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
 
JOIN_ORACLE8 - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
Deprecated.
 
joinCommands(Object[]) - Static method in class org.biojava.utils.process.ExternalProcess
Joins a command list to a single command string.
jointDistOverAlignment(Alignment, boolean, double, int[]) - Static method in class org.biojava.bio.dist.DistributionTools
Creates a joint distribution.
JOURNAL_ABBREV - Static variable in interface org.biojava.bibliography.BibRefSupport
A vocabulary name.
JOURNAL_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
JOURNAL_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
JOURNAL_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
JOURNAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
JOURNAL_TITLES - Static variable in interface org.biojava.bibliography.BibRefSupport
A vocabulary name.
jState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
Gets the J loop state
JukesCantor(String, String) - Static method in class org.biojavax.bio.phylo.MultipleHitCorrection
 
jumpTo(UkkonenSuffixTree.SuffixNode, CharSequence, int, int) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
Just like walkTo, but faster when used during tree construction, as it assumes that a mismatch can only occurs with the last character of the target string.

K

k() - Static method in class org.biojava.bio.seq.DNATools
 
k() - Static method in class org.biojava.bio.seq.NucleotideTools
 
k() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Lysine
kernel - Static variable in class org.biojava.stats.svm.SparseVector
 
KEY_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
KEY_QUERY_ID - Static variable in interface org.biojava.bio.search.BlastLikeSearchFilter
 
KeyedWeakReference - Class in org.biojava.utils.cache
Subclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has been enqueued.
KeyedWeakReference(Object, Object) - Constructor for class org.biojava.utils.cache.KeyedWeakReference
 
KeyedWeakReference(Object, Object, ReferenceQueue) - Constructor for class org.biojava.utils.cache.KeyedWeakReference
 
keys() - Method in class org.biojava.bio.AbstractAnnotation
 
keys() - Method in interface org.biojava.bio.Annotation
Get a set of key objects.
keys() - Method in class org.biojava.bio.MergeAnnotation
 
keys() - Method in class org.biojava.bio.OverlayAnnotation
Return a Set containing all key objects visible in this annotation.
keys() - Method in class org.biojavax.EmptyRichAnnotation
Get a set of key objects.
keys() - Method in class org.biojavax.SimpleRichAnnotation
Get a set of key objects.
KEYS - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
KEYS is the key used to identify the secondary namespaces in the OBDA config.dat files.
keySet() - Method in class org.biojava.utils.OverlayMap
 
keySet() - Method in class org.biojava.utils.SmallMap
 
KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
keywords - Variable in class org.biojava.bibliography.BiblioSubject
The keywords are usually (but not limited to) one word long.
KEYWORDS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
KEYWORDS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
KEYWORDS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
KimuraTwoParameter(String, String) - Static method in class org.biojavax.bio.phylo.MultipleHitCorrection
 
KLDistance(Distribution, Distribution, double) - Static method in class org.biojava.bio.dist.DistributionTools
A method to calculate the Kullback-Liebler Distance (relative entropy).
KnuthMorrisPrattSearch - Class in org.biojava.bio.search
An object to find exact subsequences within a sequence.
KnuthMorrisPrattSearch(SymbolList) - Constructor for class org.biojava.bio.search.KnuthMorrisPrattSearch
Constructs a KMP matcher to find exact occurances of pattern in text using the Knuth-Morris-Pratt algorithm.

L

l() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Leucine
L_ESCULENTUM - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
label - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement
 
Label - Class in org.biojava.utils.bytecode
A Label used to mark a position in byte code.
Label() - Constructor for class org.biojava.utils.bytecode.Label
 
Label(String) - Constructor for class org.biojava.utils.bytecode.Label
 
LABEL - Static variable in class org.biojava.bio.gui.sequence.AlignmentRenderer
 
LABEL - Static variable in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
 
LABEL_MAKER - Static variable in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
 
LabelledSequenceRenderer - Class in org.biojava.bio.gui.sequence
Renderer which draws a track of sequence with a textual label.
LabelledSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
Creates new LabelledSequenceRenderer with default width and depth;
LabelledSequenceRenderer(double, double) - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
Creates new LabelledSequenceRenderer with the specified width and depth.
LabelledSequenceRenderer(String, SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
LabelledVector(SparseVector, double) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
LabelledVector(SparseVector, double, String) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
labelOrder - Variable in class org.biojava.bio.alignment.FlexibleAlignment
 
LabelRenderer - Interface in org.biojava.bio.gui.sequence
The interface for things that can render labels for a line of information about a sequence.
LabelRenderer.RenderNothing - Class in org.biojava.bio.gui.sequence
 
labelsAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment
 
labelsAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
labelsAt(int) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment
Returns a list labels, of all seqs that cover that column
labelsInRange(Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment
 
labelsInRange(Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
labelsInRange(Location) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment
Returns list of all the labels that intersect that range
LANE - Static variable in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
language - Variable in class org.biojava.bibliography.BiblioDescription
language - Variable in class org.biojava.bibliography.BibRef
It defines a language of the intellectual contents of the cited resource.
LANGUAGES - Static variable in interface org.biojava.bibliography.BibRefSupport
A vocabulary name.
LargeBuffer - Class in org.biojava.utils.io
Wrapper arround MappedByteBuffers to allow long-indexed access to files larger than 2 gigs.
LargeBuffer(FileChannel, FileChannel.MapMode, long, long) - Constructor for class org.biojava.utils.io.LargeBuffer
 
lastCol() - Method in interface org.biojava.bio.dp.onehead.DPCursor
The previous column.
lastCol() - Method in class org.biojava.bio.dp.onehead.SmallCursor
 
lastModifiedDate - Variable in class org.biojava.bibliography.BiblioEntryStatus
It defines when the citation record was added or last modified.
lastNonGap() - Method in interface org.biojava.bio.symbol.GappedSymbolList
Return the index of the last Symbol that is not a Gap character.
lastNonGap() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
lastPage - Variable in class org.biojava.bibliography.BiblioArticle
Last page of the article.
lastRes() - Method in interface org.biojava.bio.dp.onehead.DPCursor
The previous symbol.
layer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
LayeredRenderer - Class in org.biojava.bio.gui.sequence
LayeredRenderer handles the lane offsets for MultiLineRenders.
LayeredRenderer() - Constructor for class org.biojava.bio.gui.sequence.LayeredRenderer
 
LAYOUT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext
 
LazyFeatureHolder - Class in org.biojava.bio.seq
Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.
LazyFeatureHolder() - Constructor for class org.biojava.bio.seq.LazyFeatureHolder
Construct a LazyFeatureHolder with the schema of its contained featureholder
LazyFeatureHolder(FeatureFilter) - Constructor for class org.biojava.bio.seq.LazyFeatureHolder
Construct a LazyFeatureHolder with the specified schema
LazyFilteredAnnotationDB - Class in org.biojava.bio.annodb
An implementation of AnnotationDB that lazily applies a filter.
LazyFilteredAnnotationDB(String, AnnotationDB, AnnotationType) - Constructor for class org.biojava.bio.annodb.LazyFilteredAnnotationDB
Create a new DB by wrapping another with a schema.
LazyFilterFeatureHolder - Class in org.biojava.bio.seq.impl
FeatureHolder which lazily applies a specified filter to another FeatureHolder.
LazyFilterFeatureHolder(FeatureHolder, FeatureFilter) - Constructor for class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
LazySearchedAnnotationDB - Class in org.biojava.bio.annodb
An implementation of AnnotationDB that does a JIT search on another set.
LazySearchedAnnotationDB(String, AnnotationDB, AnnotationType) - Constructor for class org.biojava.bio.annodb.LazySearchedAnnotationDB
Create a new DB from an old one by applying a schema.
le - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
leaf - Static variable in interface org.biojava.bio.seq.FeatureFilter
A filter which accepts features with no children
leaf() - Static method in class org.biojava.bio.seq.FilterUtils
Return a filter which matches features with zero children.
leftIndent(String, int) - Static method in class org.biojavax.utils.StringTools
Takes an input string and appends spaces to the left.
leftMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment
leftMost and rightMost return labels.
leftPad(String, char, int) - Static method in class org.biojavax.utils.StringTools
Pads a string to be a certain width by prepending given symbols.
leftPad(String, int) - Static method in class org.biojavax.utils.StringTools
Pads a string to be a certain width by prepending spaces.
LeftRightLocationComparator() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
 
LEFTVALUE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
length - Variable in class org.biojava.bio.symbol.Edit
 
length() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
length() - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
length() - Method in class org.biojava.bio.alignment.SimpleAlignment
 
length() - Method in interface org.biojava.bio.dp.onehead.DPCursor
The length of the sequence.
length() - Method in class org.biojava.bio.dp.onehead.SmallCursor
 
length() - Method in class org.biojava.bio.dp.SimpleStatePath
 
length() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
length() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
length() - Method in class org.biojava.bio.seq.impl.DummySequence
 
length() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
length() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
length() - Method in class org.biojava.bio.seq.impl.SubSequence
 
length() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
length() - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
 
length() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
length() - Method in class org.biojava.bio.seq.SimpleAssembly
 
length() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
 
length() - Method in class org.biojava.bio.symbol.DummySymbolList
 
length() - Method in class org.biojava.bio.symbol.PackedSymbolList
 
length() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
length() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
length() - Method in class org.biojava.bio.symbol.SimpleSymbolList
Get the length of this SymbolList.
length() - Method in interface org.biojava.bio.symbol.SymbolList
The number of symbols in this SymbolList.
length() - Method in class org.biojava.utils.io.RandomAccessReader
length returns the length of the underlying RandomAccessFile.
length() - Method in class org.biojava.utils.RepeatedCharSequence
 
length() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
The number of symbols in this SymbolList.
length() - Method in class org.biojavax.bio.seq.SimpleRichSequence
The number of symbols in this SymbolList.
length() - Method in class org.biojavax.bio.seq.ThinRichSequence
The number of symbols in this SymbolList.
LENGTH_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
lesser(int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
LessThan(double) - Constructor for class org.biojava.bio.search.FilterTest.LessThan
 
leu() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Leucine (L)
LIBRARY_ANNOTATION - Static variable in class org.biojava.bio.program.unigene.UnigeneTools
Annotation schema for all Unigene libraries.
LifeScienceIdentifier - Class in org.biojava.utils.lsid
Life Science Identifier (LSID).
LifeScienceIdentifierParseException - Exception in org.biojava.utils.lsid
Exception thrown in the event of an error in parsing a LSID-formatted string.
LifeScienceIdentifierParseException() - Constructor for exception org.biojava.utils.lsid.LifeScienceIdentifierParseException
Construct a new parse exception with no message.
LifeScienceIdentifierParseException(String) - Constructor for exception org.biojava.utils.lsid.LifeScienceIdentifierParseException
Construct a new parse exception with the specified error message.
Ligand - Class in org.biojava.bio.program.formats
 
Ligand.Compound - Class in org.biojava.bio.program.formats
 
Ligand.Enzyme - Class in org.biojava.bio.program.formats
 
Ligand.Reaction - Class in org.biojava.bio.program.formats
 
LightPairDPCursor - Class in org.biojava.bio.dp.twohead
A LIGHT implementation of PairDPCursor.
LightPairDPCursor(SymbolList, SymbolList, int, int, int, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.LightPairDPCursor
Constructor for the LightPairDPCursor object
line - Variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
line is the line to be drawn for each feature.
line - Variable in class org.biojava.ontology.obo.OboFileParser
 
LINEAGE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LINEAGE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LinearKernel - Class in org.biojava.stats.svm
Deprecated.
Just use SparseVector.kernel instead...
LinearKernel() - Constructor for class org.biojava.stats.svm.LinearKernel
Deprecated.
 
LineInfo - Class in org.biojava.bio.gui.sequence
Encapsulates the rendering info for a single line of the display.
LineInfo() - Constructor for class org.biojava.bio.gui.sequence.LineInfo
 
lineIterator() - Method in class org.biojava.bio.program.gff.GFFEntrySet
Loop over all lines in the set.
linenum - Variable in class org.biojava.ontology.obo.OboFileParser
 
LineSplitParser - Class in org.biojava.bio.program.tagvalue
A parser that splits a line into tag/value at a given column number.
LineSplitParser() - Constructor for class org.biojava.bio.program.tagvalue.LineSplitParser
 
LineSplitParser(LineSplitParser) - Constructor for class org.biojava.bio.program.tagvalue.LineSplitParser
 
lineWidth - Variable in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
The line width for output.
list(String) - Method in class org.biojava.naming.ObdaContext
 
list(Name) - Method in class org.biojava.naming.ObdaContext
 
listBindings(String) - Method in class org.biojava.naming.ObdaContext
 
listBindings(Name) - Method in class org.biojava.naming.ObdaContext
 
listener - Variable in class org.biojava.utils.IndexedChangeHub.ListenerMemento
 
ListenerMemento(ChangeType, Reference) - Constructor for class org.biojava.utils.IndexedChangeHub.ListenerMemento
 
listIntersection(List<String>, List<String>) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
ListSumKernel - Class in org.biojava.stats.svm
This kernel computes the sum of the dot products between items of two lists at corresponding indexes.
ListSumKernel() - Constructor for class org.biojava.stats.svm.ListSumKernel
 
ListTools - Class in org.biojava.utils
 
ListTools() - Constructor for class org.biojava.utils.ListTools
 
ListTools.Doublet - Class in org.biojava.utils
 
ListTools.Mapper - Interface in org.biojava.utils
Maps one object to another.
ListTools.SeriesList - Class in org.biojava.utils
A list that represents a series of values.
ListTools.Triplet - Class in org.biojava.utils
 
load(File) - Method in class org.biojava.bio.program.abi.ABIFChromatogram
 
load(File) - Method in class org.biojava.bio.program.scf.SCF
 
load(InputStream) - Method in class org.biojava.bio.program.abi.ABIFChromatogram
 
load(InputStream, long) - Method in class org.biojava.bio.program.scf.SCF
 
load(Class, String) - Method in class org.biojava.utils.TypedProperties
Reads a property list (key and element pairs) from the given file which is interpreted as a resource of the given class.
load(String) - Method in class org.biojava.utils.TypedProperties
Reads a property list (key and element pairs) from the file with the given file name.
loadAlphabets(InputSource) - Static method in class org.biojava.bio.symbol.AlphabetManager
Load additional Alphabets, defined in XML format, into the AlphabetManager's registry.
loadEnzymeFile(InputStream, boolean) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
loadEnzymeFile loads a new REBASE file (or any file using REBASE format #31).
loadUnigene(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
 
loadUnigene(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
 
loadUnigene(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
 
loadUnigene(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
Load a UnigeneDB instance referred to by a URL.
loc - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement
 
LOC_ELEMENT_ACC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOC_ELEMENT_COMPL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOC_ELEMENT_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOC_ELEMENT_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOC_FUZZY_END_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
LOC_FUZZY_START_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
LocalVariable - Class in org.biojava.utils.bytecode
A local variable.
LocalVariable(CodeClass) - Constructor for class org.biojava.utils.bytecode.LocalVariable
Create a new local variable that will store values of a given type.
LocalVariable(CodeClass, String) - Constructor for class org.biojava.utils.bytecode.LocalVariable
Create a new local variable with a type and a name.
location - Variable in class org.biojava.bio.seq.Feature.Template
 
Location - Interface in org.biojava.bio.symbol
A set of integers, often used to represent positions on biological sequences.
LOCATION - Static variable in interface org.biojava.bio.alignment.EditableAlignment
 
LOCATION - Static variable in interface org.biojava.bio.seq.Feature
The location of this feature is being altered.
LOCATION - Static variable in interface org.biojavax.bio.seq.RichFeature
 
LOCATION - Static variable in interface org.biojavax.RankedDocRef
 
LOCATION_BEGIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_COMPL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOCATION_ELEMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOCATION_END_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_POSITION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_SEQ_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LocationHandlerBase - Class in org.biojava.bio.program.xff
Handler to the XFF location type.
LocationHandlerBase() - Constructor for class org.biojava.bio.program.xff.LocationHandlerBase
 
locationToGapped(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Translate a Location onto the gapped view, splitting blocks if necessary
LocationTools - Class in org.biojava.bio.symbol
Tools class containing a number of operators for working with Location objects.
LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
locInAlignment(Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
The location of an individual SymbolList relative to overall Alignment
locInAlignment(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
The location of an individual SymbolList relative to overall Alignment
locInAlignment(Object) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment
The location of an individual SymbolList relative to overall Alignment
locInSeq(Object, Location) - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
lock() - Method in class org.biojava.utils.automata.PatternBlitz
 
lockModel() - Method in class org.biojava.bio.dp.DP
 
LOCUS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
LOCUSID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
LOG_TO_OUT - Static variable in interface org.biojava.utils.ChangeListener
Convenience implementation that echoes all events to out.
log2(double) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
 
log2(double) - Static method in class org.biojava.bio.program.hmmer.ProfileEmissionState
 
LoggingListener(PrintStream) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener
Create a LoggingListener that will log all events to 'out'.
LoggingListener(PrintStream, String) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener
Create a LoggingListener that will log all events to 'out' with a prefix.
LogoContext - Interface in org.biojava.bio.gui
 
LogoPainter - Interface in org.biojava.bio.gui
The interface for something that will draw the sequence logo for a state.
logProb(Symbol) - Method in class org.biojava.bio.program.hmmer.ProfileEmissionState
 
LongElementHandlerBase - Class in org.biojava.utils.stax
StAX handler for any element which just contains a string representation of a long.
LongElementHandlerBase() - Constructor for class org.biojava.utils.stax.LongElementHandlerBase
 
lookingAt() - Method in class org.biojava.utils.regex.Matcher
Attempts to match the input SymbolList, starting at the beginning, against the pattern.
lookup(String) - Static method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Looks up an Option instance based on its string description.
lookup(String) - Method in class org.biojava.naming.ObdaContext
 
lookup(Name) - Method in class org.biojava.naming.ObdaContext
 
lookupLink(String) - Method in class org.biojava.naming.ObdaContext
 
lookupLink(Name) - Method in class org.biojava.naming.ObdaContext
 
lowercaseName() - Method in enum org.biojava.bio.program.fastq.FastqVariant
Return the name of this FASTQ sequence format variant in lowercase-with-dashes style.
lp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
lp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
lp_ipi - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
lp_uniprot - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
lpPre87 - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
LSID_EMBL_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
LSID_EMBL_AA sequence format LSID for EMBL AA.
LSID_EMBL_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
LSID_EMBL_DNA sequence format LSID for EMBL DNA.
LSID_EMBL_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
LSID_EMBL_RNA sequence format LSID for EMBL RNA.
LSID_FASTA_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
LSID_FASTA_AA sequence format LSID for Fasta AA.
LSID_FASTA_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
LSID_FASTA_DNA sequence format LSID for Fasta DNA.
LSID_FASTA_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
LSID_FASTA_RNA sequence format LSID for Fasta RNA.
LSID_GENBANK_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
LSID_GENBANK_AA sequence format LSID for Genbank AA.
LSID_GENBANK_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
LSID_GENBANK_DNA sequence format LSID for Genbank DNA.
LSID_GENBANK_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
LSID_GENBANK_RNA sequence format LSID for Genbank RNA.
LSID_SWISSPROT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
LSID_SWISSPROT sequence format LSID for Swissprot.
lys() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Lysine (K)
LYS_C - Static variable in class org.biojava.bio.proteomics.Protease
 
LYS_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager
 

M

m() - Static method in class org.biojava.bio.seq.DNATools
 
m() - Static method in class org.biojava.bio.seq.NucleotideTools
 
m() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Methionine
M_MUSCULUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
M_TRUNCULATA - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
MAGICAL_STATE - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
 
magicalState() - Method in interface org.biojava.bio.dp.MarkovModel
The MagicalState for this model.
magicalState() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
magicalState() - Method in class org.biojava.bio.dp.WMAsMM
 
MagicalState - Class in org.biojava.bio.dp
Start/end state for HMMs.
main(String[]) - Static method in class org.biojava.App
 
main(String[]) - Static method in class org.biojava.bio.search.KnuthMorrisPrattSearch
Demo and Test method
main(String[]) - Static method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
Test this class
main(String[]) - Static method in class org.biojava.bio.seq.io.MSFAlignmentFormat
used to quick test the code
main(String[]) - Static method in class org.biojava.stats.svm.tools.ClassifierExample
Entry point for the application.
main(String[]) - Static method in class org.biojava.stats.svm.tools.Classify
 
main(String[]) - Static method in class org.biojava.stats.svm.tools.Train
 
main(String[]) - Static method in class org.biojava.stats.svm.tools.TrainRegression
 
main(String[]) - Static method in class org.biojava.utils.ExecRunner
This is for unit testing of the class.
main(String[]) - Static method in class org.biojava.utils.io.UncompressInputStream
 
main(String[]) - Static method in class org.biojava.utils.JDBCPooledDataSource
 
main(String[]) - Static method in class org.biojava.utils.process.ExternalProcess
Runs an external program from the command line.
main(String[]) - Static method in class org.biojava.utils.xml.AppBeanRunner
 
make(DP) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker
 
make(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
 
make(DP) - Method in class org.biojava.bio.dp.twohead.DPInterpreter.Maker
 
make(SymbolReader) - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
Method to create a Sequence with a SymbolReader.
make_aaload() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the aaload instruction.
make_aastore() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the aastore instruction.
make_aconst_null() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the aconst_null instruction.
make_add(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_aload(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_and(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_areturn() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the areturn instruction.
make_array_load(ParametricType) - Static method in class org.biojava.utils.bytecode.ByteCode
Load an element of a parametric type to an array.
make_arraylength() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the arraylength instruction.
make_arrayStore(ParametricType) - Static method in class org.biojava.utils.bytecode.ByteCode
Store an element of a parametric type to an array.
make_astore(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_athrow() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the athrow instruction.
make_baload() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the baload instruction.
make_bastore() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the bastore instruction.
make_breakpoint() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the breakpoint instruction.
make_caload() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the caload instruction.
make_cast(ParametricType, ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_castore() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the castore instruction.
make_checkcast(CodeClass) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_cmpg(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_cmpl(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_d2f() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the d2f instruction.
make_d2i() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the d2i instruction.
make_d2l() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the d2l instruction.
make_dadd() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dadd instruction.
make_daload() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the daload instruction.
make_dastore() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dastore instruction.
make_dcmpg() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dcmpg instruction.
make_dcmpl() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dcmpl instruction.
make_dconst(double) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_ddiv() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ddiv instruction.
make_div(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_dload(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_dmul() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dmul instruction.
make_dneg() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dneg instruction.
make_drem() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the drem instruction.
make_dreturn() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dreturn instruction.
make_dstore(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_dsub() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dsub instruction.
make_dup() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dup instruction.
make_dup(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_dup_x1() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dup_x1 instruction.
make_dup_x2() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dup_x2 instruction.
make_dup2() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dup2 instruction.
make_dup2_x1() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dup2_x1 instruction.
make_dup2_x2() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the dup2_x2 instruction.
make_f2d() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the f2d instruction.
make_f2i() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the f2i instruction.
make_f2l() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the f2l instruction.
make_fadd() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the fadd instruction.
make_faload() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the faload instruction.
make_fastore() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the fastore instruction.
make_fcmpg() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the fcmpg instruction.
make_fcmpl() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the fcmpl instruction.
make_fconst(float) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_fdiv() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the fdiv instruction.
make_fload(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_fmul() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the fmul instruction.
make_fneg() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the fneg instruction.
make_frem() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the frem instruction.
make_freturn() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the freturn instruction.
make_fstore(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_fsub() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the fsub instruction.
make_getfield(CodeField) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_getstatic(CodeField) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_goto(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_i2b() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the i2b instruction.
make_i2c() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the i2c instruction.
make_i2d() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the i2d instruction.
make_i2f() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the i2f instruction.
make_i2l() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the i2l instruction.
make_i2s() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the i2s instruction.
make_iadd() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the iadd instruction.
make_iaload() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the iaload instruction.
make_iand() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the iand instruction.
make_iastore() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the iastore instruction.
make_iconst(int) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_idiv() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the idiv instruction.
make_if(byte, Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Make an if Instruction for the opcode and label.
make_if_acmpeq(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the if_acmpeq instruction.
make_if_acmpne(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the if_acmpne instruction.
make_if_icmpeq(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the if_icmpeq instruction.
make_if_icmpge(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the if_icmpge instruction.
make_if_icmpgt(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the if_icmpgt instruction.
make_if_icmple(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the if_icmple instruction.
make_if_icmplt(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the if_icmplt instruction.
make_if_icmpne(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the if_icmpne instruction.
make_ifeq(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ifeq instruction.
make_ifge(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ifge instruction.
make_ifgt(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ifgt instruction.
make_ifle(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ifle instruction.
make_iflt(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the iflt instruction.
make_ifne(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ifne instruction.
make_ifnonnull(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ifnonnull instruction.
make_ifnull(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ifnull instruction.
make_iload(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_impdep1() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the impdep1 instruction.
make_impdep2() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the impdep2 instruction.
make_imul() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the imul instruction.
make_ineg() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ineg instruction.
make_instanceof(CodeClass) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_invoke(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode
Make an invoke opcode that is suited to the method.
make_invokeinterface(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_invokespecial(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_invokestatic(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_invokevirtual(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_invokevirtual_quick_w() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the invokevirtual_quick_w instruction.
make_ior() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ior instruction.
make_irem() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the irem instruction.
make_ireturn() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ireturn instruction.
make_ishl() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ishl instruction.
make_ishr() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ishr instruction.
make_istore(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_isub() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the isub instruction.
make_iushr() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the iushr instruction.
make_ixor() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ixor instruction.
make_jsr(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_l2d() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the l2d instruction.
make_l2f() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the l2f instruction.
make_l2i() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the l2i instruction.
make_ladd() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ladd instruction.
make_laload() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the laload instruction.
make_land() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the land instruction.
make_lastore() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lastore instruction.
make_lcmp() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lcmp instruction.
make_lconst(long) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_ldiv() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the ldiv instruction.
make_lload(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_lmul() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lmul instruction.
make_lneg() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lneg instruction.
make_load(ParametricType, LocalVariable) - Method in class org.biojava.utils.bytecode.ByteCode
Load an item of a parametric type from a local variable.
make_lor() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lor instruction.
make_lrem() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lrem instruction.
make_lreturn() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lreturn instruction.
make_lshl() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lshl instruction.
make_lshr() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lshr instruction.
make_lstore(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_lsub() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lsub instruction.
make_lushr() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lushr instruction.
make_lxor() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the lxor instruction.
make_markLabel(Label) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_monitorenter() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the monitorenter instruction.
make_monitorexit() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the monitorexit instruction.
make_mul(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_neg(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_new(CodeClass) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_newarray(CodeClass) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_newraray(ParametricType) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_nop() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the nop instruction.
make_or(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_pop() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the pop instruction.
make_pop2() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the pop2 instruction.
make_putfield(CodeField) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_putstatic(CodeField) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_rem(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_return() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the return instruction.
make_return(CodeClass) - Static method in class org.biojava.utils.bytecode.ByteCode
Creates the return Instruction suitable for a given class or type.
make_return(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode
A convenient one-stop method to get a return statement suitable for a method.
make_return(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
Make a return statement for the parametric type.
make_saload() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the saload instruction.
make_sastore() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the sastore instruction.
make_save(ParametricType, LocalVariable) - Method in class org.biojava.utils.bytecode.ByteCode
Store an item of a parametric type to a local variable.
make_sconst(String) - Static method in class org.biojava.utils.bytecode.ByteCode
 
make_shiftLeft(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_shiftRight(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_shiftRightLogical(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_sub(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
make_swap() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the swap instruction.
make_synchronizedBlock(CodeGenerator) - Static method in class org.biojava.utils.bytecode.ByteCode
Synchronize the processing of an entire block of code on the object on the top of the stack.
make_synchronizedBlock(LocalVariable, CodeGenerator) - Static method in class org.biojava.utils.bytecode.ByteCode
Synchronize the processing of an entire block of code on a local variable.
make_wide() - Static method in class org.biojava.utils.bytecode.ByteCode
Return the Instruction object for the wide instruction.
make_xor(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode
 
makeAnnotation(Map) - Static method in class org.biojava.bio.program.ssbind.AnnotationFactory
makeAnnotation creates the annotation.
makeBatchRequest(URL, Set) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.
makeBatchRequest(URL, Set) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.
makeBatchRequest(URL, Set) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.
makeCircularLocation(int, int, int) - Static method in class org.biojava.bio.symbol.LocationTools
A simple method to generate a RangeLocation wrapped in a CircularLocation.
makeConfigFile(File) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
makeConfigFile returns a file which represents an OBDA "config.dat" in the specified index directory.
makeContext(SequenceRenderContext, RangeLocation) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
 
makeEmptyFeature() - Static method in class org.biojavax.bio.seq.RichFeature.Tools
A way to make a dummy feature
makeFactory(FiniteAlphabet) - Static method in class org.biojava.utils.regex.PatternFactory
Returns a factory for Patterns in the specified Alphabet.
makeHandler(String, String) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory
 
makeHandler(String, String) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory
 
makeHandler(String, String, XMLFilterHandler) - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandlerFactory
 
makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
 
makeLabel(Feature) - Method in interface org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker
 
makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker
 
makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker
 
makeLocation(int, int) - Static method in class org.biojava.bio.symbol.LocationTools
Return a contiguous Location from min to max.
makeName(String, MarkovModel) - Static method in class org.biojava.bio.dp.twohead.DPCompiler
 
makeNewBlock() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
makeNewBlock() - Method in class org.biojavax.bio.phylo.io.nexus.DataBlockBuilder
 
makeNewInsertState(String, Annotation, int[], Distribution) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
 
makeNewMatchState(String, Annotation, int[], Distribution) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
 
makePrimaryKeyFile(File, String) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
makePrimaryKeyFile returns a file which represents an OBDA "key_<primary namespace>.key" primary key file on the specified index directory.
makeProjectionSet(FeatureHolder) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
Called internally to construct a lightweight projected view of a set of features
makeQueryViewSequence(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
 
Maker() - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter.Maker
 
makeReference(Object) - Method in interface org.biojava.utils.cache.Cache
Construct a temporary reference to an object.
makeReference(Object) - Method in class org.biojava.utils.cache.FixedSizeCache
 
makeReference(Object) - Method in class org.biojava.utils.cache.SoftReferenceCache
 
makeRichSequence() - Method in interface org.biojavax.bio.seq.io.RichSequenceBuilder
Build a RichSequence.
makeRichSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Build a RichSequence.
makeSearchResult() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
makeSearchResult() - Method in interface org.biojava.bio.search.SearchBuilder
The makeSearchResult method returns a SeqSimilaritySearchResult instance created from accumulated data.
makeSecondaryFile(File, String) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
makeSecondaryFile returns a file which represents an OBDA "id_<secondary namespace>.index" secondary key file on the specified.
makeSequence() - Method in interface org.biojava.bio.seq.io.SequenceBuilder
Return the Sequence object which has been constructed by this builder.
makeSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
makeSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
makeSequence() - Method in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
create the sequence
makeSequence() - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
 
makeSequence() - Method in class org.biojava.bio.seq.io.SimpleSequenceBuilder
 
makeSequence() - Method in class org.biojava.bio.seq.io.SmartSequenceBuilder
 
makeSequence() - Method in interface org.biojavax.bio.seq.io.RichSequenceBuilder
Return the Sequence object which has been constructed by this builder.
makeSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Return the Sequence object which has been constructed by this builder.
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.EmblProcessor.Factory
Deprecated.
 
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory
Deprecated.
 
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.GenbankProcessor.Factory
Deprecated.
 
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.OrganismParser.Factory
Deprecated.
 
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory
Deprecated.
 
makeSequenceBuilder() - Method in interface org.biojava.bio.seq.io.SequenceBuilderFactory
 
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.SwissprotProcessor.Factory
Deprecated.
 
makeSequenceBuilder() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
makeSequenceBuilder(String) - Method in class org.biojava.bio.seq.io.GenbankProcessor.Factory
Deprecated.
 
makeSequenceBuilder(String) - Method in class org.biojava.bio.seq.io.SwissprotProcessor.Factory
Deprecated.
 
makeSubjectViewSequence(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
 
makeSymbolList() - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
Converts accumulated Symbols to a SymbolList
makeSymbolList(Symbol[], int, Alphabet) - Method in class org.biojava.bio.symbol.PackedSymbolListFactory
Makes a packed SymbolList out of a list of Symbols.
makeSymbolList(Symbol[], int, Alphabet) - Method in class org.biojava.bio.symbol.SimpleSymbolListFactory
Create a factory for SimpleSymbolLists.
makeSymbolList(Symbol[], int, Alphabet) - Method in interface org.biojava.bio.symbol.SymbolListFactory
makes a SymbolList containing size Symbols from a Symbol array.
makeTemplate() - Method in interface org.biojava.bio.seq.Feature
Create a new Template that could be used to generate a feature identical to this one.
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
makeTemplate() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Create a new Template that could be used to generate a feature identical to this one.
makeTemplate(Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils
 
MAN_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
Homo sapiens codon preferences
mAnnotFilter - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
The AnnotationMap to use for getting AGAVE XML attributes from a Sequence Annotation.
ManyToOneTranslationTable - Interface in org.biojava.bio.symbol
A translation table that will handle the many-to-one mappings that you see, for example, with genetic codes.
map(Object) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
map(Object) - Method in interface org.biojava.utils.ListTools.Mapper
Map the object.
map(Set<String>) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
mapList(List, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools
 
mapLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
 
mapMap(Map, ListTools.Mapper, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools
 
MappedDataStoreFactory - Class in org.biojava.bio.program.ssaha
Builder for a data store that is backed by a java.nio.MappedByteBuffer.
MappedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.MappedDataStoreFactory
 
mapSet(Set, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools
 
mark(int) - Method in class org.biojava.utils.io.CountedBufferedReader
 
markLabel(Label) - Method in interface org.biojava.utils.bytecode.CodeContext
Mark a label at the current point in the stream.
MarkLabel - Class in org.biojava.utils.bytecode
A CodeGenerator that just marks a label that can be used for jumps.
MarkLabel(Label) - Constructor for class org.biojava.utils.bytecode.MarkLabel
 
MarkovModel - Interface in org.biojava.bio.dp
A markov model.
markSupported() - Method in class org.biojava.utils.io.CountedBufferedReader
 
markSupported() - Method in class org.biojava.utils.io.UncompressInputStream
This stream does not support mark/reset on the stream.
mask(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
Masks a token by making it lowercase
mask(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
Present the token for a Symbol as it would appear if masked
maskSequence(Sequence, RangeLocation) - Static method in class org.biojava.bio.seq.SequenceTools
Mask of a sequence.
MASS_SPECTROMETRY - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
A name for a comment type.
MassCalc - Class in org.biojava.bio.proteomics
MassCalc calculates the mass of peptides which for our purposes are SymbolLists which contain Symbolsfrom the protein Alphabet.
MassCalc(String, boolean) - Constructor for class org.biojava.bio.proteomics.MassCalc
Creates a new MassCalc.
matcher(SymbolList) - Method in interface org.biojava.bio.search.BioPattern
Get a matcher that will use these parameters to search a SymbolList.
matcher(SymbolList) - Method in class org.biojava.bio.search.MaxMismatchPattern
 
matcher(SymbolList) - Method in class org.biojava.bio.search.SeqContentPattern
 
matcher(SymbolList) - Method in class org.biojava.utils.regex.Pattern
Creates a matcher that will match the given input against this pattern.
Matcher - Class in org.biojava.utils.regex
This class is analogous to java.util.Matcher except that it works on SymbolLists instead of Strings.
matches() - Method in class org.biojava.utils.regex.Matcher
Attempts to match the entire input sequence against the pattern.
matchingTypes() - Method in class org.biojava.utils.ChangeType
Return an iterator which contains this type, and all supertypes.
MatchRegex(String) - Constructor for class org.biojava.bio.search.FilterTest.MatchRegex
 
mathExp(double) - Method in class org.biojava.bio.dp.BaumWelchTrainer
 
MatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
 
MatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.MatrixPairDPCursor
 
max - Variable in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
 
MAX_CROSSES - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
 
MaximalResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.MaximalResolver
 
MaximumGeneration(int) - Constructor for class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
Public Constructer
maximumQualityScore() - Method in enum org.biojava.bio.program.fastq.FastqVariant
Return the maximum quality score for this FASTQ sequence format variant.
maxIndex() - Method in class org.biojava.stats.svm.SparseVector
 
maxLength() - Method in class org.biojava.bio.symbol.SuffixTree
Return the length of the longest motif represented in this SuffixTree
MaxMismatchMatcher - Class in org.biojava.bio.search
A BioMatcher class returned by MaxMismatchPattern.matcher() that implements searching of a SymbolList.
MaxMismatchPattern - Class in org.biojava.bio.search
This class permits searching a SymbolList with another SymbolList while permitting a specified number of mismatches.
MaxMismatchPattern() - Constructor for class org.biojava.bio.search.MaxMismatchPattern
 
MaxMismatchPattern(SymbolList, int) - Constructor for class org.biojava.bio.search.MaxMismatchPattern
 
MEDLINE_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
Holds a reference to the key that must be used to store Medline references.
MEDLINE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
MEDLINE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
members - Variable in class org.biojavax.bio.seq.CompoundRichLocation
 
Meme - Class in org.biojava.bio.program
The results of a meme run.
Meme(InputStream, SymbolTokenization) - Constructor for class org.biojava.bio.program.Meme
 
merge(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
Takes a set of locations and tries to merge all pairs where the union operation results in a simple rich location, not a compound one.
merge(Set, Set) - Static method in class org.biojava.utils.MergingSet
 
MergeAnnotation - Class in org.biojava.bio
Merged view onto a list of underlying Annotation objects.
MergeAnnotation() - Constructor for class org.biojava.bio.MergeAnnotation
 
MergeAnnotation.PropertyForwarder - Class in org.biojava.bio
Listener used to forward changes for any of the underlying annotations to listeners on this annotation.
MergeFeatureHolder - Class in org.biojava.bio.seq
FeatureHolder which exposes all the features in a set of sub-FeatureHolders.
MergeFeatureHolder() - Constructor for class org.biojava.bio.seq.MergeFeatureHolder
Create a new, empty, MergeFeatureHolder.
MergeLocation - Class in org.biojava.bio.symbol
Produced by LocationTools as a result of union operations.
mergeLocations(List) - Static method in class org.biojava.bio.symbol.MergeLocation
Static Factory method for getting an instance of a MergeLocation
mergeLocations(Location, Location) - Static method in class org.biojava.bio.symbol.MergeLocation
 
MergingAnnotationDB - Class in org.biojava.bio.annodb
An AnnotationDB that provides a merged view of a list of underlying DBs.
MergingAnnotationDB(String) - Constructor for class org.biojava.bio.annodb.MergingAnnotationDB
Create a new MergingAnnotationDB with a name and no DBs to merge.
MergingAnnotationDB(String, List) - Constructor for class org.biojava.bio.annodb.MergingAnnotationDB
Create a new MergingAnnotationDB with a name and a list of DBs to merge.
MergingIterator - Class in org.biojava.utils
 
MergingIterator(Iterator) - Constructor for class org.biojava.utils.MergingIterator
 
MergingSet - Class in org.biojava.utils
 
MergingSet() - Constructor for class org.biojava.utils.MergingSet
 
MergingSet(Set) - Constructor for class org.biojava.utils.MergingSet
 
met() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Methionine (M)
META_DATA_TYPE - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
AnnotationType that all meta-data files should fit.
mFilter - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
writes PCDATA replacing XML characters with escape entities
midInitials - Variable in class org.biojava.bibliography.BiblioPerson
Any middle innitials.
min - Variable in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
 
min(int, int, int) - Static method in class org.biojava.bio.alignment.NeedlemanWunsch
This just computes the minimum of three integer values.
mIndent - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
Base indent
mIndent - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
indent
MinimalResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.MinimalResolver
 
minimumQualityScore() - Method in enum org.biojava.bio.program.fastq.FastqVariant
Return the minimum quality score for this FASTQ sequence format variant.
mismatchCount() - Method in class org.biojava.bio.search.MaxMismatchMatcher
Returns number of mismatches
MITOGENETICCODE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
mListeners - Variable in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
 
model - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
model() - Method in interface org.biojava.bio.dp.DPMatrix
 
model() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
model() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
 
ModelInState - Interface in org.biojava.bio.dp
A state that contains an entire sub-model.
ModelTrainer - Interface in org.biojava.bio.dp
Encapsulates the training of an entire model.
modifiableMerge() - Static method in class org.biojava.utils.MergingSet
 
modifiableMerge(Set) - Static method in class org.biojava.utils.MergingSet
 
MODIFY - Static variable in interface org.biojava.bio.program.homologene.OrthologueSet
 
MODIFY - Static variable in interface org.biojava.bio.program.homologene.OrthoPairSet
 
modifyAttributes(String, int, Attributes) - Method in class org.biojava.naming.ObdaContext
 
modifyAttributes(String, ModificationItem[]) - Method in class org.biojava.naming.ObdaContext
 
modifyAttributes(Name, int, Attributes) - Method in class org.biojava.naming.ObdaContext
 
modifyAttributes(Name, ModificationItem[]) - Method in class org.biojava.naming.ObdaContext
 
modulateCircularIndex(int, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.
modulateCircularLocation(int, int, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
Takes a start and end position on a circular location of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence.
modulateCircularLocationPair(Location, Location, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
Takes two circular locations of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence.
MOLD_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the mold mitochondrial genetic code.
MOLTYPE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
MONO_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 
MotifTools - Class in org.biojava.bio.symbol
MotifTools contains utility methods for sequence motifs.
MotifTools() - Constructor for class org.biojava.bio.symbol.MotifTools
 
MOUSE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
Mus musculus codon preferences
mouseClicked(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener
 
mouseDragged(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerMotionListener
 
mouseMoved(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerMotionListener
 
mousePressed(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener
 
mouseReleased(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener
 
mOut - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
Write to XML document
MP(TaxaBlock, CharactersBlock) - Static method in class org.biojavax.bio.phylo.ParsimonyTreeMethod
 
MSF - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
MSF indicates that the alignment format is MSF.
MSF_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
MSF_AA premade MSF | AA;
MSF_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
MSF_DNA premade MSF | DNA;
MSF_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
MSF_DNA premade MSF | RNA;
MSFAlignmentFormat - Class in org.biojava.bio.seq.io
 
MSFAlignmentFormat() - Constructor for class org.biojava.bio.seq.io.MSFAlignmentFormat
 
MultiLineRenderer - Class in org.biojava.bio.gui.sequence
MultiLineRenderer is a SequenceRenderer which collects a number of other SequenceRenderers each of which render their own view of a Sequence.
MultiLineRenderer() - Constructor for class org.biojava.bio.gui.sequence.MultiLineRenderer
 
MULTIPLE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
MULTIPLE - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
 
MultipleHitCorrection - Class in org.biojavax.bio.phylo
 
MultipleHitCorrection() - Constructor for class org.biojavax.bio.phylo.MultipleHitCorrection
 
MultipleScalar(SuffixTreeKernel.DepthScaler, SuffixTreeKernel.DepthScaler) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
 
MultiSourceCompoundRichLocation - Class in org.biojavax.bio.seq
An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.
MultiSourceCompoundRichLocation(Collection) - Constructor for class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
Constructs a MultiSourceCompoundRichLocation from the given set of members, with the default term of "join".
MultiSourceCompoundRichLocation(ComparableTerm, Collection) - Constructor for class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
Constructs a MultiSourceCompoundRichLocation from the given set of members.
MultiTagger - Class in org.biojava.bio.program.tagvalue
Partician multiple values for a tag into their own tag groups.
MultiTagger(TagValueListener, BoundaryFinder) - Constructor for class org.biojava.bio.program.tagvalue.MultiTagger
 
mutate(SymbolList) - Method in interface org.biojavax.ga.functions.MutationFunction
Produces a new SymbolList by mutation.
mutate(SymbolList) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
mutate(SymbolList) - Method in class org.biojavax.ga.functions.SimpleMutationFunction
 
mutate(SymbolList) - Method in class org.biojavax.ga.functions.SwapMutationFunction
 
MUTATION_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
 
MUTATION_PROBS - Static variable in interface org.biojavax.ga.functions.MutationFunction
 
MUTATION_SPECTRUM - Static variable in interface org.biojavax.ga.functions.MutationFunction
 
MutationFunction - Interface in org.biojavax.ga.functions
A class that mutates a SymbolList
MutationFunction.NoMutation - Class in org.biojavax.ga.functions
Place Holder class that doesn't mutate its SymbolLists
mutuallyExclusiveWith - Variable in class org.biojava.bibliography.BiblioCriterion
A list of other criteria names that this criterion is mutually exclusive with.
mWriteDocType - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
write DOCTYPE if true
myLocalName - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
MySQLDBHelper - Class in org.biojava.bio.seq.db.biosql
Deprecated.
Use hibernate and org.biojavax.bio.db.*
MySQLDBHelper(Connection) - Constructor for class org.biojava.bio.seq.db.biosql.MySQLDBHelper
Deprecated.
 

N

n() - Static method in class org.biojava.bio.seq.DNATools
 
n() - Static method in class org.biojava.bio.seq.NucleotideTools
 
n() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Asparagine
n() - Static method in class org.biojava.bio.seq.RNATools
 
name - Variable in class org.biojava.bibliography.BiblioCriterion
Each Criterion is identified by its name.
name - Variable in class org.biojava.bibliography.BiblioJournal
A journal title.
name - Variable in class org.biojava.bibliography.BiblioOrganisation
The name of the organisation.
name - Variable in class org.biojava.bibliography.BiblioService
The name of a bibliographic service.
name - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
name - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
 
name - Variable in class org.biojava.utils.bytecode.Label
 
NAME - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
NAME - Static variable in interface org.biojavax.bio.seq.RichFeature
 
NAME - Static variable in interface org.biojavax.ga.Organism
 
NAME - Static variable in interface org.biojavax.ga.Population
 
NAME - Static variable in interface org.biojavax.Namespace
 
NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
NAME_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
names - Variable in class org.biojavax.bio.taxa.SimpleNCBITaxon
 
names() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
Returns the set of unique table names.
names() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB
Returns the set of unique table names.
NAMES - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
 
NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
 
NameSetStringValue(String) - Method in interface org.biojava.bio.seq.io.game.GAMENameCallbackItf
Callback implemented by nesting class to allow nested class to pass string to nesting class for handling.
NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
 
Namespace - Interface in org.biojavax
The namespace of an entry in a database schema.
NAMESPACE - Static variable in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
 
NameTokenization - Class in org.biojava.bio.seq.io
Simple implementation of SymbolTokenization which uses the `name' field of the symbols.
NameTokenization(FiniteAlphabet) - Constructor for class org.biojava.bio.seq.io.NameTokenization
Construct a new NameTokenization, defaulting to case-insensitive.
NameTokenization(FiniteAlphabet, boolean) - Constructor for class org.biojava.bio.seq.io.NameTokenization
 
NARROW_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
NARROW_SYNONYM - Static variable in class org.biojava.ontology.Synonym
 
NATURAL_ORDER - Static variable in interface org.biojava.bio.program.gff.GFFRecord
Comparator which defines a useful sort order for GFF records.
naturalOrder - Static variable in interface org.biojava.bio.symbol.Location
Comparator which orders Locations naturally.
Navg - Static variable in class org.biojava.bio.proteomics.MassCalc
Constant value of Nitrogen average mass
NBRF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
NBRF indicates that the sequence format is NBRF.
NCBI_TAXON_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
NcbiDatabaseURLGenerator - Class in org.biojava.bio.program.blast2html
Simple URL generator for Entrez at the NCBI.
NcbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator
 
NCBIids(Connection) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Returns a Set of all NCBI-Taxon-IDs which are currently stored in the database.
NCBISequenceDB - Class in org.biojava.bio.seq.db
 
NCBISequenceDB() - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB
Default constructor, querys the Genbank nucleotide database on "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi" and retrieves sequences in FastaFormat.
NCBISequenceDB(String, String, String, SequenceFormat) - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB
Parameterized constructor
NCBISequenceDB(String, SequenceFormat) - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB
Parameterized constructor
NCBITaxon - Interface in org.biojavax.bio.taxa
Represents an NCBI Taxon entry, a combination of the taxon and taxon_name tables in BioSQL.
NCBITaxonomyLoader - Interface in org.biojavax.bio.taxa.io
Implementors are able to load taxonomy files and generate sets of NCBITaxon objects that represent them.
NeedlemanWunsch - Class in org.biojava.bio.alignment
Needleman and Wunsch defined the problem of global sequence alignments, from the first till the last symbol of a sequence.
NeedlemanWunsch(short, short, short, short, short, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.NeedlemanWunsch
Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix.
needSlots() - Method in class org.biojava.utils.bytecode.LocalVariable
 
NEGATIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature
Flag to indicate that a feature is on the negative strand.
NEGATIVE_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand
The negative strand is represented by the symbol '-' and has the number -1.
NeighborJoining(TaxaBlock, CharactersBlock) - Static method in class org.biojavax.bio.phylo.DistanceBasedTreeMethod
 
NestedKernel - Class in org.biojava.stats.svm
Encapsulates a kernel that wraps another kernel up.
NestedKernel() - Constructor for class org.biojava.stats.svm.NestedKernel
Create a new NestedKernel.
NestedKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NestedKernel
Create a new NestedKernel that wraps k.
NEW_LINE - Static variable in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat
New-line symbol.
NewAssembledSymbolList - Class in org.biojava.bio.seq.impl
Support class for applications which need to patch together sections of sequence into a single SymbolList.
NewAssembledSymbolList() - Constructor for class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
NewickTreeString() - Constructor for class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString
 
newInstance(Constructor, Object[]) - Method in interface org.biojava.bio.seq.projection.ProjectionEngine.Instantiator
 
newInstance(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
 
newInstance(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
newInstance(Location) - Method in interface org.biojava.bio.symbol.Location
Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
newInstance(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
newInstance(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
newInstance(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
newKey(String, String) - Method in interface org.biojava.ontology.obo.OboFileEventListener
found a new key in the file
newKey(String, String) - Method in class org.biojava.ontology.obo.OboFileHandler
 
newMessage(Class, String, String, String, String) - Static method in exception org.biojava.bio.seq.io.ParseException
Make a new error message.
newOboFileHeader() - Method in interface org.biojava.ontology.obo.OboFileEventListener
parsed a new OBO file header
newOboFileHeader() - Method in class org.biojava.ontology.obo.OboFileHandler
 
NewSimpleAssembly - Class in org.biojava.bio.seq
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
NewSimpleAssembly(int, String, String) - Constructor for class org.biojava.bio.seq.NewSimpleAssembly
Construct a new SimpleAssembly using the DNA alphabet.
NewSimpleAssembly(String, String) - Constructor for class org.biojava.bio.seq.NewSimpleAssembly
Construct a new NewSimpleAssembly using the DNA alphabet.
newStanza(String) - Method in interface org.biojava.ontology.obo.OboFileEventListener
parsed a new stanza in the file
newStanza(String) - Method in class org.biojava.ontology.obo.OboFileHandler
 
newSynonym(Synonym) - Method in interface org.biojava.ontology.obo.OboFileEventListener
a new synonym has been found
newSynonym(Synonym) - Method in class org.biojava.ontology.obo.OboFileHandler
 
next() - Method in class org.biojava.bio.alignment.Alignment.SymbolListIterator
 
next() - Method in class org.biojava.bio.dp.DP.ReverseIterator
 
next() - Method in class org.biojava.utils.MergingIterator
 
next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
 
next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
Description of the Method
next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.MatrixPairDPCursor
 
next(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.PairDPCursor
retrieve the next block of cells
nextBioEntry() - Method in interface org.biojavax.bio.BioEntryIterator
 
nextBioEntry() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator
 
nextBioEntry() - Method in class org.biojavax.bio.seq.io.RichStreamReader
nextBioEntry() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
nextOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthologueSet.Iterator
 
nextOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet.Iterator
 
nextOrthoPair() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet.Iterator
 
nextOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet.Iterator
 
nextRequest() - Method in class org.biojava.utils.SimpleThreadPool
nextRequest gets the next Runnable from the queue.
nextRichSequence() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator
 
nextRichSequence() - Method in class org.biojavax.bio.seq.io.RichStreamReader
nextRichSequence() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
nextRichSequence() - Method in interface org.biojavax.bio.seq.RichSequenceIterator
 
nextSequence() - Method in class org.biojava.bio.seq.io.StreamReader
Pull the next sequence out of the stream.
nextSequence() - Method in interface org.biojava.bio.seq.SequenceIterator
Returns the next sequence in the iterator.
nextSequence() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator
 
nextSequence() - Method in class org.biojavax.bio.seq.io.RichStreamReader
Returns the next sequence in the iterator.
nextSequence() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
Returns the next sequence in the iterator.
nextSet() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection.Iterator
returns the next OrthoPairSet
nextSet() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection.Iterator
 
nextTable() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
Returns the next SymbolPropertyTable object.
nextTable() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator
Returns the next SymbolPropertyTable object.
nextWord(SymbolList, int, int, int, Packing) - Static method in class org.biojava.bio.symbol.PackingFactory
 
NexusBlock - Interface in org.biojavax.bio.phylo.io.nexus
Represents a Nexus block.
NexusBlock.Abstract - Class in org.biojavax.bio.phylo.io.nexus
 
NexusBlockBuilder - Interface in org.biojavax.bio.phylo.io.nexus
Builds a Nexus block from listening to events.
NexusBlockBuilder.Abstract - Class in org.biojavax.bio.phylo.io.nexus
This abstract version knows how to build and add comments.
NexusBlockListener - Interface in org.biojavax.bio.phylo.io.nexus
Listens to events from NexusBlockParser objects to create objects.
NexusBlockParser - Interface in org.biojavax.bio.phylo.io.nexus
Parses Nexus blocks.
NexusBlockParser.Abstract - Class in org.biojavax.bio.phylo.io.nexus
All block parsers should derive from this abstract parser.
NexusComment - Class in org.biojavax.bio.phylo.io.nexus
Represents a Nexus comment, possibly nested.
NexusComment() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusComment
 
NexusFile - Class in org.biojavax.bio.phylo.io.nexus
Represents Nexus files.
NexusFile() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusFile
 
NexusFileBuilder - Class in org.biojavax.bio.phylo.io.nexus
Builds a Nexus file by listening to events.
NexusFileBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
 
NexusFileFormat - Class in org.biojavax.bio.phylo.io.nexus
Reads/writes Nexus files and fires events at a NexusFileListener object.
NexusFileListener - Interface in org.biojavax.bio.phylo.io.nexus
Listens to events fired by the Nexus parser.
NexusFileListener.Abstract - Class in org.biojavax.bio.phylo.io.nexus
Example abstract implementation which all others should extend.
NexusObject - Interface in org.biojavax.bio.phylo.io.nexus
Represents general info about nexus objects.
Nfa - Class in org.biojava.utils.automata
Class for modelling non-deterministic finite automata.
Nfa(String, FiniteAlphabet) - Constructor for class org.biojava.utils.automata.Nfa
 
NfaBuilder - Interface in org.biojava.utils.automata
 
NfaSubModel - Class in org.biojava.utils.automata
This class caches a reference to all objects that it directs its delegate to make.
NIODataStoreFactory - Class in org.biojava.bio.program.ssaha
Builder for a datastore that has no practical file size limit.
NIODataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.NIODataStoreFactory
 
nl() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
Nmono - Static variable in class org.biojava.bio.proteomics.MassCalc
Constant value of Nitrogen monoisotopic mass
NO_CROSS - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
 
NO_FRAME - Static variable in interface org.biojava.bio.program.gff.GFFRecord
Deprecated.
Use GFFTools.NO_FRAME instead
NO_FRAME - Static variable in class org.biojava.bio.program.gff.GFFTools
Flag to indicate that there is no frame info.
NO_MUTATION - Static variable in interface org.biojavax.ga.functions.MutationFunction
 
NO_SCORE - Static variable in interface org.biojava.bio.program.gff.GFFRecord
Deprecated.
Use GFFTools.NO_SCORE instead
NO_SCORE - Static variable in class org.biojava.bio.program.gff.GFFTools
Flag to indicate that there is no score info.
NoCross() - Constructor for class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
NODERANK - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
nodes - Variable in class org.biojava.utils.automata.FiniteAutomaton
 
NoMutation() - Constructor for class org.biojavax.ga.functions.MutationFunction.NoMutation
 
none - Static variable in interface org.biojava.bio.seq.FeatureFilter
No features are selected by this filter.
none - Static variable in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
No features are selected by this filter.
none() - Static method in class org.biojava.bio.seq.FilterUtils
Return a filter which matches no features.
NONE - Static variable in interface org.biojava.bio.AnnotationType
The type that accepts no annotations at all and is the subtype of all other annotations.
NONE - Static variable in class org.biojava.bio.CardinalityConstraint
This cardinality contains no intengers, not even zero.
NONE - Static variable in interface org.biojava.bio.CollectionConstraint
NONE is a constraint which accepts no value for a property under any condition.
NONE - Static variable in interface org.biojava.bio.PropertyConstraint
NONE is a constraint which accepts no value for a property under any condition.
NONE - Static variable in class org.biojava.ontology.OntoTools
 
nonRemoveIterator(Iterator) - Static method in class org.biojava.utils.ListTools
 
normalizeMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
With this method you can get a “normalized” SubstitutionMatrix object; however, since this implementation uses an short matrix, the normalized matrix will be scaled by ten.
NormalizingKernel - Class in org.biojava.stats.svm
Performs a normalization on the results of a nested kernel.
NormalizingKernel() - Constructor for class org.biojava.stats.svm.NormalizingKernel
 
NormalizingKernel(List) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel
Generate a normalizing kernel defined by the SparseVectors in vectors.
NormalizingKernel(SparseVector) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel
Generate a normalizing kernel with the normalizing vector s.
NormalizingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NormalizingKernel
 
normalLengthVector(SparseVector, double) - Static method in class org.biojava.stats.svm.SparseVector
 
not - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
not(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a new filter which is the negation of filter.
not(FeatureFilter.Not, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
not(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils
Operator: FeatureHolder 1 NOT FeatureHolder2
Not(OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Not
 
Not(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Not
 
Not(OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not
 
Not(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.Not
 
Not(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Not
 
Not(BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
 
Note - Interface in org.biojavax
Note is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank.
NOTE - Static variable in interface org.biojavax.bio.seq.RichLocation
 
NOTE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
NotFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
 
NotFilter(GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
 
notifyExit() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.ExitNotification
 
notifyHit(String, int, int, boolean) - Method in interface org.biojava.utils.automata.PatternListener
 
notifyOnExit - Variable in class org.biojava.bio.program.tagvalue.StateMachine.Transition
should the State listener be notified that this transition is leaving the state.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.program.phred.PhredFormat
Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblProcessor
Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankProcessor
Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.
nState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
Gets the n loop state
nucleotideToken(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
Get a single-character token for a Nucleotide symbol
NucleotideTools - Class in org.biojava.bio.seq
Useful functionality for processing nucleotide sequences.
NULL_MAPPER - Static variable in class org.biojava.utils.ListTools
 
NULL_MODEL - Static variable in interface org.biojava.bio.dist.Distribution
Whenever the null model distribution changes the values that would be returned by getWeight, either by being edited or by being replaced, a ChangeEvent with this object as the type should be thrown.
NULL_MODEL - Static variable in interface org.biojava.bio.dp.ScoreType
 
NullModel() - Constructor for class org.biojava.bio.dp.ScoreType.NullModel
 
nullModelForwarder - Variable in class org.biojava.bio.dist.AbstractDistribution
Forwarder for modifications to the null model.
NullModelForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.dist.Distribution.NullModelForwarder
Deprecated.
Create a new forwarder.
NullModelScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
 
numberOfElements - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
numericalEntity(char) - Method in class org.biojava.utils.xml.FastXMLWriter
 
numericalEntity(char) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
numParameters() - Method in interface org.biojava.utils.bytecode.CodeMethod
Get the number of parameters taken by this method
numParameters() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
 
numStates - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
numStates - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
Description of the Field
numTables() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
Returns the number of symbol property tables in the database.
numTables() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB
Returns the number of symbol property tables in the database.

O

o() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Pyrrolysine
O_SATIVA - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
Oavg - Static variable in class org.biojava.bio.proteomics.MassCalc
Constant value of Oxygen average mass
OBDA_SEARCH_ENV - Static variable in class org.biojava.directory.SystemRegistry
 
ObdaContext - Class in org.biojava.naming
 
ObdaInitialContextFactory - Class in org.biojava.naming
 
ObdaInitialContextFactory() - Constructor for class org.biojava.naming.ObdaInitialContextFactory
 
OBDARegistryParser - Class in org.biojava.directory
This class encapsulates all the parsing of the OBDA registry configuration file.
OBDARegistryParser() - Constructor for class org.biojava.directory.OBDARegistryParser
 
ObdaUriParser - Class in org.biojava.naming
Singleton class for parsers that understand OBDA URIs.
objectIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
Iterate over all objects in the file in order.
ObjectUtil - Class in org.biojava.utils
utility methods for implementing the equals() and hashCode() methods of Objects.
ObjectUtil() - Constructor for class org.biojava.utils.ObjectUtil
 
OboFileEventListener - Interface in org.biojava.ontology.obo
an interface for events that occur during parsing of .obo files
OboFileHandler - Class in org.biojava.ontology.obo
A file handler for .obo files
OboFileHandler(Ontology) - Constructor for class org.biojava.ontology.obo.OboFileHandler
 
OboFileParser - Class in org.biojava.ontology.obo
A class to parse the content of an OBO file.
OboFileParser() - Constructor for class org.biojava.ontology.obo.OboFileParser
 
OboFileParser.SOPair - Class in org.biojava.ontology.obo
 
OboParser - Class in org.biojava.ontology.io
Parses an OBO file.
OboParser() - Constructor for class org.biojava.ontology.io.OboParser
 
OBSOLETE - Static variable in interface org.biojavax.ontology.ComparableTerm
 
oColourClassMap - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
Stores mapping from a Colour to a FONT Class.
oColourMap - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
Map between Char and the Colour class.
oColourSet - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
Store the unique colours for markup.
Odds() - Constructor for class org.biojava.bio.dp.ScoreType.Odds
 
ODDS - Static variable in interface org.biojava.bio.dp.ScoreType
 
OFFSET - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
offsetData - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
OffsetRulerRenderer - Class in org.biojava.bio.gui.sequence
OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.
OffsetRulerRenderer() - Constructor for class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
OffsetRulerRenderer(int, int) - Constructor for class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
OFFSETS - Static variable in interface org.biojava.bio.chromatogram.Chromatogram
The sequence label for the trace offsets of the called bases.
Omono - Static variable in class org.biojava.bio.proteomics.MassCalc
Constant value of Oxygen monoisotopic mass
one() - Static method in class org.biojavax.ga.util.GATools
 
ONE - Static variable in class org.biojava.bio.CardinalityConstraint
The property should have exactly one value.
ONE_OR_MORE - Static variable in class org.biojava.bio.CardinalityConstraint
The property should have one or more values.
onlyChildren(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features whose children all match the specified filter.
onlyChildren(FeatureFilter.OnlyChildren, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
OnlyChildren(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
onlyDescendants(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features whose decendants all match the specified filter.
onlyDescendants(FeatureFilter.OnlyDescendants, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
OnlyDescendants(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
Ontology - Interface in org.biojava.ontology
An ontology.
ONTOLOGY - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
ONTOLOGY - Static variable in interface org.biojava.ontology.Term
ChangeType which indicates that this term's ontology has been altered
Ontology.Impl - Class in org.biojava.ontology
A basic in-memory implementation of an ontology
OntologyException - Exception in org.biojava.ontology
Thrown to indicate an error in an Ontology object
OntologyException() - Constructor for exception org.biojava.ontology.OntologyException
 
OntologyException(String) - Constructor for exception org.biojava.ontology.OntologyException
 
OntologyException(String, Throwable) - Constructor for exception org.biojava.ontology.OntologyException
 
OntologyException(Throwable) - Constructor for exception org.biojava.ontology.OntologyException
 
OntologyFactory - Interface in org.biojava.ontology
A factory for Ontology instances.
OntologyOps - Interface in org.biojava.ontology
This is an interface for optimizing ontology operators.
OntologyTerm - Interface in org.biojava.ontology
A term in an ontology which identifies another ontology.
OntologyTerm.Impl - Class in org.biojava.ontology
Simple in-memory implementation of a remote ontology term.
OntoTools - Class in org.biojava.ontology
Tools for manipulating ontologies.
op_aaload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_aastore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_aconst_null - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_aload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_aload_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_aload_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_aload_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_aload_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_anewarray - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_anewarray_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_areturn - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_arraylength - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_astore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_astore_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_astore_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_astore_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_astore_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_athrow - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_baload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_bastore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_bipush - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_breakpoint - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_caload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_castore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_checkcast - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_checkcast_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_d2f - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_d2i - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_d2l - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dadd - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_daload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dastore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dcmpg - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dcmpl - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dconst_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dconst_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ddiv - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dload_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dload_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dload_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dload_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dmul - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dneg - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_drem - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dreturn - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dstore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dstore_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dstore_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dstore_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dstore_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dsub - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dup - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dup_x1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dup_x2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dup2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dup2_x1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_dup2_x2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_f2d - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_f2i - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_f2l - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fadd - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_faload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fastore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fcmpg - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fcmpl - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fconst_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fconst_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fconst_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fdiv - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fload_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fload_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fload_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fload_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fmul - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fneg - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_frem - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_freturn - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fstore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fstore_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fstore_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fstore_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fstore_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_fsub - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_getfield - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_getfield_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_getfield_quick_w - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_getfield2_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_getstatic - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_getstatic_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_getstatic2_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_goto - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_goto_w - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_i2b - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_i2c - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_i2d - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_i2f - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_i2l - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_i2s - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iadd - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iaload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iand - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iastore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iconst_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iconst_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iconst_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iconst_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iconst_4 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iconst_5 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iconst_m1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_idiv - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_if_acmpeq - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_if_acmpne - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_if_icmpeq - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_if_icmpge - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_if_icmpgt - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_if_icmple - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_if_icmplt - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_if_icmpne - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ifeq - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ifge - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ifgt - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ifle - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iflt - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ifne - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ifnonnull - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ifnull - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iinc - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iload_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iload_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iload_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iload_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_impdep1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_impdep2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_imul - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ineg - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_instanceof - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_instanceof_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokeinterface - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokeinterface_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokenonvirtual_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokespecial - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokestatic - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokestatic_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokesuper_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokevirtual - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokevirtual_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokevirtual_quick_w - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_invokevirtualobject_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ior - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_irem - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ireturn - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ishl - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ishr - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_istore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_istore_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_istore_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_istore_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_istore_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_isub - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_iushr - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ixor - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_jsr - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_jsr_w - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_l2d - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_l2f - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_l2i - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ladd - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_laload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_land - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lastore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lcmp - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lconst_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lconst_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ldc - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ldc_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ldc_w - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ldc_w_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ldc2_w - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ldc2_w_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ldiv - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lload_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lload_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lload_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lload_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lmul - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lneg - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lookupswitch - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lor - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lrem - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lreturn - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lshl - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lshr - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lstore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lstore_0 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lstore_1 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lstore_2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lstore_3 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lsub - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lushr - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_lxor - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_monitorenter - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_monitorexit - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_multianewarray - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_multianewarray_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_new - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_new_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_newarray - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_nop - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_pop - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_pop2 - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_putfield - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_putfield_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_putfield_quick_w - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_putfield2_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_putstatic - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_putstatic_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_putstatic2_quick - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_ret - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_return - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_saload - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_sastore - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_sipush - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_swap - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_tableswitch - Static variable in class org.biojava.utils.bytecode.ByteCode
 
op_wide - Static variable in class org.biojava.utils.bytecode.ByteCode
 
open() - Method in interface org.biojava.utils.bytecode.CodeContext
Open the context for writing.
open(File) - Static method in class org.biojava.bio.seq.db.TabIndexStore
Open an existing index store.
openSubComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
 
openTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
openTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
openTag(String) - Method in interface org.biojava.utils.xml.XMLWriter
Open a new unqualified XML tag.
openTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
openTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
Open a new namespace-qualified XML tag.
OptimizableFilter - Interface in org.biojava.bio.seq
The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.
optimize(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with fewer terms.
optionIsTrue(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Helper method for converting a Boolean-valued option into a boolean primitive.
options - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
The map containing the ChromatogramGraphic.Options and values for this instance.
or - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
or(FeatureFilter.Or, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
or(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a new filter which matches the intersection of two filters.
or(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a new filter which matches the union of two filters.
Or(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.Or
Create a new Or from two child constraints.
Or(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Or
 
Or(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Or
 
Or(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or
 
Or(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.Or
Create a new Or from two child constraints.
Or(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.Or
 
Or(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Or
 
Or(BioSQLFeatureFilter, BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
OracleDBHelper - Class in org.biojava.bio.seq.db.biosql
Deprecated.
Use hibernate and org.biojavax.bio.db.*
OracleDBHelper(Connection) - Constructor for class org.biojava.bio.seq.db.biosql.OracleDBHelper
Deprecated.
 
OrderCrossover - Class in org.biojavax.ga.functions
This does a 2-point-crossover on two chromosomes keeping the Symbols in each chromosome constant.
OrderCrossover() - Constructor for class org.biojavax.ga.functions.OrderCrossover
Sets the maximal number of crossover points to two and the crossover probability to 0.5 and initializes this object.
orderedLables(Comparator<String>) - Method in class org.biojava.bio.alignment.AbstractULAlignment
 
OrderNDistribution - Interface in org.biojava.bio.dist
Provides an N'th order distribution.
OrderNDistributionFactory - Class in org.biojava.bio.dist
Default factory for Order-N distributions.
OrderNDistributionFactory(DistributionFactory) - Constructor for class org.biojava.bio.dist.OrderNDistributionFactory
Construct a new OrderNDistributionFactory with a specified factory for conditioned distributions.
orderNSymbolList(SymbolList, int) - Static method in class org.biojava.bio.symbol.SymbolListViews
An n-th order view of another SymbolList.
ORDLOCNAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
ORFNAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
org.biojava - package org.biojava
 
org.biojava.bibliography - package org.biojava.bibliography
The data structures and interfaces included in this package define an interoperable framework for bibliographic searches.
org.biojava.bio - package org.biojava.bio
The core classes that will be used throughout the bio packages.
org.biojava.bio.alignment - package org.biojava.bio.alignment
Classes to generate and describe sequence alignments.
org.biojava.bio.annodb - package org.biojava.bio.annodb
Databases of generic structured data (annotation) objects.
org.biojava.bio.chromatogram - package org.biojava.bio.chromatogram
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.chromatogram.graphic - package org.biojava.bio.chromatogram.graphic
Tools for displaying chromatograms.
org.biojava.bio.dist - package org.biojava.bio.dist
Probability distributions over Alphabets.
org.biojava.bio.dp - package org.biojava.bio.dp
HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead - package org.biojava.bio.dp.onehead
 
org.biojava.bio.dp.twohead - package org.biojava.bio.dp.twohead
 
org.biojava.bio.gui - package org.biojava.bio.gui
Graphical interfaces for biojava objects.
org.biojava.bio.gui.glyph - package org.biojava.bio.gui.glyph
Glyphs implementations that draw shapes into SequenceRenderers
org.biojava.bio.gui.sequence - package org.biojava.bio.gui.sequence
Graphical displays of biological sequences and associated annotations.
org.biojava.bio.gui.sequence.tracklayout - package org.biojava.bio.gui.sequence.tracklayout
Classes for the handling of the layout of a WrappedSequencePanel.
org.biojava.bio.molbio - package org.biojava.bio.molbio
The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program - package org.biojava.bio.program
Java wrappers for interacting with external bioinformatics tools.
org.biojava.bio.program.abi - package org.biojava.bio.program.abi
ABI Trace Handling.
org.biojava.bio.program.blast2html - package org.biojava.bio.program.blast2html
Code for generating HTML reports from blast output
org.biojava.bio.program.fastq - package org.biojava.bio.program.fastq
FASTQ and variants sequence format I/O.
org.biojava.bio.program.formats - package org.biojava.bio.program.formats
Experimental parsers using the tagvalue framework.
org.biojava.bio.program.gff - package org.biojava.bio.program.gff
GFF manipulation.
org.biojava.bio.program.gff3 - package org.biojava.bio.program.gff3
Support for reading and writing GFF3.
org.biojava.bio.program.hmmer - package org.biojava.bio.program.hmmer
Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.homologene - package org.biojava.bio.program.homologene
Support classes for Homologene data.
org.biojava.bio.program.indexdb - package org.biojava.bio.program.indexdb
A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.phred - package org.biojava.bio.program.phred
Parser for Phred output
org.biojava.bio.program.sax - package org.biojava.bio.program.sax
Parsers which offer XML representations of the output from common bioinformatics tools.
org.biojava.bio.program.sax.blastxml - package org.biojava.bio.program.sax.blastxml
Parsers for the XML output from NCBI blast.
org.biojava.bio.program.scf - package org.biojava.bio.program.scf
Support for the SCF chromatogram format.
org.biojava.bio.program.ssaha - package org.biojava.bio.program.ssaha
SSAHA sequence searching API.
org.biojava.bio.program.ssbind - package org.biojava.bio.program.ssbind
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.tagvalue - package org.biojava.bio.program.tagvalue
Process files as streams of records, each with tags with values.
org.biojava.bio.program.unigene - package org.biojava.bio.program.unigene
Objects for representing Unigene clusters.
org.biojava.bio.program.xff - package org.biojava.bio.program.xff
Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.program.xml - package org.biojava.bio.program.xml
Utility classes for the org.biojava.bio.program.sax package.
org.biojava.bio.proteomics - package org.biojava.bio.proteomics
Utilities to aid in performing various physical analysis of proteins.
org.biojava.bio.proteomics.aaindex - package org.biojava.bio.proteomics.aaindex
Classes and interfaces to load Amino Acid Index database files.
org.biojava.bio.search - package org.biojava.bio.search
Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq - package org.biojava.bio.seq
Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db - package org.biojava.bio.seq.db
Collections of biological sequence data.
org.biojava.bio.seq.db.biofetch - package org.biojava.bio.seq.db.biofetch
Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.biosql - package org.biojava.bio.seq.db.biosql
General purpose Sequence storage in a relational database.
org.biojava.bio.seq.db.emblcd - package org.biojava.bio.seq.db.emblcd
Readers for the EMBL CD-ROM format binary index files used by EMBOSS and Staden packages.
org.biojava.bio.seq.db.flat - package org.biojava.bio.seq.db.flat
Support for OBDA flatfile databases.
org.biojava.bio.seq.distributed - package org.biojava.bio.seq.distributed
Sequences and SequenceDBs which are composed from data taken from a number of data sources.
org.biojava.bio.seq.filter - package org.biojava.bio.seq.filter
 
org.biojava.bio.seq.homol - package org.biojava.bio.seq.homol
The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl - package org.biojava.bio.seq.impl
Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io - package org.biojava.bio.seq.io
Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.agave - package org.biojava.bio.seq.io.agave
Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.io.filterxml - package org.biojava.bio.seq.io.filterxml
Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
org.biojava.bio.seq.io.game - package org.biojava.bio.seq.io.game
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.io.game12 - package org.biojava.bio.seq.io.game12
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.projection - package org.biojava.bio.seq.projection
Code for projecting Feature objects and systematically altering their properties.
org.biojava.bio.symbol - package org.biojava.bio.symbol
Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.bio.taxa - package org.biojava.bio.taxa
Taxonomy object for representing species information.
org.biojava.directory - package org.biojava.directory
Open Bio Sequence Database Access (OBDA) registry support.
org.biojava.naming - package org.biojava.naming
 
org.biojava.ontology - package org.biojava.ontology
A general-purpose API for ontologies.
org.biojava.ontology.io - package org.biojava.ontology.io
Tools for loading and saving ontologies.
org.biojava.ontology.obo - package org.biojava.ontology.obo
 
org.biojava.stats.svm - package org.biojava.stats.svm
Support Vector Machine classification and regression.
org.biojava.stats.svm.tools - package org.biojava.stats.svm.tools
Tools for use of the SVM package.
org.biojava.utils - package org.biojava.utils
Miscellaneous utility classes used by other BioJava components.
org.biojava.utils.automata - package org.biojava.utils.automata
 
org.biojava.utils.bytecode - package org.biojava.utils.bytecode
A Java object-model for a Java Bytecode Macro-Assembler.
org.biojava.utils.cache - package org.biojava.utils.cache
A simple cache system with pluggable caching behaviours.
org.biojava.utils.candy - package org.biojava.utils.candy
The data structures and interfaces included in this package define an interoperable framework for simple controlled vocabularies.
org.biojava.utils.io - package org.biojava.utils.io
I/O utility classes.
org.biojava.utils.lsid - package org.biojava.utils.lsid
Life Science Identifier (LSID) package.
org.biojava.utils.math - package org.biojava.utils.math
Mathematical utility classes.
org.biojava.utils.net - package org.biojava.utils.net
Network programming utility classes.
org.biojava.utils.process - package org.biojava.utils.process
Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.
org.biojava.utils.regex - package org.biojava.utils.regex
This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
org.biojava.utils.stax - package org.biojava.utils.stax
The Stack API for XML (StAX).
org.biojava.utils.walker - package org.biojava.utils.walker
 
org.biojava.utils.xml - package org.biojava.utils.xml
Utility classes for handling and generating XML documents.
org.biojavax - package org.biojavax
The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio - package org.biojavax.bio
Classes to represent biological entities and their relationships.
org.biojavax.bio.alignment - package org.biojavax.bio.alignment
This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojavax.bio.alignment.blast - package org.biojavax.bio.alignment.blast
This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services through the WWW.
org.biojavax.bio.db - package org.biojavax.bio.db
Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql - package org.biojavax.bio.db.biosql
Interface between biojava and biosql databases
org.biojavax.bio.db.ncbi - package org.biojavax.bio.db.ncbi
Interfaces to NCBI data.
org.biojavax.bio.phylo - package org.biojavax.bio.phylo
Classes to support phlylogeny objects.
org.biojavax.bio.phylo.io.nexus - package org.biojavax.bio.phylo.io.nexus
Classes to support the I/O of Nexus files.
org.biojavax.bio.phylo.io.phylip - package org.biojavax.bio.phylo.io.phylip
Classes to support the reading and writing of PHYLIP format.
org.biojavax.bio.seq - package org.biojavax.bio.seq
Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io - package org.biojavax.bio.seq.io
Classes to support the I/O of RichSequence and Bioentry objects.
org.biojavax.bio.taxa - package org.biojavax.bio.taxa
Objects that model the NCBI taxonomy schema as described in the BioSQL schema.
org.biojavax.bio.taxa.io - package org.biojavax.bio.taxa.io
 
org.biojavax.ga - package org.biojavax.ga
Classes to provide a genetic algorithm framework
org.biojavax.ga.exception - package org.biojavax.ga.exception
Exceptions related to the GA framework
org.biojavax.ga.functions - package org.biojavax.ga.functions
GA functions
org.biojavax.ga.impl - package org.biojavax.ga.impl
Default implementations and abstract classes.
org.biojavax.ga.util - package org.biojavax.ga.util
Utility functions and helper classes
org.biojavax.ontology - package org.biojavax.ontology
Extensions to the biojava ontology model that represent BioSQL ontology.
org.biojavax.utils - package org.biojavax.utils
Utility classes that are used by biojavax objects but could have wider utility to other applications.
ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
Organism - Interface in org.biojavax.ga
A GA 'organism' contains one or more Chromosomes
ORGANISM_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
ORGANISM_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ORGANISM_XREF_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
OrganismParser - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.taxa framework instead
OrganismParser(SequenceBuilder, TaxonFactory, TaxonParser, String, String, String) - Constructor for class org.biojava.bio.seq.io.OrganismParser
Deprecated.
 
OrganismParser.Factory - Class in org.biojava.bio.seq.io
Deprecated.
Factory which wraps SequenceBuilders in an OrganismParser.
organisms() - Method in class org.biojavax.ga.impl.SimplePopulation
 
organisms() - Method in interface org.biojavax.ga.Population
 
ORGANISMS - Static variable in interface org.biojavax.ga.Population
 
origSeq - Variable in class org.biojava.bio.seq.impl.RevCompSequence
 
Orthologue - Interface in org.biojava.bio.program.homologene
this entry contains data about the orthologue.
OrthologueFilter - Interface in org.biojava.bio.program.homologene
 
OrthologueFilter.AcceptAll - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.And - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByAccession - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByHomologeneID - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByLocusID - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByTaxon - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByTaxonID - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByTitle - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.Not - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.Or - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.Xor - Class in org.biojava.bio.program.homologene
 
OrthologueSet - Interface in org.biojava.bio.program.homologene
Interface for classes that store and manipulate orthologues.
OrthologueSet.Iterator - Interface in org.biojava.bio.program.homologene
An iterator for the contents of an OrthologueSet.
OrthoPair - Interface in org.biojava.bio.program.homologene
Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues.
OrthoPairCollection - Interface in org.biojava.bio.program.homologene
Interface for a Set of OrthoPairSets
OrthoPairCollection.Iterator - Interface in org.biojava.bio.program.homologene
Iterator for a OrthoPairCollection
OrthoPairFilter - Interface in org.biojava.bio.program.homologene
 
OrthoPairFilter.AcceptAll - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.And - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.ByMaxIdentity - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.ByMinIdentity - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.ByRef - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.BySimilarityType - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.Not - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.Or - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.Xor - Class in org.biojava.bio.program.homologene
 
OrthoPairSet - Interface in org.biojava.bio.program.homologene
represents the Homologene Group.
OrthoPairSet.Iterator - Interface in org.biojava.bio.program.homologene
 
OrthoPairSetFilter - Interface in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.AcceptAll - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.AllPairsInCollection - Class in org.biojava.bio.program.homologene
all OrthoPairs must meet the requirement defined by filter.
OrthoPairSetFilter.And - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.ByMinIdentity - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.ByTaxon - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.Not - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.Or - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.SomePairsInCollection - Class in org.biojava.bio.program.homologene
at least one OrthoPair must meet the requirement defined by filter.
OrthoPairSetFilter.Xor - Class in org.biojava.bio.program.homologene
 
OTHER_SEQID_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
OTHER_SEQIDS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
outline - Variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
outline is the line colour.
OUTLINE - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Constant OUTLINE indicating a change to the outline paint of the features.
OUTLINE - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
OUTLINE - Static variable in class org.biojava.bio.gui.sequence.CrosshairRenderer
Constant OUTLINE indicating a change to the crosshair paint.
OUTLINE - Static variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
Constant OUTLINE indicating a change to the fill of the features.
OUTLINE - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
outlinePaint(Symbol) - Method in class org.biojava.bio.gui.DNAStyle
 
outlinePaint(Symbol) - Method in class org.biojava.bio.gui.PlainStyle
 
outlinePaint(Symbol) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
 
outlinePaint(Symbol) - Method in interface org.biojava.bio.gui.SymbolStyle
Return the outline paint for a symbol.
OutputHandler - Interface in org.biojava.utils.process
Interface to a threadable output handler for an external process.
OVERHANG_3PRIME - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
OVERHANG_3PRIME the sticky end type created by enzymes which leave a 3' overhang (e.g. a stretch of single-stranded DNA with a free 3' end).
OVERHANG_5PRIME - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
OVERHANG_5PRIME the sticky end type created by enzymes which leave a 5' overhang (e.g. a stretch of single-stranded DNA with a free 5' end).
overlaps(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
 
overlaps(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
overlaps(Location) - Method in class org.biojava.bio.symbol.CircularLocation
 
overlaps(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
overlaps(Location) - Method in interface org.biojava.bio.symbol.Location
Checks if these two locations overlap, using this location's concept of overlapping.
overlaps(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Checks if these two locations overlap, using this location's concept of overlapping.
overlaps(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Checks if these two locations overlap, using this location's concept of overlapping.
overlaps(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Checks if these two locations overlap, using this location's concept of overlapping.
overlaps(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
Determines whether the locations overlap or not.
overlapsLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features with locations contained by or overlapping the specified Location.
OverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
Creates a filter that returns everything overlapping loc.
overlapsOrigin() - Method in class org.biojava.bio.symbol.CircularLocation
Does the Location overlap the origin (position 1) of the sequence?
OverlapsRichLocation(RichLocation) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
Creates a filter that returns everything overlapping loc.
OverlayAnnotation - Class in org.biojava.bio
Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.
OverlayAnnotation(Annotation) - Constructor for class org.biojava.bio.OverlayAnnotation
Construct an annotation which can overlay new key-value pairs onto an underlying annotation.
OverlayAnnotation.PropertyForwarder - Class in org.biojava.bio
Forwards change events from the underlying Annotation to this one.
OverlayMap - Class in org.biojava.utils
Overlap one map onto another.
OverlayMap(Map) - Constructor for class org.biojava.utils.OverlayMap
Build a new map with default key-value pairs.
OverlayMap(Map, Map) - Constructor for class org.biojava.utils.OverlayMap
Build a new map with default key-value pairs.
OverlayMarker - Interface in org.biojava.bio.gui.sequence
This is a dummy interface to permit identification of renderers whose output is to be overlaid along the lines of the Marker Interface pattern.
OverlayRendererWrapper - Class in org.biojava.bio.gui.sequence
This class wraps SequenceRenderer classes to present an Overlay Marker interface that will indicate to LayeredRenderer that subsequent renderers should overdraw the same space as the wrapped renderer.
OverlayRendererWrapper() - Constructor for class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 
OverlayRendererWrapper(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 

P

p() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Proline
pack(Symbol) - Method in class org.biojava.bio.symbol.DNAAmbPack
 
pack(Symbol) - Method in class org.biojava.bio.symbol.DNANoAmbPack
 
pack(Symbol) - Method in interface org.biojava.bio.symbol.Packing
Return a byte representing the packing of a symbol.
PACKED - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory
Accessor for a factory that produces builders that compress the SymbolList of a RichSequence.
PackedSymbolList - Class in org.biojava.bio.symbol
A SymbolList that stores symbols as bit-patterns in an array of longs.
PackedSymbolList(Packing, long[], int) - Constructor for class org.biojava.bio.symbol.PackedSymbolList
Create a new PackedSymbolList directly from a bit pattern.
PackedSymbolList(Packing, Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.PackedSymbolList
Create a new PackedSymbolList from an array of Symbols.
PackedSymbolList(Packing, SymbolList) - Constructor for class org.biojava.bio.symbol.PackedSymbolList
Create a new PackedSymbolList as a packed copy of another symbol list.
PackedSymbolListFactory - Class in org.biojava.bio.symbol
This class makes PackedSymbolLists.
PackedSymbolListFactory() - Constructor for class org.biojava.bio.symbol.PackedSymbolListFactory
Create a factory for PackedSymbolLists.
PackedSymbolListFactory(boolean) - Constructor for class org.biojava.bio.symbol.PackedSymbolListFactory
Deprecated.
the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately.
Packing - Interface in org.biojava.bio.symbol
An encapsulation of the way symbols map to bit-patterns.
PackingFactory - Class in org.biojava.bio.symbol
A factory that is used to maintain associations between alphabets and preferred bit-packings for them.
PackingFactory() - Constructor for class org.biojava.bio.symbol.PackingFactory
 
PADDING - Static variable in class org.biojava.bio.gui.sequence.PaddingRenderer
Event type for when the size of the padding changes.
PaddingRenderer - Class in org.biojava.bio.gui.sequence
A renderer that adds padding before and after a delegate renderer.
PaddingRenderer() - Constructor for class org.biojava.bio.gui.sequence.PaddingRenderer
Build a new PaddingRenderer with zero padding.
PaddingRenderer(SequenceRenderer, double) - Constructor for class org.biojava.bio.gui.sequence.PaddingRenderer
Build a new PaddingRenderer that wraps renderer and has padding depth padding.
paint(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
paint(Graphics2D, List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
 
paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
 
paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
 
paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularMLR
 
paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularPaddedRenderer
 
paint(Graphics2D, CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularRenderer
Paint this renderer.
paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
 
paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
paint renders the feature as a simple line.
paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
 
paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
paint applies all renderers in the order in which they were added.
paint(Graphics2D, PairwiseRenderContext) - Method in interface org.biojava.bio.gui.sequence.PairwiseSequenceRenderer
paints some or all of the information about the sequence pair.
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
 
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in interface org.biojava.bio.gui.sequence.LabelRenderer
Render a label for the information for sp to g.
paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
 
paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
 
paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in interface org.biojava.bio.gui.BlockPainter
 
paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in class org.biojava.bio.gui.PlainBlock
 
paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in class org.biojava.bio.gui.TextBlock
 
paintComponent(Graphics) - Method in class org.biojava.bio.gui.DistributionLogo
Transforms the graphics context so that it is in bits space, and then requests the logo painter to fill the area.
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
 
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
 
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanel
Paint this component.
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Paint this component.
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
paintComponent paints this component.
paintComponent(Graphics) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Renders this component to display the points, and if present, the support vector machine.
paintLogo(LogoContext) - Method in class org.biojava.bio.gui.BarLogoPainter
 
paintLogo(LogoContext) - Method in interface org.biojava.bio.gui.LogoPainter
Render the state from sl onto the graphics object g.
paintLogo(LogoContext) - Method in class org.biojava.bio.gui.StackedLogoPainter
 
paintLogo(LogoContext) - Method in class org.biojava.bio.gui.TextLogoPainter
 
PairDistribution - Class in org.biojava.bio.dist
Class for pairing up two independant distributions.
PairDistribution(Distribution, Distribution) - Constructor for class org.biojava.bio.dist.PairDistribution
Create a new PairDistribution that represents the product of two other distributions.
PairDPCursor - Interface in org.biojava.bio.dp.twohead
A cursor over a DP matrix.
PairDPMatrix - Class in org.biojava.bio.dp.twohead
Storage structure for intermediate values from a pairwise dynamic programming run.
PairDPMatrix(DP, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.twohead.PairDPMatrix
 
PAIRWISE - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
pairwiseAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.AlignmentAlgorithm
Performs a pairwise sequence alignment of the two given sequences.
pairwiseAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.
pairwiseAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.SmithWaterman
Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment.
PairwiseDiagonalRenderer - Class in org.biojava.bio.gui.sequence
PairwiseDiagonalRenderer renders a region of similarity between two sequences as a straight line.
PairwiseDiagonalRenderer() - Constructor for class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
Creates a new PairwiseDiagonalRenderer which will draw black lines.
PairwiseDiagonalRenderer(Paint) - Constructor for class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
Creates a new PairwiseDiagonalRenderer which will draw lines using the specified Paint.
PairwiseDP - Class in org.biojava.bio.dp.twohead
Algorithms for dynamic programming (alignments) between pairs of SymbolLists.
PairwiseDP(MarkovModel, CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.twohead.PairwiseDP
 
PairwiseFilteringRenderer - Class in org.biojava.bio.gui.sequence
PairwiseFilteringRenderer wraps a PairwiseSequenceRenderer and filters the PairwiseRenderContexts passed to it.
PairwiseFilteringRenderer(PairwiseSequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
Creates a new PairwiseFilteringRenderer which uses a filter which accepts all features.
PairwiseFilteringRenderer(PairwiseSequenceRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
Creates a new PairwiseFilteringRenderer.
PairwiseOverlayRenderer - Class in org.biojava.bio.gui.sequence
PairwiseOverlayRenderer allows a list of other PairwiseSequenceRenderers to superimpose their output.
PairwiseOverlayRenderer() - Constructor for class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
Creates a new, empty PairwiseOverlayRenderer.
PairwiseRenderContext - Interface in org.biojava.bio.gui.sequence
PairwiseRenderContext encapsulates information required for the rendering of a pair of sequences.
PairwiseRendererForwarder(PairwiseSequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder
Creates a new PairwiseRendererForwarder.
PairwiseSequencePanel - Class in org.biojava.bio.gui.sequence
A PairwiseSequencePanel is a panel that displays a pair of sequences; one sequence (the primary) may be either left-to-right (HORIZONTAL) or from top-to-bottom (VERTICAL).
PairwiseSequencePanel() - Constructor for class org.biojava.bio.gui.sequence.PairwiseSequencePanel
Creates a new PairwiseSequencePanel with the default settings (primary sequence direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, secondary symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font).
PairwiseSequenceRenderer - Interface in org.biojava.bio.gui.sequence
PairwiseSequenceRenderers render information about the relationship between two sequences.
PairwiseSequenceRenderer.PairwiseRendererForwarder - Class in org.biojava.bio.gui.sequence
PairwiseRendererForwarder forward events to other renderers.
PARAMETER - Static variable in interface org.biojava.bio.dp.MarkovModel
Signals that one or more parameters have altered.
ParametricCodeGenerator - Interface in org.biojava.utils.bytecode
 
ParametricType - Class in org.biojava.utils.bytecode
A template type.
parent - Variable in class org.biojava.bio.taxa.SimpleTaxon
Deprecated.
 
parent - Variable in class org.biojava.bio.taxa.WeakTaxon
Deprecated.
 
parent() - Method in interface org.biojava.utils.automata.StateMachineInstance
 
PARENT - Static variable in interface org.biojavax.bio.seq.RichFeature
 
PARENT - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
parse(BufferedReader, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFParser
Informs handler of each line of gff read from bReader.
parse(BufferedReader, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.GFFParser
Informs handler of each line of GFF read from bReader
parse(BufferedReader, GFF3DocumentHandler, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser
Informs handler of each line of gff read from bReader.
parse(BufferedReader, GFF3DocumentHandler, Ontology, String) - Method in class org.biojava.bio.program.gff3.GFF3Parser
Informs handler of each line of GFF read from bReader
parse(BufferedReader, OntologyFactory) - Method in class org.biojava.ontology.io.TabDelimParser
Parse an ontology from a reader.
parse(File) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileParser
Returns a profile HMM representing the core HMMER hmm
parse(Object) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
 
parse(Object) - Method in class org.biojava.bio.program.tagvalue.RegexParser
 
parse(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueParser
 
parse(Readable, ParseListener) - Method in interface org.biojava.bio.program.fastq.FastqReader
Parse the specified readable.
parse(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
 
parse(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser
 
parse(String) - Method in class org.biojava.naming.ObdaUriParser
 
parse(TaxonFactory, String) - Method in class org.biojava.bio.taxa.EbiFormat
Deprecated.
 
parse(TaxonFactory, String) - Method in interface org.biojava.bio.taxa.TaxonParser
Deprecated.
Convert a stringified Taxon into a Taxon instance.
parse(PHYLIPFileListener, BufferedReader) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat
 
parse(InputSource) - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser
parse initiates the parsing operation.
parse(InputSource) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
 
parse(InputSource) - Method in class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser
Describe 'parse' method here.
parse(InputSource) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
parse(InputSource) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser
Describe 'parse' method here.
parse(InputSource) - Method in class org.biojava.bio.program.sax.PdbSAXParser
Describe 'parse' method here.
parse(InputSource) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser
Describe 'parse' method here.
parseAttribute(String) - Method in class org.biojava.bio.program.gff.GFFParser
Parse attValList into a Map of attributes and value lists.
parseAttribute(String, Annotation, Ontology, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser
Parse attValList into a Map of attributes and value lists.
parseAuthorString(String) - Static method in class org.biojavax.DocRefAuthor.Tools
Takes a list of authors and returns a set of DocRefAuthor objects.
parseComment(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Parses the comment string from the given comment and populates the internal fields appropriately.
parseComment(Comment) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Parses the comment string from the given comment and populates the internal fields appropriately.
ParseErrorEvent - Class in org.biojava.utils
Event which signals a bad line when parsing a record.
ParseErrorEvent(Object) - Constructor for class org.biojava.utils.ParseErrorEvent
Construct a ParseErrorEvent with no other information.
ParseErrorEvent(Object, String) - Constructor for class org.biojava.utils.ParseErrorEvent
Construct a ParseErrorEvent with a message.
ParseErrorListener - Interface in org.biojava.utils
Listener for a ParseErrorEvent.
ParseErrorSource - Interface in org.biojava.utils
Source for a ParseErrorEvent.
parseExample(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
ParseException - Exception in org.biojava.bio.seq.io
ParseException should be thrown to indicate that there was a problem with parsing sequence information.
ParseException() - Constructor for exception org.biojava.bio.seq.io.ParseException
 
ParseException(String) - Constructor for exception org.biojava.bio.seq.io.ParseException
 
ParseException(Throwable) - Constructor for exception org.biojava.bio.seq.io.ParseException
 
ParseException(Throwable, String) - Constructor for exception org.biojava.bio.seq.io.ParseException
 
parseFastqVariant(String) - Static method in enum org.biojava.bio.program.fastq.FastqVariant
Return the FASTQ sequence format variant with the specified name, if any.
parseFile(NexusFileListener, File) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat
Parse a file and send events to the given listener.
parseFile(PHYLIPFileListener, File) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat
 
parseFull(File) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileParser
Returns the full markov model - including the core model + J,C,N loop states.
parseGO(BufferedReader, String, String, OntologyFactory) - Method in class org.biojava.ontology.io.GOParser
 
parseInputStream(NexusFileListener, InputStream) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat
Parse a stream and send events to the given listener.
parseInputStream(PHYLIPFileListener, InputStream) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat
 
ParseListener - Interface in org.biojava.bio.program.fastq
Low-level event based parser callback.
parseLocation(String) - Static method in class org.biojavax.bio.seq.io.UniProtLocationParser
Parses a location.
parseLocation(String, Feature.Template) - Method in class org.biojava.bio.seq.io.EmblLikeLocationParser
Deprecated.
parseLocation creates a Location from the String and returns a stranded location.
parseLocation(Namespace, String, String) - Static method in class org.biojavax.bio.seq.io.GenbankLocationParser
Parses a location.
parseModel(File) - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
parseOBO(BufferedReader) - Method in class org.biojava.ontology.obo.OboFileParser
parse an ontology file
parseOBO(BufferedReader, String, String) - Method in class org.biojava.ontology.io.OboParser
Parse a OBO file and return its content as a BioJava Ontology object
Parser - Class in org.biojava.bio.program.tagvalue
Encapsulate the parsing of lines from a buffered reader into tag-value events.
Parser() - Constructor for class org.biojava.bio.program.tagvalue.Parser
 
Parser(File) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
 
Parser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
 
parseReader(NexusFileListener, Reader) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat
Parse a reader and send events to the given listener.
parseReader(PHYLIPFileListener, Reader) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat
 
parseRecord(byte[]) - Method in class org.biojava.utils.FileAsList
 
parseRegistry(BufferedReader, String) - Static method in class org.biojava.directory.OBDARegistryParser
parseRegistry parses an Open Bioinformatics Database Access (OBDA) configuration file.
ParserException - Exception in org.biojava.utils
Exception thrown when an error occurs in document parsing.
ParserException(String) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(String, String) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(String, String, int) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(String, String, int, String) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(String, String, int, String, int) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(String, Throwable) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(Throwable) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(Throwable, String) - Constructor for exception org.biojava.utils.ParserException
Deprecated.
use new ParserException(detail, t)
ParserException(Throwable, String, String) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(Throwable, String, String, int) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(Throwable, String, String, int, String) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(Throwable, String, String, int, String, int) - Constructor for exception org.biojava.utils.ParserException
 
ParserListener - Class in org.biojava.bio.program.tagvalue
ParserListener is an immutable pairing of a parser and listener.
ParserListener(TagValueParser, TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.ParserListener
Creates a new ParserListener instance.
PARSERS - Static variable in interface org.biojava.bio.symbol.Alphabet
This signals that the available parsers have changed.
parseStrand(String) - Static method in class org.biojava.bio.seq.StrandParser
 
parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.AlternateTokenization
Will throw an exception.
parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
parseStream(SeqIOListener) - Method in interface org.biojava.bio.seq.io.SymbolTokenization
Return an object which can parse an arbitrary character stream into symbols.
parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.WordTokenization
 
parseStream(SeqIOListener) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
The current implementation only supports character parsing.
parseString(String) - Method in class org.biojava.bio.seq.io.WordTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.AlternateTokenization
Will throw an exception.
parseToken(String) - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.CrossProductTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.DoubleTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.IntegerTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.NameTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.SubIntegerTokenization
 
parseToken(String) - Method in interface org.biojava.bio.seq.io.SymbolTokenization
Returns the symbol for a single token.
parseToken(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
 
parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser
 
parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser
 
parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
parseToken(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
Notifies the parser of the next token.
parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
parseToken(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Encountered a token.
parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockParser
 
parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
 
parseTokenChar(char) - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
parseXML(InputStream) - Method in class org.biojava.bio.dist.XMLDistributionReader
Reads an XML representation of a Distribution from a file.
parseXref(String, int, int) - Method in class org.biojava.ontology.obo.OboFileParser
 
ParsimonyTreeMethod - Class in org.biojavax.bio.phylo
 
ParsimonyTreeMethod() - Constructor for class org.biojavax.bio.phylo.ParsimonyTreeMethod
 
PART_OF - Static variable in class org.biojava.ontology.OntoTools
 
PARTIAL_ORDER - Static variable in class org.biojava.ontology.OntoTools
 
PATENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
pattern() - Method in class org.biojava.utils.regex.Matcher
Returns the Pattern object that compiled this Matcher.
Pattern - Class in org.biojava.utils.regex
A class analogous to java.util.regex.Pattern but for SymbolLists.
patternAsString() - Method in class org.biojava.utils.regex.Pattern
returns the Pattern to be matched as a String.
PatternBlitz - Class in org.biojava.utils.automata
 
PatternBlitz(FiniteAlphabet, StateMachineToolkit) - Constructor for class org.biojava.utils.automata.PatternBlitz
 
patternExpanded() - Method in class org.biojava.utils.regex.Pattern
returns the actual String used to construct the regex with all ambiguities expanded.
PatternFactory - Class in org.biojava.utils.regex
A class that creates Patterns for regex matching on SymbolLists of a specific Alphabet.
PatternListener - Interface in org.biojava.utils.automata
 
PatternMaker - Class in org.biojava.utils.automata
 
pcs - Variable in class org.biojava.bio.gui.sequence.SequencePanel.Border
 
pcs - Variable in class org.biojava.bio.gui.sequence.SequencePoster.Border
Deprecated.
 
PDB - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
PDB indicates that the sequence format is PDB.
PdbSAXParser - Class in org.biojava.bio.program.sax
A SAX2 parser for dealing with native PDB files.
PdbSAXParser() - Constructor for class org.biojava.bio.program.sax.PdbSAXParser
Sets namespace prefix to "biojava"
PdbToXMLConverter - Class in org.biojava.bio.program
A class that converts Protein Data Bank (PDB) to XML that will validate against the biojava:MacromolecularStructure DTD.
PdbToXMLConverter(String) - Constructor for class org.biojava.bio.program.PdbToXMLConverter
Creates a new BlastToXMLConverter instance.
PEPTIDE_FEATURE_TYPE - Static variable in class org.biojava.bio.proteomics.Digest
 
PeptideDigestRenderer - Class in org.biojava.bio.gui.sequence
A concrete AbstractPeptideDigestRenderer.
PeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer
 
PeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer
 
PeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer
 
PERCENTIDENTITY - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
performCrossOver(SymbolList, SymbolList) - Method in interface org.biojavax.ga.functions.CrossOverFunction
Performs a cross between the pair of chromosomes
performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.OrderCrossover
 
performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.SimpleCrossOverFunction
 
PERSON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
pFromQuality(double) - Static method in class org.biojava.bio.program.phred.PhredTools
Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
pFromQuality(int) - Static method in class org.biojava.bio.program.phred.PhredTools
Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
pFromQuality(IntegerAlphabet.IntegerSymbol) - Static method in class org.biojava.bio.program.phred.PhredTools
Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
phe() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Phenylalanine (F)
PHRED - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
PHRED indicates that the sequence format is PHRED.
phredAlignmentToDistArray(Alignment) - Static method in class org.biojava.bio.program.phred.PhredTools
converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment.
PhredFormat - Class in org.biojava.bio.program.phred
Format object representing Phred Quality files.
PhredFormat() - Constructor for class org.biojava.bio.program.phred.PhredFormat
 
PhredSequence - Class in org.biojava.bio.program.phred
PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.
PhredSequence(SymbolList, String, String, Annotation) - Constructor for class org.biojava.bio.program.phred.PhredSequence
Constructs a new PhredSequence.
phredToDistArray(PhredSequence) - Static method in class org.biojava.bio.program.phred.PhredTools
Converts a Phred sequence to an array of distributions.
PhredTools - Class in org.biojava.bio.program.phred
PhredTools contains static methods for working with phred quality data.
PhredTools() - Constructor for class org.biojava.bio.program.phred.PhredTools
 
PHYLIPFileBuilder - Class in org.biojavax.bio.phylo.io.phylip
Builds a PHYLIP file by listening to events.
PHYLIPFileBuilder() - Constructor for class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
 
PHYLIPFileFormat - Class in org.biojavax.bio.phylo.io.phylip
Reads PHYLIP interleaved alignment files and fires events at a PHYLIPFileListener object.
PHYLIPFileListener - Interface in org.biojavax.bio.phylo.io.phylip
Listens to events fired by the PHYLIP parser.
PK - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 
PK_Cterm - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 
PK_Nterm - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 
PlainBlock - Class in org.biojava.bio.gui
A painter that just draws a block (or bar).
PlainBlock() - Constructor for class org.biojava.bio.gui.PlainBlock
 
PlainStyle - Class in org.biojava.bio.gui
A simple implementation of SymbolStyle that just uses a single paint for outlines and a single paint for filling.
PlainStyle() - Constructor for class org.biojava.bio.gui.PlainStyle
 
PlainStyle(Paint, Paint) - Constructor for class org.biojava.bio.gui.PlainStyle
 
PLASMID_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
 
point - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer
point is the current location (in sequence coordinates) of the crosshair in the X and Y sequences.
PointClassifier() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Make a new PointClassifier.
PointLocation - Class in org.biojava.bio.symbol
A location representing a single point.
PointLocation(int) - Constructor for class org.biojava.bio.symbol.PointLocation
 
POLY - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
POLY indicates a polygonal image map hotspot.
polyKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
 
PolynomialKernel - Class in org.biojava.stats.svm
This kernel computes all possible products of order features in feature space.
PolynomialKernel() - Constructor for class org.biojava.stats.svm.PolynomialKernel
 
PolynomialKernel(SVMKernel, double, double, double) - Constructor for class org.biojava.stats.svm.PolynomialKernel
 
POMBE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
Schizosaccharomyces pombe codon preferences
pop() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
pop a StAXContentHandler off the stack.
pop() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
pop a StAXContentHandler off the stack.
populate(Feature.Template, Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils
This attempts to populate the fields of a template using the publically accessible information in a feature.
population - Variable in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
Population - Interface in org.biojavax.ga
A collection of GA organisms
POPULATION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
 
pos - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
pos - Variable in class org.biojava.bio.symbol.Edit
 
posInSeq(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
get the position in the sequence corresponding to the postion within the alignment
position() - Method in class org.biojava.utils.io.LargeBuffer
 
position(long) - Method in class org.biojava.utils.io.LargeBuffer
 
Position - Interface in org.biojavax.bio.seq
Holds info about base positions.
PositionResolver - Interface in org.biojavax.bio.seq
Resolves a position that is fuzzy or covers a range of bases by converting it to a single base.
PositionResolver.AverageResolver - Class in org.biojavax.bio.seq
The minimal resolver returns the base which provides the average range, halfway between maximal and minimal.
PositionResolver.MaximalResolver - Class in org.biojavax.bio.seq
The maximal resolver returns the base which provides the largest possible range.
PositionResolver.MinimalResolver - Class in org.biojavax.bio.seq
The minimal resolver returns the base which provides the smallest possible range.
POSITIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature
Flag to indicate that a feature is on the positive strand.
POSITIVE_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand
The positive strand is represented by the symbol '+' and has the number 1.
posmax(Position, Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
posmin(Position, Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
postalAddress - Variable in class org.biojava.bibliography.BiblioPerson
Their postal address.
postChange(ChangeEvent) - Method in class org.biojava.bio.symbol.SimpleSymbolList
 
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeAdapter
 
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder
 
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.AlwaysVetoListener
 
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.LoggingListener
 
postChange(ChangeEvent) - Method in interface org.biojava.utils.ChangeListener
Called when a change has just taken place.
PostgreSQLDBHelper - Class in org.biojava.bio.seq.db.biosql
 
PostgreSQLDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
 
PParametricCodeGenerator - Interface in org.biojava.utils.bytecode
 
preChange(ChangeEvent) - Method in class org.biojava.bio.symbol.SimpleSymbolList
On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeAdapter
 
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder
 
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.AlwaysVetoListener
 
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.ChangeEventRecorder
 
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.LoggingListener
 
preChange(ChangeEvent) - Method in interface org.biojava.utils.ChangeListener
Called before a change takes place.
press() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
press() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
Returns the minimal context of the DP matrix necessary to compute the value of a single point in that matrix.
press() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor
press out a new correctly sized cell array
PrettyXMLWriter - Class in org.biojava.utils.xml
Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter.
PrettyXMLWriter(PrintWriter) - Constructor for class org.biojava.utils.xml.PrettyXMLWriter
 
PRIMARY_KEY_NAME - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
PRIMARY_KEY_NAME is the key used to identify the primary namespace in the OBDA config.dat files.
PRIME - Static variable in class org.biojava.utils.ObjectUtil
the current hashCode is always first multiplied with this prime before the hashCode value for a particular field is added.
primeWord(SymbolList, int, Packing) - Static method in class org.biojava.bio.symbol.PackingFactory
 
print(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
print(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
print(String) - Method in interface org.biojava.utils.xml.XMLWriter
Prints some textual content in an element.
printAttributeValue(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
printAttributeValue(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
printChars(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
printChars(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
printCostMatrix(int[][], char[], char[]) - Static method in class org.biojava.bio.alignment.NeedlemanWunsch
Prints a String representation of the CostMatrix for the given Alignment on the screen.
println(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
println(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
println(String) - Method in interface org.biojava.utils.xml.XMLWriter
Prints some textual content, terminated with a newline character.
printMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
Just to perform some test.
printOutSequenceHeaderLine(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Prints out sequence header with only length data.
printRaw(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
printRaw(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
printRaw(String) - Method in interface org.biojava.utils.xml.XMLWriter
Send raw data to the stream.
printRemoteBlastInfo() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService
A simple method to check the availability of the QBlast service
printTree() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
priority - Variable in class org.biojava.utils.SimpleThreadPool
 
pro() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Proline (P)
PROB_NUC_A - Static variable in class org.biojava.bio.program.scf.SCF
Base call alignment sequence label for the probability that call should be A.
PROB_NUC_C - Static variable in class org.biojava.bio.program.scf.SCF
Base call alignment sequence label for the probability that call should be C.
PROB_NUC_G - Static variable in class org.biojava.bio.program.scf.SCF
Base call alignment sequence label for the probability that call should be G.
PROB_NUC_T - Static variable in class org.biojava.bio.program.scf.SCF
Base call alignment sequence label for the probability that call should be T.
PROB_OVERCALL - Static variable in class org.biojava.bio.program.scf.SCF
Base call alignment sequence label for the overcall probability.
PROB_SUBSTITUTION - Static variable in class org.biojava.bio.program.scf.SCF
Base call alignment sequence label for the substitution probability.
PROB_UNDERCALL - Static variable in class org.biojava.bio.program.scf.SCF
Base call alignment sequence label for the undercall probability.
Probability() - Constructor for class org.biojava.bio.dp.ScoreType.Probability
 
PROBABILITY - Static variable in interface org.biojava.bio.dp.ScoreType
 
processDB(SequenceDB, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Process all Sequences within a SequenceDB, informing handler of any suitable features.
processFeatureFilter(FeatureFilter) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
processHeader(String, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat
Parse the Header information from the Fasta Description line
processingInstruction(String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
processingInstruction(String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
processingInstruction(String, String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
processingInstruction(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
processingInstruction(String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
processingInstruction(String, String) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
processingInstruction(String, String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
processMouseEvent(List, MouseEvent, List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
 
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
processMouseEvent processes any MouseEvents directed to the renderer.
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
processMouseEvent acts on a mouse gesture.
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
 
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
processMouseEvent produces a SequenceViewerEvent in response to a mouse gesture.
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in interface org.biojava.bio.gui.sequence.PairwiseSequenceRenderer
processMouseEvent produces a SequenceViewerEvent in response to a mouse gesture.
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
Produce a SequenceViewerEvent in response to a mouse gesture.
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.StopRenderer
 
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
processMouseEvent defines the behaviour on revieving a mouse event.
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
 
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
 
processSequence(Sequence, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Process an individual Sequence, informing handler of any suitable features.
processSequenceLine(String, StreamParser) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
Dispatch symbol data from SQ-block line of an EMBL-like file.
ProcessTimeoutException - Exception in org.biojava.utils
Exception which is thrown if a child process managed by ProcessTools exceeds a specified time limit.
ProcessTimeoutException(int) - Constructor for exception org.biojava.utils.ProcessTimeoutException
 
ProcessTimeoutException(int, String) - Constructor for exception org.biojava.utils.ProcessTimeoutException
 
ProcessTools - Class in org.biojava.utils
Deprecated.
preferable to use org.biojava.utils.ExecRunner or the org.biojava.utils.process package.
ProfileEmissionState - Class in org.biojava.bio.program.hmmer
A state in a HMMer model.
ProfileEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.program.hmmer.ProfileEmissionState
 
ProfileHMM - Class in org.biojava.bio.dp
 
ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory) - Constructor for class org.biojava.bio.dp.ProfileHMM
Deprecated. 
ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory, String) - Constructor for class org.biojava.bio.dp.ProfileHMM
Create a new ProfileHMM.
PROJ_ACC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
projectChildFeatures(Feature, FeatureHolder) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
 
projectChildFeatures(Feature, FeatureHolder) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Project all features that are children of feature so that they become children of parent.
projectChildFeatures(Feature, FeatureHolder) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
ProjectedFeature - Class in org.biojava.bio.seq.projection
Internal class used by ProjectionEngine to wrap Feature objects.
ProjectedFeature(Feature, ProjectionContext) - Constructor for class org.biojava.bio.seq.projection.ProjectedFeature
 
ProjectedFeatureHolder - Class in org.biojava.bio.seq.projection
Helper class for projecting Feature objects into an alternative coordinate system.
ProjectedFeatureHolder(ProjectionContext) - Constructor for class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
projectFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
 
projectFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Project a single feature.
projectFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
Create a single projected feature using the rules of this ProjectedFeatureHolder.
projectFeature(Feature, ProjectionContext) - Method in class org.biojava.bio.seq.projection.ProjectionEngine
Return a projection of Feature f into the system defined by a given ProjectionContext.
projectFeatures(FeatureHolder) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Project all of the features in a FeatureHolder.
projectFeatures(FeatureHolder) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
projectFilter(FeatureFilter) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Transform a filter on unprojected features so that it applies to projected features.
projectFilter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
Projection - Interface in org.biojava.bio.seq.projection
Interface implemented by all projected feature objects.
ProjectionContext - Interface in org.biojava.bio.seq.projection
Interface that defines the projection between original features and projected features.
ProjectionEngine - Class in org.biojava.bio.seq.projection
Factory for proxy objects which project BioJava features into alternate coordinate systems.
ProjectionEngine.Instantiator - Interface in org.biojava.bio.seq.projection
Internal helper class.
ProjectionEngine.TemplateProjector - Interface in org.biojava.bio.seq.projection
This is an interface for things that project feature templates.
ProjectionUtils - Class in org.biojava.bio.seq.projection
Some common things you want to do while projecting features.
ProjectionUtils() - Constructor for class org.biojava.bio.seq.projection.ProjectionUtils
 
projectLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
 
projectLocation(Location) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
 
projectLocation(Location) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
projectStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
PROP_CASE_SENSITIVE - Static variable in interface org.biojava.utils.candy.CandyVocabulary
A property name.
PROP_CRITERIONS - Static variable in interface org.biojava.bibliography.BibRefQuery
A property name specifying a list of searching and ordering criteria names (type of the property value should be String[]).
PROP_ENTRY_COUNT - Static variable in interface org.biojava.utils.candy.CandyVocabulary
A property name.
PROP_EXCLUDED_ATTRS - Static variable in interface org.biojava.bibliography.BibRefQuery
A property name specifying a list of excluded attribute names (the type of the property value should be String[]).
PROP_VOCAB_DESC - Static variable in interface org.biojava.utils.candy.CandyVocabulary
A property name.
PROP_VOCAB_NAME - Static variable in interface org.biojava.utils.candy.CandyVocabulary
A property name.
PROP_VOCAB_VERSION - Static variable in interface org.biojava.utils.candy.CandyVocabulary
A property name.
PROP_VOCABULARY - Static variable in interface org.biojava.utils.candy.CandyFinder
A property name.
PROP_VOCABULARY - Static variable in interface org.biojava.utils.candy.CandyVocabulary
A property name.
PROPDETAIL_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.PropDetailHandler
 
PropDetailHandler - Class in org.biojava.bio.program.xff
StAX handler for xff:prop detail elements.
PropDetailHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.PropDetailHandler
 
properties - Variable in class org.biojava.bibliography.BiblioEntryStatus
The dynamic properties may be used to add features related to the citation itself.
properties - Variable in class org.biojava.bibliography.BiblioJournal
Additional properties used when the explicit attributes are not sufficient.
properties - Variable in class org.biojava.bibliography.BiblioProvider
Additional properties used when the explicit attributes of the sub-classes are not sufficient.
properties - Variable in class org.biojava.bibliography.BiblioScope
It may contain additional properties related to the extend or scope of the cited resource.
properties - Variable in class org.biojava.bibliography.BibRef
Additional attributes of this citation.
propertiesAllocated() - Method in class org.biojava.bio.AbstractAnnotation
A convenience method to see if we have allocated the properties Map.
propertiesAllocated() - Method in class org.biojava.bio.AnnotationChanger
propertiesAllocated is a convenience method to see if we have allocated the properties Map.
propertiesAllocated() - Method in class org.biojava.bio.AnnotationRenamer
propertiesAllocated Javadoc FIXME - this overrides a protected method and I'm not sure why (KJ).
propertiesAllocated() - Method in class org.biojava.bio.BeanAsAnnotation
 
propertiesAllocated() - Method in class org.biojava.bio.seq.io.ReferenceAnnotation
Deprecated.
 
propertiesAllocated() - Method in class org.biojava.bio.SimpleAnnotation
Test to see if any properties have been allocated
propertiesAllocated() - Method in class org.biojava.bio.SmallAnnotation
 
PROPERTY - Static variable in interface org.biojava.bio.Annotation
This type symbolizes that one or more properties have changed.
PROPERTY_DATA_KEY - Static variable in interface org.biojava.bio.seq.Feature
This is used as a key in the Annotation where it identifies internal data.
PROPERTY_DESCRIPTIONLINE - Static variable in class org.biojava.bio.program.phred.PhredFormat
Constant string which is the property key used to notify listeners of the description lines of Phred sequences.
PROPERTY_DESCRIPTIONLINE - Static variable in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
Constant string which is the property key used to notify listeners of the description lines of FASTA sequences.
PROPERTY_EMBL_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.EmblProcessor
Deprecated.
 
PROPERTY_GENBANK_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.GenbankProcessor
Deprecated.
 
PROPERTY_GFF_SCORE - Static variable in class org.biojava.bio.program.gff.GFFEntrySet
 
PROPERTY_NCBI_TAXON - Static variable in class org.biojava.bio.taxa.EbiFormat
Deprecated.
 
PROPERTY_ORGANISM - Static variable in class org.biojava.bio.seq.io.OrganismParser
Deprecated.
 
PROPERTY_SWISSPROT_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor
Deprecated.
 
PROPERTY_SWISSPROT_COMMENT - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor
Deprecated.
 
PROPERTY_SWISSPROT_FEATUREATTRIBUTE - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor
Deprecated.
 
PROPERTY_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
PROPERTY_TAXON_NAMES - Static variable in class org.biojava.bio.taxa.EbiFormat
Deprecated.
 
PROPERTY_XFF_ID - Static variable in class org.biojava.bio.program.xff.XFFFeatureSetHandler
 
PropertyChanger - Interface in org.biojava.bio.program.tagvalue
Interface for objects that change tag names or properties systematically.
PropertyConstraint - Interface in org.biojava.bio
PropertyConstraints describes a constraint applied to the members of an annotation bundle.
PropertyConstraint.And - Class in org.biojava.bio
A property constraint that accpepts items iff they are accepted by both child constraints.
PropertyConstraint.ByAnnotationType - Class in org.biojava.bio
ByAnnotationType accepts a property value if it belongs to type defined by AnnotationType.
PropertyConstraint.ByClass - Class in org.biojava.bio
ByClass accepts a property value if it is an instance of a specific Java class.
PropertyConstraint.Enumeration - Class in org.biojava.bio
Enumeration accepts a property if it is present in the specified set of values.
PropertyConstraint.ExactValue - Class in org.biojava.bio
Matches properties if they have exactly this one value.
PropertyConstraint.Or - Class in org.biojava.bio
A property constraint that accepts items iff they are accepted by either child constraints.
PropertyForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.MergeAnnotation.PropertyForwarder
Create a new forwarder on behalf of a source using the change support.
PropertyForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.OverlayAnnotation.PropertyForwarder
Forward on behalf of source using the change support provided.
PropertyWriter - Class in org.biojava.bio.program.xff
 
PropertyWriter() - Constructor for class org.biojava.bio.program.xff.PropertyWriter
 
ProportionalSelection - Class in org.biojavax.ga.functions
A Selection function that determines the proportion of individuals in a new population proportionally to their fitness.
ProportionalSelection() - Constructor for class org.biojavax.ga.functions.ProportionalSelection
 
props - Variable in class org.biojava.bio.symbol.Edit
 
Protease - Class in org.biojava.bio.proteomics
The protease class stores parameters needed by Digest to digest a protein sequence.
Protease(String, boolean) - Constructor for class org.biojava.bio.proteomics.Protease
Deprecated.
Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
Protease(String, boolean, String) - Constructor for class org.biojava.bio.proteomics.Protease
Deprecated.
Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
Protease(SymbolList, boolean, SymbolList) - Constructor for class org.biojava.bio.proteomics.Protease
Deprecated.
Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
Protease(SymbolList, boolean, SymbolList, String) - Constructor for class org.biojava.bio.proteomics.Protease
 
ProteaseManager - Class in org.biojava.bio.proteomics
Registry and utility methods for Proteases.
ProteaseManager() - Constructor for class org.biojava.bio.proteomics.ProteaseManager
 
PROTEIN - Static variable in class org.biojava.bio.seq.io.FastaAlignmentFormat
 
PROTEIN_ALPHABET - Static variable in class org.biojava.bio.proteomics.aaindex.AAindex
The alphabet of the symbol property table, that is protein.
PROTEIN_EXIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
PROTEIN_EXISTS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
PROTEIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
PROTEIN_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ProteinRefSeqFileFormer - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
ProteinRefSeqFileFormer() - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
Deprecated.
 
ProteinRefSeqFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
Deprecated.
 
ProteinRefSeqProcessor - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
ProteinRefSeqProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqProcessor
Deprecated.
 
ProteinRefSeqProcessor.Factory - Class in org.biojava.bio.seq.io
Deprecated.
Factory which wraps sequence builders in a ProteinRefSeqProcessor
ProteinTools - Class in org.biojava.bio.seq
The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.
PROVIDER_ORGANISATION - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a provider type.
PROVIDER_PERSON - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a provider type.
PROVIDER_SERVICE - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a provider type.
ProviderNotFoundException - Exception in org.biojava.directory
ProviderNotFoundException is thrown when a sequence database provider can not be located.
ProviderNotFoundException() - Constructor for exception org.biojava.directory.ProviderNotFoundException
Creates a ProviderNotFoundException with no detail message.
ProviderNotFoundException(String) - Constructor for exception org.biojava.directory.ProviderNotFoundException
Creates a ProviderNotFoundException with the specified detail message.
PTM - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
A name for a comment type.
ptr - Variable in class org.biojava.utils.io.CachingInputStream
The 0-based index into cache of the _next_ byte to return.
publisher - Variable in class org.biojava.bibliography.BibRef
A publisher is responsible for making the resource available.
PUBMED_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
Holds a reference to the key that must be used to store PubMed references.
PUBMED_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
PUBMED_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
PUBMED_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
push(StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
Push StAXContentHandler object onto stack
push(StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
Push StAXContentHandler object onto stack
pushParser(TagValueParser, TagValueListener) - Method in interface org.biojava.bio.program.tagvalue.TagValueContext
Push a parser and listener pair onto the parser stack.
put(byte) - Method in class org.biojava.utils.io.LargeBuffer
 
put(int, double) - Method in class org.biojava.stats.svm.SparseVector
Set the value at a particular dimension.
put(long, byte) - Method in class org.biojava.utils.io.LargeBuffer
 
put(Object, Object) - Method in class org.biojava.utils.BeanAsMap
 
put(Object, Object) - Method in interface org.biojava.utils.cache.CacheMap
Associate a value with a key.
put(Object, Object) - Method in class org.biojava.utils.cache.ChangeableCache
 
put(Object, Object) - Method in class org.biojava.utils.cache.FixedSizeMap
 
put(Object, Object) - Method in class org.biojava.utils.cache.WeakCacheMap
 
put(Object, Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
 
put(Object, Object) - Method in class org.biojava.utils.io.SoftHashMap
Here we put the key, value pair into the HashMap using a SoftValue object.
put(Object, Object) - Method in class org.biojava.utils.OverlayMap
 
put(Object, Object) - Method in class org.biojava.utils.SmallMap
 
put(Object, StateMachine.Transition) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
set a Transition within this TransitionTable (2-argument form)
put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
 
put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
 
put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
 
put(CodonPref) - Method in interface org.biojava.bio.symbol.CodonPrefFilter
handles storage of a CodonPref object
putChar(char) - Method in class org.biojava.utils.io.LargeBuffer
 
putChar(long, char) - Method in class org.biojava.utils.io.LargeBuffer
 
putComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
putComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
putComponent(Location, SymbolList) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
putConnection(Connection) - Method in class org.biojava.utils.JDBCConnectionPool
 
putDouble(double) - Method in class org.biojava.utils.io.LargeBuffer
 
putDouble(long, double) - Method in class org.biojava.utils.io.LargeBuffer
 
putFloat(float) - Method in class org.biojava.utils.io.LargeBuffer
 
putFloat(long, float) - Method in class org.biojava.utils.io.LargeBuffer
 
putInt(int) - Method in class org.biojava.utils.io.LargeBuffer
 
putInt(long, int) - Method in class org.biojava.utils.io.LargeBuffer
 
putLong(long) - Method in class org.biojava.utils.io.LargeBuffer
 
putLong(long, long) - Method in class org.biojava.utils.io.LargeBuffer
 
putShort(long, short) - Method in class org.biojava.utils.io.LargeBuffer
 
putShort(short) - Method in class org.biojava.utils.io.LargeBuffer
 
putStatement(Statement) - Method in class org.biojava.utils.JDBCConnectionPool
 
putTaxon(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Adds a Taxon (along with its parents) to the database.
putTokenization(String, SymbolTokenization) - Method in class org.biojava.bio.symbol.AbstractAlphabet
Assigns a symbol parser to a String object.
pyl() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Pyrrolysine (O)

Q

q() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Glutamine
QUALIFIER - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
QUALIFIER_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
QUALIFIER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
Qualitative - Interface in org.biojava.bio.program.phred
Qualitative is an interface for classes wanting to hold quality data in symbolic form such as Phred scores.
QualitativeAlignment - Interface in org.biojava.bio.alignment
 
quality(int) - Method in enum org.biojava.bio.program.fastq.FastqVariant
Convert the specified quality score to a quality in ASCII format.
quality(String) - Method in interface org.biojava.bio.program.fastq.ParseListener
Notify this listener of a quality line.
QUALITY - Static variable in class org.biojava.bio.program.abi.ABITools
The quality alphabet.
qualityAt(Object, int) - Method in interface org.biojava.bio.alignment.QualitativeAlignment
Returns a quality score for label/position
qualityFromP(double) - Static method in class org.biojava.bio.program.phred.PhredTools
The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ) where P_e is the probability that the base call is an error.
qualityScore(char) - Method in enum org.biojava.bio.program.fastq.FastqVariant
Convert the specified quality in ASCII format to a quality score.
qualityScore(double) - Method in enum org.biojava.bio.program.fastq.FastqVariant
Convert the specified error probability to a quality score.
qualityScores(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
Return the quality scores from the specified FASTQ formatted sequence.
qualityScores(Fastq, int[]) - Static method in class org.biojava.bio.program.fastq.FastqTools
Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.
query(String, Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery
It queries the current collection using a query language.
QUERY_ANCHORED - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
QUERY_ANCHORED_NO_IDENTITIES - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
QUERY_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion
A query criterion.
QUERY_LABEL - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
This object is used as the label for the query sequence in the alignment of the query sequence with this sub-hit sequence.
QUERY_LABEL - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
Constant QUERY_LABEL is the alignment label used for all query sequences.
querySeqHolder - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
 
queryViewCache - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
 

R

r() - Static method in class org.biojava.bio.seq.DNATools
 
r() - Static method in class org.biojava.bio.seq.NucleotideTools
 
r() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Arginine
R_NORVEGICUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
RadialBaseKernel - Class in org.biojava.stats.svm
This kernel computes the radial base kernel that corresponds to a gausian distribution.
RadialBaseKernel() - Constructor for class org.biojava.stats.svm.RadialBaseKernel
 
RadialBaseKernel(SVMKernel, double) - Constructor for class org.biojava.stats.svm.RadialBaseKernel
 
RAF - Class in org.biojava.utils.io
 
RAF(File, String) - Constructor for class org.biojava.utils.io.RAF
 
RAF(String, String) - Constructor for class org.biojava.utils.io.RAF
 
raIndexFile - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
 
RandomAccessReader - Class in org.biojava.utils.io
RandomAccessReader extends Reader to provide a means to create buffered Readers from RandomAccessFiles.
RandomAccessReader(RandomAccessFile) - Constructor for class org.biojava.utils.io.RandomAccessReader
Creates a new RandomAccessReader wrapping the RandomAccessFile and using a default-sized buffer (8192 bytes).
RandomAccessReader(RandomAccessFile, int) - Constructor for class org.biojava.utils.io.RandomAccessReader
Creates a new RandomAccessReader wrapping the RandomAccessFile and using a buffer of the specified size.
randomizeDistribution(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
Randomizes the weights of a Distribution.
RangeLocation - Class in org.biojava.bio.symbol
A simple implementation of Location that contains all points between getMin and getMax inclusive.
RangeLocation(int, int) - Constructor for class org.biojava.bio.symbol.RangeLocation
Construct a new RangeLocation from min to max.
RANK - Static variable in interface org.biojavax.bio.BioEntryRelationship
 
RANK - Static variable in interface org.biojavax.bio.seq.RichFeature
 
RANK - Static variable in interface org.biojavax.bio.seq.RichFeatureRelationship
 
RANK - Static variable in interface org.biojavax.bio.seq.RichLocation
 
RANK - Static variable in interface org.biojavax.Comment
 
RANK - Static variable in interface org.biojavax.Note
 
RANK - Static variable in interface org.biojavax.RankedCrossRef
 
RANK - Static variable in interface org.biojavax.RankedDocRef
 
RankedCrossRef - Interface in org.biojavax
Allows cross-references to other databases to be ranked.
RANKEDCROSSREF - Static variable in interface org.biojavax.bio.BioEntry
 
RANKEDCROSSREF - Static variable in interface org.biojavax.ontology.ComparableTerm
 
RankedCrossRefable - Interface in org.biojavax
Defines an object as being able to have ranked cross references associated with it.
rankedCrossRefs - Variable in class org.biojavax.bio.seq.RichFeature.Template
 
RankedDocRef - Interface in org.biojavax
Represents a documentary reference.
RANKEDDOCREF - Static variable in interface org.biojavax.bio.BioEntry
 
RAT_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
Rattus norvegicus codon preferences
RATIO - Static variable in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
Constant RATIO indicating a change to the minimum allowed ratio of long axis to short axis of the features.
RAW - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
RAW indicates that the alignment format is raw (symbols only).
RAW - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
RAW indicates that the sequence format is raw (symbols only).
RAW_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
RAW_AA premade RAW | AA.
RAW_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
RAW_DNA premade RAW | DNA.
RAW_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
RAW_RNA premade RAW | RNA.
rawGet(int) - Method in class org.biojava.utils.FileAsList
rawGet reads the record at the specified index as a raw byte array.
rbfKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
 
RC_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
RC_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RC_PLASMID_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RC_SPECIES_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RC_STRAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RC_TISSUE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RC_TRANSP_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
Reaction() - Constructor for class org.biojava.bio.program.formats.Ligand.Reaction
 
read() - Method in class org.biojava.utils.io.CachingInputStream
 
read() - Method in class org.biojava.utils.io.CountedBufferedReader
 
read() - Method in class org.biojava.utils.io.RandomAccessReader
read reads one byte from the underlying RandomAccessFile.
read() - Method in class org.biojava.utils.io.UncompressInputStream
 
read() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
read(byte[], int, int) - Method in class org.biojava.utils.io.CachingInputStream
 
read(byte[], int, int) - Method in class org.biojava.utils.io.UncompressInputStream
 
read(char[]) - Method in class org.biojava.utils.io.CountedBufferedReader
 
read(char[], int, int) - Method in class org.biojava.utils.io.CountedBufferedReader
 
read(char[], int, int) - Method in class org.biojava.utils.io.RandomAccessReader
read reads from the underlying RandomAccessFile into an array.
read(BufferedReader) - Method in interface org.biojava.bio.seq.io.AlignmentFormat
Read in an alignment from a buffered reader object
read(BufferedReader) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
Reads an alignment in FASTA format.
read(BufferedReader) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
Reads an MSF Alignment File
read(BufferedReader, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.Parser
 
read(File) - Method in interface org.biojava.bio.program.fastq.FastqReader
Read zero or more FASTQ formatted sequences from the specified file.
read(InputStream) - Method in interface org.biojava.bio.program.fastq.FastqReader
Read zero or more FASTQ formatted sequences from the specified input stream.
read(URL) - Method in interface org.biojava.bio.program.fastq.FastqReader
Read zero or more FASTQ formatted sequences from the specified url.
readableFileNames - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
readableFiles - Static variable in class org.biojavax.bio.seq.io.FastaFormat
 
readableFiles - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
readColourMap() - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
Read the the properties file that specifies the character/colour mapping.
readColourMapFromProperties(String) - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
Setup styles from java property file.
readDBDate() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
readDBDate reads the date from the index header.
readDBName() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
readDBName returns the database name from the index header.
readDBRelease() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
readDBRelease returns the database release from the index header.
readEmbl(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Iterate over the sequences in an EMBL-format stream.
readEMBL(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Read a EMBL file using a custom type of SymbolList.
readEMBLDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an EMBL-format stream of DNA sequences.
readEmblNucleotide(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Iterate over the sequences in an EMBL-format stream.
readEMBLProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an EMBL-format stream of Protein sequences.
readEmblRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Iterate over the sequences in an EMBL-format stream, but for RNA.
readEMBLRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an EMBL-format stream of RNA sequences.
readEMBLxml(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Read a EMBLxml file using a custom type of SymbolList.
readEMBLxmlDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an EMBLxml-format stream of DNA sequences.
readEMBLxmlProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an EMBLxml-format stream of Protein sequences.
readEMBLxmlRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an EMBLxml-format stream of RNA sequences.
ReaderInputHandler - Class in org.biojava.utils.process
Reader input handler that reads the input for an external process from a reader.
ReaderInputHandler(Reader, String) - Constructor for class org.biojava.utils.process.ReaderInputHandler
Initializes the reader input handler.
ReaderWriterPipe - Class in org.biojava.utils.process
A multi threaded class which pipes the contents of an input reader to an output writer.
ReaderWriterPipe(Reader, Writer, String) - Constructor for class org.biojava.utils.process.ReaderWriterPipe
Initializes the reader writer pipe.
readFasta(BufferedReader, SymbolTokenization) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Read a fasta file.
readFasta(BufferedReader, SymbolTokenization, SequenceBuilderFactory) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Read a fasta file using a custom type of SymbolList.
readFasta(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Read a fasta file building a custom type of RichSequence .
readFasta(BufferedReader, SymbolTokenization, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Read a fasta file.
readFasta(InputStream, Alphabet) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Create a sequence database from a fasta file provided as an input stream.
readFastaDNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Iterate over the sequences in an FASTA-format stream of DNA sequences.
readFastaDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an FASTA-format stream of DNA sequences.
readFastaProtein(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Iterate over the sequences in an FASTA-format stream of Protein sequences.
readFastaProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an FASTA-format stream of Protein sequences.
readFastaRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Iterate over the sequences in an FASTA-format stream of RNA sequences.
readFastaRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an FASTA-format stream of RNA sequences.
readFile(File, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Guess which format a file is then attempt to read it.
readFile(File, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Guess which format a file is then attempt to read it.
readFileLength() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
readFileLength returns the file length in bytes (stored within the file's header by the indexing program).
readFromXML(InputStream) - Static method in class org.biojava.bio.dist.DistributionTools
Read a distribution from XML.
readFromXML(InputStream) - Static method in class org.biojava.bio.symbol.CodonPrefTools
 
readFromXML(InputStream, String) - Static method in class org.biojava.bio.symbol.CodonPrefTools
reads a specified CodonPref from an file.
readFromXML(InputStream, CodonPrefFilter) - Static method in class org.biojava.bio.symbol.CodonPrefTools
read an CodonPref XML stream and handle it with a CodonPrefFilter object.
readGenbank(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Iterate over the sequences in an Genbank-format stream.
readGenbank(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Read a GenBank file using a custom type of SymbolList.
readGenbankDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an GenBank-format stream of DNA sequences.
readGenbankProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an GenBank-format stream of Protein sequences.
readGenbankRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an GenBank-format stream of RNA sequences.
readGenbankXml(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Iterate over the sequences in an GenbankXML-format stream.
readGenpept(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Iterate over the sequences in an Genpept-format stream.
readGFF(BufferedReader) - Static method in class org.biojava.bio.program.gff.GFFTools
Read all GFF entries from a buffered reader.
readGFF(BufferedReader, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
Read all GFF entries matching a filter from a buffered reader.
readGFF(File) - Static method in class org.biojava.bio.program.gff.GFFTools
Reads a GFFEntrySet from a file with no filtering.
readGFF(File, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
Reads a GFFEntrySet from a file with the specified filter.
readGFF(String) - Static method in class org.biojava.bio.program.gff.GFFTools
Deprecated.
use: readGff(File)
readGFF(String, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
Deprecated.
use: readGff(File,GFFRecordFilter)
readHashedFastaDNA(BufferedInputStream, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an FASTA-format stream of DNA sequences.
readingFrame - Variable in class org.biojava.bio.seq.FramedFeature.Template
 
readINSDseq(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Read a INSDseq file using a custom type of SymbolList.
readINSDseqDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an INSDseq-format stream of DNA sequences.
readINSDseqProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an INSDseq-format stream of Protein sequences.
readINSDseqRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an INSDseq-format stream of RNA sequences.
readLine() - Method in class org.biojava.utils.io.CountedBufferedReader
 
readMatrix(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
readModel(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
readModelFile(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
readName(BufferedReader) - Method in interface org.biojavax.bio.taxa.io.NCBITaxonomyLoader
Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already.
readName(BufferedReader) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already.
readNode(BufferedReader) - Method in interface org.biojavax.bio.taxa.io.NCBITaxonomyLoader
Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.
readNode(BufferedReader) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.
readPhredQuality(BufferedReader) - Static method in class org.biojava.bio.program.phred.PhredTools
Constructs a StreamReader to read in Phred quality data in FASTA format.
readPhredSequence(BufferedReader) - Static method in class org.biojava.bio.program.phred.PhredTools
Calls SeqIOTools.readFastaDNA(br), added here for convinience.
readQuotedString(String, int, int, char, boolean, boolean) - Method in class org.biojava.ontology.obo.OboFileParser
 
readRawRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
readRawRecord returns the raw bytes of a single record from the index.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.AcnumHitReader
readRecord creates an array of Objects from the raw byte array of a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.AcnumTrgReader
readRecord creates an array of Objects from the raw byte array of a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.DivisionLkpReader
readRecord creates an array of Objects from the raw byte array of a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
readRecord returns an array of objects parsed from a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
readRecord returns an array of objects parsed from a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader
readRecord creates an array of Objects from the raw byte array of a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
readRecord creates an array of Objects from the raw byte array of a single record.
readRecordCount() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
readRecordCount returns the number of records in the file.
readRecordLength() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
readRecordLength returns the record length (bytes).
readResolve() - Method in class org.biojava.bio.proteomics.Protease
Prevent duplication of the object during Serialization
readResolve() - Method in class org.biojava.bio.symbol.AbstractAlphabet
To prevent duplication of a what should be a single instance of an existing alphabet.
readResolve() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
To prevent duplication of a what should be a single instance of an existing alphabet.
readResolve() - Method in class org.biojava.utils.StaticMemberPlaceHolder
 
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.GenbankFormat
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtFormat
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.program.phred.PhredFormat
 
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
Reads information from a flatfile to a SeqIOListener using a SymbolTokenizer to convert sequence strings to Symbol objects.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GAMEFormat
this version only reads annotations (no symbols)
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GenbankXmlFormat
Deprecated.
 
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in interface org.biojava.bio.seq.io.SequenceFormat
Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.EMBLFormat
Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.FastaFormat
Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.GenbankFormat
Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.UniProtFormat
Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
Read a sequence and pass data on to a SeqIOListener.
readStream(BufferedInputStream, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Guess which format a stream is then attempt to read it.
readStream(BufferedInputStream, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Guess which format a stream is then attempt to read it.
readSwissprot(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Iterate over the sequences in an Swissprot-format stream.
readSymbol() - Method in interface org.biojava.bio.seq.io.SymbolReader
Return a single symbol from the stream.
readSymbols(Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SymbolReader
Read one or more symbols from the stream.
readUniProt(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Read a UniProt file using a custom type of SymbolList.
readUniProt(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an UniProt-format stream of RNA sequences.
readUniProtXML(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Read a UniProt XML file using a custom type of SymbolList.
readUniProtXML(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Iterate over the sequences in an UniProt XML-format stream of RNA sequences.
readXFF(File, String) - Static method in class org.biojava.bio.program.xff.XFFTools
 
readXFF(File, String, FiniteAlphabet) - Static method in class org.biojava.bio.program.xff.XFFTools
 
readXMLChunk(BufferedReader, DefaultHandler, String) - Static method in class org.biojavax.utils.XMLTools
Attempts to read XML file in chunks, passing each chunk to a SAX parser.
ready() - Method in class org.biojava.utils.io.CountedBufferedReader
 
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
realizeFeature(FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.RealizingFeatureHolder
Realize a feature template.
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
 
realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.FeatureRealizer
Install a feature on the specified sequence.
realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer
 
realizeSubFeatures(Feature) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
recursively attach children features to parent
RealizingFeatureHolder - Interface in org.biojava.bio.seq
Interface for FeatureHolder objects which know how to instantiate new child Features.
reapGarbageListeners() - Method in class org.biojava.utils.ChangeSupport
Remove all references to listeners which have been cleared by the garbage collector.
REBASE_DATA_KEY - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
REBASE_DATA_KEY the ResourceBundle key which specifies the location of the REBASE flat file.
REBASE_TAG_COMM - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
REBASE_TAG_COMM the REBASE tag containing the commercial suppliers.
REBASE_TAG_ISZR - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
REBASE_TAG_ISZR the REBASE tag containing the enzyme isoschizomers.
REBASE_TAG_METH - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
REBASE_TAG_METH the REBASE tag containing the methylation site.
REBASE_TAG_NAME - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
REBASE_TAG_NAME the REBASE tag containing the enzyme name.
REBASE_TAG_ORGN - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
REBASE_TAG_ORGN the REBASE tag containing the organism.
REBASE_TAG_REFS - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
REBASE_TAG_REFS the REBASE tag containing the references.
REBASE_TAG_SITE - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
REBASE_TAG_SITE the REBASE tag containing the enzyme site.
REBASE_TAG_SRCE - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
REBASE_TAG_SRCE the REBASE tag containing the source.
rebind(String, Object) - Method in class org.biojava.naming.ObdaContext
 
rebind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
 
rebind(Name, Object) - Method in class org.biojava.naming.ObdaContext
 
rebind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
 
recBytes - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
 
receiveSequence(String) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
 
receiveSequence(String) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
Receive sequence data for the current sequence.
Record - Interface in org.biojava.bio.program.indexdb
Record represents a record within an indexed flat file databank as defined by the OBDA standard.
Record.Impl - Class in org.biojava.bio.program.indexdb
Impl is the default implementation of Record.
recordEmittedSymbol(State, Symbol, double) - Method in interface org.biojava.bio.dp.HMMTrainer
record that the specified symbol was emitted from the specified state.
recordEmittedSymbol(State, Symbol, double) - Method in class org.biojava.bio.dp.SimpleHMMTrainer
 
recordLength - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
recordLine(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
A record line has been encountered.
recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFFilterer
Only forward the GFFRecords that match a filter.
recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFWriter
Prints record to the PrintWriter.
recordLine(GFF3Record) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
A record line has been encountered.
recordTransition(State, State, double) - Method in interface org.biojava.bio.dp.HMMTrainer
record that a transition was observed between the specified states.
recordTransition(State, State, double) - Method in class org.biojava.bio.dp.SimpleHMMTrainer
 
recParser - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
 
recParser - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
A recParser for implementing readRecord() specific to each concrete subclass.
rect - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
 
rect - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
 
RECT - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
RECT indicates a rectangular image map hotspot.
RectangleGlyph - Class in org.biojava.bio.gui.glyph
A Glyph that paints a rectangle shape within the bounds.
RectangleGlyph() - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph
 
RectangleGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph
 
RectangleGlyph(Paint) - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph
 
RectangularBeadRenderer - Class in org.biojava.bio.gui.sequence
RectangularBeadRenderer renders features as simple rectangles.
RectangularBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.RectangularBeadRenderer
Creates a new RectangularBeadRenderer with the default settings.
RectangularBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.RectangularBeadRenderer
Creates a new RectangularBeadRenderer.
RectangularImapRenderer - Class in org.biojava.bio.gui.sequence
RectangularImapRenderer is a decorator for RectangularBeadRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the RectangularBeadRenderer.
RectangularImapRenderer(RectangularBeadRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.RectangularImapRenderer
Creates a new RectangularImapRenderer.
recurse - Variable in class org.biojava.bio.gui.sequence.FilteringRenderer
 
recurse - Variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
recurse indicates whether the filter should recurse through any subfeatures.
RECURSE - Static variable in class org.biojava.bio.gui.sequence.FilteringRenderer
 
RECURSE - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
Constant RECURSE indicating a change to the renderer's filter recursion flag.
REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
REF_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
REF_POS_BEGIN_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
REF_POS_END_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
REF_XREF_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
REFERENCE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
REFERENCE_LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
REFERENCE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
REFERENCE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
ReferenceAnnotation - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
ReferenceAnnotation() - Constructor for class org.biojava.bio.seq.io.ReferenceAnnotation
Deprecated.
 
REFERENCES_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
REFLEXIVE - Static variable in class org.biojava.ontology.OntoTools
 
refp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
refRange - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
refreshSequencePanels() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
REFSEQ - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
REFSEQ indicates that the sequence format is REFSEQ.
REFSEQ_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
REFSEQ_AA premade REFSEQ | AA.
REFSEQ_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
REFSEQ_DNA premade REFSEQ | DNA.
REFSEQ_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
REFSEQ_RNA premade REFSEQ | RNA.
RegexChanger - Class in org.biojava.bio.program.tagvalue
A ValueChanger.Changer that returns a specific match value using a regex Pattern.
RegexChanger(Pattern, int) - Constructor for class org.biojava.bio.program.tagvalue.RegexChanger
Create a new RegexChanger with a pattern.
RegexException - Exception in org.biojava.utils.regex
An exception thrown by classes of this package.
RegexException(String) - Constructor for exception org.biojava.utils.regex.RegexException
 
RegexException(Throwable) - Constructor for exception org.biojava.utils.regex.RegexException
 
RegexException(Throwable, String) - Constructor for exception org.biojava.utils.regex.RegexException
 
RegexFieldFinder - Class in org.biojava.bio.program.tagvalue
 
RegexFieldFinder(TagValueListener, Pattern, String[], boolean) - Constructor for class org.biojava.bio.program.tagvalue.RegexFieldFinder
Creates a new RegexFiledFinder.
RegexParser - Class in org.biojava.bio.program.tagvalue
A TagValueParser that splits a line based upon a regular expression.
RegexParser() - Constructor for class org.biojava.bio.program.tagvalue.RegexParser
Create a new RegexParser with all boolean values set to false.
RegexSplitter - Class in org.biojava.bio.program.tagvalue
A ValueChanger.Splitter that splits a line of text using a regular expression, returning one value per match.
RegexSplitter(Pattern, int) - Constructor for class org.biojava.bio.program.tagvalue.RegexSplitter
Create a new RegexSplitter with a pattern.
Region(Location, String, boolean) - Constructor for class org.biojava.bio.seq.RemoteFeature.Region
Create a new Region.
regions - Variable in class org.biojava.bio.seq.RemoteFeature.Template
 
register(RestrictionEnzyme, Set) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
register regisiters a new RestrictionEnzyme with the manager.
registerAlphabet(String[], Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Register and Alphabet by more than one name.
registerAlphabet(String, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Register an alphabet by name.
registerCollectionHandlerFactory(String, String, XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
Register a factory used to create handlers for the specified tag in an XML AnnotationType
registerDistribution(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Register a distribution object with this context.
registerDistribution(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
registered(String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
Has a Protease been registered with that name?
registered(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Has an Alphabet been registered by that name
registerFactory(UnigeneFactory) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
Register a UnigeneFactory.
registerFormat(Class) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Register a new format with IOTools for auto-guessing.
registerHandlerFactory(String, String, XMLFilterHandler.FilterHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
Register a factory used to create handlers for the specified tag name
registerModel(MarkovModel) - Method in interface org.biojava.bio.dp.ModelTrainer
Registers an HMM with this trainer.
registerModel(MarkovModel) - Method in class org.biojava.bio.dp.SimpleModelTrainer
 
registerParametricType(ParametricType, CodeClass) - Method in interface org.biojava.utils.bytecode.CodeContext
Register a concrete type for a parametric type.
registerPropertyHandlerFactory(String, String, XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
Register a factory used to create handlers for the specified tag in an XML AnnotationType
registerProtease(Protease) - Static method in class org.biojava.bio.proteomics.ProteaseManager
Registers a protease and ensures its flyweight status
registerTrainer(Distribution, DistributionTrainer) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Register a Distribution and an associated DistributionTrainer object.
registerTrainer(Distribution, DistributionTrainer) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractDistribution
Register an IgnoreCountsTrainer instance as the trainer for this distribution.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.Distribution
Register this distribution with a training context.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.GapDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.PairDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution
Register an SimpleDistribution.Trainer instance as the trainer for this distribution.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.TranslatedDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UniformDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UntrainableDistribution
 
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dist.PairDistribution
Register this paired distribution with a model trainer.
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
registerWithTrainer(ModelTrainer) - Method in interface org.biojava.bio.dp.Trainable
Perform any registration that is necessary with mt.
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.WMAsMM
 
registrations() - Static method in class org.biojava.bio.symbol.AlphabetManager
A set of names under which Alphabets have been registered.
Registry - Class in org.biojava.directory
Registry is a factory which gets implementations of the BioJava SequenceDBLite interface.
Registry(RegistryConfiguration) - Constructor for class org.biojava.directory.Registry
Creates a new OBDA Registry with the specified configuration.
RegistryConfiguration - Interface in org.biojava.directory
The BioDirectory Registry is a simple system for specifying where to find services which provide sequence databases.
RegistryConfiguration.Composite - Class in org.biojava.directory
A RegistryConfiguration that allows you to treat other configurations as providing important or default configuration information.
RegistryConfiguration.Impl - Class in org.biojava.directory
A simple implementation of RegistryConfiguration backed by a Map.
RegistryException - Exception in org.biojava.directory
A RegistryException thrown when the registry cannot find an implementation of a requested SequenceDB.
RegistryException() - Constructor for exception org.biojava.directory.RegistryException
Creates a new RegistryException with no detail message.
RegistryException(String) - Constructor for exception org.biojava.directory.RegistryException
Creates a new RegistryException with the specified detail message.
RegistryException(String, Throwable) - Constructor for exception org.biojava.directory.RegistryException
 
RegistryException(Throwable) - Constructor for exception org.biojava.directory.RegistryException
Creates a new RegistryException with no detail message, wrapping another Throwable.
RegistryException(Throwable, String) - Constructor for exception org.biojava.directory.RegistryException
Deprecated.
use new RegistryException(message, cause)
REL_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
RelabeledAlignment - Class in org.biojava.bio.symbol
An alignment that relabels another alignment.
RelabeledAlignment(Alignment) - Constructor for class org.biojava.bio.symbol.RelabeledAlignment
 
RELATED_SYNONYM - Static variable in class org.biojava.ontology.Synonym
 
RELATION - Static variable in class org.biojava.ontology.OntoTools
 
RELATION - Static variable in interface org.biojavax.bio.seq.RichFeature
 
RELATIONS - Static variable in interface org.biojavax.bio.BioEntry
 
RELATIONSHIP - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
REMARK - Static variable in interface org.biojavax.DocRef
 
REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
RemoteFeature - Interface in org.biojava.bio.seq
A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.
RemoteFeature.Region - Class in org.biojava.bio.seq
A tuple of Location and sequence ID.
RemoteFeature.Resolver - Interface in org.biojava.bio.seq
The interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature.
RemoteFeature.Template - Class in org.biojava.bio.seq
 
RemotePairwiseAlignmentOutputProperties - Interface in org.biojavax.bio.alignment
RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object.
RemotePairwiseAlignmentProperties - Interface in org.biojavax.bio.alignment
RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties.
RemotePairwiseAlignmentService - Interface in org.biojavax.bio.alignment
This interface specifies minimal information needed to execute a pairwise alignment on a remote service.
RemoteQBlastAlignmentProperties - Class in org.biojavax.bio.alignment.blast
This class implements RemotePairwiseAlignmentProperties by specifying several convenient methods used to wrap the addition of Blast alignment parameters.
RemoteQBlastAlignmentProperties() - Constructor for class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
 
RemoteQBlastOutputFormat - Enum in org.biojavax.bio.alignment.blast
The RemoteQBlastOutputFormat enum acts like static fields for specifiying various values for certain output options.
RemoteQBlastOutputProperties - Class in org.biojavax.bio.alignment.blast
The actual implementation of the RemotePairwiseAlignmentOutputProperties interface for the QBlast service.
RemoteQBlastOutputProperties() - Constructor for class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
This constructor build the parameters for the default output of the GET command sent to the QBlast service.
RemoteQBlastService - Class in org.biojavax.bio.alignment.blast
RemoteQBlastService - A simple way of submitting BLAST request to the QBlast service at NCBI.
RemoteQBlastService() - Constructor for class org.biojavax.bio.alignment.blast.RemoteQBlastService
The constructor for a QBlast service request.
RemoteTerm - Interface in org.biojava.ontology
A term in another ontology.
RemoteTerm.Impl - Class in org.biojava.ontology
Simple in-memory implementation of a remote ontology term.
remove() - Method in class org.biojava.bio.alignment.Alignment.SymbolListIterator
 
remove() - Method in class org.biojava.bio.dp.DP.ReverseIterator
 
remove() - Method in class org.biojava.utils.MergingIterator
 
remove(int) - Method in class org.biojava.utils.bytecode.InstructionVector
 
remove(Object) - Method in interface org.biojava.utils.cache.CacheMap
Explicitly remove an object.
remove(Object) - Method in class org.biojava.utils.cache.FixedSizeMap
 
remove(Object) - Method in class org.biojava.utils.cache.WeakCacheMap
 
remove(Object) - Method in class org.biojava.utils.io.SoftHashMap
 
remove(Object) - Method in class org.biojava.utils.MergingSet
 
remove(Object) - Method in class org.biojavax.ga.util.WeightedSet
 
REMOVE_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
 
removeAllItems() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
removeAllOrganisms() - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeAllOrganisms() - Method in interface org.biojavax.ga.Population
Removes all the Organisms in this Population
removeAllOrganismsImpl() - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeAllOrganismsImpl() - Method in class org.biojavax.ga.impl.SimplePopulation
 
removeAllSymbols() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
removeAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation
Remove an Annotation from the list.
removeAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
Remove a DB from this view.
removeBioEntry(String) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
 
removeBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
removeBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite
Remove the BioEntry associated with an ID from the database.
removeBioEntry(String) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
 
removeBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB
 
removeChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Remove a ChangeListener from a projected feature.
removeChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
removeChangeListener removes a listener.
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
removeChangeListener removes a listener.
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
 
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
removeChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
 
removeChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable
Deprecated.
use removeChangeListener(cl, ChangeType.UNKNOWN)
removeChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport
Remove a listener that was interested in all types of changes.
removeChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
 
removeChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Remove a listener that was interested in all types of changes.
removeChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
removeChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
removeChangeListener removes a listener.
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
removeChangeListener removes a listener.
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
 
removeChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable
Remove a listener that was interested in a specific types of changes.
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport
Remove a listener that was interested in a specific types of changes.
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Remove a listener that was interested in a specific types of changes.
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
removeCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
removeCharState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
Deprecated.
 
removeChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
Deprecated.
Remove a Taxon as a child to this one.
removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
Deprecated.
 
removeComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Removes a comment.
removeComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Removes a comment.
removeComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Removes a comment.
removeComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Removes a comment.
removeComment(Comment) - Method in interface org.biojavax.bio.BioEntry
Removes a comment instance from this bioentry.
removeComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry
Removes a comment instance from this bioentry.
removeComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
removeComponent(Location) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
removeDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
Remove a distributed data source.
removeDelegateRenderer(OptimizableFilter) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
removeDelegateRenderer removes any association of the given OptimizableFilter with a BeadFeatureRenderer.
removeDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple
Removes a descriptor.
removeDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple
Removes a descriptor.
removeEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper
removeEnzyme removes an enzyme from those to be searched for in the Sequence.
removeEquate(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
removeFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder
Remove a feature from this FeatureHolder.
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence
Remove a feature attached to this sequence.
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence
Remove a feature from this sequence.
removeFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
removeFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Remove the dying child.
removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
 
removeFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Remove a feature from this FeatureHolder.
removeFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence
Remove a feature from this FeatureHolder.
removeFeature(Feature, Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Remove the dying child.
removeFeature(Feature, Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
removeFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder
Remove a FeatureHolder from the set of FeatureHolders which are merged.
removeFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
Removes a relationship from this feature holder.
removeFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Removes a relationship from this feature holder.
removeFilterWithGlyph(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
 
removeForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
 
removeFromEnvironment(String) - Method in class org.biojava.naming.ObdaContext
 
removeGap(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
Remove a single gap at position pos in this GappedSymbolList.
removeGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
removeGaps(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
Remove some gaps at position pos in this GappedSymbolList.
removeGaps(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
removeGaps(GappedSymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
because there is a bug in GappedSymbolList
removeGeneticCodeID(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Deletes the genetic code annotation from the taxon in the database.
removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
removeItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
removeItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
 
removeItem(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
removeKey(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
removeKey removes the specified key.
removeKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
Remove a key.
removeLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
Remove a piece of text from the label
removeLeftValue(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Deletes the left value from the specified taxon in the database.
removeListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub
remove a ChangeListener associated with given key.
removeListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub
 
removeMitochondrialGeneticCodeID(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Deletes the so called mitochondrial genetic code annotation from the given taxon.
removeName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
Removes the name from the given name class.
removeName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Removes the name from the given name class.
removeName(Connection, DBHelper, Taxon, String, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Deletes the specified name from of the taxon from the database.
removeNote(Note) - Method in class org.biojavax.EmptyRichAnnotation
Removes a note from this annotation.
removeNote(Note) - Method in interface org.biojavax.RichAnnotation
Removes a note from this annotation.
removeNote(Note) - Method in class org.biojavax.SimpleRichAnnotation
Removes a note from this annotation.
removeObject(NexusObject) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
Removes an object from the file.
removeOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeOrganism(Organism) - Method in interface org.biojavax.ga.Population
Kills off the organism
removeOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation
 
removeOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeOrganisms(Set) - Method in interface org.biojavax.ga.Population
Removes all the Organisms in orgs
removeOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population
Removes all the Organisms in orgs
removeOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
Remove an orthologue from the set.
removeOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
 
removeOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
removes a specified OrthoPair relationship from this group.
removeOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat
Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor
Deprecated.
Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor
Deprecated.
Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
Deprecated.
Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource
Removes a parse error listener from the list of listeners.
removeProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
 
removeProperty(Object) - Method in interface org.biojava.bio.Annotation
Delete a property.
removeProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
 
removeProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
 
removeProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation
Delete a property.
removeProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation
Deprecated. 
removeProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
 
removeProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType
Remove a value from the specified property slot.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
Deprecated.
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
 
removeRank(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Removes the rank persistently from the taxon in the database.
removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Removes a ranked cross reference from the existing set.
removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry
Removes a ranked cross reference from the existing set.
removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm
Removes a ranked cross reference from the existing set.
removeRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable
Removes a ranked cross reference from the existing set.
removeRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry
Removes a ranked docref instance from this bioentry.
removeRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry
Removes a ranked docref instance from this bioentry.
removeRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry
Removes a relation instance from this bioentry.
removeRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry
Removes a relation instance from this bioentry.
removeRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR
 
removeRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
 
removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
removeRenderer removes a renderer.
removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
removeRenderer removes a renderer.
removeRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes
Remove a repository from FeaturTypes.
removeRichSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
removeRichSequence(String) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
 
removeRichSequence(String) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
Remove the RichSequence associated with an ID from the database.
removeRightValue(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Deletes the right value from the specified taxon in the database.
removeSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
Remove a secondary key.
removeSequence(Object) - Method in interface org.biojava.bio.alignment.ARAlignment
 
removeSequence(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
removeSequence(String) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
 
removeSequence(String) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
 
removeSequence(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
removeSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB
 
removeSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
removeSequence always throws a ChangeVetoException as this implementation is immutable.
removeSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
removeSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDBLite
Remove the sequence associated with an ID from the database.
removeSequence(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
Not supported, you can't remove a sequence from a WebDB!
removeSequence(String) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
removeSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
removeSequence(String) - Method in class org.biojavax.bio.db.HashRichSequenceDB
 
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
removeSequenceViewerListener removes a listener for mouse click SequenceViewerEvents.
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
 
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
removeSequenceViewerListener removes a listener for mouse click SequenceViewerEvents.
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addSequenceViewerMotionListener removes a listener for mouse motion SequenceViewerEvents.
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
 
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
addSequenceViewerMotionListener removes a listener for mouse motion SequenceViewerEvents.
removeSet(Set) - Method in class org.biojava.utils.MergingSet
 
removeState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
removeState(State) - Method in interface org.biojava.bio.dp.MarkovModel
Remove a state from the model.
removeState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
removeState(State) - Method in class org.biojava.bio.dp.WMAsMM
 
removeSymbol(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
removeSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet
Remove a symbol from this alphabet.
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
SoftMaskedAlphabets cannot remove Symbols.
removeSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
removeSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl
 
removeSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl
 
removeSynonym(Object) - Method in class org.biojava.ontology.Term.Impl
 
removeSynonym(Object) - Method in interface org.biojava.ontology.Term
Remove a synonym for this term.
removeSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl
 
removeSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
Remove a synonym for this term.
removeSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
Remove a synonym for this term.
removeTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
Remove a tag so that it will not be retained.
removeTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Removes the given TAXLABEL.
removeTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Removes the given TAXLABEL.
removeTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Removes the given TAXLABEL.
removeTaxon(Connection, int, DBHelper) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the removed taxon.
removeTaxon(Connection, DBHelper, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Deletes a taxon specified by one of it's names with all it's different names, annotations and sequences from the database.
removeTranslation(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Removes the given translation.
removeTree(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Removes a tree.
removeVariableModifications(char) - Method in class org.biojava.bio.proteomics.MassCalc
Remove all variable modifications assocaited with this residue.
removeVariableModifications(Symbol) - Method in class org.biojava.bio.proteomics.MassCalc
Remove all variable modifications assocaited with this residue.
rename(String, String) - Method in class org.biojava.naming.ObdaContext
 
rename(Name, Name) - Method in class org.biojava.naming.ObdaContext
 
render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
 
render(Graphics2D) - Method in interface org.biojava.bio.gui.glyph.Glyph
 
render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.HelixGlyph
 
render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
 
render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.TurnGlyph
 
render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
 
RENDER_NOTHING - Static variable in interface org.biojava.bio.gui.sequence.LabelRenderer
 
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
renderBead should be overridden by the concrete BeadRenderer.
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
renderBead should implement rendering for this bead type only.
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
renderBead renders features as simple ellipse.
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
renderBead renders features as simple rectangle.
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
 
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
renderBead renders features as a rectangle with rounded corners.
RENDERER - Static variable in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
RENDERER - Static variable in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 
RENDERER - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
Constant RENDERER indicating a change to the renderer.
RENDERER - Static variable in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
Constant RENDERER is a ChangeType which indicates a change to the renderer, requiring a layout update.
RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequencePanel
 
RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
 
RENDERER - Static variable in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
Constant RENDERER is a ChangeType which indicates a change to the renderer, requiring a layout update.
RendererForwarder(SequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder
 
renderers - Variable in class org.biojava.bio.gui.sequence.MultiLineRenderer
 
RENDERERS - Static variable in class org.biojava.bio.gui.sequence.MultiLineRenderer
 
RENDERERS - Static variable in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
Constant RENDERERS indicating a change to the renderers handled by the overlay.
RENDERERS - Static variable in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
 
renderFeature(Graphics2D, Feature, CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
renderFeature draws a feature using the supplied graphics context.
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
 
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
 
renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
renderImageMap writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.
renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.ImageMapRenderer
renderImageMap renders the Feature as set of image map hotspots.
renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
renderImageMap writes a set of image map coordinates corresponding to the rectangle drawn by the renderer.
renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
renderImageMap writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.
renderLocation(Graphics2D, SequenceRenderContext, Location) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
Render another "exon" in the correct translation frame.
RenderNothing() - Constructor for class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
 
renumber(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Renumber the view indexes from block, adding delta to each offset.
REPAINT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext
 
ReparentContext - Class in org.biojava.bio.seq.projection
A good base class to implement ProjectionContext from.
ReparentContext(FeatureHolder, FeatureHolder) - Constructor for class org.biojava.bio.seq.projection.ReparentContext
 
repeatDescription(String) - Method in interface org.biojava.bio.program.fastq.ParseListener
Notify this parse listener of a repeat description line.
RepeatedCharSequence - Class in org.biojava.utils
 
RepeatedCharSequence() - Constructor for class org.biojava.utils.RepeatedCharSequence
 
RepeatedCharSequence(int, char) - Constructor for class org.biojava.utils.RepeatedCharSequence
 
replacement - Variable in class org.biojava.bio.symbol.Edit
 
replicate(String) - Method in class org.biojavax.ga.impl.SimpleOrganism
 
replicate(String) - Method in interface org.biojavax.ga.Organism
Creates a replica of this Organism with a new name.
reportDna(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
 
reportDna(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
reportDna(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
 
reportDna(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
 
reportExon(RangeLocation, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
 
reportExon(RangeLocation, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf
Allows nesting class that manages a transcript template to gain information about its extent from nested elements that represent exons.
reportFeature(Location) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
Allows nesting class that manages a gene template to gain information about its extent from nested elements.
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
 
reportFeature(Location) - Method in interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
 
reportFeature(Location) - Method in interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf
Allows nesting class that manages a gene template to gain information about its extent from nested elements.
reportMatch(SymbolList, Pattern, int, int) - Method in interface org.biojava.utils.regex.Search.Listener
 
reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVECallbackItf
 
reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf
 
reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
 
reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
 
reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
 
reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
 
reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
 
reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
 
reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf
 
REPOSITORY_SUBSETS - Static variable in interface org.biojava.bibliography.BibRefSupport
A vocabulary name.
RepositoryImpl(String) - Constructor for class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
Create a named repository.
repositorySubset - Variable in class org.biojava.bibliography.BiblioEntryStatus
Some bibliographic repositories consist of several, or even many, databases.
requestsQueued() - Method in class org.biojava.utils.SimpleThreadPool
requestsQueued returns the number of Runnables currently queued.
reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
 
reset() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
 
reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
 
reset() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
 
reset() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter
resets the internal state of this filter including any cached evaluations.
reset() - Method in class org.biojava.utils.io.CountedBufferedReader
 
reset() - Method in class org.biojava.utils.regex.Matcher
Resets this matcher.
reset() - Method in class org.biojavax.utils.CRC64Checksum
 
reset(SymbolList) - Method in class org.biojava.utils.regex.Matcher
Resets this matcher with a new input SymbolList.
resetRange() - Method in class org.biojava.bio.alignment.FlexibleAlignment
check that begining is at 1 otherwise shift everything over
resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
Allowed to be called by DATA subclass.
resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser
 
resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser
 
resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
This function is called when the parser is reset before starting a new block.
resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockParser
 
resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
 
resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
resizeAndValidate sets the minimum, preferred and maximum sizes of the component according to the current visible symbol count.
resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
resizeAndValidate sets the minimum, preferred and maximum sizes of the component according to the current leading and trailing borders, renderer depth and visible symbol count.
resolve(RemoteFeature) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
 
resolve(RemoteFeature) - Method in interface org.biojava.bio.seq.RemoteFeature.Resolver
Resolve rFeat.
resolve(FuzzyPointLocation) - Method in interface org.biojava.bio.symbol.FuzzyPointLocation.PointResolver
Return the actual point that the specified location should claim to occupy.
RESOLVE_AVERAGE - Static variable in class org.biojava.bio.symbol.FuzzyLocation
Use the arithmetic mean of the `inner' and `outer' values, unless the outer value is unbounded.
RESOLVE_AVERAGE - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
 
RESOLVE_INNER - Static variable in class org.biojava.bio.symbol.FuzzyLocation
Always use the `inner' values.
RESOLVE_MAX - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
 
RESOLVE_MIN - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
 
RESOLVE_OUTER - Static variable in class org.biojava.bio.symbol.FuzzyLocation
Use the `outer' values, unless they are unbounded in which case the `inner' values are used.
resolveAlphabet(String) - Static method in class org.biojava.bio.program.ssbind.AlphabetResolver
resolveAlphabet returns an appropriate Alphabet for an arbitrary identifier.
resolveClass(CodeClass) - Method in class org.biojava.utils.bytecode.ConstantPool
 
resolveCommands(String, Properties) - Static method in class org.biojava.utils.process.ExternalProcess
Resolves the given command line by replacing all placeholder of the format %NAME% with the values from the given properties for the corresponding keys of the format NAME.
resolveDouble(double) - Method in class org.biojava.utils.bytecode.ConstantPool
 
resolveEntity(String, String) - Method in class org.biojava.utils.xml.ResourceEntityResolver
 
resolveField(CodeField) - Method in class org.biojava.utils.bytecode.ConstantPool
 
resolveFloat(float) - Method in class org.biojava.utils.bytecode.ConstantPool
 
resolveInt(int) - Method in class org.biojava.ontology.IntegerOntology
 
resolveInt(int) - Method in class org.biojava.utils.bytecode.ConstantPool
 
resolveInterfaceMethod(CodeMethod) - Method in class org.biojava.utils.bytecode.ConstantPool
 
resolveLocal(LocalVariable) - Method in interface org.biojava.utils.bytecode.CodeContext
Resolve a local variable to the local variable slot assigned to it.
resolveLong(long) - Method in class org.biojava.utils.bytecode.ConstantPool
 
resolveMax(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver
Delegate for the getMax() method.
resolveMethod(CodeMethod) - Method in class org.biojava.utils.bytecode.ConstantPool
 
resolveMin(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver
Delegate for the getMin() method.
resolveNameAndType(String, String) - Method in class org.biojava.utils.bytecode.ConstantPool
 
resolveParametricType(ParametricType) - Method in interface org.biojava.utils.bytecode.CodeContext
Resolve a parametric type to a concrete class.
resolver - Variable in class org.biojava.bio.seq.RemoteFeature.Template
 
resolveString(String) - Method in class org.biojava.utils.bytecode.ConstantPool
 
resolveUtf8(String) - Method in class org.biojava.utils.bytecode.ConstantPool
 
RESOURCE_TYPES - Static variable in interface org.biojava.bibliography.BibRefSupport
A vocabulary name.
ResourceEntityResolver - Class in org.biojava.utils.xml
SAX EntityResolve which looks up system IDs as resources from a Java ClassLoader.
ResourceEntityResolver(String) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
Construct a resolver which searches for resources in the specified path relative to the current classloader.
ResourceEntityResolver(String[]) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
Construct a resolver which searches for resources in the specified list of directories relative to the current classloader.
ResourceEntityResolver(String[], ClassLoader) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
Construct a resolver which searches for resources in the specified list of directories relative to the supplied classloader.
ResourceEntityResolver(String, ClassLoader) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
Construct a resolver which searches for resources in the specified path relative to the supplied classloader.
RestrictionEnzyme - Class in org.biojava.bio.molbio
RestrictionEnzyme represents a restriction enzyme according to the REBASE standard.
RestrictionEnzyme(String, SymbolList, int, int) - Constructor for class org.biojava.bio.molbio.RestrictionEnzyme
Creates a new RestrictionEnzyme which cuts within or downstream of the recognition site.
RestrictionEnzyme(String, SymbolList, int, int, int, int) - Constructor for class org.biojava.bio.molbio.RestrictionEnzyme
Creates a new RestrictionEnzyme of the unusual type which cuts both upstream and downstream of its recognition site.
RestrictionEnzymeManager - Class in org.biojava.bio.molbio
RestrictionEnzymeManager manages collections of static RestrictionEnzyme instances.
RestrictionMapper - Class in org.biojava.bio.molbio
RestrictionMapper is a class for annotating Sequences with Features which represent restriction sites.
RestrictionMapper(ExecutorService) - Constructor for class org.biojava.bio.molbio.RestrictionMapper
Creates a new RestrictionMapper which will use the specified ExecutorService.
RestrictionMapper(ThreadPool) - Constructor for class org.biojava.bio.molbio.RestrictionMapper
Creates a new RestrictionMapper which will use the specified ThreadPool.
RestrictionSite - Interface in org.biojava.bio.molbio
RestrictionSite represents the recognition site of a restriction enzyme.
RestrictionSite.Template - Class in org.biojava.bio.molbio
Template for construction of RestrictionSites.
RESULT_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
retainAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
 
returnData(Object) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
provides a standardised way of returning an object that represents the result of parsing the child element
Retyper(Object, ChangeSupport, ChangeType) - Constructor for class org.biojava.utils.ChangeForwarder.Retyper
Create a new Retyper for forwarding events.
RevCompSequence - Class in org.biojava.bio.seq.impl
A reverse complement view onto Sequence interface.
RevCompSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.RevCompSequence
URN, Name and Annotation are copied as is from the original Sequence, unless you use the the other contructor that sets these.
RevCompSequence(Sequence, String, String, Annotation) - Constructor for class org.biojava.bio.seq.impl.RevCompSequence
 
reverse(int[]) - Static method in class org.biojava.bio.chromatogram.AbstractChromatogram
Utility method for reversing an int[] array.
reverse(SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews
A reversed view onto a SymbolList.
reverseComplement() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
 
reverseComplement() - Method in interface org.biojava.bio.chromatogram.Chromatogram
Returns a new Chromatogram representing the reverse complement of this one.
reverseComplement(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools
Reverse-complement a sequence, and flip all of its features.
reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
Retrieve a reverse-complement view of list.
reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools
Retrieve a reverse-complement view of list.
reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
Retrieve a reverse-complement view of list.
reverseComplementBaseCallList(Object) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
Return a symbol list containing the reverse complement of the base call data for the given label.
reverseComplementBaseCallList(String) - Method in class org.biojava.bio.program.scf.SCF
Overrides AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object) to support the 7 quality values from the SCF.
reverseComplementBaseCalls() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
Returns a new base call alignment that is the reverse complement of one in this chromatogram.
reverseComplementInstance() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
Returns a new instance of this AbstractChromatogram subclass for use in AbstractChromatogram.reverseComplement().
reverseComplementInstance() - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
 
reverseComplementInstance() - Method in class org.biojava.bio.program.abi.ABIFChromatogram
 
reverseComplementInstance() - Method in class org.biojava.bio.program.scf.SCF
 
ReverseIterator(SymbolList) - Constructor for class org.biojava.bio.dp.DP.ReverseIterator
 
reverseRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
ReversibleTranslationTable - Interface in org.biojava.bio.symbol
A translation table that can also translate from the target to source alphabet.
revertFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
 
revertFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Unproject a feature.
revertFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
revertFilter(FeatureFilter) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Transform a filter on projected features so that it applies to unprojected features.
revertFilter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
revertLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
 
revertLocation(Location) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
revertLocation(Location, int, boolean) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
Revert a location, translating and flipping as required.
revertStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
revertTemplate(Feature.Template, ProjectionContext) - Method in class org.biojava.bio.seq.projection.ProjectionEngine
Revert a template so that it can be used on the original feature-space.
revertTemplate(ProjectionContext, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionEngine.TemplateProjector
 
RichAnnotatable - Interface in org.biojavax
Annotatable objects that can have rich annotations.
RichAnnotation - Interface in org.biojavax
An annotation collection which stores annotations as Note objects.
RichFeature - Interface in org.biojavax.bio.seq
Represents a feature that can be given name and rank and be moved from one sequence to another.
RichFeature.Template - Class in org.biojavax.bio.seq
Added-value extension of Feature.Template including bits we're interested in, eg. featureRelationshipSet for relationships with other features, and rankedCrossRefs for lookups into other databases.
RichFeature.Tools - Class in org.biojavax.bio.seq
Some useful tools for working with features.
RichFeatureRelationship - Interface in org.biojavax.bio.seq
Represents the relation between two features.
RichFeatureRelationshipHolder - Interface in org.biojavax.bio.seq
Holds feature relationships.
RichLocation - Interface in org.biojavax.bio.seq
Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
RichLocation.Strand - Class in org.biojavax.bio.seq
This class represents a strand on which a location may lie.
RichLocation.Tools - Class in org.biojavax.bio.seq
Some useful tools for working with Locations.
RichObjectBuilder - Interface in org.biojavax
This interface allows a class to generate Rich objects based on a class name and some parameters.
RichObjectFactory - Class in org.biojavax
Runs a service that builds rich objects, and provides some default values for things like default ontology, default namespace, etc.
RichSeqIOAdapter - Class in org.biojavax.bio.seq.io
This class implements all methods of RichSeqIOListener and takes no action.
RichSeqIOAdapter() - Constructor for class org.biojavax.bio.seq.io.RichSeqIOAdapter
Creates a new instance of RichSeqIOAdapter
RichSeqIOListener - Interface in org.biojavax.bio.seq.io
An interface for classes that listen to BioEntry or RichSequence I/O streams.
RichSequence - Interface in org.biojavax.bio.seq
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
RichSequence.IOTools - Class in org.biojavax.bio.seq
A set of convenience methods for handling common file formats.
RichSequence.IOTools.SingleRichSeqIterator - Class in org.biojavax.bio.seq
Used to iterate over a single rich sequence
RichSequence.Terms - Class in org.biojavax.bio.seq
Stores a number of useful terms used across many sequence formats for consistency's sake.
RichSequence.Tools - Class in org.biojavax.bio.seq
Some useful tools for working with RichSequence objects.
RichSequenceBuilder - Interface in org.biojavax.bio.seq.io
An interface for objects that can build RichSequences.
RichSequenceBuilderFactory - Interface in org.biojavax.bio.seq.io
Simple factory for constructing new RichSequenceBuilder objects.
RichSequenceDB - Interface in org.biojavax.bio.db
A database of RichSequences with accessible keys and iterators over all sequences.
RichSequenceDBLite - Interface in org.biojavax.bio.db
A database of RichSequences.
RichSequenceFormat - Interface in org.biojavax.bio.seq.io
Allows a file format to be read/written as RichSequences.
RichSequenceFormat.BasicFormat - Class in org.biojavax.bio.seq.io
Provides a basic format with simple things like line-widths precoded.
RichSequenceFormat.HeaderlessFormat - Class in org.biojavax.bio.seq.io
Provides the basic implementation required for simple header/footer-less files such as Genbank.
RichSequenceHandler - Interface in org.biojavax.bio.seq
An interface for classes that know how to handle subsequence operations.
RichSequenceIterator - Interface in org.biojavax.bio.seq
Essentially the same as SequenceIterator.
RichStreamReader - Class in org.biojavax.bio.seq.io
Parses a stream into sequences.
RichStreamReader(BufferedReader, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Constructor for class org.biojavax.bio.seq.io.RichStreamReader
Creates a new stream reader on the given reader, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.
RichStreamReader(InputStream, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Constructor for class org.biojavax.bio.seq.io.RichStreamReader
Creates a new stream reader on the given input stream, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.
RichStreamWriter - Class in org.biojavax.bio.seq.io
Writes all of the sequences from a SequenceIterator to a stream with a particular format.
RichStreamWriter(OutputStream, RichSequenceFormat) - Constructor for class org.biojavax.bio.seq.io.RichStreamWriter
Generate a new RichStreamWriter to the stream os and using format.
rightMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment
 
rightPad(String, char, int) - Static method in class org.biojavax.utils.StringTools
Pads a string to be a certain width by appending given symbols.
rightPad(String, int) - Static method in class org.biojavax.utils.StringTools
Pads a string to be a certain width by appending spaces.
rights - Variable in class org.biojava.bibliography.BibRef
It specifies information about rights over the cited resource.
RIGHTVALUE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
RNA indicates that a sequence contains RNA (ribonucleic acid) symbols.
RNATools - Class in org.biojava.bio.seq
Useful functionality for processing DNA and RNA sequences.
ROLE_ATTR_QUERYABLE - Static variable in interface org.biojava.bibliography.BibRefSupport
A role of an attribute.
ROLE_ATTR_RETRIEVABLE - Static variable in interface org.biojava.bibliography.BibRefSupport
A role of an attribute.
rollback() - Method in class org.biojava.bio.seq.db.BioIndex
 
rollback() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
rollback rolls back changes made since the last commit.
rollback() - Method in interface org.biojava.bio.seq.db.IndexStore
Discard all uncommited changes.
rollback() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
rollback() - Method in interface org.biojava.utils.Commitable
rollback reverses pending changes to restore initial (or prior commit) state.
rollback() - Method in class org.biojava.utils.FileAsList
 
RoundRectangularBeadRenderer - Class in org.biojava.bio.gui.sequence
RoundRectangularBeadRenderer renders features as rectangles with rounded corners.
RoundRectangularBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
Creates a new RoundRectangularBeadRenderer object with the default settings.
RoundRectangularBeadRenderer(double, double, Paint, Paint, Stroke, double, double) - Constructor for class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
Creates a new RoundRectangularBeadRenderer.
RP_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
RP_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
rpp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
rppat - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
rppat - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RulerRenderer - Class in org.biojava.bio.gui.sequence
RulerRenderer renders numerical scales in sequence coordinates.
RulerRenderer() - Constructor for class org.biojava.bio.gui.sequence.RulerRenderer
Creates a new RulerRenderer with the default setting of ticks pointing downwards.
RulerRenderer(int) - Constructor for class org.biojava.bio.gui.sequence.RulerRenderer
Creates a new RulerRenderer with the specified tick direction.
run() - Method in class org.biojava.utils.process.ReaderInputHandler
run() - Method in class org.biojava.utils.process.ReaderWriterPipe
run() - Method in class org.biojava.utils.process.SimpleInputHandler
run() - Method in class org.biojava.utils.process.StreamPipe
run(GAStoppingCriteria) - Method in interface org.biojavax.ga.GeneticAlgorithm
Iterates the Algorithm until the stopping criteria are met.
run(GAStoppingCriteria) - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm
 

S

s() - Static method in class org.biojava.bio.seq.DNATools
 
s() - Static method in class org.biojava.bio.seq.NucleotideTools
 
s() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Serine
S_SCROFA - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
sample() - Method in class org.biojavax.ga.util.WeightedSet
Randomly samples an Object from the Set according to its weight.
sampleSymbol() - Method in class org.biojava.bio.dist.AbstractDistribution
 
sampleSymbol() - Method in interface org.biojava.bio.dist.Distribution
Sample a symbol from this state's probability distribution.
sampleSymbol() - Method in class org.biojava.bio.dist.GapDistribution
 
sampleSymbol() - Method in class org.biojava.bio.dist.PairDistribution
 
sampleSymbol() - Method in class org.biojava.bio.dist.TranslatedDistribution
 
SangerFastqReader - Class in org.biojava.bio.program.fastq
Reader for FastqVariant.FASTQ_SANGER formatted sequences.
SangerFastqReader() - Constructor for class org.biojava.bio.program.fastq.SangerFastqReader
 
SangerFastqWriter - Class in org.biojava.bio.program.fastq
Writer for FastqVariant.FASTQ_SANGER formatted sequences.
SangerFastqWriter() - Constructor for class org.biojava.bio.program.fastq.SangerFastqWriter
 
SAX2StAXAdaptor - Class in org.biojava.bio.seq.io.agave
Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services.
SAX2StAXAdaptor - Class in org.biojava.utils.stax
Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services.
SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
Construct a new SAX Content handler which wraps a StAX handler.
SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.utils.stax.SAX2StAXAdaptor
Construct a new SAX Content handler which wraps a StAX handler.
sb - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
 
scale(Chromatogram, int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity
 
scale(Chromatogram, int) - Method in interface org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler
Returns the remapped coordinate for the provided trace sample index of the given chromatogram.
scale(Chromatogram, int) - Method in class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler
 
scaleHeight - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
 
SCENE_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the scenedesmus obliquus mitochondrial genetic code.
SCF - Class in org.biojava.bio.program.scf
A Chromatogram as loaded from an SCF v2 or v3 file.
SCF() - Constructor for class org.biojava.bio.program.scf.SCF
Creates a new, completely empty SCF.
SCF_MAGIC - Static variable in class org.biojava.bio.chromatogram.ChromatogramFactory
The magic number for SCF files.
SCHEMA - Static variable in interface org.biojava.bio.seq.FeatureHolder
Signals that the schema of this FeatureHolder has changed.
SCI_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
SCIENTIFIC - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
Use this to define scientific names for things.
SCIENTIFIC_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
SCINAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SCOOP - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
score - Variable in class org.biojava.bio.dp.BackPointer
The score of this element of the DP matrix.
score - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
score - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
score of the search which produced the alignment.
scores - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
scores - Variable in class org.biojava.bio.dp.twohead.Cell
 
SCORES - Static variable in interface org.biojava.bio.dp.StatePath
Alignment label for the likelyhood at each step.
ScoreType - Interface in org.biojava.bio.dp
This class computes the score that is used to be used in a DP optimisation.
ScoreType.NullModel - Class in org.biojava.bio.dp
In this class, calculateScore returns the probability of a Symbol being emitted by the null model.
ScoreType.Odds - Class in org.biojava.bio.dp
In this class, calculateScore returns the odds ratio of a symbol being emitted.
ScoreType.Probability - Class in org.biojava.bio.dp
In this class, calculateScore returns the probability of a Symbol being emitted.
scoreWeightMatrix(WeightMatrix, SymbolList, int) - Static method in class org.biojava.bio.dp.DP
Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.
scoreWeightMatrix(WeightMatrix, SymbolList, ScoreType, int) - Static method in class org.biojava.bio.dp.DP
Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType.
search(Object) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
Deprecated.
 
search(Object) - Method in interface org.biojava.bio.taxa.TaxonFactory
Deprecated.
Retrieve a Taxon that matches some ID.
search(Object) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
Deprecated.
 
search(String, String, Object[], SearchControls) - Method in class org.biojava.naming.ObdaContext
 
search(String, String, SearchControls) - Method in class org.biojava.naming.ObdaContext
 
search(String, Attributes) - Method in class org.biojava.naming.ObdaContext
 
search(String, Attributes, String[]) - Method in class org.biojava.naming.ObdaContext
 
search(String, SymbolList, SearchListener) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
 
search(String, SymbolList, SearchListener) - Method in interface org.biojava.bio.program.ssaha.DataStore
Search the DataStore with a symbol list.
search(Name, String, Object[], SearchControls) - Method in class org.biojava.naming.ObdaContext
 
search(Name, String, SearchControls) - Method in class org.biojava.naming.ObdaContext
 
search(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
 
search(Name, Attributes, String[]) - Method in class org.biojava.naming.ObdaContext
 
search(AnnotationType) - Method in interface org.biojava.bio.annodb.AnnotationDB
Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType.
search(AnnotationType) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
 
search(AnnotationType) - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
 
search(AnnotationType) - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
 
search(AnnotationType) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
 
search(AnnotationType) - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
 
search(SymbolList) - Method in class org.biojava.utils.automata.PatternBlitz
 
search(SymbolList) - Method in class org.biojava.utils.regex.Search
search the Sequence with the patterns already registered with this object.
search(SymbolList, int, int) - Method in class org.biojava.utils.regex.Search
search part of the SymbolList with the patterns already registered with this object.
search(SymbolList, SequenceDB, Map) - Method in interface org.biojava.bio.search.SeqSimilaritySearcher
Using this sequence similarity searcher, search with the given sequence against the given sequence database.
Search - Class in org.biojava.utils.regex
A utility class to make searching a Sequence with many regex patterns easier.
Search(FiniteAlphabet) - Constructor for class org.biojava.utils.regex.Search
 
Search.Listener - Interface in org.biojava.utils.regex
Interface for a class that will recieve match information from this class.
searchAnnotation(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.
SearchBuilder - Interface in org.biojava.bio.search
The SearchBuilder interface is to be used by objects which accumulate state via a SearchContentHandler and then construct a SeqSimilaritySearchResult object.
SearchContentAdapter - Class in org.biojava.bio.search
An adapter for SearchContentHandler.
SearchContentAdapter() - Constructor for class org.biojava.bio.search.SearchContentAdapter
 
SearchContentFilter - Class in org.biojava.bio.search
Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain.
SearchContentFilter(SearchContentHandler) - Constructor for class org.biojava.bio.search.SearchContentFilter
 
SearchContentHandler - Interface in org.biojava.bio.search
SearchContentHandler is a notification interface for objects which listen to search stream parsers.
SearchContentHandlerDebugger - Class in org.biojava.bio.search
This class prints to a PrintStream calls to the SearchContentHandler interface in human readable form.
SearchContentHandlerDebugger() - Constructor for class org.biojava.bio.search.SearchContentHandlerDebugger
Create an instance that dumps to System.out.
SearchContentHandlerDebugger(PrintStream) - Constructor for class org.biojava.bio.search.SearchContentHandlerDebugger
 
SearchException - Exception in org.biojava.bio.program.ssaha
There has been some failure that prevents a search from completing.
SearchException(String) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
 
SearchException(String, Throwable) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
 
SearchException(Throwable) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
 
SearchListener - Interface in org.biojava.bio.program.ssaha
The interface used to inform interested parties that some sequence has been searched and something found.
SearchListener.Echo - Class in org.biojava.bio.program.ssaha
A SearchListener that prints events out to a PrintStream.
SearchListener.FilterByLength - Class in org.biojava.bio.program.ssaha
A simple listener that filters out all hits that are too short.
SearchListener.Tee - Class in org.biojava.bio.program.ssaha
A SearchListener that passes events on to two delegate listeners.
SearchListener.Wrapper - Class in org.biojava.bio.program.ssaha
A simple wrapper implementation.
sec() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Selenocysteine (U)
SEC_ACC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SECONDARY_ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
SECONDARY_ACCESSIONS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
secondarySequenceToGraphics(int) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
secondarySequenceToGraphics converts a sequence coordinate on the secondary sequence to a graphical position.
secondarySequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
secondarySequenceToGraphics converts a sequence index to a graphical position.
secondarySequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
SecondaryStructureFeatureRenderer - Class in org.biojava.bio.gui.sequence
A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).
SecondaryStructureFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer
 
sectp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
seek(long) - Method in class org.biojava.utils.io.CachingInputStream
 
seek(long) - Method in class org.biojava.utils.io.RandomAccessReader
seek moves the pointer to the specified position.
seek(long) - Method in interface org.biojava.utils.io.Seekable
Moves the pointer in the inputstream such that the byte starting at pos are returned by the next read.
Seekable - Interface in org.biojava.utils.io
This interface provides a collective name for IO classes that implement a seek function (e.g., RandomAccessFile).
select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.ProportionalSelection
 
select(Population, GeneticAlgorithm) - Method in interface org.biojavax.ga.functions.SelectionFunction
Selects a Population of Organisms for replication based on their fitness.
select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
 
select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold
Selects individuals whose fitness (as determined by the FitnessFunction) is more than the cutoff.
select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.TournamentSelection
Standard call to select organisms, will select a number of Organisms corresponding to 75 % of the population.
SelectAll() - Constructor for class org.biojavax.ga.functions.SelectionFunction.SelectAll
 
SELECTION_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
 
SelectionFunction - Interface in org.biojavax.ga.functions
Selects Organisms for Replication and returns the offspring.
SelectionFunction.SelectAll - Class in org.biojavax.ga.functions
 
SelectionFunction.Threshold - Class in org.biojavax.ga.functions
Selects individuals who's fitness exceeds a threshold value.
SelectionScalar(BitSet) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
Make a new SelectionScalar that masks in different depths.
selectNIndividuals(Population, GeneticAlgorithm, int) - Method in class org.biojavax.ga.functions.TournamentSelection
This method selects n Organism from the population it is given, using the tournament selection method
sendAlignmentRequest(int, RemotePairwiseAlignmentProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService
This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a GenBank GID.
sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService
This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a string representing the sequence.
sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService
Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object
sendAlignmentRequest(RichSequence, RemotePairwiseAlignmentProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService
This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a RichSequence.
sendAlignmentRequest(RichSequence, RemotePairwiseAlignmentProperties) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService
Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object
SEPARATED - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
 
SEPARATOR_COLOR - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating the color that the call separators should be.
SEPARATOR_STROKE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option providing the the stroke to use for drawing call separators.
SEPARATOR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
seq - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement
 
seq - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
 
SeqCaution() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
Creates a new instance.
SeqContentPattern - Class in org.biojava.bio.search
A pattern that can be used to find regions with given sequence content.
SeqContentPattern(FiniteAlphabet) - Constructor for class org.biojava.bio.search.SeqContentPattern
Create a new SeqContentPattern over an alphabet.
SeqFileFormer - Interface in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
SeqIOAdapter - Class in org.biojava.bio.seq.io
Adapter class for SeqIOListener that has empty methods.
SeqIOAdapter() - Constructor for class org.biojava.bio.seq.io.SeqIOAdapter
 
SeqIOConstants - Class in org.biojava.bio.seq.io
SeqIOConstants contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing sequences.
SeqIOConstants() - Constructor for class org.biojava.bio.seq.io.SeqIOConstants
 
SeqIOEventEmitter - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
SeqIOEventEmitter(Comparator, Comparator) - Constructor for class org.biojava.bio.seq.io.SeqIOEventEmitter
Deprecated.
 
SeqIOFilter - Class in org.biojava.bio.seq.io
Base-class for listeners that pass filtered events onto another listener.
SeqIOFilter(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.SeqIOFilter
Create a new SeqIOFilter that will forward events on to another listener.
SeqIOListener - Interface in org.biojava.bio.seq.io
Notification interface for objects which listen to a sequence stream parser.
SeqIOTools - Class in org.biojava.bio.seq.io
Deprecated.
use org.biojavax.bio.seq.RichSequence.IOTools
seqNameForID(int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
 
seqNameForID(int) - Method in interface org.biojava.bio.program.ssaha.DataStore
Resolve an ID to a sequence name.
seqPanels - Variable in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
seqs - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
SeqSimilarityAdapter - Class in org.biojava.bio.program.ssbind
A SeqSimilarityAdapter converts SAX events into method calls on a SearchContentHandler implementation.
SeqSimilarityAdapter() - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
SeqSimilaritySearcher - Interface in org.biojava.bio.search
Objects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP.
SeqSimilaritySearchHit - Interface in org.biojava.bio.search
Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
SeqSimilaritySearchHit.ByScoreComparator - Class in org.biojava.bio.search
ByScoreComparator compares SeqSimilaritySearchHits by their score.
SeqSimilaritySearchHit.BySubHitCountComparator - Class in org.biojava.bio.search
BySubHitCountComparator compares SeqSimilaritySearchHits by their number of sub-hits.
SeqSimilaritySearchResult - Interface in org.biojava.bio.search
Objects of this type represent one particular result of a sequence similarity search.
SeqSimilaritySearchSubHit - Interface in org.biojava.bio.search
Objects of this type represent one particular sub-hit (one concrete sequence stretch within a sequence and associated information) from a sequence similarity search hit.
SeqSimilaritySearchSubHit.ByScoreComparator - Class in org.biojava.bio.search
ByScoreComparator compares SeqSimilaritySearchSubHits by their score.
SeqSimilaritySearchSubHit.BySubjectStartComparator - Class in org.biojava.bio.search
BySubjectStartComparator compares SeqSimilaritySearchSubHits by their start position on the subject sequence.
SeqSimilarityStAXAdapter - Class in org.biojava.bio.program.ssbind
SeqSimilarityStAXAdapter is a handler for XML conforming to the BioJava BlastLike DTD.
SeqSimilarityStAXAdapter() - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
 
SeqSimilarityStAXHandler - Class in org.biojava.bio.program.ssbind
SeqSimilarityStAXHandler is a base class for creating modular StAX handlers which send callbacks to a SeqSimilarityStAXAdapter.
SeqSimilarityStAXHandler(SeqSimilarityStAXAdapter) - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
Creates a new SeqSimilarityStAXHandler which simply maintains a list of StAXHandlerBindings and delegates to any suitable StAXContentHandler bound by one of them.
seqString() - Method in class org.biojava.bio.dp.SimpleStatePath
 
seqString() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
seqString() - Method in class org.biojava.bio.seq.impl.DummySequence
 
seqString() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
seqString() - Method in class org.biojava.bio.seq.impl.SubSequence
 
seqString() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
seqString() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
seqString() - Method in class org.biojava.bio.seq.SimpleAssembly
 
seqString() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
seqString() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
seqString() - Method in interface org.biojava.bio.symbol.SymbolList
Stringify this symbol list.
seqString() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Stringify this symbol list.
seqString() - Method in class org.biojavax.bio.seq.ThinRichSequence
Stringify this symbol list.
seqString(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
Stringify this Sequences.
seqString(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
Stringify this Sequences.
seqString(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
Stringify this Sequences.
sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
 
sequence(String) - Method in interface org.biojava.bio.program.fastq.ParseListener
Notify this parse listener of a sequence line.
Sequence - Interface in org.biojava.bio.seq
A biological sequence.
SEQUENCE - Static variable in interface org.biojava.bio.dp.StatePath
Alignment label for the emitted sequence.
SEQUENCE - Static variable in class org.biojava.bio.program.abi.ABITools
Alignment label for the DNA sequence row.
SEQUENCE_CAUTION - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
A name for a comment type.
SEQUENCE_CHECKSUM_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SEQUENCE_FORMAT - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
SEQUENCE_FORMAT is the key used to identify the format of the indexed sequence files represented by the store in the OBDA config.dat files.
SEQUENCE_LENGTH_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SEQUENCE_LENGTH_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SEQUENCE_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SEQUENCE_MODIFIED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SEQUENCE_TOPOLOGY_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SEQUENCE_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SEQUENCE_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SEQUENCE_VERSION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SequenceAlignmentSAXParser - Class in org.biojava.bio.program.sax
A SAX2 parser for dealing with a sequence alignments.
SequenceAlignmentSAXParser() - Constructor for class org.biojava.bio.program.sax.SequenceAlignmentSAXParser
Initialises internal state Sets namespace prefix to "biojava"
sequenceAndQualityLengthsMatch() - Method in class org.biojava.bio.program.fastq.FastqBuilder
Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.
SequenceAnnotator - Interface in org.biojava.bio.seq
An object which adds some additional information to a Sequence.
SequenceBuilder - Interface in org.biojava.bio.seq.io
Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object.
SequenceBuilderBase - Class in org.biojava.bio.seq.io
Basic SequenceBuilder implementation which accumulates all notified information.
SequenceBuilderBase() - Constructor for class org.biojava.bio.seq.io.SequenceBuilderBase
 
SequenceBuilderFactory - Interface in org.biojava.bio.seq.io
Simple factory for constructing new SequenceBuilder objects.
SequenceBuilderFilter - Class in org.biojava.bio.seq.io
Base-class for builders that pass filtered events onto another builder.
SequenceBuilderFilter(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SequenceBuilderFilter
Create a new SeqIOFilter that will forward events on to another listener.
SequenceContentHandlerBase - Class in org.biojava.bio.seq.io.game
StAX handler for elements containing sequence
SequenceContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
 
SequenceDB - Interface in org.biojava.bio.seq.db
A database of sequences with accessible keys and iterators over all sequences.
SequenceDBDataSource - Class in org.biojava.bio.seq.distributed
Turn an entire SequenceDB instance into a DistDataSource.
SequenceDBDataSource(SequenceDB) - Constructor for class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
SequenceDBInstallation - Interface in org.biojava.bio.seq.db
A SequenceDBInstallation has the functionality of a factory for SequenceDB objects and additionally manages the SequenceDB objects created by itself such that the minimum number of SequenceDB objects is created by a particular SequenceDBInstallation object.
SequenceDBLite - Interface in org.biojava.bio.seq.db
A database of sequences.
SequenceDBProvider - Interface in org.biojava.directory
Interfaces for named resources that can provide sequences via a database given some configuration information as defined by the OBDA standard.
SequenceDBSearchHit - Class in org.biojava.bio.search
Deprecated.
SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.
SequenceDBSearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List) - Constructor for class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
Creates a new SequenceDBSearchHit object.
SequenceDBSearchResult - Class in org.biojava.bio.search
Deprecated.
SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.
SequenceDBSearchResult(Sequence, SequenceDB, Map, List, Annotation) - Constructor for class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
Creates a new SequenceDBSearchResult.
SequenceDBSearchSubHit - Class in org.biojava.bio.search
Deprecated.
SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.
SequenceDBSearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation) - Constructor for class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
Creates a new SequenceDBSearchSubHit object.
SequenceDBSequenceBuilder - Class in org.biojava.bio.seq.io
This SequenceBuilder has a variety of modes of operation.
SequenceDBSequenceBuilder(SequenceDB, int) - Constructor for class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
constructor
SequenceDBStreamer(SequenceDB) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
 
SequenceDBWrapper - Class in org.biojava.bio.seq.db
An abstract implementation of SequenceDB that wraps up another database.
SequenceDBWrapper(SequenceDB) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper
 
SequenceDBWrapper.SequencesForwarder - Class in org.biojava.bio.seq.db
 
sequenceExtentOfPixels(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
SequenceFactory - Interface in org.biojava.bio.seq
Deprecated.
use org.biojavax.bio.seq.io.RichSequenceBuilder or use org.biojavax.bio.seq.io.SequenceBuilder
SequenceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
 
SequenceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
 
SequenceFormat - Interface in org.biojava.bio.seq.io
Defines what a sequence format does.
SequenceHandler - Interface in org.biojava.bio.seq.io.agave
mark interface
sequenceIterator() - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.DummySequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
 
sequenceIterator() - Method in interface org.biojava.bio.seq.db.SequenceDB
Returns a SequenceIterator over all sequences in the database.
sequenceIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
sequenceIterator() - Method in interface org.biojavax.bio.db.RichSequenceDB
Returns a SequenceIterator over all sequences in the database.
SequenceIterator - Interface in org.biojava.bio.seq
An iterator over a bag of sequences.
SequencePanel - Class in org.biojava.bio.gui.sequence
A panel that displays a Sequence.
SequencePanel() - Constructor for class org.biojava.bio.gui.sequence.SequencePanel
Create a new SequencePanel.
SequencePanel.Border - Class in org.biojava.bio.gui.sequence
 
SequencePanelWrapper - Class in org.biojava.bio.gui.sequence
Handles multiple SequencePanels and Ranges so that a Sequence can be wrapped over more than one line on screen.
SequencePanelWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequencePanelWrapper
Creates a new instance of WrappedSequencePanel
SequencePoster - Class in org.biojava.bio.gui.sequence
Deprecated.
This doesn't handle loads of stuff. Use SequencePoster.
SequencePoster() - Constructor for class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Create a new SeqeuncePanel.
SequencePoster.Border - Class in org.biojava.bio.gui.sequence
Deprecated.
 
SequenceRenderContext - Interface in org.biojava.bio.gui.sequence
A context within which sequence information may be rendered.
SequenceRenderContext.Border - Class in org.biojava.bio.gui.sequence
The metric object for the 'border' area - the area between the extent of the rendered area and the beginning or end of the sequence.
SequenceRenderer - Interface in org.biojava.bio.gui.sequence
The interface for things that can render a line of information about a sequence.
SequenceRenderer.RendererForwarder - Class in org.biojava.bio.gui.sequence
 
SequenceRendererWrapper - Class in org.biojava.bio.gui.sequence
An implementation of SequenceRenderer that delegates rendering to another renderer.
SequenceRendererWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper
Create a new renderer with no wrapped renderer.
SequenceRendererWrapper(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper
Create a new wrapper with a wrapped renderer
SEQUENCES - Static variable in interface org.biojava.bio.seq.db.SequenceDBLite
Signals that sequences are being added to or remove from the database.
SequencesAsGFF - Class in org.biojava.bio.program.gff
Turns a sequence database into a GFF event stream.
SequencesAsGFF() - Constructor for class org.biojava.bio.program.gff.SequencesAsGFF
 
SequencesForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
 
SequenceStreamer - Interface in org.biojava.bio.program.ssaha
 
SequenceStreamer.FileStreamer - Class in org.biojava.bio.program.ssaha
 
SequenceStreamer.SequenceDBStreamer - Class in org.biojava.bio.program.ssaha
 
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
 
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
sequenceToGraphics converts a sequence index to a graphical position.
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
sequenceToGraphics(int) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
Converts a sequence index into a graphical coordinate.
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
sequenceToGraphics converts a sequence index to a graphical position.
SequenceTools - Class in org.biojava.bio.seq
Methods for manipulating sequences.
SequenceViewerEvent - Class in org.biojava.bio.gui.sequence
An event indicating that a mouse gesture was recognised within a widget that renders sequences.
SequenceViewerEvent(Object, Object, int, MouseEvent, List) - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerEvent
Construct a SequenceViewerEvent with the given source, target, mouseEvent and path.
SequenceViewerListener - Interface in org.biojava.bio.gui.sequence
 
SequenceViewerMotionListener - Interface in org.biojava.bio.gui.sequence
 
SequenceViewerMotionSupport - Class in org.biojava.bio.gui.sequence
 
SequenceViewerMotionSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
 
SequenceViewerSupport - Class in org.biojava.bio.gui.sequence
 
SequenceViewerSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerSupport
 
SEQVERSION - Static variable in interface org.biojavax.bio.BioEntry
 
ser() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Serine (S)
serialize(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat
Deprecated.
 
serialize(Taxon) - Method in interface org.biojava.bio.taxa.TaxonParser
Deprecated.
Convert a Taxon into a stringified representation.
serializeSource(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat
Deprecated.
 
serializeXRef(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat
Deprecated.
 
serialVersionUID - Static variable in class org.biojava.bio.dp.SimpleMarkovModel
 
serialVersionUID - Static variable in class org.biojava.bio.symbol.AbstractAlphabet
 
serialVersionUID - Static variable in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties
 
serialVersionUID - Static variable in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties
 
series - Variable in class org.biojava.bibliography.BiblioBook
Book series.
ServerSide() - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ServerSide
Creates a new ServerSide image map.
Services - Class in org.biojava.utils
Utility methods for handling META-INF/services files
Services() - Constructor for class org.biojava.utils.Services
 
set(int, Object) - Method in class org.biojava.utils.FileAsList
This always returns null, not the previous object.
set(Object, Object) - Method in class org.biojava.utils.ListTools.Doublet
 
set(Object, Object, Object) - Method in class org.biojava.utils.ListTools.Triplet
 
setA(Object) - Method in class org.biojava.utils.ListTools.Doublet
 
setA(Object) - Method in class org.biojava.utils.ListTools.Triplet
 
setAbsorptionMax(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property absorptionMax.
setAbsorptionNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property absorptionNote.
setAccession(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setAccession(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setAccession(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener the accession of the record being read.
setAccession(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener the accession of the record being read.
setAcronym(String) - Method in interface org.biojavax.Namespace
Sets an optional acronym for the namespace.
setAcronym(String) - Method in class org.biojavax.SimpleNamespace
Sets an optional acronym for the namespace.
setAddPos(boolean) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Set a flag so that newly added points will be in the positive class or negative class, depending on wether addPos is true or false respectively.
setAdvance(int[]) - Method in interface org.biojava.bio.dp.EmissionState
Set the advance array.
setAdvance(int[]) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setAdvancedOptions(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
This method is to be used if a request is to use non-default values at submission.
setAlignementOption(String, String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
 
setAlignementOption(String, String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties
Method to set the value for a specific alignment parameter using a key to store in a map.
setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
 
setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
Deprecated.
 
setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
Sets the Alignment attribute of the Border object.
setAlignment(Alignment) - Method in class org.biojava.bio.seq.homol.SimpleHomology
setAlignment sets the alignment which describes the homology.
setAlignmentNumber(int) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
A method to set the number of alignments to fetch to the GET command.
setAlignmentOutputFormat(RemoteQBlastOutputFormat) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
This method is use to set the alignment output format to get from the QBlast service
setAlpha(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
setAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
setAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
setAlphabetName(String) - Method in class org.biojavax.bio.seq.SimpleRichSequence
 
setAlphabetName(String) - Method in class org.biojavax.bio.seq.ThinRichSequence
 
setAlphaStar(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setAnnotation(Annotation) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setAnnotation(Annotation) - Method in class org.biojava.ontology.Term.Impl
 
setApplicationClass(Class, Class) - Static method in class org.biojavax.RichObjectFactory
Allow application to override the default biojava class created in getObject - subclass restriction is checked in the builder.
setArrowHeadSize(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
setArticleAuthors(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Sets the names of the authors which first published an article about the AAindex entry.
setArticleTitle(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Sets the title of the article which describes the AAindex entry.
setAuthority(String) - Method in interface org.biojavax.Namespace
This method sets the authority that governs the namespace.
setAuthority(String) - Method in class org.biojavax.SimpleNamespace
This method sets the authority that governs the namespace.
setB(Object) - Method in class org.biojava.utils.ListTools.Doublet
 
setB(Object) - Method in class org.biojava.utils.ListTools.Triplet
 
setBaseCallAlignment(Alignment) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
Provides the list of base calls.
setBaseColor(Symbol, Color) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Maps a color to a DNA symbol.
setBeadDepth(double) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
setBeadDepth sets the depth of a single bead produced by this renderer.
setBeadDisplacement(double) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
setBeadDisplacement sets the displacement of beads from the centre line of the renderer.
setBeadFill(Paint) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
setBeadFill sets the bead fill paint.
setBeadOutline(Paint) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
setBeadOutline sets the bead outline paint.
setBeadStroke(Stroke) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
setBeadStroke sets the bead outline stroke.
setBits(int) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
Sets the number of significant bits in the trace samples.
setBlastDatabase(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
This method set the database to be use with blastall
setBlastProgram(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
This method set the program to be use with blastall.
setBlockDepth(double) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
 
setBlockDepth(double) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
 
setBlockPainter(BlockPainter) - Method in class org.biojava.bio.gui.DistributionLogo
 
setBlockParser(String, NexusBlockParser) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
setBlockParser(String, NexusBlockParser) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Sets the parser to use for a given block.
setBlockWidth(double) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
setBooleanValue(boolean) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
Override this method to do something useful with the boolean we collect.
setBoundaryFinder(BoundaryFinder) - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
 
setBounds(Rectangle2D.Float) - Method in interface org.biojava.bio.gui.glyph.Glyph
 
setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.HelixGlyph
 
setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
 
setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.TurnGlyph
 
setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
 
setByteValue(byte) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
Override this method to do something useful with the byte we collect.
setC(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer
 
setC(double) - Method in class org.biojava.stats.svm.SMOTrainer
 
setC(Object) - Method in class org.biojava.utils.ListTools.Triplet
 
setCategory(String) - Method in class org.biojava.ontology.Synonym
 
setChanger(Object, ChangeTable.Changer) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
Set the Changer to be used for all values of a particular tag.
setChangeTable(ChangeTable) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
 
setCharacter(char) - Method in class org.biojava.utils.RepeatedCharSequence
 
setCharStateLabel(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setCharStateLabel(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setCharStateLabel(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setCharValue(char) - Method in class org.biojava.utils.stax.CharElementHandlerBase
Override this method to do something useful with the char we collect.
setChildrenRaw(Set) - Method in class org.biojava.bio.taxa.WeakTaxon
Deprecated.
 
setChromatogram(Chromatogram) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Sets the chromatogram to draw.
setChromImpl(SymbolList[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
 
setChromImpl(SymbolList[]) - Method in class org.biojavax.ga.impl.SimpleOrganism
 
setChromosome(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setChromosomes(SymbolList[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
 
setChromosomes(SymbolList[]) - Method in interface org.biojavax.ga.Organism
Sets the organisms 'chromosome' sequences.
setCircular(boolean) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setCircular(boolean) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setCircular(boolean) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Defined this sequence being parser as circular.
setCircular(boolean) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Defined this sequence being parser as circular.
setCircular(boolean) - Method in interface org.biojavax.bio.seq.RichSequence
Circularises the Sequence.
setCircular(boolean) - Method in class org.biojavax.bio.seq.ThinRichSequence
Circularises the Sequence.
setCircularLength(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Sets the circular length of this location.
setCircularLength(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Sets the circular length of this location.
setCircularLength(int) - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
Sets the circular length of this location.
setCircularLength(int) - Method in interface org.biojavax.bio.seq.RichLocation
Sets the circular length of this location.
setCircularLength(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Sets the circular length of this location.
setCodeGenerator(CodeMethod, CodeGenerator) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
 
setCollapsing(boolean) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
Specifies if the renderer should collapse to zero depth when no features are visible (default true).
setCommands(String) - Method in class org.biojava.utils.process.ExternalProcess
Sets the command line including the path or name of the external program and its command line arguments.
setComment(Object, String) - Method in class org.biojava.bio.AnnotationType.Impl
 
setComment(Object, String) - Method in interface org.biojava.bio.AnnotationType
Set the comment for a particular property.
setComment(String) - Method in class org.biojava.bio.AnnotationType.Impl
 
setComment(String) - Method in interface org.biojava.bio.AnnotationType
Set the comment for the whole AnnotationType.
setComment(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the comment to comment.
setComment(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Sets the user comment for the AAindex entry.
setComment(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setComment(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setComment(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener about a comment in the record being read.
setComment(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener about a comment in the record being read.
setComment(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
Setter for property comment.
setComment(String) - Method in class org.biojavax.SimpleComment
 
setCommentType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property commentType.
setCommonName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
setCommonName(String) - Method in interface org.biojava.bio.taxa.Taxon
Deprecated.
Set the new common name of this Taxon.
setCommonName(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
With this method the common name of the given taxon can be changed or created, if there was none before.
setConstant(double) - Method in class org.biojava.stats.svm.PolynomialKernel
 
setConstant(double) - Method in class org.biojava.stats.svm.SigmoidKernel
 
setConstraint(Object, CollectionConstraint) - Method in class org.biojava.bio.AnnotationType.Impl
 
setConstraint(Object, CollectionConstraint) - Method in interface org.biojava.bio.AnnotationType
Specifies the constraint to apply to the specified property.
setConstraints(Object, PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract
 
setConstraints(Object, PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType
Set the constraints associated with a property.
setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser
sets the ContentHandler for this object
setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
this sets the ContentHandler that receives SAX events from the internal Blast XML parser which is the actual ContentHandler.
setContinueOnEmptyTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
Choose whether to treat empty tags as a continuation of previous tags or as a new tag with the value of the empty string.
setContinueOnEmptyTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
Decide whether to treat empty tags as continuations of the previous non -empty tag.
setCount(AtomicSymbol, double) - Method in interface org.biojava.bio.dist.Count
Set the count for the Symbol s.
setCount(AtomicSymbol, double) - Method in class org.biojava.bio.dist.IndexedCount
 
setCounts(Count) - Method in interface org.biojava.bio.dist.Count
Set the counts in this Counts to be equal to the counts in c.
setCounts(Count) - Method in class org.biojava.bio.dist.IndexedCount
 
setCreateOnUnderlyingSequence(boolean) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
setCrossOverFunction(CrossOverFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
Changes the CrossOverFunction used to CrossOver Chromosomes
setCrossOverFunction(CrossOverFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
setCrossOverProbs(double[]) - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
 
setCrossOverProbs(double[]) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
setCrossOverProbs(double[]) - Method in interface org.biojavax.ga.functions.CrossOverFunction
Sets the probability of crossing at each base.
setCrossref(CrossRef) - Method in interface org.biojavax.DocRef
The document reference may refer to an object in another database.
setCrossref(CrossRef) - Method in class org.biojavax.SimpleDocRef
The document reference may refer to an object in another database.
setCrossRef(CrossRef) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Sets the cross ref resolver to use when retrieving remote symbols.
setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Sets the cross ref resolver to use when retrieving remote symbols.
setCrossRefResolver(CrossReferenceResolver) - Method in interface org.biojavax.bio.seq.RichLocation
Sets the cross ref resolver to use when retrieving remote symbols.
setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Sets the cross ref resolver to use when retrieving remote symbols.
setCurrentSequenceName(String) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
 
setCurrentSequenceName(String) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
Set the name of the sequence which is about to be received.
setDatabase(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
 
setDatabaseID(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
setDatabaseID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
setDatabaseID(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
 
setDatabaseID(String) - Method in class org.biojava.bio.search.FilteringContentHandler
 
setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentAdapter
 
setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentFilter
 
setDatabaseID(String) - Method in interface org.biojava.bio.search.SearchContentHandler
setDatabaseID identifies the database searched by a name, ID or URN.
setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
setDatabaseName(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property databaseName.
setDataType(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setDataType(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setDataType(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setDbCode(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
 
setDefaultBlockParsers() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
 
setDefaultBlockParsers() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
setDefaultBlockParsers() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Causes the default block parsers to be assigned.
setDefaultChanger(ChangeTable.Changer) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
The changer that will be applied to the values of tags not registered explicitly to any changer or splitter instance.
setDefaultConstraint(CollectionConstraint) - Method in class org.biojava.bio.AnnotationType.Impl
 
setDefaultConstraint(CollectionConstraint) - Method in interface org.biojava.bio.AnnotationType
Specifies the default constraint to apply to properties where no other constraint is specified.
setDefaultConstraints(PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract
 
setDefaultConstraints(PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType
Set the constraints that will apply to all properties without an explicitly defined set of constraints.
setDefaultCrossReferenceResolver(CrossReferenceResolver) - Static method in class org.biojavax.RichObjectFactory
Sets the default crossref resolver to use when resolving remote entries.
setDefaultNamespaceName(String) - Static method in class org.biojavax.RichObjectFactory
Sets the default namespace name to use when loading sequences.
setDefaultOntologyName(String) - Static method in class org.biojavax.RichObjectFactory
Sets the default ontology name to use when loading sequences.
setDefaultPaint(Paint) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
 
setDefaultPositionResolver(PositionResolver) - Static method in class org.biojavax.RichObjectFactory
Sets the default position resolver to use when creating new rich feature locations.
setDefaultRichSequenceHandler(RichSequenceHandler) - Static method in class org.biojavax.RichObjectFactory
Sets the default sequence handler to use when performing sequence manipulation.
setDefaultSplitter(ChangeTable.Splitter) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
The splitter that will be applied to the values of tags not registered explicitly to any changer or splitter instance.
setDefaultTransitions(StateMachine.TransitionTable) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
specify fallback TransitionTable for this State
setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.StateMachine
TagValueWrapper interface
setDelegate(TagValueListener) - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper
set listener to which all calls will be delegated
setDelegateParser(TagValueParser) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
setDelegateRenderer associates an OptimizableFilter with a BeadFeatureRenderer.
setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
setDelegateRenderer associates an OptimizableFilter with a BeadFeatureRenderer.
setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
setDelegateRenderer for the specified filter.
setDelete(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Sets the penalty for a delete operation to the specified value.
setDelete(short) - Method in class org.biojava.bio.alignment.SmithWaterman
Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a delete operation to the specified value.
setDeprecated(boolean) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
Set the deprecation flag.
setDepth(double) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
setDepth(double) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
 
setDepth(double) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
setDepth(SequenceRenderer, double) - Method in class org.biojava.bio.gui.sequence.LineInfo
 
setDepthScaler(SuffixTreeKernel.DepthScaler) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
Change the current DepthScaler to depthScaler.
setDescription(String) - Method in class org.biojava.bio.alignment.SubstitutionMatrix
Sets the description to the given value.
setDescription(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Sets the description for the AAindex entry.
setDescription(String) - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
 
setDescription(String) - Method in class org.biojava.ontology.AbstractTerm
 
setDescription(String) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
setDescription(String) - Method in class org.biojava.ontology.IntegerOntology
 
setDescription(String) - Method in class org.biojava.ontology.Ontology.Impl
 
setDescription(String) - Method in interface org.biojava.ontology.Ontology
set the description of this ontology
setDescription(String) - Method in class org.biojava.ontology.OntologyTerm.Impl
 
setDescription(String) - Method in interface org.biojava.ontology.Term
set the description of the term;
setDescription(String) - Method in class org.biojava.ontology.Triple.Impl
 
setDescription(String) - Method in interface org.biojavax.bio.BioEntry
Sets the description for this bioentry.
setDescription(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setDescription(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setDescription(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener the description of the record being read.
setDescription(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener the description of the record being read.
setDescription(String) - Method in class org.biojavax.bio.SimpleBioEntry
Sets the description for this bioentry.
setDescription(String) - Method in interface org.biojavax.Namespace
This method sets a description for the namespace.
setDescription(String) - Method in interface org.biojavax.ontology.ComparableOntology
Sets a human-readable description of this ontology.
setDescription(String) - Method in interface org.biojavax.ontology.ComparableTerm
Sets the description associated with this term.
setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
Sets a human-readable description of this ontology.
setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableTerm
Sets the description associated with this term.
setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableTriple
set the description of the term;
setDescription(String) - Method in class org.biojavax.SimpleNamespace
This method sets a description for the namespace.
setDescriptionNumber(int) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
A method to set the number of descriptions to fetch to the GET command.
setDescriptors(Set) - Method in interface org.biojavax.ontology.ComparableTriple
Clears the current set of descriptors and replaces it with the content of the set passed.
setDescriptors(Set) - Method in class org.biojavax.ontology.SimpleComparableTriple
Clears the current set of descriptors and replaces it with the content of the set passed.
setDiagonal(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
setDiagonal(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
setDiagonal(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
 
setDimensionRatio(double) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
setDimensionRatio sets the minimum ratio of long dimension to short dimension of the bead.
setDimensionsNChar(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Set the NCHAR value.
setDimensionsNChar(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setDimensionsNChar(int) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
Set the NCHAR value.
setDimensionsNChar(int) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Set the NCHAR value.
setDimensionsNChar(int) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
setDimensionsNChar(int) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
Set the NCHAR value.
setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Set the NTAX value.
setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setDimensionsNTax(int) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
Set the NTAX value.
setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Set the NTAX value.
setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
setDimensionsNTax(int) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
Set the NTAX value.
setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Set the NTAX value.
setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
 
setDimensionsNTax(int) - Method in interface org.biojavax.bio.phylo.io.nexus.TaxaBlockListener
Set the DIMENSIONS NTAX value.
setDirection(int) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
This method allows you to decide in which direction the arrow has to point.
setDirection(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
setDirection sets the direction in which this context will render the sequence - HORIZONTAL or VERTICAL.
setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel
Set the direction that this SequencePanel renders in.
setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Set the direction that this SequencePoster renders in.
setDirection(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
setDirection sets the direction in which this context will render sequences - HORIZONTAL or VERTICAL.
setDistanceBetweenFeatures(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
setDistribution(Distribution) - Method in interface org.biojava.bio.dp.EmissionState
Set the Distribution associated with this state.
setDistribution(Distribution) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setDistribution(Distribution) - Method in class org.biojava.bio.gui.DistributionLogo
Set the dist to render.
setDistribution(Symbol, Distribution) - Method in interface org.biojava.bio.dist.OrderNDistribution
Set the distribution assocated with a symbol.
setDivision(String) - Method in interface org.biojavax.bio.BioEntry
Sets the division of this bioentry.
setDivision(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setDivision(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setDivision(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener the division of the record being read.
setDivision(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener the division of the record being read.
setDivision(String) - Method in class org.biojavax.bio.SimpleBioEntry
Sets the division of this bioentry.
setDocumentLocator(Locator) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
setDocumentLocator(Locator) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
setDocumentLocator(Locator) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
setDocumentLocator(Locator) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
setDocumentLocator(Locator) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
setDocumentLocator(Locator) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
setDocumentLocator(Locator) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
setDoubleProperty(Symbol, String) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
 
setDoubleValue(double) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
Override this method to do something useful with the double we collect.
setDTDHandler(DTDHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
 
setElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
setElideComments(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Use this method to toggle reading of comments data.
setElideComments(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Use this method to toggle reading of comments data.
setElideFeatures(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Use this method to toggle reading of feature data.
setElideFeatures(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Use this method to toggle reading of feature data.
setElideReferences(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Use this method to toggle reading of bibliographic reference data.
setElideReferences(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Use this method to toggle reading of bibliographic reference data.
setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
Specifies whether the symbols (SQ) part of the entry should be ignored.
setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
Use this method to toggle reading of sequence data.
setElideSymbols(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Use this method to toggle reading of sequence data.
setElideSymbols(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Use this method to toggle reading of sequence data.
setEliminateEnd(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setEliminateEnd(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setEliminateEnd(int) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setEliminateStart(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setEliminateStart(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setEliminateStart(int) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setEmail(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService
Set the email for QBlast.
setEmail(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Set the email for Entrez.
setEnd(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the end coordinate to end.
setEnd(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setEnd(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
setEnd(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
Set the string indicating that a record has ended.
setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.RegexParser
Set the explicit end-of-record string.
setEntityResolver(EntityResolver) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries.
setEnvironmentProperties(String[]) - Method in class org.biojava.utils.process.ExternalProcess
Sets environment variables for the external process.
setEpsilon(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer
 
setEpsilon(double) - Method in class org.biojava.stats.svm.SMOTrainer
 
setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff.GFFParser
Set the error handler used by this parser.
setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff3.GFF3Parser
Set the error handler used by this parser.
setErrorHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess
Sets the output error handler which is responsible for the standard error output of the external process.
setErrorHandler(ErrorHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
 
setEvents(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property events.
setExceptionOnNullDelegate(boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
determines if an exception is thrown when an event arrives without the delegate being set.
setFactory(RichSequenceBuilderFactory) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Setter for property factory.
setFactory(RichSequenceBuilderFactory) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
Setter for property factory.
setFallback(StateMachine.TransitionTable) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
set the specified TransitionTable to be looked looked up if the Transition cannot be found in this one.
setFeature(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
Set the feature to feature.
setFeature(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the feature type to type.
setFeature(String, boolean) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
by default, we set the parser to non-validating.
setFeature(RichFeature) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Sets the feature this location is associated with.
setFeature(RichFeature) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Sets the feature this location is associated with.
setFeature(RichFeature) - Method in interface org.biojavax.bio.seq.RichLocation
Sets the feature this location is associated with.
setFeature(RichFeature) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Sets the feature this location is associated with.
setFeatureFilter(FeatureFilter) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Replace the current FeatureFilter with filter.
setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
Set the object which receives startFeature/endFeature notifications.
setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
setFeatureProperty(Object, Object) - Method in class org.biojava.bio.program.xff.FeatureHandler
Set a property.
setFeatureRealizer(FeatureRealizer) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
Set the FeatureRealizer used by new sequences created by this factory.
setFeatureRelationshipSet(Set<RichFeatureRelationship>) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
Clears the relations from this feature holder and replaces them with a new set.
setFeatureRelationshipSet(Set<RichFeatureRelationship>) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Clears the relations from this feature holder and replaces them with a new set.
setFeatureRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
setFeatureRenderer sets the renderer to be used.
setFeatureSet(Set<Feature>) - Method in interface org.biojavax.bio.seq.RichSequence
Sets the features of this sequence.
setFeatureSet(Set<Feature>) - Method in class org.biojavax.bio.seq.ThinRichSequence
Sets the features of this sequence.
setFeatureSource(FeatureSource) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
 
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
 
setFillColor(Color) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
Set the background color of the label area.
setFillPaint(Paint) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
Allows you to set the paint properties of this glyph.
setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle
 
setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
 
setFilter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
 
setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
setFilter sets the filter.
setFirstIntActID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Setter for property firstIntActID.
setFitness(double[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
 
setFitness(double[]) - Method in interface org.biojavax.ga.Organism
This method allows to set the fitness of this organism to the specified value.
setFitnessFunction(FitnessFunction) - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
 
setFitnessFunction(FitnessFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
The fitness function that will be used to compute the fitness of each organism.
setFitnessFunction(FitnessFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
setFloatValue(float) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
Override this method to do something useful with the float we collect.
setFont(Font) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
setFrame(int) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
 
setFrame(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the frame to frame.
setGap(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setGap(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setGap(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setGapExt(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Sets the penalty for an extension of any gap (insert or delete) to the specified value.
setGapExt(short) - Method in class org.biojava.bio.alignment.SmithWaterman
Overrides the method inherited from the NeedlemanWunsch and sets the penalty for an extension of any gap (insert or delete) to the specified value.
setGenerateSequenceHeader(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Specify whether a per-sequence header line, giving the length of the sequence, should be generated.
setGeneticCode(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
Sets the genetic code of this taxon, which may be null, which will unset it.
setGeneticCode(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Sets the genetic code of this taxon, which may be null, which will unset it.
setGeneticCodeID(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Updates the taxon in the database and sets its genetic code id to the specified value.
setGlyphForFilter(FeatureFilter, Glyph) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
Allows setting another Glyph object to be painted for the given FeatureFilter.
setGroupAttributes(Map) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Replace the group-attribute Map with ga.
setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
Sets the element name that the class responds to.
setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
Sets the element name that the class responds to.
setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
Sets the element name that the class responds to.
setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
Sets the element name that the class responds to.
setHeader(FastaHeader) - Method in class org.biojavax.bio.seq.io.FastaFormat
 
setHeight(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Sets the height (in pixels).
setHeightScaling(boolean) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
setHeightScaling sets the height scaling policy.
setHeightScaling(boolean) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
setHeightScaling sets the height scaling policy.
setHorizontalScale(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Sets the horizontal scale (proportional).
setId(Integer) - Method in class org.biojavax.bio.seq.SimplePosition
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.bio.SimpleBioEntry
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableOntology
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableTerm
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableTriple
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.SimpleComment
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.SimpleCrossRef
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.SimpleDocRef
Sets the Hibernate ID.
setId(Integer) - Method in class org.biojavax.SimpleNamespace
Sets the Hibernate ID.
setId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
setID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Setter for property ID.
setIdentifier(String) - Method in interface org.biojavax.bio.BioEntry
Sets the identifier of this bioentry.
setIdentifier(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setIdentifier(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setIdentifier(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener the identifier of the record being read.
setIdentifier(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener the identifier of the record being read.
setIdentifier(String) - Method in class org.biojavax.bio.SimpleBioEntry
Sets the identifier of this bioentry.
setIdentifier(String) - Method in interface org.biojavax.ontology.ComparableTerm
Sets the (optional) identifier associated with this term.
setIdentifier(String) - Method in class org.biojavax.ontology.SimpleComparableTerm
Sets the (optional) identifier associated with this term.
setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
setImageMap sets the current image map.
setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
setImageMap sets the current image map.
setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
setImageMap sets the current image map.
setInput(InputStream) - Method in interface org.biojava.utils.process.OutputHandler
Sets the input stream.
setInput(InputStream) - Method in class org.biojava.utils.process.StreamPipe
Sets the input stream
setInput(InputStream) - Method in class org.biojava.utils.process.WriterOutputHandler
Sets the input stream.
setInputHandler(InputHandler) - Method in class org.biojava.utils.process.ExternalProcess
Sets the input handler which is responsible for the standard input of the external process.
setInsert(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Sets the penalty for an insert operation to the specified value.
setInsert(short) - Method in class org.biojava.bio.alignment.SmithWaterman
Overrides the method inherited from the NeedlemanWunsch and sets the penalty for an insert operation to the specified value.
setInteractions(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property interactions.
setInterleaved(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setInterleaved(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setInterleaved(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setInterleaved(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
setInterleaved(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
setInterleaved(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
 
setIntValue(int) - Method in class org.biojava.utils.stax.IntElementHandlerBase
Override this method to do something useful with the int we collect.
setIsoforms(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property isoforms.
setIsoIDs(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Setter for property isoIDs.
setIsStrict(boolean) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
Selects strict mode.
setIsStrict(boolean) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
Selects strict mode.
setJoiner(String) - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
setJournalReference(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Sets a reference to the journal which published the article about the AAindex entry.
setKernel(SVMKernel) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setKernel(SVMKernel) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Set the kernel used for classification.
setKey(Object) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
 
setKineticsNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property kineticsNote.
setKMs(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property KMs.
setLabel(String) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
 
setLabel(String) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
 
setLabel(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Setter for property label.
setLabelMaker(FeatureLabelRenderer.LabelMaker) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
 
setLabels(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setLabels(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setLabels(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setLabels(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
setLabels(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
setLabels(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
 
setLambda(double) - Method in class org.biojava.stats.svm.DiagonalAddKernel
Set the scale factor.
setLeadingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
setLeftValue(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
Sets the left value.
setLeftValue(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Sets the left value.
setLeftValue(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Updates the taxon and sets the left value to the specified value.
setLength(int) - Method in class org.biojava.bio.search.SeqContentPattern
Set the pattern length.
setLength(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
setLength(int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
setLength(int) - Method in class org.biojava.utils.RepeatedCharSequence
 
setLimit(int) - Method in class org.biojava.utils.cache.FixedSizeCache
 
setLines(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Set the absolute number of lines that the sequence will be rendered on.
setLineWidth(int) - Method in class org.biojava.bio.program.phred.PhredFormat
Set the line width.
setLineWidth(int) - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
Set the line width.
setLineWidth(int) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Set the line width.
setLineWidth(int) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Set the line width.
setListener(Object, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
setListener(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
set a TagValueListener for this State.
setListener(PatternListener) - Method in class org.biojava.utils.automata.PatternBlitz
 
setListener(PatternListener) - Method in interface org.biojava.utils.automata.StateMachineFactory
 
setListener(Search.Listener) - Method in class org.biojava.utils.regex.Search
 
setLITDBEntryNumbers(String[]) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Sets the list of literature database identifiers for the AAindex entry.
setLoc(Location) - Method in interface org.biojava.bio.alignment.AlignmentElement
 
setLoc(Location) - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
 
setLocation(Location) - Method in interface org.biojava.bio.seq.Feature
The new location for this feature.
setLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
setLocation(Location) - Method in class org.biojavax.bio.seq.SimpleRichFeature
The new location for this feature.
setLocation(RichLocation) - Method in interface org.biojavax.RankedDocRef
Set the location of this reference.
setLocation(RichLocation) - Method in class org.biojavax.SimpleRankedDocRef
Set the location of this reference.
setLocationValue(Location) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
Override this method to do something useful with the location we collect.
setLogoFont(Font) - Method in class org.biojava.bio.gui.TextBlock
Set the current logo font.
setLogoFont(Font) - Method in class org.biojava.bio.gui.TextLogoPainter
Set the current logo font.
setLogoPainter(LogoPainter) - Method in class org.biojava.bio.gui.DistributionLogo
Set the logo painter.
setLongValue(long) - Method in class org.biojava.utils.stax.LongElementHandlerBase
Override this method to do something useful with the long we collect.
setLRUCacheSize(int) - Static method in class org.biojavax.RichObjectFactory
Sets the size of the LRU cache.
setLRUCacheSize(Class, int) - Static method in class org.biojavax.RichObjectFactory
Sets the size of the LRU cache.
setMapAll(boolean) - Method in class org.biojava.bio.molbio.RestrictionMapper
setMapAll sets whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it.
setMapType(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setMatch(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Sets the penalty for a match operation to the specified value.
setMatch(short) - Method in class org.biojava.bio.alignment.SmithWaterman
Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a match operation to the specified value.
setMatchChar(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setMatchChar(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setMatchChar(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setMaxCounts(AtomicSymbol, int) - Method in class org.biojava.bio.search.SeqContentPattern
Set the maximum counts required for a symbol.
setMaxCrossOvers(int) - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
 
setMaxCrossOvers(int) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
setMaxCrossOvers(int) - Method in interface org.biojavax.ga.functions.CrossOverFunction
Sets an upper limit on the number of crosses.
setMaxMissedCleavages(int) - Method in class org.biojava.bio.proteomics.Digest
Sets the maximum number of partial digest products to be annotated.
setMaxPosition(Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
setMaxRunTimeSecs(int) - Method in class org.biojava.utils.ExecRunner
Sets the maximum run time in seconds.
setMergeAnnotation(Annotation) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
 
setMergeSameTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
Enable or disable treating runs of identical tags as a single tag start event with multiple values or each as a separate tag start, value, and tag end.
setMergeSameTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
Decide if multiple examples of a single tag should be merged into a single start/endTag pair with multiple values, or multiple start/endTag pairs each with a single value.
setMinCounts(AtomicSymbol, int) - Method in class org.biojava.bio.search.SeqContentPattern
Set the minimum counts required for a symbol.
setMinPosition(Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
setMismatches(int) - Method in class org.biojava.bio.search.MaxMismatchPattern
 
setMissing(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setMissing(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setMissing(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setMissing(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
setMissing(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
setMissing(String) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
 
setMitochondrialGeneticCodeID(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Updates the given taxon and sets it's so called mitochondrial genetic code id to the specified value.
setMitoGeneticCode(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
Sets the mitochondrial genetic code of this taxon, which may be null, which will unset it.
setMitoGeneticCode(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Sets the mitochondrial genetic code of this taxon, which may be null, which will unset it.
setModel(MarkovModel) - Method in class org.biojava.bio.dp.DP
 
setModeLazy() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
 
setModeLazy() - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser
Setting the mode to lazy means that, if the program is recognised, e.g.
setModeStrict() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
 
setModeStrict() - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser
This is the default, parsing will be attempted only if both the program e.g.
setMolecularWeight(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property molecularWeight.
setMolWeightError(Integer) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property molWeightError.
setMolWeightMethod(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property molWeightMethod.
setMolWeightRangeEnd(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property molWeightRangeEnd.
setMolWeightRangeStart(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property molWeightRangeStart.
setMoreSearches(boolean) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentAdapter
 
setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentFilter
 
setMoreSearches(boolean) - Method in interface org.biojava.bio.search.SearchContentHandler
setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results.
setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
setMultiplier(double) - Method in class org.biojava.stats.svm.PolynomialKernel
 
setMultiplier(double) - Method in class org.biojava.stats.svm.SigmoidKernel
 
setMutationFunction(MutationFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
Sets the current MutationFunction
setMutationFunction(MutationFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
setMutationProbs(double[]) - Method in class org.biojavax.ga.functions.AbstractMutationFunction
 
setMutationProbs(double[]) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
setMutationProbs(double[]) - Method in interface org.biojavax.ga.functions.MutationFunction
Set the probability of a mutation occuring at a certain position Position 0 in the array corresponds to the probability of the first residue of seq mutating.
setMutationSpectrum(OrderNDistribution) - Method in class org.biojavax.ga.functions.AbstractMutationFunction
 
setMutationSpectrum(OrderNDistribution) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
setMutationSpectrum(OrderNDistribution) - Method in interface org.biojavax.ga.functions.MutationFunction
Sets the Distribution of Symbols that will be selected from when a mutation occurs.
setName(String) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setName(String) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
set the name of this group.
setName(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
setName(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence
Assign a name to this sequence
setName(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
setName(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
setName(String) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
setName(String) - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
setName(String) - Method in interface org.biojava.bio.seq.io.SeqIOListener
Notify the listener that the current sequence is generally known by a particular name.
setName(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
setName(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
setName(String) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
The name is printed out as part of the identifier line.
setName(String) - Method in class org.biojava.bio.symbol.SimpleAlphabet
Assign a name to the alphabet
setName(String) - Method in class org.biojava.ontology.IntegerOntology
 
setName(String) - Method in class org.biojava.ontology.Ontology.Impl
 
setName(String) - Method in interface org.biojava.ontology.Ontology
Set the name for this ontology
setName(String) - Method in class org.biojava.ontology.Synonym
 
setName(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setName(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setName(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Notify the listener that the current sequence is generally known by a particular name.
setName(String) - Method in interface org.biojavax.bio.seq.RichFeature
Sets the name of this feature.
setName(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Sets the name of this feature.
setName(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
Changes the name.
setName(String) - Method in class org.biojavax.ga.impl.AbstractOrganism
 
setName(String) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
setName(String) - Method in interface org.biojavax.ga.Organism
Sets the organisms name
setName(String) - Method in interface org.biojavax.ga.Population
Sets the name of the population
setName(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
 
setNameClass(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
Changes the class of this name.
setNamedIsoforms(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
Setter for property namedIsoforms.
setNames(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Setter for property names.
setNamespace(Namespace) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Setter for property namespace.
setNamespace(Namespace) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
Setter for property namespace.
setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setNamespace(Namespace) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener the namespace of the record being read.
setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener the namespace of the record being read.
setNegShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Set the Shape to represent the negative points.
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.CachingKernel
 
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.DiagonalCachingKernel
Set the kernel to nest.
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.NestedKernel
Set the SVMKernel to nest to k.
setNewTag(Object, Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper
setNewTag.
setNodePrefix(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Sets the node prefix of intermediate nodes for returned graphs.
setNodeRank(String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
Sets the node rank of this taxon.
setNodeRank(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Setter for property nodeRank.
setNormalizingVector(SparseVector) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
Set the normalizing vector.
setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Setter for property note.
setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property note.
setNoteSet(Set) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Clears the notes associated with this object and replaces them with the contents of this set.
setNoteSet(Set) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Clears the notes associated with this object and replaces them with the contents of this set.
setNoteSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Clears the notes associated with this object and replaces them with the contents of this set.
setNoteSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Clears the notes associated with this object and replaces them with the contents of this set.
setNoteSet(Set) - Method in class org.biojavax.EmptyRichAnnotation
Clears the notes from this annotation and replaces them with those from the given set.
setNoteSet(Set) - Method in class org.biojavax.SimpleCrossRef
Clears the notes associated with this object and replaces them with the contents of this set.
setNoteSet(Set<Note>) - Method in class org.biojavax.bio.SimpleBioEntry
Clears the notes associated with this object and replaces them with the contents of this set.
setNoteSet(Set<Note>) - Method in interface org.biojavax.RichAnnotatable
Clears the notes associated with this object and replaces them with the contents of this set.
setNoteSet(Set<Note>) - Method in interface org.biojavax.RichAnnotation
Clears the notes from this annotation and replaces them with those from the given set.
setNoteSet(Set<Note>) - Method in class org.biojavax.SimpleRichAnnotation
Clears the notes from this annotation and replaces them with those from the given set.
setNullModel(Distribution) - Method in class org.biojava.bio.dist.AbstractDistribution
 
setNullModel(Distribution) - Method in interface org.biojava.bio.dist.Distribution
Set the null model Distribution that this Distribution recognizes.
setNullModel(Distribution) - Method in class org.biojava.bio.dist.GapDistribution
 
setNullModel(Distribution) - Method in class org.biojava.bio.dist.PairDistribution
 
setNullModel(Distribution) - Method in class org.biojava.bio.dist.TranslatedDistribution
 
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.AbstractDistribution
Implement this to set the null model.
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
 
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.SimpleDistribution
 
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.UniformDistribution
Assign a background distribution.
setNullModelWeight(double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Set the number of pseudocounts to add when training the distribution.
setNullModelWeight(double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
setNumber(float) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
Set the number associated with this node.
setNumberExperiments(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Setter for property numberExperiments.
setObsolete(Boolean) - Method in interface org.biojavax.ontology.ComparableTerm
Sets the obsolescence flag associated with this term.
setObsolete(Boolean) - Method in class org.biojavax.ontology.SimpleComparableTerm
Sets the obsolescence flag associated with this term.
setOffset(double) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
 
setOption(ChromatogramGraphic.Option, Object) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Sets a new value for the specified option.
setOrder(double) - Method in class org.biojava.stats.svm.PolynomialKernel
 
setOrganismsDiffer(boolean) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Setter for property organismsDiffer.
setOrientation(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setOuterPaint(Paint) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
Allows setting the paint properties of the outer line of this glyph to the given value.
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
 
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
setOutline sets the the colour used to draw the lines.
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
setOutline sets the the colour used to draw the lines.
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
 
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
 
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
 
setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle
 
setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
 
setOutput(OutputStream) - Method in interface org.biojava.utils.process.InputHandler
Sets the output stream.
setOutput(OutputStream) - Method in class org.biojava.utils.process.ReaderInputHandler
Sets the output stream.
setOutput(OutputStream) - Method in class org.biojava.utils.process.StreamPipe
Sets the output stream
setOutputFormat(RemoteQBlastOutputFormat) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
This method is use to set the stream output format to get from the QBlast service
setOutputHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess
Sets the output handler which is responsible for the standard output of the external process.
setOutputOption(String, String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
 
setOutputOption(String, String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties
Method to set the value for a specific output parameter using a key to store in a map.
setPadding(double) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
Set the padding.
setPaint(Paint) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
Allows you to set the paint properties of this glyph, i.e., its color.
setPaint(Paint) - Method in class org.biojava.bio.gui.glyph.TurnGlyph
Allows you to set the paint properties of this glyph, i.e., its color.
setParent(Connection, Taxon, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
This updates the taxonomic tree in the database and sets the parent of the given child taxon to the parent taxon.
setParent(FeatureHolder) - Method in interface org.biojavax.bio.seq.RichFeature
Sets the parent of this feature.
setParent(FeatureHolder) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Sets the parent of this feature.
setParentNCBITaxID(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
Sets the parent NCBI taxon ID.
setParentNCBITaxID(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Sets the parent NCBI taxon ID.
setParserListener(Object, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
setPathPrefix(File) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
setPathPrefix sets the abstract path to be appended to sequence database filenames retrieved from the binary index.
setPattern(Pattern) - Method in class org.biojava.bio.program.tagvalue.RegexParser
Set the Pattern used to split lines.
setPattern(SymbolList) - Method in class org.biojava.bio.search.MaxMismatchPattern
 
setPhase(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setPHDependence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property PHDependence.
setPopulation(Population) - Method in interface org.biojavax.ga.GeneticAlgorithm
Sets the Population of Organisms to the Algorithm.
setPopulation(Population) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
setPos(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
 
setPositionResolver(PositionResolver) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Sets the resolver to use when working out actual base coordinates from fuzzy positions.
setPositionResolver(PositionResolver) - Method in interface org.biojavax.bio.seq.RichLocation
Sets the resolver to use when working out actual base coordinates from fuzzy positions.
setPositionResolver(PositionResolver) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Sets the resolver to use when working out actual base coordinates from fuzzy positions.
setPositions(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
setPosShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Set the Shape to represent the positive points.
setPrimaryKey(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
setPrimaryKey sets the primary identifier namespace.
setPrimaryKeyName(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
Set the tag to use as a primary key in the index.
setPrimaryKeyName(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
Set the tag to use as a primary key in the index.
setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
setPrintStream(PrintStream) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
Deprecated.
setPrintStream informs an instance which PrintStream to use.
setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
setPrintStream informs an instance which PrintStream to use.
setPrintStream(PrintStream) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
Sets the stream to write to.
setPrintStream(PrintStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Sets the stream to write to.
setPrintWriter(PrintWriter) - Method in class org.biojava.bio.program.blast2html.HTMLRenderer
Set the PrintWriter to output the HTML to.
setProfileHMM() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
setProperty(Object, Object) - Method in class org.biojava.bio.AbstractAnnotation
 
setProperty(Object, Object) - Method in interface org.biojava.bio.Annotation
Set the value of a property.
setProperty(Object, Object) - Method in class org.biojava.bio.MergeAnnotation
 
setProperty(Object, Object) - Method in class org.biojava.bio.OverlayAnnotation
 
setProperty(Object, Object) - Method in class org.biojavax.EmptyRichAnnotation
Set the value of a property.
setProperty(Object, Object) - Method in class org.biojavax.SimpleRichAnnotation
Deprecated. 
setProperty(String, Object) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
 
setProperty(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
 
setProperty(String, String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
setProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
 
setProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType
Set the property in an annotation bundle according to the type we believe it should be.
setProtease(Protease) - Method in class org.biojava.bio.proteomics.Digest
 
setProtype(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionEnzyme
Set the prototype of this RestrictionEnzyme.
setQueryID(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
setQueryID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
setQueryID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
setQueryID(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
setQueryID(String) - Method in class org.biojava.bio.search.FilteringContentHandler
 
setQueryID(String) - Method in class org.biojava.bio.search.SearchContentAdapter
 
setQueryID(String) - Method in class org.biojava.bio.search.SearchContentFilter
 
setQueryID(String) - Method in interface org.biojava.bio.search.SearchContentHandler
setQueryID identifies the query sequence by a name, ID or URN.
setQueryID(String) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
setQuerySeq(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
Deprecated.
use setQueryID instead.
setQuerySeqHolder(SequenceDB) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
setQuerySeqHolder sets the query sequence holder to a specific database.
setQuerySeqHolder(SequenceDB) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
setQuerySeqHolder sets the query sequence holder to a specific database.
setRadius(double) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
 
setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
 
setRange(RangeLocation) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
 
setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
 
setRank(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Sets the rank for this location.
setRank(int) - Method in interface org.biojavax.bio.seq.RichFeature
Sets the rank of this feature.
setRank(int) - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
Sets the rank of this relationship.
setRank(int) - Method in interface org.biojavax.bio.seq.RichLocation
Sets the rank for this location.
setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Sets the rank of this feature.
setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Sets the rank of this relationship.
setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Sets the rank for this location.
setRank(int) - Method in interface org.biojavax.Comment
Sets the rank of this comment.
setRank(int) - Method in interface org.biojavax.Note
Sets the rank for this note.
setRank(int) - Method in interface org.biojavax.RankedCrossRef
Set the rank associated with the cross reference.
setRank(int) - Method in interface org.biojavax.RankedDocRef
Set the rank of this reference.
setRank(int) - Method in class org.biojavax.SimpleComment
Sets the rank of this comment.
setRank(int) - Method in class org.biojavax.SimpleNote
Sets the rank for this note.
setRank(int) - Method in class org.biojavax.SimpleRankedCrossRef
Set the rank associated with the cross reference.
setRank(int) - Method in class org.biojavax.SimpleRankedDocRef
Set the rank of this reference.
setRank(Integer) - Method in interface org.biojavax.bio.BioEntryRelationship
Sets the rank of this relationship.
setRank(Integer) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
Sets the rank of this relationship.
setRank(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Updates a taxon and sets it's rank to the specified String.
setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener about a cross reference.
setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener about a cross reference.
setRankedCrossRefs(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Sets the ranked cross references associated with an object.
setRankedCrossRefs(Set) - Method in class org.biojavax.ontology.SimpleComparableTerm
Sets the ranked cross references associated with an object.
setRankedCrossRefs(Set<RankedCrossRef>) - Method in class org.biojavax.bio.SimpleBioEntry
 
setRankedCrossRefs(Set<RankedCrossRef>) - Method in interface org.biojavax.RankedCrossRefable
Sets the ranked cross references associated with an object.
setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener about a literature reference in the record being read.
setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener about a literature reference in the record being read.
setReader(Reader) - Method in class org.biojava.utils.process.ReaderWriterPipe
Sets the reader.
setRecurse(boolean) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
setRecurse(boolean) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
setRecurse sets the recursion flag on the filter.
setRecurse(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Set whether features will be filtered recursively to recurse.
setRecursive(boolean) - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
 
setRedoxPotential(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property redoxPotential.
setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
 
setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry.
setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry.
setRemark(String) - Method in interface org.biojavax.DocRef
Set the remarks for this document reference using this method.
setRemark(String) - Method in class org.biojavax.SimpleDocRef
Set the remarks for this document reference using this method.
setRenderer(CircularFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
 
setRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
 
setRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
setRenderer sets the renderer.
setRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
setRenderer sets the current PairwiseSequenceRenderer.
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
Set the child renderer responsible for drawing the contents of this track
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
 
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
 
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
setRenderer sets the current SequenceRenderer.
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.DistributionLogo
 
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
setRenderingHints sets the RenderingHints which will be used by the Graphics2D instances of delegate renderers.
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePanel
Use this to switch on effects like Anti-aliasing etc
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Use this to switch on effects like Anti-aliasing etc
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
setRenderingHints sets the RenderingHints which will be used by the Graphics2D instances of delegate renderers.
setReplace(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Sets the penalty for a replace operation to the specified value.
setReplace(short) - Method in class org.biojava.bio.alignment.SmithWaterman
Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a replace operation to the specified value.
setRespectCase(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setRespectCase(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setRespectCase(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setRetain(boolean) - Method in class org.biojava.bio.program.tagvalue.TagDropper
Set wether known tags are to be retained or dropped.
setRichObjectBuilder(RichObjectBuilder) - Static method in class org.biojavax.RichObjectFactory
Sets the builder to use when instantiating new Rich objects.
setRightValue(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
Sets the right value.
setRightValue(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Sets the right value.
setRightValue(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Updates the taxon in the database and sets the right value to the specified value.
setRootType(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString
Make the tree (un)rooted.
setScale(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
setScale sets the scale in pixels per Symbol.
setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePanel
Set the scale.
setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Set the scale.
setScale(double) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
setScale sets the scale in pixels per Symbol.
setScaleByInformation(boolean) - Method in class org.biojava.bio.gui.DistributionLogo
 
setScientificName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
setScientificName(String) - Method in interface org.biojava.bio.taxa.Taxon
Deprecated.
Change the scientific name of this species.
setScientificName(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
This changes the scientific name of the given taxon and stores the new name persistent in the database.
setScope(int) - Method in class org.biojava.ontology.Synonym
 
setScore(double) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
setScore(double) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the score to score.
setScore(double) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setScore(int) - Method in class org.biojava.bio.alignment.SimpleAlignment
 
setScore(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
setSearchContentHandler sets the handler which will recieve the method calls generated by the adapter.
setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
setSearchContentHandler sets the handler which will recieve the method calls generated by the adapter.
setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.search.FilteringContentHandler
 
setSecondarySequence(Sequence) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
setSecondarySequence sets the secondary Sequence to be rendered.
setSecondarySymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
setSecondarySymbolTranslation sets the translation in Symbols which will be applied when rendering.
setSecondIntActID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
Setter for property secondIntActID.
setSelectionFunction(SelectionFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
Changes the SelectionFunction used to select candidates for the next generation
setSelectionFunction(SelectionFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
setSelectionPressure(int) - Method in class org.biojavax.ga.functions.TournamentSelection
sets the parameter controlling selection pressure
setSeqCautions(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property seqCautions.
setSeqID(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
Deprecated.
 
setSeqName(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
Set the sequence name to seqName.
setSeqName(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the sequence name to seqName.
setSequence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
setSequence sets the Sequence to be rendered.
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Set the SymboList to be rendered.
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
 
setSequence(Sequence) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
 
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
 
setSequence(Sequence) - Method in class org.biojava.bio.proteomics.Digest
 
setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
 
setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.SequencePanel
Set the SymboList to be rendered.
setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
setSequence sets the Sequence to be rendered.
setSequenceCount(int) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
 
setSequenceCount(int) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
Set the number of sequences in the alignment.
setSequenceDB(SequenceDB) - Method in class org.biojava.bio.gui.FeatureTree
Use this method to provide the sequences for the tree to work with.
setSequenceFormat(SequenceFormat) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
 
setSequenceFormat(LifeScienceIdentifier) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
setSequenceFormat sets the sequence format name which will be indicated in the index.
setSequenceID(String) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setSequenceLength(int) - Method in class org.biojavax.bio.seq.SimpleRichSequence
 
setSequenceLength(int) - Method in class org.biojavax.bio.seq.ThinRichSequence
 
setSequenceOffset(int) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
setSequenceRef(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Setter for property sequenceRef.
setSequenceType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
Setter for property sequenceType.
setSeqVersion(Double) - Method in interface org.biojavax.bio.seq.RichSequence
Sets the version of the associated symbol list.
setSeqVersion(Double) - Method in class org.biojavax.bio.seq.ThinRichSequence
Sets the version of the associated symbol list.
setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setSeqVersion(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener the version of the sequence of the record being read.
setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener the version of the sequence of the record being read.
setShatter(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Specify whether features with non-contiguous locations should be broken up such that a GFF feature line is emitted for each contiguous block.
setShowAccession(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
 
setShowDescription(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
 
setShowIdentifier(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
 
setShowName(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
 
setShowNamespace(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
 
setShowVersion(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
Determines if the version number of a sequence should be displayed.
setSibling(SimilarityPairFeature) - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
setSibling sets the sibling feature of the pair.
setSibling(SimilarityPairFeature) - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
 
setSignificantBits(int) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
Sets the number of significant bits in the data.
setSitesCount(int) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
 
setSitesCount(int) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
Set the number of sites in the alignment
setSize(double) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
Sets the size of the border in number of pixels.
setSleepTime(int) - Method in class org.biojava.utils.process.ExternalProcess
Sets the number of milliseconds the ExternalProcess.execute(Properties) method should pauses after the external process is terminated.
setSource(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
Set the source to source.
setSource(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the feature source to source.
setSource(String) - Method in interface org.biojava.bio.seq.Feature
Change the source of the Feature.
setSource(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
setSource(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setSource(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Change the source of the Feature.
setSource(Term) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setSourceFile(String) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
Set the source file associated with this code class.
setSourceTerm(Term) - Method in interface org.biojava.bio.seq.Feature
Set the source ontology-term for this feature.
setSourceTerm(Term) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
setSourceTerm(Term) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Set the source ontology-term for this feature.
setSpacer(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
Set the number of pixels to leave blank between each block of sequence information.
setSplitOffset(int) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
Set the offset to split lines at.
setSplitter(Object, ChangeTable.Splitter) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
Set the Splitter to be used for all values of a particular tag.
setStarred(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString
Sets whether this tree has a star before it's name.
setStart(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the start coordinate to start.
setStart(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
setStatesFormat(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setStatesFormat(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setStatesFormat(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setStoreLocation(File) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
setStoreLocation sets the directory of the new index.
setStoreName(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
setStoreName sets the name to be given to the new index.
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
 
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the strand to strand.
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
setStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.StrandedFeature
Set the strand that this feature lies upon.
setStrand(StrandedFeature.Strand) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Set the strand that this feature lies upon.
setStrand(RichLocation.Strand) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
setStreamParser(StreamParser) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
assign a StreamParser object to instance.
setStringSequence(String) - Method in class org.biojavax.bio.seq.SimpleRichSequence
 
setStringValue(String) - Method in class org.biojava.bio.program.xff.PropDetailHandler
 
setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
 
setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMENamePropHandler
 
setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMETypePropHandler
 
setStringValue(String) - Method in class org.biojava.utils.stax.StringElementHandlerBase
Override this method to do something useful with the string we collect.
setStyle(SymbolStyle) - Method in class org.biojava.bio.gui.DistributionLogo
Set the symbol style.
setSubjectDB(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
Deprecated.
use setDatabaseID instead.
setSubjectDBInstallation(SequenceDBInstallation) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
setSubjectDBInstallation sets the subject database holder to a specific installation.
setSubjectDBInstallation(SequenceDBInstallation) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
setSubjectDBInstallation sets the subject database holder to a specific installation.
setSubMatrix(SubstitutionMatrix) - Method in class org.biojava.bio.alignment.SmithWaterman
 
setSubSeqStart(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setSubstitutionMatrix(SubstitutionMatrix) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
Sets the substitution matrix to be used to the specified one.
setSymbolList(SymbolList) - Method in class org.biojava.bio.molbio.Composition
Set the SymbolList to calculation the composition of.
setSymbolLists(SymbolList, SymbolList) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
Set the DNA and OFFSETS symbol lists for the basecall alignment.
setSymbolModification(char, double) - Method in class org.biojava.bio.proteomics.MassCalc
Use this to set a post translational modification for the Symbol represented by this character.
setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
setSymbolTranslation sets the translation in Symbols which will be applied when rendering.
setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
setSymbolTranslation sets the translation in Symbols which will be applied when rendering.
setSynonyms(Set<Object>) - Method in class org.biojava.ontology.Term.Impl
 
setTableNumber(int) - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
 
setTagGroup(int) - Method in class org.biojava.bio.program.tagvalue.RegexParser
Set the group number that will match the tag.
setTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
setTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
setTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
 
setTaxon(NCBITaxon) - Method in interface org.biojavax.bio.BioEntry
Sets the taxon for this bioentry.
setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setTaxon(NCBITaxon) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener the Taxon of the record being read.
setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener the Taxon of the record being read.
setTaxon(NCBITaxon) - Method in class org.biojavax.bio.SimpleBioEntry
Sets the taxon for this bioentry.
setTaxonHidden(boolean) - Method in interface org.biojavax.bio.taxa.NCBITaxon
determines whether this taxonomy level is displayed in etNameHierarchy()
setTaxonHidden(boolean) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
 
setTemperatureDependence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property temperatureDependence.
setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Sets the term for this location.
setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Sets the term for this location.
setTerm(ComparableTerm) - Method in interface org.biojavax.bio.seq.RichLocation
Sets the term for this location.
setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Sets the term for this location.
setTerm(ComparableTerm) - Method in interface org.biojavax.Note
Sets the term for this note.
setTerm(ComparableTerm) - Method in class org.biojavax.SimpleNote
Sets the term for this note.
setTermSet(Set) - Method in interface org.biojavax.ontology.ComparableOntology
Clears out all the terms and populates the ontology with the contents of the set passed.
setTermSet(Set) - Method in class org.biojavax.ontology.SimpleComparableOntology
Clears out all the terms and populates the ontology with the contents of the set passed.
setText(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property text.
setTextColor(Color) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
Set the color of the label text
setThreshold() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
setThreshold(double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
setThreshold(double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
setThreshold(double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setTickDirection(int) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
setTitle(String) - Method in interface org.biojava.bio.program.homologene.Orthologue
 
setTitle(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
 
setTokens(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setTokens(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setTokens(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setTool(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService
Set the tool identifier for QBlast.
setTool(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
Set the tool identifier for Entrez.
setTrace(ABITrace) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
setTrace(AtomicSymbol, int[], int) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
Provides the trace samples for a particular nucleotide.
setTraceValues(AtomicSymbol, int[], int) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
Sets the trace array for one of the DNA nucleotides.
setTrackLayout(TrackLayout) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
setTrailingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
 
setTransition(Object, StateMachine.State) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
set a Transition for this State setting notifyOnExit to false.
setTransition(Object, StateMachine.State, boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
set a Transition for this State
setTransition(Object, StateMachine.State, boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
set a Transition within this TransitionTable (3-argument form)
setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
Alter the translation mapping.
setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
Alter the translation mapping.
setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
Alter the translation mapping.
setTransposed(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
setTransposed(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
setTransposed(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
setTreeString(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString
Set the Newick string describing the tree.
setTriangle(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
setTriangle(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
setTriangle(String) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
 
setTrimTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
Enable or disable trimming of tags.
setTrimTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
Enable trimming of the tag using String.trim().
setTrimValue(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
Enable or disable trimming of values.
setTrimValue(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
Enable trimming of the value using String.trim().
setTripleSet(Set) - Method in interface org.biojavax.ontology.ComparableOntology
Clears out all the triples and populates the ontology with the contents of the set passed.
setTripleSet(Set) - Method in class org.biojavax.ontology.SimpleComparableOntology
Clears out all the triples and populates the ontology with the contents of the set passed.
setType(String) - Method in interface org.biojava.bio.seq.Feature
Change the type of this feature.
setType(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
setType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
Setter for property type.
setType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
setType(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Change the type of this feature.
setType(AnnotationType) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
setType(Term) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setTypeTerm(Term) - Method in interface org.biojava.bio.seq.Feature
Set the type ontology-term for this feature.
setTypeTerm(Term) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
setTypeTerm(Term) - Method in class org.biojavax.bio.seq.SimpleRichFeature
Set the type ontology-term for this feature.
setUnits(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setUri(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property uri.
setURI(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
setURI(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
setURI(String) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
setURI(String) - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
setURI(String) - Method in interface org.biojava.bio.seq.io.SeqIOListener
Notify the listener of a URI identifying the current sequence.
setURI(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
setURI(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
setURI(String) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Null implementation.
setURI(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setURI(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setURI(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Deprecated.
There is no clear mapping between URI and BioSQL. This method is no longer used or supported in biojavax. Don't use it. Calling it may result in exceptions. Use instead setName(String name), setAccession(String accession), setVersion(int version) etc as appropriate.
setURI(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Notify the listener of a URI identifying the current sequence.
setURI(URI) - Method in interface org.biojavax.Namespace
Sets an optional URI for the namespace.
setURI(URI) - Method in class org.biojavax.SimpleNamespace
Sets an optional URI for the namespace.
setURN(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence
Provide the URN for this sequence
setUserObject(Object) - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
setUserObject sets the user object.
setValue(double) - Method in interface org.biojava.stats.svm.ItemValue
 
setValue(double) - Method in class org.biojava.stats.svm.SimpleItemValue
 
setValue(String) - Method in interface org.biojavax.Note
Sets the value for this note, or null for no value.
setValue(String) - Method in class org.biojavax.SimpleNote
Sets the value for this note, or null for no value.
setValueGroup(int) - Method in class org.biojava.bio.program.tagvalue.RegexParser
Set the group number that will match the value.
setVectorNTISupport(boolean) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
VectorNTI requires GenBank format to be a little more specific than required by the GenBank definition.
setVersion(int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setVersion(int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setVersion(int) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
Call back method so the event emitter can tell the listener the version of the record being read.
setVersion(int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Call back method so the event emitter can tell the listener the version of the record being read.
setVersion(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
setVerticalScale(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Sets the vertical scale (proportional).
setVMaxes(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
Setter for property VMaxes.
setWeight(Object, double) - Method in class org.biojavax.ga.util.WeightedSet
Sets the weight of an Object.
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution
Set the weight of a given symbol in this distribution.
setWeight(Symbol, double) - Method in interface org.biojava.bio.dist.Distribution
Set the probability or odds that Symbol s is emitted by this state.
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.GapDistribution
 
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.PairDistribution
 
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.TranslatedDistribution
 
setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution
Implement this to actually set the weight.
setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
Set a weight in one of the conditioned distributions.
setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution
 
setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.UniformDistribution
 
setWeightMatrixID(String) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
Set the weight matrix id.
setWeights(State, Distribution) - Method in interface org.biojava.bio.dp.MarkovModel
Set the probability distribution over the transitions from 'source'.
setWeights(State, Distribution) - Method in class org.biojava.bio.dp.SimpleMarkovModel
Use this methods to customize the transition probabilities.
setWeights(State, Distribution) - Method in class org.biojava.bio.dp.WMAsMM
 
setWidth(double) - Method in class org.biojava.stats.svm.RadialBaseKernel
 
setWidth(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Sets the width of the whole graphic (in pixels).
setWorkingDirectory(File) - Method in class org.biojava.utils.process.ExternalProcess
Sets the working directory for the external process.
setWrap(int) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
 
setWrap(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
 
setWrap(int) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
 
setWrap(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
 
setWrapIncrement(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
 
setWrapIncrement(int) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
 
setWrapIncrement(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
 
setWrappedKernel(SVMKernel) - Method in class org.biojava.stats.svm.SigmoidKernel
 
setWriteDocType(boolean) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
Set flag that determines if XML DOCTYPE is written or not.
setWriter(Writer) - Method in class org.biojava.utils.process.ReaderWriterPipe
Sets the writer.
shadow(Location) - Static method in class org.biojava.bio.symbol.LocationTools
Return a contiguous location running from the minimum to the maximum points of the specified location.
shadowContainedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features with locations where the interval between the min and max positions are contained by the specified Location.
ShadowContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
Creates a filter that returns everything contained within loc.
shadowOverlapsLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features with locations where the interval between the min and max positions are contained by or overlap the specified Location.
ShadowOverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
Creates a filter that returns everything overlapping loc.
shannonEntropy(Distribution, double) - Static method in class org.biojava.bio.dist.DistributionTools
A method to calculate the Shannon Entropy for a Distribution.
shift(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
moves the whole sequence
shiftAll(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
shiftAtAlignmentLoc(Object, Location, int) - Method in interface org.biojava.bio.alignment.EditableAlignment
loc in this case is the Alignment Location
shiftAtAlignmentLoc(Object, Location, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
loc in this case is the Alignment Location
shiftAtSequenceLoc(Object, Location, int) - Method in interface org.biojava.bio.alignment.EditableAlignment
loc in this case is the SymbolList Location
shiftAtSequenceLoc(Object, Location, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
loc in this case is the SymbolList Location
SHORT_MAX_VALUE - Static variable in class org.biojava.bio.program.scf.SCF
Represents the maximum unsigned value of a short for wrapping purposes
SHOW_ALL - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
Return default styles
SHOW_DIFF - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
As NORMAL except only return if the two colour classes for query and subject are the different
SHOW_SAME - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
Only return if the two colour classes for query and subject are the same
sibling - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
sibling SimilarityPairFeature field.
SIBLING - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
The sibling of this feature has altered.
SigmoidKernel - Class in org.biojava.stats.svm
This kernel implements a three layer neural net.
SigmoidKernel() - Constructor for class org.biojava.stats.svm.SigmoidKernel
 
sign(double) - Static method in class org.biojava.stats.svm.tools.Classify
 
similarEntries() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Returns a map with the names of similar AAindex entries and its correlation coefficients.
SIMILARITY_PAIR_FEATURE_TYPE - Static variable in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
Constant SIMILARITY_PAIR_FEATURE_TYPE the type String used by SimilarityPairBuilder when creating SimilarityPairFeatures.
SimilarityPairBuilder - Class in org.biojava.bio.program.ssbind
SimilarityPairBuilder annotates query and subject Sequence with SimilarityPairFeatures created from SAX events supplied via a SeqSimilarityAdapter.
SimilarityPairBuilder() - Constructor for class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
SimilarityPairFeature - Interface in org.biojava.bio.seq.homol
SimilarityPairFeature describes a pairwise similarity between two nucleotide sequences (as it extends StrandedFeature).
SimilarityPairFeature.EmptyPairwiseAlignment - Class in org.biojava.bio.seq.homol
EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists.
SimilarityPairFeature.Template - Class in org.biojava.bio.seq.homol
Template for construction of SimilarityPairFeatures.
SimilarityType - Interface in org.biojava.bio.program.homologene
Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues.
SIMILARITYTYPE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
SimilarityType.PlaceHolder - Class in org.biojava.bio.program.homologene
 
SIMPLE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
SimpleAlignment - Class in org.biojava.bio.alignment
A simple implementation of an Alignment.
SimpleAlignment(Map<String, SymbolList>) - Constructor for class org.biojava.bio.alignment.SimpleAlignment
Generate an alignment from a list of SymbolLists.
SimpleAlignmentElement - Class in org.biojava.bio.alignment
SimpleSimpleAlignment is a simple implementation of AlignmentElement.
SimpleAlignmentElement(String, SymbolList, Location) - Constructor for class org.biojava.bio.alignment.SimpleAlignmentElement
 
SimpleAlignmentStyler - Class in org.biojava.bio.program.blast2html
Simple implementation for specifying markup styles.
SimpleAlignmentStyler(int) - Constructor for class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
Creates a new SimpleAlignmentStyler instance.
SimpleAlphabet - Class in org.biojava.bio.symbol
A simple no-frills implementation of the FiniteAlphabet interface.
SimpleAlphabet() - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
 
SimpleAlphabet(String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
 
SimpleAlphabet(Set) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
 
SimpleAlphabet(Set, String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
 
SimpleAnnotation - Class in org.biojava.bio
A no-frills implementation of Annotation that is just a wrapper around a LinkedHashMap.
SimpleAnnotation() - Constructor for class org.biojava.bio.SimpleAnnotation
Create a new, empty SimpleAnnotation instance.
SimpleAnnotation(Map) - Constructor for class org.biojava.bio.SimpleAnnotation
Create a new SimpleAnnotation using the values in a Map.
SimpleAnnotation(Annotation) - Constructor for class org.biojava.bio.SimpleAnnotation
Create a new SimpleAnnotation by copying the properties from another one.
SimpleAnnotationDB - Class in org.biojava.bio.annodb
A no-frills implementation of AnnotationDB.
SimpleAnnotationDB(String, Set, AnnotationType) - Constructor for class org.biojava.bio.annodb.SimpleAnnotationDB
Create a no-frills AnnotationDB instancec.
SimpleAnnotFilter - Class in org.biojava.bio.seq.io.agave
Basic implementation of AGAVEAnnotFilter
SimpleAssembly - Class in org.biojava.bio.seq
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
SimpleAssembly(int, String, String) - Constructor for class org.biojava.bio.seq.SimpleAssembly
Construct a new SimpleAssembly using the DNA alphabet.
SimpleAssembly(String, String) - Constructor for class org.biojava.bio.seq.SimpleAssembly
Construct a new SimpleAssembly using the DNA alphabet.
SimpleAssemblyBuilder - Class in org.biojava.bio.seq.io
Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.
SimpleAssemblyBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleAssemblyBuilder
 
SimpleAtomicSymbol - Class in org.biojava.bio.symbol
A basic implementation of AtomicSymbol.
SimpleAtomicSymbol(Annotation, List) - Constructor for class org.biojava.bio.symbol.SimpleAtomicSymbol
 
SimpleBioEntry - Class in org.biojavax.bio
Reference implementation of a BioEntry object which has no features or sequence.
SimpleBioEntry() - Constructor for class org.biojavax.bio.SimpleBioEntry
 
SimpleBioEntry(Namespace, String, String, int) - Constructor for class org.biojavax.bio.SimpleBioEntry
Creates a new bioentry representing the sequence in the given namespace with the given name, accession and version.
SimpleBioEntryRelationship - Class in org.biojavax.bio
Represents a relationship between two bioentries that is described by a term and given a rank.
SimpleBioEntryRelationship() - Constructor for class org.biojavax.bio.SimpleBioEntryRelationship
 
SimpleBioEntryRelationship(BioEntry, BioEntry, ComparableTerm, Integer) - Constructor for class org.biojavax.bio.SimpleBioEntryRelationship
Creates a new instance of SimpleBioEntryRelationship.
SimpleChromatogram - Class in org.biojava.bio.chromatogram
A basic chromatogram implementation which provides public mutators for setting the various attributes of the chromatogram.
SimpleChromatogram() - Constructor for class org.biojava.bio.chromatogram.SimpleChromatogram
Creates a new instance of SimpleChromatogram.
SimpleCodonPref - Class in org.biojava.bio.symbol
a simple no-frills implementation of the CodonPref object that encapsulates codon preference data.
SimpleCodonPref(String, Distribution, String) - Constructor for class org.biojava.bio.symbol.SimpleCodonPref
 
SimpleComment - Class in org.biojavax
An implementaion of Comment.
SimpleComment() - Constructor for class org.biojavax.SimpleComment
 
SimpleComment(String, int) - Constructor for class org.biojavax.SimpleComment
Constructs a new, immutable comment, given some text and a rank.
SimpleComparableOntology - Class in org.biojavax.ontology
Represents an ontology that can be compared to other ontologies.
SimpleComparableOntology() - Constructor for class org.biojavax.ontology.SimpleComparableOntology
 
SimpleComparableOntology(String) - Constructor for class org.biojavax.ontology.SimpleComparableOntology
Creates a new instance of SimpleComparableOntology with the given, immutable, non-nullable name.
SimpleComparableTerm - Class in org.biojavax.ontology
A Term object that can be compared and thus sorted.
SimpleComparableTerm() - Constructor for class org.biojavax.ontology.SimpleComparableTerm
 
SimpleComparableTriple - Class in org.biojavax.ontology
Basic comparable triple, BioSQL style.
SimpleComparableTriple() - Constructor for class org.biojavax.ontology.SimpleComparableTriple
 
SimpleCrossOverFunction - Class in org.biojavax.ga.functions
Simple Implementation of the CrossOverFunction interface
SimpleCrossOverFunction() - Constructor for class org.biojavax.ga.functions.SimpleCrossOverFunction
 
SimpleCrossRef - Class in org.biojavax
A basic CrossRef implementation.
SimpleCrossRef() - Constructor for class org.biojavax.SimpleCrossRef
 
SimpleCrossRef(String, String, int) - Constructor for class org.biojavax.SimpleCrossRef
Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version.
SimpleCrossRef(String, String, Integer) - Constructor for class org.biojavax.SimpleCrossRef
Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version.
SimpleDistribution - Class in org.biojava.bio.dist
A simple implementation of a distribution, which works with any finite alphabet.
SimpleDistribution(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistribution
make an instance of SimpleDistribution with weights identical to the specified Distribution.
SimpleDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.SimpleDistribution
make an instance of SimpleDistribution for the specified Alphabet.
SimpleDistribution.Trainer - Class in org.biojava.bio.dist
A simple implementation of a trainer for this class.
SimpleDistributionTrainer - Class in org.biojava.bio.dist
Deprecated.
Distribution impls should be providing custom trainers.
SimpleDistributionTrainer(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainer
Deprecated.
 
SimpleDistributionTrainerContext - Class in org.biojava.bio.dist
A no-frills implementation of DistributionTrainerContext.
SimpleDistributionTrainerContext() - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainerContext
Create a new context with no initial distributions or trainers.
SimpleDocRef - Class in org.biojavax
A basic DocRef implementation.
SimpleDocRef() - Constructor for class org.biojavax.SimpleDocRef
 
SimpleDocRef(String, String) - Constructor for class org.biojavax.SimpleDocRef
Creates a new document reference from the given immutable authors and location and title.
SimpleDocRef(String, String, String) - Constructor for class org.biojavax.SimpleDocRef
Creates a new document reference from the given immutable authors and location and title.
SimpleDocRef(String, String, String, String, String, Integer) - Constructor for class org.biojavax.SimpleDocRef
Construct a doc ref with populated cross ref.
SimpleDocRef(List<DocRefAuthor>, String) - Constructor for class org.biojavax.SimpleDocRef
Creates a new document reference from the given immutable authors and location and title.
SimpleDocRef(List<DocRefAuthor>, String, String) - Constructor for class org.biojavax.SimpleDocRef
Creates a new document reference from the given immutable authors and location and title.
SimpleDocRef(List, String, String, String, String, Integer) - Constructor for class org.biojavax.SimpleDocRef
Construct a doc ref with populated cross ref.
SimpleDocRefAuthor - Class in org.biojavax
Represents an author of a documentary reference.
SimpleDocRefAuthor(String) - Constructor for class org.biojavax.SimpleDocRefAuthor
Constructs a new author instance from a string.
SimpleDocRefAuthor(String, boolean, boolean) - Constructor for class org.biojavax.SimpleDocRefAuthor
Constructs a new author instance.
SimpleDotState - Class in org.biojava.bio.dp
A Dot state that you can make and use.
SimpleDotState(char, String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState
Deprecated.
token is ignored since 1.2. Use the 2-arg constructor instead.
SimpleDotState(String) - Constructor for class org.biojava.bio.dp.SimpleDotState
 
SimpleDotState(String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState
Construct a new state with the specified name and annotation
SimpleEmissionState - Class in org.biojava.bio.dp
 
SimpleEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.dp.SimpleEmissionState
 
SimpleFeature - Class in org.biojava.bio.seq.impl
A no-frills implementation of a feature.
SimpleFeature(Sequence, FeatureHolder, Feature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFeature
Create a SimpleFeature on the given sequence.
SimpleFeatureHolder - Class in org.biojava.bio.seq
A no-frills implementation of FeatureHolder.
SimpleFeatureHolder() - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder
Construct a new SimpleFeatureHolder with a non-informative schema.
SimpleFeatureHolder(FeatureFilter) - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder
Construct a new SimpleFeatureHolder with the specified schema.
SimpleFeatureRealizer - Class in org.biojava.bio.seq
FeatureRealizer which uses a lookup table to map template classes to implementations.
SimpleFeatureRealizer() - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer
 
SimpleFeatureRealizer(FeatureRealizer) - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer
 
SimpleFramedFeature - Class in org.biojava.bio.seq.impl
Title: SimpleFramedFeature.
SimpleFramedFeature(Sequence, FeatureHolder, FramedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFramedFeature
 
SimpleGACrossResult - Class in org.biojavax.ga.functions
Simple implementation of the GACross interface.
SimpleGACrossResult(PointLocation[], SymbolList[]) - Constructor for class org.biojavax.ga.functions.SimpleGACrossResult
 
SimpleGappedSequence - Class in org.biojava.bio.seq.impl
Simple implementation of GappedSequence.
SimpleGappedSequence(GappedSequence) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence
 
SimpleGappedSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence
 
SimpleGappedSequence(Alphabet) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence
 
SimpleGappedSequence.GappedContext - Class in org.biojava.bio.seq.impl
 
SimpleGappedSymbolList - Class in org.biojava.bio.symbol
This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
SimpleGappedSymbolList(Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList
 
SimpleGappedSymbolList(GappedSymbolList) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList
Create a new SimpleGappedSymbolList that will view source, inheriting all existing gaps.
SimpleGappedSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList
Create a new SimpleGappedSymbolList that will view source.
SimpleGappedSymbolList.Block - Class in org.biojava.bio.symbol
An aligned block.
SimpleGeneticAlgorithm - Class in org.biojavax.ga.impl
A simple implementation of the GeneticAlgorithm interface it is not intended that this class be overidden, hence it is final.
SimpleGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.SimpleGeneticAlgorithm
 
SimpleGeneticAlgorithm(Population, MutationFunction, CrossOverFunction, SelectionFunction) - Constructor for class org.biojavax.ga.impl.SimpleGeneticAlgorithm
 
SimpleGeneticCodeTable - Class in org.biojava.bio.symbol
A genetic code translation table representing a translation table in the DDBJ/EMBL/GenBank Feature Table (appendix V).
SimpleGeneticCodeTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleGeneticCodeTable
Creates a new instance of SimpleGeneticCodeTable
SimpleGFFRecord - Class in org.biojava.bio.program.gff
A no-frills implementation of a GFFRecord.
SimpleGFFRecord() - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
Create a new SimpleGFFRecord with values set to null or zero
SimpleGFFRecord(String, String, String, int, int, double, StrandedFeature.Strand, int, String, Map) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
 
SimpleGFFRecord(GFFRecord) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
Create a new SimpleGFFRecord from GFFRecord object
SimpleHMMTrainer - Class in org.biojava.bio.dp
 
SimpleHMMTrainer(MarkovModel) - Constructor for class org.biojava.bio.dp.SimpleHMMTrainer
 
SimpleHomologeneBuilder - Class in org.biojava.bio.program.homologene
A simple no-frills implementation of the HomologeneBuilder interface.
SimpleHomologeneBuilder() - Constructor for class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
SimpleHomologeneDB - Class in org.biojava.bio.program.homologene
 
SimpleHomologeneDB() - Constructor for class org.biojava.bio.program.homologene.SimpleHomologeneDB
 
SimpleHomology - Class in org.biojava.bio.seq.homol
A no-frills implementation of Homology.
SimpleHomology() - Constructor for class org.biojava.bio.seq.homol.SimpleHomology
Creates a new empty SimpleHomology containing no Alignment and no FeatureHolder.
SimpleHomologyFeature - Class in org.biojava.bio.seq.impl
 
SimpleHomologyFeature(Sequence, FeatureHolder, HomologyFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleHomologyFeature
 
SimpleIndex - Class in org.biojava.bio.seq.db
This is a no-frills implementation of the Index interface.
SimpleIndex(File, long, int, String) - Constructor for class org.biojava.bio.seq.db.SimpleIndex
Build the index using the given file, start and id
SimpleInputHandler - Class in org.biojava.utils.process
Simple input handler that reads the input for an external process from an input stream.
SimpleInputHandler(InputStream, String) - Constructor for class org.biojava.utils.process.SimpleInputHandler
Initializes the simple input handler.
SimpleItemValue - Class in org.biojava.stats.svm
A no-frills implementation of ItemValue.
SimpleItemValue(Object, double) - Constructor for class org.biojava.stats.svm.SimpleItemValue
 
SimpleLabelRenderer - Class in org.biojava.bio.gui.sequence
 
SimpleLabelRenderer() - Constructor for class org.biojava.bio.gui.sequence.SimpleLabelRenderer
 
SimpleManyToOneTranslationTable - Class in org.biojava.bio.symbol
A no-frills implementation of a translation table that maps between two alphabets.
SimpleManyToOneTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
Construct a new translation table.
SimpleMarkovModel - Class in org.biojava.bio.dp
 
SimpleMarkovModel(int, Alphabet) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
Deprecated. 
SimpleMarkovModel(int, Alphabet, String) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
 
SimpleModelInState - Class in org.biojava.bio.dp
 
SimpleModelInState(MarkovModel, String) - Constructor for class org.biojava.bio.dp.SimpleModelInState
 
SimpleModelTrainer - Class in org.biojava.bio.dp
 
SimpleModelTrainer() - Constructor for class org.biojava.bio.dp.SimpleModelTrainer
 
SimpleMutationFunction - Class in org.biojavax.ga.functions
Simple no frills Implementation of the MutationFunction interface
SimpleMutationFunction() - Constructor for class org.biojavax.ga.functions.SimpleMutationFunction
 
SimpleNamespace - Class in org.biojavax
A basic Namespace implemenation.
SimpleNamespace() - Constructor for class org.biojavax.SimpleNamespace
 
SimpleNamespace(String) - Constructor for class org.biojavax.SimpleNamespace
Creates a new instance of SimpleNamespace with the given name, which cannot be null.
SimpleNCBITaxon - Class in org.biojavax.bio.taxa
Reference implementation of NCBITaxon.
SimpleNCBITaxon() - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon
 
SimpleNCBITaxon(int) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon
Creates a new instance of SimpleNCBITaxon based on the given taxon ID.
SimpleNCBITaxon(Integer) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon
Creates a new instance of SimpleNCBITaxon based on the given taxon ID.
SimpleNCBITaxonName - Class in org.biojavax.bio.taxa
Represents a name class plus name combination for an NCBITaxon object.
SimpleNCBITaxonName() - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxonName
 
SimpleNCBITaxonName(String, String) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxonName
Creates a new taxon name based on the given class and name, both of which cannot be null.
SimpleNCBITaxonomyLoader - Class in org.biojavax.bio.taxa.io
Loads NCBI taxon information from names.dmp and nodes.dmp, which are two of the files in the archive downloadable at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ .
SimpleNCBITaxonomyLoader() - Constructor for class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
 
SimpleNote - Class in org.biojavax
Simple implementation of Note.
SimpleNote() - Constructor for class org.biojavax.SimpleNote
 
SimpleNote(ComparableTerm, String, int) - Constructor for class org.biojavax.SimpleNote
Creates a new instance of SimpleNote with a given term, value and rank.
SimpleOrganism - Class in org.biojavax.ga.impl
A Simple Haploid Organism implementation
SimpleOrganism() - Constructor for class org.biojavax.ga.impl.SimpleOrganism
 
SimpleOrganism(String) - Constructor for class org.biojavax.ga.impl.SimpleOrganism
 
SimpleOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.SimpleOrganism
 
SimpleOrthologue - Class in org.biojava.bio.program.homologene
this entry contains data about the orthologue.
SimpleOrthologue(int, String, String, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologue
this constructor does the Taxon lookup for you too
SimpleOrthologue(Taxon, String, String, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologue
 
SimpleOrthologueSet - Class in org.biojava.bio.program.homologene
 
SimpleOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologueSet
 
SimpleOrthologueSet.Iterator - Class in org.biojava.bio.program.homologene
 
SimpleOrthoPair - Class in org.biojava.bio.program.homologene
A no-frills implementation of the OrthoPair interface
SimpleOrthoPair(Orthologue, Orthologue, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPair
constructor for the curated form of an orthology relationship
SimpleOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPair
constructor for the computed form of an orthology relationship.
SimpleOrthoPairCollection - Class in org.biojava.bio.program.homologene
 
SimpleOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
 
SimpleOrthoPairCollection.Iterator - Class in org.biojava.bio.program.homologene
 
SimpleOrthoPairSet - Class in org.biojava.bio.program.homologene
a no-frills implementation of a Homologene Group
SimpleOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
SimpleOrthoPairSet.Iterator - Class in org.biojava.bio.program.homologene
 
SimpleOutputHandler - Class in org.biojava.utils.process
Simple output handler that pipes the output of an external process to an output stream.
SimpleOutputHandler(OutputStream, String) - Constructor for class org.biojava.utils.process.SimpleOutputHandler
Initializes the simple output handler.
SimplePopulation - Class in org.biojavax.ga.impl
Simple concrete implementation of the Population interface
SimplePopulation() - Constructor for class org.biojavax.ga.impl.SimplePopulation
 
SimplePopulation(String) - Constructor for class org.biojavax.ga.impl.SimplePopulation
 
SimplePosition - Class in org.biojavax.bio.seq
A simple implementation of the Position interface.
SimplePosition() - Constructor for class org.biojavax.bio.seq.SimplePosition
 
SimplePosition(boolean, boolean, int) - Constructor for class org.biojavax.bio.seq.SimplePosition
Constructs a point position, with optionally fuzzy start and end.
SimplePosition(boolean, boolean, int, int, String) - Constructor for class org.biojavax.bio.seq.SimplePosition
Constructs a range position, with optionally fuzzy start and end.
SimplePosition(int) - Constructor for class org.biojavax.bio.seq.SimplePosition
Constructs a point position, with no fuzzy start or end.
SimplePosition(int, int) - Constructor for class org.biojavax.bio.seq.SimplePosition
Constructs a range position, with no fuzzy start or end.
SimpleRankedCrossRef - Class in org.biojavax
Simple implementation of RankedCrossRef.
SimpleRankedCrossRef() - Constructor for class org.biojavax.SimpleRankedCrossRef
 
SimpleRankedCrossRef(CrossRef, int) - Constructor for class org.biojavax.SimpleRankedCrossRef
Constructs a new crossref with a rank.
SimpleRankedDocRef - Class in org.biojavax
Represents a documentary reference.
SimpleRankedDocRef() - Constructor for class org.biojavax.SimpleRankedDocRef
 
SimpleRankedDocRef(DocRef, Integer, Integer, int) - Constructor for class org.biojavax.SimpleRankedDocRef
Constructs a new docref for a given location.
SimpleRankedDocRef(DocRef, RichLocation, int) - Constructor for class org.biojavax.SimpleRankedDocRef
Constructs a new docref for a given location.
SimpleRemoteFeature - Class in org.biojava.bio.seq.impl
A no-frills implementation of a remote feature.
SimpleRemoteFeature(Sequence, FeatureHolder, RemoteFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature
 
SimpleRemoteFeature.DBResolver - Class in org.biojava.bio.seq.impl
 
SimpleRestrictionSite - Class in org.biojava.bio.seq.impl
SimpleRestrictionSite represents the recognition site of a restriction enzyme.
SimpleRestrictionSite(Sequence, FeatureHolder, RestrictionSite.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleRestrictionSite
Creates a new SimpleRestrictionSite.
SimpleReversibleTranslationTable - Class in org.biojava.bio.symbol
A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
SimpleReversibleTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleReversibleTranslationTable
Construct a new translation table.
SimpleRichAnnotation - Class in org.biojavax
Simple annotation wrapper.
SimpleRichAnnotation() - Constructor for class org.biojavax.SimpleRichAnnotation
Creates a new, empty instance of SimpleRichAnnotation
SimpleRichFeature - Class in org.biojavax.bio.seq
A simple implementation of RichFeature.
SimpleRichFeature() - Constructor for class org.biojavax.bio.seq.SimpleRichFeature
 
SimpleRichFeature(FeatureHolder, Feature.Template) - Constructor for class org.biojavax.bio.seq.SimpleRichFeature
Creates a new instance of SimpleRichFeature based on a template.
SimpleRichFeatureRelationship - Class in org.biojavax.bio.seq
Represents a relationship between two features that is described by a term.
SimpleRichFeatureRelationship() - Constructor for class org.biojavax.bio.seq.SimpleRichFeatureRelationship
 
SimpleRichFeatureRelationship(RichFeature, RichFeature, ComparableTerm, int) - Constructor for class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Creates a new instance of SimpleRichFeatureRelationship.
SimpleRichLocation - Class in org.biojavax.bio.seq
A simple implementation of RichLocation.
SimpleRichLocation() - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
 
SimpleRichLocation(Position, int) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
Creates a new instance of SimpleRichSequenceLocation that points to a single position on the positive strand.
SimpleRichLocation(Position, int, RichLocation.Strand) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
Creates a new instance of SimpleRichSequenceLocation that points to a single position.
SimpleRichLocation(Position, int, RichLocation.Strand, CrossRef) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
Creates a new instance of SimpleRichSequenceLocation that points to a single position on another sequence.
SimpleRichLocation(Position, Position, int) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
Creates a new instance of SimpleRichSequenceLocation that points to a range position on the positive strand.
SimpleRichLocation(Position, Position, int, RichLocation.Strand) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
Creates a new instance of SimpleRichSequenceLocation that points to a range position.
SimpleRichLocation(Position, Position, int, RichLocation.Strand, CrossRef) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
Creates a new instance of SimpleRichSequenceLocation that points to a range position on another sequence.
SimpleRichObjectBuilder - Class in org.biojavax
Creates objects and returns them, and stores them in an internal map of singletons for reference.
SimpleRichObjectBuilder() - Constructor for class org.biojavax.SimpleRichObjectBuilder
 
SimpleRichSequence - Class in org.biojavax.bio.seq
A simple implementation of RichSequence.
SimpleRichSequence() - Constructor for class org.biojavax.bio.seq.SimpleRichSequence
 
SimpleRichSequence(Namespace, String, String, int, SymbolList, Double) - Constructor for class org.biojavax.bio.seq.SimpleRichSequence
Creates a new instance of SimpleRichSequence.
SimpleRichSequenceBuilder - Class in org.biojavax.bio.seq.io
Constructs BioEntry objects by listening to events.
SimpleRichSequenceBuilder() - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Creates a new instance of SimpleRichSequenceBuilder using a SimpleSymbolListFactory with a threshold of zero.
SimpleRichSequenceBuilder(SymbolListFactory) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Creates a new instance of SimpleRichSequenceBuilder with the desired symbollistfactory and threshold of zero.
SimpleRichSequenceBuilder(SymbolListFactory, int) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Creates a new instance of SimpleRichSequenceBuilder with the desired symbollistfactory and threshold.
SimpleRichSequenceBuilderFactory - Class in org.biojavax.bio.seq.io
Generates RichSequenceBuilder objects.
SimpleRichSequenceBuilderFactory() - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
Creates a new instance of SimpleRichSequenceBuilderFactory
SimpleRichSequenceBuilderFactory(SymbolListFactory) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
Creates a new instance of SimpleRichSequenceBuilderFactory
SimpleRichSequenceBuilderFactory(SymbolListFactory, int) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
Creates a new instance of SimpleRichSequenceBuilderFactory that uses a specified factory for SymbolLists longer than a specified length.
SimpleSeqSimilaritySearchHit - Class in org.biojava.bio.search
SimpleSeqSimilaritySearchHit objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.
SimpleSeqSimilaritySearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
Creates a new SimpleSeqSimilaritySearchHit object.
SimpleSeqSimilaritySearchResult - Class in org.biojava.bio.search
SimpleSeqSimilaritySearchResult objects represent a result of a search of a SymbolList against the sequences within a SequenceDB object.
SimpleSeqSimilaritySearchResult(Sequence, SequenceDB, Map, List, Annotation) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
Creates a new SimpleSeqSimilaritySearchResult.
SimpleSeqSimilaritySearchSubHit - Class in org.biojava.bio.search
SimpleSeqSimilaritySearchSubHit objects represent sub-hits which make up a hit.
SimpleSeqSimilaritySearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
Creates a new SimpleSeqSimilaritySearchSubHit object.
SimpleSequence - Class in org.biojava.bio.seq.impl
A basic implementation of the Sequence interface.
SimpleSequence(SymbolList, String, String, Annotation) - Constructor for class org.biojava.bio.seq.impl.SimpleSequence
Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed.
SimpleSequence(SymbolList, String, String, Annotation, FeatureRealizer) - Constructor for class org.biojava.bio.seq.impl.SimpleSequence
Create a SimpleSequence using a specified FeatureRealizer.
SimpleSequenceBuilder - Class in org.biojava.bio.seq.io
Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.
SimpleSequenceBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleSequenceBuilder
 
SimpleSequenceDBInstallation - Class in org.biojava.bio.seq.db
This class is an implementation of interface SequenceDBInstallation that manages a set of SequenceDB objects.
SimpleSequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
create an initially empty SimpleSequenceDBInstallation
SimpleSequenceFactory - Class in org.biojava.bio.seq.impl
A no-frills implementation of SequenceFactory that produces SimpleSequence objects.
SimpleSequenceFactory() - Constructor for class org.biojava.bio.seq.impl.SimpleSequenceFactory
 
SimpleSimilarityPairFeature - Class in org.biojava.bio.seq.impl
SimpleSimilarityPairFeature represents a similarity between a query sequence and a subject sequence as produced by a search program.
SimpleSimilarityPairFeature(Sequence, FeatureHolder, SimilarityPairFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
Creates a new SimpleSimilarityPairFeature.
SimpleStateListener() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
 
SimpleStatePath - Class in org.biojava.bio.dp
A no-frills implementation of StatePath.
SimpleStatePath(double, SymbolList, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.SimpleStatePath
 
SimpleStrandedFeature - Class in org.biojava.bio.seq.impl
A no-frills implementation of StrandedFeature.
SimpleStrandedFeature(Sequence, FeatureHolder, StrandedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
SimpleSVMClassifierModel - Class in org.biojava.stats.svm
A no-frills implementation of an SVM classifier model.
SimpleSVMClassifierModel(SVMKernel) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
 
SimpleSVMClassifierModel(SVMKernel, Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
 
SimpleSVMClassifierModel(SVMKernel, SVMTarget) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
 
SimpleSVMTarget - Class in org.biojava.stats.svm
No-frills implementation of SVMTarget.
SimpleSVMTarget() - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
 
SimpleSVMTarget(Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
 
SimpleSymbolList - Class in org.biojava.bio.symbol
Basic implementation of SymbolList.
SimpleSymbolList(SymbolTokenization, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
Construct a SymbolList from a string.
SimpleSymbolList(Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
Construct an empty SimpleSymbolList.
SimpleSymbolList(Alphabet, List) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
Construct a SymbolList containing the symbols in the specified list.
SimpleSymbolList(Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
Construct a SimpleSymbolList given the Symbol array that backs it.
SimpleSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
Construct a copy of an existing SymbolList.
SimpleSymbolListFactory - Class in org.biojava.bio.symbol
This class makes SimpleSymbolLists.
SimpleSymbolListFactory() - Constructor for class org.biojava.bio.symbol.SimpleSymbolListFactory
 
SimpleSymbolPropertyTable - Class in org.biojava.bio.symbol
Class that implements the SymbolPropertyTable interface
SimpleSymbolPropertyTable(Alphabet, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolPropertyTable
 
SimpleSymbolPropertyTableDB - Class in org.biojava.bio.proteomics.aaindex
A simple implementation of a symbol property table database.
SimpleSymbolPropertyTableDB() - Constructor for class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
Initializes the database.
SimpleSymbolPropertyTableDB(SymbolPropertyTableIterator) - Constructor for class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
Initializes the database by copying all symbol property tables from a given iterator into the database.
SimpleSymbolStyle - Class in org.biojava.bio.gui
A no-frills implementation of SymbolStyle.
SimpleSymbolStyle(FiniteAlphabet) - Constructor for class org.biojava.bio.gui.SimpleSymbolStyle
 
SimpleTagValueWrapper - Class in org.biojava.bio.program.tagvalue
Helper class to wrap one TagValueListener inside another one.
SimpleTagValueWrapper() - Constructor for class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
SimpleTagValueWrapper(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
Build a SimpleTagValueWrapper that will forward everything to a delegate.
SimpleTaxon - Class in org.biojava.bio.taxa
Deprecated.
replaced by classes in org.biojavax.bio.taxa
SimpleTaxon() - Constructor for class org.biojava.bio.taxa.SimpleTaxon
Deprecated.
 
SimpleTaxon(String, String) - Constructor for class org.biojava.bio.taxa.SimpleTaxon
Deprecated.
Create a new instance with no parent, no children and given scientific and common names.
SimpleTaxonFactory - Class in org.biojava.bio.taxa
Deprecated.
replaced by classes in org.biojavax.bio.taxa
SimpleTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.SimpleTaxonFactory
Deprecated.
 
SimpleThreadPool - Class in org.biojava.utils
SimpleThreadPool is a basic implementation of ThreadPool for use where we don't wish to introduce a dependency on a 3rd-party pool.
SimpleThreadPool() - Constructor for class org.biojava.utils.SimpleThreadPool
Creates a new SimpleThreadPool containing 4 non-daemon threads and starts them.
SimpleThreadPool(int, boolean) - Constructor for class org.biojava.utils.SimpleThreadPool
Creates a new SimpleThreadPool containing the specified number of threads and starts them.
SimpleThreadPool(int, boolean, int) - Constructor for class org.biojava.utils.SimpleThreadPool
Creates a new SimpleThreadPool containing the specified number of threads and starts them.
SimpleTrackLayout - Class in org.biojava.bio.gui.sequence.tracklayout
A TrackLayout implenentation that wraps the sequence smoothly after a set number of residues
SimpleTrackLayout() - Constructor for class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
 
SimpleTrackLayout(Sequence, int) - Constructor for class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
 
SimpleTranslationTable - Class in org.biojava.bio.symbol
A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
SimpleTranslationTable(FiniteAlphabet, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable
Create a new translation table that will translate symbols from source to target.
SimpleTranslationTable(FiniteAlphabet, Alphabet, Map) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable
Create a new translation table that will translate symbols from source to target.
SimpleWeightMatrix - Class in org.biojava.bio.dp
 
SimpleWeightMatrix(Distribution[]) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
 
SimpleWeightMatrix(Alphabet, int, DistributionFactory) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
 
SimpleXMLEmitter - Class in org.biojava.bio.program.xml
A simple XML DocumentHandler that processes SAX2 events to create a sensibly formatted XML as it parsed without populating objects with data.
SimpleXMLEmitter() - Constructor for class org.biojava.bio.program.xml.SimpleXMLEmitter
 
SimpleXMLEmitter(boolean) - Constructor for class org.biojava.bio.program.xml.SimpleXMLEmitter
 
SingleDP - Class in org.biojava.bio.dp.onehead
An implementation of DP that aligns a single sequence against a single model.
SingleDP(MarkovModel) - Constructor for class org.biojava.bio.dp.onehead.SingleDP
 
SingleDPMatrix - Class in org.biojava.bio.dp.onehead
The dynamic programming matrix for a single sequence.
SingleDPMatrix(DP, SymbolList) - Constructor for class org.biojava.bio.dp.onehead.SingleDPMatrix
 
SingleRichSeqIterator(Sequence) - Constructor for class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
Creates an iterator over a single sequence.
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.AbstractTrainer
 
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchSampler
 
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchTrainer
 
singleSequenceIteration(ModelTrainer, SymbolList, ScoreType) - Method in class org.biojava.bio.dp.BaumWelchSampler
 
SingletonAlphabet - Class in org.biojava.bio.symbol
An alphabet that contains a single atomic symbol.
SingletonAlphabet(AtomicSymbol) - Constructor for class org.biojava.bio.symbol.SingletonAlphabet
 
SingletonList - Class in org.biojava.utils
 
SingletonList(Object) - Constructor for class org.biojava.utils.SingletonList
 
site - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
SITE_FEATURE_SOURCE - Static variable in class org.biojava.bio.molbio.RestrictionMapper
SITE_FEATURE_SOURCE the source String used by RestrictionMapper when creating restriction site Features.
SITE_FEATURE_TYPE - Static variable in class org.biojava.bio.molbio.RestrictionMapper
SITE_FEATURE_TYPE the type String used by RestrictionMapper when creating restriction site Features.
SixFrameRenderer - Class in org.biojava.bio.gui.sequence
Class that handles drawing in six frames for other classes.
SixFrameRenderer() - Constructor for class org.biojava.bio.gui.sequence.SixFrameRenderer
 
SixFrameZiggyRenderer - Class in org.biojava.bio.gui.sequence
A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.
SixFrameZiggyRenderer(SixFrameRenderer) - Constructor for class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
 
size - Variable in class org.biojavax.bio.seq.CompoundRichLocation
 
size() - Method in interface org.biojava.bio.annodb.AnnotationDB
The number of Annotation instances in the DB.
size() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
 
size() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
 
size() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
 
size() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
 
size() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
 
size() - Method in class org.biojava.bio.program.gff.GFFEntrySet
Return how many lines are in this set.
size() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
returns an iterator to the contents of the set. /** no. of entries in this Homologene group
size() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
size() - Method in interface org.biojava.bio.symbol.FiniteAlphabet
The number of symbols in the alphabet.
size() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
size() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
size() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
size() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
 
size() - Method in class org.biojava.stats.svm.SparseVector
The number of used dimensions.
size() - Method in class org.biojava.stats.svm.SVMRegressionModel
 
size() - Method in class org.biojava.utils.BeanAsMap
 
size() - Method in class org.biojava.utils.bytecode.InstructionVector
 
size() - Method in class org.biojava.utils.FileAsList
 
size() - Method in class org.biojava.utils.io.FlatFileCache
 
size() - Method in class org.biojava.utils.io.SoftHashMap
 
size() - Method in class org.biojava.utils.ListTools.Doublet
 
size() - Method in class org.biojava.utils.ListTools.SeriesList
 
size() - Method in class org.biojava.utils.ListTools.Triplet
 
size() - Method in class org.biojava.utils.MergingSet
 
size() - Method in class org.biojava.utils.SingletonList
 
size() - Method in class org.biojava.utils.SmallMap
 
size() - Method in class org.biojava.utils.SmallSet
 
size() - Method in class org.biojavax.ga.impl.SimplePopulation
 
size() - Method in interface org.biojavax.ga.Population
Gets the Size of the population
size() - Method in class org.biojavax.ga.util.WeightedSet
 
SIZE - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
SIZE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
SIZE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
skip(long) - Method in class org.biojava.utils.io.CachingInputStream
 
skip(long) - Method in class org.biojava.utils.io.CountedBufferedReader
 
skip(long) - Method in class org.biojava.utils.io.UncompressInputStream
 
SKIP_RECORD - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
 
skippedEntity(String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
skippedEntity(String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
skippedEntity(String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
skippedEntity(String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
skippedEntity(String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
skippedEntity(String) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
skippedEntity(String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
SkipRecordErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
SLEEP_TIME - Static variable in class org.biojava.utils.process.ExternalProcess
Number of milliseconds the execute method should pauses after the external process has finished the execution.
SmallAnnotation - Class in org.biojava.bio
Annotation that is optimized for memory usage.
SmallAnnotation() - Constructor for class org.biojava.bio.SmallAnnotation
Return a new SmallAnnotation optimised for small sets of properties.
SmallAnnotation(Map) - Constructor for class org.biojava.bio.SmallAnnotation
Return a new SmallAnnotation that copies all values from a Map.
SmallAnnotation(Annotation) - Constructor for class org.biojava.bio.SmallAnnotation
Return a new SmallAnnotation that copies all values from another annoation.
SmallCursor - Class in org.biojava.bio.dp.onehead
Constant-memory implementation of single-head DP cursor.
SmallCursor(State[], SymbolList, Iterator) - Constructor for class org.biojava.bio.dp.onehead.SmallCursor
 
SmallMap - Class in org.biojava.utils
Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability.
SmallMap() - Constructor for class org.biojava.utils.SmallMap
 
SmallMap(int) - Constructor for class org.biojava.utils.SmallMap
 
SmallMap(Map) - Constructor for class org.biojava.utils.SmallMap
 
SmallSet - Class in org.biojava.utils
Lightweight implementation of Set which uses little memory to store a small number of items, at the expense of scalability.
SmallSet() - Constructor for class org.biojava.utils.SmallSet
 
SmallSet(int) - Constructor for class org.biojava.utils.SmallSet
 
SmallSet(Collection) - Constructor for class org.biojava.utils.SmallSet
 
SmartSequenceBuilder - Class in org.biojava.bio.seq.io
Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.
sMatrix - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
SmithWaterman - Class in org.biojava.bio.alignment
Smith and Waterman developed an efficient dynamic programming algorithm to perform local sequence alignments, which returns the most conserved region of two sequences (longest common substring with modifications).
SmithWaterman() - Constructor for class org.biojava.bio.alignment.SmithWaterman
Default constructor.
SmithWaterman(short, short, short, short, short, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.SmithWaterman
Constructs the new SmithWaterman alignment object.
SMORegressionTrainer - Class in org.biojava.stats.svm
Train a regression support vector machine using the Sequential Minimal Optimization algorithm.
SMORegressionTrainer() - Constructor for class org.biojava.stats.svm.SMORegressionTrainer
 
SMOTrainer - Class in org.biojava.stats.svm
Train a support vector machine using the Sequential Minimal Optimization algorithm.
SMOTrainer() - Constructor for class org.biojava.stats.svm.SMOTrainer
 
SoftHashMap - Class in org.biojava.utils.io
A in memory cache using soft references.
SoftHashMap() - Constructor for class org.biojava.utils.io.SoftHashMap
 
SoftHashMap(int) - Constructor for class org.biojava.utils.io.SoftHashMap
 
SoftMaskedAlphabet - Class in org.biojava.bio.symbol
Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.
SoftMaskedAlphabet.CaseSensitiveTokenization - Class in org.biojava.bio.symbol
This SymbolTokenizer works with a delegate to softmask symbol tokenization as appropriate.
SoftMaskedAlphabet.MaskingDetector - Interface in org.biojava.bio.symbol
Implementations will define how soft masking looks.
SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector - Class in org.biojava.bio.symbol
 
SoftReferenceCache - Class in org.biojava.utils.cache
Cache which is cleared according to memory pressure.
SoftReferenceCache() - Constructor for class org.biojava.utils.cache.SoftReferenceCache
 
SolexaFastqReader - Class in org.biojava.bio.program.fastq
Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.
SolexaFastqReader() - Constructor for class org.biojava.bio.program.fastq.SolexaFastqReader
 
SolexaFastqWriter - Class in org.biojava.bio.program.fastq
Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.
SolexaFastqWriter() - Constructor for class org.biojava.bio.program.fastq.SolexaFastqWriter
 
solve(double, double, double, ComputeObject) - Static method in class org.biojava.utils.math.BinarySearch
method that will attempt solving the equation.
SomePairsInCollection(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection
 
SOPair(String, int) - Constructor for class org.biojava.ontology.obo.OboFileParser.SOPair
 
SOPair(String, int, int) - Constructor for class org.biojava.ontology.obo.OboFileParser.SOPair
 
sort() - Method in class org.biojavax.bio.seq.CompoundRichLocation
Sorts the member locations of a compound location.
sort() - Method in class org.biojavax.bio.seq.EmptyRichLocation
Sorts the member locations of a compound location.
sort() - Method in interface org.biojavax.bio.seq.RichLocation
Sorts the member locations of a compound location.
sort() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Sorts the member locations of a compound location.
sort(String[], Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery
It sorts the current collection and returns another collection which is a sorted copy of the current collection.
SORT_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion
A sort criterion.
sortPeptidesIntoLanes() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
source - Variable in class org.biojava.bio.seq.Feature.Template
 
SOURCE - Static variable in interface org.biojava.bio.seq.Feature
The source of this feature has altered
SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
sourceEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
SourceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
 
SourceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
 
SourceLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker
 
sourceStart - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
sourceTerm - Variable in class org.biojava.bio.seq.Feature.Template
 
SOURCETERM - Static variable in interface org.biojava.bio.seq.Feature
The ontological source of this feature has altered
SOURCETERM - Static variable in interface org.biojavax.bio.seq.RichFeature
 
sourceToView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
Coordinate conversion from source to view.
sourceToView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
sourceToView(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Coordinate conversion from source to view.
SparseVector - Class in org.biojava.stats.svm
An implementation of a sparse vector.
SparseVector() - Constructor for class org.biojava.stats.svm.SparseVector
 
SparseVector(int) - Constructor for class org.biojava.stats.svm.SparseVector
 
SparseVector.NormalizingKernel - Class in org.biojava.stats.svm
A version of the standard dot-product kernel that scales each column independently.
spatialLocation - Variable in class org.biojava.bibliography.BiblioScope
It defines a spatial location of the cited resource.
SPECIES_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
 
split(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Splitter
Produce a list of values from an old value.
split(Object) - Method in class org.biojava.bio.program.tagvalue.RegexSplitter
 
splitString(String) - Method in class org.biojava.bio.seq.io.WordTokenization
 
SQLUnigeneFactory - Class in org.biojava.bio.program.unigene
An implementatoin of UnigeneFactory that manages it's data in an SQL database.
SQLUnigeneFactory() - Constructor for class org.biojava.bio.program.unigene.SQLUnigeneFactory
 
ssContext - Variable in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
 
stackDelta() - Method in interface org.biojava.utils.bytecode.CodeGenerator
Return the change in the stack dept this generator will cause.
stackDelta() - Method in class org.biojava.utils.bytecode.IfExpression
 
stackDelta() - Method in class org.biojava.utils.bytecode.InstructionVector
 
stackDelta() - Method in class org.biojava.utils.bytecode.Label
 
stackDelta() - Method in class org.biojava.utils.bytecode.MarkLabel
 
stackDepth() - Method in interface org.biojava.utils.bytecode.CodeGenerator
Return the total depth of the stack required by this CodeGenerator.
stackDepth() - Method in class org.biojava.utils.bytecode.IfExpression
 
stackDepth() - Method in class org.biojava.utils.bytecode.InstructionVector
 
stackDepth() - Method in class org.biojava.utils.bytecode.Label
 
stackDepth() - Method in class org.biojava.utils.bytecode.MarkLabel
 
StackedFeatureRenderer - Class in org.biojava.bio.gui.sequence
Allows you to stack multiple feature renderers up (for example a label renderer and a beaded renderer) and have them treated as a single renderer for layout.
StackedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.StackedFeatureRenderer
 
StackedLogoPainter - Class in org.biojava.bio.gui
A logo painter that paints in stacked areas.
StackedLogoPainter() - Constructor for class org.biojava.bio.gui.StackedLogoPainter
 
stackLevel - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
stackLevel - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
standardMutationDistribution(FiniteAlphabet) - Static method in class org.biojavax.ga.util.GATools
Makes a mutation Distribution where the probability of a Symbol being mutated to itself is zero and the probability of it being changed to any other Symbol in the Alphabet a is 1.0 / (a.size() - 1.0)
start - Variable in class org.biojava.utils.automata.FiniteAutomaton
 
start() - Method in interface org.biojava.bio.search.BioMatcher
Get the first symbol index that matches the pattern.
start() - Method in class org.biojava.bio.search.MaxMismatchMatcher
 
start() - Method in class org.biojava.utils.regex.Matcher
Returns the start index of the previous match.
start(int) - Method in class org.biojava.utils.regex.Matcher
Returns the start index of the subsequence captured by the given group during the previous match operation.
start(String[]) - Method in interface org.biojava.utils.xml.AppEntry
 
START_RECORD_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
 
START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
startBlock(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
 
startBlock(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
Notifies the parser that a new block is starting.
startBlock(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
startBlock(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
Notifies the parser that a new block is starting.
startBlock(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
startBlock(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
About to start a new block.
startBlockObject() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
startBlockObject() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
startBlockObject() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
Tell the builder to start a new block object.
startBlockObject() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
 
startBlockObject() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
 
startCycle() - Method in interface org.biojava.bio.dp.HMMTrainer
called to put the trainer into an initial state for a new round of training.
startCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer
 
startDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
indicates start of data for a HomologeneDB
startDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
startDocument() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
startDocument() - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
startDocument() - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
startDocument(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
Indicates that a new GFF document has been started.
startDocument(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
 
startDocument(String) - Method in class org.biojava.bio.program.gff.GFFWriter
 
startDocument(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
Indicates that a new GFF document has been started.
startedActivity(Object) - Method in interface org.biojava.utils.ActivityListener
Notification that an activity has started.
startElement(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.dist.XMLDistributionReader
Required by SAXParser to be public.
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler
This is called when an element is entered.
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
 
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
startElement(String, String, String, Attributes) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
startElement(String, String, String, Attributes, DelegationManager) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
Handles basic entry processing for all feature handlers.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
Override this to do any processing required but call this prior to returning.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser
we override the superclass startElement method so we can determine the the start tag type and use it to set up delegation for the superclass.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.FeatureHandler
StAX callback for element starts.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.PropDetailHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMENamePropHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMETypePropHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
Handles basic entry processing for all feature handlers.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
Override this to do any processing required but call this prior to returning.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
Handles basic entry processing for all feature handlers.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.CharElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.IntElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.LongElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StringElementHandlerBase
 
startElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVECdsHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
currently we do not handler >computation< as subtag of sciobj yet
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
Element-specific handler.
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
Element-specific handler.
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
Element-specific handler.
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
Element-specific handler.
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEHandler
Description of the Method
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
Element-specific handler.
startElementHandler(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
 
startElementHandler(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEHandler
 
startFeature(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
Deprecated.
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
Deprecated.
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
startFeature(Feature.Template) - Method in interface org.biojava.bio.seq.io.SeqIOListener
Notify the listener that a new feature object is starting.
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Null implementation.
startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Notify the listener that a new feature object is starting.
startFile() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
 
startFile() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
About to start a new file.
startFile() - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
 
startFile() - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
About to start a new file.
startGroup() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
indicates start of data for a OrthoPairSet
startGroup() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
startHeader() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
startHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
startHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
startHeader() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
startHeader() - Method in class org.biojava.bio.search.FilteringContentHandler
 
startHeader() - Method in class org.biojava.bio.search.SearchContentAdapter
 
startHeader() - Method in class org.biojava.bio.search.SearchContentFilter
 
startHeader() - Method in interface org.biojava.bio.search.SearchContentHandler
The startHeader method indicates the start of a formatted header.
startHeader() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
startHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
startHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
startHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
startHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
startHit() - Method in class org.biojava.bio.search.FilteringContentHandler
 
startHit() - Method in class org.biojava.bio.search.SearchContentAdapter
 
startHit() - Method in class org.biojava.bio.search.SearchContentFilter
 
startHit() - Method in interface org.biojava.bio.search.SearchContentHandler
The startHit method indicates the start of a formatted hit.
startHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
startInstance(int, int) - Method in interface org.biojava.utils.automata.StateMachineFactory
Return a StateMachineInstance if the Symbol represented by the symbol index is valid as the initial symbol of the pattern.
startLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
startLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
startOrthologue() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
indicates start of data for an orthologue
startOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
startOrthoPair() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
indicates start of data for an OrthoPair
startOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
startPrefixMapping(String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
 
startPrefixMapping(String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
startPrefixMapping(String, String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
startPrefixMapping(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
startPrefixMapping(String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
startPrefixMapping(String, String) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
startPrefixMapping(String, String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.Echo
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer2
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
startRecord() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
A new record is about to start.
startSearch() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
startSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
startSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
startSearch() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
startSearch() - Method in class org.biojava.bio.search.FilteringContentHandler
 
startSearch() - Method in class org.biojava.bio.search.SearchContentAdapter
 
startSearch() - Method in class org.biojava.bio.search.SearchContentFilter
 
startSearch() - Method in interface org.biojava.bio.search.SearchContentHandler
The startSearch method indicates the start of useful search information.
startSearch() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
startSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger
 
startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
 
startSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener
Indicates that a sequence is about to be searched against a DataStore.
startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
 
startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
 
startSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer
Deprecated.
 
startSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
Deprecated.
 
startSequence() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
startSequence() - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
startSequence() - Method in interface org.biojava.bio.seq.io.SeqIOListener
Start the processing of a sequence.
startSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
startSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
startSequence() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Start the processing of a sequence.
startSequence() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
startSequence() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
startSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
Start the processing of a sequence.
startSubHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
 
startSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
 
startSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
 
startSubHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
 
startSubHit() - Method in class org.biojava.bio.search.FilteringContentHandler
 
startSubHit() - Method in class org.biojava.bio.search.SearchContentAdapter
 
startSubHit() - Method in class org.biojava.bio.search.SearchContentFilter
 
startSubHit() - Method in interface org.biojava.bio.search.SearchContentHandler
The startSubHit method indicates the start of a formatted subhit.
startSubHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Echo
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Indexer
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Indexer2
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.MultiTagger
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine
TagValueListener interface
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagRenamer
 
startTag(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
Start a new tag.
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
 
startThreads() - Method in class org.biojava.utils.SimpleThreadPool
 
startThreads() - Method in interface org.biojava.utils.ThreadPool
startThreads starts all the threads running and opens the pool to requests.
startTree() - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
startTree() - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
startTree() - Method in interface org.biojava.utils.stax.StAXContentHandler
 
startTree() - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
startZiggy(StrandedFeature.Strand) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
Used to initialise the spliced transcript renderer for a CDS feature where the ends of the feature define the frame of the feature.
startZiggy(StrandedFeature.Strand, int) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
This method is called to initialise the renderer for a spliced transcript.
state - Variable in class org.biojava.bio.dp.BackPointer
The state with which this backpointer is associated.
State - Interface in org.biojava.bio.dp
A state in a markov process.
stateAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel
FiniteAlphabet of the states.
stateAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
stateAlphabet() - Method in class org.biojava.bio.dp.WMAsMM
 
stateList(MarkovModel) - Method in class org.biojava.bio.dp.DP
 
StateMachine - Class in org.biojava.bio.program.tagvalue
This class implements a state machine for parsing events from the Parser class.
StateMachine() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine
 
StateMachine.BasicState - Class in org.biojava.bio.program.tagvalue
Implementation of a State in a state machine
StateMachine.ExitNotification - Interface in org.biojava.bio.program.tagvalue
Interface implemented by State listeners that want notification when a transition leaves the State.
StateMachine.SimpleStateListener - Class in org.biojava.bio.program.tagvalue
a basic listener for a State.
StateMachine.State - Interface in org.biojava.bio.program.tagvalue
Interface for a State within this StateMachine
StateMachine.Transition - Class in org.biojava.bio.program.tagvalue
class to represent a State Transition
StateMachine.TransitionTable - Class in org.biojava.bio.program.tagvalue
Table of Transition destination States and their corresponding Tags.
StateMachineFactory - Interface in org.biojava.utils.automata
Class that produces StateMachineInstance objects.
StateMachineInstance - Interface in org.biojava.utils.automata
 
StatePath - Interface in org.biojava.bio.dp
Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods.
states - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
states() - Method in interface org.biojava.bio.dp.DPMatrix
 
states() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
states() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
 
STATES - Static variable in interface org.biojava.bio.dp.StatePath
Alignment label for the state path.
StaticMemberPlaceHolder - Class in org.biojava.utils
 
StaticMemberPlaceHolder() - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
 
StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
 
StaticMethodRPFactory(Method) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
Create a new StaticMethodRPFactory for a method.
STATUS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
StAXContentHandler - Interface in org.biojava.bio.seq.io.agave
Interface for StAX content handlers.
StAXContentHandler - Interface in org.biojava.utils.stax
Interface for StAX content handlers.
StAXContentHandlerBase - Class in org.biojava.bio.seq.io.agave
Simple implementation of the StAXContentHandler interface, with empty implementations for all the methods.
StAXContentHandlerBase - Class in org.biojava.utils.stax
Simple implementation of the StAXContentHandler interface, with empty implementations for all the methods.
StAXContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
StAXContentHandlerBase() - Constructor for class org.biojava.utils.stax.StAXContentHandlerBase
 
staxenv - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
staxenv - Variable in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
 
staxenv - Variable in class org.biojava.bio.seq.io.game.StAXPropertyHandler
 
staxenv - Variable in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
Nesting class that provides callback interfaces to nested class
StAXFeatureHandler - Class in org.biojava.bio.seq.io.agave
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXFeatureHandler - Class in org.biojava.bio.seq.io.game
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXFeatureHandler - Class in org.biojava.bio.seq.io.game12
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXFeatureHandler() - Constructor for class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
StAXHandlerBinding - Class in org.biojava.bio.program.ssbind
StAXHandlerBindings associates an ElementRecognizer with a factory which creates StAXContentHandlers for elements which it the ElementRecognizer accepts.
StAXHandlerFactory - Interface in org.biojava.bio.program.ssbind
StAXHandlerFactory is an interface for factories producing StAXContentHandlers which are used by the SeqSimilarityStAXAdapter.
StAXHandlerFactory - Interface in org.biojava.bio.seq.io.agave
Factory for StAX content handlers.
StAXHandlerFactory - Interface in org.biojava.bio.seq.io.game
Factory for StAX content handlers.
StAXHandlerFactory - Interface in org.biojava.bio.seq.io.game12
Factory for StAX content handlers.
StAXPropertyHandler - Class in org.biojava.bio.seq.io.agave
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXPropertyHandler - Class in org.biojava.bio.seq.io.game
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
stop(GeneticAlgorithm) - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
Stops the Algorithm if the iterations are >= maxGenerations
stop(GeneticAlgorithm) - Method in interface org.biojavax.ga.GAStoppingCriteria
Determines if an Algorithm should stop spawning new generations
StoppingCriteria - Interface in org.biojava.bio.dp
A callback that is invoked during the training of an HMM.
StopRenderer - Class in org.biojava.bio.gui.sequence
Compute sites of stop codons.
StopRenderer(SixFrameRenderer, int, StrandedFeature.Strand) - Constructor for class org.biojava.bio.gui.sequence.StopRenderer
 
stopThreads() - Method in class org.biojava.utils.SimpleThreadPool
Waits for all working threads to return and then stops them.
stopThreads() - Method in interface org.biojava.utils.ThreadPool
stopThreads causes all running threads to stop when their current task is complete.
store(Index) - Method in class org.biojava.bio.seq.db.BioIndex
 
store(Index) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
store adds an Index to the store.
store(Index) - Method in interface org.biojava.bio.seq.db.IndexStore
Add the Index to the store.
store(Index) - Method in class org.biojava.bio.seq.db.TabIndexStore
 
STORE_NAME - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
STORE_NAME is the key used to identify the arbitrary name of the store in the OBDA config.dat files.
str - Variable in class org.biojava.ontology.obo.OboFileParser.SOPair
 
STRAIN_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
 
strand - Variable in class org.biojava.bio.seq.StrandedFeature.Template
 
STRAND - Static variable in interface org.biojava.bio.seq.StrandedFeature
The strand of this feature is being altered.
STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
STRANDED_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
StrandedFeature - Interface in org.biojava.bio.seq
Adds the concept of 'strand' to features.
STRANDEDFEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.StrandedFeatureHandler
 
StrandedFeature.Strand - Class in org.biojava.bio.seq
Class to represent the 'strandedness' of a feature.
StrandedFeature.Template - Class in org.biojava.bio.seq
Template class for parameterizing the creation of a new StrandedFeature.
StrandedFeatureHandler - Class in org.biojava.bio.program.xff
StAX handler for XFF strandedFeature type.
StrandedFeatureHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.StrandedFeatureHandler
 
StrandFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
 
StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
 
StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.seq.FeatureFilter.StrandFilter
Build a new filter that matches all features of a given strand.
StrandParser - Class in org.biojava.bio.seq
Process strings and return strand objects.
StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser
 
stream(Readable, StreamListener) - Method in interface org.biojava.bio.program.fastq.FastqReader
Stream the specified readable.
StreamListener - Interface in org.biojava.bio.program.fastq
Event based parser callback.
streamNext(SeqIOListener) - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
 
streamNext(SeqIOListener) - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
 
streamNext(SeqIOListener) - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
 
StreamParser - Interface in org.biojava.bio.seq.io
Parse a stream of characters into BioJava symbols.
StreamPipe - Class in org.biojava.utils.process
A multi threaded class which pipes the contents of an input stream to an output stream.
StreamPipe(InputStream, OutputStream, String) - Constructor for class org.biojava.utils.process.StreamPipe
Initializes the stream pipe.
StreamReader - Class in org.biojava.bio.seq.io
Parses a stream into sequences.
StreamReader(BufferedReader, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
 
StreamReader(InputStream, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
 
streamRecords(GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFEntrySet
Write all records in this set out to a handler.
StreamWriter - Class in org.biojava.bio.seq.io
Writes all of the sequences from a SequenceIterator to a stream with a particular format.
StreamWriter(OutputStream, SequenceFormat) - Constructor for class org.biojava.bio.seq.io.StreamWriter
Generate a new StreamWriter to the stream os and using format.
STRING_TO_INT - Static variable in class org.biojava.bio.program.tagvalue.ChangeTable
 
StringElementHandlerBase - Class in org.biojava.utils.stax
StAX handler for any element which just contains a string.
StringElementHandlerBase() - Constructor for class org.biojava.utils.stax.StringElementHandlerBase
 
stringifyAttributes(Map) - Static method in class org.biojava.bio.program.gff.SimpleGFFRecord
Create a String representation of attMap.
stringnifyDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
Converts the description of the matrix to a String.
stringnifyMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
Creates a String representation of this matrix.
stringToClob(Connection, ResultSet, int, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
Deprecated.
 
StringTools - Class in org.biojavax.utils
Utility class for formatting strings into regular-sized blocks.
STROKE - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Constant STROKE indicating a change to the outline stroke of the features.
StructureTools - Class in org.biojava.bio.proteomics
Simple access to protein seccondary structure assignments.
StructureTools() - Constructor for class org.biojava.bio.proteomics.StructureTools
 
subAlignment(Set<String>, int, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment
Retreives a subAlignment
subAlignment(Set<String>, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment
Retrieves a subalignment specified by the location.
subAlignment(Set<String>, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
subAlignment(Set<String>, Location) - Method in interface org.biojava.bio.alignment.Alignment
Make a view onto this alignment.
subAlignment(Set<String>, Location) - Method in class org.biojava.bio.alignment.SimpleAlignment
 
subAlignment(Set<String>, Location) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
subAlignment(Set<String>, Location) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
subAlignment(Set, Location) - Method in class org.biojava.bio.dp.SimpleStatePath
 
SubCircularRendererContext - Class in org.biojava.bio.gui.sequence
A renderer context that allows some or all properties of another context to be over-ridden.
SubCircularRendererContext(CircularRendererContext, SymbolList, FeatureHolder, double) - Constructor for class org.biojava.bio.gui.sequence.SubCircularRendererContext
Create a new sub context.
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.And
 
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.Contains
 
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.Or
 
subConstraintOf(CollectionConstraint) - Method in interface org.biojava.bio.CollectionConstraint
subConstraintOf returns true if the constraint is a sub-constraint.
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.And
 
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
 
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ByClass
 
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
 
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
 
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.Or
 
subConstraintOf(PropertyConstraint) - Method in interface org.biojava.bio.PropertyConstraint
subConstraintOf returns true if the constraint is a sub-constraint.
subContext() - Method in interface org.biojava.utils.bytecode.CodeContext
Open a sub context.
subFeatures - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
SubIntegerTokenization - Class in org.biojava.bio.seq.io
 
SubIntegerTokenization(IntegerAlphabet.SubIntegerAlphabet) - Constructor for class org.biojava.bio.seq.io.SubIntegerTokenization
 
subject - Variable in class org.biojava.bibliography.BibRef
It defines the topic of the content of the cited resource.
SUBJECT_HEADINGS - Static variable in interface org.biojava.bibliography.BibRefSupport
A vocabulary name.
SUBJECT_LABEL - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
Constant SUBJECT_LABEL is the alignment label used for all subject sequences.
subjectDBs - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
 
subjectHeadings - Variable in class org.biojava.bibliography.BiblioSubject
The subject headings usually come from standard lists such as Sears List of Subject Headings, or Library of Congress Subject Headings (LCSH).
subjectHeadingsSource - Variable in class org.biojava.bibliography.BiblioSubject
The source of subject headings.
subjectViewCache - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
 
subList(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
subList(int, int) - Method in class org.biojava.bio.seq.CircularView
Over rides ViewSequence.
subList(int, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.DummySequence
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.SubSequence
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
subList(int, int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
subList(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly
 
subList(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
subList(int, int) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
 
subList(int, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
subList(int, int) - Method in class org.biojava.bio.symbol.SimpleSymbolList
create a subList of the original, this will be a view until either the original symbolList or the sublist is edited
subList(int, int) - Method in interface org.biojava.bio.symbol.SymbolList
Return a new SymbolList for the symbols start to end inclusive.
subList(int, int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Return a new SymbolList for the symbols start to end inclusive.
subList(int, int) - Method in class org.biojavax.bio.seq.ThinRichSequence
Return a new SymbolList for the symbols start to end inclusive.
subList(SymbolList, int, int) - Static method in class org.biojava.bio.symbol.SymbolListViews
View a portion of a SymbolList.
subList(RichSequence, int, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
Return a new SymbolList for the symbols start to end inclusive.
subList(RichSequence, int, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
Return a new SymbolList for the symbols start to end inclusive.
subList(RichSequence, int, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
Return a new SymbolList for the symbols start to end inclusive.
subMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch
A matrix with the size length(alphabet) times length(alphabet)
SubPairwiseRenderContext - Class in org.biojava.bio.gui.sequence
SubPairwiseRenderContext is a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own.
SubPairwiseRenderContext(PairwiseRenderContext, SymbolList, SymbolList, FeatureHolder, FeatureHolder, RangeLocation, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
Creates a new SubPairwiseRenderContext.
SUBPATH_LENGTH - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
To improve performance, the drawing objects for the chromatogram traces are precomputed.
subpathsValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Flag for subpaths.
subSequence(int, int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
 
subSequence(int, int) - Method in class org.biojava.utils.RepeatedCharSequence
 
subSequence(Sequence, int, int) - Static method in class org.biojava.bio.seq.SequenceTools
Extract a sub-sequence from a sequence.
subSequence(Sequence, int, int, String) - Static method in class org.biojava.bio.seq.SequenceTools
Extract a sub-sequence from a sequence.
subSequence(Sequence, int, int, String, StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.SequenceTools
Extract a sub-sequence from a sequence.
subSequence(RichSequence, int, int, Namespace, String, String, String, int, Double) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
Creates a new sequence from a subregion of another sequence.
SubSequence - Class in org.biojava.bio.seq.impl
View a sub-section of a given sequence object, including all the features intersecting that region.
SubSequence(Sequence, int, int) - Constructor for class org.biojava.bio.seq.impl.SubSequence
Construct a new SubSequence of the specified sequence.
SubSequence(Sequence, int, int, String) - Constructor for class org.biojava.bio.seq.impl.SubSequence
Construct a new SubSequence of the specified sequence.
SubSequence.SubProjectedFeatureContext - Class in org.biojava.bio.seq.impl
TargetContext that implements the mapping between the parent sequence and this sub-sequence.
SubSequenceDB - Class in org.biojava.bio.seq.db
 
SubSequenceDB(SequenceDB, Set) - Constructor for class org.biojava.bio.seq.db.SubSequenceDB
 
SubSequenceRenderContext - Class in org.biojava.bio.gui.sequence
Allows a new renderer to "wrap" another one, replacing one or more values.
SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation, int) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext
 
SUBSET - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
SubstitutionMatrix - Class in org.biojava.bio.alignment
This object is able to read a substitution matrix file and constructs a short matrix in memory.
SubstitutionMatrix(File) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
This constructor can be used to guess the alphabet of this substitution matrix.
SubstitutionMatrix(FiniteAlphabet, short, short) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters.
SubstitutionMatrix(FiniteAlphabet, File) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
This constructs a SubstitutionMatrix object that contains two Map data structures having BioJava symbols as keys and the value being the index of the matrix containing the substitution score.
SubstitutionMatrix(FiniteAlphabet, String, String) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file.
subStr(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
subStr(int, int) - Method in class org.biojava.bio.seq.CircularView
Over rides ViewSequence.
subStr(int, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
subStr(int, int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
subStr(int, int) - Method in class org.biojava.bio.seq.impl.DummySequence
 
subStr(int, int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
subStr(int, int) - Method in class org.biojava.bio.seq.impl.SubSequence
 
subStr(int, int) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
subStr(int, int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
subStr(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly
 
subStr(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
subStr(int, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
subStr(int, int) - Method in interface org.biojava.bio.symbol.SymbolList
Return a region of this symbol list as a String.
subStr(int, int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Return a region of this symbol list as a String.
subStr(int, int) - Method in class org.biojavax.bio.seq.ThinRichSequence
Return a region of this symbol list as a String.
subStr(RichSequence, int, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
Return a region of this sequence as a String.
subStr(RichSequence, int, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
Return a region of this sequence as a String.
subStr(RichSequence, int, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
Return a region of this sequence as a String.
subStringExists(String) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
subtract(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
Subtract one location from another.
subTypeOf(AnnotationType) - Method in class org.biojava.bio.AnnotationType.Abstract
 
subTypeOf(AnnotationType) - Method in interface org.biojava.bio.AnnotationType
See if an AnnotationType is a specialisation of this type.
SubULAlignment(Set<String>, Location) - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
SuffixNode() - Constructor for class org.biojava.bio.symbol.SuffixTree.SuffixNode
 
SuffixNode() - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode
 
SuffixTree - Class in org.biojava.bio.symbol
Suffix tree implementation.
SuffixTree(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SuffixTree
Construct a new SuffixTree to contain motifs over the specified alphabet.
SuffixTree.SuffixNode - Class in org.biojava.bio.symbol
A node in the suffix tree.
SuffixTreeKernel - Class in org.biojava.stats.svm.tools
Computes the dot-product of two suffix-trees as the sum of the products of the counts of all nodes they have in common.
SuffixTreeKernel() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel
 
SuffixTreeKernel.DepthScaler - Interface in org.biojava.stats.svm.tools
Encapsulates the scale factor to apply at a given depth.
SuffixTreeKernel.MultipleScalar - Class in org.biojava.stats.svm.tools
Scale using a multiple of two DepthScalers.
SuffixTreeKernel.NullModelScaler - Class in org.biojava.stats.svm.tools
Scales by 4^depth - equivalent to dividing by a probablistic flatt prior null model
SuffixTreeKernel.SelectionScalar - Class in org.biojava.stats.svm.tools
Scale using a BitSet to allow/disallow depths.
SuffixTreeKernel.UniformScaler - Class in org.biojava.stats.svm.tools
Scale all depths by 1.0
SUPPORT - Static variable in class org.biojava.bio.program.abi.ABITools
Alignment label for the support row.
surname - Variable in class org.biojava.bibliography.BiblioPerson
The person's sirname (family name).
SVM_Light - Class in org.biojava.stats.svm.tools
 
SVM_Light() - Constructor for class org.biojava.stats.svm.tools.SVM_Light
 
SVM_Light.LabelledVector - Class in org.biojava.stats.svm.tools
 
SVMClassifierModel - Interface in org.biojava.stats.svm
An SVM classifier model.
SVMKernel - Interface in org.biojava.stats.svm
Kernel for support vector machines and related methods.
SVMRegressionModel - Class in org.biojava.stats.svm
 
SVMRegressionModel() - Constructor for class org.biojava.stats.svm.SVMRegressionModel
 
SVMRegressionModel(int) - Constructor for class org.biojava.stats.svm.SVMRegressionModel
 
SVMTarget - Interface in org.biojava.stats.svm
An SVM classifier model.
SwapMutationFunction - Class in org.biojavax.ga.functions
This class does a sort of mutation by exchanging two positions on the chromosome.
SwapMutationFunction(double[]) - Constructor for class org.biojavax.ga.functions.SwapMutationFunction
Sets the mutation probabilities to the designated values.
Swissprot - Class in org.biojava.bio.program.formats
 
Swissprot() - Constructor for class org.biojava.bio.program.formats.Swissprot
 
SWISSPROT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
SWISSPROT indicates that the sequence format is SWISSPROT.
SWISSPROT_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
 
SwissprotFileFormer - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
SwissprotFileFormer() - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Creates a new SwissprotFileFormer using System.out stream.
SwissprotFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer
Deprecated.
Creates a new SwissprotFileFormer using the specified stream.
SwissprotProcessor - Class in org.biojava.bio.seq.io
Deprecated.
Use org.biojavax.bio.seq.io framework instead
SwissprotProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor
Deprecated.
 
SwissprotProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor
Deprecated.
Constructor that sets the source of the feature to theSource.
SwissprotProcessor.Factory - Class in org.biojava.bio.seq.io
Deprecated.
Factory which wraps SequenceBuilders in a SwissprotProcessor
SwissprotSequenceDB - Class in org.biojava.bio.seq.db
This class contains functions accessing sequences in swiss-prot.
SwissprotSequenceDB() - Constructor for class org.biojava.bio.seq.db.SwissprotSequenceDB
 
Symbol - Interface in org.biojava.bio.symbol
A single symbol.
symbolAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
symbolAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment
this will return the ambiguity symbol associated with all symbols in that column
symbolAt(int) - Method in class org.biojava.bio.alignment.SimpleAlignment
 
symbolAt(int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolAt(int) - Method in class org.biojava.bio.seq.CircularView
Over rides ViewSequence.
symbolAt(int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.DummySequence
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.SubSequence
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
symbolAt(int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
symbolAt(int) - Method in class org.biojava.bio.seq.SimpleAssembly
 
symbolAt(int) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.DummySymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.PackedSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleSymbolList
Find a symbol at a specified offset in the SymbolList.
symbolAt(int) - Method in interface org.biojava.bio.symbol.SymbolList
Return the symbol at index, counting from 1.
symbolAt(int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Return the symbol at index, counting from 1.
symbolAt(int) - Method in class org.biojavax.bio.seq.ThinRichSequence
Return the symbol at index, counting from 1.
symbolAt(String, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
symbolAt(String, int) - Method in interface org.biojava.bio.alignment.Alignment
Retrieve a symbol by label and column.
symbolAt(String, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
This gets the symbol for an individual sequence at position in the overall alignment If the sequence is not aligned at that location it returns null
symbolAt(String, int) - Method in class org.biojava.bio.alignment.SimpleAlignment
 
symbolAt(String, int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolAt(String, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
symbolAt(String, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
symbolAt(RichSequence, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
Return the symbol at index, counting from 1.
symbolAt(RichSequence, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
Return the symbol at index, counting from 1.
symbolAt(RichSequence, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
Return the symbol at index, counting from 1.
symbolForIndex(int) - Method in interface org.biojava.bio.symbol.AlphabetIndex
Retrieve the symbol for an index.
symbolForLifeScienceID(LifeScienceIdentifier) - Static method in class org.biojava.bio.symbol.AlphabetManager
Retreives the Symbol for the LSID
symbolForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Deprecated.
use symbolForLifeScienceID() instead
SymbolList - Interface in org.biojava.bio.symbol
A sequence of symbols that belong to an alphabet.
SymbolListCharSequence - Class in org.biojava.bio.seq.io
SymbolListCharSequence is a CharSequence implementation which wraps a SymbolList.
SymbolListCharSequence(SymbolList) - Constructor for class org.biojava.bio.seq.io.SymbolListCharSequence
Creates a new SymbolListCharSequence wrapping a SymbolList.
SymbolListFactory - Interface in org.biojava.bio.symbol
This interface exists to hide implementational details of SymbolLists when making chunked symbol lists.
symbolListForLabel(String) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
symbolListForLabel(String) - Method in interface org.biojava.bio.alignment.Alignment
Retrieve a single row of the alignment by label.
symbolListForLabel(String) - Method in class org.biojava.bio.alignment.FlexibleAlignment
 
symbolListForLabel(String) - Method in class org.biojava.bio.alignment.SimpleAlignment
 
symbolListForLabel(String) - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolListForLabel(String) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
symbolListForLabel(String) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment
 
symbolListIterator() - Method in interface org.biojava.bio.alignment.Alignment
Creates an Iterator over the SymbolLists in the alignment.
symbolListIterator() - Method in class org.biojava.bio.alignment.SimpleAlignment
 
symbolListIterator() - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolListIterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
symbolListIterator() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
SymbolListIterator(Alignment) - Constructor for class org.biojava.bio.alignment.Alignment.SymbolListIterator
Creates a SymbolListIterator for a given alignment object.
SymbolListViews - Class in org.biojava.bio.symbol
Tools class for constructing views of SymbolList objects.
SymbolPropertyTable - Interface in org.biojava.bio.symbol
class for maintaining properties associated with a symbol
SymbolPropertyTableDB - Interface in org.biojava.bio.proteomics.aaindex
Database of SymbolPropertyTable objects.
SymbolPropertyTableIterator - Interface in org.biojava.bio.proteomics.aaindex
Iterator over SymbolPropertyTable objects.
SymbolReader - Interface in org.biojava.bio.seq.io
Encapsulate a stream of Symbols being parsed from some input stream.
symbols(SymbolList) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
symbols(SymbolList) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
 
symbols(SymbolList) - Method in class org.biojava.bio.symbol.CircularLocation
 
symbols(SymbolList) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
symbols(SymbolList) - Method in interface org.biojava.bio.symbol.Location
Return the symbols in a sequence that fall within this range.
symbols(SymbolList) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Return the symbols in a sequence that fall within this range.
symbols(SymbolList) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Return the symbols in a sequence that fall within this range.
symbols(SymbolList) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Return the symbols in a sequence that fall within this range.
SYMBOLS - Static variable in interface org.biojava.bio.symbol.Alphabet
This ChangeType indicates that some symbols have been added or removed from the alphabet.
SymbolSequenceRenderer - Class in org.biojava.bio.gui.sequence
SymbolSequenceRenderer renders symbols of a SymbolList.
SymbolSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
SymbolStyle - Interface in org.biojava.bio.gui
The interface for things that say how to paint a symbol.
SymbolTokenization - Interface in org.biojava.bio.seq.io
Encapsulate a mapping between BioJava Symbol objects and some string representation.
SymbolTokenization.TokenType - Class in org.biojava.bio.seq.io
 
symList - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
symList() - Method in interface org.biojava.bio.dp.DPMatrix
 
symList() - Method in interface org.biojava.bio.dp.onehead.DPCursor
The symbol list being looped over.
symList() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
symList() - Method in class org.biojava.bio.dp.onehead.SmallCursor
 
symList() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
 
SYMLISTVERSION - Static variable in interface org.biojavax.bio.seq.RichSequence
 
SYMMETRIC - Static variable in class org.biojava.ontology.OntoTools
 
Synonym - Class in org.biojava.ontology
 
Synonym() - Constructor for class org.biojava.ontology.Synonym
 
SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
SYNONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
Use this to define common names for things.
SYNONYM_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
SystemRegistry - Class in org.biojava.directory
A registry that loads up the standard biodirectory files.
SystemRegistry() - Constructor for class org.biojava.directory.SystemRegistry
 

T

t() - Static method in class org.biojava.bio.seq.DNATools
 
t() - Static method in class org.biojava.bio.seq.NucleotideTools
 
t() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Threonine
T_AESTIVUM - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
TabDelimParser - Class in org.biojava.ontology.io
Parse tab-delimited ontology files into Ontology objects.
TabDelimParser() - Constructor for class org.biojava.ontology.io.TabDelimParser
 
TabIndexStore - Class in org.biojava.bio.seq.db
Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets.
TabIndexStore(File, File, String, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.TabIndexStore
Create a new TabIndexStore.
table(String) - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
Returns the table with the specified name.
table(String) - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB
Returns the table with the specified name.
tableIterator() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
Returns an iterator over SymbolPropertyTable objects.
tableIterator() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB
Returns an iterator over SymbolPropertyTable objects.
tableOfContents - Variable in class org.biojava.bibliography.BiblioDescription
It is a table of contents of the cited resource.
tableOfContentsType - Variable in class org.biojava.bibliography.BiblioDescription
It specifies how BiblioDescription.tableOfContents is coded.
TABULAR - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
TagDelegator - Class in org.biojava.bio.program.tagvalue
Pushes a new parser and listener, or delegate to a listener depending on the tag.
TagDelegator() - Constructor for class org.biojava.bio.program.tagvalue.TagDelegator
 
TagDelegator(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.TagDelegator
 
TagDropper - Class in org.biojava.bio.program.tagvalue
Silently drop all tags except those specified, and pass the rest onto a delegate.
TagDropper() - Constructor for class org.biojava.bio.program.tagvalue.TagDropper
 
TagDropper(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.TagDropper
Create a new TagDropper that will pass on all retained tags and values to tvl.
TaggedDataRecord(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
Creates a new TaggedDataRecord from the next 28 bytes of din.
TagMapper - Class in org.biojava.bio.program.tagvalue
TagMapper maps arbitrary object keys to new keys.
TagMapper() - Constructor for class org.biojava.bio.program.tagvalue.TagMapper
Creates a new, empty TagMapper.
tagName - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
tagNumber - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
 
TagRenamer - Class in org.biojava.bio.program.tagvalue
Rename tags using a TagMapper.
TagRenamer(TagValueListener, PropertyChanger) - Constructor for class org.biojava.bio.program.tagvalue.TagRenamer
Build a new TagRenamer with a delegate and mapper.
TagValue - Class in org.biojava.bio.program.tagvalue
Utility class for representing tag-value pairs for TagValueParser implementors.
TagValue(Object, Object, boolean) - Constructor for class org.biojava.bio.program.tagvalue.TagValue
Build a new TagValue with a tag, a value and a flag indicating if this is a new example of this tag or a continuation of an old example.
TagValueContext - Interface in org.biojava.bio.program.tagvalue
Communication interface between Parser and a TagValueListener that allows listeners to request that a parser/listener pair be pushed onto the stack to handle the current tag.
TagValueListener - Interface in org.biojava.bio.program.tagvalue
An object that wishes to be informed of events during the parsing of a file.
TagValueParser - Interface in org.biojava.bio.program.tagvalue
Tokenize single records (lines of text, objects) into a tag and a value.
TagValueWrapper - Interface in org.biojava.bio.program.tagvalue
Interface for TagValueListeners that wrap other TagValueListeners
takeConnection() - Method in class org.biojava.utils.JDBCConnectionPool
 
takeStatement() - Method in class org.biojava.utils.JDBCConnectionPool
 
tanh(double) - Method in class org.biojava.stats.svm.SigmoidKernel
 
taxa - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
TAXA_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
A constant representing the name of Taxa blocks.
TaxaBlock - Class in org.biojavax.bio.phylo.io.nexus
Represents Nexus taxa blocks.
TaxaBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Delegates to NexusBlock.Abstract constructor using TaxaBlock.TAXA_BLOCK as the name.
TaxaBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus
Builds Nexus taxa blocks.
TaxaBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
 
TaxaBlockListener - Interface in org.biojavax.bio.phylo.io.nexus
Listens to events that represent Nexus taxa blocks.
TaxaBlockParser - Class in org.biojavax.bio.phylo.io.nexus
Parses Nexus taxa blocks.
TaxaBlockParser(TaxaBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.TaxaBlockParser
Delegates to NexusBlockParser.Abstract.
TAXID_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
Taxon - Interface in org.biojava.bio.program.homologene
 
Taxon - Interface in org.biojava.bio.taxa
Deprecated.
replaced by classes in org.biojavax.bio.taxa
TAXON - Static variable in interface org.biojavax.bio.BioEntry
 
TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
Taxon.TaxonStub - Class in org.biojava.bio.program.homologene
 
TaxonFactory - Interface in org.biojava.bio.taxa
Deprecated.
replaced by classes in org.biojavax.bio.taxa
TAXONID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
TAXONOMY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
TaxonParser - Interface in org.biojava.bio.taxa
Deprecated.
replaced by classes in org.biojavax.bio.taxa
TaxonSQL - Class in org.biojava.bio.seq.db.biosql
Deprecated.
Use hibernate and org.biojavax.bio.db.*
TaxonSQL() - Constructor for class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
 
Tee(SearchListener, SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Tee
 
tempBuffer - Variable in class org.biojava.ontology.obo.OboFileParser
 
Template() - Constructor for class org.biojava.bio.molbio.RestrictionSite.Template
 
Template() - Constructor for class org.biojava.bio.seq.ComponentFeature.Template
 
Template() - Constructor for class org.biojava.bio.seq.Feature.Template
 
Template() - Constructor for class org.biojava.bio.seq.FramedFeature.Template
 
Template() - Constructor for class org.biojava.bio.seq.homol.HomologyFeature.Template
 
Template() - Constructor for class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
 
Template() - Constructor for class org.biojava.bio.seq.RemoteFeature.Template
 
Template() - Constructor for class org.biojava.bio.seq.StrandedFeature.Template
 
Template() - Constructor for class org.biojavax.bio.seq.RichFeature.Template
 
Template(Feature.Template) - Constructor for class org.biojava.bio.seq.RemoteFeature.Template
Creates a RemoteFeature.Template that has the same values as the template passed in.
TemplateUtils - Class in org.biojava.bio.seq.impl
Common things you may want to do with feature templates.
temporalPeriod - Variable in class org.biojava.bibliography.BiblioScope
It defines temporal period of the cited resource.
ter() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the termination (*) placeholder
term - Variable in class org.biojavax.bio.seq.SimpleRichLocation
 
Term - Interface in org.biojava.ontology
A term in an ontology.
TERM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
TERM - Static variable in interface org.biojava.ontology.Ontology
 
TERM - Static variable in interface org.biojavax.bio.seq.RichLocation
 
TERM - Static variable in interface org.biojavax.Note
 
TERM - Static variable in interface org.biojavax.ontology.ComparableOntology
 
Term.Impl - Class in org.biojava.ontology
Simple in-memory implementation of an ontology term.
Terms() - Constructor for class org.biojavax.bio.seq.io.EMBLFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.io.INSDseqFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.io.UniProtFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.RichSequence.Terms
 
TEXT - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
TEXT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
TextBlock - Class in org.biojava.bio.gui
A BlockPainter that renders letters in proportion to the size of the signal.
TextBlock() - Constructor for class org.biojava.bio.gui.TextBlock
 
TextLogoPainter - Class in org.biojava.bio.gui
A logo painter that paints in stacked letters.
TextLogoPainter() - Constructor for class org.biojava.bio.gui.TextLogoPainter
 
theAbstract - Variable in class org.biojava.bibliography.BiblioDescription
It is an abstract of the cited resource.
ThinRichSequence - Class in org.biojavax.bio.seq
A simple implementation of RichSequence.
ThinRichSequence() - Constructor for class org.biojavax.bio.seq.ThinRichSequence
 
ThinRichSequence(Namespace, String, String, int, Alphabet, Double) - Constructor for class org.biojavax.bio.seq.ThinRichSequence
Creates a new instance of ThinRichSequence.
thr() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Threonine (T)
THREAD_POOL_SIZE - Static variable in class org.biojava.utils.process.ExternalProcess
Size of the thread pool for the static execute methods.
threadPool() - Method in class org.biojava.utils.process.ExternalProcess
Gets the thread pool which is used for the input and output handlers.
ThreadPool - Interface in org.biojava.utils
ThreadPool specifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava.
threads - Variable in class org.biojava.utils.SimpleThreadPool
 
threadsAlive() - Method in class org.biojava.utils.SimpleThreadPool
threadsAlive returns the number of threads currently alive.
threadsIdle() - Method in class org.biojava.utils.SimpleThreadPool
threadsIdle returns the number of threads currently waiting for work.
threadsWorking() - Method in class org.biojava.utils.SimpleThreadPool
threadsWorking returns the number of threads currently performing work.
Threshold(double) - Constructor for class org.biojavax.ga.functions.SelectionFunction.Threshold
 
THRESHOLD - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory
Accessor for a factory that produces builders that compress the SymbolList of a RichSequence when the length of the SymbolList exceeds THRESHOLD.
THRESHOLD_VALUE - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory
The value that will be used as a threshold for the THRESHOLD builder.
TickFeatureRenderer - Class in org.biojava.bio.gui.sequence
 
TickFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.TickFeatureRenderer
 
TICKS - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
TICKS_DOWN - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
TICKS_DOWN - Static variable in class org.biojava.bio.gui.sequence.RulerRenderer
TICKS_DOWN indicates that the ticks will point downwards from a baseline.
TICKS_UP - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
 
TICKS_UP - Static variable in class org.biojava.bio.gui.sequence.RulerRenderer
TICKS_UP indicates that the ticks will point upwards from a baseline.
TISSUE_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
 
title - Variable in class org.biojava.bibliography.BibRef
A title given to the cited resource (a name by which the resource is formally known).
TITLE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
TITLE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
to - Variable in class org.biojava.bio.dp.TrainerTransition
 
to - Variable in class org.biojava.bio.dp.Transition
 
TO_A_LEAF - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree
 
TO_TRACE_SAMPLE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating the highest (rightmost) trace sample that should be drawn.
toArray() - Method in class org.biojavax.ga.util.WeightedSet
 
toggleSelectionStatus() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.AlternateTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.CrossProductTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.DoubleTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.IntegerTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.NameTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.SubIntegerTokenization
 
tokenizeSymbol(Symbol) - Method in interface org.biojava.bio.seq.io.SymbolTokenization
Return a token representing a single symbol.
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
 
tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.AlternateTokenization
 
tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
tokenizeSymbolList(SymbolList) - Method in interface org.biojava.bio.seq.io.SymbolTokenization
Return a string representation of a list of symbols.
tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.WordTokenization
 
tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
 
toLink(String, Properties) - Method in interface org.biojava.bio.program.blast2html.DatabaseURLGenerator
Returns a full retrieve item anchor for the given database id.
toLink(String, Properties) - Method in class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
 
toLink(String, Properties) - Method in class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator
 
toList() - Method in class org.biojava.bio.dp.SimpleStatePath
 
toList() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
toList() - Method in class org.biojava.bio.seq.impl.DummySequence
 
toList() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
toList() - Method in class org.biojava.bio.seq.impl.SubSequence
 
toList() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
toList() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
toList() - Method in class org.biojava.bio.seq.SimpleAssembly
 
toList() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
toList() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
toList() - Method in interface org.biojava.bio.symbol.SymbolList
Returns a List of symbols.
toList() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Returns a List of symbols.
toList() - Method in class org.biojavax.bio.seq.ThinRichSequence
Returns a List of symbols.
toList(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
Returns a List of symbols.
toList(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
Returns a List of symbols.
toList(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
Returns a List of symbols.
Tools() - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools
 
top_level - Static variable in interface org.biojava.bio.seq.FeatureFilter
A filter which accepts only top-level Features.
topLevel() - Static method in class org.biojava.bio.seq.FilterUtils
Return a filter which matches all top-level features.
TOPOLOGY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
toProtein(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
Convenience method that directly converts a DNA sequence to RNA then to protein.
toProtein(SymbolList, int, int) - Static method in class org.biojava.bio.seq.DNATools
Convenience method to translate a region of a DNA sequence directly into protein.
toRNA(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
Converts a SymbolList from the DNA Alphabet to the RNA Alphabet.
toString() - Method in class org.biojava.bio.AbstractAnnotation
 
toString() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
Overrides the inherited method.
toString() - Method in class org.biojava.bio.AnnotationType.Abstract
 
toString() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
 
toString() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
toString() - Method in class org.biojava.bio.CollectionConstraint.And
 
toString() - Method in class org.biojava.bio.CollectionConstraint.Contains
 
toString() - Method in class org.biojava.bio.CollectionConstraint.Or
 
toString() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
toString() - Method in class org.biojava.bio.EcNumber.Impl
 
toString() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide
 
toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
 
toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide
 
toString() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
 
toString() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
 
toString() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
 
toString() - Method in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
A very verbose toString that dumps all of the data in this record in a human-readable format.
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
 
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
 
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
 
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
 
toString() - Method in class org.biojava.bio.PropertyConstraint.And
 
toString() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
 
toString() - Method in class org.biojava.bio.PropertyConstraint.ByClass
 
toString() - Method in class org.biojava.bio.PropertyConstraint.Enumeration
 
toString() - Method in class org.biojava.bio.PropertyConstraint.ExactValue
 
toString() - Method in class org.biojava.bio.PropertyConstraint.Or
 
toString() - Method in class org.biojava.bio.search.SequenceDBSearchHit
Deprecated.
 
toString() - Method in class org.biojava.bio.search.SequenceDBSearchResult
Deprecated.
 
toString() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
Deprecated.
 
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
toString() - Method in class org.biojava.bio.seq.db.biosql.DBHelper.BioSequenceStyle
Deprecated.
 
toString() - Method in class org.biojava.bio.seq.db.biosql.DBHelper.DeleteStyle
Deprecated.
 
toString() - Method in class org.biojava.bio.seq.db.biosql.DBHelper.JoinStyle
Deprecated.
 
toString() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
 
toString() - Method in class org.biojava.bio.seq.Feature.Template
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.And
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.Not
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
 
toString() - Method in class org.biojava.bio.seq.FramedFeature.ReadingFrame
 
toString() - Method in class org.biojava.bio.seq.homol.SimpleHomology
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
toString() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
Return the current indent
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
return the agave xml representation of this instance
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
the agave xml representation of xrefs
toString() - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
 
toString() - Method in class org.biojava.bio.seq.io.SymbolTokenization.TokenType
 
toString() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
 
toString() - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
toString() - Method in class org.biojava.bio.symbol.AbstractSymbol
 
toString() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
toString() - Method in class org.biojava.bio.symbol.CircularLocation
 
toString() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
toString() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
toString() - Method in class org.biojava.bio.symbol.PointLocation
 
toString() - Method in class org.biojava.bio.symbol.RangeLocation
 
toString() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
toString() - Method in class org.biojava.bio.taxa.AbstractTaxon
Deprecated.
 
toString() - Method in class org.biojava.ontology.Ontology.Impl
 
toString() - Method in class org.biojava.ontology.OntologyTerm.Impl
 
toString() - Method in class org.biojava.ontology.RemoteTerm.Impl
 
toString() - Method in class org.biojava.ontology.Synonym
 
toString() - Method in class org.biojava.ontology.Term.Impl
 
toString() - Method in class org.biojava.ontology.Triple.Impl
 
toString() - Method in class org.biojava.stats.svm.CachingKernel
 
toString() - Method in class org.biojava.stats.svm.DiagonalAddKernel
 
toString() - Method in class org.biojava.stats.svm.DiagonalCachingKernel
 
toString() - Method in class org.biojava.stats.svm.ListSumKernel
 
toString() - Method in class org.biojava.stats.svm.NormalizingKernel
 
toString() - Method in class org.biojava.stats.svm.PolynomialKernel
 
toString() - Method in class org.biojava.stats.svm.RadialBaseKernel
 
toString() - Method in class org.biojava.stats.svm.SigmoidKernel
 
toString() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
 
toString() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
 
toString() - Method in class org.biojava.utils.automata.FiniteAutomaton
dumps internal data of Nodes and Transitions that describe this FiniteAutomaton.
toString() - Method in interface org.biojava.utils.automata.NfaBuilder
 
toString() - Method in class org.biojava.utils.automata.NfaSubModel
 
toString() - Method in class org.biojava.utils.bytecode.CodeField
 
toString() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
 
toString() - Method in class org.biojava.utils.bytecode.Label
 
toString() - Method in class org.biojava.utils.bytecode.LocalVariable
 
toString() - Method in class org.biojava.utils.bytecode.ParametricType
 
toString() - Method in class org.biojava.utils.candy.CandyEntry
It prints the entry contents.
toString() - Method in class org.biojava.utils.ChangeEvent
 
toString() - Method in class org.biojava.utils.ChangeType
Return a string representation of this change.
toString() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
 
toString() - Method in class org.biojava.utils.ParseErrorEvent
 
toString() - Method in exception org.biojava.utils.ParserException
Represent this exception as a string.
toString() - Method in class org.biojava.utils.RepeatedCharSequence
 
toString() - Method in class org.biojava.utils.TypedProperties
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
 
toString() - Method in class org.biojavax.bio.seq.CompoundRichLocation
Form: "start..end" or just "point" for point locations
toString() - Method in class org.biojavax.bio.seq.EmptyRichLocation
ALWAYS RETURNS "empty"
toString() - Method in class org.biojavax.bio.seq.RichLocation.Strand
Form: "symbol" (eg. +,-,?)
toString() - Method in class org.biojavax.bio.seq.SimplePosition
toString() - Method in class org.biojavax.bio.seq.SimpleRichFeature
Form: "(#rank) parent:type,source(location)"
toString() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
Form: "(#rank) term(object,subject)"
toString() - Method in class org.biojavax.bio.seq.SimpleRichLocation
Form: "start..end" or just "point" for point locations
toString() - Method in class org.biojavax.bio.SimpleBioEntry
Form: namespace:name/accession.version
toString() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
Form is "(#rank) term(object,subject)"
toString() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
Form: "taxid:[name,name...]"
toString() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
Form: "class:name"
toString() - Method in class org.biojavax.ontology.SimpleComparableOntology
Form: "name"
toString() - Method in class org.biojavax.ontology.SimpleComparableTerm
Form: "ontology:name [obsolete]" where [obsolete] is optional
toString() - Method in class org.biojavax.ontology.SimpleComparableTriple
Form: "ontology:predicate(subject,object)"
toString() - Method in class org.biojavax.SimpleComment
Form: "(#rank) comment"
toString() - Method in class org.biojavax.SimpleCrossRef
Form: "dbname:accession.version"
toString() - Method in class org.biojavax.SimpleDocRef
Form: "authors; location"
toString() - Method in class org.biojavax.SimpleDocRefAuthor
Form: "name (consortium) (ed.)" where sections in brackets are optional.
toString() - Method in class org.biojavax.SimpleNamespace
Form: "name"
toString() - Method in class org.biojavax.SimpleNote
Form: "(#rank) term: value"
toString() - Method in class org.biojavax.SimpleRankedCrossRef
Form: "(#rank) crossref"
toString() - Method in class org.biojavax.SimpleRankedDocRef
Form: "(#rank) docref"
toString() - Method in class org.biojavax.SimpleRichAnnotation
Form: list of "[note]" values separated by commas
toString() - Method in class org.biojavax.utils.CRC64Checksum
Returns a zero-padded 16 character wide string containing the current value of this checksum in uppercase hexadecimal format.
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
return the agave xml representation of this instance
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
 
totalBits(Distribution) - Static method in class org.biojava.bio.gui.DistributionLogo
Retrieve the maximal number of bits possible for this type of dist.
totalEntropy(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
Calculates the total Entropy for a Distribution.
totalInformation(Distribution) - Static method in class org.biojava.bio.gui.DistributionLogo
Calculates the total information of the dist in bits.
totalSize - Variable in class org.biojava.ontology.obo.OboFileParser
 
toURL(String, Properties) - Method in interface org.biojava.bio.program.blast2html.DatabaseURLGenerator
Returns a string representation of a URL to the specified ID.
toURL(String, Properties) - Method in class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
 
toURL(String, Properties) - Method in class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator
 
TournamentSelection - Class in org.biojavax.ga.functions
Tournament Selection chooses the best organisms from n random subsets of a given population.
TournamentSelection() - Constructor for class org.biojavax.ga.functions.TournamentSelection
Default constructor: sets the selection pressure to the value of 10.
TPA_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
TRACE - Static variable in class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
TRACE_STROKE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option providing the the stroke to use for drawing the chromatogram traces.
TrackLayout - Interface in org.biojava.bio.gui.sequence.tracklayout
An interface for the handling of the layout of a WrappedSequencePanel.
train() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Trains the Distribution, given a null model.
train() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
train(double, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
Trains the transition, given an expected probability, and a weight for that probability.
train(DistributionTrainerContext, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
Trains the Distribution, given a null model.
train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
 
train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
 
train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
Deprecated.
 
train(SequenceDB, double, StoppingCriteria) - Method in class org.biojava.bio.dp.AbstractTrainer
Trains the sequences in db until stopper says to finnish.
train(SequenceDB, double, StoppingCriteria) - Method in interface org.biojava.bio.dp.TrainingAlgorithm
Trains the sequences in db untill stopper says to finnish.
Train - Class in org.biojava.stats.svm.tools
 
Train() - Constructor for class org.biojava.stats.svm.tools.Train
 
Trainable - Interface in org.biojava.bio.dp
Flags an object as being able to register itself with a model trainer.
trainer - Variable in class org.biojava.bio.dp.TrainerTransition
 
trainer - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
 
Trainer() - Constructor for class org.biojava.bio.dist.SimpleDistribution.Trainer
Create a new trainer.
TrainerTransition - Class in org.biojava.bio.dp
This is a small and ugly class for storing a trainer and a transition.
TrainerTransition(TransitionTrainer, State, State) - Constructor for class org.biojava.bio.dp.TrainerTransition
 
trainImpl(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
 
TrainingAlgorithm - Interface in org.biojava.bio.dp
 
trainingComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener
 
TrainingContext - Interface in org.biojava.stats.svm
 
trainingCycleComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener
 
TrainingEvent - Class in org.biojava.stats.svm
 
TrainingEvent(TrainingContext) - Constructor for class org.biojava.stats.svm.TrainingEvent
 
TrainingListener - Interface in org.biojava.stats.svm
 
trainModel(SVMRegressionModel, double[]) - Method in class org.biojava.stats.svm.SMORegressionTrainer
 
trainModel(SVMTarget, SVMKernel, TrainingListener) - Method in class org.biojava.stats.svm.SMOTrainer
 
TrainRegression - Class in org.biojava.stats.svm.tools
 
TrainRegression() - Constructor for class org.biojava.stats.svm.tools.TrainRegression
 
transcribe(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes
Transcribe DNA into RNA.
transcribe(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
Deprecated.
The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.
transcribeToRNA(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
Transcribes DNA to RNA.
transcriptionTable() - Static method in class org.biojava.bio.seq.RNATools
Get a translation table for converting DNA to RNA.
transform(FeatureFilter) - Method in class org.biojava.bio.seq.FilterUtils.DelegatingTransformer
 
transform(FeatureFilter) - Method in interface org.biojava.bio.seq.FilterUtils.FilterTransformer
Transform a filter, or return null if it can not be transformed.
transformFilter(FeatureFilter, FilterUtils.FilterTransformer) - Static method in class org.biojava.bio.seq.FilterUtils
This is a general framework method for transforming one filter into another.
transformLocation(Location, int, boolean) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
Transform a location, translating and flipping as required.
transit(int) - Method in interface org.biojava.utils.automata.StateMachineInstance
invoke transition from current state indicated by Symbol represented by symbol index.
transit(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
Find the destination State when the specified tag is encountered.
transit(Object) - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
 
Transition - Class in org.biojava.bio.dp
This is a small and ugly class for storing a transition.
Transition(State, State) - Constructor for class org.biojava.bio.dp.Transition
 
transitions - Variable in class org.biojava.utils.automata.FiniteAutomaton
 
transitionsFrom(State) - Method in interface org.biojava.bio.dp.MarkovModel
Returns the FiniteAlphabet of all states that have a transition from 'source'.
transitionsFrom(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
transitionsFrom(State) - Method in class org.biojava.bio.dp.WMAsMM
 
transitionsTo(State) - Method in interface org.biojava.bio.dp.MarkovModel
Returns the FiniteAlphabet of all states that have a transition to 'dest'.
transitionsTo(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
transitionsTo(State) - Method in class org.biojava.bio.dp.WMAsMM
 
TransitionTable() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
 
TransitionTrainer - Interface in org.biojava.bio.dp
An object that can be used to train the transitions within a MarkovModel.
TRANSITIVE - Static variable in class org.biojava.ontology.OntoTools
 
translate(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
translate(int) - Method in class org.biojava.bio.symbol.FuzzyLocation
 
translate(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
translate(int) - Method in interface org.biojava.bio.symbol.Location
Create a location that is a translation of this location.
translate(int) - Method in class org.biojava.bio.symbol.PointLocation
 
translate(int) - Method in class org.biojava.bio.symbol.RangeLocation
 
translate(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Create a location that is a translation of this location.
translate(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Create a location that is a translation of this location.
translate(int) - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
Create a location that is a translation of this location.
translate(int) - Method in interface org.biojavax.bio.seq.Position
Takes this position and returns a copy translated by 'distance' bases.
translate(int) - Method in class org.biojavax.bio.seq.SimplePosition
Takes this position and returns a copy translated by 'distance' bases.
translate(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Create a location that is a translation of this location.
translate(Symbol) - Method in interface org.biojava.bio.symbol.TranslationTable
Translate a single symbol from source alphabet to the target alphabet.
translate(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes
Translate RNA into protein (with termination symbols).
translate(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
Translate RNA into protein (with termination symbols).
translate(SymbolList, TranslationTable) - Static method in class org.biojava.bio.symbol.SymbolListViews
Provides a 'translated' view of an underlying SymbolList.
translateCUD(InputStream, OutputStream) - Static method in class org.biojava.bio.symbol.CodonPrefTools
reads in a file in Codon Usage Database format and translate it into our XML format These can be obtained from the Codon Usage Database.
TranslatedDistribution - Class in org.biojava.bio.dist
A translated view of some underlying distribution.
TranslatedDistribution(ReversibleTranslationTable, Distribution, DistributionFactory) - Constructor for class org.biojava.bio.dist.TranslatedDistribution
Create a new TranslatedDistribution.
TranslatedSequencePanel - Class in org.biojava.bio.gui.sequence
TranslatedSequencePanel is a panel that displays a Sequence.
TranslatedSequencePanel() - Constructor for class org.biojava.bio.gui.sequence.TranslatedSequencePanel
Creates a new TranslatedSequencePanel with the default settings (direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font).
TranslateFlipContext - Class in org.biojava.bio.seq.projection
A ProjectionContext that translates and optionaly flips features.
TranslateFlipContext(FeatureHolder, FeatureHolder, int) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext
Create a new TranslateFlipContext with translation only.
TranslateFlipContext(FeatureHolder, FeatureHolder, int, boolean) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext
Create a new TranslateFlipContext with explicit translation and flip.
TranslateFlipContext(FeatureHolder, FeatureHolder, int, int) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext
Create a new TranslateFlipContext that flips all featurs arround min and max.
TRANSLATION - Static variable in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
Constant TRANSLATION is a ChangeType which indicates a change to the translation, requiring a paint update.
TRANSLATION - Static variable in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
Constant TRANSLATION is a ChangeType which indicates a change to the translation, requiring a paint update.
TranslationTable - Interface in org.biojava.bio.symbol
Encapsulates the mapping from a source to a destination alphabet.
TRANSPOSON_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
 
transScore(State, State, Symbol, Symbol) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
 
TREES_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.TreesBlock
A constant representing the name of Trees blocks.
TreesBlock - Class in org.biojavax.bio.phylo.io.nexus
Represents Nexus trees blocks.
TreesBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.TreesBlock
Delegates to NexusBlock.Abstract constructor using TreesBlock.TREES_BLOCK as the name.
TreesBlock.NewickTreeString - Class in org.biojavax.bio.phylo.io.nexus
A simple representation of a Newick tree as a single string.
TreesBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus
Builds Nexus taxa blocks.
TreesBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
 
TreesBlockListener - Interface in org.biojavax.bio.phylo.io.nexus
Listens to events that represent Nexus trees blocks.
TreesBlockParser - Class in org.biojavax.bio.phylo.io.nexus
Parses Nexus taxa blocks.
TreesBlockParser(TreesBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
Delegates to NexusBlockParser.Abstract.
TREMA_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the trematode mitochondrial genetic code.
Triple - Interface in org.biojava.ontology
A triple in an ontology.
TRIPLE - Static variable in interface org.biojava.ontology.Ontology
 
TRIPLE - Static variable in interface org.biojavax.ontology.ComparableOntology
 
Triple.Impl - Class in org.biojava.ontology
Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple
Triplet() - Constructor for class org.biojava.utils.ListTools.Triplet
 
Triplet(Object, Object, Object) - Constructor for class org.biojava.utils.ListTools.Triplet
 
TriState - Class in org.biojava.utils
Class that represents the tristate values possible in a logical operation: true, false and indeterminate.
trp() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Tryptophan (W)
TRUE - Static variable in class org.biojava.utils.TriState
 
TRYPSIN - Static variable in class org.biojava.bio.proteomics.Protease
 
TRYPSIN - Static variable in class org.biojava.bio.proteomics.ProteaseManager
 
TurnGlyph - Class in org.biojava.bio.gui.glyph
A Glyph that paints a wide 'H' line within the bounds
TurnGlyph() - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph
 
TurnGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph
 
TurnGlyph(Paint, Stroke) - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph
 
TWIN - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
TWIN - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
 
TwoHeadedArrowGlyph - Class in org.biojava.bio.gui.glyph
A Glyph that paints a two headed arrow within the bounds
TwoHeadedArrowGlyph() - Constructor for class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
 
TwoHeadedArrowGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
 
type - Variable in class org.biojava.bibliography.BiblioCriterion
The criteria can be used for defining rules for matching (type BiblioCriterion.QUERY_CRITERION), or for ordering (type BiblioCriterion.SORT_CRITERION).
type - Variable in class org.biojava.bibliography.BibRef
It defines the nature or genre of the cited resource.
type - Variable in class org.biojava.bio.seq.Feature.Template
 
type - Variable in class org.biojava.utils.IndexedChangeHub.ListenerMemento
 
TYPE - Static variable in interface org.biojava.bio.seq.Feature
The type of this feature has altered.
TYPE_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a bibliographic resource type.
TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
TYPE_BOOK - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a bibliographic resource type.
TYPE_BOOK_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a bibliographic resource type.
TYPE_BOOLEAN - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
TYPE_BYTE - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
TYPE_CHAR - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
TYPE_DOUBLE - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
TYPE_FLOAT - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
TYPE_INT - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
TYPE_JOURNAL_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a bibliographic resource type.
TYPE_LONG - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
TYPE_OBJECT - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
TYPE_PATENT - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a bibliographic resource type.
TYPE_PROCEEDING - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a bibliographic resource type.
TYPE_SHORT - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
TYPE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
TYPE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
TYPE_TECH_REPORT - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a bibliographic resource type.
TYPE_THESIS - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a bibliographic resource type.
TYPE_VOID - Static variable in class org.biojava.utils.bytecode.CodeUtils
 
TYPE_WEB_RESOURCE - Static variable in interface org.biojava.bibliography.BibRefSupport
A name of a bibliographic resource type.
TYPEDEF - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
TypedProperties - Class in org.biojava.utils
a sub-class of java.util.Properties that provides the same constructors, adds two convenient load methods to load the properties from files and, most importantly, adds getPropertyAsXXX() methods to get a property as an object of type XXX.
TypedProperties() - Constructor for class org.biojava.utils.TypedProperties
Creates an empty property list with no default values.
TypedProperties(Properties) - Constructor for class org.biojava.utils.TypedProperties
Creates an empty property list with the specified defaults.
TypeLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker
 
typeTerm - Variable in class org.biojava.bio.seq.Feature.Template
 
TYPETERM - Static variable in interface org.biojava.bio.seq.Feature
The ontological type of this feature has altered.
TYPETERM - Static variable in interface org.biojavax.bio.seq.RichFeature
 
tyr() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Tyrosine (Y)

U

u() - Static method in class org.biojava.bio.seq.NucleotideTools
 
u() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Selenocysteine
u() - Static method in class org.biojava.bio.seq.RNATools
 
UkkonenSuffixTree - Class in org.biojava.bio.symbol
A suffix tree is an efficient method for encoding the frequencies of motifs in a sequence.
UkkonenSuffixTree() - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree
Initializes a new UkkonenSuffixTree instance.
UkkonenSuffixTree(String) - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree
 
UkkonenSuffixTree(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree
 
UkkonenSuffixTree.SuffixNode - Class in org.biojava.bio.symbol
end Tree modification methods
unbind(String) - Method in class org.biojava.naming.ObdaContext
 
unbind(Name) - Method in class org.biojava.naming.ObdaContext
 
Unchangeable - Class in org.biojava.utils
This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
Unchangeable() - Constructor for class org.biojava.utils.Unchangeable
 
UNCLASSIFIED - Static variable in interface org.biojava.bio.EcNumber
Constant that represents EC number components that are as yet unclassified.
uncompress(String, FileOutputStream) - Static method in class org.biojava.utils.io.UncompressInputStream
 
UncompressInputStream - Class in org.biojava.utils.io
This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).
UncompressInputStream(InputStream) - Constructor for class org.biojava.utils.io.UncompressInputStream
 
UNDEFINED - Static variable in interface org.biojava.bio.EcNumber
Constant that represents EC number components that are not defined.
UnequalLengthAlignment - Interface in org.biojava.bio.alignment
UnequalLengthAlignment has the following behavior.
unescape(String) - Method in class org.biojava.ontology.obo.OboFileParser
 
unescape(String, char, int, boolean) - Method in class org.biojava.ontology.obo.OboFileParser
 
unescape(String, char, int, int, boolean) - Method in class org.biojava.ontology.obo.OboFileParser
 
unescapeChars - Static variable in class org.biojava.ontology.obo.OboFileParser
 
UniformDistribution - Class in org.biojava.bio.dist
An implementation of an uniform distribution
UniformDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.UniformDistribution
Create a new UniformDistribution.
uniformMutationDistribution(FiniteAlphabet) - Static method in class org.biojavax.ga.util.GATools
Makes a 1st order distribution which is infact uniform (equivalent to a uniform zero order distribution).
UniformScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
 
UNIGENE_ANNOTATION - Static variable in class org.biojava.bio.program.unigene.UnigeneTools
Annotation schema for all UnigeneCluster instances.
UnigeneCluster - Interface in org.biojava.bio.program.unigene
A single unigene cluster.
UnigeneDB - Interface in org.biojava.bio.program.unigene
A database of Unigene clusters.
UnigeneFactory - Interface in org.biojava.bio.program.unigene
Objects that can be used to produce a UnigeneDB instance given a URL.
UnigeneTools - Class in org.biojava.bio.program.unigene
Usefull tools for working with Unigene.
UnigeneTools() - Constructor for class org.biojava.bio.program.unigene.UnigeneTools
 
unIndent() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
Remove a level of indentation
union(Collection) - Static method in class org.biojava.bio.symbol.LocationTools
The n-way union of a Collection of locations.
union(BibRefQuery[], Hashtable) - Method in interface org.biojava.bibliography.BibRefSupport
It merges all given collections together.
union(AnnotationType, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
Create an AnnotationType that matches all Anntotations that are accepted by two others.
union(CollectionConstraint, CollectionConstraint) - Static method in class org.biojava.bio.AnnotationTools
Calculate a CollectionConstaint that will accept all items accepted by either constraint.
union(PropertyConstraint, PropertyConstraint) - Static method in class org.biojava.bio.AnnotationTools
Create a PropertyConstraint that matches all Objects that are accepted by two others.
union(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils
Operator: Union of FeatureHolder1 and FeatureHolder2
union(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
 
union(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
union(Location) - Method in class org.biojava.bio.symbol.CircularLocation
 
union(Location) - Method in interface org.biojava.bio.symbol.Location
Return a Location containing all points in either ranges.
union(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Return a Location containing all points in either ranges.
union(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Return a Location containing all points in either ranges.
union(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Return a Location containing all points in either ranges.
union(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
Return the union of two locations.
UNIPROT_FORMAT - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
The name of this format
UniProtCommentParser - Class in org.biojavax.bio.seq.io
 
UniProtCommentParser() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser
Creates a new instance of UniProtCommentParser.
UniProtCommentParser.Event - Class in org.biojavax.bio.seq.io
A class to describe events for alternative product comments.
UniProtCommentParser.Interaction - Class in org.biojavax.bio.seq.io
A class to describe protein-protein interactions.
UniProtCommentParser.Isoform - Class in org.biojavax.bio.seq.io
A class to describe isoforms for alternative product comments.
UniProtCommentParser.SeqCaution - Class in org.biojavax.bio.seq.io
A class to describe seq caution entries.
UniProtFormat - Class in org.biojavax.bio.seq.io
Format reader for UniProt files.
UniProtFormat() - Constructor for class org.biojavax.bio.seq.io.UniProtFormat
 
UniProtFormat.Terms - Class in org.biojavax.bio.seq.io
Implements some UniProt-specific terms.
UniProtLocationParser - Class in org.biojavax.bio.seq.io
Parses UniProt location strings into RichLocation objects.
UNIPROTXML_FORMAT - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
The name of this format
UniProtXMLFormat - Class in org.biojavax.bio.seq.io
Format reader for UniProtXML files.
UniProtXMLFormat() - Constructor for class org.biojavax.bio.seq.io.UniProtXMLFormat
 
UniProtXMLFormat.Terms - Class in org.biojavax.bio.seq.io
Implements some UniProtXML-specific terms.
UNIVERSAL - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the universal genetic code.
UNKNOWN - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
UNKNOWN indicates that the alignment format is unknown.
UNKNOWN - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
UNKNOWN indicates that the sequence format is unknown.
UNKNOWN - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
 
UNKNOWN - Static variable in interface org.biojava.bio.seq.StrandedFeature
Flag to indicate that a feature has an unknown strand.
UNKNOWN - Static variable in class org.biojava.utils.ChangeType
Constant ChangeType field which indicates that a change has occured which can't otherwise be represented.
UNKNOWN_BLOCK - Static variable in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
The name for an unknown block parser.
UNKNOWN_SCOPE - Static variable in class org.biojava.ontology.Synonym
 
UNKNOWN_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand
The unknown strand is represented by the symbol '?'
UnknownDBHelper - Class in org.biojava.bio.seq.db.biosql
Deprecated.
Use hibernate and org.biojavax.bio.db.*
UnknownDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.UnknownDBHelper
Deprecated.
 
unlockModel() - Method in class org.biojava.bio.dp.DP
 
unmask(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
Un-masks the token by making it upper case.
unmask(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
Present the token for a Symbol as it would appear if it wasn't softmasked
unpack(byte) - Method in class org.biojava.bio.symbol.DNAAmbPack
 
unpack(byte) - Method in class org.biojava.bio.symbol.DNANoAmbPack
 
unpack(byte) - Method in interface org.biojava.bio.symbol.Packing
Return the symbol for a packing.
unregisterFactory(UnigeneFactory) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
Register a UnigeneFactory.
UnsupportedChromatogramFormatException - Exception in org.biojava.bio.chromatogram
Exception indicating that some provided data does not represent a supported chromatogram format.
UnsupportedChromatogramFormatException() - Constructor for exception org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException
Create a new UnsupportedChromatogramFormatException.
UnsupportedChromatogramFormatException(String) - Constructor for exception org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException
Create a new UnsupportedChromatogramFormatException with a message.
UntrainableDistribution - Class in org.biojava.bio.dist
A distribution which does not interact with the training framework.
UntrainableDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.UntrainableDistribution
Construct a new untrainable distribution over the specified alphabet.
untranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet.
untranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
 
untranslate(Symbol) - Method in interface org.biojava.bio.symbol.ManyToOneTranslationTable
Translate a single symbol from target alphabet to the source alphabet.
untranslate(Symbol) - Method in interface org.biojava.bio.symbol.ReversibleTranslationTable
Translate a single symbol from target alphabet to the source alphabet.
update() - Method in class org.biojava.bio.dp.DP
 
update() - Method in class org.biojava.bio.dp.onehead.SingleDP
 
update() - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
update(byte[], int, int) - Method in class org.biojavax.utils.CRC64Checksum
 
update(int) - Method in class org.biojavax.utils.CRC64Checksum
 
update(String) - Method in class org.biojavax.utils.CRC64Checksum
 
UPDATE_DATE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
UPDATE_REL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
Upgma(TaxaBlock, CharactersBlock) - Static method in class org.biojavax.bio.phylo.DistanceBasedTreeMethod
 
uri - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
 
URI - Static variable in interface org.biojavax.Namespace
 
URI_PREFIX - Static variable in class org.biojava.bio.seq.FeatureTypes
The standard prefix for all type URIs
url - Variable in class org.biojava.bibliography.BiblioWebResource
The URL of the resource.
urlBatchSequences - Static variable in class org.biojava.bio.seq.db.GenbankSequenceDB
 
urlBatchSequences - Static variable in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
 
urlBatchSequences - Static variable in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
 
URLFactory - Interface in org.biojava.utils.net
URLFactory defines a means of obtaining a URL associated with an object.
URLGeneratorFactory - Interface in org.biojava.bio.program.blast2html
Interface for a factory method to return a list of 0, 1 or more DatabaseURLGenerator instances.
usCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
USE_CUSTOM_STROKE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to use custom strokes when drawing traces and separators.
USE_PER_SHAPE_TRANSFORM - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether to apply scaling and translation transforms to each shape individually or to apply a single transform to the graphics context.
UserDefinedTrackLayout - Class in org.biojava.bio.gui.sequence.tracklayout
An implementation of TrackLayout that that wraps a sequence over an arbitrary set of ranges
UserDefinedTrackLayout(RangeLocation[]) - Constructor for class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
 
useSuppliedSymListFactory() - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
Call this to convert from default SymbolList implementation to user-supplied implementation.
UtilHelper - Class in org.biojava.bio.seq.io.agave
Just make the property follow the common case
UtilHelper() - Constructor for class org.biojava.bio.seq.io.agave.UtilHelper
 

V

v() - Static method in class org.biojava.bio.seq.DNATools
 
v() - Static method in class org.biojava.bio.seq.NucleotideTools
 
v() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Valine
val() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Valine (V)
validate(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
validate(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
validate(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
validate(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
validate(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
validate(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
 
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.And
 
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
 
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Or
 
validateAddValue(Collection, Object) - Method in interface org.biojava.bio.CollectionConstraint
Return true iff the Collection formed by adding newValue to current would be accepted by this constraint.
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.And
 
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
 
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Or
 
validateRemoveValue(Collection, Object) - Method in interface org.biojava.bio.CollectionConstraint
Return true iff the Collection formed by removing newValue from current would be accepted by this constraint.
validLen - Variable in class org.biojava.utils.io.CachingInputStream
A count of the number of bytes in CachingInputStream.cache that contain data read from the stream.
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Echo
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Indexer
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Indexer2
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.MultiTagger
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
 
value(TagValueContext, Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
A value has been seen.
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
 
VALUE - Static variable in interface org.biojavax.Note
 
VALUE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ValueChanger - Class in org.biojava.bio.program.tagvalue
Intercept the values associated with some tags and change them systematically.
ValueChanger(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.ValueChanger
 
ValueChanger(TagValueListener, ChangeTable) - Constructor for class org.biojava.bio.program.tagvalue.ValueChanger
Create a new changer that will pass the modified event stream to a delegate.
valueOf(String) - Static method in class org.biojava.bio.EcNumber.Impl
Process a string into an EcNumber.
valueOf(String) - Static method in enum org.biojava.bio.program.fastq.FastqVariant
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier
Create a new LifeScienceIdentifier parsed from the properly formatted string lsid.
valueOf(String) - Static method in enum org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
Returns the enum constant of this type with the specified name.
valueOf(String, String, String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier
Create a new LifeScienceIdentifier from the specified parameters.
valueOf(String, String, String, String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier
Create a new LifeScienceIdentifier from the specified parameters.
values() - Static method in enum org.biojava.bio.program.fastq.FastqVariant
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
Returns an array containing the constants of this enum type, in the order they are declared.
VALUES - Static variable in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
Variable - Interface in org.biojava.ontology
 
Variable.Impl - Class in org.biojava.ontology
 
vectorToString(SparseVector) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
VERSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
VERSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
VERT_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the vertebrate mitochondrial genetic code.
view(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools
Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly.
view(Sequence, String) - Static method in class org.biojava.bio.seq.SequenceTools
Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly.
view(Sequence, FeatureRealizer) - Static method in class org.biojava.bio.seq.SequenceTools
Creates a new Sequence with the data of the old but with a different FeatureRealizer that will be applied to new Features.
viewEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
ViewingSequenceDB - Class in org.biojava.bio.seq.db
SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.
ViewingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.ViewingSequenceDB
Create a new ViewingSequenceDB that views the sequences in parent.
ViewSequence - Class in org.biojava.bio.seq.impl
A view onto another Sequence object.
ViewSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.ViewSequence
Construct a view onto an existing sequence which takes on that sequence's name.
ViewSequence(Sequence, String) - Constructor for class org.biojava.bio.seq.impl.ViewSequence
Construct a view onto an existing sequence and give it a new name.
ViewSequence(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.impl.ViewSequence
Construct a view onto a sequence, using a specific FeatureRealizer.
ViewSequenceFactory - Class in org.biojava.bio.program.ssbind
ViewSequenceFactory is a base class for creating search handlers which create and cache views on the query and subject sequences.
ViewSequenceFactory() - Constructor for class org.biojava.bio.program.ssbind.ViewSequenceFactory
 
viewStart - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
viewToSource(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
Coordinate conversion from view to source.
viewToSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
viewToSource(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
Coordinate conversion from view to source.
visitFilter(FeatureFilter, Visitor) - Static method in class org.biojava.bio.seq.FilterUtils
Applies a visitor to a filter, and returns the visitor's result or null.
Visitor - Interface in org.biojava.utils.walker
Things that will be shown filters.
viterbi(ScoreType, BackPointer) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
 
viterbi(ScoreType, BackPointer) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
 
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
 
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
volume - Variable in class org.biojava.bibliography.BiblioBook
Book volume.
volume - Variable in class org.biojava.bibliography.BiblioJournalArticle
The journal volume.
vp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
vp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 

W

w() - Static method in class org.biojava.bio.seq.DNATools
 
w() - Static method in class org.biojava.bio.seq.NucleotideTools
 
w() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Tryptophan
waitForThreads() - Method in class org.biojava.utils.SimpleThreadPool
 
waitForThreads() - Method in interface org.biojava.utils.ThreadPool
waitForThreads temporarily closes the pool to new requests until such time as the current request queue has been emptied and all running tasks completed.
walk(Object, Visitor) - Method in interface org.biojava.utils.walker.Walker
This walks the feature tree, showing the visitor each filter in the expression.
Walker - Interface in org.biojava.utils.walker
Objects that can walk over a filter expression, showing each element to a visitor.
WalkerFactory - Class in org.biojava.utils.walker
 
walkTo(UkkonenSuffixTree.SuffixNode, String, int, int) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
This method is used to walk down the tree, from a given node.
wantsBracketsAndBraces() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser
 
wantsBracketsAndBraces() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser
 
wantsBracketsAndBraces() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
 
wantsBracketsAndBraces() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
Does the listener want to know about brackets and braces as separate tokens?
wantsBracketsAndBraces() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
 
wantsBracketsAndBraces() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
Does the listener want to know about brackets and braces as separate tokens?
wasEmpty() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer
Returns true if no HitSummary and no Hit elements were encountered
WeakCacheMap - Class in org.biojava.utils.cache
A cache which retains weak references to objects
WeakCacheMap() - Constructor for class org.biojava.utils.cache.WeakCacheMap
 
WeakTaxon - Class in org.biojava.bio.taxa
Deprecated.
replaced by classes in org.biojavax.bio.taxa
WeakTaxon() - Constructor for class org.biojava.bio.taxa.WeakTaxon
Deprecated.
 
WeakTaxon(String, String) - Constructor for class org.biojava.bio.taxa.WeakTaxon
Deprecated.
 
WeakTaxonFactory - Class in org.biojava.bio.taxa
Deprecated.
replaced by classes in org.biojavax.bio.taxa
WeakTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.WeakTaxonFactory
Deprecated.
 
WeakValueHashMap - Class in org.biojava.utils.cache
Map implementation which keeps weak references to values.
WeakValueHashMap() - Constructor for class org.biojava.utils.cache.WeakValueHashMap
 
WebSequenceDB - Class in org.biojava.bio.seq.db
Functions for access to a web based database that returns sequences in a variety of formats.
WebSequenceDB() - Constructor for class org.biojava.bio.seq.db.WebSequenceDB
 
WeightedSet - Class in org.biojavax.ga.util
Inspred by the BioJava Distribution objects the WeightedSet is a map from a Key to a Weight.
WeightedSet() - Constructor for class org.biojavax.ga.util.WeightedSet
 
weightForwarder - Variable in class org.biojava.bio.dist.AbstractOrderNDistribution
The listener that will forward events from the underlying distributions to listeners for this distribution.
WeightMatrix - Interface in org.biojava.bio.dp
A log odds weight matrix.
WeightMatrixAnnotator - Class in org.biojava.bio.dp
Annotates a sequence with hits to a weight-matrix.
WeightMatrixAnnotator(WeightMatrix, double) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator
Create a new annotator that uses PROBABILITY score type.
WeightMatrixAnnotator(WeightMatrix, ScoreType, double) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator
Create a new annotator that uses a specific score type.
WeightMatrixAnnotator(WeightMatrix, ScoreType, double, String) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator
Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix.
WEIGHTS - Static variable in interface org.biojava.bio.dist.Distribution
Whenever a distribution changes the values that would be returned by getWeight, they should fire a ChangeEvent with this object as the type.
WIDTH_IS_AUTHORITATIVE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Option indicating whether width or horizontal scale is the authoritative measure.
windowedSymbolList(SymbolList, int) - Static method in class org.biojava.bio.symbol.SymbolListViews
A view of windows onto another SymbolList.
withDescription(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified description.
withQuality(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified quality scores.
withSequence(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified sequence.
withVariant(FastqVariant) - Method in class org.biojava.bio.program.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.
WMAsMM - Class in org.biojava.bio.dp
Wraps a weight matrix up so that it appears to be a very simple HMM.
WMAsMM(WeightMatrix) - Constructor for class org.biojava.bio.dp.WMAsMM
 
WobbleDistribution - Interface in org.biojava.bio.symbol
an object to return statistics about the frequency of the wobble base in a set of synonymous codons.
wordsForType(CodeClass) - Static method in class org.biojava.utils.bytecode.CodeUtils
Number of words needed for local variables of this type.
wordSize() - Method in class org.biojava.bio.symbol.DNAAmbPack
 
wordSize() - Method in class org.biojava.bio.symbol.DNANoAmbPack
 
wordSize() - Method in interface org.biojava.bio.symbol.Packing
The number of bits required to pack a symbol.
WordTokenization - Class in org.biojava.bio.seq.io
Base class for tokenizations which accept whitespace-separated `words'.
WordTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.WordTokenization
 
wordWrap(String, String, int) - Static method in class org.biojavax.utils.StringTools
Word-wraps a string into an array of lines of no more than the given width.
WORM_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
Caenorhabditis elegans codon preferences
Wrapper(SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Wrapper
 
write(File, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified file.
write(File, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified file.
write(OutputStream, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified output stream.
write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
Writes out the alignment to an FASTA file.
write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
 
write(OutputStream, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified output stream.
write(Sequence) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
Writing Sequence.
writeAnnotations(FeatureHolder) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeAnnotationType(AnnotationType, XMLWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
Write an AnnotationType to the specified XMLWriter.
writeAssembly(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeBioSequence(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeBlockContents(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
writeBlockContents(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
 
writeBlockContents(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
Implement this to write out block contents, not including the BEGIN and END tags.
writeBlockContents(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
 
writeBlockContents(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
 
writeByte(byte) - Method in interface org.biojava.utils.bytecode.CodeContext
Write a single byte to the context.
writeClassification(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeCode(CodeContext) - Method in interface org.biojava.utils.bytecode.CodeGenerator
Write the byte or bytes for this CodeGenerator to a CodeContext.
writeCode(CodeContext) - Method in class org.biojava.utils.bytecode.IfExpression
 
writeCode(CodeContext) - Method in class org.biojava.utils.bytecode.InstructionVector
 
writeCode(CodeContext) - Method in class org.biojava.utils.bytecode.Label
 
writeCode(CodeContext) - Method in class org.biojava.utils.bytecode.MarkLabel
 
writeCollectionConstraint(CollectionConstraint, XMLWriter, XMLAnnotationTypeWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLCollectionConstraintWriter
 
writeCompResult(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeConstantPool(DataOutput) - Method in class org.biojava.utils.bytecode.ConstantPool
 
writeContig(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeDetails(XMLWriter, Feature) - Method in class org.biojava.bio.program.xff.BasicXFFHelper
 
writeDetails(XMLWriter, Feature) - Method in class org.biojava.bio.program.xff.PropertyWriter
 
writeDetails(XMLWriter, Feature) - Method in interface org.biojava.bio.program.xff.XFFHelper
 
writeDistribution(Distribution, OutputStream) - Method in class org.biojava.bio.dist.XMLDistributionWriter
Writes an OrderNDistribution or simple Distribution to an XML file.
writeDna(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
 
writeDna(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
 
writeEmbl(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes a single Sequence to an OutputStream in EMBL format.
writeEmbl(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes a stream of Sequences to an OutputStream in EMBL format.
writeEMBL(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes sequences from a SequenceIterator to an OutputStream in EMBL Format.
writeEMBL(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes a single Sequence to an OutputStream in EMBL format.
writeEMBLxml(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes sequences from a SequenceIterator to an OutputStream in EMBLxml Format.
writeEMBLxml(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes a single Sequence to an OutputStream in EMBLxml format.
writeEmptyElement(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
writeEmptyElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
writeFasta(OutputStream, SequenceDB) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Write a sequenceDB to an output stream in fasta format.
writeFasta(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes a single Sequence to an OutputStream in Fasta format.
writeFasta(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes sequences from a SequenceIterator to an OutputStream in Fasta Format.
writeFasta(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes Sequences from a SequenceIterator to an OutputStream in Fasta Format.
writeFasta(OutputStream, SequenceIterator, Namespace, FastaHeader) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes Sequences from a SequenceIterator to an OutputStream in Fasta Format.
writeFasta(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes a single Sequence to an OutputStream in Fasta format.
writeFasta(OutputStream, Sequence, Namespace, FastaHeader) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes a single Sequence to an OutputStream in Fasta format.
writeFeatureSet(FeatureHolder, XMLWriter) - Method in class org.biojava.bio.program.xff.XFFWriter
 
writeFile(File, Alignment) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat
Writes the given Alignment in PHYLIP format to a file.
writeFile(File, NexusFile) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat
Writes the given Nexus output to a file.
writeFilter(FeatureFilter, XMLWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
Write a FeatureFilter to the supplied XMLWriter
writeFilter(FeatureFilter, XMLWriter, XMLFilterWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterWriter.FilterWriter
 
writeFooter() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
Write </sciobj>
writeGenbank(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes a single Sequence to an OutputStream in Genbank format.
writeGenbank(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes a stream of Sequences to an OutputStream in Genbank format.
writeGenbank(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes sequences from a SequenceIterator to an OutputStream in GenBank Format.
writeGenbank(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes a single Sequence to an OutputStream in GenBank format.
writeGene(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeGenpept(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes a single Sequence to an OutputStream in Genpept format.
writeGenpept(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes a stream of Sequences to an OutputStream in Genpept format.
writeGFF(File, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
Writes a GFFEntrySet to a file.
writeGFF(PrintWriter, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
Writes a GFFEntrySet to a PrintWriter.
writeGFF(String, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
Writes a GFFEntrySet to a file.
writeHeader() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
writeHeader() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
Write <sciobj>
writeIndent() - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
writeINSDseq(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes sequences from a SequenceIterator to an OutputStream in INSDseq Format.
writeINSDseq(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes a single Sequence to an OutputStream in INSDseq format.
writeKeyValueLine(String, String, int, int, PrintStream) - Static method in class org.biojavax.utils.StringTools
Writes some text to the output stream in the following format: key text continuation of text where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth, and the text is split over multiple lines at the nearest occurrence of whitespace.
writeKeyValueLine(String, String, int, int, String, PrintStream) - Static method in class org.biojavax.utils.StringTools
Writes some text to the output stream in the following format: key text continuation of text where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth, and the text is split over multiple lines at the nearest occurrence of separator sep.
writeKeyValueLine(String, String, int, int, String, String, PrintStream) - Static method in class org.biojavax.utils.StringTools
Writes some text to the output stream in the following format: key text wrappedKey continuation of text where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth, and the text is split over multiple lines at the nearest occurrence of separator sep.
writeLabel(Label) - Method in interface org.biojava.utils.bytecode.CodeContext
Write the offset of a Label to the context.
writeLocation(RichLocation) - Static method in class org.biojavax.bio.seq.io.GenbankLocationParser
Writes a location in Genbank format.
writeLocation(RichLocation) - Static method in class org.biojavax.bio.seq.io.UniProtLocationParser
Writes a location in UniProt format.
writeMatrix(WeightMatrix, PrintStream) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
writeModel(MarkovModel, PrintStream) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
writeModelFile(SVMClassifierModel, String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
writeObject(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
 
writeObject(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
 
writeObject(Writer) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusObject
Writes this object to the given writer.
writePCData(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
writePhredQuality(OutputStream, OutputStream, SequenceDB) - Static method in class org.biojava.bio.program.phred.PhredTools
Writes Phred quality data in a Fasta type format.
writePropertyConstraint(PropertyConstraint, XMLWriter, XMLAnnotationTypeWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLPropertyConstraintWriter
 
writeProtein(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
 
writeProtein(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
 
writeRecord(RAF, long, int, String, Map) - Method in class org.biojava.bio.program.indexdb.BioStore
 
writeRecord(RAF, long, int, String, Map) - Method in interface org.biojava.bio.program.indexdb.IndexStore
writeRecord creates and writes a new Record
WriterOutputHandler - Class in org.biojava.utils.process
Simple output handler that writes the output of an external process to an writer.
WriterOutputHandler(Writer, String) - Constructor for class org.biojava.utils.process.WriterOutputHandler
Initializes the writer output handler.
writeSeqFeature(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
Write SeqFeature XML
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.program.phred.PhredFormat
This method will print symbols to the line width followed by a new line etc.
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
Write sequence into AGAVE XML format.
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
 
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
Writes a Sequence or RichSequence to a PrintStream in FASTA format.
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GAMEFormat
 
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
 
writeSequence(Sequence, PrintStream) - Method in interface org.biojava.bio.seq.io.SequenceFormat
writeSequence writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
writeSequence writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
writeSequence writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
writeSequence writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
writeSequence writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
writeSequence writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
writeSequence writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
writeSequence writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.program.phred.PhredFormat
Deprecated.
use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.
use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat
Deprecated.
use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.GAMEFormat
 
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.
use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, String, PrintStream) - Method in interface org.biojava.bio.seq.io.SequenceFormat
Deprecated.
use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
writeSequence writes a sequence to the specified PrintStream, using the specified format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
writeSequence writes a sequence to the specified PrintStream, using the specified format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
writeSequence writes a sequence to the specified PrintStream, using the specified format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
writeSequence writes a sequence to the specified PrintStream, using the specified format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
writeSequence writes a sequence to the specified PrintStream, using the specified format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
writeSequence writes a sequence to the specified PrintStream, using the specified format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
writeSequence writes a sequence to the specified PrintStream, using the specified format.
writeSequence(Sequence, String, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat
As per EMBLFormat.writeSequence(Sequence, Namespace), except that it also takes a format parameter.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.GenbankFormat
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
writeSequence(Sequence, Namespace) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtFormat
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
writeSequenceMap(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
group sequence_map by getSource()
writeSequenceMap2(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
Write SequenceMap XML
writeShort(int) - Method in interface org.biojava.utils.bytecode.CodeContext
Write a short (2 bytes) to the context.
writeStream(OutputStream, Alignment) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat
Writes the given Alignment in PHYLIP format to a stream.
writeStream(OutputStream, NexusFile) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat
Writes the given Nexus output to a stream.
writeStream(SequenceIterator) - Method in class org.biojava.bio.seq.io.StreamWriter
Write each of the sequences in ss to the stream in the given format.
writeStream(SequenceIterator, Namespace) - Method in class org.biojavax.bio.seq.io.RichStreamWriter
Write each of the sequences in ss to the stream in the given format.
writeSwissprot(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes a single Sequence to an OutputStream in SwissProt format.
writeSwissprot(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Writes a stream of Sequences to an OutputStream in SwissProt format.
writeToken(Writer, String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
Writes a token and correctly substitutes all symbols in it.
writeToXML(Distribution, OutputStream) - Static method in class org.biojava.bio.dist.DistributionTools
Writes a Distribution to XML that can be read with the readFromXML method.
writeToXML(CodonPref, PrintWriter) - Static method in class org.biojava.bio.symbol.CodonPrefTools
write out a specified CodonPref object in XML format.
writeTranscript(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeUniProt(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes sequences from a SequenceIterator to an OutputStream in UniProt Format.
writeUniProt(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes a single Sequence to an OutputStream in UniProt format.
writeUniProtXML(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes sequences from a SequenceIterator to an OutputStream in UniProt XML Format.
writeUniProtXML(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
Writes a single Sequence to an OutputStream in UniProt XML format.
writeWriter(Writer, Alignment) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat
Writes the given Alignment in PHYLIP format to a writer.
writeWriter(Writer, NexusFile) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat
Writes the given Nexus output to a writer.
writeXFF(File, FeatureHolder) - Static method in class org.biojava.bio.program.xff.XFFTools
 
writeXFF(PrintWriter, FeatureHolder) - Static method in class org.biojava.bio.program.xff.XFFTools
 
writeXML(XMLWriter) - Method in interface org.biojava.utils.xml.XMLWritable
 

X

X_LAEVIS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
XFF_BIOJAVA_NS - Static variable in class org.biojava.bio.program.xff.XFFTools
 
XFF_NS - Static variable in class org.biojava.bio.program.xff.XFFTools
 
XFFFeatureSetHandler - Class in org.biojava.bio.program.xff
StAX handler which converts and stream of parse events for an XFF featureSet element into BioJava SeqIO events.
XFFFeatureSetHandler() - Constructor for class org.biojava.bio.program.xff.XFFFeatureSetHandler
Construct a new XFFFeatureSetHandler with the default set of handlers.
XFFHelper - Interface in org.biojava.bio.program.xff
 
XFFPartHandlerFactory - Interface in org.biojava.bio.program.xff
Factory for StAX content handlers.
XFFTools - Class in org.biojava.bio.program.xff
Common functionality for manipulating XFF.
XFFTools() - Constructor for class org.biojava.bio.program.xff.XFFTools
 
XFFWriter - Class in org.biojava.bio.program.xff
Simple XFF writing code, ripped off from Dazzle 0.08.
XFFWriter() - Constructor for class org.biojava.bio.program.xff.XFFWriter
 
XFFWriter(XFFHelper) - Constructor for class org.biojava.bio.program.xff.XFFWriter
 
xHair - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer
xHair is the vertical line positioned along the X-axis.
XML - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
XML_ANNOTATIONTYPE_NS - Static variable in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
XML namespace string used to the AnnotationType representation
XML_FILTER_NS - Static variable in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
 
XMLAnnotationTypeHandler - Class in org.biojava.bio.seq.io.filterxml
StAX handler for parsing AnnotationTypes in FilterXML documents.
XMLAnnotationTypeHandler() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
Construct a new XMLAnnotationTypeHandler which can parse the builtin PropertyConstraints.
XMLAnnotationTypeHandler.CollectionConstraintHandler - Interface in org.biojava.bio.seq.io.filterxml
Handler for an individual CollectionConstraint in an AnnotationType.
XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml
Handler Factory for a CollectionConstraint in an AnnotationType.
XMLAnnotationTypeHandler.PropertyConstraintHandler - Interface in org.biojava.bio.seq.io.filterxml
Handler for an individual PropertyConstraint in an AnnotationType.
XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml
Handler Factory for a PropertyConstraint in an AnnotationType.
XMLAnnotationTypeWriter - Class in org.biojava.bio.seq.io.filterxml
Main class for writing AnnotationTypes as XML.
XMLAnnotationTypeWriter() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
Construct a new AnnotationTypeWriter which knows about the builtin types of PropertyConstraint
XMLAnnotationTypeWriter.XMLCollectionConstraintWriter - Interface in org.biojava.bio.seq.io.filterxml
Writer for types of CollectionConstraint.
XMLAnnotationTypeWriter.XMLPropertyConstraintWriter - Interface in org.biojava.bio.seq.io.filterxml
Writer for types of PropertyConstraint.
XMLBeans - Class in org.biojava.utils.xml
Construct java beans from XML elements
XMLBeans() - Constructor for class org.biojava.utils.xml.XMLBeans
 
XMLDistributionReader - Class in org.biojava.bio.dist
A SAX parser that reads an XML representation of a Distribution from a file and recreates it as a Distribution Object.
XMLDistributionReader() - Constructor for class org.biojava.bio.dist.XMLDistributionReader
 
XMLDistributionWriter - Class in org.biojava.bio.dist
Writes an OrderNDistribution or simple Distribution to an XML file.
XMLDistributionWriter() - Constructor for class org.biojava.bio.dist.XMLDistributionWriter
 
XMLFilterHandler - Class in org.biojava.bio.seq.io.filterxml
Factory producing content handlers for parsing FilterXML elements.
XMLFilterHandler() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
Construct a new XMLFilterHandler which can parse the builtin types of FeatureFilter.
XMLFilterHandler.FilterHandler - Interface in org.biojava.bio.seq.io.filterxml
StAXContentHandler for a particular type of FeatureFilter.
XMLFilterHandler.FilterHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml
Factory of StAXContentHandlers for a particular type of FeatureFilter.
XMLFilterWriter - Class in org.biojava.bio.seq.io.filterxml
Write FeatureFilters in XML format.
XMLFilterWriter() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
Construct a new XMLFilterWriter which can serialize the buildin types of FeatureFilter.
XMLFilterWriter.FilterWriter - Interface in org.biojava.bio.seq.io.filterxml
Interface for an object which can write a FeatureFilter as XML.
XmlMarkovModel - Class in org.biojava.bio.dp
 
XmlMarkovModel() - Constructor for class org.biojava.bio.dp.XmlMarkovModel
 
xmlSchema - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
xmlSchema - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
xmlSchema - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
XMLTools - Class in org.biojavax.utils
Utility class for reading chunks of XML files and feeding them to SAX.
XMLWritable - Interface in org.biojava.utils.xml
Object which knows how to represent itself as an XML element.
XMLWriter - Interface in org.biojava.utils.xml
Simple interface for building XML documents.
Xor(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Xor
 
Xor(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Xor
 
Xor(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor
 
XREF_ANALOG - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
XREF_DBNAME_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
XREF_ID_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
XREF_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
XREF_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 

Y

y() - Static method in class org.biojava.bio.seq.DNATools
 
y() - Static method in class org.biojava.bio.seq.NucleotideTools
 
y() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Tyrosine
YEAST_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
Translation table name for the yeast mitochondrial genetic code.
yHair - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer
yHair is the horizontal line positioned along the Y-axis.

Z

Z_MAYS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
zero() - Static method in class org.biojavax.ga.util.GATools
 
ZERO - Static variable in class org.biojava.bio.CardinalityConstraint
The property should have zero values.
ZERO_OR_ONE - Static variable in class org.biojava.bio.CardinalityConstraint
The property should have zero or one values.
zeroCol - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
zeroCol - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
Description of the Field
zeroCounts() - Method in interface org.biojava.bio.dist.Count
Reset all the counts to zero.
zeroCounts() - Method in class org.biojava.bio.dist.IndexedCount
 
ZiggyFeatureRenderer - Class in org.biojava.bio.gui.sequence
A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags.
ZiggyFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
 
ZiggyImapRenderer - Class in org.biojava.bio.gui.sequence
ZiggyImapRenderer is a decorator for ZiggyFeatureRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the ZiggyFeatureRenderer.
ZiggyImapRenderer(ZiggyFeatureRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.ZiggyImapRenderer
Creates a new ZiggyImapRenderer.

_

_0 - Static variable in class org.biojava.bio.program.abi.ABITools
The poorly supported symbol.
_1 - Static variable in class org.biojava.bio.program.abi.ABITools
The well supported symbol.
_addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
 
_addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
 
_addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
 
_removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
 
_removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
 
_setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
_setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
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