A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ 

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(Reader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
Initializes the iterator.
AAindexStreamReader(BufferedReader) - 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.
ABIFChromatogram.Parser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
 
ABIFChromatogram.Parser(File) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
 
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.
ABIFParser.TaggedDataRecord(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
Creates a new TaggedDataRecord from the next 28 bytes of din.
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(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.
ABITrace(byte[]) - Constructor for class org.biojava.bio.program.abi.ABITrace
The byte[] constructor parses an ABI file represented as a byte array.
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
 
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(Annotation) - Constructor for class org.biojava.bio.AbstractAnnotation
Copy-constructor.
AbstractAnnotation(Map) - Constructor for class org.biojava.bio.AbstractAnnotation
Create a new Annotation by copying the key-value pairs from a map.
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.EditScreener(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
 
AbstractSymbolList.EditTranslater - Class in org.biojava.bio.symbol
This translates edit events that fall within a window into window co-ordinates.
AbstractSymbolList.EditTranslater(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
 
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(DP) - Constructor for class org.biojava.bio.dp.AbstractTrainer
 
AbstractTrainer() - 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.LeftRightLocationComparator() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
 
AbstractULAlignment.SubULAlignment - Class in org.biojava.bio.alignment
 
AbstractULAlignment.SubULAlignment(Set<String>, Location) - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
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(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(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(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() - 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.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(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.
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(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(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_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(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
addBioEntry(String, BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
 
addBottomConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
Add a configuration as the most default place to look.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addChangeListener adds a listener for all types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addChangeListener adds a listener for specific types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.
 
addChangeListener(ChangeListener, ChangeType) - 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, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
addChangeListener adds a listener for specific types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
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) - Method in class org.biojava.bio.seq.impl.SubSequence
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
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.utils.AbstractChangeable
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
 
addChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable
Deprecated.
use addChangeListener(cl, ChangeType.UNKNOWN)
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) - Method in class org.biojava.utils.ChangeSupport
Add a listener that will be informed of all changes.
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) - Method in class org.biojava.utils.Unchangeable
 
addChangeListener(ChangeListener, ChangeType) - 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, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Add a listener that will be informed of changes of a given type.
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
addChangeListener(ChangeListener, ChangeType) - 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.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(Comment) - Method in interface org.biojavax.bio.BioEntry
Adds a comment instance to this bioentry.
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 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(DistributionTrainerContext, AtomicSymbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
Registers that sym was counted in this state.
addCount(Distribution, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
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(Distribution, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
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(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.
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.
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(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
addOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
addOrganisms(Population) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
addOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population
Adds several organisms to the population
addOrganisms(Set) - Method in interface org.biojavax.ga.Population
Adds several organisms to the population
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(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
 
addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
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(String, 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.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(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
addRenderer adds a renderer as a new track.
addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
addRenderer adds a renderer.
addRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
 
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(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(String, RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
 
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(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(String, Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
Add a sequence under a particular id.
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(String, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
Add a sequence into the tree.
addSequence(Sequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
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(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.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(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
 
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
 
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(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.
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
 
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(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.
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.
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, 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.
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.
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, double, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
addVector(Object) - 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 - Static variable in interface org.biojava.bio.dp.EmissionState
This signals that the advance array has been altered.
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
 
affiliation - Variable in class org.biojava.bibliography.BiblioPerson
Their affiliation.
Agave2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave
Dumping the data from biojava with source of agave into agave format
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
 
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.
AgaveWriter.Indent() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
 
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 - 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 - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
alignment Alignment field.
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(List, SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews
View a SymbolList over a cross-product Alphabet as an Alignment.
Alignment.SymbolListIterator - Class in org.biojava.bio.alignment
Iterator implementation looping over symbol lists in an alignment using the labels.
Alignment.SymbolListIterator(Alignment) - Constructor for class org.biojava.bio.alignment.Alignment.SymbolListIterator
Creates a SymbolListIterator for a given alignment object.
ALIGNMENT_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.AlignmentStAXHandler
 
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.program.xff.ElementRecognizer
 
all - Static variable in interface org.biojava.bio.seq.FeatureFilter
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.seq.io.agave.ElementRecognizer
 
ALL - Static variable in interface org.biojava.bio.seq.io.game.ElementRecognizer
 
all - Static variable in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
All features are selected by this filter.
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.
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.
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(FeatureFilter.And, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
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(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils
Constructs a new filter which matches the intersection of a set of filters.
and - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
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
Annotatable.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.
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 - Static variable in interface org.biojava.bio.Annotatable
Signals that the associated Annotation has altered in some way.
Annotation - Interface in org.biojava.bio
Arbitrary annotation associated with one or more objects.
annotation - Variable in class org.biojava.bio.seq.Feature.Template
 
annotation - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
 
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.
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
 
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.Abstract() - Constructor for class org.biojava.bio.AnnotationType.Abstract
 
AnnotationType.Impl - Class in org.biojava.bio
An implementation of AnnotationType.
AnnotationType.Impl() - Constructor for class org.biojava.bio.AnnotationType.Impl
Create a new Impl with no constraints.
AnnotationType.Impl(PropertyConstraint, Location) - Constructor for class org.biojava.bio.AnnotationType.Impl
Create a new Impl with a default property and cardinality constraint.
AnnotationType.Impl(CollectionConstraint) - Constructor for class org.biojava.bio.AnnotationType.Impl
Create a new Impl with a default collection constraint.
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(T, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
Append the specified FASTQ formatted sequences to the specified appendable.
append(T, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
Append the specified FASTQ formatted sequences to the specified appendable.
append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel
 
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 distributions.
areEmissionSpectraEqual(Distribution[], Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
Compares the emission spectra of two distribution arrays.
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(Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
Creates a new ArrowGlyph, which is filled with the given color.
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.
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(Throwable) - Constructor for error org.biojava.utils.AssertionFailure
 
AssertionFailure(String, Throwable) - Constructor for error org.biojava.utils.AssertionFailure
 
AtomicSymbol - Interface in org.biojava.bio.symbol
A symbol that is not ambiguous.
attemptClose(Statement) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Attempt to close the Statement.
attemptClose(ResultSet) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
Deprecated.
Attempt to close the ResultSet.
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, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
attribute(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.
attribute(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
Add an un-qualified 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.
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, BackPointer, double) - Constructor for class org.biojava.bio.dp.BackPointer
 
BackPointer(State) - Constructor for class org.biojava.bio.dp.BackPointer
 
backPointers - Variable in class org.biojava.bio.dp.twohead.Cell
 
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
 
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
backward(DPCursor, 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[], ScoreType) - Method in class org.biojava.bio.dp.DP
 
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
 
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
backwardMatrix(SymbolList[], DPMatrix, 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
 
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.
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(Throwable) - Constructor for exception org.biojava.bibliography.BibRefException
Create a new BibRefException with a root cause.
BibRefException(String, Throwable) - Constructor for exception org.biojava.bibliography.BibRefException
Create a nw BibRefException with a message and 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(long) - Static method in class org.biojava.bio.symbol.PackingFactory
 
binary(int) - 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(Name, Object) - Method in class org.biojava.naming.ObdaContext
 
bind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
 
bind(String, Object) - Method in class org.biojava.naming.ObdaContext
 
bind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
 
bindSymbol(Symbol, String) - Method in class org.biojava.bio.seq.io.AlternateTokenization
Bind a Symbol to a string.
bindSymbol(Symbol, char) - Method in class org.biojava.bio.seq.io.CharacterTokenization
Bind a Symbol to a character.
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(String) - Constructor for error org.biojava.bio.BioError
Create a new BioError with 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.
BioError(String, Throwable) - Constructor for error org.biojava.bio.BioError
Create a new BioError with a cause and a message.
BioError() - Constructor for error org.biojava.bio.BioError
Create a new BioError.
BioException - Exception in org.biojava.bio
A nestable biological exception.
BioException(String) - Constructor for exception org.biojava.bio.BioException
Create a new BioException with 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
BioException(String, Throwable) - Constructor for exception org.biojava.bio.BioException
Create a new BioException with a cause and a message.
BioException() - Constructor for exception org.biojava.bio.BioException
Create a new BioException.
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, String, int) - Constructor for class org.biojava.bio.seq.db.BioIndex
 
BioIndex(File) - Constructor for class org.biojava.bio.seq.db.BioIndex
Load an existing index file.
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
biojavaToFile(int, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools
Deprecated.
Converts a Biojava object to the given filetype.
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(String) - Constructor for exception org.biojava.bio.BioRuntimeException
Create a new BioRuntimeException with 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
BioRuntimeException(String, Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException
Create a new BioRuntimeException with a cause and a message.
BioRuntimeException() - Constructor for exception org.biojava.bio.BioRuntimeException
Create a new BioRuntimeException.
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.And(BioSQLFeatureFilter, BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
BioSQLFeatureFilter.ByName - Class in org.biojavax.bio.db.biosql
Construct one of these to filter features by display name.
BioSQLFeatureFilter.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.
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.ByNote(Note) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
 
BioSQLFeatureFilter.ByNoteTermOnly - Class in org.biojavax.bio.db.biosql
A filter that returns all features that have a note with the given term.
BioSQLFeatureFilter.ByNoteTermOnly(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
 
BioSQLFeatureFilter.ByRank - Class in org.biojavax.bio.db.biosql
Construct one of these to filter features by rank.
BioSQLFeatureFilter.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.
BioSQLFeatureFilter.BySequenceName - Class in org.biojavax.bio.db.biosql
Accept features that reside on a sequence with a particular name.
BioSQLFeatureFilter.BySequenceName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
 
BioSQLFeatureFilter.BySourceTerm - Class in org.biojavax.bio.db.biosql
Construct one of these to filter features by source.
BioSQLFeatureFilter.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.
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.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.
BioSQLFeatureFilter.ByStrand - Class in org.biojavax.bio.db.biosql
A filter that returns all features having locations on a given strand.
BioSQLFeatureFilter.ByStrand(RichLocation.Strand) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
Creates a filter that returns everything on strand str.
BioSQLFeatureFilter.ByTypeTerm - Class in org.biojavax.bio.db.biosql
Construct one of these to filter features by type.
BioSQLFeatureFilter.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.
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.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.
BioSQLFeatureFilter.ContainedByRichLocation - Class in org.biojavax.bio.db.biosql
A filter that returns all features contained within a location.
BioSQLFeatureFilter.ContainedByRichLocation(RichLocation) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
Creates a filter that returns everything contained within loc.
BioSQLFeatureFilter.HibernateFeatureFilter - Class in org.biojavax.bio.db.biosql
A filter for Hibernate-BioSQL filters to extend.
BioSQLFeatureFilter.HibernateFeatureFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
 
BioSQLFeatureFilter.Not - Class in org.biojavax.bio.db.biosql
A filter that returns all features not accepted by a child filter.
BioSQLFeatureFilter.Not(BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
 
BioSQLFeatureFilter.Or - Class in org.biojavax.bio.db.biosql
A filter that returns all features accepted by at least one child filter.
BioSQLFeatureFilter.Or(BioSQLFeatureFilter, BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
BioSQLFeatureFilter.OverlapsRichLocation - Class in org.biojavax.bio.db.biosql
A filter that returns all features overlapping a location.
BioSQLFeatureFilter.OverlapsRichLocation(RichLocation) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
Creates a filter that returns everything overlapping loc.
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).
BioSQLFeatureFilter.Tools() - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools
 
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, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
Deprecated.
Connect to a BioSQL database.
BioSQLSequenceDB(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.And(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.And
 
BlastLikeSearchFilter.ByHitProperty - Class in org.biojava.bio.search
Applies test to the value specified by the key in hit properties.
BlastLikeSearchFilter.ByHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
 
BlastLikeSearchFilter.BySearchProperty - Class in org.biojava.bio.search
Applies test to the value specified by the key in search properties.
BlastLikeSearchFilter.BySearchProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
 
BlastLikeSearchFilter.BySubHitProperty - Class in org.biojava.bio.search
Applies test to the value specified by the key in subhit properties.
BlastLikeSearchFilter.BySubHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
 
BlastLikeSearchFilter.Node - Interface in org.biojava.bio.search
 
BlastLikeSearchFilter.Not - Class in org.biojava.bio.search
 
BlastLikeSearchFilter.Not(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.Not
 
BlastLikeSearchFilter.Or - Class in org.biojava.bio.search
 
BlastLikeSearchFilter.Or(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.Or
 
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.
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.biojava.bio.symbol.SimpleGappedSymbolList
Get list of the un-gapped region of the SymbolList.
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.
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
 
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, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
 
buildDataStore(File, SequenceStreamer, Packing, int, 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.
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
 
byAncestor(FeatureFilter.ByAncestor, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
byAncestor(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where at least one of the ancestors matches the specified filter.
byAnnotation(Object, Object) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where the annotation property named key is equal to value.
byAnnotationType(AnnotationType) - Static method in class org.biojava.bio.seq.FilterUtils
Match features with annotations matching the specified AnnotationType
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.
byChild(FeatureFilter.ByChild, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
byChild(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where at least one child feature matches the supplied filter.
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.
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
byDescendant(FeatureFilter.ByDescendant, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
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.
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
 
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.
byName - Static variable in interface org.biojava.bio.seq.db.IDMaker
A simple implementation of IDMaker that hashes by sequence name.
byPairwiseScore(double, double) - Static method in class org.biojava.bio.seq.FilterUtils
Match SeqSimilaritiy features with scores in the specified range.
byParent(FeatureFilter.ByParent, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
byParent(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
Match features where the parent feature matches the specified filter.
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.
bySearchProperty(BlastLikeSearchFilter.BySearchProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
 
bySequenceName(String) - Static method in class org.biojava.bio.seq.FilterUtils
Match features attached to sequences with a specified name.
bySource(String) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features with a specific source value.
byStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.FilterUtils
Match StrandedFeatures on the specified strand.
bySubHitCount - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit
bySubHitCount contains a SeqSimilaritySearchHit comparator which compares by their number of sub-hits.
bySubHitProperty(BlastLikeSearchFilter.BySubHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
 
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.
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
 
byType(String) - Static method in class org.biojava.bio.seq.FilterUtils
Construct a filter which matches features with a specific type value.
byURN - Static variable in interface org.biojava.bio.seq.db.IDMaker
A simple implementation of IDMaker that hashes by URN.

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 - Interface in org.biojava.utils.cache
Interface for managing caches of objects.
cache - Variable in class org.biojava.utils.io.CachingInputStream
The byte cache itself.
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(Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
 
CandyException(String, 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(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat
Check to see if a given file is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
Check to see if a given stream 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(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
Check to see if a given stream 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(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
Check to see if a given stream 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(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
Check to see if a given stream 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(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
Check to see if a given stream 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(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
Check to see if a given stream 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(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
Check to see if a given stream 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.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
Check to see if a given stream 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
change(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
 
change(Object, Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
 
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_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.
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.
ChangeForwarder.Retyper(Object, ChangeSupport, ChangeType) - Constructor for class org.biojava.utils.ChangeForwarder.Retyper
Create a new Retyper for forwarding events.
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.AlwaysVetoListener() - Constructor for class org.biojava.utils.ChangeListener.AlwaysVetoListener
Private constructor.
ChangeListener.ChangeEventRecorder - Class in org.biojava.utils
A listener that remembers the ChangeEvent of the last change.
ChangeListener.ChangeEventRecorder() - Constructor for class org.biojava.utils.ChangeListener.ChangeEventRecorder
 
ChangeListener.LoggingListener - Class in org.biojava.utils
A listener that writes information about the event stream to a PrintStream.
ChangeListener.LoggingListener(PrintStream) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener
Create a LoggingListener that will log all events to 'out'.
ChangeListener.LoggingListener(PrintStream, String) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener
Create a LoggingListener that will log all events to 'out' with a prefix.
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.ChainedChanger(ChangeTable.Changer[]) - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
 
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, Field, 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, 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, String, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
 
ChangeType(String, String, String) - 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(ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException
Construct an exception to veto a change without explanation.
ChangeVetoException(String) - Constructor for exception org.biojava.utils.ChangeVetoException
Create an exception with a detail message
ChangeVetoException(ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException
Construct an exception to veto a change for a specified reason.
ChangeVetoException(Throwable, ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException
Propogate an exception without (additional) explanation.
ChangeVetoException(Throwable, String) - Constructor for exception org.biojava.utils.ChangeVetoException
Deprecated.
use new ChangeVetoException(reason, ex);
ChangeVetoException(String, Throwable) - Constructor for exception org.biojava.utils.ChangeVetoException
 
ChangeVetoException(Throwable, ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException
Propogate an exception, giving a detail message
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(CircularRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
 
CircularPaddedRenderer(double, double) - 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(Throwable) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
Deprecated.
 
CircularReferenceException(String) - 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, FeatureRealizer) - Constructor for class org.biojava.bio.seq.CircularView
 
CircularView(Sequence) - 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.
ClassifierExample.PointClassifier() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Make a new PointClassifier.
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() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Learn a model from the current points.
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(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.DistributionTrainer
Clears all of the counts to zero.
clearCounts() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
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.
 
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.
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.
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, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
closeTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
closeTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
Closes an element
closeTag(String) - Method in interface org.biojava.utils.xml.XMLWriter
Closes an un-qualified 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.AcceptAll() - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
 
CodonPrefFilter.ByName - Class in org.biojava.bio.symbol
 
CodonPrefFilter.ByName(String) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.ByName
 
CodonPrefFilter.EverythingToXML - Class in org.biojava.bio.symbol
 
CodonPrefFilter.EverythingToXML(PrintWriter) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
 
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.AllValuesIn(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.AllValuesIn
Create an AllValuesIn based upon a PropertyConstraint and a cardinality.
CollectionConstraint.And - Class in org.biojava.bio
A collection constraint that accpepts collections iff they are accepted by both child constraints.
CollectionConstraint.And(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.And
Create a new And from two child constraints.
CollectionConstraint.Contains - Class in org.biojava.bio
CollectionConstraint which validates a portion of a Collection.
CollectionConstraint.Contains(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.Contains
Create a Contains based upon a PropertyConstraint and a cardinality.
CollectionConstraint.Or - Class in org.biojava.bio
A collection constraint that accepts items iff they are accepted by either child constraints.
CollectionConstraint.Or(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.Or
Create a new Or from two 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() - 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 - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
columns() - Method in interface org.biojava.bio.dp.WeightMatrix
The number of columns modeled by the weight matrix.
COMMENT - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
COMMENT - Static variable in interface org.biojavax.bio.BioEntry
 
Comment - Interface in org.biojavax
A simple ranked comment designed to be used for BioEntry comments in BioSQL.
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(Throwable) - Constructor for exception org.biojava.utils.CommitFailure
 
CommitFailure(String, 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(Synonym) - Method in class org.biojava.ontology.Synonym
 
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.
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(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
Retrieve a complement view of list.
COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
 
complement(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools
Retrieve a complement view of list.
complement(Symbol) - Static method in class org.biojava.bio.seq.RNATools
Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
Retrieve a complement view of list.
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.
ComponentFeature.Template() - Constructor for class org.biojava.bio.seq.ComponentFeature.Template
 
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(Name, Name) - Method in class org.biojava.naming.ObdaContext
 
composeName(String, String) - Method in class org.biojava.naming.ObdaContext
 
Composition - Class in org.biojava.bio.molbio
Computes composition statistics about a SymbolList.
Composition() - Constructor for class org.biojava.bio.molbio.Composition
 
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(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.
CompoundRichLocation() - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
 
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(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.
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.
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
 
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.
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(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
 
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
contains(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
contains(int) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
 
contains(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet
Returns whether or not this Alphabet contains the symbol.
contains(int) - Method in class org.biojava.bio.symbol.CircularLocation
 
contains(Location) - Method in class org.biojava.bio.symbol.CircularLocation
 
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
contains(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
contains(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
contains(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
contains(Location) - Method in interface org.biojava.bio.symbol.Location
Checks if this location contains the other.
contains(int) - Method in interface org.biojava.bio.symbol.Location
Checks if this location contains a point.
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(int) - Method in class org.biojava.bio.symbol.PointLocation
 
contains(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
 
contains(String) - Method in interface org.biojava.utils.candy.CandyVocabulary
It checks if a given entry exists in this vocabulary.
contains(Object) - Method in class org.biojava.utils.MergingSet
 
contains(Object) - Method in class org.biojava.utils.SmallSet
 
contains(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Checks if this location contains a point.
contains(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
Checks if this location contains the other.
contains(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Checks if this location contains a point.
contains(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
Checks if this location contains the other.
contains(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Checks if this location contains a point.
contains(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
Checks if this location contains the other.
contains(Note) - Method in class org.biojavax.EmptyRichAnnotation
Returns true if the given note exists in this annotation.
contains(Object) - Method in class org.biojavax.ga.util.WeightedSet
 
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_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(FeatureFilter) - Static method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools
Convert a non-BioSQL FeatureFilter into a BioSQL one.
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(InputStream) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
Creates a new Chromatogram object from the supplied stream.
create(File) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
Create a new ABIF object from a file.
create(InputStream) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
Create a new ABIF object from a stream of bytes.
create(File) - Static method in class org.biojava.bio.program.scf.SCF
 
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(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
Create and return a new DNA SymbolList from the specified FASTQ formatted sequence.
createDNA(String) - Static method in class org.biojava.bio.seq.DNATools
Return a new DNA SymbolList 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.
createDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools
Return a new DNA Sequence for dna.
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(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
Deprecated.
Please use new 1-arg createFeature instead.
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, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Create a new projected feature.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
createFeature(Feature, 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.
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(List) - Static method in class org.biojava.utils.ListTools
 
createList(Object[]) - Static method in class org.biojava.utils.ListTools
 
createMatches() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
 
createMethod(String, CodeClass, CodeClass[], String[], int) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
Create a new method.
createMethod(String, CodeClass, CodeClass[], 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(Taxon, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
Create an orthologue.
createOrthologue(int, 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
 
createOrthologue(int, String, String, 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, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
Create a curated orthology entry.
createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
 
createOrthoPair(Orthologue, Orthologue, String) - 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(SymbolList, boolean, SymbolList, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
Creates and registers a new Protease.
createProtease(SymbolList, 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(String, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
 
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, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
Create a new RichSequence in the default namespace.
createRichSequence(String, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
Create a new RichSequence in the specified 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(String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
Create a new RichSequence in the default 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(Name) - Method in class org.biojava.naming.ObdaContext
 
createSubcontext(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
 
createSubcontext(String) - Method in class org.biojava.naming.ObdaContext
 
createSubcontext(String, Attributes) - Method in class org.biojava.naming.ObdaContext
 
createSwissprotParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
 
createSymbol(String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generate a new AtomicSymbol instance with a name and Annotation.
createSymbol(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generate a new AtomicSymbol instance with a name and an Empty Annotation.
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(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(char, Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Deprecated.
use the three-arg version of this method instead.
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, String) - Method in class org.biojava.ontology.IntegerOntology
 
createTerm(String, String, Object[]) - 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, String) - Method in interface org.biojava.ontology.Ontology
Create a new term in this ontology.
createTerm(String, String, Object[]) - 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, String) - Method in class org.biojava.ontology.Ontology.Impl
 
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.
createTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
Create a new term in this ontology.
createTerm(String, String) - 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, FeatureFilter, Set) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
Create a new type in this repository.
createType(String) - Static method in class org.biojava.utils.bytecode.ParametricType
Create a new ParametricType that claims nothing.
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
CrossOverFunction.NoCross() - Constructor for class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
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 - Static variable in interface org.biojavax.bio.seq.RichFeature
 
CrossRef - Interface in org.biojavax
Represents a cross reference to another database.
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
 
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.
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
 
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(String) - Method in interface org.biojava.bio.program.fastq.ParseListener
Notify this parse listener of a description line.
description - Variable in class org.biojava.ontology.AbstractTerm
 
description - Variable in class org.biojava.utils.candy.CandyEntry
A value of this entry.
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(Name) - Method in class org.biojava.naming.ObdaContext
 
destroySubcontext(String) - 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 - Static variable in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
DIGEST - Static variable in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
 
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
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, double) - Static method in class org.biojava.bio.dist.DistributionTools
Creates an array of distributions, one for each column of the alignment.
distOverAlignment(Alignment, boolean) - 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
Distribution.NullModelForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.dist.Distribution.NullModelForwarder
Deprecated.
Create a new forwarder.
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.
DistributionFactory.DefaultDistributionFactory() - Constructor for class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
 
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
 
domain1 - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
DOMAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
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.DoubleRange(double, double) - Constructor for class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
 
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
 
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 - Class in org.biojava.bio.dp
Objects that can perform dymamic programming operations upon sequences with HMMs.
DP(MarkovModel) - Constructor for class org.biojava.bio.dp.DP
 
DP() - Constructor for class org.biojava.bio.dp.DP
This method will result in a DP with no model.
dp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
dp - Static variable in class org.biojavax.bio.seq.io.FastaFormat
 
DP.ReverseIterator - Class in org.biojava.bio.dp
 
DP.ReverseIterator(SymbolList) - Constructor for class org.biojava.bio.dp.DP.ReverseIterator
 
dp_ipi - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
dp_uniprot - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
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
 
DPFactory.DefaultFactory(CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.DPFactory.DefaultFactory
 
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
 
DPInterpreter.Maker() - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter.Maker
 
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(FiniteAlphabet, int) - Constructor for class org.biojava.bio.symbol.DummySymbolList
 
DummySymbolList(Alphabet, int, Symbol) - 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
 
EcNumber - Interface in org.biojava.bio
An ec (enzyme classification) number.
EcNumber.Impl - Class in org.biojava.bio
A simple implementation of EcNumber.
EcNumber.Impl(int, int, int, int) - Constructor for class org.biojava.bio.EcNumber.Impl
Make a new EcNumber.Impl with the data provided.
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 - 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, Alphabet, Symbol) - Constructor for class org.biojava.bio.symbol.Edit
Convenience construtor for making single residue changes
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 - Static variable in interface org.biojava.bio.symbol.SymbolList
Signals that the SymbolList is being edited.
edit(Edit) - Method in interface org.biojava.bio.symbol.SymbolList
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(Edit) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Apply an edit to the SymbolList 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(Edit) - Method in class org.biojavax.bio.seq.ThinRichSequence
Apply an edit to the SymbolList as specified by the edit object.
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
 
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() - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
 
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.seq.io.agave
 
ElementRecognizer.AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
 
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.seq.io.game
 
ElementRecognizer.AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
 
ElementRecognizer.ByLocalName - Class in org.biojava.bio.program.xff
Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
 
ElementRecognizer.ByLocalName - Class in org.biojava.bio.seq.io.agave
Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
 
ElementRecognizer.ByLocalName - Class in org.biojava.bio.seq.io.game
Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
 
ElementRecognizer.ByNSName - Class in org.biojava.bio.program.xff
Filter elements by name and namespace.
ElementRecognizer.ByNSName(String, String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
 
ElementRecognizer.ByNSName - Class in org.biojava.bio.seq.io.agave
Filter elements by name and namespace.
ElementRecognizer.ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
 
ElementRecognizer.ByNSName - Class in org.biojava.bio.seq.io.game
Filter elements by name and namespace.
ElementRecognizer.ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
 
ElementRecognizer.HasAttribute - Class in org.biojava.bio.program.xff
Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
 
ElementRecognizer.HasAttribute - Class in org.biojava.bio.seq.io.agave
Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute
 
ElementRecognizer.HasAttribute - Class in org.biojava.bio.seq.io.game
Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute
 
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.
Embl2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave
Map EMBL data into AGAVE format
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
 
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, 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, 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.
EMBLFormat.Terms() - Constructor for class org.biojavax.bio.seq.io.EMBLFormat.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
EmblProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.EmblProcessor.Factory
Deprecated.
 
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