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 _
All Classes All Packages
All Classes All Packages
A
- a() - Static method in class org.biojava.bio.seq.DNATools
- a() - Static method in class org.biojava.bio.seq.NucleotideTools
- a() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the
AtomicSymbol
for the amino acid Alanine - a() - Static method in class org.biojava.bio.seq.RNATools
- A_THALIANA - Static variable in interface org.biojava.bio.program.homologene.Taxon
- AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
AA
indicates that a sequence contains AA (amino acid) symbols. - AAindex - Class in org.biojava.bio.proteomics.aaindex
-
Symbol property table based on the Amino Acid Index Database.
- AAindex(String) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindex
-
Initializes the AAindex symbol property table.
- AAindexStreamReader - Class in org.biojava.bio.proteomics.aaindex
-
Iterator over
AAindex
objects that are stored in a stream in the AAindex1 file format. - AAindexStreamReader(BufferedReader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
-
Initializes the iterator.
- AAindexStreamReader(Reader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
-
Initializes the iterator.
- ABBREV_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
- abbreviation - Variable in class org.biojava.bibliography.BiblioJournal
-
An abbreviation of the journal title.
- ABI_MAGIC - Static variable in class org.biojava.bio.chromatogram.ChromatogramFactory
-
The magic number for ABIF files.
- ABIFChromatogram - Class in org.biojava.bio.program.abi
-
An implementation of
Chromatogram
to encapulsulate chromatogram data extracted from the files produced by ABI sequencers, such as the the 377 and the 3700. - ABIFChromatogram() - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram
- ABIFChromatogram.Parser - Class in org.biojava.bio.program.abi
-
An extension of
ABIFParser
that reads the particular fields from the ABIF that contain the chromatogram data and initializes the fields in its enclosingABIFChromatogram
instance. - ABIFParser - Class in org.biojava.bio.program.abi
-
A general base parser for files produced by ABI software.
- ABIFParser(File) - Constructor for class org.biojava.bio.program.abi.ABIFParser
-
Creates a new ABIFParser for a file.
- ABIFParser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFParser
-
Creates a new ABIFParser for an input stream.
- ABIFParser(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser
-
Creates a new ABIFParser for the specified
ABIFParser.DataAccess
object. - ABIFParser.DataAccess - Interface in org.biojava.bio.program.abi
- ABIFParser.TaggedDataRecord - Class in org.biojava.bio.program.abi
-
An aggregate immutable type for an ABIF tagged data record.
- ABITools - Class in org.biojava.bio.program.abi
-
Useful functionality for working with fasta files where the quality of the DNA is encoded as upper and lower case DNA characters.
- ABITools() - Constructor for class org.biojava.bio.program.abi.ABITools
- ABITrace - Class in org.biojava.bio.program.abi
-
Title: ABITrace
ABITrace is a class for managing ABI file information, it is capable of opening an ABI file and storing the most important fields, which can be recalled as simple java types. - ABITrace(byte[]) - Constructor for class org.biojava.bio.program.abi.ABITrace
-
The
byte[]
constructor parses an ABI file represented as a byte array. - ABITrace(File) - Constructor for class org.biojava.bio.program.abi.ABITrace
-
The File constructor opens a local ABI file and parses the content.
- ABITrace(URL) - Constructor for class org.biojava.bio.program.abi.ABITrace
-
The URL constructor opens an ABI file from any URL.
- AbiTraceRenderer - Class in org.biojava.bio.gui.sequence
-
Renders an ABI trace file as a chromatogram graph.
- AbiTraceRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbiTraceRenderer
- ABORT_PARSING - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
- AbortErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
- Abstract() - Constructor for class org.biojava.bio.AnnotationType.Abstract
- Abstract() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
- Abstract() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
- Abstract(String) - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
-
Construct a block with a given name.
- Abstract(NexusBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
- AbstractAlignmentStyler - Class in org.biojava.bio.program.blast2html
-
Abstract implementation of
AlignmentStyler
, contains utility methods for generating a set of HTML styles from a list of RGB colours. - AbstractAlignmentStyler() - Constructor for class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
- AbstractAlphabet - Class in org.biojava.bio.symbol
-
An abstract implementation of
Alphabet
. - AbstractAlphabet() - Constructor for class org.biojava.bio.symbol.AbstractAlphabet
- AbstractAnnotation - Class in org.biojava.bio
-
A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
- AbstractAnnotation() - Constructor for class org.biojava.bio.AbstractAnnotation
-
Protected no-args constructor intended for sub-classes.
- AbstractAnnotation(Map) - Constructor for class org.biojava.bio.AbstractAnnotation
-
Create a new Annotation by copying the key-value pairs from a map.
- AbstractAnnotation(Annotation) - Constructor for class org.biojava.bio.AbstractAnnotation
-
Copy-constructor.
- AbstractBeadRenderer - Class in org.biojava.bio.gui.sequence
-
AbstractBeadRenderer
is a an abstract base class for the creation ofFeatureRenderer
s which use a 'string of beads' metaphor for displaying features. - AbstractBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
Creates a new
AbstractBeadRenderer
with no delegates. - AbstractBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
Creates a new
AbstractBeadRenderer
object. - AbstractBioEntryDB - Class in org.biojavax.bio.db
-
An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.
- AbstractBioEntryDB() - Constructor for class org.biojavax.bio.db.AbstractBioEntryDB
- AbstractChangeable - Class in org.biojava.utils
-
Useful base-class for objects implementing Changeable
- AbstractChangeable() - Constructor for class org.biojava.utils.AbstractChangeable
- AbstractChromatogram - Class in org.biojava.bio.chromatogram
-
A basic, abstract implementation of
Chromatogram
. - AbstractChromatogram() - Constructor for class org.biojava.bio.chromatogram.AbstractChromatogram
-
Create a new AbstractChromatogram.
- AbstractCrossOverFunction - Class in org.biojavax.ga.functions
-
Abstract implementation of
CrossOverFunction
. - AbstractCrossOverFunction() - Constructor for class org.biojavax.ga.functions.AbstractCrossOverFunction
- AbstractDistribution - Class in org.biojava.bio.dist
-
An abstract implementation of Distribution.
- AbstractDistribution() - Constructor for class org.biojava.bio.dist.AbstractDistribution
- AbstractFeatureHolder - Class in org.biojava.bio.seq
-
An abstract implementation of FeatureHolder.
- AbstractFeatureHolder() - Constructor for class org.biojava.bio.seq.AbstractFeatureHolder
- AbstractGeneticAlgorithm - Class in org.biojavax.ga.impl
-
Base class from which most implementations of GeneticAlgorithm will inherit.
- AbstractGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.AbstractGeneticAlgorithm
- AbstractLocation - Class in org.biojava.bio.symbol
-
An abstract implementation of
Location
. - AbstractLocation() - Constructor for class org.biojava.bio.symbol.AbstractLocation
- AbstractLocationDecorator - Class in org.biojava.bio.symbol
-
Abstract
Location
decorator (wrapper). - AbstractLocationDecorator(Location) - Constructor for class org.biojava.bio.symbol.AbstractLocationDecorator
-
Construct a new decorator wrapping the specified Location.
- AbstractManyToOneTranslationTable - Class in org.biojava.bio.symbol
-
an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
- AbstractManyToOneTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
- AbstractMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
- AbstractMatrixPairDPCursor(SymbolList, SymbolList, int, int, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
- AbstractMutationFunction - Class in org.biojavax.ga.functions
-
Abstract implementation of
MutationFunction
all custom implementations should inherit from here. - AbstractMutationFunction() - Constructor for class org.biojavax.ga.functions.AbstractMutationFunction
- AbstractOrderNDistribution - Class in org.biojava.bio.dist
-
Simple base class for OrderNDistributions.
- AbstractOrderNDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.AbstractOrderNDistribution
-
Construct a new NthOrderDistribution.
- AbstractOrganism - Class in org.biojavax.ga.impl
-
Abstract implementation of Organism.
- AbstractOrganism() - Constructor for class org.biojavax.ga.impl.AbstractOrganism
- AbstractOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.AbstractOrganism
- AbstractOrthologueSet - Class in org.biojava.bio.program.homologene
- AbstractOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthologueSet
- AbstractOrthoPairCollection - Class in org.biojava.bio.program.homologene
-
An abstract implementation of the OrthoPairCollection interface.
- AbstractOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
- AbstractOrthoPairSet - Class in org.biojava.bio.program.homologene
-
represents the Homologene Group.
- AbstractOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairSet
- AbstractPeptideDigestRenderer - Class in org.biojava.bio.gui.sequence
-
A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.
- AbstractPeptideDigestRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
- AbstractPeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
- AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
- AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
- AbstractPopulation - Class in org.biojavax.ga.impl
-
Most Population implementations will want to inherit from here.
- AbstractPopulation() - Constructor for class org.biojavax.ga.impl.AbstractPopulation
- AbstractPopulation(String) - Constructor for class org.biojavax.ga.impl.AbstractPopulation
- AbstractRangeLocation - Class in org.biojava.bio.symbol
-
Base class for simple contiguous Location implementations.
- AbstractRangeLocation() - Constructor for class org.biojava.bio.symbol.AbstractRangeLocation
- AbstractReversibleTranslationTable - Class in org.biojava.bio.symbol
-
an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
- AbstractReversibleTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractReversibleTranslationTable
- AbstractRichSequenceDB - Class in org.biojavax.bio.db
-
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
- AbstractRichSequenceDB() - Constructor for class org.biojavax.bio.db.AbstractRichSequenceDB
- AbstractSequenceDB - Class in org.biojava.bio.seq.db
-
An abstract implementation of SequenceDB that provides the sequenceIterator method.
- AbstractSequenceDB() - Constructor for class org.biojava.bio.seq.db.AbstractSequenceDB
- AbstractSVMClassifierModel - Class in org.biojava.stats.svm
-
Abstract implementation of SVMClassifierModel.
- AbstractSVMClassifierModel() - Constructor for class org.biojava.stats.svm.AbstractSVMClassifierModel
- AbstractSVMTarget - Class in org.biojava.stats.svm
-
An abstract implementation of an SVMModel.
- AbstractSVMTarget() - Constructor for class org.biojava.stats.svm.AbstractSVMTarget
- AbstractSymbol - Class in org.biojava.bio.symbol
-
The base-class for Symbol implementations.
- AbstractSymbol() - Constructor for class org.biojava.bio.symbol.AbstractSymbol
- AbstractSymbolList - Class in org.biojava.bio.symbol
-
Abstract helper implementation of the SymbolList core interface.
- AbstractSymbolList() - Constructor for class org.biojava.bio.symbol.AbstractSymbolList
- AbstractSymbolList.EditScreener - Class in org.biojava.bio.symbol
-
This adapter screens all edit events to see if they overlap with a window of interest.
- AbstractSymbolList.EditTranslater - Class in org.biojava.bio.symbol
-
This translates edit events that fall within a window into window co-ordinates.
- AbstractTaxon - Class in org.biojava.bio.taxa
-
Deprecated.replaced by classes in
org.biojavax.bio.taxa
- AbstractTaxon() - Constructor for class org.biojava.bio.taxa.AbstractTaxon
-
Deprecated.
- AbstractTaxon(String, String) - Constructor for class org.biojava.bio.taxa.AbstractTaxon
-
Deprecated.
- AbstractTerm - Class in org.biojava.ontology
-
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
- AbstractTerm() - Constructor for class org.biojava.ontology.AbstractTerm
- AbstractTrainer - Class in org.biojava.bio.dp
-
An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.
- AbstractTrainer() - Constructor for class org.biojava.bio.dp.AbstractTrainer
- AbstractTrainer(DP) - Constructor for class org.biojava.bio.dp.AbstractTrainer
- abstractType - Variable in class org.biojava.bibliography.BiblioDescription
-
It specifies how
BiblioDescription.theAbstract
is coded. - AbstractULAlignment - Class in org.biojava.bio.alignment
- AbstractULAlignment() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment
- AbstractULAlignment.LeftRightLocationComparator<T> - Class in org.biojava.bio.alignment
-
Orders by location left to right.
- AbstractULAlignment.SubULAlignment - Class in org.biojava.bio.alignment
- AbstractWrapper - Class in org.biojava.bio.program.tagvalue
-
An abstract TagValueWrapper that does nothing!
- AbstractWrapper() - Constructor for class org.biojava.bio.program.tagvalue.AbstractWrapper
- ACC_ABSTRACT - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_FINAL - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_INTERFACE - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_NATIVE - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_PRIVATE - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_PROTECTED - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_PUBLIC - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_STATIC - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_STRICT - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_SUPER - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_SYNCHRONIZED - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_TRANSIENT - Static variable in class org.biojava.utils.bytecode.CodeUtils
- ACC_VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- ACC_VOLATILE - Static variable in class org.biojava.utils.bytecode.CodeUtils
- accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
- accept() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter
-
returns a TriState indicating the current outcome of evaluating this filter.
- accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.And
- accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
- accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Or
- accept(Object) - Method in interface org.biojava.bio.CollectionConstraint
-
accept
returns true if the value fulfills the constraint. - accept(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
- accept(Object) - Method in class org.biojava.bio.CollectionConstraint.And
- accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
- accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Or
- accept(Object) - Method in interface org.biojava.bio.PropertyConstraint
-
accept
returns true if the value fulfills the constraint. - accept(Object) - Method in class org.biojava.bio.PropertyConstraint.And
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByClass
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Or
- accept(Object) - Method in interface org.biojava.bio.search.FilterTest
- accept(Object) - Method in class org.biojava.bio.search.FilterTest.Equals
- accept(Object) - Method in class org.biojava.bio.search.FilterTest.FindRegex
- accept(Object) - Method in class org.biojava.bio.search.FilterTest.GreaterThan
- accept(Object) - Method in class org.biojava.bio.search.FilterTest.LessThan
- accept(Object) - Method in class org.biojava.bio.search.FilterTest.MatchRegex
- accept(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFRecordFilter
-
Return whether or not to accept record.
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
- accept(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueFilter
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.And
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Not
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Or
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Xor
- accept(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairFilter
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.And
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Not
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Or
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Xor
- accept(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairSetFilter
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor
- accept(Feature) - Method in interface org.biojava.bio.seq.FeatureFilter
-
This method determines whether a feature is to be accepted.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.And
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
-
Accept a Feature if it is an instance of SimilarityPairFeature and its score is <= filter's minimum score and >= filter's maximum score.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
-
Returns true if the feature has a matching type property.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
-
Returns true if the feature is within this filter's location.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
-
Accept the Feature if it is an instance of FramedFeature and matches the value of getFrame().
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Not
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Or
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
-
Returns true if the feature overlaps this filter's location.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
-
Returns true if the feature is within this filter's location.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
-
Returns true if the feature overlaps this filter's location.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
-
Accept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
-
Returns true if the feature has a matching type property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
-
Returns true if the feature has a matching type property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
-
Returns true if the feature has a matching source property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
-
Returns true if the feature has a matching source property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
-
Returns true if the feature overlaps this filter's location.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
-
Returns true if the feature has a matching type property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
-
Returns true if the feature has a matching type property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
-
Returns true if the feature is within this filter's location.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
-
Returns true if the feature overlaps this filter's location.
- ACCEPT_ALL - Static variable in interface org.biojava.bio.program.gff.GFFRecordFilter
-
A GFFRecordFilter that accepts everything.
- AcceptAll() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
- AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
- AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
- AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
- AcceptAll() - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
- ACCESSION - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
- ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
- ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
- ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- accessionNumber() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Gets the accession number of the AAindex entry.
- AcnumHitReader - Class in org.biojava.bio.seq.db.emblcd
-
AcnumHitReader
reads the "acnum.hit" file of an EMBL CD-ROM format binary index. - AcnumHitReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumHitReader
-
Creates a new
AcnumHitReader
. - AcnumTrgReader - Class in org.biojava.bio.seq.db.emblcd
-
AcnumTrgReader
reads the "acnum.trg" file of an EMBL CD-ROM format binary index. - AcnumTrgReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumTrgReader
-
Creates a new
AcnumTrgReader
. - ACRONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
-
Use this to define acronyms for things.
- ACRONYM - Static variable in interface org.biojavax.Namespace
- activityFailed(Object, Exception) - Method in interface org.biojava.utils.ActivityListener
-
Notification of errors behind the scenes.
- ActivityListener - Interface in org.biojava.utils
-
Interface for object which monitor long-running activities.
- activityProgress(Object, int, int) - Method in interface org.biojava.utils.ActivityListener
-
Estimated progress of an activity.
- add(int, CodeGenerator) - Method in class org.biojava.utils.bytecode.InstructionVector
- add(Object) - Method in class org.biojava.utils.FileAsList
- add(Object) - Method in class org.biojava.utils.MergingSet
- add(Object) - Method in class org.biojava.utils.SmallSet
- add(Object) - Method in class org.biojavax.ga.util.WeightedSet
-
Adds a new
Object
with a weight of zero. - add(String) - Method in class org.biojava.bio.program.gff.GFFEntrySet
-
Add a comment to the end of this set.
- add(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFEntrySet
-
Add a GFFRecord to the end of this set.
- add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
- add(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
- add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
- add(CodeGenerator) - Method in class org.biojava.utils.bytecode.InstructionVector
- ADD_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
- addAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
- addAllFeatures(Sequence, FeatureHolder) - Static method in class org.biojava.bio.seq.SequenceTools
-
Add features to a sequence that contain the same information as all those in a feature holder.
- addAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation
-
Add a new Annotation to to the end of the list to be merged.
- addAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
-
Add a DB to be merged in this view.
- addBioEntry(String, BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
- addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
- addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
- addBioEntry(BioEntry) - Method in interface org.biojavax.bio.db.BioEntryDBLite
-
Adds a sequence to the database.
- addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
- addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
-
Add a BioEntry, the name of the BioEntry will be used as the ID
- addBottomConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
-
Add a configuration as the most default place to look.
- addChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Add a ChangeListener to a projected feature.
- addChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
addChangeListener
adds a listener for all types of change. - addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
addChangeListener
adds a listener for all types of change. - addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
- addChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
- addChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable
-
Deprecated.use addChangeListener(cl, ChangeType.UNKNOWN)
- addChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport
-
Add a listener that will be informed of all changes.
- addChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
- addChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Add a listener that will be informed of all changes.
- addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
- addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
addChangeListener
adds a listener for specific types of change. - addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
addChangeListener
adds a listener for specific types of change. - addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
- addChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable
-
Add a listener that will be informed of changes of a given type.
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport
-
Add a listener that will be informed of changes of a given type (and it's subtypes)
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Add a listener that will be informed of changes of a given type.
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
- addCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- addCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addCharLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
- addCharState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- addCharState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addCharState(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
- addCharStateKeyword(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- addCharStateKeyword(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addCharStateKeyword(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
- addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
-
Deprecated.
- addChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
-
Deprecated.Add a taxon as a child to a parent.
- addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
-
Deprecated.
- addCluster(UnigeneCluster) - Method in interface org.biojava.bio.program.unigene.UnigeneDB
-
Add a cluster to a database.
- addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
Adds a comment.
- addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
-
Adds a comment.
- addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
- addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
-
Tell the builder to add the given comment at the current location.
- addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
-
Adds a comment.
- addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
- addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
-
Adds a comment.
- addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
- addComment(Comment) - Method in interface org.biojavax.bio.BioEntry
-
Adds a comment instance to this bioentry.
- addComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry
-
Adds a comment instance to this bioentry.
- addCommentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
- addComponentSequence(ComponentFeature.Template) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
- addCount(Distribution, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
-
Registers that sym was counted in this state.
- addCount(Distribution, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
- addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
-
Registers that sym was counted in this state.
- addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
- addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
- addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
-
Deprecated.
- addCount(State, State, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
-
Add 'count' to the transition from->to.
- addDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
Add a distributed data source.
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
- addDbId(AGAVEDbId) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
-
add @param id
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
- addDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple
-
Adds a descriptor.
- addDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Adds a descriptor.
- addDetailHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
Extend this FeatureSetHandler to delegate certain detail elements to the specified handler type.
- addDigestFeatures() - Method in class org.biojava.bio.proteomics.Digest
-
Adds peptides as features to the Sequence in this class.
- addElementId(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf
- addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
- addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
- addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
- addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
- addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
- addEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper
-
addEnzyme
adds an enzyme to be searched for in theSequence
. - addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
-
Add a silent optimisable transition to instance.
- addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
- addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
- addEquate(String, List) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- addEquate(String, List) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addEquate(String, List) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
- addExceptionTableEntry(Label, Label, CodeClass, Label) - Method in interface org.biojava.utils.bytecode.CodeContext
-
Add an exception table entry.
- addFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
-
Add a feature to the featureholder
- addFeatureHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
Extend this FeatureSetHandler to delegate certain feature elements to the specified handler type.
- addFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder
-
Add an extra FeatureHolder to the set of FeatureHolders which are merged.
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
- addFeatureProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener
-
Notify the listener of a feature property.
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
-
Add an annotation-bundle entry to the feature.
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.Null implementation
- addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
- addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
- addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Notify the listener of a feature property.
- addFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
-
Adds a relationship to this feature holder.
- addFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Adds a relationship to this feature holder.
- addFeatureToSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
- addFile(File) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
-
Add sequences from a file to the sequence database.
- addFile(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
- addFilterAndGlyph(FeatureFilter, Glyph) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
- addForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
- addGapInSource(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Add a gap at pos within the source coordinates.
- addGapInSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
- addGapInView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Add a single gap at pos within the view coordintates.
- addGapInView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
- addGapsInSource(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Add length gaps at pos within the source coordinates.
- addGapsInSource(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
- addGapsInView(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Add length gaps at pos within the view coordinates.
- addGapsInView(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
-
Adds a feature to the Handler attribute of the StAXFeatureHandler object
- addHitProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
- addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
- addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
- addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
- addHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
- addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
- addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
- addHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
-
The
addHitProperty
method adds a key/value pair containing some property of a particular hit. - addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
- addHotSpot(ImageMap.HotSpot) - Method in interface org.biojava.bio.gui.sequence.ImageMap
-
addHotSpot
adds a hotspot to the map. - addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide
- addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide
- addIdAlias(AGAVEIdAlias) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
- addIdAlias(AGAVEIdAlias) - Method in interface org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf
- addImplementation(Class, Class) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer
-
Install a new mapping from a class of Feature.Template to a class of Feature implementations.
- addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
- addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
- addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
- addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
- addItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
- addItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
- addItem(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- addItem(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addItem(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
- addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
- addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
- addItemAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
- addItemTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
- addItemTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
- addItemTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
- addKey(String, int) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
addKey
adds a new identifier namespace. - addKeyPath(String, Object[]) - Method in class org.biojava.bio.program.tagvalue.Index2Model
-
Add a key and a path to that key in the tag-value hierachy.
- addLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
Add a piece of text to this renderer's label
- addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
-
Add a silent persistent transition to instance.
- addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
- addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
- addListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub
-
add a ChangeListener associated with given key.
- addListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub
- addMapPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
- addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addMatrixEntry(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
- addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
- addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
- addMatrixEntry(String) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
- addName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Adds the name to this taxon in the given name class.
- addName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Adds the name to this taxon in the given name class.
- addName(Connection, Taxon, String, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.Adds a new name of the given
nameClass
to the taxon. - addNeg(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
- addNode(boolean) - Method in class org.biojava.utils.automata.FiniteAutomaton
-
Add a node to the FA.
- addNode(boolean) - Method in interface org.biojava.utils.automata.NfaBuilder
- addNode(boolean) - Method in class org.biojava.utils.automata.NfaSubModel
- addNote(Note) - Method in class org.biojavax.EmptyRichAnnotation
-
Adds a note to this annotation.
- addNote(Note) - Method in interface org.biojavax.RichAnnotation
-
Adds a note to this annotation.
- addNote(Note) - Method in class org.biojavax.SimpleRichAnnotation
-
Adds a note to this annotation.
- addObject(NexusObject) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
-
Appends an object to the end of the file.
- addOboFileEventListener(OboFileEventListener) - Method in class org.biojava.ontology.obo.OboFileParser
- addOntology(Ontology) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- addOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
- addOrganism(Organism) - Method in interface org.biojavax.ga.Population
-
Adds an Organism to the Population
- addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
- addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation
- addOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
- addOrganisms(Set) - Method in interface org.biojavax.ga.Population
-
Adds several organisms to the population
- addOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
- addOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population
-
Adds several organisms to the population
- addOrganisms(Population) - Method in class org.biojavax.ga.impl.AbstractPopulation
- addOrganisms(Population) - Method in interface org.biojavax.ga.Population
-
Adds the residents of one population to this one
- addOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
-
Add an orthologue to the set.
- addOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
- addOrthologueProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
add a property to the current Orthologue
- addOrthologueProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
- addOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
-
adds a specified OrthoPair relationship to this group.
- addOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
- addOrthoPairProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
add a property to the current OrthoPair
- addOrthoPairProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat
-
Adds a parse error listener to the list of listeners if it isn't already included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor
-
Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat
-
Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor
-
Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
-
Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.
- addParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource
-
Adds a parse error listener to the list of listeners.
- addPattern(String) - Method in class org.biojava.utils.automata.PatternBlitz
-
add the specified regex to the patterns used for searching.
- addPattern(String, boolean) - Method in class org.biojava.utils.regex.Search
-
add a search pattern to the searches to be conducted by this object.
- addPattern(String, String, boolean) - Method in class org.biojava.utils.regex.Search
-
add a search pattern to the searches to be conducted by this object.
- addPos(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
- addPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
- addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
- addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
- addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
- addProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType
-
Add a value to the specified property slot.
- addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
- addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
- addProperty(AGAVEProperty) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf
- addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
- addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
- addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
- addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
-
Deprecated.
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
- addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Adds a ranked cross reference to the existing set.
- addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry
-
Adds a ranked cross reference to the existing set.
- addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Adds a ranked cross reference to the existing set.
- addRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable
-
Adds a ranked cross reference to the existing set.
- addRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry
-
Adds a ranked docref instance to this bioentry.
- addRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry
-
Adds a ranked docref instance to this bioentry.
- addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
- addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
- addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
- addRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry
-
Adds a relation instance to this bioentry.
- addRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry
-
Adds a relation instance to this bioentry.
- addRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR
- addRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
- addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
-
addRenderer
adds a renderer. - addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
addRenderer
adds a renderer as a new track. - addRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes
-
Add a repository to FeatureTypes.
- addRequest(Runnable) - Method in class org.biojava.utils.SimpleThreadPool
- addRequest(Runnable) - Method in interface org.biojava.utils.ThreadPool
-
addRequest
requests that aRunnable
be scheduled to be run by one of the threads in the pool. - addRichSequence(String, RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
- addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
- addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
- addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
-
Add a sequence.
- addRichSequence(RichSequence) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
-
Adds a sequence to the database.
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
- addSearchProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
-
The
addSearchProperty
method adds a key/value pair containing some property of the overall search result. - addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
- addSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
-
Add a secondary key.
- addSequence(String, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
Add a sequence into the tree.
- addSequence(String, Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
-
Add a sequence under a particular id.
- addSequence(AlignmentElement) - Method in interface org.biojava.bio.alignment.ARAlignment
- addSequence(AlignmentElement) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
add a new a alignment usings a location to the reference sequence.
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.DummySequenceDB
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
-
addSequence
always throws aChangeVetoException
as this implementation is immutable. - addSequence(Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
- addSequence(Sequence) - Method in interface org.biojava.bio.seq.db.SequenceDBLite
-
Adds a sequence to the database.
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.WebSequenceDB
-
Not supported, You can't add sequences to a WebDB!
- addSequence(Sequence) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
- addSequence(Sequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
- addSequenceDB(String, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
-
This method creates a new (and empty) HashSequenceDB with the given name that will be accessible through this sequence db installation through this name and all given other identifiers.
- addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
-
As this is a dummy implementation adding a sequenceDB doesn't do anything
- addSequenceDB(SequenceDBLite, Set) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
-
addSequenceDB
adds a newSequenceDB
under its own identifier which will additionally be recognised by the set of other identifiers. - addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
-
addSequenceDB
adds a new SequenceDB which will be accessible via the name returned by its getName() method and via all other given identifiers. - addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblProcessor
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankProcessor
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.OrganismParser
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
- addSequenceProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener
-
Notify the listener of a sequence-wide property.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
-
Add an annotation-bundle entry to the sequence.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.Notify the listener of a sequence-wide property.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
- addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
- addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Notify the listener of a sequence-wide property.
- addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
addSequenceViewerListener
adds a listener for mouse clickSequenceViewerEvent
s. - 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 clickSequenceViewerEvent
s. - addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
addSequenceViewerMotionListener
adds a listener for mouse motionSequenceViewerEvent
s. - 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 motionSequenceViewerEvent
s. - addSet(Set) - Method in class org.biojava.utils.MergingSet
- addState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- addState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addState(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
- addState(State) - Method in interface org.biojava.bio.dp.MarkovModel
-
Adds a state to the model.
- addState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
- addState(State) - Method in class org.biojava.bio.dp.WMAsMM
- addStateLabel(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- addStateLabel(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addStateLabel(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
- addStyle(String, String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
-
Add a colour style to this Styler.
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
- addSubHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
-
The
addSubHitProperty
method adds a key/value pair containing some property of a particular subhit. - addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
- addSymbol(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- addSymbol(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addSymbol(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
- addSymbol(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
- addSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet
-
Adds a symbol to this alphabet.
- addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolList
-
Add a new Symbol to the end of this list.
- addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
SoftMaskedAlphabet
s cannot add newSymbol
s. - addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
- addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
- addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
- addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
- addSymbolList(SymbolList, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
-
tool to construct the SymbolList by adding Symbols.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
-
Deprecated.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOFilter
- addSymbols(Alphabet, Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SeqIOListener
-
Notify the listener of symbol data.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
-
does nothing for now.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleSequenceBuilder
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SmartSequenceBuilder
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.Prints out the sequences properties in order.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Notify the listener of symbol data.
- addSymbols(SymbolList, int) - Method in class org.biojava.bio.symbol.SuffixTree
-
Add a count for all motifs with length of up to
window
to this tree. - addSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
- addSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl
- addSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl
- addSynonym(Object) - Method in interface org.biojava.ontology.Term
-
Add a synonym for this term.
- addSynonym(Object) - Method in class org.biojava.ontology.Term.Impl
- addSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl
- addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Add a synonym for this term.
- addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Add a synonym for this term.
- addTable(SymbolPropertyTable) - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
-
Adds a symbol property table to the database.
- addTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
-
Add a tag to retain.
- addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
Add a TAXLABEL.
- addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- addTaxLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
-
Add a TAXLABEL.
- addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
-
Add a TAXLABEL.
- addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
- addTaxLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
-
Add a TAXLABEL.
- addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
-
Add a TAXLABEL.
- addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
- addTaxLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.TaxaBlockListener
-
Add another value after the TAXLABEL tag.
- addThrownException(CodeClass) - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
-
Adds a feature to the ThrownException attribute of the GeneratedCodeMethod object
- addTitle(int, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
add title information to an Orthologue (this is not in enclosed in the Orthologue element because it comes completely separate in the Homologene data files.
- addTitle(int, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
- addToCache(String, File) - Static method in class org.biojava.utils.io.FlatFileCache
- addToEnvironment(String, Object) - Method in class org.biojava.naming.ObdaContext
- addTopConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
-
Add a configuration as the most authoritative place to look.
- addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
- addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in interface org.biojava.utils.automata.NfaBuilder
- addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.NfaSubModel
- addTranslation(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
-
Add a translation.
- addTranslation(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
- addTranslation(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.TreesBlockListener
-
Add a translation.
- addTree(String, TreesBlock.NewickTreeString) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
-
Adds a tree.
- addTree(String, TreesBlock.NewickTreeString) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
- addTree(String, TreesBlock.NewickTreeString) - Method in interface org.biojavax.bio.phylo.io.nexus.TreesBlockListener
-
Adds a tree.
- addTree(String, WeightedGraph<String, DefaultWeightedEdge>) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
-
Deprecated.
- addTree(String, WeightedGraph<String, DefaultWeightedEdge>, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
-
Add a tree, converting weighted graph (JGraphT) to NewickString.
- addTypeWithParent(Class) - Method in class org.biojava.utils.walker.WalkerFactory
-
Register a type as being a 'container' class.
- addVariableModification(char, double[]) - Method in class org.biojava.bio.proteomics.MassCalc
-
Add Variable modifications.
- addVariableModification(Symbol, double[]) - Method in class org.biojava.bio.proteomics.MassCalc
-
Add Variable modifications.
- addVector(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
- addVector(Object, double, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
- addXMLCollectionConstraintWriter(Class, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
-
Register a writer for the specified class of collection constraint
- addXMLCollectionConstraintWriter(CollectionConstraint, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
-
Register a writer for a singleton property constraint.
- addXMLFilterWriter(Class, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
-
Add a writer for the specified class of filters
- addXMLFilterWriter(FeatureFilter, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
-
Add a writer for a singleton filter.
- addXMLPropertyConstraintWriter(Class, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
-
Register a writer for the specified class of property constraint
- addXMLPropertyConstraintWriter(PropertyConstraint, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
-
Register a writer for a singleton property constraint.
- addXref(AGAVEXref) - Method in interface org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf
- addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
-
add @param xref
- addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
- advance() - Method in interface org.biojava.bio.dp.MarkovModel
-
The maximum advance for this model.
- advance() - Method in interface org.biojava.bio.dp.onehead.DPCursor
-
Advance.
- advance() - Method in class org.biojava.bio.dp.onehead.SmallCursor
- advance() - Method in class org.biojava.bio.dp.SimpleMarkovModel
- advance() - Method in class org.biojava.bio.dp.WMAsMM
- ADVANCE - Static variable in interface org.biojava.bio.dp.EmissionState
-
This signals that the advance array has been altered.
- affiliation - Variable in class org.biojava.bibliography.BiblioPerson
-
Their affiliation.
- AGAVE_AGAVE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
- AGAVE_ALT_IDS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
- AGAVE_ANNOTATIONS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler
- AGAVE_ASSEMBLY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler
- AGAVE_BIO_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
- AGAVE_BIO_SEQUENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
- AGAVE_CDS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECdsHandler
- AGAVE_CHROMOSOME_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
- AGAVE_CLASSIFICATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
- AGAVE_COMP_RESULT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
- AGAVE_COMPUTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
- AGAVE_CONTIG_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
- AGAVE_DBID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
- AGAVE_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
- AGAVE_ELEMENT_ID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
- AGAVE_EVIDENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
- AGAVE_EXONS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler
- AGAVE_FRAGMENT_ORDER_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
- AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
- AGAVE_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
- AGAVE_ID_ALIAS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
- AGAVE_KEYWORD_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
- AGAVE_MAP_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
- AGAVE_MAP_POSITION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
- AGAVE_MATCH_ALIGN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
- AGAVE_MATCH_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
- AGAVE_MATCH_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
- AGAVE_MRNA_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
- AGAVE_NOTE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
- AGAVE_PREDICTED_PROTEIN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
- AGAVE_QUALIFIER_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
- AGAVE_QUERY_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
- AGAVE_RELATED_ANNOT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
- AGAVE_RESULT_GROUP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
- AGAVE_RESULT_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
- AGAVE_SCI_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
- AGAVE_SEQ_FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
- AGAVE_SEQ_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
- AGAVE_SEQ_MAP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
- AGAVE_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
- AGAVE_TRANSCRIPT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
- AGAVE_UNORDERED_FRAGMENTS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler
- AGAVE_VIEW_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
- AGAVE_XREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
- AGAVE_XREF_PROP_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
- AGAVE_XREFS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
- Agave2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave
-
Dumping the data from biojava with source of agave into agave format
- AGAVEAltIdsPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with alternate sequence IDs
- AGAVEAnnotationsHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEAnnotFilter - Interface in org.biojava.bio.seq.io.agave
-
This interface defines mapping from BioJava into AGAVE format.
- AGAVEAnnotFilterFactory - Interface in org.biojava.bio.seq.io.agave
- AGAVEAssemblyHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEBioSeqCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
An interface that can be tested for by nested handlers when trying to do a callback.
- AGAVEBioSeqHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <bio_sequence> element
- AGAVEBioSequenceHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <bio_sequence> element
- AGAVECallbackItf - Interface in org.biojava.bio.seq.io.agave
-
An interface that can be tested for by nested handlers when trying to do a callback.
- AGAVECdsHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <cds> element
- AGAVEChromosomeCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
An interface that can be tested for by nested handlers when trying to do a callback.
- AGAVEChromosomeHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <chromosome> element
- AGAVEClassificationHandler - Class in org.biojava.bio.seq.io.agave
- AGAVECompResultHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEComputationHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEContigCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
An interface that can be tested for by nested handlers when trying to do a callback.
- AGAVEContigHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <contig> element
- AGAVEDbId - Class in org.biojava.bio.seq.io.agave
- AGAVEDbId() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEDbId
- AGAVEDbIdCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
this is the interface implemented by several classes
- AGAVEDbIdPropCallbackItf - Interface in org.biojava.bio.seq.io.agave
- AGAVEDbIdPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with database crossreferences
- AGAVEDescPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with database crossreferences
- AGAVEElementIdPropHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEEvidenceCallbackItf - Interface in org.biojava.bio.seq.io.agave
- AGAVEEvidenceHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEExonsPropHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
An interface that can be tested for by nested handlers when trying to do a callback.
- AGAVEFragmentOrderHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEFragmentOrientationHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEGeneHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the root AGAVE element modified for agave format
- AGAVEHandler() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEHandler
- AGAVEIdAlias - Class in org.biojava.bio.seq.io.agave
- AGAVEIdAliasCallbackItf - Interface in org.biojava.bio.seq.io.agave
- AGAVEIdAliasPropHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEKeywordPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with AGAVE keywords
- AGAVEMapLocation - Class in org.biojava.bio.seq.io.agave
- AGAVEMapLocation() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapLocation
- AGAVEMapLocationPropHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEMapPosition - Class in org.biojava.bio.seq.io.agave
- AGAVEMapPosition() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapPosition
- AGAVEMapPositionPropHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEMatchAlignPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with match_align
- AGAVEMatchDescPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with match_desc
- AGAVEMatchRegion - Class in org.biojava.bio.seq.io.agave
-
match_region
- AGAVEMatchRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
- AGAVEMatchRegionPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with match_region
- AGAVEMrnaHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <mrna> element
- AGAVENotePropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with note
- AGAVEPredictedProteinHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <predicted_protein> element
- AGAVEProperty - Class in org.biojava.bio.seq.io.agave
- AGAVEProperty(String, String, String, String) - Constructor for class org.biojava.bio.seq.io.agave.AGAVEProperty
- AGAVEQualifierPropHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEQueryRegion - Class in org.biojava.bio.seq.io.agave
- AGAVEQueryRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
- AGAVEQueryRegionPropHandler - Class in org.biojava.bio.seq.io.agave
- AGAVERelatedAnnot - Class in org.biojava.bio.seq.io.agave
- AGAVERelatedAnnot() - Constructor for class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
construct..
- AGAVERelatedAnnotPropHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEResultGroupHandler - Class in org.biojava.bio.seq.io.agave
- AGAVEResultPropertyPropHandler - Class in org.biojava.bio.seq.io.agave
- AGAVESciPropertyPropHandler - Class in org.biojava.bio.seq.io.agave
-
sci_property
- AGAVESeqFeatureHandler - Class in org.biojava.bio.seq.io.agave
-
seq_feature
- AGAVESeqLocationPropHandler - Class in org.biojava.bio.seq.io.agave
-
seq_location
- AGAVESeqMapHandler - Class in org.biojava.bio.seq.io.agave
-
sequence_map
- AGAVESeqPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with sequence code
- AGAVETranscriptHandler - Class in org.biojava.bio.seq.io.agave
-
transcript
- AGAVEUnorderedFragmentsHandler - Class in org.biojava.bio.seq.io.agave
-
unordered_fragments
- AGAVEViewPropHandler - Class in org.biojava.bio.seq.io.agave
-
Moves view attributes into annotation properties.
- AgaveWriter - Class in org.biojava.bio.seq.io.agave
-
Writes Sequence into AGAVE XML document.
- AgaveWriter() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter
-
Default constructor uses generic annotation to attribute mapping.
- AgaveWriter(AGAVEAnnotFilter) - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter
-
Construct with data source specific annotation to attribute mapping.
- AgaveWriter.Indent - Class in org.biojava.bio.seq.io.agave
-
Implements indenting for elements.
- AGAVEXref - Class in org.biojava.bio.seq.io.agave
-
xref
- AGAVEXref() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXref
- AGAVEXrefCallbackItf - Interface in org.biojava.bio.seq.io.agave
- AGAVEXrefPropHandler - Class in org.biojava.bio.seq.io.agave
-
handle AGAVE xref
- AGAVEXrefPropPropHandler - Class in org.biojava.bio.seq.io.agave
-
xref_property
- AGAVEXrefs - Class in org.biojava.bio.seq.io.agave
-
xrefs
- AGAVEXrefs() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXrefs
- AGAVEXrefsPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with database crossreferences (xrefs)
- Aggregator - Class in org.biojava.bio.program.tagvalue
-
Joins multipel values into single values.
- Aggregator(TagValueListener, BoundaryFinder, String) - Constructor for class org.biojava.bio.program.tagvalue.Aggregator
- ala() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the
AtomicSymbol
for the amino acid Alanine (A) - align(Sequence, Sequence, AlignmentAlgorithm) - Static method in class org.biojava.bio.alignment.AlignmentPair
- alignAll(SequenceIterator, SequenceDB) - Method in class org.biojava.bio.alignment.AlignmentAlgorithm
- AlignIOConstants - Class in org.biojava.bio.seq.io
-
AlignIOConstants
contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing alignments. - AlignIOConstants() - Constructor for class org.biojava.bio.seq.io.AlignIOConstants
- alignment - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
-
alignment
Alignment
field. - alignment(List, SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews
-
View a SymbolList over a cross-product Alphabet as an Alignment.
- alignment(Map) - Static method in class org.biojava.bio.symbol.SymbolListViews
-
Construct an alignment of the SymbolLists contained in the values collection of
labelToSymList
. - Alignment - Interface in org.biojava.bio.alignment
-
An alignment containing multiple SymbolLists.
- ALIGNMENT - Static variable in interface org.biojava.bio.seq.homol.Homology
-
Signals that the alignment describing the homologous sequences has changed.
- ALIGNMENT_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.AlignmentStAXHandler
- Alignment.SymbolListIterator - Class in org.biojava.bio.alignment
-
Iterator implementation looping over symbol lists in an alignment using the labels.
- AlignmentAlgorithm - Class in org.biojava.bio.alignment
-
This Interface provides methods for the alignment of bio-sequences.
- AlignmentAlgorithm() - Constructor for class org.biojava.bio.alignment.AlignmentAlgorithm
- AlignmentElement - Interface in org.biojava.bio.alignment
-
AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.
- AlignmentFormat - Interface in org.biojava.bio.seq.io
- AlignmentMarker - Class in org.biojava.bio.program.blast2html
-
Class to do simple HTML colouring of sequence alignments.
- AlignmentMarker(ColourCommand, AlignmentStyler) - Constructor for class org.biojava.bio.program.blast2html.AlignmentMarker
-
Creates a new
AlignmentMarker
instance. - AlignmentPair - Class in org.biojava.bio.alignment
-
This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.
- AlignmentPair(Sequence, Sequence, int, int, int, int, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.AlignmentPair
- AlignmentPair(Sequence, Sequence, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.AlignmentPair
- alignmentRange - Variable in class org.biojava.bio.alignment.FlexibleAlignment
- AlignmentRenderer - Class in org.biojava.bio.gui.sequence
- AlignmentRenderer() - Constructor for class org.biojava.bio.gui.sequence.AlignmentRenderer
- AlignmentStAXHandler - Class in org.biojava.bio.program.ssbind
-
AlignmentStAXHandler
handles the BlastLikeAlignment element of BioJava BlastLike XML. - all - Static variable in interface org.biojava.bio.seq.FeatureFilter
-
All features are selected by this filter.
- all - Static variable in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
-
All features are selected by this filter.
- all() - Static method in class org.biojava.bio.seq.FilterUtils
-
Return a filter which matches all features.
- ALL - Static variable in interface org.biojava.bio.program.xff.ElementRecognizer
- ALL - Static variable in interface org.biojava.bio.seq.io.agave.ElementRecognizer
- ALL - Static variable in interface org.biojava.bio.seq.io.game.ElementRecognizer
- AllElementRecognizer() - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
- AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
- AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
- allGaps(SymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
make sure that all Symbols in this range are gaps
- allIn(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
-
Destructive down-cast an annotation to a type.
- allOut(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
-
allOut
returns a newAnnotation
containing only those values in theAnnotation
argument which are not of a type specified by theAnnotationType
. - AllPairsInCollection(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
- AllValuesIn(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.AllValuesIn
-
Create an AllValuesIn based upon a PropertyConstraint and a cardinality.
- alph - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
- alphabet - Variable in class org.biojava.bio.alignment.AbstractULAlignment
- Alphabet - Interface in org.biojava.bio.symbol
-
The set of AtomicSymbols which can be concatenated together to make a SymbolList.
- alphabetForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Retrieve the alphabet for a specific name.
- AlphabetIndex - Interface in org.biojava.bio.symbol
-
Map between Symbols and index numbers.
- AlphabetManager - Class in org.biojava.bio.symbol
-
Utility methods for working with Alphabets.
- AlphabetManager() - Constructor for class org.biojava.bio.symbol.AlphabetManager
- AlphabetResolver - Class in org.biojava.bio.program.ssbind
-
AlphabetResolver
s are helpers which determine which type of sequenceAlphabet
to expect from a search result. - AlphabetResolver() - Constructor for class org.biojava.bio.program.ssbind.AlphabetResolver
- alphabets() - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Get an iterator over all alphabets known.
- alphaIndex(Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
- alphaIndex(Symbol) - Method in class org.biojava.utils.automata.Nfa
- AlreadyExistsException - Exception in org.biojava.ontology
-
Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
- AlreadyExistsException() - Constructor for exception org.biojava.ontology.AlreadyExistsException
- AlreadyExistsException(String) - Constructor for exception org.biojava.ontology.AlreadyExistsException
- ALT_ID - Static variable in class org.biojava.ontology.obo.OboFileHandler
- ALT_YEAST_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the alternative yeast nuclear genetic code.
- AlternateTokenization - Class in org.biojava.bio.seq.io
-
Implementation of SymbolTokenization which binds symbols to strings of characters.
- AlternateTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.AlternateTokenization
- ALTERNATIVE_PRODUCTS - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
-
A name for a comment type.
- ALWAYS_VETO - Static variable in interface org.biojava.utils.ChangeListener
-
Convenience implementation which vetoes every change of which it is notified.
- AlwaysVetoListener() - Constructor for class org.biojava.utils.ChangeListener.AlwaysVetoListener
-
Private constructor.
- AMBIGUOUS - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
AMBIGUOUS
indicates that a sequence contains ambiguity symbols. - aminoAcids - Static variable in class org.biojavax.bio.seq.io.FastaFormat
- and - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
- and(FeatureFilter.And, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
- and(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils
-
Constructs a new filter which matches the intersection of a set of filters.
- and(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a new filter which matches the intersection of two other filters.
- And(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.And
-
Create a new
And
from two child constraints. - And(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.And
- And(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.And
- And(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
- And(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.And
-
Create a new
And
from two child constraints. - And(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.And
- And(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.And
- And(BioSQLFeatureFilter, BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
- annot - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
- Annotatable - Interface in org.biojava.bio
-
Indicates that an object has an associated annotation.
- Annotatable.AnnotationForwarder - Class in org.biojava.bio
-
Deprecated.use
new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)
instead - annotate(Sequence) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
- annotate(Sequence) - Method in class org.biojava.bio.molbio.RestrictionMapper
-
annotate
addsFeature
s which represent restriction sites. - annotate(Sequence) - Method in interface org.biojava.bio.seq.SequenceAnnotator
-
Return an annotated version of a sequence.
- ANNOTATE_EXISTING - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
- AnnotatedSequenceDB - Class in org.biojava.bio.seq.db
-
SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
- AnnotatedSequenceDB(SequenceDB, SequenceAnnotator) - Constructor for class org.biojava.bio.seq.db.AnnotatedSequenceDB
- annotateSequence(Sequence, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
- annotateSequence(Sequence, GFFEntrySet, boolean) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Annotates a sequence with the features from a GFF entry set.
- annotateSequences(SequenceDB, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Annotates all sequences in a sequence DB with features from a GFF entry set.
- annotateXFF(File, Sequence) - Static method in class org.biojava.bio.program.xff.XFFTools
- annotateXFF(File, Sequence, Annotation) - Static method in class org.biojava.bio.program.xff.XFFTools
- annotation - Variable in class org.biojava.bio.seq.Feature.Template
- annotation - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
- Annotation - Interface in org.biojava.bio
-
Arbitrary annotation associated with one or more objects.
- ANNOTATION - Static variable in interface org.biojava.bio.Annotatable
-
Signals that the associated Annotation has altered in some way.
- ANNOTATION_ADD - Static variable in class org.biojava.bio.MergeAnnotation
-
ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
- ANNOTATION_CHANGED - Static variable in class org.biojava.bio.MergeAnnotation
-
ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
- ANNOTATION_REMOVE - Static variable in class org.biojava.bio.MergeAnnotation
-
ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
- AnnotationBuilder - Class in org.biojava.bio.program.tagvalue
-
Builds an Annotation tree from TagValue events using an AnnotationType to work out which fields are of what type.
- AnnotationBuilder(AnnotationType) - Constructor for class org.biojava.bio.program.tagvalue.AnnotationBuilder
-
Make a new AnnotationBuilder that will build Annotation instances of a given type.
- AnnotationChanger - Class in org.biojava.bio
-
AnnotationChanger
remaps the values of anAnnotation
to new values specified by aValueChanger
. - AnnotationChanger(Annotation, ChangeTable) - Constructor for class org.biojava.bio.AnnotationChanger
-
Creates a new
AnnotationChanger
using the specifiedValueChanger
to remap its values. - AnnotationContains(Object, Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.AnnotationContains
-
Make a new AnnotationContains that will accept features with an annotation bundle where the value-set assosiated with the property
key
contains a member equal tovalue
. - 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 makingAnnotation
s fromMap
s. - AnnotationFactory() - Constructor for class org.biojava.bio.program.ssbind.AnnotationFactory
- annotationForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
- annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchResult
-
Deprecated.
- annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
- annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
- annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
- annotationForwarder - Variable in class org.biojava.bio.seq.impl.SubSequence
- annotationForwarder - Variable in class org.biojava.bio.seq.NewSimpleAssembly
- annotationForwarder - Variable in class org.biojava.bio.seq.SimpleAssembly
- annotationForwarder - Variable in class org.biojava.bio.symbol.AbstractSymbol
- annotationForwarder - Variable in class org.biojava.bio.symbol.SimpleAlphabet
- AnnotationForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.Annotatable.AnnotationForwarder
-
Deprecated.Create a new AnnotationForwarder that will forward events for a source using a change support.
- AnnotationLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
- AnnotationLabelMaker(Object) - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
- AnnotationRenamer - Class in org.biojava.bio
-
AnnotationRenamer
remaps the keys of anAnnotation
to new keys specified by aTagMapper
. - AnnotationRenamer(Annotation, PropertyChanger) - Constructor for class org.biojava.bio.AnnotationRenamer
-
Creates a new
AnnotationRenamer
using the specifiedTagMapper
to remap its keys. - AnnotationTools - Class in org.biojava.bio
-
AnnotationTools
is a set of static utility methods for manipulatingAnnotation
s andAnnotationType
s. - AnnotationTools() - Constructor for class org.biojava.bio.AnnotationTools
- AnnotationType - Interface in org.biojava.bio
-
A set of constraints on the data contained in an
Annotation
. - AnnotationType.Abstract - Class in org.biojava.bio
-
An abstract base class useful for implementing AnnotationType instances.
- AnnotationType.Impl - Class in org.biojava.bio
-
An implementation of
AnnotationType
. - ANY - Static variable in interface org.biojava.bio.AnnotationType
-
The type that accepts all annotations and is the supertype of all other annotations.
- ANY - Static variable in class org.biojava.bio.CardinalityConstraint
-
The property can have any number of values, including none.
- ANY - Static variable in interface org.biojava.bio.CollectionConstraint
-
ANY
is a constraint which accepts a property for addition under all conditions. - ANY - Static variable in interface org.biojava.bio.PropertyConstraint
-
ANY
is a constraint which accepts a property for addition under all conditions. - ANY - Static variable in class org.biojava.ontology.OntoTools
- App - Class in org.biojava
-
Hello world!
- App() - Constructor for class org.biojava.App
- AppBeanRunner - Class in org.biojava.utils.xml
-
Create a bean from an XML file, then attempt to enter it.
- AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner
- append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel
- append(T, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
-
Append the specified FASTQ formatted sequences to the specified appendable.
- append(T, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
-
Append the specified FASTQ formatted sequences to the specified appendable.
- appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- appendMatrixData(String, Object) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
- appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
- appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
- appendMatrixData(String, Object) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
- appendQuality(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder
-
Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.
- appendQuality(String) - Method in interface org.biojava.bio.program.fastq.ParseListener
-
Notify this listener of a quality line.
- appendSequence(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder
-
Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.
- appendSequence(String) - Method in interface org.biojava.bio.program.fastq.ParseListener
-
Notify this parse listener of an additional sequence line.
- AppEntry - Interface in org.biojava.utils.xml
- AppException - Exception in org.biojava.utils.xml
- AppException(String) - Constructor for exception org.biojava.utils.xml.AppException
- applicants - Variable in class org.biojava.bibliography.BiblioPatent
-
Array of applicants.
- ARAlignment - Interface in org.biojava.bio.alignment
-
ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
- arcHeight - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
- ARCHITECTURE - Static variable in interface org.biojava.bio.dp.MarkovModel
-
Signals that the architecture of the model is changing.
- arcWidth - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
- areDisjoint(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Determines if two queries can be proven to be disjoint.
- areEmissionSpectraEqual(Distribution[], Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
-
Compares the emission spectra of two distribution arrays.
- areEmissionSpectraEqual(Distribution, Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
-
Compares the emission spectra of two distributions.
- areEqual(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Decide if two feature filters accept exactly the same set of features.
- areEqual(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Return whether two locations are equal.
- areProperSubset(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Determines if the set of features matched by sub can be
proven
to be a proper subset of the features matched by sup. - arg() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the
AtomicSymbol
for the amino acid Arginine (R) - ARG_C - Static variable in class org.biojava.bio.proteomics.Protease
- ARG_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager
- ArrayStateMachineToolkit - Class in org.biojava.utils.automata
- ArrowedFeatureRenderer - Class in org.biojava.bio.gui.sequence
-
A Feature Renderer that paints the Feature as a right facing arrow Based heavily on BasicFeatureRenderer
- ArrowedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
- ArrowGlyph - Class in org.biojava.bio.gui.glyph
-
A Glyph that paints an arrow shape within the bounds.
- ArrowGlyph() - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
-
Creates a new
ArrowGlyph
, which is filled with the color blue by default. - ArrowGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
-
This constructs an arrow in the given bounds, which is colored blue.
- ArrowGlyph(Rectangle2D.Float, Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
-
Constructor which sets both the size of this arrow and its color.
- ArrowGlyph(Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
-
Creates a new
ArrowGlyph
, which is filled with the given color. - ASCID_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the ascidian mitochondrial genetic code.
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
- asCriterion() - Method in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
-
This method returns a Hibernate Criterion object that can be used to query the database.
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
- asMap() - Method in class org.biojava.bio.AbstractAnnotation
- asMap() - Method in interface org.biojava.bio.Annotation
-
Return a map that contains the same key/values as this Annotation.
- asMap() - Method in class org.biojava.bio.MergeAnnotation
- asMap() - Method in class org.biojava.bio.OverlayAnnotation
-
Return a
Map
view onto this annotation. - asMap() - Method in class org.biojavax.EmptyRichAnnotation
-
Return a map that contains the same key/values as this Annotation.
- asMap() - Method in class org.biojavax.ga.util.WeightedSet
-
Converts the Set to a map from key
Objects
toDouble
weights. - asMap() - Method in class org.biojavax.SimpleRichAnnotation
-
Return a map that contains the same key/values as this Annotation.
- asn() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the
AtomicSymbol
for the amino acid Asparagine (N) - asp() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the
AtomicSymbol
for the amino acid Aspartic Acid (D) - ASP_N - Static variable in class org.biojava.bio.proteomics.Protease
- ASP_N - Static variable in class org.biojava.bio.proteomics.ProteaseManager
- AssembledSymbolList - Class in org.biojava.bio.seq.impl
-
Support class for applications which need to patch together sections of sequence into a single SymbolList.
- AssembledSymbolList() - Constructor for class org.biojava.bio.seq.impl.AssembledSymbolList
- AssertionFailure - Error in org.biojava.utils
-
An unchecked exception representing an Assertion failure.
- AssertionFailure(String) - Constructor for error org.biojava.utils.AssertionFailure
- AssertionFailure(String, Throwable) - Constructor for error org.biojava.utils.AssertionFailure
- AssertionFailure(Throwable) - Constructor for error org.biojava.utils.AssertionFailure
- AtomicSymbol - Interface in org.biojava.bio.symbol
-
A symbol that is not ambiguous.
- attemptClose(ResultSet) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.Attempt to close the ResultSet.
- attemptClose(Statement) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.Attempt to close the Statement.
- ATTR_FORMAT - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A vocabulary name, or a part of a vocabulary name.
- ATTR_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A part of a vocabulary name.
- ATTR_SCOPE - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A vocabulary name, or a part of a vocabulary name.
- attribute(String, String) - Method in class org.biojava.utils.xml.FastXMLWriter
- attribute(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
- attribute(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
-
Add an un-qualified attribute to an element.
- attribute(String, String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
- attribute(String, String, String) - Method in interface org.biojava.utils.xml.XMLWriter
-
Add an attribute to an element.
- AUTHOR_LIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- AUTHORITY - Static variable in interface org.biojavax.Namespace
- authors - Variable in class org.biojava.bibliography.BibRef
-
The authors and contributors are responsible for creating the contents of the cited resource.
- AUTHORS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
- AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
- automaticUpdate(Connection, DBHelper, TaxonFactory, File, File) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.This method tries to perform a complete update according to the given
TaxonFactory
, which already contains the newes taxa and the files available at the NCBI-FTP-Site. - AutomatonException - Exception in org.biojava.utils.automata
-
An exception thrown by classes of this package.
- AutomatonException(String) - Constructor for exception org.biojava.utils.automata.AutomatonException
- AutomatonException(Throwable) - Constructor for exception org.biojava.utils.automata.AutomatonException
- AutomatonException(Throwable, String) - Constructor for exception org.biojava.utils.automata.AutomatonException
- available() - Method in class org.biojava.utils.io.UncompressInputStream
- average(Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
-
Averages two or more distributions.
- AverageResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.AverageResolver
- AVG_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
B
- b() - Static method in class org.biojava.bio.seq.DNATools
- b() - Static method in class org.biojava.bio.seq.NucleotideTools
- B_TAURUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
- back - Variable in class org.biojava.bio.dp.BackPointer
-
The previous backpointer (towards origin of DP matrix) in traceback.
- BackMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
- BackMatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
- BackPointer - Class in org.biojava.bio.dp
-
A backpointer.
- BackPointer(State) - Constructor for class org.biojava.bio.dp.BackPointer
- BackPointer(State, BackPointer, double) - Constructor for class org.biojava.bio.dp.BackPointer
- backPointers - Variable in class org.biojava.bio.dp.twohead.Cell
- backward(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
- backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
- backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
- backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
- backward_initialize(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
- backward_recurse(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
- backward_termination(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
- backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
- backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
- backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
- backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
- backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
- backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
- backwards(ScoreType) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
- backwards(ScoreType) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
- backwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
- backwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP
- BACTERIAL - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the bacterial and plant plastid genetic code.
- BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.program.phred.PhredFormat
-
This method determines the behaviour when a bad line is processed.
- BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.This method determines the behaviour when a bad line is processed.
- BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat
-
Deprecated.This method determines the behaviour when a bad line is processed.
- BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.This method determines the behaviour when a bad line is processed.
- BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.StreamReader
-
This method determines the behaviour when a bad line is processed.
- BadLineParsed(ParseErrorEvent) - Method in interface org.biojava.utils.ParseErrorListener
-
Method called when the parser encounters a bad line.
- BarLogoPainter - Class in org.biojava.bio.gui
-
A logo painter that paints in bars.
- BarLogoPainter() - Constructor for class org.biojava.bio.gui.BarLogoPainter
- BASE_COUNT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- BASE_COUNT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
- BASE_COUNT_TAG_FULL - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
- BASEPOSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- BASEPOSITION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- BaseXMLWriter - Class in org.biojava.bio.program.xml
-
Base XMLWriter class for writing XML representations of Java Value Objects with bespoke architectures.
- BaseXMLWriter() - Constructor for class org.biojava.bio.program.xml.BaseXMLWriter
- BasicFeatureRenderer - Class in org.biojava.bio.gui.sequence
- BasicFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.BasicFeatureRenderer
- BasicFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
- BasicImapRenderer - Class in org.biojava.bio.gui.sequence
-
BasicImapRenderer
is a decorator forBasicFeatureRenderer
which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by theBasicFeatureRenderer
. - BasicImapRenderer(BasicFeatureRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.BasicImapRenderer
-
Creates a new
BasicImapRenderer
. - BasicState(String) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
This is the default constructor
- BasicState(String, TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
when this constructor is used, a fixed listener is used with this state.
- BasicXFFHelper - Class in org.biojava.bio.program.xff
- BasicXFFHelper() - Constructor for class org.biojava.bio.program.xff.BasicXFFHelper
- BasisSymbol - Interface in org.biojava.bio.symbol
-
A symbol that can be represented as a string of Symbols.
- BaumWelchSampler - Class in org.biojava.bio.dp
-
Train a hidden markov model using a sampling algorithm.
- BaumWelchSampler(DP) - Constructor for class org.biojava.bio.dp.BaumWelchSampler
- BaumWelchTrainer - Class in org.biojava.bio.dp
-
Train a hidden markov model using maximum likelihood.
- BaumWelchTrainer(DP) - Constructor for class org.biojava.bio.dp.BaumWelchTrainer
- beadDepth - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
- beadDisplacement - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
- BeadFeatureRenderer - Interface in org.biojava.bio.gui.sequence
-
BeadFeatureRenderer
s use a 'string of beads' metaphor for displaying features. - beadFill - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
- beadOutline - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
- beadStroke - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
- BeanAsAnnotation - Class in org.biojava.bio
-
Create an Annotation with properties matching those of a JavaBean instance.
- BeanAsAnnotation(Object) - Constructor for class org.biojava.bio.BeanAsAnnotation
-
Create a new BeanAsAnnotation for a bean.
- BeanAsMap - Class in org.biojava.utils
- BeanAsMap(Object) - Constructor for class org.biojava.utils.BeanAsMap
- beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
- beginComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
-
Opening a comment tag.
- beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
- beginComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
-
Opening a comment tag.
- beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
- beginComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
-
Opening a comment tag.
- beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
- beginFileComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
- beginFileComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
-
This method will get called when a comment is started on the file, and not any block within it.
- beginWriting() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
Informs the writer that we want to start writing.
- beginWriting() - Method in class org.biojavax.bio.seq.io.INSDseqFormat
-
Informs the writer that we want to start writing.
- beginWriting() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Informs the writer that we want to start writing.
- beginWriting() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
-
Informs the writer that we want to start writing.
- beginWriting() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
Informs the writer that we want to start writing.
- BETWEEN_BASES - Static variable in interface org.biojavax.bio.seq.Position
-
A symbol representing a position that falls in between two bases, eg. 2^3 falls somewhere in the gap between 2 and 3.
- BetweenLocation - Class in org.biojava.bio.symbol
-
Between view onto an underlying Location instance.
- BetweenLocation(Location) - Constructor for class org.biojava.bio.symbol.BetweenLocation
- BiblioArticle - Class in org.biojava.bibliography
-
It represents an article.
- BiblioArticle() - Constructor for class org.biojava.bibliography.BiblioArticle
- BiblioBook - Class in org.biojava.bibliography
-
It represents a book.
- BiblioBook() - Constructor for class org.biojava.bibliography.BiblioBook
- BiblioBookArticle - Class in org.biojava.bibliography
-
It represents a book article.
- BiblioBookArticle() - Constructor for class org.biojava.bibliography.BiblioBookArticle
- BiblioCriterion - Class in org.biojava.bibliography
-
The criteria define how the matching or ordering should be done during queries.
- BiblioCriterion() - Constructor for class org.biojava.bibliography.BiblioCriterion
- BiblioDescription - Class in org.biojava.bibliography
-
It represents an account of the content of the cited resource.
- BiblioDescription() - Constructor for class org.biojava.bibliography.BiblioDescription
- BiblioEntryStatus - Class in org.biojava.bibliography
-
It defines information related to the citation itself rather than to the cited resource.
- BiblioEntryStatus() - Constructor for class org.biojava.bibliography.BiblioEntryStatus
- BiblioJournal - Class in org.biojava.bibliography
-
A class describing journals.
- BiblioJournal() - Constructor for class org.biojava.bibliography.BiblioJournal
- BiblioJournalArticle - Class in org.biojava.bibliography
-
It represents a journal article.
- BiblioJournalArticle() - Constructor for class org.biojava.bibliography.BiblioJournalArticle
- BiblioOrganisation - Class in org.biojava.bibliography
-
It represents an organisation dealing with the bibliographic resources.
- BiblioOrganisation() - Constructor for class org.biojava.bibliography.BiblioOrganisation
- BiblioPatent - Class in org.biojava.bibliography
-
It represents a patent.
- BiblioPatent() - Constructor for class org.biojava.bibliography.BiblioPatent
- BiblioPerson - Class in org.biojava.bibliography
-
It represents a person dealing with the bibliographic resources.
- BiblioPerson() - Constructor for class org.biojava.bibliography.BiblioPerson
- BiblioProceeding - Class in org.biojava.bibliography
-
It represents a conference proceeding.
- BiblioProceeding() - Constructor for class org.biojava.bibliography.BiblioProceeding
- BiblioProvider - Class in org.biojava.bibliography
-
This class and its sub-classes define active participants of the process of creation and dissemination of the bibliographic resources.
- BiblioProvider() - Constructor for class org.biojava.bibliography.BiblioProvider
- BiblioScope - Class in org.biojava.bibliography
-
It represent an extent or scope of the content of the cited resource.
- BiblioScope() - Constructor for class org.biojava.bibliography.BiblioScope
- BiblioService - Class in org.biojava.bibliography
-
It represents a service dealing with the bibliographic resources.
- BiblioService() - Constructor for class org.biojava.bibliography.BiblioService
- BiblioSubject - Class in org.biojava.bibliography
-
It represents the topic of the content of the cited resource.
- BiblioSubject() - Constructor for class org.biojava.bibliography.BiblioSubject
- BiblioTechReport - Class in org.biojava.bibliography
-
It represents a technical report.
- BiblioTechReport() - Constructor for class org.biojava.bibliography.BiblioTechReport
- BiblioThesis - Class in org.biojava.bibliography
-
It represents a thesis.
- BiblioThesis() - Constructor for class org.biojava.bibliography.BiblioThesis
- BiblioWebResource - Class in org.biojava.bibliography
-
It represents a WWW resource.
- BiblioWebResource() - Constructor for class org.biojava.bibliography.BiblioWebResource
- BibRef - Class in org.biojava.bibliography
-
This class is a core class of the bibliographic data model - it represents a bibliographic reference, a citation.
- BibRef() - Constructor for class org.biojava.bibliography.BibRef
- BibRefException - Exception in org.biojava.bibliography
-
An exception raised when communciation with the BibRef APIs fails.
- BibRefException(String) - Constructor for exception org.biojava.bibliography.BibRefException
-
Create a new BibRefException with a message.
- BibRefException(String, Throwable) - Constructor for exception org.biojava.bibliography.BibRefException
-
Create a nw BibRefException with a message and a root cause.
- BibRefException(Throwable) - Constructor for exception org.biojava.bibliography.BibRefException
-
Create a new BibRefException with a root cause.
- BibRefQuery - Interface in org.biojava.bibliography
-
The interface BibRefQuery is a fundamental part of the Bibliographic Query Service.
- BibRefSupport - Interface in org.biojava.bibliography
-
This interface defines supporting utilities for working with bibliographic repositories.
- binary(int) - Static method in class org.biojava.bio.symbol.PackingFactory
- binary(long) - Static method in class org.biojava.bio.symbol.PackingFactory
- BinarySearch - Class in org.biojava.utils.math
-
solves y = f(x) = 0 by binary search.
- BinarySearch() - Constructor for class org.biojava.utils.math.BinarySearch
- bind(String, Object) - Method in class org.biojava.naming.ObdaContext
- bind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
- bind(Name, Object) - Method in class org.biojava.naming.ObdaContext
- bind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
- bindSymbol(Symbol, char) - Method in class org.biojava.bio.seq.io.CharacterTokenization
-
Bind a Symbol to a character.
- bindSymbol(Symbol, String) - Method in class org.biojava.bio.seq.io.AlternateTokenization
-
Bind a Symbol to a string.
- BioEntry - Interface in org.biojavax.bio
-
This class relates to the bioentry table in BioSQL.
- BioEntryDB - Interface in org.biojavax.bio.db
-
.
- BioEntryDBLite - Interface in org.biojavax.bio.db
-
A database of BioEntrys.
- BioEntryIterator - Interface in org.biojavax.bio
-
Essentially the same as SequenceIterator.
- BioEntryRelationship - Interface in org.biojavax.bio
-
Represents the relation between two bioentries.
- BIOENTRYS - Static variable in interface org.biojavax.bio.db.BioEntryDBLite
-
Signals that sequences are being added to or remove from the database.
- BioError - Error in org.biojava.bio
-
A nestable biological error.
- BioError() - Constructor for error org.biojava.bio.BioError
-
Create a new BioError.
- BioError(String) - Constructor for error org.biojava.bio.BioError
-
Create a new BioError with a message.
- BioError(String, Throwable) - Constructor for error org.biojava.bio.BioError
-
Create a new BioError with a cause and a message.
- BioError(Throwable) - Constructor for error org.biojava.bio.BioError
-
Create a new BioError with a cause.
- BioError(Throwable, String) - Constructor for error org.biojava.bio.BioError
-
Deprecated.Use BioError(message, ex) instead.
- BioException - Exception in org.biojava.bio
-
A nestable biological exception.
- BioException() - Constructor for exception org.biojava.bio.BioException
-
Create a new BioException.
- BioException(String) - Constructor for exception org.biojava.bio.BioException
-
Create a new BioException with a message.
- BioException(String, Throwable) - Constructor for exception org.biojava.bio.BioException
-
Create a new BioException with a cause and a message.
- BioException(Throwable) - Constructor for exception org.biojava.bio.BioException
-
Create a new BioException with a cause.
- BioException(Throwable, String) - Constructor for exception org.biojava.bio.BioException
-
Deprecated.use new BioException(message, ex) instead
- BioFetchSequenceDB - Class in org.biojava.bio.seq.db.biofetch
-
Simple SequenceDB implementation backed by a BioFetch (HTTP) server.
- BioFetchSequenceDB(String, String) - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
-
Construct a BioFetchSequenceDB which connects to the specified BioFetch server.
- BioFetchSequenceDBProvider - Class in org.biojava.bio.seq.db.biofetch
-
Directory-services plugin for biofetch databases.
- BioFetchSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
- BioIndex - Class in org.biojava.bio.seq.db
-
The original object for indexing sequence files.
- BioIndex(File) - Constructor for class org.biojava.bio.seq.db.BioIndex
-
Load an existing index file.
- BioIndex(File, String, int) - Constructor for class org.biojava.bio.seq.db.BioIndex
- biojavaToFile(int, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.Converts a Biojava object to the given filetype.
- biojavaToFile(String, String, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.Writes a Biojava
SequenceIterator
,SequenceDB
,Sequence
orAligment
to anOutputStream
- BioMatcher - Interface in org.biojava.bio.search
-
Interface for things that perform matches.
- BioPattern - Interface in org.biojava.bio.search
- BIOPHYSICOCHEMICAL_PROPERTIES - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
-
A name for a comment type.
- BioRuntimeException - Exception in org.biojava.bio
-
A nestable biological exception.
- BioRuntimeException() - Constructor for exception org.biojava.bio.BioRuntimeException
-
Create a new BioRuntimeException.
- BioRuntimeException(String) - Constructor for exception org.biojava.bio.BioRuntimeException
-
Create a new BioRuntimeException with a message.
- BioRuntimeException(String, Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException
-
Create a new BioRuntimeException with a cause and a message.
- BioRuntimeException(Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException
-
Create a new BioRuntimeException with a cause.
- BioRuntimeException(Throwable, String) - Constructor for exception org.biojava.bio.BioRuntimeException
-
Deprecated.use new BioRuntimeException(message, ex) instead
- BIOSEQUENCE_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
- BIOSEQUENCE_ORACLECLOB - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
- BioSQLAcceptAllFilter - Class in org.biojavax.bio.db.biosql
-
The class that accepts all features.
- BioSQLAcceptAllFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
- BioSQLAcceptNoneFilter - Class in org.biojavax.bio.db.biosql
-
The class that accepts no features.
- BioSQLAcceptNoneFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
- BioSQLBioEntryDB - Class in org.biojavax.bio.db.biosql
- BioSQLBioEntryDB(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
-
Creates a new instance of BioSQLBioEntryDB
- BioSQLBioEntryDB(String, Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
-
Creates a new instance of BioSQLBioEntryDB
- BioSQLCrossReferenceResolver - Class in org.biojavax.bio.db.biosql
-
A simple implementation of CrossReferenceResolver
- BioSQLCrossReferenceResolver(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
-
Requires a Hibernate session to work correctly.
- BioSQLFeatureFilter - Interface in org.biojavax.bio.db.biosql
-
A filter for accepting or rejecting a feature.
- BioSQLFeatureFilter.And - Class in org.biojavax.bio.db.biosql
-
A filter that returns all features accepted by both child filter.
- BioSQLFeatureFilter.ByName - Class in org.biojavax.bio.db.biosql
-
Construct one of these to filter features by display name.
- BioSQLFeatureFilter.ByNote - Class in org.biojavax.bio.db.biosql
-
A filter that returns all features that have the given note, and the value and rank is checked as well.
- BioSQLFeatureFilter.ByNoteTermOnly - Class in org.biojavax.bio.db.biosql
-
A filter that returns all features that have a note with the given term.
- BioSQLFeatureFilter.ByRank - Class in org.biojavax.bio.db.biosql
-
Construct one of these to filter features by rank.
- BioSQLFeatureFilter.BySequenceName - Class in org.biojavax.bio.db.biosql
-
Accept features that reside on a sequence with a particular name.
- BioSQLFeatureFilter.BySourceTerm - Class in org.biojavax.bio.db.biosql
-
Construct one of these to filter features by source.
- BioSQLFeatureFilter.BySourceTermName - Class in org.biojavax.bio.db.biosql
-
Construct one of these to filter features by source (name only - parent ontology is ignored).
- BioSQLFeatureFilter.ByStrand - Class in org.biojavax.bio.db.biosql
-
A filter that returns all features having locations on a given strand.
- BioSQLFeatureFilter.ByTypeTerm - Class in org.biojavax.bio.db.biosql
-
Construct one of these to filter features by type.
- BioSQLFeatureFilter.ByTypeTermName - Class in org.biojavax.bio.db.biosql
-
Construct one of these to filter features by type (name only - parent ontology is ignored).
- BioSQLFeatureFilter.ContainedByRichLocation - Class in org.biojavax.bio.db.biosql
-
A filter that returns all features contained within a location.
- BioSQLFeatureFilter.HibernateFeatureFilter - Class in org.biojavax.bio.db.biosql
-
A filter for Hibernate-BioSQL filters to extend.
- BioSQLFeatureFilter.Not - Class in org.biojavax.bio.db.biosql
-
A filter that returns all features not accepted by a child filter.
- BioSQLFeatureFilter.Or - Class in org.biojavax.bio.db.biosql
-
A filter that returns all features accepted by at least one child filter.
- BioSQLFeatureFilter.OverlapsRichLocation - Class in org.biojavax.bio.db.biosql
-
A filter that returns all features overlapping a location.
- BioSQLFeatureFilter.Tools - Class in org.biojavax.bio.db.biosql
-
A class representing some useful stuff you can do with BioSQLFeatureFilters, for instance converting plain FeatureFilters into a their BioSQLFeatureFilter equivalents (where possible).
- BioSQLRichObjectBuilder - Class in org.biojavax.bio.db.biosql
-
Takes requests for RichObjects and sees if it can load them from a Hibernate database.
- BioSQLRichObjectBuilder(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder
-
Creates a new instance of SimpleRichObjectBuilder.
- BioSQLRichSequenceDB - Class in org.biojavax.bio.db.biosql
- BioSQLRichSequenceDB(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
Creates a new instance of BioSQLRichSequenceDB
- BioSQLRichSequenceDB(String, Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
Creates a new instance of BioSQLRichSequenceDB
- BioSQLRichSequenceHandler - Class in org.biojavax.bio.db.biosql
-
A handler which loads sequence data from a BioSQL database, caching it where possible.
- BioSQLRichSequenceHandler(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
-
Requires a Hibernate session to work correctly.
- BioSQLSequenceDB - Class in org.biojava.bio.seq.db.biosql
-
Deprecated.Use hibernate and org.biojavax.bio.db.*
- BioSQLSequenceDB(String, String, String, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.Connect to a BioSQL database.
- BioSQLSequenceDB(String, String, String, String, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.Connect to a BioSQL database.
- BioSQLSequenceDB(DataSource, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- BioSQLSequenceDBProvider - Class in org.biojava.bio.seq.db.biosql
-
Deprecated.Use hibernate and org.biojavax.bio.db.*
- BioSQLSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
-
Deprecated.
- BioStore - Class in org.biojava.bio.program.indexdb
-
BioStore
s 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
createsBioStore
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 aList
withHomology
instances created from SAX events supplied via aSeqSimilarityAdapter
. - BlastLikeHomologyBuilder(List) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
Creates a new
BlastLikeHomologyBuilder
which will instantiateHomology
objects into theList
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 createSeqSimilaritySearchResult
s from SAX events via aSeqSimilarityAdapter
. - BlastLikeSearchBuilder(List) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
Creates a new
BlastLikeSearchBuilder
which will instantiate results into theList
target. - BlastLikeSearchBuilder(List, SequenceDB, SequenceDBInstallation) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
Creates a new
BlastLikeSearchBuilder
which will instantiate results into theList
target. - BlastLikeSearchFilter - Interface in org.biojava.bio.search
-
A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.
- BlastLikeSearchFilter.AbstractBlastLikeSearchFilter - Class in org.biojava.bio.search
- BlastLikeSearchFilter.And - Class in org.biojava.bio.search
- BlastLikeSearchFilter.ByHitProperty - Class in org.biojava.bio.search
-
Applies test to the value specified by the key in hit properties.
- BlastLikeSearchFilter.BySearchProperty - Class in org.biojava.bio.search
-
Applies test to the value specified by the key in search properties.
- BlastLikeSearchFilter.BySubHitProperty - Class in org.biojava.bio.search
-
Applies test to the value specified by the key in subhit properties.
- BlastLikeSearchFilter.Node - Interface in org.biojava.bio.search
- BlastLikeSearchFilter.Not - Class in org.biojava.bio.search
- BlastLikeSearchFilter.Or - Class in org.biojava.bio.search
- BlastLikeToXMLConverter - Class in org.biojava.bio.program
-
A class that converts the raw output from a variety of bioinformatics software and converts it to XML that will validate against the biojava:BlastLikeDataSetCollection DTD.
- BlastLikeToXMLConverter(String) - Constructor for class org.biojava.bio.program.BlastLikeToXMLConverter
-
Creates a new
BlastToXMLConverter
instance. - BlastXMLParser - Class in org.biojava.bio.program.sax.blastxml
-
This class parses NCBI Blast XML output.
- BlastXMLParser() - Constructor for class org.biojava.bio.program.sax.blastxml.BlastXMLParser
- BlastXMLParserFacade - Class in org.biojava.bio.program.sax.blastxml
-
A facade class that wraps the NCBI Blast XML parsing framework in a more user-friendly form.
- BlastXMLParserFacade() - Constructor for class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
- BLEPH_MNUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the blepharisma macronuclear genetic code.
- Block(int, int, int, int) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
- Block(SimpleGappedSymbolList.Block) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
- blockCount(Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Return the number of contiguous blocks in a location.
- blockEnded(NexusBlockParser) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
- blockEnded(NexusBlockParser) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
-
This method gets called when the block parser is expected to have finished parsing a block.
- blockIterator() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
- blockIterator() - Method in class org.biojava.bio.symbol.AbstractRangeLocation
- blockIterator() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
- blockIterator() - Method in interface org.biojava.bio.symbol.Location
-
Return an Iterator over the set of maximal contiguous sub-locations.
- blockIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
-
Iterate over all blocks in the file in order.
- blockIterator() - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Return an Iterator over the set of maximal contiguous sub-locations.
- blockIterator() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Return an Iterator over the set of maximal contiguous sub-locations.
- blockIterator() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Return an Iterator over the set of maximal contiguous sub-locations.
- BlockIterator() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
Get list of the un-gapped region of the SymbolList.
- BlockPainter - Interface in org.biojava.bio.gui
- BLUNT - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
-
BLUNT
the end type created by enzymes which leave a blunt end. - BooleanElementHandlerBase - Class in org.biojava.utils.stax
-
StAX handler for any element which just contains a string representation of an boolean.
- BooleanElementHandlerBase() - Constructor for class org.biojava.utils.stax.BooleanElementHandlerBase
- Border() - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
- BOTH_FORWARD_COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
- BoundaryFinder - Interface in org.biojava.bio.program.tagvalue
- bPointers - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
- bPointers - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
-
Description of the Field
- breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
-
Deprecated.Converts the symbol list passed in into an array of strings.
- breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.Converts the symbol list passed in into an array of strings.
- BROAD_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
- BROAD_SYNONYM - Static variable in class org.biojava.ontology.Synonym
- build() - Method in class org.biojava.bio.program.fastq.FastqBuilder
-
Build and return a new FASTQ formatted sequence configured from the properties of this builder.
- buildDataParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
-
Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener.
- buildDataStore(File, SequenceStreamer, Packing, int, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
- buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
- buildDataStore(File, SequenceDB, Packing, int, int) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory
-
Build a new DataStore.
- buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory
- buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory
- builder() - Static method in class org.biojava.bio.program.fastq.Fastq
-
Create and return a new FastqBuilder.
- builder(Fastq) - Static method in class org.biojava.bio.program.fastq.Fastq
-
Create and return a new FastqBuilder configured from the specified FASTQ formatted sequence.
- buildLibInfoParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
-
Generate a tag-value parser for the library info unigene files.
- buildObject(Class, List) - Method in class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder
-
This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
- buildObject(Class, List) - Method in interface org.biojavax.RichObjectBuilder
-
This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
- buildObject(Class, List) - Method in class org.biojavax.SimpleRichObjectBuilder
-
This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
- BumpedRenderer - Class in org.biojava.bio.gui.sequence
- BumpedRenderer() - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
- BumpedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
- BumpedRenderer(SequenceRenderer, int, int) - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
- ByAccession(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
- byAncestor(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Match features where at least one of the ancestors matches the specified filter.
- byAncestor(FeatureFilter.ByAncestor, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
- ByAncestor(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAncestor
- byAnnotation(Object, Object) - Static method in class org.biojava.bio.seq.FilterUtils
-
Match features where the annotation property named
key
is equal tovalue
. - ByAnnotation(Object, Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotation
-
Make a new ByAnnotation that will accept features with an annotation bundle containing 'value' associated with 'key'.
- byAnnotationType(Object, Class) - Static method in class org.biojava.bio.seq.FilterUtils
-
Match features where the annotation property named
key
is an instance ofvalClass
. - byAnnotationType(AnnotationType) - Static method in class org.biojava.bio.seq.FilterUtils
-
Match features with annotations matching the specified
AnnotationType
- ByAnnotationType() - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
- ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.PropertyConstraint.ByAnnotationType
-
Create a new constraint by type.
- ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
- byChild(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Match features where at least one child feature matches the supplied filter.
- byChild(FeatureFilter.ByChild, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
- ByChild(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByChild
- byClass(Class) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a filter which matches features which are assignable to the specified class or interface.
- ByClass(Class) - Constructor for class org.biojava.bio.PropertyConstraint.ByClass
-
Create a new ByClass instance.
- ByClass(Class) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByClass
- byComponentName(String) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a filter which matches all features which implement the
ComponentFeature
interface and have acomponentName
property equal to the specified value - ByComponentName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByComponentName
- byDescendant(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Match features where at least one decendant feature -- possibly but not necessarily an immediate child -- matches the specified filter.
- byDescendant(FeatureFilter.ByDescendant, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
- ByDescendant(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByDescendant
- ByFeature(Feature) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByFeature
- byFrame(FramedFeature.ReadingFrame) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a filter which matches FramedFeatures with the specified reading frame.
- byHitProperty(BlastLikeSearchFilter.ByHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
- ByHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
- ByHomologeneID(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
- ByLocalName(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
- ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
- ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
- ByLocationComparator() - Constructor for class org.biojava.bio.seq.Feature.ByLocationComparator
- ByLocationMinMaxComparator - Class in org.biojava.bio.seq
-
A Comparator similar to Feature.ByLocationComparator except that the min and max positions of the location are both compared
- ByLocationMinMaxComparator() - Constructor for class org.biojava.bio.seq.ByLocationMinMaxComparator
- ByLocationMinMaxFeatureComparator - Class in org.biojava.bio.seq
-
Comparator that compares the min and max positions of Features Required by org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer instances.
- ByLocationMinMaxFeatureComparator() - Constructor for class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
- byLocationOrder - Static variable in interface org.biojava.bio.seq.Feature
-
byLocationOrder
contains aFeature
comparator which compares by the minimum base position of theirLocation
. - ByLocusID(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
- ByMaxIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
- ByMinIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
- ByMinIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
- byName - Static variable in interface org.biojava.bio.seq.db.IDMaker
-
A simple implementation of IDMaker that hashes by sequence name.
- ByName() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByName
- ByName(String) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.ByName
- ByName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
-
Create a ByType filter that filters in all features with type fields equal to type.
- ByNote(Note) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
- ByNoteTermOnly(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
- ByNSName(String, String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
- ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
- ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
- byPairwiseScore(double, double) - Static method in class org.biojava.bio.seq.FilterUtils
-
Match SeqSimilaritiy features with scores in the specified range.
- ByPairwiseScore(double, double) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
-
Creates a new
ByPairwiseScore
. - byParent(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Match features where the parent feature matches the specified filter.
- byParent(FeatureFilter.ByParent, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
- ByParent(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByParent
- ByRank(int) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
-
Create a Rank filter that filters in all features with rank fields equal to rank.
- ByRef(String) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
- byScore - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
byScore
contains aSeqSimilaritySearchHit
comparator which compares by their score. - byScore - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
byScore
contains aSeqSimilaritySearchSubHit
comparator which compares by the score of the sub-hit. - ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
- ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
- bySearchProperty(BlastLikeSearchFilter.BySearchProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
- BySearchProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
- bySequenceName(String) - Static method in class org.biojava.bio.seq.FilterUtils
-
Match features attached to sequences with a specified name.
- BySequenceName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySequenceName
- BySequenceName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
- BySimilarityType(SimilarityType) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
- bySource(String) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a filter which matches features with a specific
source
value. - BySource(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySource
-
Create a BySource filter that filters in all features which have sources equal to source.
- BySourceTerm(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
-
Create a BySourceTerm filter that filters in all features with sourceTerm fields equal to source.
- BySourceTermName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
-
Create a BySourceTerm filter that filters in all features with sourceTerm fields having name equal to sourceTermName.
- byStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.FilterUtils
-
Match StrandedFeatures on the specified strand.
- ByStrand(RichLocation.Strand) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
-
Creates a filter that returns everything on strand str.
- bySubHitCount - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
bySubHitCount
contains aSeqSimilaritySearchHit
comparator which compares by their number of sub-hits. - BySubHitCountComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
- bySubHitProperty(BlastLikeSearchFilter.BySubHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
- BySubHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
- bySubjectStart - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
bySubjectStart
contains aSeqSimilaritySearchSubHit
comparator which compares by the start position of the sub-hit on the subject sequence. - BySubjectStartComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
- ByTaxon(Taxon) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
- ByTaxon(Taxon) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
- ByTaxonID(int) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
- BYTE_MAX_VALUE - Static variable in class org.biojava.bio.program.scf.SCF
-
Represents the maximum unsigned value of a byte for wrapping purposes
- ByteCode - Class in org.biojava.utils.bytecode
-
Factory for objects which encapsulate individual Java bytecode instructions.
- ByteCode() - Constructor for class org.biojava.utils.bytecode.ByteCode
- ByteElementHandlerBase - Class in org.biojava.utils.stax
-
StAX handler for any element which just contains a string representation of a byte.
- ByteElementHandlerBase() - Constructor for class org.biojava.utils.stax.ByteElementHandlerBase
- BYTES_IN_BYTE - Static variable in class org.biojava.utils.Constants
- BYTES_IN_CHAR - Static variable in class org.biojava.utils.Constants
- BYTES_IN_DOUBLE - Static variable in class org.biojava.utils.Constants
- BYTES_IN_FLOAT - Static variable in class org.biojava.utils.Constants
- BYTES_IN_INT - Static variable in class org.biojava.utils.Constants
- BYTES_IN_LONG - Static variable in class org.biojava.utils.Constants
- BYTES_IN_SHORT - Static variable in class org.biojava.utils.Constants
- bytesRead - Variable in class org.biojava.ontology.obo.OboFileParser
- ByTitle(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
- byType(String) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a filter which matches features with a specific
type
value. - ByType(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByType
-
Create a ByType filter that filters in all features with type fields equal to type.
- ByTypeTerm(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
-
Create a ByTypeTerm filter that filters in all features with typeTerm fields equal to typeTerm.
- ByTypeTermName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
-
Create a ByTypeTermName filter that filters in all features with typeTerm fields having name equal to typeTermName.
- byURN - Static variable in interface org.biojava.bio.seq.db.IDMaker
-
A simple implementation of IDMaker that hashes by URN.
- ByURN() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByURN
C
- c() - Static method in class org.biojava.bio.seq.DNATools
- c() - Static method in class org.biojava.bio.seq.NucleotideTools
- c() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the
AtomicSymbol
for the amino acid Cysteine - c() - Static method in class org.biojava.bio.seq.RNATools
- C_ELEGANS - Static variable in interface org.biojava.bio.program.homologene.Taxon
- cache - Variable in class org.biojava.utils.io.CachingInputStream
-
The byte cache itself.
- Cache - Interface in org.biojava.utils.cache
-
Interface for managing caches of objects.
- CACHE_PROPERTY - Static variable in class org.biojava.utils.io.InputStreamProvider
- cachedOutcome - Variable in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
- CacheMap - Interface in org.biojava.utils.cache
-
Interface for managing caches of objects fetchable by key.
- CacheReference - Interface in org.biojava.utils.cache
-
Interface for a reference to an object, analogous to
java.lang.ref.Referencce
, but more flexible. - CachingInputStream - Class in org.biojava.utils.io
-
A wrapper around
InputStream
that provides in-memory caching of the input data. - CachingInputStream(InputStream) - Constructor for class org.biojava.utils.io.CachingInputStream
- CachingKernel - Class in org.biojava.stats.svm
-
Caches the results of a nested kernel so that k(a, b) need only be calculated once.
- CachingKernel() - Constructor for class org.biojava.stats.svm.CachingKernel
- CachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.CachingKernel
- CachingSequenceDB - Class in org.biojava.bio.seq.db
-
SequenceDB implementation that caches the results of another SequenceDB.
- CachingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.CachingSequenceDB
-
Create a new CachingSequenceDB that caches the sequences in parent.
- calcCell(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator
-
Calculate the 'scores' array in the cell at cells[0][0].
- calcDist() - Method in class org.biojava.bio.gui.sequence.SequencePanel
- calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByName
- calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByURN
- calcID(Sequence) - Method in interface org.biojava.bio.seq.db.IDMaker
-
Calculate the id for a sequence.
- calcKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
- calcLineExtent(MouseEvent) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- calculatePrimRecLen(int) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
calculatePrimRecLen
calculates the byte length of primary namespace records. - calculateScore(Distribution, Symbol) - Method in interface org.biojava.bio.dp.ScoreType
-
Calculates the score associated with a distribution and a symbol.
- calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.NullModel
- calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Odds
- calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Probability
- calculateSecRecLen(int, String, Map) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
calculateSecRecLen
calculates the byte length of secondary namespace records. - callbackStack - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
this is the stack of handler objects for the current feature.
- callbackStack - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
this is the stack of handler objects for the current feature.
- callboxesValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Flag for call boxes.
- canAccept(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
-
Accepts all URLs that are of the file protocol.
- canAccept(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
-
Accepts all URLs that are of the jdbc protocol.
- canAccept(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
- canAccept(CodeClass) - Method in class org.biojava.utils.bytecode.ParametricType
- canAdvance() - Method in interface org.biojava.bio.dp.onehead.DPCursor
-
Can we advance?
- CANDIES_NOT_SORTED - Static variable in interface org.biojava.utils.candy.CandyVocabulary
-
A property name.
- CandyEntry - Class in org.biojava.utils.candy
-
This is a basic container for a vocabulary entry.
- CandyEntry() - Constructor for class org.biojava.utils.candy.CandyEntry
-
An empty constructor.
- CandyEntry(String) - Constructor for class org.biojava.utils.candy.CandyEntry
-
It creates an entry instance with given name and empty value.
- CandyEntry(String, String) - Constructor for class org.biojava.utils.candy.CandyEntry
-
It creates an entry instance with given name and value.
- CandyEntry(String, String, Hashtable) - Constructor for class org.biojava.utils.candy.CandyEntry
-
It creates an entry instance with given name, value and additional properties.
- CandyException - Exception in org.biojava.utils.candy
- CandyException(String) - Constructor for exception org.biojava.utils.candy.CandyException
- CandyException(String, Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
- CandyException(Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
- CandyFinder - Interface in org.biojava.utils.candy
-
This interface is a main entry point to a set of controlled vocabularies.
- CandyVocabulary - Interface in org.biojava.utils.candy
-
This interface defines functionality of a controlled vocabulary.
- canMerge(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Determines whether the locations are touching or not (if they could be merged in a single Location.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
-
Check to see if a given stream is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
Check to see if a given stream is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
-
Check to see if a given stream is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
-
Check to see if a given stream is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
-
Check to see if a given stream is in our format.
- canRead(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Check to see if a given stream is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
-
Check to see if a given stream is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
Check to see if a given stream is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat
-
Check to see if a given file is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
Check to see if a given file is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.FastaFormat
-
Check to see if a given file is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat
-
Check to see if a given file is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
-
Check to see if a given file is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Check to see if a given file is in our format.
- canRead(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Check to see if a given file is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat
-
Check to see if a given file is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
Check to see if a given file is in our format.
- CardinalityConstraint - Class in org.biojava.bio
-
A constraint on the number of values a property can have.
- Cavg - Static variable in class org.biojava.bio.proteomics.MassCalc
-
Constant value of Carbon average mass
- Cell - Class in org.biojava.bio.dp.twohead
-
A single cell in the DP matrix.
- Cell() - Constructor for class org.biojava.bio.dp.twohead.Cell
- CellCalculator - Interface in org.biojava.bio.dp.twohead
-
The interface for all functions that can calculate the 'scores' array for a given cell.
- CellCalculatorFactory - Interface in org.biojava.bio.dp.twohead
- CellCalculatorFactoryMaker - Interface in org.biojava.bio.dp.twohead
-
The interface for all functions that can calculate the 'scores' array for a given cell.
- CEREVISIAE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
-
Saccharomyces cerevisiae codon preferences
- ChainedChanger(ChangeTable.Changer[]) - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
- change(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
- change(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Changer
-
Produce a modified value from an old value.
- change(Object) - Method in class org.biojava.bio.program.tagvalue.RegexChanger
- change(Object, Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
- CHANGE_COMMON_NAME - Static variable in interface org.biojava.bio.taxa.Taxon
-
Deprecated.Change type to indicate that the common name of this Taxon is changing.
- CHANGE_SCIENTIFIC_NAME - Static variable in interface org.biojava.bio.taxa.Taxon
-
Deprecated.Change type to indicate that the scientific name of this Taxon is changing.
- Changeable - Interface in org.biojava.utils
-
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
- ChangeableCache - Class in org.biojava.utils.cache
-
A cache that clears values as the keys fire ChangeEvents of a given type.
- ChangeableCache(ChangeType) - Constructor for class org.biojava.utils.cache.ChangeableCache
- ChangeAdapter - Class in org.biojava.utils
-
This is a ChangeListener that ignores everything.
- ChangeAdapter() - Constructor for class org.biojava.utils.ChangeAdapter
- ChangeEvent - Class in org.biojava.utils
-
Event which encapsulates a change in any mutable BioJava object.
- ChangeEvent(Object, ChangeType) - Constructor for class org.biojava.utils.ChangeEvent
-
Construct a ChangeEvent with no change details.
- ChangeEvent(Object, ChangeType, Object) - Constructor for class org.biojava.utils.ChangeEvent
-
Construct a ChangeEvent specifying a new value for a property, or an object to be added to a collection.
- ChangeEvent(Object, ChangeType, Object, Object) - Constructor for class org.biojava.utils.ChangeEvent
-
Construct a ChangeEvent specifying a new value for a property, and giving the previous value.
- ChangeEvent(Object, ChangeType, Object, Object, ChangeEvent) - Constructor for class org.biojava.utils.ChangeEvent
-
Construct a ChangeEvent to be fired because another ChangeEvent has been received from a property object.
- ChangeEventRecorder() - Constructor for class org.biojava.utils.ChangeListener.ChangeEventRecorder
- ChangeForwarder - Class in org.biojava.utils
-
This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
- ChangeForwarder(Object, ChangeSupport) - Constructor for class org.biojava.utils.ChangeForwarder
-
Create a new ChangeForwarder for forwarding events.
- ChangeForwarder.Retyper - Class in org.biojava.utils
-
A ChangeForwarder that systematically uses a given type and wraps the old event.
- ChangeHub - Interface in org.biojava.utils
-
Interface implemented by ChangeHubs, i.e.
- ChangeListener - Interface in org.biojava.utils
-
Interface for objects which listen to ChangeEvents.
- ChangeListener.AlwaysVetoListener - Class in org.biojava.utils
-
An implementation that always vetoes everything.
- ChangeListener.ChangeEventRecorder - Class in org.biojava.utils
-
A listener that remembers the ChangeEvent of the last change.
- ChangeListener.LoggingListener - Class in org.biojava.utils
-
A listener that writes information about the event stream to a PrintStream.
- changeSupport() - Method in class org.biojava.utils.ChangeForwarder
-
Return the underlying
ChangeSupport
instance that can be used to fireChangeEvent
s and mannage listeners. - ChangeSupport - Class in org.biojava.utils
-
A utility class to provide management for informing ChangeListeners of ChangeEvents.
- ChangeSupport() - Constructor for class org.biojava.utils.ChangeSupport
-
Generate a new ChangeSupport instance.
- ChangeSupport(int) - Constructor for class org.biojava.utils.ChangeSupport
-
Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources.
- ChangeSupport(int, int) - Constructor for class org.biojava.utils.ChangeSupport
-
Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources, and which will grow by delta each time.
- ChangeSupport(Set) - Constructor for class org.biojava.utils.ChangeSupport
- ChangeSupport(Set, int, int) - Constructor for class org.biojava.utils.ChangeSupport
-
Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources, and which will grow by delta each time.
- ChangeTable - Class in org.biojava.bio.program.tagvalue
-
A mapping between keys and actions to turn old values into new values.
- ChangeTable() - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable
- ChangeTable.ChainedChanger - Class in org.biojava.bio.program.tagvalue
-
An implementation of Changer that applies a list of Changer instances to the value in turn.
- ChangeTable.Changer - Interface in org.biojava.bio.program.tagvalue
-
Callback used to produce a new value from an old one.
- ChangeTable.Splitter - Interface in org.biojava.bio.program.tagvalue
-
Callback used to produce a list of values from a single old one.
- ChangeType - Class in org.biojava.utils
-
Class for all constants which are used to indicate change types.
- ChangeType(String, Class, String) - Constructor for class org.biojava.utils.ChangeType
-
Construct a new ChangeType with supertype UNKNOWN.
- ChangeType(String, Class, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
-
Construct a new ChangeType.
- ChangeType(String, Field) - Constructor for class org.biojava.utils.ChangeType
-
Construct a new ChangeType with superType UNKNOWN.
- ChangeType(String, Field, ChangeType) - Constructor for class org.biojava.utils.ChangeType
-
Construct a new ChangeType.
- ChangeType(String, String, String) - Constructor for class org.biojava.utils.ChangeType
- ChangeType(String, String, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
- ChangeVetoException - Exception in org.biojava.utils
-
Exception which is thrown when a ChangeListener does not wish a change to take place.
- ChangeVetoException() - Constructor for exception org.biojava.utils.ChangeVetoException
- ChangeVetoException(String) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Create an exception with a detail message
- ChangeVetoException(String, Throwable) - Constructor for exception org.biojava.utils.ChangeVetoException
- ChangeVetoException(Throwable, String) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Deprecated.use new ChangeVetoException(reason, ex);
- ChangeVetoException(Throwable, ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Propogate an exception without (additional) explanation.
- ChangeVetoException(Throwable, ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Propogate an exception, giving a detail message
- ChangeVetoException(ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Construct an exception to veto a change without explanation.
- ChangeVetoException(ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Construct an exception to veto a change for a specified reason.
- CHARACTER - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
- characters(char[], int, int) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler
-
Describe
characters
method here. - characters(char[], int, int) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
- characters(char[], int, int) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
- characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
-
Signal a span of character data in the XML input.
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
- characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.StreamParser
- characters(char[], int, int) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
- characters(char[], int, int) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
- characters(char[], int, int) - Method in class org.biojava.utils.stax.CharElementHandlerBase
- characters(char[], int, int) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
- characters(char[], int, int) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
- characters(char[], int, int) - Method in class org.biojava.utils.stax.IntElementHandlerBase
- characters(char[], int, int) - Method in class org.biojava.utils.stax.LongElementHandlerBase
- characters(char[], int, int) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
- characters(char[], int, int) - Method in interface org.biojava.utils.stax.StAXContentHandler
- characters(char[], int, int) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
-
Signal a span of character data in the XML input.
- characters(char[], int, int) - Method in class org.biojava.utils.stax.StringElementHandlerBase
- CHARACTERS_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
A constant representing the name of Characters blocks.
- CharactersBlock - Class in org.biojavax.bio.phylo.io.nexus
-
Represents Nexus characters blocks.
- CharactersBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
Delegates to NexusBlock.Abstract constructor using CharactersBlock.CHARACTERS_BLOCK as the name.
- CharactersBlock(String) - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
For the DATA block subclass.
- CharactersBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus
-
Builds Nexus characters blocks.
- CharactersBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
- CharactersBlockListener - Interface in org.biojavax.bio.phylo.io.nexus
-
Listens to events that represent Nexus characters blocks.
- CharactersBlockParser - Class in org.biojavax.bio.phylo.io.nexus
-
Parses Nexus characters blocks.
- CharactersBlockParser(CharactersBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser
-
Delegates to NexusBlockParser.Abstract.
- CharacterTokenization - Class in org.biojava.bio.seq.io
-
Implementation of SymbolTokenization which binds symbols to single unicode characters.
- CharacterTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.CharacterTokenization
- charAt(int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
- charAt(int) - Method in class org.biojava.utils.RepeatedCharSequence
- CharElementHandlerBase - Class in org.biojava.utils.stax
-
StAX handler for any element which just contains a string representation of a char.
- CharElementHandlerBase() - Constructor for class org.biojava.utils.stax.CharElementHandlerBase
- charValue(Symbol) - Method in class org.biojava.utils.regex.PatternFactory
-
Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for.
- charValue(Symbol) - Method in class org.biojava.utils.regex.Search
- checkException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
- checkException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
- checkIOException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
- checkIOException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
- checkIOException() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
- children - Variable in class org.biojava.bio.taxa.SimpleTaxon
-
Deprecated.
- CHLORO_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the chlorophycean mitochondrial genetic code.
- Chromatogram - Interface in org.biojava.bio.chromatogram
-
Encapsulates the basic information you would want from a chromatogram.
- ChromatogramFactory - Class in org.biojava.bio.chromatogram
-
A factory that creates
Chromatogram
objects from files or streams. - ChromatogramFactory() - Constructor for class org.biojava.bio.chromatogram.ChromatogramFactory
- ChromatogramGraphic - Class in org.biojava.bio.chromatogram.graphic
-
Encapsulates a configurable method for drawing a
Chromatogram
into a graphics context. - ChromatogramGraphic() - Constructor for class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Default constructor with no Chromatogram.
- ChromatogramGraphic(Chromatogram) - Constructor for class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Creates a new
ChromatogramGraphic
, initially displaying the given chromatogram. - ChromatogramGraphic.Option - Class in org.biojava.bio.chromatogram.graphic
-
A typesafe enumeration of the options available for configuring the behavior of a
ChromatogramGraphic
instance. - ChromatogramNonlinearScaler - Interface in org.biojava.bio.chromatogram.graphic
-
Provides the mechanism whereby a ChromatogramGraphic can display a Chromatogram with a non-linear horizontal scale.
- ChromatogramNonlinearScaler.Identity - Class in org.biojava.bio.chromatogram.graphic
-
The default scaler that displays the chromatogram 1:1.
- ChromatogramTools - Class in org.biojava.bio.chromatogram
-
Utility class for dealing with
Chromatogram
s. - chromosomes - Variable in class org.biojavax.ga.impl.AbstractOrganism
- CHROMOSOMES - Static variable in interface org.biojavax.ga.Organism
- ChunkedSymbolList - Class in org.biojava.bio.symbol
-
SymbolList implementation using constant-size chunks.
- ChunkedSymbolList(SymbolList[], int, int, Alphabet) - Constructor for class org.biojava.bio.symbol.ChunkedSymbolList
- ChunkedSymbolListFactory - Class in org.biojava.bio.seq.io
-
class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves.
- ChunkedSymbolListFactory(SymbolListFactory) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
- ChunkedSymbolListFactory(SymbolListFactory, int) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
- CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.Protease
- CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.ProteaseManager
- CILIATE_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the ciliate nuclear genetic code.
- CIRCLE - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
-
CIRCLE
indicates a circular image map hotspot. - CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichLocation
- CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichSequence
- CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- CircularFeatureFilteringRenderer - Class in org.biojava.bio.gui.sequence
- CircularFeatureFilteringRenderer(CircularRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
- CircularFeatureRenderer - Interface in org.biojava.bio.gui.sequence
- CircularFeaturesRenderer - Class in org.biojava.bio.gui.sequence
- CircularFeaturesRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
- CircularFeaturesRenderer(CircularFeatureRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
- circularLength - Variable in class org.biojavax.bio.seq.SimpleRichLocation
- CircularLocation - Class in org.biojava.bio.symbol
-
Circular view onto an underlying Location instance.
- CircularLocation(Location, int) - Constructor for class org.biojava.bio.symbol.CircularLocation
-
Constructs a CircularLocation by wrapping another Location It is preferable to use LocationTools to make CircularLocations
- CircularLocation(Location, int, int) - Constructor for class org.biojava.bio.symbol.CircularLocation
-
Makes a CircularLocation where the 5' end of the Location is specified.
- CircularMLR - Class in org.biojava.bio.gui.sequence
-
Renders multiple renderers, each in their own concentric rings.
- CircularMLR() - Constructor for class org.biojava.bio.gui.sequence.CircularMLR
- CircularPaddedRenderer - Class in org.biojava.bio.gui.sequence
- CircularPaddedRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
- CircularPaddedRenderer(double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
- CircularPaddedRenderer(CircularRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
- CircularPaddedRenderer(CircularRenderer, double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
- CircularReferenceException - Exception in org.biojava.bio.taxa
-
Deprecated.replaced by classes in
org.biojavax.bio.taxa
- CircularReferenceException() - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
-
Deprecated.
- CircularReferenceException(String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
-
Deprecated.
- CircularReferenceException(Throwable) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
-
Deprecated.
- CircularReferenceException(Throwable, String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
-
Deprecated.
- CircularRenderer - Interface in org.biojava.bio.gui.sequence
-
Render information from a CircularRendererContext onto a graphics context.
- CircularRendererContext - Interface in org.biojava.bio.gui.sequence
-
A context providing information for rendering sequences into circular coordinate systems.
- CircularRendererPanel - Class in org.biojava.bio.gui.sequence
-
Renders a sequence as a circle using a CircularRenderer.
- CircularRendererPanel() - Constructor for class org.biojava.bio.gui.sequence.CircularRendererPanel
- CircularView - Class in org.biojava.bio.seq
-
A circular view onto another Sequence object.
- CircularView(Sequence) - Constructor for class org.biojava.bio.seq.CircularView
- CircularView(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.CircularView
- CITATION_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_FIRST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_ID_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_INSTITUTE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_ISSUE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_LAST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_PATENT_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_PUB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- CITATION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_VOL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CITATION_YEAR_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- ClassifierExample - Class in org.biojava.stats.svm.tools
-
A simple toy example that allows you to put points on a canvas, and find a polynomial hyperplane to seperate them.
- ClassifierExample() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample
- ClassifierExample.PointClassifier - Class in org.biojava.stats.svm.tools
-
An extention of JComponent that contains the points & encapsulates the classifier.
- classify() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Learn a model from the current points.
- classify(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
- classify(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
- classify(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
- Classify - Class in org.biojava.stats.svm.tools
- Classify() - Constructor for class org.biojava.stats.svm.tools.Classify
- classListToString(CodeClass[]) - Static method in class org.biojava.utils.bytecode.CodeUtils
-
Format an array of classes as a comma-seperated list.
- ClassTools - Class in org.biojava.utils
-
Utility methods for manipulating class objects and resources.
- clear() - Method in class org.biojava.bio.dp.twohead.EmissionCache
- clear() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
- clear() - Method in class org.biojava.stats.svm.AbstractSVMTarget
- clear() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
- clear() - Method in class org.biojava.stats.svm.SimpleSVMTarget
- clear() - Method in interface org.biojava.stats.svm.SVMClassifierModel
- clear() - Method in interface org.biojava.stats.svm.SVMTarget
- clear() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Remove all points from the canvas, and discard any model.
- clear() - Method in interface org.biojava.utils.cache.CacheReference
- clear() - Method in class org.biojava.utils.FileAsList
- clear() - Method in class org.biojava.utils.io.FlatFileCache
- clear() - Method in class org.biojava.utils.io.SoftHashMap
- clear() - Method in class org.biojavax.EmptyRichAnnotation
-
Removes all notes from this annotation object.
- clear() - Method in class org.biojavax.ga.util.WeightedSet
- clear() - Method in interface org.biojavax.RichAnnotation
-
Removes all notes from this annotation object.
- clear() - Method in class org.biojavax.SimpleRichAnnotation
-
Removes all notes from this annotation object.
- clearCounts() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
-
Clears all of the counts to zero.
- clearCounts() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
- clearCounts() - Method in interface org.biojava.bio.dp.TransitionTrainer
-
Clears all of the counts to zero.
- clearCounts(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.DistributionTrainer
-
Clears all of the counts to zero.
- clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
- clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
- clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
-
Deprecated.
- clearEnzymes() - Method in class org.biojava.bio.molbio.RestrictionMapper
-
clearEnzymes
removes all enzymes from those to be searched for in theSequence
. - clearLRUCache() - Static method in class org.biojavax.RichObjectFactory
-
Removes all objects from the LRU cache.
- clearLRUCache(Class) - Static method in class org.biojavax.RichObjectFactory
-
Removes all objects of the specified class from the LRU cache.
- clearPatterns() - Method in class org.biojava.utils.regex.Search
-
remove all patterns from the pattern cache.
- clearRenderers() - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
clearRenderers
removes all renderers from this renderer. - clearRenderers() - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
-
clearRenderers
removes all the renderers. - clearTraces() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Sets the trace data structures to null.
- clearTraceValues() - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
-
Sets all the traces to null.
- ClientSide(String) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ClientSide
-
Creates a new
ClientSide
image map. - clobToString(Connection, ResultSet, int) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
-
Deprecated.
- clone() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Performs a partial deep copy and invalidates regenerable structures.
- clone() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
- clone() - Method in class org.biojava.bio.seq.Feature.Template
- clone() - Method in class org.biojava.bio.seq.impl.RevCompSequence
-
clone() should make a complete copy of the Sequence with all features (and children) and return a SimpleSequence that is unconnected from the original sequence.
- clone() - Method in class org.biojava.utils.ExecRunner
-
We override the
clone
method here to prevent cloning of our class. - clone() - Method in class org.biojava.utils.TypedProperties
- close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
close
closes the underlyingInputStream
. - close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
-
close
closes the underlyingRandomAccessFile
. - close() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
close
closes the underlyingEntryNamRandomAccess
which in turn closes the lower levelRandomAccessFile
. - 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 underlyingRandomAccessFile
. - close() - Method in class org.biojava.utils.xml.PrettyXMLWriter
- close() - Method in interface org.biojava.utils.xml.XMLWriter
-
Close this XMLWriter, and it's underlying stream.
- closeSubComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
- closeTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
- closeTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
- closeTag(String) - Method in interface org.biojava.utils.xml.XMLWriter
-
Closes an un-qualified element.
- closeTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
- closeTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
-
Closes an element
- CLUSTAL - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
CLUSTAL
indicates that the alignment format is Clustal. - CLUSTAL_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
CLUSTAL_AA
premade CLUSTAL | AA; - CLUSTAL_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
CLUSTAL_DNA
premade CLUSTAL | DNA; - CLUSTAL_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
CLUSTAL_RNA
premade CLUSTAL | RNA; - ClustalWAlignmentSAXParser - Class in org.biojava.bio.program.sax
-
A SAX2 parser for dealing with a multiple sequence alignment as produced by ClustalW outputing .aln format.
- ClustalWAlignmentSAXParser() - Constructor for class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser
-
Initialises internal state Sets namespace prefix to "biojava"
- Cmono - Static variable in class org.biojava.bio.proteomics.MassCalc
-
Constant value of Carbon monoisotopic mass
- CNBr - Static variable in class org.biojava.bio.proteomics.Protease
- CNBr - Static variable in class org.biojava.bio.proteomics.ProteaseManager
- CodeClass - Interface in org.biojava.utils.bytecode
-
Interface for Java classes within the bytecode generation framework.
- CodeContext - Interface in org.biojava.utils.bytecode
-
Interface which encapsulates the stream to which Java bytecode can be written.
- CodeException - Exception in org.biojava.utils.bytecode
-
An exception indicating that something went wrong generating byte code.
- CodeException() - Constructor for exception org.biojava.utils.bytecode.CodeException
- CodeException(String) - Constructor for exception org.biojava.utils.bytecode.CodeException
- CodeField - Class in org.biojava.utils.bytecode
-
Wrap up details about a field in a Java class file.
- CodeGenerator - Interface in org.biojava.utils.bytecode
-
Interface for an object which can produce Java bytecode.
- CodeMethod - Interface in org.biojava.utils.bytecode
-
Wrap up details about a method in a Java class file
- codes - Variable in class org.biojava.bibliography.BiblioSubject
-
Classification code (call number) is usually either Dewey decimal or Congress classification.
- CodeUtils - Class in org.biojava.utils.bytecode
-
Utility code for things you will frequently need.
- CodeUtils() - Constructor for class org.biojava.utils.bytecode.CodeUtils
- CodonPref - Interface in org.biojava.bio.symbol
- CodonPrefFilter - Interface in org.biojava.bio.symbol
- CodonPrefFilter.AcceptAll - Class in org.biojava.bio.symbol
- CodonPrefFilter.ByName - Class in org.biojava.bio.symbol
- CodonPrefFilter.EverythingToXML - Class in org.biojava.bio.symbol
- CodonPrefTools - Class in org.biojava.bio.symbol
-
An utility class for codon preferences
- CodonPrefTools() - Constructor for class org.biojava.bio.symbol.CodonPrefTools
- CollectionConstraint - Interface in org.biojava.bio
-
Used by
AnnotationType
to represent the constraint on the collection of values in a property-slot. - CollectionConstraint.AllValuesIn - Class in org.biojava.bio
-
CollectionConstraint which validates all members of a Collection.
- CollectionConstraint.And - Class in org.biojava.bio
-
A collection constraint that accpepts collections iff they are accepted by both child constraints.
- CollectionConstraint.Contains - Class in org.biojava.bio
-
CollectionConstraint which validates a portion of a Collection.
- CollectionConstraint.Or - Class in org.biojava.bio
-
A collection constraint that accepts items iff they are accepted by either child constraints.
- colors - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
The map containing the colors for drawing traces.
- ColourCommand - Interface in org.biojava.bio.program.blast2html
-
Interface for specifying whether a particular pair of residues/bases should be coloured.
- columns - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
- columns() - Method in class org.biojava.bio.dp.ProfileHMM
-
Retrieve the number of columns in the model.
- columns() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
- columns() - Method in interface org.biojava.bio.dp.WeightMatrix
-
The number of columns modeled by the weight matrix.
- Comment - Interface in org.biojavax
-
A simple ranked comment designed to be used for BioEntry comments in BioSQL.
- COMMENT - Static variable in class org.biojava.ontology.obo.OboFileHandler
- COMMENT - Static variable in interface org.biojavax.bio.BioEntry
- COMMENT_ABS_MAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_ABSORPTION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_ERROR_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_EVENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_EXPERIMENTS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_INTERACT_INTACT_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_INTERACT_LABEL_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_INTERACTANT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_ISOFORM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_KIN_KM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_KIN_VMAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_KINETICS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_LINK_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_LINK_URI_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_LOCTYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_METHOD_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_ORGANISMS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_PH_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_REDOX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- COMMENT_TEMPERATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- commentIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
-
This iterator iterates over all parts of the comment.
- commentIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
-
Iterate over all comments in the file in order.
- commentLine(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
-
A comment line has been encountered.
- commentLine(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
- commentLine(String) - Method in class org.biojava.bio.program.gff.GFFWriter
-
Prints the comment directly to the PrintWriter after adding a leading '
#
'. - commentLine(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
-
A comment line has been encountered.
- commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
- commentText(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
-
Receiving free text inside a comment tag.
- commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
- commentText(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser
-
Receiving free text inside a comment tag.
- commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
- commentText(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener
-
Receiving free text inside a comment tag.
- commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
- commit() - Method in class org.biojava.bio.program.indexdb.BioStore
-
commit
writes an index to disk. - commit() - Method in class org.biojava.bio.seq.db.BioIndex
- commit() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
commit
commits changes. - commit() - Method in interface org.biojava.bio.seq.db.IndexStore
-
Commit the stored indices to permanent storage.
- commit() - Method in class org.biojava.bio.seq.db.TabIndexStore
- commit() - Method in interface org.biojava.utils.Commitable
-
commit
commits pending changes. - commit() - Method in class org.biojava.utils.FileAsList
- Commitable - Interface in org.biojava.utils
-
Implementations of
Commitable
support atomic changes from one known state to another via commit/rollback semantics. - CommitFailure - Exception in org.biojava.utils
- CommitFailure(String) - Constructor for exception org.biojava.utils.CommitFailure
- CommitFailure(String, Throwable) - Constructor for exception org.biojava.utils.CommitFailure
- CommitFailure(Throwable) - Constructor for exception org.biojava.utils.CommitFailure
- commitStore() - Method in class org.biojava.bio.seq.db.TabIndexStore
- COMMON - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
-
Use this to define common names for things.
- COMMON_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
- COMNAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CompactedDataStore - Class in org.biojava.bio.program.ssaha
-
An implementation of DataStore that will map onto a file using the NIO constructs.
- CompactedDataStoreFactory - Class in org.biojava.bio.program.ssaha
-
Builder for a data store that is backed by a java.nio.MappedByteBuffer.
- CompactedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
- ComparableOntology - Interface in org.biojavax.ontology
-
An Ontology that can be compared to another.
- ComparableTerm - Interface in org.biojavax.ontology
-
Makes Term objects comparable properly and adds some extra features to them.
- ComparableTriple - Interface in org.biojavax.ontology
-
Comparable triples, obviously.
- comparator() - Static method in class org.biojava.bio.seq.ByLocationMinMaxComparator
- COMPARATOR - Static variable in class org.biojava.ontology.Synonym
- compare(Object, Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
- compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
- compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
- compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
- compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
- compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxComparator
- compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
- compare(Object, Object) - Method in class org.biojava.bio.seq.Feature.ByLocationComparator
- compare(Object, Object) - Method in class org.biojava.bio.seq.io.EmblReferenceComparator
- compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblFeatureComparator
-
Deprecated.
- compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblPropertyComparator
-
Deprecated.
- compareTo(Object) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
- compareTo(Object) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Empty Rich Locations return 0 when compared to other Empty ones, or -1 otherwise.
- compareTo(Object) - Method in class org.biojavax.bio.seq.RichLocation.Strand
-
Strands are compared first by symbol, then by number.
- compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Features are sorted first by rank, then parent, type, and source.
- compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Relations are compared first by rank, then object, subject, then finally term.
- compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
- compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntry
-
Bioentries are ordered first by namespace, then name, accession, and finally version.
- compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
-
A relationship is compared first by rank, then object, subject, and term.
- compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
NCBITaxon objects are compared only by their NCBITaxID fields.
- compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
-
Taxon names are sorted by class first, then name.
- compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Ontologies are compared only by name.
- compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Terms are sorted by ontology first, then name.
- compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Triples are sorted in order of ontology, subject, object, and finally predicate.
- compareTo(Object) - Method in class org.biojavax.SimpleComment
-
Comments are ordered first by their rank, then by a string comparison of their text values.
- compareTo(Object) - Method in class org.biojavax.SimpleCrossRef
-
Compares cross references first by database name, then by accession, then by version.
- compareTo(Object) - Method in class org.biojavax.SimpleDocRef
-
Document references are compared first by author, then by location, then by title.
- compareTo(Object) - Method in class org.biojavax.SimpleDocRefAuthor
-
Document authors are compared first by name, then consortium status, then editor status.
- compareTo(Object) - Method in class org.biojavax.SimpleNamespace
-
Namespaces are compared only by name.
- compareTo(Object) - Method in class org.biojavax.SimpleNote
-
Notes are compared first by rank, then by the term.
- compareTo(Object) - Method in class org.biojavax.SimpleRankedCrossRef
-
Ranked cross references are sorted first by rank, then by cross reference.
- compareTo(Object) - Method in class org.biojavax.SimpleRankedDocRef
-
Ranked document references are sorted first by rank then location then by actual document reference.
- compareTo(Synonym) - Method in class org.biojava.ontology.Synonym
- compile(String) - Method in class org.biojava.utils.regex.PatternFactory
-
Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
- compile(String, String) - Method in class org.biojava.utils.regex.PatternFactory
-
Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
- complement(Symbol) - Static method in class org.biojava.bio.seq.DNATools
-
Complement the symbol.
- complement(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
-
Complement the symbol.
- complement(Symbol) - Static method in class org.biojava.bio.seq.RNATools
-
Complement the symbol.
- complement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
-
Retrieve a complement view of list.
- complement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools
-
Retrieve a complement view of list.
- complement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
-
Retrieve a complement view of list.
- COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
- complementTable() - Static method in class org.biojava.bio.seq.DNATools
-
Get a translation table for complementing DNA symbols.
- complementTable() - Static method in class org.biojava.bio.seq.NucleotideTools
-
Get a translation table for complementing Nucleotide symbols.
- complementTable() - Static method in class org.biojava.bio.seq.RNATools
-
Get a translation table for complementing DNA symbols.
- complete() - Method in interface org.biojava.bio.program.fastq.ParseListener
-
Notify this listener the FASTQ formatted sequence is complete.
- completeCycle() - Method in interface org.biojava.bio.dp.HMMTrainer
-
indicate that a cycle of training is completed and the emission/transition matrices should be updated.
- completeCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer
- completedActivity(Object) - Method in interface org.biojava.utils.ActivityListener
-
Notification that an activity is complete.
- COMPONENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- ComponentFeature - Interface in org.biojava.bio.seq
-
Feature which represents a component in an assembly (contig).
- ComponentFeature.Template - Class in org.biojava.bio.seq
-
Template for constructing a new ComponentFeature.
- componentLocation - Variable in class org.biojava.bio.seq.ComponentFeature.Template
- componentLocationIterator() - Method in class org.biojava.bio.symbol.MergeLocation
- componentSequence - Variable in class org.biojava.bio.seq.ComponentFeature.Template
- componentSequenceName - Variable in class org.biojava.bio.seq.ComponentFeature.Template
- composeName(String, String) - Method in class org.biojava.naming.ObdaContext
- composeName(Name, Name) - Method in class org.biojava.naming.ObdaContext
- Composite() - Constructor for class org.biojava.directory.RegistryConfiguration.Composite
- Composition - Class in org.biojava.bio.molbio
-
Computes composition statistics about a
SymbolList
. - Composition() - Constructor for class org.biojava.bio.molbio.Composition
- Compound() - Constructor for class org.biojava.bio.program.formats.Ligand.Compound
- CompoundRichLocation - Class in org.biojavax.bio.seq
-
An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
- CompoundRichLocation() - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
- CompoundRichLocation(Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
-
Constructs a CompoundRichLocation from the given set of members, with the default term of "join".
- CompoundRichLocation(ComparableTerm, Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
-
Constructs a CompoundRichLocation from the given set of members.
- compute(double) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc.ChargeCalculator
-
computes charge at given pH
- compute(double) - Method in interface org.biojava.utils.math.ComputeObject
-
workhorse method for this class.
- ComputeObject - Interface in org.biojava.utils.math
-
interface for classes that return a single double precision value for a single double precision argument.
- conditionedDistributions() - Method in interface org.biojava.bio.dist.OrderNDistribution
-
Get the conditioned distributions.
- CONFIG_FILE - Static variable in class org.biojava.directory.SystemRegistry
- CONFIG_LOCATOR - Static variable in class org.biojava.directory.SystemRegistry
- conjunctAdd - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
- conjunction - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
- connect() - Method in interface org.biojava.bibliography.BibRefQuery
-
It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication.
- connect() - Method in interface org.biojava.bibliography.BibRefSupport
-
It creates a connection to an object providing the supporting utilities, or/and it makes all necessary initialization steps needed for further communication.
- connect() - Method in interface org.biojava.utils.candy.CandyFinder
-
It creates a connection to an object representing a vocabulary finder, or/and it makes all necessary initialization steps needed for further communication.
- connect(byte[]) - Method in interface org.biojava.bibliography.BibRefQuery
-
It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication, and it makes the collection described by collectionId the current collection.
- connectModel() - Method in class org.biojava.bio.dp.ProfileHMM
-
This is called by constructor in setting up the allowed transitions in the model
- connectModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
-
This is called by constructor in setting up the allowed transitions in the model
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- ConstantPool - Class in org.biojava.utils.bytecode
-
Build a Java class file constant pool.
- ConstantPool() - Constructor for class org.biojava.utils.bytecode.ConstantPool
- constantPoolSize() - Method in class org.biojava.utils.bytecode.ConstantPool
- Constants - Class in org.biojava.utils
-
Some usefull constants for working with binary files.
- Constants() - Constructor for class org.biojava.utils.Constants
- constrain(double) - Method in enum org.biojava.bio.program.fastq.FastqVariant
-
Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.
- construct(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
-
Constructs a RichLocation object based on the given collection of members.
- constructSubsets() - Method in class org.biojava.utils.automata.DfaBuilder
- containedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a filter which matches features with locations wholly contained by the specified
Location
. - ContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
-
Creates a filter that returns everything contained within loc.
- ContainedByRichLocation(RichLocation) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
-
Creates a filter that returns everything contained within loc.
- contains(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
- contains(int) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
- contains(int) - Method in class org.biojava.bio.symbol.CircularLocation
- contains(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
- contains(int) - Method in interface org.biojava.bio.symbol.Location
-
Checks if this location contains a point.
- contains(int) - Method in class org.biojava.bio.symbol.PointLocation
- contains(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Checks if this location contains a point.
- contains(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Checks if this location contains a point.
- contains(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Checks if this location contains a point.
- contains(Object) - Method in class org.biojava.utils.MergingSet
- contains(Object) - Method in class org.biojava.utils.SmallSet
- contains(Object) - Method in class org.biojavax.ga.util.WeightedSet
- contains(String) - Method in interface org.biojava.utils.candy.CandyVocabulary
-
It checks if a given entry exists in this vocabulary.
- contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
- contains(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
- contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
- contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
- contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
- contains(Location) - Method in class org.biojava.bio.symbol.CircularLocation
- contains(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
- contains(Location) - Method in interface org.biojava.bio.symbol.Location
-
Checks if this location contains the other.
- contains(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Checks if this location contains the other.
- contains(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Checks if this location contains the other.
- contains(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Checks if this location contains the other.
- contains(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Return
true
iff all indices inlocB
are also contained bylocA
. - contains(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
- contains(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet
-
Returns whether or not this Alphabet contains the symbol.
- contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
- contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
- contains(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
- contains(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
- contains(Note) - Method in class org.biojavax.EmptyRichAnnotation
-
Returns true if the given note exists in this annotation.
- contains(Note) - Method in interface org.biojavax.RichAnnotation
-
Returns true if the given note exists in this annotation.
- contains(Note) - Method in class org.biojavax.SimpleRichAnnotation
-
Returns true if the given note exists in this annotation.
- Contains(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.Contains
-
Create a Contains based upon a PropertyConstraint and a cardinality.
- CONTAINS_PREFIX - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
- containsAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
- containsCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- containsFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder
-
Check if the feature is present in this holder.
- containsFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
-
containsFeature() will return true if this seq contains the feature in question, or if if the original (non reverse complement) sequence contains the feature;
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence
- containsFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder
- containsFeature(Feature) - Method in class org.biojava.bio.seq.MergeFeatureHolder
- containsFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly
- containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
- containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
- containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly
- containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
- containsFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Check if the feature is present in this holder.
- containsFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Check if the feature is present in this holder.
- containsFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
Returns true if the given
FeatureFilter
is already contained in this renderer. - containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
- containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
- containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
- containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
- containsKey(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
- containsKey(Object) - Method in class org.biojava.utils.OverlayMap
- containsKey(Object) - Method in class org.biojava.utils.SmallMap
- containsName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Tests for the presence of a name in a given class.
- containsName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Tests for the presence of a name in a given class.
- containsNode(FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
- containsObject(NexusObject) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile
-
Checks to see if we contain an object.
- containsProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
- containsProperty(Object) - Method in interface org.biojava.bio.Annotation
-
Returns whether there the property is defined.
- containsProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
- containsProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
- containsProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation
-
Returns whether there the property is defined.
- containsProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation
-
Deprecated.
- containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.Detects whether a particular table is present in the database.
- containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.HypersonicDBHelper
-
Deprecated.
- containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
-
Deprecated.
- containsTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
Checks to see if we contain the given TAXLABEL.
- containsTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
-
Checks to see if we contain the given TAXLABEL.
- containsTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
-
Checks to see if we contain the given TAXLABEL.
- containsTerm(String) - Method in class org.biojava.ontology.IntegerOntology
- containsTerm(String) - Method in interface org.biojava.ontology.Ontology
-
Determines if this ontology currently contains a term named
name
- containsTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
- containsTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Determines if this ontology currently contains a term named
name
- containsTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
-
Returns wether a transition exists or not.
- containsTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
- containsTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
- containsTranslation(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
-
Checks to see if we contain the given translation.
- containsTree(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
-
Checks to see if we contain the given tree.
- containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology
- containsTriple(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology
-
See if a triple exists in this ontology
- containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl
- containsTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
See if a triple exists in this ontology
- CONTENT - Static variable in interface org.biojava.bio.alignment.Alignment
-
Signals that SymbolLists will be added to or removed from an alignment.
- contextForLabel(SequenceRenderContext, String) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
- CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- contributors - Variable in class org.biojava.bibliography.BibRef
-
The authors and contributors are responsible for creating the contents of the cited resource.
- convert() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
- convert() - Method in class org.biojava.bio.program.PdbToXMLConverter
- convert(Fastq) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
- convert(Fastq) - Method in class org.biojava.bio.program.fastq.SangerFastqWriter
- convert(Fastq) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter
- convert(Fastq, FastqVariant) - Static method in class org.biojava.bio.program.fastq.FastqTools
-
Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
- convert(FeatureFilter) - Static method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools
-
Convert a non-BioSQL FeatureFilter into a BioSQL one.
- convertTo(FastqVariant) - Method in class org.biojava.bio.program.fastq.Fastq
-
Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.
- convertValueToText(Object, boolean, boolean, boolean, int, boolean) - Method in class org.biojava.bio.gui.FeatureTree
-
Labels
Sequence
objects with their name,Annotations
with the tag Annotations,Features
with the tag Features and other objects with thetoString
value. - COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- coordinateDisplayOn(boolean) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
-
coordinateDisplayOn
toggles the display of sequence coordinates. - COPYRIGHT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- cost - Variable in class org.biojava.bibliography.BiblioWebResource
-
The cost of accessing the resource.
- CostMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch
-
A matrix with the size length(sequence1) times length(sequence2)
- Count - Interface in org.biojava.bio.dist
-
An encapsulation of a count over the Symbols within an alphabet.
- CountedBufferedReader - Class in org.biojava.utils.io
- CountedBufferedReader(Reader) - Constructor for class org.biojava.utils.io.CountedBufferedReader
- countFeatures() - Method in interface org.biojava.bio.seq.FeatureHolder
-
Count how many features are contained.
- countFeatures() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
- countFeatures() - Method in class org.biojava.bio.seq.impl.DummySequence
- countFeatures() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
- countFeatures() - Method in class org.biojava.bio.seq.impl.RevCompSequence
- countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleFeature
- countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
- countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleSequence
- countFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
- countFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
- countFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
- countFeatures() - Method in class org.biojava.bio.seq.MergeFeatureHolder
- countFeatures() - Method in class org.biojava.bio.seq.NewSimpleAssembly
- countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
- countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
- countFeatures() - Method in class org.biojava.bio.seq.SimpleAssembly
- countFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
- countFeatures() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Count how many features are contained.
- countFeatures() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Count how many features are contained.
- COUNTS - Static variable in interface org.biojava.bio.dist.Count
-
Whenever a component count changes the values that would be returned by getCount, they should fire a ChangeEvent with this object as the type.
- countToDistribution(Count) - Static method in class org.biojava.bio.dist.DistributionTools
-
Make a distribution from a count.
- coverage - Variable in class org.biojava.bibliography.BibRef
-
It defines an extent or scope of the content of the cited resource.
- coverage(Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Return the number of positions which are covered by a
Location
- CRC64Checksum - Class in org.biojavax.utils
-
Utility class that calculates a CRC64 checksum on a stream of bytes.
- CRC64Checksum() - Constructor for class org.biojavax.utils.CRC64Checksum
- create(File) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
-
Creates a new
Chromatogram
object from the named file. - create(File) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
-
Create a new ABIF object from a file.
- create(File) - Static method in class org.biojava.bio.program.scf.SCF
- create(InputStream) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
-
Creates a new
Chromatogram
object from the supplied stream. - create(InputStream) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
-
Create a new ABIF object from a stream of bytes.
- create(InputStream, long) - Static method in class org.biojava.bio.program.scf.SCF
- CREATE_DATE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- CREATE_DUMMYSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
- CREATE_REALSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
- CREATE_REL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- createArrayType(String) - Static method in class org.biojava.utils.bytecode.ParametricType
-
Create a new ParametricType that claims to resolve to an array type.
- createBinary(String) - Static method in class org.biojavax.ga.util.GATools
-
Creates a
SymbolList
in the GABinaryAlphabet
- createBioStore() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
createBioStore
creates aBioStore
reflecting the current state of the factory and returns a reference to it. - createCode(OutputStream) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
- createDistribution(Alphabet) - Method in interface org.biojava.bio.dist.DistributionFactory
-
Generate a new Distribution as requested.
- createDistribution(Alphabet) - Method in class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
- createDistribution(Alphabet) - Method in class org.biojava.bio.dist.OrderNDistributionFactory
-
Creates an OrderNDistribution of the appropriate type.
- createDNA(String) - Static method in class org.biojava.bio.seq.DNATools
-
Return a new DNA SymbolList for dna.
- createDNA(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
-
Create and return a new DNA
SymbolList
from the specified FASTQ formatted sequence. - createDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools
-
Return a new DNA Sequence for dna.
- createDNASequence(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
-
Create and return a new DNA
Sequence
from the specified FASTQ formatted sequence. - createDP(MarkovModel) - Method in interface org.biojava.bio.dp.DPFactory
- createDP(MarkovModel) - Method in class org.biojava.bio.dp.DPFactory.DefaultFactory
- createDummy(String, String) - Static method in class org.biojava.bio.seq.SequenceTools
-
Create a new Sequence that has no annotation, no features and a zero-length symbol list.
- createDummy(Alphabet, int, Symbol, String, String) - Static method in class org.biojava.bio.seq.SequenceTools
-
Create a new Sequence that contains a single symbol repeated over and over.
- createDummySequence(String, Alphabet, int) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- createEmblParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.CircularView
-
Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
- createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.FeatureHolder
-
Create a new Feature, and add it to this FeatureHolder.
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.DummySequence
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.RevCompSequence
-
createFeature() will call createFeature() on the underlying Sequence.
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SubSequence
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.LazyFeatureHolder
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
- createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Create a projected feature with properties matching the template.
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
- createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Create a new Feature, and add it to this FeatureHolder.
- createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Create a new Feature, and add it to this FeatureHolder.
- createFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
Deprecated.Please use new 1-arg createFeature instead.
- createFeature(Feature, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Create a new projected feature.
- createFeature(Feature, Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
- createFeatureHolder() - Method in class org.biojava.bio.seq.LazyFeatureHolder
- createFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler
-
Create a new template of the appropriate type.
- createFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
- createField(String, CodeClass, int) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
- createGappedDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools
-
Get a new dna as a GappedSequence
- createGappedProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools
-
Get a new protein as a GappedSequence
- createGFFRecord(Feature, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Internal method to create a GFFRecord from an individual Feature.
- createImmutableAlignment(Map) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
A factory method for creating new immutable alignments, particularly for use as base call alignments.
- createImmutableSymbolList(Alphabet, List) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
A factory method for creating new symbol lists with a given alphabet.
- createInnerBounds(CircularRendererContext) - Static method in class org.biojava.bio.gui.sequence.GUITools
- createList(Object[]) - Static method in class org.biojava.utils.ListTools
- createList(List) - Static method in class org.biojava.utils.ListTools
- createMatches() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
- createMethod(String, CodeClass, CodeClass[], int) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
-
Create a new method.
- createMethod(String, CodeClass, CodeClass[], String[], int) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
-
Create a new method.
- createNodeSet() - Method in class org.biojava.utils.automata.FiniteAutomaton
- createNodeSet() - Method in interface org.biojava.utils.automata.NfaBuilder
- createNodeSet() - Method in class org.biojava.utils.automata.NfaSubModel
- createNucleotide(String) - Static method in class org.biojava.bio.seq.NucleotideTools
-
Return a new Nucleotide SymbolList for nucleotide.
- createNucleotideSequence(String, String) - Static method in class org.biojava.bio.seq.NucleotideTools
-
Return a new Nucleotide Sequence for nucleotide.
- createObjectType(String) - Static method in class org.biojava.utils.bytecode.ParametricType
-
Create a new ParametricType that claims to resolve to an object type.
- createOntology(String, String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- createOntology(String, String) - Method in interface org.biojava.ontology.OntologyFactory
-
Creates a new Ontology
- createOntologyTerm(Ontology) - Method in class org.biojava.ontology.Ontology.Impl
- createOrthologue(int, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Create an orthologue.
- createOrthologue(int, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
- createOrthologue(Taxon, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Create an orthologue.
- createOrthologue(Taxon, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
- createOrthoPair(Orthologue, Orthologue, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Create a curated orthology entry.
- createOrthoPair(Orthologue, Orthologue, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
- createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Create a computed orthology entry.
- createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
- createOrthoPairSet() - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Create a Homologene Group.
- createOrthoPairSet() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
- createOuterBounds(CircularRendererContext, double) - Static method in class org.biojava.bio.gui.sequence.GUITools
- createPhred(SymbolList, SymbolList) - Static method in class org.biojava.bio.program.phred.PhredTools
-
Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.
- createPhredSequence(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
-
Create and return a new
PhredSequence
from the specified FASTQ formatted sequence. - createPrimitiveType(String) - Static method in class org.biojava.utils.bytecode.ParametricType
-
Create a new ParametricType that claims to resolve to a primative type.
- createProtease(String, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
- createProtease(String, boolean, String, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
- createProtease(SymbolList, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
- createProtease(SymbolList, boolean, SymbolList, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
Creates and registers a new Protease.
- createProtein(String) - Static method in class org.biojava.bio.seq.ProteinTools
-
Return a new Protein SymbolList for protein.
- createProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools
-
Return a new PROTEIN Sequence for protein.
- createQualityScores(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
-
Create and return a new
SymbolList
of quality scores from the specified FASTQ formatted sequence. - createRecord(GFFDocumentHandler, List, String, String) - Method in class org.biojava.bio.program.gff.GFFParser
-
Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
- createRecord(GFF3DocumentHandler, List, String, String, Ontology, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser
-
Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.
- createRegex(SymbolList) - Static method in class org.biojava.bio.symbol.MotifTools
-
createRegex
creates a regular expression which matches theSymbolList
. - createRenderer(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
- createRenderer(int) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
- createRichSequence(String, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Create a new RichSequence in the specified namespace.
- createRichSequence(String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Create a new RichSequence in the default namespace.
- createRichSequence(String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Create a new RichSequence in the default namespace.
- createRichSequence(Namespace, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Create a new RichSequence in the specified namespace.
- createRichSequence(Namespace, String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Create a new RichSequence in the specified namespace.
- createRNA(String) - Static method in class org.biojava.bio.seq.RNATools
-
Return a new RNA SymbolList for rna.
- createRNASequence(String, String) - Static method in class org.biojava.bio.seq.RNATools
-
Return a new RNA Sequence for rna.
- createSequence(SymbolList, String, String, Annotation) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
- createSequence(SymbolList, String, String, Annotation) - Method in interface org.biojava.bio.seq.SequenceFactory
-
Deprecated.Creates a sequence using these parameters.
- createSequence(SymbolList, String, String, Annotation) - Static method in class org.biojava.bio.seq.SequenceTools
- createSeriesList(String, String, int) - Static method in class org.biojava.utils.ListTools
-
Create a new SeriesList with the given leader, trailer and size.
- createState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine
- createSubcontext(String) - Method in class org.biojava.naming.ObdaContext
- createSubcontext(String, Attributes) - Method in class org.biojava.naming.ObdaContext
- createSubcontext(Name) - Method in class org.biojava.naming.ObdaContext
- createSubcontext(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
- createSwissprotParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
- createSymbol(char, String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Deprecated.Use the two-arg version of this method instead.
- createSymbol(char, Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Deprecated.use the new version, without the token argument
- createSymbol(char, Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Deprecated.use the three-arg version of this method instead.
- createSymbol(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Generate a new AtomicSymbol instance with a name and an Empty Annotation.
- createSymbol(String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Generate a new AtomicSymbol instance with a name and Annotation.
- createSymbol(Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Generates a new Symbol instance that represents the tuple of Symbols in symList.
- createSymbol(Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Generates a new Symbol instance that represents the tuple of Symbols in symList.
- createSymbolDistribution(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools
-
Create and return a new array of symbol
Distribution
s from the specified FASTQ formatted sequence. - createTaxon(int, String) - Static method in class org.biojava.bio.program.homologene.HomologeneTools
-
add a Taxon
- createTaxon(String, String) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
-
Deprecated.
- createTaxon(String, String) - Method in interface org.biojava.bio.taxa.TaxonFactory
-
Deprecated.Create a new orphan Taxon with a given scientific and common name.
- createTaxon(String, String) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
-
Deprecated.
- createTemplate() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
generates a very basic Template for the feature with SmallAnnotation in the annotation field.
- createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
- createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
- createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
- createTemplate() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
generates a very basic Template for the feature with SmallAnnotation in the annotation field.
- createTerm(String) - Method in class org.biojava.ontology.IntegerOntology
- createTerm(String) - Method in interface org.biojava.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
- createTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Create a new term in this ontology.
- createTerm(String, String) - Method in class org.biojava.ontology.IntegerOntology
- createTerm(String, String) - Method in interface org.biojava.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String, String) - Method in class org.biojava.ontology.Ontology.Impl
- createTerm(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Create a new term in this ontology.
- createTerm(String, String, Object[]) - Method in class org.biojava.ontology.IntegerOntology
- createTerm(String, String, Object[]) - Method in interface org.biojava.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String, String, Object[]) - Method in class org.biojava.ontology.Ontology.Impl
- createTerm(String, String, Object[]) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Create a new term in this ontology.
- createTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
-
Makes a transition between two states legal.
- createTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
- createTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
- createTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine
- createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.IntegerOntology
- createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.ontology.Ontology
-
Creates a new Triple.
- createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.Ontology.Impl
- createTriple(Term, Term, Term, String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Creates a new Triple.
- createType(String) - Static method in class org.biojava.utils.bytecode.ParametricType
-
Create a new ParametricType that claims nothing.
- createType(String, FeatureFilter, Set) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
-
Create a new type in this repository.
- createType(String, CodeClass[]) - Static method in class org.biojava.utils.bytecode.ParametricType
-
Create a new ParametricType that claims to be castable to all the classes in a list.
- createUnigene(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
- createUnigene(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
- createUnigene(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
- createUnigene(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
-
Create a new UnigeneDB instance referred to by a URL.
- createURL(Object) - Method in interface org.biojava.utils.net.URLFactory
-
createURL
returns a URL which is relevant to the object in a way specified by the implementation. - createVariable(String, String) - Method in class org.biojava.ontology.IntegerOntology
- createVariable(String, String) - Method in interface org.biojava.ontology.Ontology
-
Create a new term in this ontology that is used as a variable.
- createVariable(String, String) - Method in class org.biojava.ontology.Ontology.Impl
- createVariable(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Create a new term in this ontology that is used as a variable.
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
- criterionAliasMap() - Method in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
-
Returns a map of property names (keys) to aliases (values), if the criterion returned by asCriterion() uses aliases at all.
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
- CROSS_OVER_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
- CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
- CrosshairRenderer - Class in org.biojava.bio.gui.sequence
-
CrosshairRenderer
draws a crosshair, optionally with coordinates. - CrosshairRenderer() - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer
-
Creates a new
CrosshairRenderer
in light grey with coordinates displayed. - CrosshairRenderer(Paint) - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer
-
Creates a new
CrosshairRenderer
of the specified colour, with coordinates displayed. - CrossOverFunction - Interface in org.biojavax.ga.functions
-
Crosses two chromosomes.
- CrossOverFunction.NoCross - Class in org.biojavax.ga.functions
-
A place holder CrossOverFunction that doesn't perform cross overs
- CrossProductTokenization - Class in org.biojava.bio.seq.io
-
Tokenization for cross-product alphabets.
- CrossProductTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
- CrossProductTokenization(Alphabet, List) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
- CrossRef - Interface in org.biojavax
-
Represents a cross reference to another database.
- CROSSREF - Static variable in interface org.biojavax.bio.seq.RichFeature
- CROSSREF - Static variable in interface org.biojavax.DocRef
- CrossReferenceResolutionException - Exception in org.biojavax
-
An exception that indicates that an attempt to resolve a
CrossRef
has failed. - CrossReferenceResolutionException() - Constructor for exception org.biojavax.CrossReferenceResolutionException
-
Creates a new instance of CrossReferenceResolutionException
- CrossReferenceResolutionException(String) - Constructor for exception org.biojavax.CrossReferenceResolutionException
-
Creates a new instance of CrossReferenceResolutionException with a message.
- CrossReferenceResolutionException(String, Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException
-
Creates a new instance of CrossReferenceResolutionException with a message and a cause.
- CrossReferenceResolutionException(Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException
-
Creates a new instance of CrossReferenceResolutionException with a cause.
- CrossReferenceResolver - Interface in org.biojavax
-
This interface returns symbols or sequence for a given cross-reference.
- crossReferences - Variable in class org.biojava.bibliography.BibRef
-
It is an array of identifiers, all of them pointing to the same cited source but usually stored in different bibliographic repositories.
- crypticVariable - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
- cState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
-
Gets the c loop state
- CURATED - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
- CURATED - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
- currentCol() - Method in interface org.biojava.bio.dp.onehead.DPCursor
-
The current column of the matrix.
- currentCol() - Method in class org.biojava.bio.dp.onehead.SmallCursor
- currentRes() - Method in interface org.biojava.bio.dp.onehead.DPCursor
-
The current symbol.
- CUT_COMPOUND - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
-
CUT_COMPOUND
a cut type where the enzyme cuts in two positions relative to the recognition site. - CUT_SIMPLE - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
-
CUT_SIMPLE
a cut type where the enzyme cuts in one position relative to the recognition site. - cutType - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
- cys() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the
AtomicSymbol
for the amino acid Cysteine (C)
D
- d() - Static method in class org.biojava.bio.seq.DNATools
- d() - Static method in class org.biojava.bio.seq.NucleotideTools
- d() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the
AtomicSymbol
for the amino acid Aspartic Acid - D_MELANOGASTER - Static variable in interface org.biojava.bio.program.homologene.Taxon
- D_RERIO - Static variable in interface org.biojava.bio.program.homologene.Taxon
- data - Variable in class org.biojava.bio.alignment.FlexibleAlignment
- DATA_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.DataBlock
-
A constant representing the name of Data blocks.
- DATA_TYPE_ASCII_ARRAY - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
- DATA_TYPE_DATE - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
- DATA_TYPE_FLOAT - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
- DATA_TYPE_INTEGER - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
- DATA_TYPE_PSTRING - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
- DATA_TYPE_TIME - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
- DATABASE - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
-
A name for a comment type.
- DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
- databaseID - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
- DatabaseURLGenerator - Interface in org.biojava.bio.program.blast2html
-
Takes a database ID and some configuration properties ( such as base URL ) and returns either a URL or a full anchor tag.
- DataBlock - Class in org.biojavax.bio.phylo.io.nexus
-
Represents Nexus data blocks.
- DataBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.DataBlock
-
Delegates to NexusBlock.Abstract constructor using DataBlock.DATA_BLOCK as the name.
- DataBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus
-
Builds Nexus characters blocks.
- DataBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.DataBlockBuilder
- DataBlockListener - Interface in org.biojavax.bio.phylo.io.nexus
-
Listens to events that represent Nexus data blocks.
- DataBlockParser - Class in org.biojavax.bio.phylo.io.nexus
-
Parses Nexus data blocks.
- DataBlockParser(DataBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.DataBlockParser
-
Delegates to CharactersBlockParser.
- dataRecord - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
- DATASOURCE - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
- DATASOURCE_SELECTION - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
- DataStore - Interface in org.biojava.bio.program.ssaha
-
A repository that can be searched with a sequence.
- DataStoreFactory - Interface in org.biojava.bio.program.ssaha
-
Builder for a data store.
- dataType - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
- date - Variable in class org.biojava.bibliography.BibRef
-
Defines a date associated with an event in the life cycle of the cited resource when this resource became available.
- DATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- DATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- DATE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- DATE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
- dateFormat - Variable in class org.biojava.ontology.obo.OboFileParser
- DB_NUCLEOTIDE - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
- DB_PROTEIN - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
- DBHelper - Class in org.biojava.bio.seq.db.biosql
-
Deprecated.Use hibernate and org.biojavax.bio.db.*
- DBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
- DBHelper.BioSequenceStyle - Class in org.biojava.bio.seq.db.biosql
-
Deprecated.
- DBHelper.DeleteStyle - Class in org.biojava.bio.seq.db.biosql
-
Deprecated.
- DBHelper.JoinStyle - Class in org.biojava.bio.seq.db.biosql
-
Deprecated.
- DBREF_DB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- DBREF_PRIMARY_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- DBREF_SEC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- DBREFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- DBResolver(SequenceDB) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
- dbxp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- dbxp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
- dbxp - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- DBXREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- debug(String) - Method in class org.biojava.bio.alignment.AbstractULAlignment
- DEBUG - Static variable in class org.biojava.utils.io.SoftHashMap
- DebuggingRichSeqIOListener - Class in org.biojavax.bio.seq.io
-
This is purely for debugging purposes.
- DebuggingRichSeqIOListener(InputStream) - Constructor for class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
- declareNamespace(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
- declareNamespace(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
-
Hints that a namespace is going to be used in a sub-tree.
- decodeDNAToken(char) - Static method in class org.biojava.bio.program.abi.ABIFParser
-
Decodes a character into a
Symbol
in the DNA alphabet. - decorate(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
- decorate(Location) - Method in class org.biojava.bio.symbol.BetweenLocation
- decorate(Location) - Method in class org.biojava.bio.symbol.CircularLocation
- DEF - Static variable in class org.biojava.ontology.obo.OboFileHandler
- DEFAULT - Static variable in interface org.biojava.bio.dist.DistributionFactory
-
The default DistributionFactory object.
- DEFAULT - Static variable in class org.biojava.bio.dist.OrderNDistributionFactory
-
Factory which used DistributionFactory.DEFAULT to create conditioned distributions.
- DEFAULT - Static variable in interface org.biojava.bio.dp.DPFactory
- DEFAULT - Static variable in class org.biojava.bio.program.phred.PhredFormat
- DEFAULT - Static variable in class org.biojava.bio.seq.impl.FeatureImpl
-
Default implementation of FeatureRealizer, which wraps simple implementations of Feature and StrandedFeature.
- DEFAULT - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- DEFAULT - Static variable in class org.biojava.bio.seq.io.FastaFormat
-
Deprecated.
- DEFAULT - Static variable in class org.biojava.bio.seq.io.GAMEFormat
- DEFAULT - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- DEFAULT - Static variable in class org.biojava.bio.seq.projection.ProjectionEngine
-
The standard projection engine object.
- DEFAULT - Static variable in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
- DEFAULT - Static variable in interface org.biojavax.ga.functions.SelectionFunction
-
Selects all members of a population for replication
- DEFAULT_CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
- DEFAULT_DELIMITERS - Static variable in class org.biojava.utils.TypedProperties
-
the default string of delimiter characters used by getAsStringList()
- DEFAULT_FINDER_NAME - Static variable in interface org.biojava.utils.candy.CandyFinder
-
A default name of this (and any) finder.
- DEFAULT_LIMIT - Static variable in class org.biojava.utils.io.SoftHashMap
- DEFAULT_MAX_CROSS - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
- DEFAULT_MUTATION_PROBS - Static variable in interface org.biojavax.ga.functions.MutationFunction
- DEFAULT_TERM_CHAR - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree
- DEFAULT_VARIANT - Static variable in class org.biojava.bio.program.fastq.FastqBuilder
-
Default FASTQ sequence format variant,
FastqVariant.FASTQ_SANGER
. - DefaultDistributionFactory() - Constructor for class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
- DefaultFactory(CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.DPFactory.DefaultFactory
- DefaultMaskingDetector() - Constructor for class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
- DefaultOps - Class in org.biojava.ontology
-
Default implementation of OntologyOps.
- DefaultOps() - Constructor for class org.biojava.ontology.DefaultOps
- DefaultURLGeneratorFactory - Class in org.biojava.bio.program.blast2html
-
A simple default
URLGeneratorFactory
which returns a singleNcbiDatabaseURLGenerator
instance. - DefaultURLGeneratorFactory() - Constructor for class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
- defineClass(GeneratedCodeClass) - Method in class org.biojava.utils.bytecode.GeneratedClassLoader
-
Define a class based upon a GeneratedCodeClass.
- DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
- DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
- delegate - Variable in class org.biojava.bio.program.tagvalue.StateMachine
- delegate(StAXContentHandler) - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
- delegate(StAXContentHandler) - Method in interface org.biojava.utils.stax.DelegationManager
- delegates - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
- DelegatingTransformer(FilterUtils.FilterTransformer, FilterUtils.FilterTransformer) - Constructor for class org.biojava.bio.seq.FilterUtils.DelegatingTransformer
-
Create a new DelegatingTransformer that will apply t1 and then t2 if t1 fails.
- delegationCache - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
- DelegationManager - Interface in org.biojava.bio.seq.io.agave
-
Interface which exposes delegation services offered by a StAX event source.
- DelegationManager - Interface in org.biojava.utils.stax
-
Interface which exposes delegation services offered by a StAX event source.
- DELETE_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
- DELETE_MYSQL4 - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
- DELETE_POSTGRESQL - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
- deleteTerm(Term) - Method in class org.biojava.ontology.IntegerOntology
- deleteTerm(Term) - Method in interface org.biojava.ontology.Ontology
-
Remove a term from an ontology, together with all triples which refer to it.
- deleteTerm(Term) - Method in class org.biojava.ontology.Ontology.Impl
- deleteTerm(Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Remove a term from an ontology, together with all triples which refer to it.
- DELIMITER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- depth - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
- depth - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
-
Description of the Field
- DEPTH - Static variable in class org.biojava.bio.gui.sequence.AbiTraceRenderer
- DEPTH - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
Constant
DEPTH
indicating a change to the depth of the renderer. - DEPTH - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer
- DESC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
- describeSequence(Sequence) - Method in class org.biojava.bio.program.phred.PhredFormat
-
Return a suitable description line for a Sequence.
- describeSequence(Sequence) - Method in class org.biojava.bio.seq.io.FastaFormat
-
Deprecated.Return a suitable description line for a Sequence.
- description - Variable in class org.biojava.bibliography.BibRef
-
An account of the content of the cited resource.
- description - Variable in class org.biojava.ontology.AbstractTerm
- description - Variable in class org.biojava.utils.candy.CandyEntry
-
A value of this entry.
- description(String) - Method in interface org.biojava.bio.program.fastq.ParseListener
-
Notify this parse listener of a description line.
- DESCRIPTION - Static variable in interface org.biojavax.bio.BioEntry
- DESCRIPTION - Static variable in interface org.biojavax.Namespace
- DESCRIPTION - Static variable in interface org.biojavax.ontology.ComparableOntology
- DESCRIPTION - Static variable in interface org.biojavax.ontology.ComparableTerm
- DESCRIPTOR - Static variable in interface org.biojavax.ontology.ComparableTriple
- destination - Variable in class org.biojava.bio.program.tagvalue.StateMachine.Transition
-
the terminus of this Transition
- destroy() - Method in interface org.biojava.bibliography.BibRefQuery
-
It frees all resources related to this query collection.
- destroy() - Method in interface org.biojava.utils.candy.CandyVocabulary
-
It frees all resources related to this vocabulary.
- destroy() - Static method in class org.biojava.utils.io.FlatFileCache
- destroySubcontext(String) - Method in class org.biojava.naming.ObdaContext
- destroySubcontext(Name) - Method in class org.biojava.naming.ObdaContext
- destroyTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
-
Breaks a transition between two states legal.
- destroyTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
- destroyTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
- DfaBuilder - Class in org.biojava.utils.automata
- DiagonalAddKernel - Class in org.biojava.stats.svm
-
Adds a class specific constant to k(x, x).
- DiagonalAddKernel() - Constructor for class org.biojava.stats.svm.DiagonalAddKernel
- DiagonalCachingKernel - Class in org.biojava.stats.svm
-
Caches the leading diagonal of a kernel matrix.
- DiagonalCachingKernel() - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel
-
Create a new CachingKernel.
- DiagonalCachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel
-
Creates a new DiagonalCachingKernel that nests k.
- diddleQueue() - Method in class org.biojava.utils.IndexedChangeHub
- Digest - Class in org.biojava.bio.proteomics
-
This class contains methods for calculating the results of proteolytic digestion of a protein sequence this class is not designed to be thread safe
- Digest() - Constructor for class org.biojava.bio.proteomics.Digest
-
Creates a new Digest Bean
- DIGEST - Static variable in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
- DIGEST - Static variable in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
- dimensionRatio - Variable in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
- disconnect() - Method in interface org.biojava.bibliography.BibRefQuery
-
It disconnects from the repository.
- disconnect() - Method in interface org.biojava.bibliography.BibRefSupport
-
It closes connection with a utility object.
- disconnect() - Method in interface org.biojava.utils.candy.CandyFinder
-
It closes connection with the finder object.
- DISJOINT_FROM - Static variable in class org.biojava.ontology.obo.OboFileHandler
- disjunctAdd - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
- disjunction - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
- DISPLACEMENT - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
Constant
DISPLACEMENT
indicating a change to the Y-axis displacement of the features. - displayString() - Method in class org.biojava.utils.ChangeSupport
- DistanceBasedTreeMethod - Class in org.biojavax.bio.phylo
- DistanceBasedTreeMethod() - Constructor for class org.biojavax.bio.phylo.DistanceBasedTreeMethod
- DISTANCES_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
-
A constant representing the name of Distances blocks.
- DistancesBlock - Class in org.biojavax.bio.phylo.io.nexus
-
Represents Nexus distances blocks.
- DistancesBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.DistancesBlock
-
Delegates to NexusBlock.Abstract constructor using DistancesBlock.DISTANCES_BLOCK as the name.
- DistancesBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus
-
Builds Nexus distances blocks.
- DistancesBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
- DistancesBlockListener - Interface in org.biojavax.bio.phylo.io.nexus
-
Listens to events that represent Nexus distances blocks.
- DistancesBlockParser - Class in org.biojavax.bio.phylo.io.nexus
-
Parses Nexus distances blocks.
- DistancesBlockParser(DistancesBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser
-
Delegates to NexusBlockParser.Abstract.
- DistDataSource - Interface in org.biojava.bio.seq.distributed
-
Object which contributes data to a DistributedSequenceDB.
- distForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
- distOverAlignment(Alignment) - Static method in class org.biojava.bio.dist.DistributionTools
-
Equivalent to distOverAlignment(a, false, 0.0).
- distOverAlignment(Alignment, boolean) - Static method in class org.biojava.bio.dist.DistributionTools
-
Creates an array of distributions, one for each column of the alignment.
- distOverAlignment(Alignment, boolean, double) - Static method in class org.biojava.bio.dist.DistributionTools
-
Creates an array of distributions, one for each column of the alignment.
- DistributedSequenceDB - Class in org.biojava.bio.seq.distributed
-
Sequence database from the meta-DAS system.
- DistributedSequenceDB() - Constructor for class org.biojava.bio.seq.distributed.DistributedSequenceDB
- Distribution - Interface in org.biojava.bio.dist
-
An encapsulation of a probability distribution over the Symbols within an alphabet.
- DISTRIBUTION - Static variable in interface org.biojava.bio.dp.EmissionState
-
This signals that the distribution associate with an EmissionState has been altered.
- Distribution.NullModelForwarder - Class in org.biojava.bio.dist
-
Deprecated.use
new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)
instead - DistributionFactory - Interface in org.biojava.bio.dist
-
A thing that can make Distributions.
- DistributionFactory.DefaultDistributionFactory - Class in org.biojava.bio.dist
-
The default DistributionFactory implementation.
- DistributionLogo - Class in org.biojava.bio.gui
-
The GUI component for rendering a DistributionLogo.
- DistributionLogo() - Constructor for class org.biojava.bio.gui.DistributionLogo
-
Create a new DistributionLogo object.
- DistributionTools - Class in org.biojava.bio.dist
-
A class to hold static methods for calculations and manipulations using Distributions.
- DistributionTrainer - Interface in org.biojava.bio.dist
-
An object that can be used to train a distribution up.
- DistributionTrainerContext - Interface in org.biojava.bio.dist
-
A context within a group of DistributionTrainers can be trained together.
- DIVISION - Static variable in interface org.biojavax.bio.BioEntry
- DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- DIVISION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
- DivisionLkpReader - Class in org.biojava.bio.seq.db.emblcd
-
DivisionLkpReader
reads the "division.lkp" file of an EMBL CD-ROM format binary index. - DivisionLkpReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.DivisionLkpReader
-
Creates a new
DivisionLkpReader
. - DNA - Static variable in interface org.biojava.bio.chromatogram.Chromatogram
-
The sequence label for the list of called bases.
- DNA - Static variable in class org.biojava.bio.seq.io.FastaAlignmentFormat
- DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
DNA
indicates that a sequence contains DNA (deoxyribonucleic acid) symbols. - DNAAmbPack - Class in org.biojava.bio.symbol
-
Packing utility class for DNA.
- DNAAmbPack() - Constructor for class org.biojava.bio.symbol.DNAAmbPack
- DNAComposition - Class in org.biojava.bio.molbio
-
Computes composition statistics about a DNA
SymbolList
. - DNAComposition() - Constructor for class org.biojava.bio.molbio.DNAComposition
- DNANoAmbPack - Class in org.biojava.bio.symbol
-
A
Packing
implementation which handles the DNA alphabet, without any support for ambiguity symbols. - DNANoAmbPack(byte) - Constructor for class org.biojava.bio.symbol.DNANoAmbPack
-
Construct a new packing which returns the specified byte value for unknown Symbols (such as ambiguity symbols).
- DNANoAmbPack(Symbol) - Constructor for class org.biojava.bio.symbol.DNANoAmbPack
-
Construct a new packing which translates unknown symbols into the specified symbol.
- DNAStyle - Class in org.biojava.bio.gui
-
A simple implementation of SymbolStyle optimized for DNA.
- DNAStyle() - Constructor for class org.biojava.bio.gui.DNAStyle
- dnaSymbolFromPhred(Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools
-
Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
- dnaToken(Symbol) - Static method in class org.biojava.bio.seq.DNATools
-
Get a single-character token for a DNA symbol
- DNATools - Class in org.biojava.bio.seq
-
Useful functionality for processing DNA sequences.
- DO_NOTHING - Static variable in class org.biojava.utils.bytecode.CodeUtils
- doAnnotation(Sequence) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
-
Apply the annotation to a sequence.
- docNumber - Variable in class org.biojava.bibliography.BiblioPatent
-
The document number.
- docOffice - Variable in class org.biojava.bibliography.BiblioPatent
-
Document office.
- DocRef - Interface in org.biojavax
-
Represents a documentary reference.
- DocRefAuthor - Interface in org.biojavax
-
Represents an author of a documentary reference.
- DocRefAuthor.Tools - Class in org.biojavax
-
Useful tools for working with authors.
- docType - Variable in class org.biojava.bibliography.BiblioPatent
-
Document type.
- documentEnd() - Method in interface org.biojava.ontology.obo.OboFileEventListener
-
end of parsing a new OBO file
- documentEnd() - Method in class org.biojava.ontology.obo.OboFileHandler
- documentStart() - Method in interface org.biojava.ontology.obo.OboFileEventListener
-
starting to parse a new OBO file
- documentStart() - Method in class org.biojava.ontology.obo.OboFileHandler
- DOI_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
-
Holds a reference to the key that must be used to store DOI references.
- doLayer(SequenceRenderContext, FeatureFilter) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
- DOMAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
- domain1 - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
- doPreProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Emit any per-sequence header information.
- doProcessFeature(Feature, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Internal method to process an individual Feature.
- doProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Internal method to process an individual Sequence.
- doRefreshRenderers() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
- doRetain() - Method in class org.biojava.bio.program.tagvalue.TagDropper
-
Find out if known tags are retained or dropped.
- doSortPeptides() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
- doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
- doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
- doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
- DotState - Interface in org.biojava.bio.dp
-
A Dot state.
- DoubleAlphabet - Class in org.biojava.bio.symbol
-
An efficient implementation of an Alphabet over the infinite set of double values.
- DoubleAlphabet.DoubleRange - Class in org.biojava.bio.symbol
-
A range of double values.
- DoubleAlphabet.DoubleSymbol - Class in org.biojava.bio.symbol
-
A single double value.
- DoubleAlphabet.SubDoubleAlphabet - Class in org.biojava.bio.symbol
-
A class to represent a contiguous range of double symbols.
- DoubleElementHandlerBase - Class in org.biojava.utils.stax
-
StAX handler for any element which just contains a string representation of a double.
- DoubleElementHandlerBase() - Constructor for class org.biojava.utils.stax.DoubleElementHandlerBase
- DoubleRange(double, double) - Constructor for class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
- Doublet() - Constructor for class org.biojava.utils.ListTools.Doublet
- Doublet(Object, Object) - Constructor for class org.biojava.utils.ListTools.Doublet
- DoubleTokenization - Class in org.biojava.bio.seq.io
- DoubleTokenization() - Constructor for class org.biojava.bio.seq.io.DoubleTokenization
- doubleValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
- doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
-
this method is expected to reverse-translate any symbol in the source alphabet.
- doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
-
this method is expected to reverse-translate any symbol in the source alphabet.
- doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
- doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
- dp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
- dp - Static variable in class org.biojavax.bio.seq.io.FastaFormat
- DP - Class in org.biojava.bio.dp
-
Objects that can perform dymamic programming operations upon sequences with HMMs.
- DP() - Constructor for class org.biojava.bio.dp.DP
-
This method will result in a DP with no model.
- DP(MarkovModel) - Constructor for class org.biojava.bio.dp.DP
- dp_ipi - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
- dp_uniprot - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
- DP.ReverseIterator - Class in org.biojava.bio.dp
- DPCompiler - Class in org.biojava.bio.dp.twohead
-
This is an implementation of CellCalculatorFactoryMaker that compiles the HMM object down to Java byte-code that is equivalent in behaviour to the interpreter.
- DPCompiler(boolean) - Constructor for class org.biojava.bio.dp.twohead.DPCompiler
- DPCursor - Interface in org.biojava.bio.dp.onehead
-
Encapsulates the dynamic programmming matrix, and the context within algorithms work.
- DPFactory - Interface in org.biojava.bio.dp
-
The interface for objects that can generate a DP object for a MarkovModel.
- DPFactory.DefaultFactory - Class in org.biojava.bio.dp
- DPInterpreter - Class in org.biojava.bio.dp.twohead
- DPInterpreter(DP) - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter
- DPInterpreter.Maker - Class in org.biojava.bio.dp.twohead
- DPMatrix - Interface in org.biojava.bio.dp
- DR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- DRAW_CALL_A - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating whether to fill in the callboxes for calls of nucleotide A.
- DRAW_CALL_C - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating whether to fill in the callboxes for calls of nucleotide C.
- DRAW_CALL_G - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating whether to fill in the callboxes for calls of nucleotide G.
- DRAW_CALL_OTHER - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating whether to fill in the callboxes for non-base calls (gaps, ambiguities).
- DRAW_CALL_SEPARATORS - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating whether to draw vertical lines separating the calls.
- DRAW_CALL_T - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating whether to fill in the callboxes for calls of nucleotide T.
- DRAW_TRACE_A - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating whether to draw the chromatogram trace for nucleotide A.
- DRAW_TRACE_C - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating whether to draw the chromatogram trace for nucleotide C.
- DRAW_TRACE_G - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating whether to draw the chromatogram trace for nucleotide G.
- DRAW_TRACE_T - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating whether to draw the chromatogram trace for nucleotide T.
- drawableCallboxesValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Flag for drawable call boxes.
- drawLine(Graphics2D, SequenceRenderContext, int, StrandedFeature.Strand) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
draws required bar in correct translation frame.
- drawTo(Graphics2D) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Draws the chromatogram onto the provided graphics context.
- dropBoundaryValues() - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
- DROSOPHILA_MELANOGASTER_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
-
Drosophila melanogaster codon preferences
- dsCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
- DummyCrossReferenceResolver - Class in org.biojavax
-
A simple implementation of CrossReferenceResolver.
- DummyCrossReferenceResolver() - Constructor for class org.biojavax.DummyCrossReferenceResolver
- DummyRichSequenceHandler - Class in org.biojavax.bio.seq
- DummyRichSequenceHandler() - Constructor for class org.biojavax.bio.seq.DummyRichSequenceHandler
- DummySequence - Class in org.biojava.bio.seq.impl
-
A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
- DummySequence(String, String) - Constructor for class org.biojava.bio.seq.impl.DummySequence
- DummySequenceDB - Class in org.biojava.bio.seq.db
-
DummySequenceDB
is an implementation which contains only aDummySequence
. - 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 sameDummySequenceDB
instance regardless of the identifier used to retrieve a database. - DummySequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.DummySequenceDBInstallation
- DummySymbolList - Class in org.biojava.bio.symbol
-
Symbol list which just consists of non-informative symbols.
- DummySymbolList(Alphabet, int, Symbol) - Constructor for class org.biojava.bio.symbol.DummySymbolList
- DummySymbolList(FiniteAlphabet, int) - Constructor for class org.biojava.bio.symbol.DummySymbolList
- dumpBlocks() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
Debugging method
- duplicate() - Method in class org.biojava.utils.automata.NfaSubModel
-
Makes a deep clone of this instance.
- DuplicateTaxonException - Exception in org.biojava.bio.program.homologene
- DuplicateTaxonException() - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
- DuplicateTaxonException(String) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
- DuplicateTaxonException(Throwable) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
- DuplicateTaxonException(Throwable, String) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
E
- e() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the
AtomicSymbol
for the amino acid Glutamic Acid - EbiDatabaseURLGenerator - Class in org.biojava.bio.program.blast2html
-
Simple URL generator for EMBL at the EBI.
- EbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
- EbiFormat - Class in org.biojava.bio.taxa
-
Deprecated.replaced by classes in
org.biojavax.bio.taxa
- EbiFormat() - Constructor for class org.biojava.bio.taxa.EbiFormat
-
Deprecated.
- EC_FROM_STRING - Static variable in class org.biojava.bio.program.formats.FormatTools
- EC_PATTERN - Static variable in interface org.biojava.bio.EcNumber
-
A Pattern that can be used to parse EC strings into the indiidual numbers.
- eCache - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
- eCache - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
-
Description of the Field
- ECHIN_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the echinoderm mitochondrial genetic code.
- Echo - Class in org.biojava.bio.program.tagvalue
-
A simple listener that just echoes events back to the console.
- Echo() - Constructor for class org.biojava.bio.program.tagvalue.Echo
- Echo(PrintStream) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Echo
- EcNumber - Interface in org.biojava.bio
-
An ec (enzyme classification) number.
- EcNumber.Impl - Class in org.biojava.bio
-
A simple implementation of EcNumber.
- ECOLI - Static variable in class org.biojava.bio.symbol.CodonPrefTools
-
Escherichia coli codon preferences
- edit(Object, Edit) - Method in interface org.biojava.bio.alignment.EditableAlignment
-
edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
- edit(Object, Edit) - Method in class org.biojava.bio.alignment.FlexibleAlignment
- edit(Edit) - Method in class org.biojava.bio.dp.SimpleStatePath
- edit(Edit) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
- edit(Edit) - Method in class org.biojava.bio.seq.impl.DummySequence
- edit(Edit) - Method in class org.biojava.bio.seq.impl.RevCompSequence
-
edit() will try to edit the underlying Sequence.
- edit(Edit) - Method in class org.biojava.bio.seq.impl.SimpleSequence
- edit(Edit) - Method in class org.biojava.bio.seq.impl.SubSequence
- edit(Edit) - Method in class org.biojava.bio.seq.impl.ViewSequence
- edit(Edit) - Method in class org.biojava.bio.seq.NewSimpleAssembly
- edit(Edit) - Method in class org.biojava.bio.seq.SimpleAssembly
- edit(Edit) - Method in class org.biojava.bio.symbol.AbstractSymbolList
- edit(Edit) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
- edit(Edit) - Method in class org.biojava.bio.symbol.RelabeledAlignment
- edit(Edit) - Method in class org.biojava.bio.symbol.SimpleSymbolList
-
Apply and edit to the SymbolList as specified by Edit.
- edit(Edit) - Method in interface org.biojava.bio.symbol.SymbolList
-
Apply an edit to the SymbolList as specified by the edit object.
- edit(Edit) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Apply an edit to the SymbolList as specified by the edit object.
- edit(Edit) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Apply an edit to the SymbolList as specified by the edit object.
- edit(RichSequence, Edit) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
-
Apply an edit to the Sequence as specified by the edit object.
- edit(RichSequence, Edit) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
-
Apply an edit to the Sequence as specified by the edit object.
- edit(RichSequence, Edit) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
-
Apply an edit to the Sequence as specified by the edit object.
- Edit - Class in org.biojava.bio.symbol
-
Encapsulates an edit operation on a SymbolList.
- Edit(int, int, SymbolList) - Constructor for class org.biojava.bio.symbol.Edit
-
Create a new Edit.
- Edit(int, int, SymbolList, Map<String, Object>) - Constructor for class org.biojava.bio.symbol.Edit
-
Create a new Edit with some properties.
- Edit(int, Alphabet, Symbol) - Constructor for class org.biojava.bio.symbol.Edit
-
Convenience construtor for making single residue changes
- EDIT - Static variable in interface org.biojava.bio.symbol.