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

A

a() - Static method in class org.biojava.bio.seq.DNATools
 
a() - Static method in class org.biojava.bio.seq.NucleotideTools
 
a() - Static method in class org.biojava.bio.seq.ProteinTools
Returns the AtomicSymbol for the amino acid Alanine
a() - Static method in class org.biojava.bio.seq.RNATools
 
A_THALIANA - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
AA indicates that a sequence contains AA (amino acid) symbols.
AAindex - Class in org.biojava.bio.proteomics.aaindex
Symbol property table based on the Amino Acid Index Database.
AAindex(String) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindex
Initializes the AAindex symbol property table.
AAindexStreamReader - Class in org.biojava.bio.proteomics.aaindex
Iterator over AAindex objects that are stored in a stream in the AAindex1 file format.
AAindexStreamReader(Reader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
Initializes the iterator.
AAindexStreamReader(BufferedReader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
Initializes the iterator.
ABBREV_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
abbreviation - Variable in class org.biojava.bibliography.BiblioJournal
An abbreviation of the journal title.
ABI_MAGIC - Static variable in class org.biojava.bio.chromatogram.ChromatogramFactory
The magic number for ABIF files.
ABIFChromatogram - Class in org.biojava.bio.program.abi
An implementation of Chromatogram to encapulsulate chromatogram data extracted from the files produced by ABI sequencers, such as the the 377 and the 3700.
ABIFChromatogram() - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram
 
ABIFChromatogram.Parser - Class in org.biojava.bio.program.abi
An extension of ABIFParser that reads the particular fields from the ABIF that contain the chromatogram data and initializes the fields in its enclosing ABIFChromatogram instance.
ABIFChromatogram.Parser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
 
ABIFChromatogram.Parser(File) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
 
ABIFParser - Class in org.biojava.bio.program.abi
A general base parser for files produced by ABI software.
ABIFParser(File) - Constructor for class org.biojava.bio.program.abi.ABIFParser
Creates a new ABIFParser for a file.
ABIFParser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFParser
Creates a new ABIFParser for an input stream.
ABIFParser(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser
Creates a new ABIFParser for the specified ABIFParser.DataAccess object.
ABIFParser.DataAccess - Interface in org.biojava.bio.program.abi
Concatenation of the Seekable and DataInput interfaces.
ABIFParser.TaggedDataRecord - Class in org.biojava.bio.program.abi
An aggregate immutable type for an ABIF tagged data record.
ABIFParser.TaggedDataRecord(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
Creates a new TaggedDataRecord from the next 28 bytes of din.
ABITools - Class in org.biojava.bio.program.abi
Useful functionality for working with fasta files where the quality of the DNA is encoded as upper and lower case DNA characters.
ABITools() - Constructor for class org.biojava.bio.program.abi.ABITools
 
ABITrace - Class in org.biojava.bio.program.abi
Title: ABITrace

ABITrace is a class for managing ABI file information, it is capable of opening an ABI file and storing the most important fields, which can be recalled as simple java types.
ABITrace(File) - Constructor for class org.biojava.bio.program.abi.ABITrace
The File constructor opens a local ABI file and parses the content.
ABITrace(URL) - Constructor for class org.biojava.bio.program.abi.ABITrace
The URL constructor opens an ABI file from any URL.
ABITrace(byte[]) - Constructor for class org.biojava.bio.program.abi.ABITrace
The byte[] constructor parses an ABI file represented as a byte array.
AbiTraceRenderer - Class in org.biojava.bio.gui.sequence
Renders an ABI trace file as a chromatogram graph.
AbiTraceRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbiTraceRenderer
 
ABORT_PARSING - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
 
AbstractAlignmentStyler - Class in org.biojava.bio.program.blast2html
Abstract implementation of AlignmentStyler, contains utility methods for generating a set of HTML styles from a list of RGB colours.
AbstractAlignmentStyler() - Constructor for class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
 
AbstractAlphabet - Class in org.biojava.bio.symbol
An abstract implementation of Alphabet.
AbstractAlphabet() - Constructor for class org.biojava.bio.symbol.AbstractAlphabet
 
AbstractAnnotation - Class in org.biojava.bio
A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
AbstractAnnotation() - Constructor for class org.biojava.bio.AbstractAnnotation
Protected no-args constructor intended for sub-classes.
AbstractAnnotation(Annotation) - Constructor for class org.biojava.bio.AbstractAnnotation
Copy-constructor.
AbstractAnnotation(Map) - Constructor for class org.biojava.bio.AbstractAnnotation
Create a new Annotation by copying the key-value pairs from a map.
AbstractBeadRenderer - Class in org.biojava.bio.gui.sequence
AbstractBeadRenderer is a an abstract base class for the creation of FeatureRenderers which use a 'string of beads' metaphor for displaying features.
AbstractBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Creates a new AbstractBeadRenderer with no delegates.
AbstractBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Creates a new AbstractBeadRenderer object.
AbstractBioEntryDB - Class in org.biojavax.bio.db
An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.
AbstractBioEntryDB() - Constructor for class org.biojavax.bio.db.AbstractBioEntryDB
 
AbstractChangeable - Class in org.biojava.utils
Useful base-class for objects implementing Changeable
AbstractChangeable() - Constructor for class org.biojava.utils.AbstractChangeable
 
AbstractChromatogram - Class in org.biojava.bio.chromatogram
A basic, abstract implementation of Chromatogram.
AbstractChromatogram() - Constructor for class org.biojava.bio.chromatogram.AbstractChromatogram
Create a new AbstractChromatogram.
AbstractCrossOverFunction - Class in org.biojavax.ga.functions
Abstract implementation of CrossOverFunction.
AbstractCrossOverFunction() - Constructor for class org.biojavax.ga.functions.AbstractCrossOverFunction
 
AbstractDistribution - Class in org.biojava.bio.dist
An abstract implementation of Distribution.
AbstractDistribution() - Constructor for class org.biojava.bio.dist.AbstractDistribution
 
AbstractFeatureHolder - Class in org.biojava.bio.seq
An abstract implementation of FeatureHolder.
AbstractFeatureHolder() - Constructor for class org.biojava.bio.seq.AbstractFeatureHolder
 
AbstractGeneticAlgorithm - Class in org.biojavax.ga.impl
Base class from which most implementations of GeneticAlgorithm will inherit.
AbstractGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
AbstractLocation - Class in org.biojava.bio.symbol
An abstract implementation of Location.
AbstractLocation() - Constructor for class org.biojava.bio.symbol.AbstractLocation
 
AbstractLocationDecorator - Class in org.biojava.bio.symbol
Abstract Location decorator (wrapper).
AbstractLocationDecorator(Location) - Constructor for class org.biojava.bio.symbol.AbstractLocationDecorator
Construct a new decorator wrapping the specified Location.
AbstractManyToOneTranslationTable - Class in org.biojava.bio.symbol
an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractManyToOneTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
 
AbstractMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
 
AbstractMatrixPairDPCursor(SymbolList, SymbolList, int, int, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
AbstractMutationFunction - Class in org.biojavax.ga.functions
Abstract implementation of MutationFunction all custom implementations should inherit from here.
AbstractMutationFunction() - Constructor for class org.biojavax.ga.functions.AbstractMutationFunction
 
AbstractOrderNDistribution - Class in org.biojava.bio.dist
Simple base class for OrderNDistributions.
AbstractOrderNDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.AbstractOrderNDistribution
Construct a new NthOrderDistribution.
AbstractOrganism - Class in org.biojavax.ga.impl
Abstract implementation of Organism.
AbstractOrganism() - Constructor for class org.biojavax.ga.impl.AbstractOrganism
 
AbstractOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.AbstractOrganism
 
AbstractOrthologueSet - Class in org.biojava.bio.program.homologene
 
AbstractOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthologueSet
 
AbstractOrthoPairCollection - Class in org.biojava.bio.program.homologene
An abstract implementation of the OrthoPairCollection interface.
AbstractOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
 
AbstractOrthoPairSet - Class in org.biojava.bio.program.homologene
represents the Homologene Group.
AbstractOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairSet
 
AbstractPeptideDigestRenderer - Class in org.biojava.bio.gui.sequence
A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.
AbstractPeptideDigestRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
AbstractPeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
 
AbstractPopulation - Class in org.biojavax.ga.impl
Most Population implementations will want to inherit from here.
AbstractPopulation() - Constructor for class org.biojavax.ga.impl.AbstractPopulation
 
AbstractPopulation(String) - Constructor for class org.biojavax.ga.impl.AbstractPopulation
 
AbstractRangeLocation - Class in org.biojava.bio.symbol
Base class for simple contiguous Location implementations.
AbstractRangeLocation() - Constructor for class org.biojava.bio.symbol.AbstractRangeLocation
 
AbstractReversibleTranslationTable - Class in org.biojava.bio.symbol
an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractReversibleTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractReversibleTranslationTable
 
AbstractRichSequenceDB - Class in org.biojavax.bio.db
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
AbstractRichSequenceDB() - Constructor for class org.biojavax.bio.db.AbstractRichSequenceDB
 
AbstractSequenceDB - Class in org.biojava.bio.seq.db
An abstract implementation of SequenceDB that provides the sequenceIterator method.
AbstractSequenceDB() - Constructor for class org.biojava.bio.seq.db.AbstractSequenceDB
 
AbstractSVMClassifierModel - Class in org.biojava.stats.svm
Abstract implementation of SVMClassifierModel.
AbstractSVMClassifierModel() - Constructor for class org.biojava.stats.svm.AbstractSVMClassifierModel
 
AbstractSVMTarget - Class in org.biojava.stats.svm
An abstract implementation of an SVMModel.
AbstractSVMTarget() - Constructor for class org.biojava.stats.svm.AbstractSVMTarget
 
AbstractSymbol - Class in org.biojava.bio.symbol
The base-class for Symbol implementations.
AbstractSymbol() - Constructor for class org.biojava.bio.symbol.AbstractSymbol
 
AbstractSymbolList - Class in org.biojava.bio.symbol
Abstract helper implementation of the SymbolList core interface.
AbstractSymbolList() - Constructor for class org.biojava.bio.symbol.AbstractSymbolList
 
AbstractSymbolList.EditScreener - Class in org.biojava.bio.symbol
This adapter screens all edit events to see if they overlap with a window of interest.
AbstractSymbolList.EditScreener(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
 
AbstractSymbolList.EditTranslater - Class in org.biojava.bio.symbol
This translates edit events that fall within a window into window co-ordinates.
AbstractSymbolList.EditTranslater(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
 
AbstractTaxon - Class in org.biojava.bio.taxa
Deprecated. replaced by classes in org.biojavax.bio.taxa
AbstractTaxon() - Constructor for class org.biojava.bio.taxa.AbstractTaxon
Deprecated.  
AbstractTaxon(String, String) - Constructor for class org.biojava.bio.taxa.AbstractTaxon
Deprecated.  
AbstractTerm - Class in org.biojava.ontology
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
AbstractTerm() - Constructor for class org.biojava.ontology.AbstractTerm
 
AbstractTrainer - Class in org.biojava.bio.dp
An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.
AbstractTrainer(DP) - Constructor for class org.biojava.bio.dp.AbstractTrainer
 
AbstractTrainer() - Constructor for class org.biojava.bio.dp.AbstractTrainer
 
abstractType - Variable in class org.biojava.bibliography.BiblioDescription
It specifies how BiblioDescription.theAbstract is coded.
AbstractULAlignment - Class in org.biojava.bio.alignment
 
AbstractULAlignment() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment
 
AbstractULAlignment.LeftRightLocationComparator - Class in org.biojava.bio.alignment
Orders by location left to right.
AbstractULAlignment.LeftRightLocationComparator() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
 
AbstractULAlignment.SubULAlignment - Class in org.biojava.bio.alignment
 
AbstractULAlignment.SubULAlignment(Set, Location) - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
 
AbstractWrapper - Class in org.biojava.bio.program.tagvalue
An abstract TagValueWrapper that does nothing!
AbstractWrapper() - Constructor for class org.biojava.bio.program.tagvalue.AbstractWrapper
 
ACC_VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
accept(Object) - Method in interface org.biojava.bio.CollectionConstraint
accept returns true if the value fulfills the constraint.
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.And
 
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
 
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Or
 
accept(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFRecordFilter
Return whether or not to accept record.
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
 
accept(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueFilter
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.And
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Not
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Or
 
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Xor
 
accept(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairFilter
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.And
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Not
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Or
 
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Xor
 
accept(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairSetFilter
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection
 
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor
 
accept(Object) - Method in interface org.biojava.bio.PropertyConstraint
accept returns true if the value fulfills the constraint.
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.And
 
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
 
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByClass
 
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
 
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
 
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Or
 
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
 
accept() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter
returns a TriState indicating the current outcome of evaluating this filter.
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.And
 
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
 
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Or
 
accept(Object) - Method in interface org.biojava.bio.search.FilterTest
 
accept(Object) - Method in class org.biojava.bio.search.FilterTest.Equals
 
accept(Object) - Method in class org.biojava.bio.search.FilterTest.FindRegex
 
accept(Object) - Method in class org.biojava.bio.search.FilterTest.GreaterThan
 
accept(Object) - Method in class org.biojava.bio.search.FilterTest.LessThan
 
accept(Object) - Method in class org.biojava.bio.search.FilterTest.MatchRegex
 
accept(Feature) - Method in interface org.biojava.bio.seq.FeatureFilter
This method determines whether a feature is to be accepted.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.And
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
Accept a Feature if it is an instance of SimilarityPairFeature and its score is <= filter's minimum score and >= filter's maximum score.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
Accept the Feature if it is an instance of FramedFeature and matches the value of getFrame().
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Not
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
Accept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().
accept(PDBHeader) - Method in interface org.biojava.bio.structure.server.PDBFilter
return true if this PDBHeader is passing this filter.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
Returns true if the feature has a matching source property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
Returns true if the feature has a matching source property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
 
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
Returns true if the feature overlaps this filter's location.
ACCEPT_ALL - Static variable in interface org.biojava.bio.program.gff.GFFRecordFilter
A GFFRecordFilter that accepts everything.
ACCESSION - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
Deprecated.  
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
Deprecated.  
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
accessionNumber() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
Gets the accession number of the AAindex entry.
AcnumHitReader - Class in org.biojava.bio.seq.db.emblcd
AcnumHitReader reads the "acnum.hit" file of an EMBL CD-ROM format binary index.
AcnumHitReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumHitReader
Creates a new AcnumHitReader.
AcnumTrgReader - Class in org.biojava.bio.seq.db.emblcd
AcnumTrgReader reads the "acnum.trg" file of an EMBL CD-ROM format binary index.
AcnumTrgReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumTrgReader
Creates a new AcnumTrgReader.
ACRONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
Use this to define acronyms for things.
ACRONYM - Static variable in interface org.biojavax.Namespace
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.gui.RasmolCommandListener
 
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) - Static method in class org.biojava.bio.program.das.DAS
 
activityProgress(Object, int, int) - Method in interface org.biojava.utils.ActivityListener
Estimated progress of an activity.
adapter - Static variable in class org.biojava.bio.structure.gui.BiojavaJmol
 
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(int, int, int, int) - Method in class org.biojava.bio.structure.align.helper.JointFragments
 
add(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
add two atoms ( a + b).
add(Object) - Method in class org.biojava.utils.FileAsList
 
add(Object) - Method in class org.biojava.utils.MergingSet
 
add(Object) - Method in class org.biojava.utils.SmallSet
 
add(Object) - Method in class org.biojavax.ga.util.WeightedSet
Adds a new Object with a weight of zero.
ADD_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
 
addActivityListener(ActivityListener) - Static method in class org.biojava.bio.program.das.DAS
 
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.
addAnnotationSource(URL) - Method in class org.biojava.bio.program.das.DASSequence
 
addAtom(Atom) - Method in interface org.biojava.bio.structure.Group
add an atom to this group.
addAtom(Atom) - Method in class org.biojava.bio.structure.HetatomImpl
add an atom to this group.
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
 
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
addBioEntry(BioEntry) - Method in interface org.biojavax.bio.db.BioEntryDBLite
Adds a sequence to the database.
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
 
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
Add a BioEntry, the name of the BioEntry will be used as the ID
addBioEntry(String, BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
 
addBlock(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
Add a "Block" Annotation.
addBottomConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
Add a configuration as the most default place to look.
addChain(Chain) - Method in class org.biojava.bio.structure.Compound
 
addChain(Chain) - Method in interface org.biojava.bio.structure.Structure
add a new chain.
addChain(Chain, int) - Method in interface org.biojava.bio.structure.Structure
add a new chain, if several models are available.
addChain(Chain) - Method in class org.biojava.bio.structure.StructureImpl
add a new chain.
addChain(Chain, int) - Method in class org.biojava.bio.structure.StructureImpl
add a new chain, if several models are available.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addChangeListener adds a listener for all types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addChangeListener adds a listener for specific types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.  
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
Deprecated.  
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
addChangeListener adds a listener for all types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
addChangeListener adds a listener for specific types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.program.das.ReferenceServer
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
 
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
addChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
Add a ChangeListener to a projected feature.
addChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
addChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
 
addChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable
Deprecated. use addChangeListener(cl, ChangeType.UNKNOWN)
addChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable
Add a listener that will be informed of changes of a given type.
addChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport
Add a listener that will be informed of all changes.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport
Add a listener that will be informed of changes of a given type (and it's subtypes)
addChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
 
addChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Add a listener that will be informed of all changes. IGNORED
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
Add a listener that will be informed of changes of a given type. IGNORED
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
addCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addCharLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addCharState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addCharState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addCharState(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addCharStateKeyword(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
 
addCharStateKeyword(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addCharStateKeyword(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
 
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
Deprecated.  
addChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
Deprecated. Add a taxon as a child to a parent.
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
Deprecated.  
addCluster(UnigeneCluster) - Method in interface org.biojava.bio.program.unigene.UnigeneDB
Add a cluster to a database.
addComment(Comment) - Method in interface org.biojavax.bio.BioEntry
Adds a comment instance to this bioentry.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
 
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
 
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
Tell the builder to add the given comment at the current location.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
 
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
 
addComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry
Adds a comment instance to this bioentry.
addCommentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
 
addComponentSequence(ComponentFeature.Template) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
 
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
Registers that sym was counted in this state.
addCount(Distribution, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Registers that sym was counted in this state.
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
 
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
 
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
Deprecated.  
addCount(Distribution, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
addCount(State, State, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
Add 'count' to the transition from->to.
addDasURL(URL) - Method in class org.biojava.bio.program.das.DAS
 
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.