Index (biojava-legacy 1.9.5 API)

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

A

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

ABITrace is a class for managing ABI file information, it is capable of opening an ABI file and storing the most important fields, which can be recalled as simple java types.
ABITrace(byte[]) - Constructor for class org.biojava.bio.program.abi.ABITrace: The byte[] constructor parses an ABI file represented as a byte array.
ABITrace(File) - Constructor for class org.biojava.bio.program.abi.ABITrace: The File constructor opens a local ABI file and parses the content.
ABITrace(URL) - Constructor for class org.biojava.bio.program.abi.ABITrace: The URL constructor opens an ABI file from any URL.
AbiTraceRenderer - Class in org.biojava.bio.gui.sequence: Renders an ABI trace file as a chromatogram graph.
AbiTraceRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbiTraceRenderer
ABORT_PARSING - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
AbortErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
Abstract() - Constructor for class org.biojava.bio.AnnotationType.Abstract
Abstract() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
Abstract() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
Abstract(String) - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract: Construct a block with a given name.
Abstract(NexusBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
AbstractAlignmentStyler - Class in org.biojava.bio.program.blast2html: Abstract implementation of AlignmentStyler, contains utility methods for generating a set of HTML styles from a list of RGB colours.
AbstractAlignmentStyler() - Constructor for class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
AbstractAlphabet - Class in org.biojava.bio.symbol: An abstract implementation of Alphabet.
AbstractAlphabet() - Constructor for class org.biojava.bio.symbol.AbstractAlphabet
AbstractAnnotation - Class in org.biojava.bio: A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
AbstractAnnotation() - Constructor for class org.biojava.bio.AbstractAnnotation: Protected no-args constructor intended for sub-classes.
AbstractAnnotation(Map) - Constructor for class org.biojava.bio.AbstractAnnotation: Create a new Annotation by copying the key-value pairs from a map.
AbstractAnnotation(Annotation) - Constructor for class org.biojava.bio.AbstractAnnotation: Copy-constructor.
AbstractBeadRenderer - Class in org.biojava.bio.gui.sequence: AbstractBeadRenderer is a an abstract base class for the creation of FeatureRenderers which use a 'string of beads' metaphor for displaying features.
AbstractBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer: Creates a new AbstractBeadRenderer with no delegates.
AbstractBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer: Creates a new AbstractBeadRenderer object.
AbstractBioEntryDB - Class in org.biojavax.bio.db: An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.
AbstractBioEntryDB() - Constructor for class org.biojavax.bio.db.AbstractBioEntryDB
AbstractChangeable - Class in org.biojava.utils: Useful base-class for objects implementing Changeable
AbstractChangeable() - Constructor for class org.biojava.utils.AbstractChangeable
AbstractChromatogram - Class in org.biojava.bio.chromatogram: A basic, abstract implementation of Chromatogram.
AbstractChromatogram() - Constructor for class org.biojava.bio.chromatogram.AbstractChromatogram: Create a new AbstractChromatogram.
AbstractCrossOverFunction - Class in org.biojavax.ga.functions: Abstract implementation of CrossOverFunction.
AbstractCrossOverFunction() - Constructor for class org.biojavax.ga.functions.AbstractCrossOverFunction
AbstractDistribution - Class in org.biojava.bio.dist: An abstract implementation of Distribution.
AbstractDistribution() - Constructor for class org.biojava.bio.dist.AbstractDistribution
AbstractFeatureHolder - Class in org.biojava.bio.seq: An abstract implementation of FeatureHolder.
AbstractFeatureHolder() - Constructor for class org.biojava.bio.seq.AbstractFeatureHolder
AbstractGeneticAlgorithm - Class in org.biojavax.ga.impl: Base class from which most implementations of GeneticAlgorithm will inherit.
AbstractGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.AbstractGeneticAlgorithm
AbstractLocation - Class in org.biojava.bio.symbol: An abstract implementation of Location.
AbstractLocation() - Constructor for class org.biojava.bio.symbol.AbstractLocation
AbstractLocationDecorator - Class in org.biojava.bio.symbol: Abstract Location decorator (wrapper).
AbstractLocationDecorator(Location) - Constructor for class org.biojava.bio.symbol.AbstractLocationDecorator: Construct a new decorator wrapping the specified Location.
AbstractManyToOneTranslationTable - Class in org.biojava.bio.symbol: an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractManyToOneTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
AbstractMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
AbstractMatrixPairDPCursor(SymbolList, SymbolList, int, int, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
AbstractMutationFunction - Class in org.biojavax.ga.functions: Abstract implementation of MutationFunction all custom implementations should inherit from here.
AbstractMutationFunction() - Constructor for class org.biojavax.ga.functions.AbstractMutationFunction
AbstractOrderNDistribution - Class in org.biojava.bio.dist: Simple base class for OrderNDistributions.
AbstractOrderNDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.AbstractOrderNDistribution: Construct a new NthOrderDistribution.
AbstractOrganism - Class in org.biojavax.ga.impl: Abstract implementation of Organism.
AbstractOrganism() - Constructor for class org.biojavax.ga.impl.AbstractOrganism
AbstractOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.AbstractOrganism
AbstractOrthologueSet - Class in org.biojava.bio.program.homologene
AbstractOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthologueSet
AbstractOrthoPairCollection - Class in org.biojava.bio.program.homologene: An abstract implementation of the OrthoPairCollection interface.
AbstractOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
AbstractOrthoPairSet - Class in org.biojava.bio.program.homologene: represents the Homologene Group.
AbstractOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairSet
AbstractPeptideDigestRenderer - Class in org.biojava.bio.gui.sequence: A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.
AbstractPeptideDigestRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
AbstractPeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
AbstractPopulation - Class in org.biojavax.ga.impl: Most Population implementations will want to inherit from here.
AbstractPopulation() - Constructor for class org.biojavax.ga.impl.AbstractPopulation
AbstractPopulation(String) - Constructor for class org.biojavax.ga.impl.AbstractPopulation
AbstractRangeLocation - Class in org.biojava.bio.symbol: Base class for simple contiguous Location implementations.
AbstractRangeLocation() - Constructor for class org.biojava.bio.symbol.AbstractRangeLocation
AbstractReversibleTranslationTable - Class in org.biojava.bio.symbol: an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractReversibleTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractReversibleTranslationTable
AbstractRichSequenceDB - Class in org.biojavax.bio.db: An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
AbstractRichSequenceDB() - Constructor for class org.biojavax.bio.db.AbstractRichSequenceDB
AbstractSequenceDB - Class in org.biojava.bio.seq.db: An abstract implementation of SequenceDB that provides the sequenceIterator method.
AbstractSequenceDB() - Constructor for class org.biojava.bio.seq.db.AbstractSequenceDB
AbstractSVMClassifierModel - Class in org.biojava.stats.svm: Abstract implementation of SVMClassifierModel.
AbstractSVMClassifierModel() - Constructor for class org.biojava.stats.svm.AbstractSVMClassifierModel
AbstractSVMTarget - Class in org.biojava.stats.svm: An abstract implementation of an SVMModel.
AbstractSVMTarget() - Constructor for class org.biojava.stats.svm.AbstractSVMTarget
AbstractSymbol - Class in org.biojava.bio.symbol: The base-class for Symbol implementations.
AbstractSymbol() - Constructor for class org.biojava.bio.symbol.AbstractSymbol
AbstractSymbolList - Class in org.biojava.bio.symbol: Abstract helper implementation of the SymbolList core interface.
AbstractSymbolList() - Constructor for class org.biojava.bio.symbol.AbstractSymbolList
AbstractSymbolList.EditScreener - Class in org.biojava.bio.symbol: This adapter screens all edit events to see if they overlap with a window of interest.
AbstractSymbolList.EditTranslater - Class in org.biojava.bio.symbol: This translates edit events that fall within a window into window co-ordinates.
AbstractTaxon - Class in org.biojava.bio.taxa: Deprecated.
replaced by classes in org.biojavax.bio.taxa
AbstractTaxon() - Constructor for class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
AbstractTaxon(String, String) - Constructor for class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
AbstractTerm - Class in org.biojava.ontology: Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
AbstractTerm() - Constructor for class org.biojava.ontology.AbstractTerm
AbstractTrainer - Class in org.biojava.bio.dp: An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.
AbstractTrainer() - Constructor for class org.biojava.bio.dp.AbstractTrainer
AbstractTrainer(DP) - Constructor for class org.biojava.bio.dp.AbstractTrainer
abstractType - Variable in class org.biojava.bibliography.BiblioDescription: It specifies how BiblioDescription.theAbstract is coded.
AbstractULAlignment - Class in org.biojava.bio.alignment
AbstractULAlignment() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment
AbstractULAlignment.LeftRightLocationComparator<T> - Class in org.biojava.bio.alignment: Orders by location left to right.
AbstractULAlignment.SubULAlignment - Class in org.biojava.bio.alignment
AbstractWrapper - Class in org.biojava.bio.program.tagvalue: An abstract TagValueWrapper that does nothing!
AbstractWrapper() - Constructor for class org.biojava.bio.program.tagvalue.AbstractWrapper
ACC_ABSTRACT - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_FINAL - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_INTERFACE - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_NATIVE - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_PRIVATE - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_PROTECTED - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_PUBLIC - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_STATIC - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_STRICT - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_SUPER - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_SYNCHRONIZED - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_TRANSIENT - Static variable in class org.biojava.utils.bytecode.CodeUtils
ACC_VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
ACC_VOLATILE - Static variable in class org.biojava.utils.bytecode.CodeUtils
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
accept() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter: returns a TriState indicating the current outcome of evaluating this filter.
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.And
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Or
accept(Object) - Method in interface org.biojava.bio.CollectionConstraint: accept returns true if the value fulfills the constraint.
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.And
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Or
accept(Object) - Method in interface org.biojava.bio.PropertyConstraint: accept returns true if the value fulfills the constraint.
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.And
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByClass
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Or
accept(Object) - Method in interface org.biojava.bio.search.FilterTest
accept(Object) - Method in class org.biojava.bio.search.FilterTest.Equals
accept(Object) - Method in class org.biojava.bio.search.FilterTest.FindRegex
accept(Object) - Method in class org.biojava.bio.search.FilterTest.GreaterThan
accept(Object) - Method in class org.biojava.bio.search.FilterTest.LessThan
accept(Object) - Method in class org.biojava.bio.search.FilterTest.MatchRegex
accept(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFRecordFilter: Return whether or not to accept record.
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
accept(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueFilter
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.And
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Not
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Or
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Xor
accept(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairFilter
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.And
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Not
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Or
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Xor
accept(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairSetFilter
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor
accept(Feature) - Method in interface org.biojava.bio.seq.FeatureFilter: This method determines whether a feature is to be accepted.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.And
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore: Accept a Feature if it is an instance of SimilarityPairFeature and its score is <= filter's minimum score and >= filter's maximum score.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByType: Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation: Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter: Accept the Feature if it is an instance of FramedFeature and matches the value of getFrame().
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Not
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Or
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation: Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation: Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation: Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter: Accept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName: Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank: Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm: Returns true if the feature has a matching source property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName: Returns true if the feature has a matching source property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand: Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm: Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName: Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation: Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation: Returns true if the feature overlaps this filter's location.
ACCEPT_ALL - Static variable in interface org.biojava.bio.program.gff.GFFRecordFilter: A GFFRecordFilter that accepts everything.
AcceptAll() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
AcceptAll() - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
ACCESSION - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
accessionNumber() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the accession number of the AAindex entry.
AcnumHitReader - Class in org.biojava.bio.seq.db.emblcd: AcnumHitReader reads the "acnum.hit" file of an EMBL CD-ROM format binary index.
AcnumHitReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumHitReader: Creates a new AcnumHitReader.
AcnumTrgReader - Class in org.biojava.bio.seq.db.emblcd: AcnumTrgReader reads the "acnum.trg" file of an EMBL CD-ROM format binary index.
AcnumTrgReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumTrgReader: Creates a new AcnumTrgReader.
ACRONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon: Use this to define acronyms for things.
ACRONYM - Static variable in interface org.biojavax.Namespace
activityFailed(Object, Exception) - Method in interface org.biojava.utils.ActivityListener: Notification of errors behind the scenes.
ActivityListener - Interface in org.biojava.utils: Interface for object which monitor long-running activities.
activityProgress(Object, int, int) - Method in interface org.biojava.utils.ActivityListener: Estimated progress of an activity.
add(int, CodeGenerator) - Method in class org.biojava.utils.bytecode.InstructionVector
add(Object) - Method in class org.biojava.utils.FileAsList
add(Object) - Method in class org.biojava.utils.MergingSet
add(Object) - Method in class org.biojava.utils.SmallSet
add(Object) - Method in class org.biojavax.ga.util.WeightedSet: Adds a new Object with a weight of zero.
add(String) - Method in class org.biojava.bio.program.gff.GFFEntrySet: Add a comment to the end of this set.
add(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFEntrySet: Add a GFFRecord to the end of this set.
add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
add(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
add(CodeGenerator) - Method in class org.biojava.utils.bytecode.InstructionVector
ADD_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
addAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
addAllFeatures(Sequence, FeatureHolder) - Static method in class org.biojava.bio.seq.SequenceTools: Add features to a sequence that contain the same information as all those in a feature holder.
addAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation: Add a new Annotation to to the end of the list to be merged.
addAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB: Add a DB to be merged in this view.
addBioEntry(String, BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
addBioEntry(BioEntry) - Method in interface org.biojavax.bio.db.BioEntryDBLite: Adds a sequence to the database.
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB: Add a BioEntry, the name of the BioEntry will be used as the ID
addBottomConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite: Add a configuration as the most default place to look.
addChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext: Add a ChangeListener to a projected feature.
addChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel: addChangeListener adds a listener for all types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster: Deprecated.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel: addChangeListener adds a listener for all types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
addChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
addChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable: Deprecated.
use addChangeListener(cl, ChangeType.UNKNOWN)
addChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport: Add a listener that will be informed of all changes.
addChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
addChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList: Add a listener that will be informed of all changes.
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel: addChangeListener adds a listener for specific types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster: Deprecated.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel: addChangeListener adds a listener for specific types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
addChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable: Add a listener that will be informed of changes of a given type.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport: Add a listener that will be informed of changes of a given type (and it's subtypes)
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList: Add a listener that will be informed of changes of a given type.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
addCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
addCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addCharLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
addCharState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
addCharState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addCharState(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
addCharStateKeyword(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
addCharStateKeyword(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addCharStateKeyword(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory: Deprecated.
addChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory: Deprecated.

Add a taxon as a child to a parent.
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory: Deprecated.
addCluster(UnigeneCluster) - Method in interface org.biojava.bio.program.unigene.UnigeneDB: Add a cluster to a database.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock: Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock: Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract: Tell the builder to add the given comment at the current location.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock: Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock: Adds a comment.
addComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
addComment(Comment) - Method in interface org.biojavax.bio.BioEntry: Adds a comment instance to this bioentry.
addComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry: Adds a comment instance to this bioentry.
addCommentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
addComponentSequence(ComponentFeature.Template) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
addCount(Distribution, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext: Registers that sym was counted in this state.
addCount(Distribution, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainer: Registers that sym was counted in this state.
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer: Deprecated.
addCount(State, State, double) - Method in interface org.biojava.bio.dp.TransitionTrainer: Add 'count' to the transition from->to.
addDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB: Add a distributed data source.
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
addDbId(AGAVEDbId) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs: add @param id
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
addDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple: Adds a descriptor.
addDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple: Adds a descriptor.
addDetailHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler: Extend this FeatureSetHandler to delegate certain detail elements to the specified handler type.
addDigestFeatures() - Method in class org.biojava.bio.proteomics.Digest: Adds peptides as features to the Sequence in this class.
addElementId(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
addEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper: addEnzyme adds an enzyme to be searched for in the Sequence.
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa: Add a silent optimisable transition to instance.
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
addEquate(String, List) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
addEquate(String, List) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addEquate(String, List) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
addExceptionTableEntry(Label, Label, CodeClass, Label) - Method in interface org.biojava.utils.bytecode.CodeContext: Add an exception table entry.
addFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder: Add a feature to the featureholder
addFeatureHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler: Extend this FeatureSetHandler to delegate certain feature elements to the specified handler type.
addFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder: Add an extra FeatureHolder to the set of FeatureHolders which are merged.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
addFeatureProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener: Notify the listener of a feature property.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase: Add an annotation-bundle entry to the feature.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Null implementation
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Notify the listener of a feature property.
addFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder: Adds a relationship to this feature holder.
addFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Adds a relationship to this feature holder.
addFeatureToSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
addFile(File) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB: Add sequences from a file to the sequence database.
addFile(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
addFilterAndGlyph(FeatureFilter, Glyph) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
addForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
addGapInSource(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList: Add a gap at pos within the source coordinates.
addGapInSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addGapInView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList: Add a single gap at pos within the view coordintates.
addGapInView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addGapsInSource(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList: Add length gaps at pos within the source coordinates.
addGapsInSource(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addGapsInView(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList: Add length gaps at pos within the view coordinates.
addGapsInView(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler: Adds a feature to the Handler attribute of the StAXFeatureHandler object
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
addHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler: The addHitProperty method adds a key/value pair containing some property of a particular hit.
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
addHotSpot(ImageMap.HotSpot) - Method in interface org.biojava.bio.gui.sequence.ImageMap: addHotSpot adds a hotspot to the map.
addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide
addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide
addIdAlias(AGAVEIdAlias) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
addIdAlias(AGAVEIdAlias) - Method in interface org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf
addImplementation(Class, Class) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer: Install a new mapping from a class of Feature.Template to a class of Feature implementations.
addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
addItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
addItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
addItem(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
addItem(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addItem(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
addItemAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
addItemTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
addKey(String, int) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory: addKey adds a new identifier namespace.
addKeyPath(String, Object[]) - Method in class org.biojava.bio.program.tagvalue.Index2Model: Add a key and a path to that key in the tag-value hierachy.
addLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer: Add a piece of text to this renderer's label
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa: Add a silent persistent transition to instance.
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
addListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub: add a ChangeListener associated with given key.
addListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub
addMapPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addMatrixEntry(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
addMatrixEntry(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
addMatrixEntry(String) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
addName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon: Adds the name to this taxon in the given name class.
addName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Adds the name to this taxon in the given name class.
addName(Connection, Taxon, String, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL: Deprecated.

Adds a new name of the given nameClass to the taxon.
addNeg(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
addNode(boolean) - Method in class org.biojava.utils.automata.FiniteAutomaton: Add a node to the FA.
addNode(boolean) - Method in interface org.biojava.utils.automata.NfaBuilder
addNode(boolean) - Method in class org.biojava.utils.automata.NfaSubModel
addNote(Note) - Method in class org.biojavax.EmptyRichAnnotation: Adds a note to this annotation.
addNote(Note) - Method in interface org.biojavax.RichAnnotation: Adds a note to this annotation.
addNote(Note) - Method in class org.biojavax.SimpleRichAnnotation: Adds a note to this annotation.
addObject(NexusObject) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile: Appends an object to the end of the file.
addOboFileEventListener(OboFileEventListener) - Method in class org.biojava.ontology.obo.OboFileParser
addOntology(Ontology) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB: Deprecated.
addOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganism(Organism) - Method in interface org.biojavax.ga.Population: Adds an Organism to the Population
addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation
addOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganisms(Set) - Method in interface org.biojavax.ga.Population: Adds several organisms to the population
addOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population: Adds several organisms to the population
addOrganisms(Population) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganisms(Population) - Method in interface org.biojavax.ga.Population: Adds the residents of one population to this one
addOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet: Add an orthologue to the set.
addOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
addOrthologueProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: add a property to the current Orthologue
addOrthologueProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
addOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet: adds a specified OrthoPair relationship to this group.
addOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
addOrthoPairProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: add a property to the current OrthoPair
addOrthoPairProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat: Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource: Adds a parse error listener to the list of listeners.
addPattern(String) - Method in class org.biojava.utils.automata.PatternBlitz: add the specified regex to the patterns used for searching.
addPattern(String, boolean) - Method in class org.biojava.utils.regex.Search: add a search pattern to the searches to be conducted by this object.
addPattern(String, String, boolean) - Method in class org.biojava.utils.regex.Search: add a search pattern to the searches to be conducted by this object.
addPos(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
addPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
addProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType: Add a value to the specified property slot.
addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
addProperty(AGAVEProperty) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border: Deprecated.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry: Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm: Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable: Adds a ranked cross reference to the existing set.
addRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry: Adds a ranked docref instance to this bioentry.
addRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry: Adds a ranked docref instance to this bioentry.
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
addRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry: Adds a relation instance to this bioentry.
addRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry: Adds a relation instance to this bioentry.
addRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR
addRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer: addRenderer adds a renderer.
addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer: addRenderer adds a renderer as a new track.
addRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes: Add a repository to FeatureTypes.
addRequest(Runnable) - Method in class org.biojava.utils.SimpleThreadPool
addRequest(Runnable) - Method in interface org.biojava.utils.ThreadPool: addRequest requests that a Runnable be scheduled to be run by one of the threads in the pool.
addRichSequence(String, RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB: Add a sequence.
addRichSequence(RichSequence) - Method in interface org.biojavax.bio.db.RichSequenceDBLite: Adds a sequence to the database.
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
addSearchProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler: The addSearchProperty method adds a key/value pair containing some property of the overall search result.
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
addSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer: Add a secondary key.
addSequence(String, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree: Add a sequence into the tree.
addSequence(String, Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB: Add a sequence under a particular id.
addSequence(AlignmentElement) - Method in interface org.biojava.bio.alignment.ARAlignment
addSequence(AlignmentElement) - Method in class org.biojava.bio.alignment.FlexibleAlignment: add a new a alignment usings a location to the reference sequence.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB: Deprecated.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.DummySequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB: addSequence always throws a ChangeVetoException as this implementation is immutable.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
addSequence(Sequence) - Method in interface org.biojava.bio.seq.db.SequenceDBLite: Adds a sequence to the database.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.WebSequenceDB: Not supported, You can't add sequences to a WebDB!
addSequence(Sequence) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
addSequence(Sequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
addSequenceDB(String, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation: This method creates a new (and empty) HashSequenceDB with the given name that will be accessible through this sequence db installation through this name and all given other identifiers.
addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation: As this is a dummy implementation adding a sequenceDB doesn't do anything
addSequenceDB(SequenceDBLite, Set) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation: addSequenceDB adds a new SequenceDB under its own identifier which will additionally be recognised by the set of other identifiers.
addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation: addSequenceDB adds a new SequenceDB which will be accessible via the name returned by its getName() method and via all other given identifiers.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblProcessor: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.OrganismParser: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
addSequenceProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener: Notify the listener of a sequence-wide property.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase: Add an annotation-bundle entry to the sequence.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Notify the listener of a sequence-wide property.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotProcessor: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Notify the listener of a sequence-wide property.
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel: addSequenceViewerListener adds a listener for mouse click SequenceViewerEvents.
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster: Deprecated.
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel: addSequenceViewerListener adds a listener for mouse click SequenceViewerEvents.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel: addSequenceViewerMotionListener adds a listener for mouse motion SequenceViewerEvents.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster: Deprecated.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel: addSequenceViewerMotionListener adds a listener for mouse motion SequenceViewerEvents.
addSet(Set) - Method in class org.biojava.utils.MergingSet
addState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
addState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addState(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
addState(State) - Method in interface org.biojava.bio.dp.MarkovModel: Adds a state to the model.
addState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
addState(State) - Method in class org.biojava.bio.dp.WMAsMM
addStateLabel(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
addStateLabel(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addStateLabel(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
addStyle(String, String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler: Add a colour style to this Styler.
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
addSubHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler: The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
addSymbol(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
addSymbol(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addSymbol(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
addSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet: Adds a symbol to this alphabet.
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolList: Add a new Symbol to the end of this list.
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: SoftMaskedAlphabets cannot add new Symbols.
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
addSymbolList(SymbolList, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory: tool to construct the SymbolList by adding Symbols.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer: Deprecated.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOFilter
addSymbols(Alphabet, Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SeqIOListener: Notify the listener of symbol data.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder: does nothing for now.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleSequenceBuilder
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SmartSequenceBuilder
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Prints out the sequences properties in order.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Notify the listener of symbol data.
addSymbols(SymbolList, int) - Method in class org.biojava.bio.symbol.SuffixTree: Add a count for all motifs with length of up to window to this tree.
addSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
addSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl
addSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl
addSynonym(Object) - Method in interface org.biojava.ontology.Term: Add a synonym for this term.
addSynonym(Object) - Method in class org.biojava.ontology.Term.Impl
addSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl
addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm: Add a synonym for this term.
addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple: Add a synonym for this term.
addTable(SymbolPropertyTable) - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB: Adds a symbol property table to the database.
addTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper: Add a tag to retain.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock: Add a TAXLABEL.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
addTaxLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener: Add a TAXLABEL.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock: Add a TAXLABEL.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
addTaxLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener: Add a TAXLABEL.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock: Add a TAXLABEL.
addTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
addTaxLabel(String) - Method in interface org.biojavax.bio.phylo.io.nexus.TaxaBlockListener: Add another value after the TAXLABEL tag.
addThrownException(CodeClass) - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod: Adds a feature to the ThrownException attribute of the GeneratedCodeMethod object
addTitle(int, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: add title information to an Orthologue (this is not in enclosed in the Orthologue element because it comes completely separate in the Homologene data files.
addTitle(int, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
addToCache(String, File) - Static method in class org.biojava.utils.io.FlatFileCache
addToEnvironment(String, Object) - Method in class org.biojava.naming.ObdaContext
addTopConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite: Add a configuration as the most authoritative place to look.
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in interface org.biojava.utils.automata.NfaBuilder
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.NfaSubModel
addTranslation(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock: Add a translation.
addTranslation(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
addTranslation(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.TreesBlockListener: Add a translation.
addTree(String, TreesBlock.NewickTreeString) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock: Adds a tree.
addTree(String, TreesBlock.NewickTreeString) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
addTree(String, TreesBlock.NewickTreeString) - Method in interface org.biojavax.bio.phylo.io.nexus.TreesBlockListener: Adds a tree.
addTree(String, WeightedGraph<String, DefaultWeightedEdge>) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock: Deprecated.
addTree(String, WeightedGraph<String, DefaultWeightedEdge>, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock: Add a tree, converting weighted graph (JGraphT) to NewickString.
addTypeWithParent(Class) - Method in class org.biojava.utils.walker.WalkerFactory: Register a type as being a 'container' class.
addVariableModification(char, double[]) - Method in class org.biojava.bio.proteomics.MassCalc: Add Variable modifications.
addVariableModification(Symbol, double[]) - Method in class org.biojava.bio.proteomics.MassCalc: Add Variable modifications.
addVector(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
addVector(Object, double, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
addXMLCollectionConstraintWriter(Class, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter: Register a writer for the specified class of collection constraint
addXMLCollectionConstraintWriter(CollectionConstraint, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter: Register a writer for a singleton property constraint.
addXMLFilterWriter(Class, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter: Add a writer for the specified class of filters
addXMLFilterWriter(FeatureFilter, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter: Add a writer for a singleton filter.
addXMLPropertyConstraintWriter(Class, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter: Register a writer for the specified class of property constraint
addXMLPropertyConstraintWriter(PropertyConstraint, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter: Register a writer for a singleton property constraint.
addXref(AGAVEXref) - Method in interface org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf
addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs: add @param xref
addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
advance() - Method in interface org.biojava.bio.dp.MarkovModel: The maximum advance for this model.
advance() - Method in interface org.biojava.bio.dp.onehead.DPCursor: Advance.
advance() - Method in class org.biojava.bio.dp.onehead.SmallCursor
advance() - Method in class org.biojava.bio.dp.SimpleMarkovModel
advance() - Method in class org.biojava.bio.dp.WMAsMM
ADVANCE - Static variable in interface org.biojava.bio.dp.EmissionState: This signals that the advance array has been altered.
affiliation - Variable in class org.biojava.bibliography.BiblioPerson: Their affiliation.
AGAVE_AGAVE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
AGAVE_ALT_IDS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
AGAVE_ANNOTATIONS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler
AGAVE_ASSEMBLY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler
AGAVE_BIO_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
AGAVE_BIO_SEQUENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
AGAVE_CDS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECdsHandler
AGAVE_CHROMOSOME_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
AGAVE_CLASSIFICATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
AGAVE_COMP_RESULT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
AGAVE_COMPUTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
AGAVE_CONTIG_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
AGAVE_DBID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
AGAVE_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
AGAVE_ELEMENT_ID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
AGAVE_EVIDENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
AGAVE_EXONS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler
AGAVE_FRAGMENT_ORDER_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
AGAVE_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
AGAVE_ID_ALIAS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
AGAVE_KEYWORD_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
AGAVE_MAP_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
AGAVE_MAP_POSITION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
AGAVE_MATCH_ALIGN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
AGAVE_MATCH_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
AGAVE_MATCH_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
AGAVE_MRNA_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
AGAVE_NOTE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
AGAVE_PREDICTED_PROTEIN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
AGAVE_QUALIFIER_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
AGAVE_QUERY_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
AGAVE_RELATED_ANNOT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
AGAVE_RESULT_GROUP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
AGAVE_RESULT_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
AGAVE_SCI_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
AGAVE_SEQ_FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
AGAVE_SEQ_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
AGAVE_SEQ_MAP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
AGAVE_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
AGAVE_TRANSCRIPT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
AGAVE_UNORDERED_FRAGMENTS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler
AGAVE_VIEW_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
AGAVE_XREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
AGAVE_XREF_PROP_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
AGAVE_XREFS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
Agave2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave: Dumping the data from biojava with source of agave into agave format
AGAVEAltIdsPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with alternate sequence IDs
AGAVEAnnotationsHandler - Class in org.biojava.bio.seq.io.agave
AGAVEAnnotFilter - Interface in org.biojava.bio.seq.io.agave: This interface defines mapping from BioJava into AGAVE format.
AGAVEAnnotFilterFactory - Interface in org.biojava.bio.seq.io.agave
AGAVEAssemblyHandler - Class in org.biojava.bio.seq.io.agave
AGAVEBioSeqCallbackItf - Interface in org.biojava.bio.seq.io.agave: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEBioSeqHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <bio_sequence> element
AGAVEBioSequenceHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <bio_sequence> element
AGAVECallbackItf - Interface in org.biojava.bio.seq.io.agave: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVECdsHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <cds> element
AGAVEChromosomeCallbackItf - Interface in org.biojava.bio.seq.io.agave: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEChromosomeHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <chromosome> element
AGAVEClassificationHandler - Class in org.biojava.bio.seq.io.agave
AGAVECompResultHandler - Class in org.biojava.bio.seq.io.agave
AGAVEComputationHandler - Class in org.biojava.bio.seq.io.agave
AGAVEContigCallbackItf - Interface in org.biojava.bio.seq.io.agave: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEContigHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <contig> element
AGAVEDbId - Class in org.biojava.bio.seq.io.agave
AGAVEDbId() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEDbId
AGAVEDbIdCallbackItf - Interface in org.biojava.bio.seq.io.agave: this is the interface implemented by several classes
AGAVEDbIdPropCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEDbIdPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with database crossreferences
AGAVEDescPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with database crossreferences
AGAVEElementIdPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEEvidenceCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEEvidenceHandler - Class in org.biojava.bio.seq.io.agave
AGAVEExonsPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.agave: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEFragmentOrderHandler - Class in org.biojava.bio.seq.io.agave
AGAVEFragmentOrientationHandler - Class in org.biojava.bio.seq.io.agave
AGAVEGeneHandler - Class in org.biojava.bio.seq.io.agave
AGAVEHandler - Class in org.biojava.bio.seq.io.agave: Handles the root AGAVE element modified for agave format
AGAVEHandler() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEHandler
AGAVEIdAlias - Class in org.biojava.bio.seq.io.agave
AGAVEIdAliasCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEIdAliasPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEKeywordPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with AGAVE keywords
AGAVEMapLocation - Class in org.biojava.bio.seq.io.agave
AGAVEMapLocation() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapLocation
AGAVEMapLocationPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEMapPosition - Class in org.biojava.bio.seq.io.agave
AGAVEMapPosition() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapPosition
AGAVEMapPositionPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEMatchAlignPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with match_align
AGAVEMatchDescPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with match_desc
AGAVEMatchRegion - Class in org.biojava.bio.seq.io.agave: match_region
AGAVEMatchRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
AGAVEMatchRegionPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with match_region
AGAVEMrnaHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <mrna> element
AGAVENotePropHandler - Class in org.biojava.bio.seq.io.agave: Deals with note
AGAVEPredictedProteinHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <predicted_protein> element
AGAVEProperty - Class in org.biojava.bio.seq.io.agave
AGAVEProperty(String, String, String, String) - Constructor for class org.biojava.bio.seq.io.agave.AGAVEProperty
AGAVEQualifierPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEQueryRegion - Class in org.biojava.bio.seq.io.agave
AGAVEQueryRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
AGAVEQueryRegionPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVERelatedAnnot - Class in org.biojava.bio.seq.io.agave
AGAVERelatedAnnot() - Constructor for class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot: construct..
AGAVERelatedAnnotPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEResultGroupHandler - Class in org.biojava.bio.seq.io.agave
AGAVEResultPropertyPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVESciPropertyPropHandler - Class in org.biojava.bio.seq.io.agave: sci_property
AGAVESeqFeatureHandler - Class in org.biojava.bio.seq.io.agave: seq_feature
AGAVESeqLocationPropHandler - Class in org.biojava.bio.seq.io.agave: seq_location
AGAVESeqMapHandler - Class in org.biojava.bio.seq.io.agave: sequence_map
AGAVESeqPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with sequence code
AGAVETranscriptHandler - Class in org.biojava.bio.seq.io.agave: transcript
AGAVEUnorderedFragmentsHandler - Class in org.biojava.bio.seq.io.agave: unordered_fragments
AGAVEViewPropHandler - Class in org.biojava.bio.seq.io.agave: Moves view attributes into annotation properties.
AgaveWriter - Class in org.biojava.bio.seq.io.agave: Writes Sequence into AGAVE XML document.
AgaveWriter() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter: Default constructor uses generic annotation to attribute mapping.
AgaveWriter(AGAVEAnnotFilter) - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter: Construct with data source specific annotation to attribute mapping.
AgaveWriter.Indent - Class in org.biojava.bio.seq.io.agave: Implements indenting for elements.
AGAVEXref - Class in org.biojava.bio.seq.io.agave: xref
AGAVEXref() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXref
AGAVEXrefCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEXrefPropHandler - Class in org.biojava.bio.seq.io.agave: handle AGAVE xref
AGAVEXrefPropPropHandler - Class in org.biojava.bio.seq.io.agave: xref_property
AGAVEXrefs - Class in org.biojava.bio.seq.io.agave: xrefs
AGAVEXrefs() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXrefs
AGAVEXrefsPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with database crossreferences (xrefs)
Aggregator - Class in org.biojava.bio.program.tagvalue: Joins multipel values into single values.
Aggregator(TagValueListener, BoundaryFinder, String) - Constructor for class org.biojava.bio.program.tagvalue.Aggregator
ala() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Alanine (A)
align(Sequence, Sequence, AlignmentAlgorithm) - Static method in class org.biojava.bio.alignment.AlignmentPair
alignAll(SequenceIterator, SequenceDB) - Method in class org.biojava.bio.alignment.AlignmentAlgorithm
AlignIOConstants - Class in org.biojava.bio.seq.io: AlignIOConstants contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing alignments.
AlignIOConstants() - Constructor for class org.biojava.bio.seq.io.AlignIOConstants
alignment - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template: alignment Alignment field.
alignment(List, SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews: View a SymbolList over a cross-product Alphabet as an Alignment.
alignment(Map) - Static method in class org.biojava.bio.symbol.SymbolListViews: Construct an alignment of the SymbolLists contained in the values collection of labelToSymList.
Alignment - Interface in org.biojava.bio.alignment: An alignment containing multiple SymbolLists.
ALIGNMENT - Static variable in interface org.biojava.bio.seq.homol.Homology: Signals that the alignment describing the homologous sequences has changed.
ALIGNMENT_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.AlignmentStAXHandler
Alignment.SymbolListIterator - Class in org.biojava.bio.alignment: Iterator implementation looping over symbol lists in an alignment using the labels.
AlignmentAlgorithm - Class in org.biojava.bio.alignment: This Interface provides methods for the alignment of bio-sequences.
AlignmentAlgorithm() - Constructor for class org.biojava.bio.alignment.AlignmentAlgorithm
AlignmentElement - Interface in org.biojava.bio.alignment: AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.
AlignmentFormat - Interface in org.biojava.bio.seq.io
AlignmentMarker - Class in org.biojava.bio.program.blast2html: Class to do simple HTML colouring of sequence alignments.
AlignmentMarker(ColourCommand, AlignmentStyler) - Constructor for class org.biojava.bio.program.blast2html.AlignmentMarker: Creates a new AlignmentMarker instance.
AlignmentPair - Class in org.biojava.bio.alignment: This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.
AlignmentPair(Sequence, Sequence, int, int, int, int, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.AlignmentPair
AlignmentPair(Sequence, Sequence, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.AlignmentPair
alignmentRange - Variable in class org.biojava.bio.alignment.FlexibleAlignment
AlignmentRenderer - Class in org.biojava.bio.gui.sequence
AlignmentRenderer() - Constructor for class org.biojava.bio.gui.sequence.AlignmentRenderer
AlignmentStAXHandler - Class in org.biojava.bio.program.ssbind: AlignmentStAXHandler handles the BlastLikeAlignment element of BioJava BlastLike XML.
all - Static variable in interface org.biojava.bio.seq.FeatureFilter: All features are selected by this filter.
all - Static variable in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter: All features are selected by this filter.
all() - Static method in class org.biojava.bio.seq.FilterUtils: Return a filter which matches all features.
ALL - Static variable in interface org.biojava.bio.program.xff.ElementRecognizer
ALL - Static variable in interface org.biojava.bio.seq.io.agave.ElementRecognizer
ALL - Static variable in interface org.biojava.bio.seq.io.game.ElementRecognizer
AllElementRecognizer() - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
allGaps(SymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment: make sure that all Symbols in this range are gaps
allIn(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools: Destructive down-cast an annotation to a type.
allOut(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools: allOut returns a new Annotation containing only those values in the Annotation argument which are not of a type specified by the AnnotationType.
AllPairsInCollection(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
AllValuesIn(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.AllValuesIn: Create an AllValuesIn based upon a PropertyConstraint and a cardinality.
alph - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
alphabet - Variable in class org.biojava.bio.alignment.AbstractULAlignment
Alphabet - Interface in org.biojava.bio.symbol: The set of AtomicSymbols which can be concatenated together to make a SymbolList.
alphabetForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager: Retrieve the alphabet for a specific name.
AlphabetIndex - Interface in org.biojava.bio.symbol: Map between Symbols and index numbers.
AlphabetManager - Class in org.biojava.bio.symbol: Utility methods for working with Alphabets.
AlphabetManager() - Constructor for class org.biojava.bio.symbol.AlphabetManager
AlphabetResolver - Class in org.biojava.bio.program.ssbind: AlphabetResolvers are helpers which determine which type of sequence Alphabet to expect from a search result.
AlphabetResolver() - Constructor for class org.biojava.bio.program.ssbind.AlphabetResolver
alphabets() - Static method in class org.biojava.bio.symbol.AlphabetManager: Get an iterator over all alphabets known.
alphaIndex(Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
alphaIndex(Symbol) - Method in class org.biojava.utils.automata.Nfa
AlreadyExistsException - Exception in org.biojava.ontology: Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
AlreadyExistsException() - Constructor for exception org.biojava.ontology.AlreadyExistsException
AlreadyExistsException(String) - Constructor for exception org.biojava.ontology.AlreadyExistsException
ALT_ID - Static variable in class org.biojava.ontology.obo.OboFileHandler
ALT_YEAST_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the alternative yeast nuclear genetic code.
AlternateTokenization - Class in org.biojava.bio.seq.io: Implementation of SymbolTokenization which binds symbols to strings of characters.
AlternateTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.AlternateTokenization
ALTERNATIVE_PRODUCTS - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser: A name for a comment type.
ALWAYS_VETO - Static variable in interface org.biojava.utils.ChangeListener: Convenience implementation which vetoes every change of which it is notified.
AlwaysVetoListener() - Constructor for class org.biojava.utils.ChangeListener.AlwaysVetoListener: Private constructor.
AMBIGUOUS - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: AMBIGUOUS indicates that a sequence contains ambiguity symbols.
aminoAcids - Static variable in class org.biojavax.bio.seq.io.FastaFormat
and - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
and(FeatureFilter.And, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
and(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils: Constructs a new filter which matches the intersection of a set of filters.
and(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a new filter which matches the intersection of two other filters.
And(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.And: Create a new And from two child constraints.
And(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.And
And(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.And
And(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
And(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.And: Create a new And from two child constraints.
And(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.And
And(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.And
And(BioSQLFeatureFilter, BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
annot - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
Annotatable - Interface in org.biojava.bio: Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder - Class in org.biojava.bio: Deprecated.
use new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY) instead
annotate(Sequence) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
annotate(Sequence) - Method in class org.biojava.bio.molbio.RestrictionMapper: annotate adds Features which represent restriction sites.
annotate(Sequence) - Method in interface org.biojava.bio.seq.SequenceAnnotator: Return an annotated version of a sequence.
ANNOTATE_EXISTING - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
AnnotatedSequenceDB - Class in org.biojava.bio.seq.db: SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
AnnotatedSequenceDB(SequenceDB, SequenceAnnotator) - Constructor for class org.biojava.bio.seq.db.AnnotatedSequenceDB
annotateSequence(Sequence, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools: Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
annotateSequence(Sequence, GFFEntrySet, boolean) - Static method in class org.biojava.bio.program.gff.GFFTools: Annotates a sequence with the features from a GFF entry set.
annotateSequences(SequenceDB, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools: Annotates all sequences in a sequence DB with features from a GFF entry set.
annotateXFF(File, Sequence) - Static method in class org.biojava.bio.program.xff.XFFTools
annotateXFF(File, Sequence, Annotation) - Static method in class org.biojava.bio.program.xff.XFFTools
annotation - Variable in class org.biojava.bio.seq.Feature.Template
annotation - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
Annotation - Interface in org.biojava.bio: Arbitrary annotation associated with one or more objects.
ANNOTATION - Static variable in interface org.biojava.bio.Annotatable: Signals that the associated Annotation has altered in some way.
ANNOTATION_ADD - Static variable in class org.biojava.bio.MergeAnnotation: ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
ANNOTATION_CHANGED - Static variable in class org.biojava.bio.MergeAnnotation: ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
ANNOTATION_REMOVE - Static variable in class org.biojava.bio.MergeAnnotation: ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
AnnotationBuilder - Class in org.biojava.bio.program.tagvalue: Builds an Annotation tree from TagValue events using an AnnotationType to work out which fields are of what type.
AnnotationBuilder(AnnotationType) - Constructor for class org.biojava.bio.program.tagvalue.AnnotationBuilder: Make a new AnnotationBuilder that will build Annotation instances of a given type.
AnnotationChanger - Class in org.biojava.bio: AnnotationChanger remaps the values of an Annotation to new values specified by a ValueChanger.
AnnotationChanger(Annotation, ChangeTable) - Constructor for class org.biojava.bio.AnnotationChanger: Creates a new AnnotationChanger using the specified ValueChanger to remap its values.
AnnotationContains(Object, Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.AnnotationContains: Make a new AnnotationContains that will accept features with an annotation bundle where the value-set assosiated with the property key contains a member equal to value.
AnnotationDB - Interface in org.biojava.bio.annodb: A database of Annotation instances.
AnnotationFactory - Class in org.biojava.bio.program.ssbind: AnnotationFactory is a utility class for making Annotations from Maps.
AnnotationFactory() - Constructor for class org.biojava.bio.program.ssbind.AnnotationFactory
annotationForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
annotationForwarder - Variable in class org.biojava.bio.seq.impl.SubSequence
annotationForwarder - Variable in class org.biojava.bio.seq.NewSimpleAssembly
annotationForwarder - Variable in class org.biojava.bio.seq.SimpleAssembly
annotationForwarder - Variable in class org.biojava.bio.symbol.AbstractSymbol
annotationForwarder - Variable in class org.biojava.bio.symbol.SimpleAlphabet
AnnotationForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.Annotatable.AnnotationForwarder: Deprecated.

Create a new AnnotationForwarder that will forward events for a source using a change support.
AnnotationLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
AnnotationLabelMaker(Object) - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
AnnotationRenamer - Class in org.biojava.bio: AnnotationRenamer remaps the keys of an Annotation to new keys specified by a TagMapper.
AnnotationRenamer(Annotation, PropertyChanger) - Constructor for class org.biojava.bio.AnnotationRenamer: Creates a new AnnotationRenamer using the specified TagMapper to remap its keys.
AnnotationTools - Class in org.biojava.bio: AnnotationTools is a set of static utility methods for manipulating Annotations and AnnotationTypes.
AnnotationTools() - Constructor for class org.biojava.bio.AnnotationTools
AnnotationType - Interface in org.biojava.bio: A set of constraints on the data contained in an Annotation.
AnnotationType.Abstract - Class in org.biojava.bio: An abstract base class useful for implementing AnnotationType instances.
AnnotationType.Impl - Class in org.biojava.bio: An implementation of AnnotationType.
ANY - Static variable in interface org.biojava.bio.AnnotationType: The type that accepts all annotations and is the supertype of all other annotations.
ANY - Static variable in class org.biojava.bio.CardinalityConstraint: The property can have any number of values, including none.
ANY - Static variable in interface org.biojava.bio.CollectionConstraint: ANY is a constraint which accepts a property for addition under all conditions.
ANY - Static variable in interface org.biojava.bio.PropertyConstraint: ANY is a constraint which accepts a property for addition under all conditions.
ANY - Static variable in class org.biojava.ontology.OntoTools
App - Class in org.biojava: Hello world!
App() - Constructor for class org.biojava.App
AppBeanRunner - Class in org.biojava.utils.xml: Create a bean from an XML file, then attempt to enter it.
AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner
append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel
append(T, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter: Append the specified FASTQ formatted sequences to the specified appendable.
append(T, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter: Append the specified FASTQ formatted sequences to the specified appendable.
appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
appendMatrixData(String, Object) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
appendMatrixData(String, Object) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
appendQuality(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder: Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.
appendQuality(String) - Method in interface org.biojava.bio.program.fastq.ParseListener: Notify this listener of a quality line.
appendSequence(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder: Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.
appendSequence(String) - Method in interface org.biojava.bio.program.fastq.ParseListener: Notify this parse listener of an additional sequence line.
AppEntry - Interface in org.biojava.utils.xml
AppException - Exception in org.biojava.utils.xml
AppException(String) - Constructor for exception org.biojava.utils.xml.AppException
applicants - Variable in class org.biojava.bibliography.BiblioPatent: Array of applicants.
ARAlignment - Interface in org.biojava.bio.alignment: ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
arcHeight - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
ARCHITECTURE - Static variable in interface org.biojava.bio.dp.MarkovModel: Signals that the architecture of the model is changing.
arcWidth - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
areDisjoint(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Determines if two queries can be proven to be disjoint.
areEmissionSpectraEqual(Distribution[], Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools: Compares the emission spectra of two distribution arrays.
areEmissionSpectraEqual(Distribution, Distribution) - Static method in class org.biojava.bio.dist.DistributionTools: Compares the emission spectra of two distributions.
areEqual(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Decide if two feature filters accept exactly the same set of features.
areEqual(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools: Return whether two locations are equal.
areProperSubset(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Determines if the set of features matched by sub can be proven to be a proper subset of the features matched by sup.
arg() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Arginine (R)
ARG_C - Static variable in class org.biojava.bio.proteomics.Protease
ARG_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager
ArrayStateMachineToolkit - Class in org.biojava.utils.automata
ArrowedFeatureRenderer - Class in org.biojava.bio.gui.sequence: A Feature Renderer that paints the Feature as a right facing arrow Based heavily on BasicFeatureRenderer
ArrowedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
ArrowGlyph - Class in org.biojava.bio.gui.glyph: A Glyph that paints an arrow shape within the bounds.
ArrowGlyph() - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph: Creates a new ArrowGlyph, which is filled with the color blue by default.
ArrowGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph: This constructs an arrow in the given bounds, which is colored blue.
ArrowGlyph(Rectangle2D.Float, Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph: Constructor which sets both the size of this arrow and its color.
ArrowGlyph(Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph: Creates a new ArrowGlyph, which is filled with the given color.
ASCID_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the ascidian mitochondrial genetic code.
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
asCriterion() - Method in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter: This method returns a Hibernate Criterion object that can be used to query the database.
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
asMap() - Method in class org.biojava.bio.AbstractAnnotation
asMap() - Method in interface org.biojava.bio.Annotation: Return a map that contains the same key/values as this Annotation.
asMap() - Method in class org.biojava.bio.MergeAnnotation
asMap() - Method in class org.biojava.bio.OverlayAnnotation: Return a Map view onto this annotation.
asMap() - Method in class org.biojavax.EmptyRichAnnotation: Return a map that contains the same key/values as this Annotation.
asMap() - Method in class org.biojavax.ga.util.WeightedSet: Converts the Set to a map from key Objects to Double weights.
asMap() - Method in class org.biojavax.SimpleRichAnnotation: Return a map that contains the same key/values as this Annotation.
asn() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Asparagine (N)
asp() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Aspartic Acid (D)
ASP_N - Static variable in class org.biojava.bio.proteomics.Protease
ASP_N - Static variable in class org.biojava.bio.proteomics.ProteaseManager
AssembledSymbolList - Class in org.biojava.bio.seq.impl: Support class for applications which need to patch together sections of sequence into a single SymbolList.
AssembledSymbolList() - Constructor for class org.biojava.bio.seq.impl.AssembledSymbolList
AssertionFailure - Error in org.biojava.utils: An unchecked exception representing an Assertion failure.
AssertionFailure(String) - Constructor for error org.biojava.utils.AssertionFailure
AssertionFailure(String, Throwable) - Constructor for error org.biojava.utils.AssertionFailure
AssertionFailure(Throwable) - Constructor for error org.biojava.utils.AssertionFailure
AtomicSymbol - Interface in org.biojava.bio.symbol: A symbol that is not ambiguous.
attemptClose(ResultSet) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL: Deprecated.

Attempt to close the ResultSet.
attemptClose(Statement) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL: Deprecated.

Attempt to close the Statement.
ATTR_FORMAT - Static variable in interface org.biojava.bibliography.BibRefSupport: A vocabulary name, or a part of a vocabulary name.
ATTR_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport: A part of a vocabulary name.
ATTR_SCOPE - Static variable in interface org.biojava.bibliography.BibRefSupport: A vocabulary name, or a part of a vocabulary name.
attribute(String, String) - Method in class org.biojava.utils.xml.FastXMLWriter
attribute(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
attribute(String, String) - Method in interface org.biojava.utils.xml.XMLWriter: Add an un-qualified attribute to an element.
attribute(String, String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
attribute(String, String, String) - Method in interface org.biojava.utils.xml.XMLWriter: Add an attribute to an element.
AUTHOR_LIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
AUTHORITY - Static variable in interface org.biojavax.Namespace
authors - Variable in class org.biojava.bibliography.BibRef: The authors and contributors are responsible for creating the contents of the cited resource.
AUTHORS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
automaticUpdate(Connection, DBHelper, TaxonFactory, File, File) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL: Deprecated.

This method tries to perform a complete update according to the given TaxonFactory, which already contains the newes taxa and the files available at the NCBI-FTP-Site.
AutomatonException - Exception in org.biojava.utils.automata: An exception thrown by classes of this package.
AutomatonException(String) - Constructor for exception org.biojava.utils.automata.AutomatonException
AutomatonException(Throwable) - Constructor for exception org.biojava.utils.automata.AutomatonException
AutomatonException(Throwable, String) - Constructor for exception org.biojava.utils.automata.AutomatonException
available() - Method in class org.biojava.utils.io.UncompressInputStream
average(Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools: Averages two or more distributions.
AverageResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.AverageResolver
AVG_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable

B

b() - Static method in class org.biojava.bio.seq.DNATools
b() - Static method in class org.biojava.bio.seq.NucleotideTools
B_TAURUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
back - Variable in class org.biojava.bio.dp.BackPointer: The previous backpointer (towards origin of DP matrix) in traceback.
BackMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
BackMatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
BackPointer - Class in org.biojava.bio.dp: A backpointer.
BackPointer(State) - Constructor for class org.biojava.bio.dp.BackPointer
BackPointer(State, BackPointer, double) - Constructor for class org.biojava.bio.dp.BackPointer
backPointers - Variable in class org.biojava.bio.dp.twohead.Cell
backward(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backward_initialize(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward_recurse(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward_termination(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backwards(ScoreType) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
backwards(ScoreType) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
backwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
backwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP
BACTERIAL - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the bacterial and plant plastid genetic code.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.program.phred.PhredFormat: This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.

This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat: Deprecated.

This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.

This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.StreamReader: This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in interface org.biojava.utils.ParseErrorListener: Method called when the parser encounters a bad line.
BarLogoPainter - Class in org.biojava.bio.gui: A logo painter that paints in bars.
BarLogoPainter() - Constructor for class org.biojava.bio.gui.BarLogoPainter
BASE_COUNT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
BASE_COUNT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
BASE_COUNT_TAG_FULL - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
BASEPOSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
BASEPOSITION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
BaseXMLWriter - Class in org.biojava.bio.program.xml: Base XMLWriter class for writing XML representations of Java Value Objects with bespoke architectures.
BaseXMLWriter() - Constructor for class org.biojava.bio.program.xml.BaseXMLWriter
BasicFeatureRenderer - Class in org.biojava.bio.gui.sequence
BasicFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.BasicFeatureRenderer
BasicFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
BasicImapRenderer - Class in org.biojava.bio.gui.sequence: BasicImapRenderer is a decorator for BasicFeatureRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the BasicFeatureRenderer.
BasicImapRenderer(BasicFeatureRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.BasicImapRenderer: Creates a new BasicImapRenderer.
BasicState(String) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState: This is the default constructor
BasicState(String, TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState: when this constructor is used, a fixed listener is used with this state.
BasicXFFHelper - Class in org.biojava.bio.program.xff
BasicXFFHelper() - Constructor for class org.biojava.bio.program.xff.BasicXFFHelper
BasisSymbol - Interface in org.biojava.bio.symbol: A symbol that can be represented as a string of Symbols.
BaumWelchSampler - Class in org.biojava.bio.dp: Train a hidden markov model using a sampling algorithm.
BaumWelchSampler(DP) - Constructor for class org.biojava.bio.dp.BaumWelchSampler
BaumWelchTrainer - Class in org.biojava.bio.dp: Train a hidden markov model using maximum likelihood.
BaumWelchTrainer(DP) - Constructor for class org.biojava.bio.dp.BaumWelchTrainer
beadDepth - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
beadDisplacement - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
BeadFeatureRenderer - Interface in org.biojava.bio.gui.sequence: BeadFeatureRenderers use a 'string of beads' metaphor for displaying features.
beadFill - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
beadOutline - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
beadStroke - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
BeanAsAnnotation - Class in org.biojava.bio: Create an Annotation with properties matching those of a JavaBean instance.
BeanAsAnnotation(Object) - Constructor for class org.biojava.bio.BeanAsAnnotation: Create a new BeanAsAnnotation for a bean.
BeanAsMap - Class in org.biojava.utils
BeanAsMap(Object) - Constructor for class org.biojava.utils.BeanAsMap
beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
beginComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener: Opening a comment tag.
beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
beginComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser: Opening a comment tag.
beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
beginComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener: Opening a comment tag.
beginComment() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
beginFileComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
beginFileComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract: This method will get called when a comment is started on the file, and not any block within it.
beginWriting() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.INSDseqFormat: Informs the writer that we want to start writing.
beginWriting() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat: Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: Informs the writer that we want to start writing.
BETWEEN_BASES - Static variable in interface org.biojavax.bio.seq.Position: A symbol representing a position that falls in between two bases, eg. 2^3 falls somewhere in the gap between 2 and 3.
BetweenLocation - Class in org.biojava.bio.symbol: Between view onto an underlying Location instance.
BetweenLocation(Location) - Constructor for class org.biojava.bio.symbol.BetweenLocation
BiblioArticle - Class in org.biojava.bibliography: It represents an article.
BiblioArticle() - Constructor for class org.biojava.bibliography.BiblioArticle
BiblioBook - Class in org.biojava.bibliography: It represents a book.
BiblioBook() - Constructor for class org.biojava.bibliography.BiblioBook
BiblioBookArticle - Class in org.biojava.bibliography: It represents a book article.
BiblioBookArticle() - Constructor for class org.biojava.bibliography.BiblioBookArticle
BiblioCriterion - Class in org.biojava.bibliography: The criteria define how the matching or ordering should be done during queries.
BiblioCriterion() - Constructor for class org.biojava.bibliography.BiblioCriterion
BiblioDescription - Class in org.biojava.bibliography: It represents an account of the content of the cited resource.
BiblioDescription() - Constructor for class org.biojava.bibliography.BiblioDescription
BiblioEntryStatus - Class in org.biojava.bibliography: It defines information related to the citation itself rather than to the cited resource.
BiblioEntryStatus() - Constructor for class org.biojava.bibliography.BiblioEntryStatus
BiblioJournal - Class in org.biojava.bibliography: A class describing journals.
BiblioJournal() - Constructor for class org.biojava.bibliography.BiblioJournal
BiblioJournalArticle - Class in org.biojava.bibliography: It represents a journal article.
BiblioJournalArticle() - Constructor for class org.biojava.bibliography.BiblioJournalArticle
BiblioOrganisation - Class in org.biojava.bibliography: It represents an organisation dealing with the bibliographic resources.
BiblioOrganisation() - Constructor for class org.biojava.bibliography.BiblioOrganisation
BiblioPatent - Class in org.biojava.bibliography: It represents a patent.
BiblioPatent() - Constructor for class org.biojava.bibliography.BiblioPatent
BiblioPerson - Class in org.biojava.bibliography: It represents a person dealing with the bibliographic resources.
BiblioPerson() - Constructor for class org.biojava.bibliography.BiblioPerson
BiblioProceeding - Class in org.biojava.bibliography: It represents a conference proceeding.
BiblioProceeding() - Constructor for class org.biojava.bibliography.BiblioProceeding
BiblioProvider - Class in org.biojava.bibliography: This class and its sub-classes define active participants of the process of creation and dissemination of the bibliographic resources.
BiblioProvider() - Constructor for class org.biojava.bibliography.BiblioProvider
BiblioScope - Class in org.biojava.bibliography: It represent an extent or scope of the content of the cited resource.
BiblioScope() - Constructor for class org.biojava.bibliography.BiblioScope
BiblioService - Class in org.biojava.bibliography: It represents a service dealing with the bibliographic resources.
BiblioService() - Constructor for class org.biojava.bibliography.BiblioService
BiblioSubject - Class in org.biojava.bibliography: It represents the topic of the content of the cited resource.
BiblioSubject() - Constructor for class org.biojava.bibliography.BiblioSubject
BiblioTechReport - Class in org.biojava.bibliography: It represents a technical report.
BiblioTechReport() - Constructor for class org.biojava.bibliography.BiblioTechReport
BiblioThesis - Class in org.biojava.bibliography: It represents a thesis.
BiblioThesis() - Constructor for class org.biojava.bibliography.BiblioThesis
BiblioWebResource - Class in org.biojava.bibliography: It represents a WWW resource.
BiblioWebResource() - Constructor for class org.biojava.bibliography.BiblioWebResource
BibRef - Class in org.biojava.bibliography: This class is a core class of the bibliographic data model - it represents a bibliographic reference, a citation.
BibRef() - Constructor for class org.biojava.bibliography.BibRef
BibRefException - Exception in org.biojava.bibliography: An exception raised when communciation with the BibRef APIs fails.
BibRefException(String) - Constructor for exception org.biojava.bibliography.BibRefException: Create a new BibRefException with a message.
BibRefException(String, Throwable) - Constructor for exception org.biojava.bibliography.BibRefException: Create a nw BibRefException with a message and a root cause.
BibRefException(Throwable) - Constructor for exception org.biojava.bibliography.BibRefException: Create a new BibRefException with a root cause.
BibRefQuery - Interface in org.biojava.bibliography: The interface BibRefQuery is a fundamental part of the Bibliographic Query Service.
BibRefSupport - Interface in org.biojava.bibliography: This interface defines supporting utilities for working with bibliographic repositories.
binary(int) - Static method in class org.biojava.bio.symbol.PackingFactory
binary(long) - Static method in class org.biojava.bio.symbol.PackingFactory
BinarySearch - Class in org.biojava.utils.math: solves y = f(x) = 0 by binary search.
BinarySearch() - Constructor for class org.biojava.utils.math.BinarySearch
bind(String, Object) - Method in class org.biojava.naming.ObdaContext
bind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
bind(Name, Object) - Method in class org.biojava.naming.ObdaContext
bind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
bindSymbol(Symbol, char) - Method in class org.biojava.bio.seq.io.CharacterTokenization: Bind a Symbol to a character.
bindSymbol(Symbol, String) - Method in class org.biojava.bio.seq.io.AlternateTokenization: Bind a Symbol to a string.
BioEntry - Interface in org.biojavax.bio: This class relates to the bioentry table in BioSQL.
BioEntryDB - Interface in org.biojavax.bio.db: .
BioEntryDBLite - Interface in org.biojavax.bio.db: A database of BioEntrys.
BioEntryIterator - Interface in org.biojavax.bio: Essentially the same as SequenceIterator.
BioEntryRelationship - Interface in org.biojavax.bio: Represents the relation between two bioentries.
BIOENTRYS - Static variable in interface org.biojavax.bio.db.BioEntryDBLite: Signals that sequences are being added to or remove from the database.
BioError - Error in org.biojava.bio: A nestable biological error.
BioError() - Constructor for error org.biojava.bio.BioError: Create a new BioError.
BioError(String) - Constructor for error org.biojava.bio.BioError: Create a new BioError with a message.
BioError(String, Throwable) - Constructor for error org.biojava.bio.BioError: Create a new BioError with a cause and a message.
BioError(Throwable) - Constructor for error org.biojava.bio.BioError: Create a new BioError with a cause.
BioError(Throwable, String) - Constructor for error org.biojava.bio.BioError: Deprecated.
Use BioError(message, ex) instead.
BioException - Exception in org.biojava.bio: A nestable biological exception.
BioException() - Constructor for exception org.biojava.bio.BioException: Create a new BioException.
BioException(String) - Constructor for exception org.biojava.bio.BioException: Create a new BioException with a message.
BioException(String, Throwable) - Constructor for exception org.biojava.bio.BioException: Create a new BioException with a cause and a message.
BioException(Throwable) - Constructor for exception org.biojava.bio.BioException: Create a new BioException with a cause.
BioException(Throwable, String) - Constructor for exception org.biojava.bio.BioException: Deprecated.
use new BioException(message, ex) instead
BioFetchSequenceDB - Class in org.biojava.bio.seq.db.biofetch: Simple SequenceDB implementation backed by a BioFetch (HTTP) server.
BioFetchSequenceDB(String, String) - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB: Construct a BioFetchSequenceDB which connects to the specified BioFetch server.
BioFetchSequenceDBProvider - Class in org.biojava.bio.seq.db.biofetch: Directory-services plugin for biofetch databases.
BioFetchSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
BioIndex - Class in org.biojava.bio.seq.db: The original object for indexing sequence files.
BioIndex(File) - Constructor for class org.biojava.bio.seq.db.BioIndex: Load an existing index file.
BioIndex(File, String, int) - Constructor for class org.biojava.bio.seq.db.BioIndex
biojavaToFile(int, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Converts a Biojava object to the given filetype.
biojavaToFile(String, String, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Writes a Biojava SequenceIterator, SequenceDB, Sequence or Aligment to an OutputStream
BioMatcher - Interface in org.biojava.bio.search: Interface for things that perform matches.
BioPattern - Interface in org.biojava.bio.search
BIOPHYSICOCHEMICAL_PROPERTIES - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser: A name for a comment type.
BioRuntimeException - Exception in org.biojava.bio: A nestable biological exception.
BioRuntimeException() - Constructor for exception org.biojava.bio.BioRuntimeException: Create a new BioRuntimeException.
BioRuntimeException(String) - Constructor for exception org.biojava.bio.BioRuntimeException: Create a new BioRuntimeException with a message.
BioRuntimeException(String, Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException: Create a new BioRuntimeException with a cause and a message.
BioRuntimeException(Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException: Create a new BioRuntimeException with a cause.
BioRuntimeException(Throwable, String) - Constructor for exception org.biojava.bio.BioRuntimeException: Deprecated.
use new BioRuntimeException(message, ex) instead
BIOSEQUENCE_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.
BIOSEQUENCE_ORACLECLOB - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.
BioSQLAcceptAllFilter - Class in org.biojavax.bio.db.biosql: The class that accepts all features.
BioSQLAcceptAllFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
BioSQLAcceptNoneFilter - Class in org.biojavax.bio.db.biosql: The class that accepts no features.
BioSQLAcceptNoneFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
BioSQLBioEntryDB - Class in org.biojavax.bio.db.biosql
BioSQLBioEntryDB(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLBioEntryDB: Creates a new instance of BioSQLBioEntryDB
BioSQLBioEntryDB(String, Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLBioEntryDB: Creates a new instance of BioSQLBioEntryDB
BioSQLCrossReferenceResolver - Class in org.biojavax.bio.db.biosql: A simple implementation of CrossReferenceResolver
BioSQLCrossReferenceResolver(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver: Requires a Hibernate session to work correctly.
BioSQLFeatureFilter - Interface in org.biojavax.bio.db.biosql: A filter for accepting or rejecting a feature.
BioSQLFeatureFilter.And - Class in org.biojavax.bio.db.biosql: A filter that returns all features accepted by both child filter.
BioSQLFeatureFilter.ByName - Class in org.biojavax.bio.db.biosql: Construct one of these to filter features by display name.
BioSQLFeatureFilter.ByNote - Class in org.biojavax.bio.db.biosql: A filter that returns all features that have the given note, and the value and rank is checked as well.
BioSQLFeatureFilter.ByNoteTermOnly - Class in org.biojavax.bio.db.biosql: A filter that returns all features that have a note with the given term.
BioSQLFeatureFilter.ByRank - Class in org.biojavax.bio.db.biosql: Construct one of these to filter features by rank.
BioSQLFeatureFilter.BySequenceName - Class in org.biojavax.bio.db.biosql: Accept features that reside on a sequence with a particular name.
BioSQLFeatureFilter.BySourceTerm - Class in org.biojavax.bio.db.biosql: Construct one of these to filter features by source.
BioSQLFeatureFilter.BySourceTermName - Class in org.biojavax.bio.db.biosql: Construct one of these to filter features by source (name only - parent ontology is ignored).
BioSQLFeatureFilter.ByStrand - Class in org.biojavax.bio.db.biosql: A filter that returns all features having locations on a given strand.
BioSQLFeatureFilter.ByTypeTerm - Class in org.biojavax.bio.db.biosql: Construct one of these to filter features by type.
BioSQLFeatureFilter.ByTypeTermName - Class in org.biojavax.bio.db.biosql: Construct one of these to filter features by type (name only - parent ontology is ignored).
BioSQLFeatureFilter.ContainedByRichLocation - Class in org.biojavax.bio.db.biosql: A filter that returns all features contained within a location.
BioSQLFeatureFilter.HibernateFeatureFilter - Class in org.biojavax.bio.db.biosql: A filter for Hibernate-BioSQL filters to extend.
BioSQLFeatureFilter.Not - Class in org.biojavax.bio.db.biosql: A filter that returns all features not accepted by a child filter.
BioSQLFeatureFilter.Or - Class in org.biojavax.bio.db.biosql: A filter that returns all features accepted by at least one child filter.
BioSQLFeatureFilter.OverlapsRichLocation - Class in org.biojavax.bio.db.biosql: A filter that returns all features overlapping a location.
BioSQLFeatureFilter.Tools - Class in org.biojavax.bio.db.biosql: A class representing some useful stuff you can do with BioSQLFeatureFilters, for instance converting plain FeatureFilters into a their BioSQLFeatureFilter equivalents (where possible).
BioSQLRichObjectBuilder - Class in org.biojavax.bio.db.biosql: Takes requests for RichObjects and sees if it can load them from a Hibernate database.
BioSQLRichObjectBuilder(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder: Creates a new instance of SimpleRichObjectBuilder.
BioSQLRichSequenceDB - Class in org.biojavax.bio.db.biosql
BioSQLRichSequenceDB(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB: Creates a new instance of BioSQLRichSequenceDB
BioSQLRichSequenceDB(String, Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB: Creates a new instance of BioSQLRichSequenceDB
BioSQLRichSequenceHandler - Class in org.biojavax.bio.db.biosql: A handler which loads sequence data from a BioSQL database, caching it where possible.
BioSQLRichSequenceHandler(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler: Requires a Hibernate session to work correctly.
BioSQLSequenceDB - Class in org.biojava.bio.seq.db.biosql: Deprecated.
Use hibernate and org.biojavax.bio.db.*
BioSQLSequenceDB(String, String, String, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB: Deprecated.

Connect to a BioSQL database.
BioSQLSequenceDB(String, String, String, String, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB: Deprecated.

Connect to a BioSQL database.
BioSQLSequenceDB(DataSource, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB: Deprecated.
BioSQLSequenceDBProvider - Class in org.biojava.bio.seq.db.biosql: Deprecated.
Use hibernate and org.biojavax.bio.db.*
BioSQLSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider: Deprecated.
BioStore - Class in org.biojava.bio.program.indexdb: BioStores represent directory and file structures which index flat files according to the OBDA specification.
BioStore(File, boolean) - Constructor for class org.biojava.bio.program.indexdb.BioStore: Creates a new BioStore flatfile index at the specified location with the specified caching behaviour.
BioStoreFactory - Class in org.biojava.bio.program.indexdb: BioStoreFactory creates BioStore instances.
BioStoreFactory() - Constructor for class org.biojava.bio.program.indexdb.BioStoreFactory: Creates a new BioStoreFactory.
BIT_PACKED - Static variable in class org.biojava.bio.seq.io.SmartSequenceBuilder
bitsOfInformation(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools: Calculates the total bits of information for a distribution.
Blast2HTMLHandler - Class in org.biojava.bio.program.blast2html: Takes a SAX event stream and a HTMLRenderer to produce a HTML Blast like program report.
Blast2HTMLHandler(HTMLRenderer) - Constructor for class org.biojava.bio.program.blast2html.Blast2HTMLHandler: A content handler for rendering blast like outputs into HTML.
BlastLikeHomologyBuilder - Class in org.biojava.bio.program.ssbind: BlastLikeHomologyBuilder populates a List with Homology instances created from SAX events supplied via a SeqSimilarityAdapter.
BlastLikeHomologyBuilder(List) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder: Creates a new BlastLikeHomologyBuilder which will instantiate Homology objects into the List target.
BlastLikeSAXParser - Class in org.biojava.bio.program.sax: A facade class allowing for direct SAX2-like parsing of the native output from Blast-like bioinformatics software.
BlastLikeSAXParser() - Constructor for class org.biojava.bio.program.sax.BlastLikeSAXParser: Initialises SAXParser, and sets default namespace prefix to "biojava".
BlastLikeSearchBuilder - Class in org.biojava.bio.program.ssbind: BlastLikeSearchBuilder will create SeqSimilaritySearchResults from SAX events via a SeqSimilarityAdapter.
BlastLikeSearchBuilder(List) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder: Creates a new BlastLikeSearchBuilder which will instantiate results into the List target.
BlastLikeSearchBuilder(List, SequenceDB, SequenceDBInstallation) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder: Creates a new BlastLikeSearchBuilder which will instantiate results into the List target.
BlastLikeSearchFilter - Interface in org.biojava.bio.search: A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter - Class in org.biojava.bio.search
BlastLikeSearchFilter.And - Class in org.biojava.bio.search
BlastLikeSearchFilter.ByHitProperty - Class in org.biojava.bio.search: Applies test to the value specified by the key in hit properties.
BlastLikeSearchFilter.BySearchProperty - Class in org.biojava.bio.search: Applies test to the value specified by the key in search properties.
BlastLikeSearchFilter.BySubHitProperty - Class in org.biojava.bio.search: Applies test to the value specified by the key in subhit properties.
BlastLikeSearchFilter.Node - Interface in org.biojava.bio.search
BlastLikeSearchFilter.Not - Class in org.biojava.bio.search
BlastLikeSearchFilter.Or - Class in org.biojava.bio.search
BlastLikeToXMLConverter - Class in org.biojava.bio.program: A class that converts the raw output from a variety of bioinformatics software and converts it to XML that will validate against the biojava:BlastLikeDataSetCollection DTD.
BlastLikeToXMLConverter(String) - Constructor for class org.biojava.bio.program.BlastLikeToXMLConverter: Creates a new BlastToXMLConverter instance.
BlastXMLParser - Class in org.biojava.bio.program.sax.blastxml: This class parses NCBI Blast XML output.
BlastXMLParser() - Constructor for class org.biojava.bio.program.sax.blastxml.BlastXMLParser
BlastXMLParserFacade - Class in org.biojava.bio.program.sax.blastxml: A facade class that wraps the NCBI Blast XML parsing framework in a more user-friendly form.
BlastXMLParserFacade() - Constructor for class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
BLEPH_MNUC - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the blepharisma macronuclear genetic code.
Block(int, int, int, int) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
Block(SimpleGappedSymbolList.Block) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
blockCount(Location) - Static method in class org.biojava.bio.symbol.LocationTools: Return the number of contiguous blocks in a location.
blockEnded(NexusBlockParser) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
blockEnded(NexusBlockParser) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract: This method gets called when the block parser is expected to have finished parsing a block.
blockIterator() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
blockIterator() - Method in class org.biojava.bio.symbol.AbstractRangeLocation
blockIterator() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
blockIterator() - Method in interface org.biojava.bio.symbol.Location: Return an Iterator over the set of maximal contiguous sub-locations.
blockIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile: Iterate over all blocks in the file in order.
blockIterator() - Method in class org.biojavax.bio.seq.CompoundRichLocation: Return an Iterator over the set of maximal contiguous sub-locations.
blockIterator() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Return an Iterator over the set of maximal contiguous sub-locations.
blockIterator() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Return an Iterator over the set of maximal contiguous sub-locations.
BlockIterator() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Get list of the un-gapped region of the SymbolList.
BlockPainter - Interface in org.biojava.bio.gui
BLUNT - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme: BLUNT the end type created by enzymes which leave a blunt end.
BooleanElementHandlerBase - Class in org.biojava.utils.stax: StAX handler for any element which just contains a string representation of an boolean.
BooleanElementHandlerBase() - Constructor for class org.biojava.utils.stax.BooleanElementHandlerBase
Border() - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
BOTH_FORWARD_COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
BoundaryFinder - Interface in org.biojava.bio.program.tagvalue
bPointers - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
bPointers - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor: Description of the Field
breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer: Deprecated.

Converts the symbol list passed in into an array of strings.
breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Converts the symbol list passed in into an array of strings.
BROAD_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
BROAD_SYNONYM - Static variable in class org.biojava.ontology.Synonym
build() - Method in class org.biojava.bio.program.fastq.FastqBuilder: Build and return a new FASTQ formatted sequence configured from the properties of this builder.
buildDataParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools: Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener.
buildDataStore(File, SequenceStreamer, Packing, int, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
buildDataStore(File, SequenceDB, Packing, int, int) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory: Build a new DataStore.
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory
builder() - Static method in class org.biojava.bio.program.fastq.Fastq: Create and return a new FastqBuilder.
builder(Fastq) - Static method in class org.biojava.bio.program.fastq.Fastq: Create and return a new FastqBuilder configured from the specified FASTQ formatted sequence.
buildLibInfoParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools: Generate a tag-value parser for the library info unigene files.
buildObject(Class, List) - Method in class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder: This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
buildObject(Class, List) - Method in interface org.biojavax.RichObjectBuilder: This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
buildObject(Class, List) - Method in class org.biojavax.SimpleRichObjectBuilder: This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
BumpedRenderer - Class in org.biojava.bio.gui.sequence
BumpedRenderer() - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
BumpedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
BumpedRenderer(SequenceRenderer, int, int) - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
ByAccession(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
byAncestor(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where at least one of the ancestors matches the specified filter.
byAncestor(FeatureFilter.ByAncestor, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
ByAncestor(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAncestor
byAnnotation(Object, Object) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where the annotation property named key is equal to value.
ByAnnotation(Object, Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotation: Make a new ByAnnotation that will accept features with an annotation bundle containing 'value' associated with 'key'.
byAnnotationType(Object, Class) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where the annotation property named key is an instance of valClass.
byAnnotationType(AnnotationType) - Static method in class org.biojava.bio.seq.FilterUtils: Match features with annotations matching the specified AnnotationType
ByAnnotationType() - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.PropertyConstraint.ByAnnotationType: Create a new constraint by type.
ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
byChild(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where at least one child feature matches the supplied filter.
byChild(FeatureFilter.ByChild, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
ByChild(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByChild
byClass(Class) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches features which are assignable to the specified class or interface.
ByClass(Class) - Constructor for class org.biojava.bio.PropertyConstraint.ByClass: Create a new ByClass instance.
ByClass(Class) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByClass
byComponentName(String) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches all features which implement the ComponentFeature interface and have a componentName property equal to the specified value
ByComponentName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByComponentName
byDescendant(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where at least one decendant feature -- possibly but not necessarily an immediate child -- matches the specified filter.
byDescendant(FeatureFilter.ByDescendant, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
ByDescendant(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByDescendant
ByFeature(Feature) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByFeature
byFrame(FramedFeature.ReadingFrame) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches FramedFeatures with the specified reading frame.
byHitProperty(BlastLikeSearchFilter.ByHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
ByHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
ByHomologeneID(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
ByLocalName(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
ByLocationComparator() - Constructor for class org.biojava.bio.seq.Feature.ByLocationComparator
ByLocationMinMaxComparator - Class in org.biojava.bio.seq: A Comparator similar to Feature.ByLocationComparator except that the min and max positions of the location are both compared
ByLocationMinMaxComparator() - Constructor for class org.biojava.bio.seq.ByLocationMinMaxComparator
ByLocationMinMaxFeatureComparator - Class in org.biojava.bio.seq: Comparator that compares the min and max positions of Features Required by org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer instances.
ByLocationMinMaxFeatureComparator() - Constructor for class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
byLocationOrder - Static variable in interface org.biojava.bio.seq.Feature: byLocationOrder contains a Feature comparator which compares by the minimum base position of their Location.
ByLocusID(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
ByMaxIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
ByMinIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
ByMinIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
byName - Static variable in interface org.biojava.bio.seq.db.IDMaker: A simple implementation of IDMaker that hashes by sequence name.
ByName() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByName
ByName(String) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.ByName
ByName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName: Create a ByType filter that filters in all features with type fields equal to type.
ByNote(Note) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
ByNoteTermOnly(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
ByNSName(String, String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
byPairwiseScore(double, double) - Static method in class org.biojava.bio.seq.FilterUtils: Match SeqSimilaritiy features with scores in the specified range.
ByPairwiseScore(double, double) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore: Creates a new ByPairwiseScore.
byParent(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where the parent feature matches the specified filter.
byParent(FeatureFilter.ByParent, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
ByParent(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByParent
ByRank(int) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank: Create a Rank filter that filters in all features with rank fields equal to rank.
ByRef(String) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
byScore - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit: byScore contains a SeqSimilaritySearchHit comparator which compares by their score.
byScore - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: byScore contains a SeqSimilaritySearchSubHit comparator which compares by the score of the sub-hit.
ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
bySearchProperty(BlastLikeSearchFilter.BySearchProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
BySearchProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
bySequenceName(String) - Static method in class org.biojava.bio.seq.FilterUtils: Match features attached to sequences with a specified name.
BySequenceName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySequenceName
BySequenceName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
BySimilarityType(SimilarityType) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
bySource(String) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches features with a specific source value.
BySource(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySource: Create a BySource filter that filters in all features which have sources equal to source.
BySourceTerm(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm: Create a BySourceTerm filter that filters in all features with sourceTerm fields equal to source.
BySourceTermName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName: Create a BySourceTerm filter that filters in all features with sourceTerm fields having name equal to sourceTermName.
byStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.FilterUtils: Match StrandedFeatures on the specified strand.
ByStrand(RichLocation.Strand) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand: Creates a filter that returns everything on strand str.
bySubHitCount - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit: bySubHitCount contains a SeqSimilaritySearchHit comparator which compares by their number of sub-hits.
BySubHitCountComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
bySubHitProperty(BlastLikeSearchFilter.BySubHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
BySubHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
bySubjectStart - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: bySubjectStart contains a SeqSimilaritySearchSubHit comparator which compares by the start position of the sub-hit on the subject sequence.
BySubjectStartComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
ByTaxon(Taxon) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
ByTaxon(Taxon) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
ByTaxonID(int) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
BYTE_MAX_VALUE - Static variable in class org.biojava.bio.program.scf.SCF: Represents the maximum unsigned value of a byte for wrapping purposes
ByteCode - Class in org.biojava.utils.bytecode: Factory for objects which encapsulate individual Java bytecode instructions.
ByteCode() - Constructor for class org.biojava.utils.bytecode.ByteCode
ByteElementHandlerBase - Class in org.biojava.utils.stax: StAX handler for any element which just contains a string representation of a byte.
ByteElementHandlerBase() - Constructor for class org.biojava.utils.stax.ByteElementHandlerBase
BYTES_IN_BYTE - Static variable in class org.biojava.utils.Constants
BYTES_IN_CHAR - Static variable in class org.biojava.utils.Constants
BYTES_IN_DOUBLE - Static variable in class org.biojava.utils.Constants
BYTES_IN_FLOAT - Static variable in class org.biojava.utils.Constants
BYTES_IN_INT - Static variable in class org.biojava.utils.Constants
BYTES_IN_LONG - Static variable in class org.biojava.utils.Constants
BYTES_IN_SHORT - Static variable in class org.biojava.utils.Constants
bytesRead - Variable in class org.biojava.ontology.obo.OboFileParser
ByTitle(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
byType(String) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches features with a specific type value.
ByType(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByType: Create a ByType filter that filters in all features with type fields equal to type.
ByTypeTerm(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm: Create a ByTypeTerm filter that filters in all features with typeTerm fields equal to typeTerm.
ByTypeTermName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName: Create a ByTypeTermName filter that filters in all features with typeTerm fields having name equal to typeTermName.
byURN - Static variable in interface org.biojava.bio.seq.db.IDMaker: A simple implementation of IDMaker that hashes by URN.
ByURN() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByURN

C

c() - Static method in class org.biojava.bio.seq.DNATools
c() - Static method in class org.biojava.bio.seq.NucleotideTools
c() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Cysteine
c() - Static method in class org.biojava.bio.seq.RNATools
C_ELEGANS - Static variable in interface org.biojava.bio.program.homologene.Taxon
cache - Variable in class org.biojava.utils.io.CachingInputStream: The byte cache itself.
Cache - Interface in org.biojava.utils.cache: Interface for managing caches of objects.
CACHE_PROPERTY - Static variable in class org.biojava.utils.io.InputStreamProvider
cachedOutcome - Variable in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
CacheMap - Interface in org.biojava.utils.cache: Interface for managing caches of objects fetchable by key.
CacheReference - Interface in org.biojava.utils.cache: Interface for a reference to an object, analogous to java.lang.ref.Referencce, but more flexible.
CachingInputStream - Class in org.biojava.utils.io: A wrapper around InputStream that provides in-memory caching of the input data.
CachingInputStream(InputStream) - Constructor for class org.biojava.utils.io.CachingInputStream
CachingKernel - Class in org.biojava.stats.svm: Caches the results of a nested kernel so that k(a, b) need only be calculated once.
CachingKernel() - Constructor for class org.biojava.stats.svm.CachingKernel
CachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.CachingKernel
CachingSequenceDB - Class in org.biojava.bio.seq.db: SequenceDB implementation that caches the results of another SequenceDB.
CachingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.CachingSequenceDB: Create a new CachingSequenceDB that caches the sequences in parent.
calcCell(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator: Calculate the 'scores' array in the cell at cells[0][0].
calcDist() - Method in class org.biojava.bio.gui.sequence.SequencePanel
calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByName
calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByURN
calcID(Sequence) - Method in interface org.biojava.bio.seq.db.IDMaker: Calculate the id for a sequence.
calcKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
calcLineExtent(MouseEvent) - Method in class org.biojava.bio.gui.sequence.SequencePoster: Deprecated.
calculatePrimRecLen(int) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory: calculatePrimRecLen calculates the byte length of primary namespace records.
calculateScore(Distribution, Symbol) - Method in interface org.biojava.bio.dp.ScoreType: Calculates the score associated with a distribution and a symbol.
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.NullModel
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Odds
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Probability
calculateSecRecLen(int, String, Map) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory: calculateSecRecLen calculates the byte length of secondary namespace records.
callbackStack - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: this is the stack of handler objects for the current feature.
callbackStack - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler: this is the stack of handler objects for the current feature.
callboxesValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Flag for call boxes.
canAccept(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory: Accepts all URLs that are of the file protocol.
canAccept(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory: Accepts all URLs that are of the jdbc protocol.
canAccept(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
canAccept(CodeClass) - Method in class org.biojava.utils.bytecode.ParametricType
canAdvance() - Method in interface org.biojava.bio.dp.onehead.DPCursor: Can we advance?
CANDIES_NOT_SORTED - Static variable in interface org.biojava.utils.candy.CandyVocabulary: A property name.
CandyEntry - Class in org.biojava.utils.candy: This is a basic container for a vocabulary entry.
CandyEntry() - Constructor for class org.biojava.utils.candy.CandyEntry: An empty constructor.
CandyEntry(String) - Constructor for class org.biojava.utils.candy.CandyEntry: It creates an entry instance with given name and empty value.
CandyEntry(String, String) - Constructor for class org.biojava.utils.candy.CandyEntry: It creates an entry instance with given name and value.
CandyEntry(String, String, Hashtable) - Constructor for class org.biojava.utils.candy.CandyEntry: It creates an entry instance with given name, value and additional properties.
CandyException - Exception in org.biojava.utils.candy
CandyException(String) - Constructor for exception org.biojava.utils.candy.CandyException
CandyException(String, Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
CandyException(Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
CandyFinder - Interface in org.biojava.utils.candy: This interface is a main entry point to a set of controlled vocabularies.
CandyVocabulary - Interface in org.biojava.utils.candy: This interface defines functionality of a controlled vocabulary.
canMerge(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools: Determines whether the locations are touching or not (if they could be merged in a single Location.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: Check to see if a given stream is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.FastaFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Check to see if a given file is in our format.
canRead(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: Check to see if a given file is in our format.
CardinalityConstraint - Class in org.biojava.bio: A constraint on the number of values a property can have.
Cavg - Static variable in class org.biojava.bio.proteomics.MassCalc: Constant value of Carbon average mass
Cell - Class in org.biojava.bio.dp.twohead: A single cell in the DP matrix.
Cell() - Constructor for class org.biojava.bio.dp.twohead.Cell
CellCalculator - Interface in org.biojava.bio.dp.twohead: The interface for all functions that can calculate the 'scores' array for a given cell.
CellCalculatorFactory - Interface in org.biojava.bio.dp.twohead
CellCalculatorFactoryMaker - Interface in org.biojava.bio.dp.twohead: The interface for all functions that can calculate the 'scores' array for a given cell.
CEREVISIAE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools: Saccharomyces cerevisiae codon preferences
ChainedChanger(ChangeTable.Changer[]) - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
change(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
change(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Changer: Produce a modified value from an old value.
change(Object) - Method in class org.biojava.bio.program.tagvalue.RegexChanger
change(Object, Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
CHANGE_COMMON_NAME - Static variable in interface org.biojava.bio.taxa.Taxon: Deprecated.

Change type to indicate that the common name of this Taxon is changing.
CHANGE_SCIENTIFIC_NAME - Static variable in interface org.biojava.bio.taxa.Taxon: Deprecated.

Change type to indicate that the scientific name of this Taxon is changing.
Changeable - Interface in org.biojava.utils: This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeableCache - Class in org.biojava.utils.cache: A cache that clears values as the keys fire ChangeEvents of a given type.
ChangeableCache(ChangeType) - Constructor for class org.biojava.utils.cache.ChangeableCache
ChangeAdapter - Class in org.biojava.utils: This is a ChangeListener that ignores everything.
ChangeAdapter() - Constructor for class org.biojava.utils.ChangeAdapter
ChangeEvent - Class in org.biojava.utils: Event which encapsulates a change in any mutable BioJava object.
ChangeEvent(Object, ChangeType) - Constructor for class org.biojava.utils.ChangeEvent: Construct a ChangeEvent with no change details.
ChangeEvent(Object, ChangeType, Object) - Constructor for class org.biojava.utils.ChangeEvent: Construct a ChangeEvent specifying a new value for a property, or an object to be added to a collection.
ChangeEvent(Object, ChangeType, Object, Object) - Constructor for class org.biojava.utils.ChangeEvent: Construct a ChangeEvent specifying a new value for a property, and giving the previous value.
ChangeEvent(Object, ChangeType, Object, Object, ChangeEvent) - Constructor for class org.biojava.utils.ChangeEvent: Construct a ChangeEvent to be fired because another ChangeEvent has been received from a property object.
ChangeEventRecorder() - Constructor for class org.biojava.utils.ChangeListener.ChangeEventRecorder
ChangeForwarder - Class in org.biojava.utils: This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeForwarder(Object, ChangeSupport) - Constructor for class org.biojava.utils.ChangeForwarder: Create a new ChangeForwarder for forwarding events.
ChangeForwarder.Retyper - Class in org.biojava.utils: A ChangeForwarder that systematically uses a given type and wraps the old event.
ChangeHub - Interface in org.biojava.utils: Interface implemented by ChangeHubs, i.e.
ChangeListener - Interface in org.biojava.utils: Interface for objects which listen to ChangeEvents.
ChangeListener.AlwaysVetoListener - Class in org.biojava.utils: An implementation that always vetoes everything.
ChangeListener.ChangeEventRecorder - Class in org.biojava.utils: A listener that remembers the ChangeEvent of the last change.
ChangeListener.LoggingListener - Class in org.biojava.utils: A listener that writes information about the event stream to a PrintStream.
changeSupport() - Method in class org.biojava.utils.ChangeForwarder: Return the underlying ChangeSupport instance that can be used to fire ChangeEvents and mannage listeners.
ChangeSupport - Class in org.biojava.utils: A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeSupport() - Constructor for class org.biojava.utils.ChangeSupport: Generate a new ChangeSupport instance.
ChangeSupport(int) - Constructor for class org.biojava.utils.ChangeSupport: Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources.
ChangeSupport(int, int) - Constructor for class org.biojava.utils.ChangeSupport: Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources, and which will grow by delta each time.
ChangeSupport(Set) - Constructor for class org.biojava.utils.ChangeSupport
ChangeSupport(Set, int, int) - Constructor for class org.biojava.utils.ChangeSupport: Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources, and which will grow by delta each time.
ChangeTable - Class in org.biojava.bio.program.tagvalue: A mapping between keys and actions to turn old values into new values.
ChangeTable() - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable
ChangeTable.ChainedChanger - Class in org.biojava.bio.program.tagvalue: An implementation of Changer that applies a list of Changer instances to the value in turn.
ChangeTable.Changer - Interface in org.biojava.bio.program.tagvalue: Callback used to produce a new value from an old one.
ChangeTable.Splitter - Interface in org.biojava.bio.program.tagvalue: Callback used to produce a list of values from a single old one.
ChangeType - Class in org.biojava.utils: Class for all constants which are used to indicate change types.
ChangeType(String, Class, String) - Constructor for class org.biojava.utils.ChangeType: Construct a new ChangeType with supertype UNKNOWN.
ChangeType(String, Class, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType: Construct a new ChangeType.
ChangeType(String, Field) - Constructor for class org.biojava.utils.ChangeType: Construct a new ChangeType with superType UNKNOWN.
ChangeType(String, Field, ChangeType) - Constructor for class org.biojava.utils.ChangeType: Construct a new ChangeType.
ChangeType(String, String, String) - Constructor for class org.biojava.utils.ChangeType
ChangeType(String, String, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
ChangeVetoException - Exception in org.biojava.utils: Exception which is thrown when a ChangeListener does not wish a change to take place.
ChangeVetoException() - Constructor for exception org.biojava.utils.ChangeVetoException
ChangeVetoException(String) - Constructor for exception org.biojava.utils.ChangeVetoException: Create an exception with a detail message
ChangeVetoException(String, Throwable) - Constructor for exception org.biojava.utils.ChangeVetoException
ChangeVetoException(Throwable, String) - Constructor for exception org.biojava.utils.ChangeVetoException: Deprecated.
use new ChangeVetoException(reason, ex);
ChangeVetoException(Throwable, ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException: Propogate an exception without (additional) explanation.
ChangeVetoException(Throwable, ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException: Propogate an exception, giving a detail message
ChangeVetoException(ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException: Construct an exception to veto a change without explanation.
ChangeVetoException(ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException: Construct an exception to veto a change for a specified reason.
CHARACTER - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
characters(char[], int, int) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler: Describe characters method here.
characters(char[], int, int) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
characters(char[], int, int) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase: Signal a span of character data in the XML input.
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.StreamParser
characters(char[], int, int) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.CharElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.IntElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.LongElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
characters(char[], int, int) - Method in interface org.biojava.utils.stax.StAXContentHandler
characters(char[], int, int) - Method in class org.biojava.utils.stax.StAXContentHandlerBase: Signal a span of character data in the XML input.
characters(char[], int, int) - Method in class org.biojava.utils.stax.StringElementHandlerBase
CHARACTERS_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.CharactersBlock: A constant representing the name of Characters blocks.
CharactersBlock - Class in org.biojavax.bio.phylo.io.nexus: Represents Nexus characters blocks.
CharactersBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlock: Delegates to NexusBlock.Abstract constructor using CharactersBlock.CHARACTERS_BLOCK as the name.
CharactersBlock(String) - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlock: For the DATA block subclass.
CharactersBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus: Builds Nexus characters blocks.
CharactersBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
CharactersBlockListener - Interface in org.biojavax.bio.phylo.io.nexus: Listens to events that represent Nexus characters blocks.
CharactersBlockParser - Class in org.biojavax.bio.phylo.io.nexus: Parses Nexus characters blocks.
CharactersBlockParser(CharactersBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser: Delegates to NexusBlockParser.Abstract.
CharacterTokenization - Class in org.biojava.bio.seq.io: Implementation of SymbolTokenization which binds symbols to single unicode characters.
CharacterTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.CharacterTokenization
charAt(int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
charAt(int) - Method in class org.biojava.utils.RepeatedCharSequence
CharElementHandlerBase - Class in org.biojava.utils.stax: StAX handler for any element which just contains a string representation of a char.
CharElementHandlerBase() - Constructor for class org.biojava.utils.stax.CharElementHandlerBase
charValue(Symbol) - Method in class org.biojava.utils.regex.PatternFactory: Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for.
charValue(Symbol) - Method in class org.biojava.utils.regex.Search
checkException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
checkException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
checkIOException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
checkIOException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
checkIOException() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
children - Variable in class org.biojava.bio.taxa.SimpleTaxon: Deprecated.
CHLORO_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the chlorophycean mitochondrial genetic code.
Chromatogram - Interface in org.biojava.bio.chromatogram: Encapsulates the basic information you would want from a chromatogram.
ChromatogramFactory - Class in org.biojava.bio.chromatogram: A factory that creates Chromatogram objects from files or streams.
ChromatogramFactory() - Constructor for class org.biojava.bio.chromatogram.ChromatogramFactory
ChromatogramGraphic - Class in org.biojava.bio.chromatogram.graphic: Encapsulates a configurable method for drawing a Chromatogram into a graphics context.
ChromatogramGraphic() - Constructor for class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Default constructor with no Chromatogram.
ChromatogramGraphic(Chromatogram) - Constructor for class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Creates a new ChromatogramGraphic, initially displaying the given chromatogram.
ChromatogramGraphic.Option - Class in org.biojava.bio.chromatogram.graphic: A typesafe enumeration of the options available for configuring the behavior of a ChromatogramGraphic instance.
ChromatogramNonlinearScaler - Interface in org.biojava.bio.chromatogram.graphic: Provides the mechanism whereby a ChromatogramGraphic can display a Chromatogram with a non-linear horizontal scale.
ChromatogramNonlinearScaler.Identity - Class in org.biojava.bio.chromatogram.graphic: The default scaler that displays the chromatogram 1:1.
ChromatogramTools - Class in org.biojava.bio.chromatogram: Utility class for dealing with Chromatograms.
chromosomes - Variable in class org.biojavax.ga.impl.AbstractOrganism
CHROMOSOMES - Static variable in interface org.biojavax.ga.Organism
ChunkedSymbolList - Class in org.biojava.bio.symbol: SymbolList implementation using constant-size chunks.
ChunkedSymbolList(SymbolList[], int, int, Alphabet) - Constructor for class org.biojava.bio.symbol.ChunkedSymbolList
ChunkedSymbolListFactory - Class in org.biojava.bio.seq.io: class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves.
ChunkedSymbolListFactory(SymbolListFactory) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
ChunkedSymbolListFactory(SymbolListFactory, int) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.Protease
CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.ProteaseManager
CILIATE_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the ciliate nuclear genetic code.
CIRCLE - Static variable in interface org.biojava.bio.gui.sequence.ImageMap: CIRCLE indicates a circular image map hotspot.
CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichLocation
CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichSequence
CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
CircularFeatureFilteringRenderer - Class in org.biojava.bio.gui.sequence
CircularFeatureFilteringRenderer(CircularRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
CircularFeatureRenderer - Interface in org.biojava.bio.gui.sequence
CircularFeaturesRenderer - Class in org.biojava.bio.gui.sequence
CircularFeaturesRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
CircularFeaturesRenderer(CircularFeatureRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
circularLength - Variable in class org.biojavax.bio.seq.SimpleRichLocation
CircularLocation - Class in org.biojava.bio.symbol: Circular view onto an underlying Location instance.
CircularLocation(Location, int) - Constructor for class org.biojava.bio.symbol.CircularLocation: Constructs a CircularLocation by wrapping another Location It is preferable to use LocationTools to make CircularLocations
CircularLocation(Location, int, int) - Constructor for class org.biojava.bio.symbol.CircularLocation: Makes a CircularLocation where the 5' end of the Location is specified.
CircularMLR - Class in org.biojava.bio.gui.sequence: Renders multiple renderers, each in their own concentric rings.
CircularMLR() - Constructor for class org.biojava.bio.gui.sequence.CircularMLR
CircularPaddedRenderer - Class in org.biojava.bio.gui.sequence
CircularPaddedRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
CircularPaddedRenderer(double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
CircularPaddedRenderer(CircularRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
CircularPaddedRenderer(CircularRenderer, double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
CircularReferenceException - Exception in org.biojava.bio.taxa: Deprecated.
replaced by classes in org.biojavax.bio.taxa
CircularReferenceException() - Constructor for exception org.biojava.bio.taxa.CircularReferenceException: Deprecated.
CircularReferenceException(String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException: Deprecated.
CircularReferenceException(Throwable) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException: Deprecated.
CircularReferenceException(Throwable, String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException: Deprecated.
CircularRenderer - Interface in org.biojava.bio.gui.sequence: Render information from a CircularRendererContext onto a graphics context.
CircularRendererContext - Interface in org.biojava.bio.gui.sequence: A context providing information for rendering sequences into circular coordinate systems.
CircularRendererPanel - Class in org.biojava.bio.gui.sequence: Renders a sequence as a circle using a CircularRenderer.
CircularRendererPanel() - Constructor for class org.biojava.bio.gui.sequence.CircularRendererPanel
CircularView - Class in org.biojava.bio.seq: A circular view onto another Sequence object.
CircularView(Sequence) - Constructor for class org.biojava.bio.seq.CircularView
CircularView(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.CircularView
CITATION_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_FIRST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_ID_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_INSTITUTE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_ISSUE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_LAST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_PATENT_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_PUB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
CITATION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_VOL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_YEAR_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ClassifierExample - Class in org.biojava.stats.svm.tools: A simple toy example that allows you to put points on a canvas, and find a polynomial hyperplane to seperate them.
ClassifierExample() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample
ClassifierExample.PointClassifier - Class in org.biojava.stats.svm.tools: An extention of JComponent that contains the points & encapsulates the classifier.
classify() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier: Learn a model from the current points.
classify(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
classify(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
classify(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
Classify - Class in org.biojava.stats.svm.tools
Classify() - Constructor for class org.biojava.stats.svm.tools.Classify
classListToString(CodeClass[]) - Static method in class org.biojava.utils.bytecode.CodeUtils: Format an array of classes as a comma-seperated list.
ClassTools - Class in org.biojava.utils: Utility methods for manipulating class objects and resources.
clear() - Method in class org.biojava.bio.dp.twohead.EmissionCache
clear() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
clear() - Method in class org.biojava.stats.svm.AbstractSVMTarget
clear() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
clear() - Method in class org.biojava.stats.svm.SimpleSVMTarget
clear() - Method in interface org.biojava.stats.svm.SVMClassifierModel
clear() - Method in interface org.biojava.stats.svm.SVMTarget
clear() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier: Remove all points from the canvas, and discard any model.
clear() - Method in interface org.biojava.utils.cache.CacheReference
clear() - Method in class org.biojava.utils.FileAsList
clear() - Method in class org.biojava.utils.io.FlatFileCache
clear() - Method in class org.biojava.utils.io.SoftHashMap
clear() - Method in class org.biojavax.EmptyRichAnnotation: Removes all notes from this annotation object.
clear() - Method in class org.biojavax.ga.util.WeightedSet
clear() - Method in interface org.biojavax.RichAnnotation: Removes all notes from this annotation object.
clear() - Method in class org.biojavax.SimpleRichAnnotation: Removes all notes from this annotation object.
clearCounts() - Method in interface org.biojava.bio.dist.DistributionTrainerContext: Clears all of the counts to zero.
clearCounts() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
clearCounts() - Method in interface org.biojava.bio.dp.TransitionTrainer: Clears all of the counts to zero.
clearCounts(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.DistributionTrainer: Clears all of the counts to zero.
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer: Deprecated.
clearEnzymes() - Method in class org.biojava.bio.molbio.RestrictionMapper: clearEnzymes removes all enzymes from those to be searched for in the Sequence.
clearLRUCache() - Static method in class org.biojavax.RichObjectFactory: Removes all objects from the LRU cache.
clearLRUCache(Class) - Static method in class org.biojavax.RichObjectFactory: Removes all objects of the specified class from the LRU cache.
clearPatterns() - Method in class org.biojava.utils.regex.Search: remove all patterns from the pattern cache.
clearRenderers() - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer: clearRenderers removes all renderers from this renderer.
clearRenderers() - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer: clearRenderers removes all the renderers.
clearTraces() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram: Sets the trace data structures to null.
clearTraceValues() - Method in class org.biojava.bio.chromatogram.SimpleChromatogram: Sets all the traces to null.
ClientSide(String) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ClientSide: Creates a new ClientSide image map.
clobToString(Connection, ResultSet, int) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper: Deprecated.
clone() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Performs a partial deep copy and invalidates regenerable structures.
clone() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
clone() - Method in class org.biojava.bio.seq.Feature.Template
clone() - Method in class org.biojava.bio.seq.impl.RevCompSequence: clone() should make a complete copy of the Sequence with all features (and children) and return a SimpleSequence that is unconnected from the original sequence.
clone() - Method in class org.biojava.utils.ExecRunner: We override the clone method here to prevent cloning of our class.
clone() - Method in class org.biojava.utils.TypedProperties
close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader: close closes the underlying InputStream.
close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess: close closes the underlying RandomAccessFile.
close() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore: close closes the underlying EntryNamRandomAccess which in turn closes the lower level RandomAccessFile.
close() - Method in interface org.biojava.bio.seq.io.StreamParser
close() - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
close() - Method in class org.biojava.naming.ObdaContext
close() - Method in interface org.biojava.utils.bytecode.CodeContext: Close the context for writing.
close() - Method in class org.biojava.utils.io.CountedBufferedReader
close() - Method in class org.biojava.utils.io.RandomAccessReader: close closes the underlying RandomAccessFile.
close() - Method in class org.biojava.utils.xml.PrettyXMLWriter
close() - Method in interface org.biojava.utils.xml.XMLWriter: Close this XMLWriter, and it's underlying stream.
closeSubComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment
closeTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
closeTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
closeTag(String) - Method in interface org.biojava.utils.xml.XMLWriter: Closes an un-qualified element.
closeTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
closeTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter: Closes an element
CLUSTAL - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: CLUSTAL indicates that the alignment format is Clustal.
CLUSTAL_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: CLUSTAL_AA premade CLUSTAL | AA;
CLUSTAL_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: CLUSTAL_DNA premade CLUSTAL | DNA;
CLUSTAL_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: CLUSTAL_RNA premade CLUSTAL | RNA;
ClustalWAlignmentSAXParser - Class in org.biojava.bio.program.sax: A SAX2 parser for dealing with a multiple sequence alignment as produced by ClustalW outputing .aln format.
ClustalWAlignmentSAXParser() - Constructor for class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Initialises internal state Sets namespace prefix to "biojava"
Cmono - Static variable in class org.biojava.bio.proteomics.MassCalc: Constant value of Carbon monoisotopic mass
CNBr - Static variable in class org.biojava.bio.proteomics.Protease
CNBr - Static variable in class org.biojava.bio.proteomics.ProteaseManager
CodeClass - Interface in org.biojava.utils.bytecode: Interface for Java classes within the bytecode generation framework.
CodeContext - Interface in org.biojava.utils.bytecode: Interface which encapsulates the stream to which Java bytecode can be written.
CodeException - Exception in org.biojava.utils.bytecode: An exception indicating that something went wrong generating byte code.
CodeException() - Constructor for exception org.biojava.utils.bytecode.CodeException
CodeException(String) - Constructor for exception org.biojava.utils.bytecode.CodeException
CodeField - Class in org.biojava.utils.bytecode: Wrap up details about a field in a Java class file.
CodeGenerator - Interface in org.biojava.utils.bytecode: Interface for an object which can produce Java bytecode.
CodeMethod - Interface in org.biojava.utils.bytecode: Wrap up details about a method in a Java class file
codes - Variable in class org.biojava.bibliography.BiblioSubject: Classification code (call number) is usually either Dewey decimal or Congress classification.
CodeUtils - Class in org.biojava.utils.bytecode: Utility code for things you will frequently need.
CodeUtils() - Constructor for class org.biojava.utils.bytecode.CodeUtils
CodonPref - Interface in org.biojava.bio.symbol
CodonPrefFilter - Interface in org.biojava.bio.symbol
CodonPrefFilter.AcceptAll - Class in org.biojava.bio.symbol
CodonPrefFilter.ByName - Class in org.biojava.bio.symbol
CodonPrefFilter.EverythingToXML - Class in org.biojava.bio.symbol
CodonPrefTools - Class in org.biojava.bio.symbol: An utility class for codon preferences
CodonPrefTools() - Constructor for class org.biojava.bio.symbol.CodonPrefTools
CollectionConstraint - Interface in org.biojava.bio: Used by AnnotationType to represent the constraint on the collection of values in a property-slot.
CollectionConstraint.AllValuesIn - Class in org.biojava.bio: CollectionConstraint which validates all members of a Collection.
CollectionConstraint.And - Class in org.biojava.bio: A collection constraint that accpepts collections iff they are accepted by both child constraints.
CollectionConstraint.Contains - Class in org.biojava.bio: CollectionConstraint which validates a portion of a Collection.
CollectionConstraint.Or - Class in org.biojava.bio: A collection constraint that accepts items iff they are accepted by either child constraints.
colors - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: The map containing the colors for drawing traces.
ColourCommand - Interface in org.biojava.bio.program.blast2html: Interface for specifying whether a particular pair of residues/bases should be coloured.
columns - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
columns() - Method in class org.biojava.bio.dp.ProfileHMM: Retrieve the number of columns in the model.
columns() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
columns() - Method in interface org.biojava.bio.dp.WeightMatrix: The number of columns modeled by the weight matrix.
Comment - Interface in org.biojavax: A simple ranked comment designed to be used for BioEntry comments in BioSQL.
COMMENT - Static variable in class org.biojava.ontology.obo.OboFileHandler
COMMENT - Static variable in interface org.biojavax.bio.BioEntry
COMMENT_ABS_MAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ABSORPTION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ERROR_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_EVENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_EXPERIMENTS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_INTERACT_INTACT_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_INTERACT_LABEL_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_INTERACTANT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ISOFORM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_KIN_KM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_KIN_VMAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_KINETICS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_LINK_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_LINK_URI_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_LOCTYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_METHOD_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ORGANISMS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_PH_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_REDOX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_TEMPERATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
commentIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment: This iterator iterates over all parts of the comment.
commentIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile: Iterate over all comments in the file in order.
commentLine(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler: A comment line has been encountered.
commentLine(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
commentLine(String) - Method in class org.biojava.bio.program.gff.GFFWriter: Prints the comment directly to the PrintWriter after adding a leading '#'.
commentLine(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler: A comment line has been encountered.
commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
commentText(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener: Receiving free text inside a comment tag.
commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
commentText(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser: Receiving free text inside a comment tag.
commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
commentText(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener: Receiving free text inside a comment tag.
commentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
commit() - Method in class org.biojava.bio.program.indexdb.BioStore: commit writes an index to disk.
commit() - Method in class org.biojava.bio.seq.db.BioIndex
commit() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore: commit commits changes.
commit() - Method in interface org.biojava.bio.seq.db.IndexStore: Commit the stored indices to permanent storage.
commit() - Method in class org.biojava.bio.seq.db.TabIndexStore
commit() - Method in interface org.biojava.utils.Commitable: commit commits pending changes.
commit() - Method in class org.biojava.utils.FileAsList
Commitable - Interface in org.biojava.utils: Implementations of Commitable support atomic changes from one known state to another via commit/rollback semantics.
CommitFailure - Exception in org.biojava.utils
CommitFailure(String) - Constructor for exception org.biojava.utils.CommitFailure
CommitFailure(String, Throwable) - Constructor for exception org.biojava.utils.CommitFailure
CommitFailure(Throwable) - Constructor for exception org.biojava.utils.CommitFailure
commitStore() - Method in class org.biojava.bio.seq.db.TabIndexStore
COMMON - Static variable in interface org.biojavax.bio.taxa.NCBITaxon: Use this to define common names for things.
COMMON_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
COMNAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CompactedDataStore - Class in org.biojava.bio.program.ssaha: An implementation of DataStore that will map onto a file using the NIO constructs.
CompactedDataStoreFactory - Class in org.biojava.bio.program.ssaha: Builder for a data store that is backed by a java.nio.MappedByteBuffer.
CompactedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
ComparableOntology - Interface in org.biojavax.ontology: An Ontology that can be compared to another.
ComparableTerm - Interface in org.biojavax.ontology: Makes Term objects comparable properly and adds some extra features to them.
ComparableTriple - Interface in org.biojavax.ontology: Comparable triples, obviously.
comparator() - Static method in class org.biojava.bio.seq.ByLocationMinMaxComparator
COMPARATOR - Static variable in class org.biojava.ontology.Synonym
compare(Object, Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.Feature.ByLocationComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.io.EmblReferenceComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblFeatureComparator: Deprecated.
compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblPropertyComparator: Deprecated.
compareTo(Object) - Method in class org.biojavax.bio.seq.CompoundRichLocation: Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
compareTo(Object) - Method in class org.biojavax.bio.seq.EmptyRichLocation: Empty Rich Locations return 0 when compared to other Empty ones, or -1 otherwise.
compareTo(Object) - Method in class org.biojavax.bio.seq.RichLocation.Strand: Strands are compared first by symbol, then by number.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Features are sorted first by rank, then parent, type, and source.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Relations are compared first by rank, then object, subject, then finally term.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichLocation: Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntry: Bioentries are ordered first by namespace, then name, accession, and finally version.
compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntryRelationship: A relationship is compared first by rank, then object, subject, and term.
compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: NCBITaxon objects are compared only by their NCBITaxID fields.
compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName: Taxon names are sorted by class first, then name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableOntology: Ontologies are compared only by name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm: Terms are sorted by ontology first, then name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple: Triples are sorted in order of ontology, subject, object, and finally predicate.
compareTo(Object) - Method in class org.biojavax.SimpleComment: Comments are ordered first by their rank, then by a string comparison of their text values.
compareTo(Object) - Method in class org.biojavax.SimpleCrossRef: Compares cross references first by database name, then by accession, then by version.
compareTo(Object) - Method in class org.biojavax.SimpleDocRef: Document references are compared first by author, then by location, then by title.
compareTo(Object) - Method in class org.biojavax.SimpleDocRefAuthor: Document authors are compared first by name, then consortium status, then editor status.
compareTo(Object) - Method in class org.biojavax.SimpleNamespace: Namespaces are compared only by name.
compareTo(Object) - Method in class org.biojavax.SimpleNote: Notes are compared first by rank, then by the term.
compareTo(Object) - Method in class org.biojavax.SimpleRankedCrossRef: Ranked cross references are sorted first by rank, then by cross reference.
compareTo(Object) - Method in class org.biojavax.SimpleRankedDocRef: Ranked document references are sorted first by rank then location then by actual document reference.
compareTo(Synonym) - Method in class org.biojava.ontology.Synonym
compile(String) - Method in class org.biojava.utils.regex.PatternFactory: Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
compile(String, String) - Method in class org.biojava.utils.regex.PatternFactory: Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
complement(Symbol) - Static method in class org.biojava.bio.seq.DNATools: Complement the symbol.
complement(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools: Complement the symbol.
complement(Symbol) - Static method in class org.biojava.bio.seq.RNATools: Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools: Retrieve a complement view of list.
complement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools: Retrieve a complement view of list.
complement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools: Retrieve a complement view of list.
COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
complementTable() - Static method in class org.biojava.bio.seq.DNATools: Get a translation table for complementing DNA symbols.
complementTable() - Static method in class org.biojava.bio.seq.NucleotideTools: Get a translation table for complementing Nucleotide symbols.
complementTable() - Static method in class org.biojava.bio.seq.RNATools: Get a translation table for complementing DNA symbols.
complete() - Method in interface org.biojava.bio.program.fastq.ParseListener: Notify this listener the FASTQ formatted sequence is complete.
completeCycle() - Method in interface org.biojava.bio.dp.HMMTrainer: indicate that a cycle of training is completed and the emission/transition matrices should be updated.
completeCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer
completedActivity(Object) - Method in interface org.biojava.utils.ActivityListener: Notification that an activity is complete.
COMPONENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ComponentFeature - Interface in org.biojava.bio.seq: Feature which represents a component in an assembly (contig).
ComponentFeature.Template - Class in org.biojava.bio.seq: Template for constructing a new ComponentFeature.
componentLocation - Variable in class org.biojava.bio.seq.ComponentFeature.Template
componentLocationIterator() - Method in class org.biojava.bio.symbol.MergeLocation
componentSequence - Variable in class org.biojava.bio.seq.ComponentFeature.Template
componentSequenceName - Variable in class org.biojava.bio.seq.ComponentFeature.Template
composeName(String, String) - Method in class org.biojava.naming.ObdaContext
composeName(Name, Name) - Method in class org.biojava.naming.ObdaContext
Composite() - Constructor for class org.biojava.directory.RegistryConfiguration.Composite
Composition - Class in org.biojava.bio.molbio: Computes composition statistics about a SymbolList.
Composition() - Constructor for class org.biojava.bio.molbio.Composition
Compound() - Constructor for class org.biojava.bio.program.formats.Ligand.Compound
CompoundRichLocation - Class in org.biojavax.bio.seq: An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
CompoundRichLocation() - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
CompoundRichLocation(Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation: Constructs a CompoundRichLocation from the given set of members, with the default term of "join".
CompoundRichLocation(ComparableTerm, Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation: Constructs a CompoundRichLocation from the given set of members.
compute(double) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc.ChargeCalculator: computes charge at given pH
compute(double) - Method in interface org.biojava.utils.math.ComputeObject: workhorse method for this class.
ComputeObject - Interface in org.biojava.utils.math: interface for classes that return a single double precision value for a single double precision argument.
conditionedDistributions() - Method in interface org.biojava.bio.dist.OrderNDistribution: Get the conditioned distributions.
CONFIG_FILE - Static variable in class org.biojava.directory.SystemRegistry
CONFIG_LOCATOR - Static variable in class org.biojava.directory.SystemRegistry
conjunctAdd - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
conjunction - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
connect() - Method in interface org.biojava.bibliography.BibRefQuery: It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication.
connect() - Method in interface org.biojava.bibliography.BibRefSupport: It creates a connection to an object providing the supporting utilities, or/and it makes all necessary initialization steps needed for further communication.
connect() - Method in interface org.biojava.utils.candy.CandyFinder: It creates a connection to an object representing a vocabulary finder, or/and it makes all necessary initialization steps needed for further communication.
connect(byte[]) - Method in interface org.biojava.bibliography.BibRefQuery: It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication, and it makes the collection described by collectionId the current collection.
connectModel() - Method in class org.biojava.bio.dp.ProfileHMM: This is called by constructor in setting up the allowed transitions in the model
connectModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM: This is called by constructor in setting up the allowed transitions in the model
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ConstantPool - Class in org.biojava.utils.bytecode: Build a Java class file constant pool.
ConstantPool() - Constructor for class org.biojava.utils.bytecode.ConstantPool
constantPoolSize() - Method in class org.biojava.utils.bytecode.ConstantPool
Constants - Class in org.biojava.utils: Some usefull constants for working with binary files.
Constants() - Constructor for class org.biojava.utils.Constants
constrain(double) - Method in enum org.biojava.bio.program.fastq.FastqVariant: Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.
construct(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools: Constructs a RichLocation object based on the given collection of members.
constructSubsets() - Method in class org.biojava.utils.automata.DfaBuilder
containedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches features with locations wholly contained by the specified Location.
ContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ContainedByLocation: Creates a filter that returns everything contained within loc.
ContainedByRichLocation(RichLocation) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation: Creates a filter that returns everything contained within loc.
contains(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
contains(int) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
contains(int) - Method in class org.biojava.bio.symbol.CircularLocation
contains(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
contains(int) - Method in interface org.biojava.bio.symbol.Location: Checks if this location contains a point.
contains(int) - Method in class org.biojava.bio.symbol.PointLocation
contains(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation: Checks if this location contains a point.
contains(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation: Checks if this location contains a point.
contains(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation: Checks if this location contains a point.
contains(Object) - Method in class org.biojava.utils.MergingSet
contains(Object) - Method in class org.biojava.utils.SmallSet
contains(Object) - Method in class org.biojavax.ga.util.WeightedSet
contains(String) - Method in interface org.biojava.utils.candy.CandyVocabulary: It checks if a given entry exists in this vocabulary.
contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
contains(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
contains(Location) - Method in class org.biojava.bio.symbol.CircularLocation
contains(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
contains(Location) - Method in interface org.biojava.bio.symbol.Location: Checks if this location contains the other.
contains(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation: Checks if this location contains the other.
contains(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation: Checks if this location contains the other.
contains(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation: Checks if this location contains the other.
contains(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools: Return true iff all indices in locB are also contained by locA.
contains(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
contains(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet: Returns whether or not this Alphabet contains the symbol.
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
contains(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
contains(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
contains(Note) - Method in class org.biojavax.EmptyRichAnnotation: Returns true if the given note exists in this annotation.
contains(Note) - Method in interface org.biojavax.RichAnnotation: Returns true if the given note exists in this annotation.
contains(Note) - Method in class org.biojavax.SimpleRichAnnotation: Returns true if the given note exists in this annotation.
Contains(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.Contains: Create a Contains based upon a PropertyConstraint and a cardinality.
CONTAINS_PREFIX - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
containsAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
containsCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
containsFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder: Check if the feature is present in this holder.
containsFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence: containsFeature() will return true if this seq contains the feature in question, or if if the original (non reverse complement) sequence contains the feature;
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.MergeFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly
containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly
containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
containsFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Check if the feature is present in this holder.
containsFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence: Check if the feature is present in this holder.
containsFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Returns true if the given FeatureFilter is already contained in this renderer.
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
containsKey(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
containsKey(Object) - Method in class org.biojava.utils.OverlayMap
containsKey(Object) - Method in class org.biojava.utils.SmallMap
containsName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon: Tests for the presence of a name in a given class.
containsName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Tests for the presence of a name in a given class.
containsNode(FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
containsObject(NexusObject) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile: Checks to see if we contain an object.
containsProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
containsProperty(Object) - Method in interface org.biojava.bio.Annotation: Returns whether there the property is defined.
containsProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
containsProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
containsProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation: Returns whether there the property is defined.
containsProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation: Deprecated.
containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.

Detects whether a particular table is present in the database.
containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.HypersonicDBHelper: Deprecated.
containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper: Deprecated.
containsTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock: Checks to see if we contain the given TAXLABEL.
containsTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock: Checks to see if we contain the given TAXLABEL.
containsTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock: Checks to see if we contain the given TAXLABEL.
containsTerm(String) - Method in class org.biojava.ontology.IntegerOntology
containsTerm(String) - Method in interface org.biojava.ontology.Ontology: Determines if this ontology currently contains a term named name
containsTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
containsTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Determines if this ontology currently contains a term named name
containsTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel: Returns wether a transition exists or not.
containsTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
containsTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
containsTranslation(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock: Checks to see if we contain the given translation.
containsTree(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock: Checks to see if we contain the given tree.
containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology
containsTriple(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology: See if a triple exists in this ontology
containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl
containsTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology: See if a triple exists in this ontology
CONTENT - Static variable in interface org.biojava.bio.alignment.Alignment: Signals that SymbolLists will be added to or removed from an alignment.
contextForLabel(SequenceRenderContext, String) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
contributors - Variable in class org.biojava.bibliography.BibRef: The authors and contributors are responsible for creating the contents of the cited resource.
convert() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
convert() - Method in class org.biojava.bio.program.PdbToXMLConverter
convert(Fastq) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
convert(Fastq) - Method in class org.biojava.bio.program.fastq.SangerFastqWriter
convert(Fastq) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter
convert(Fastq, FastqVariant) - Static method in class org.biojava.bio.program.fastq.FastqTools: Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
convert(FeatureFilter) - Static method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools: Convert a non-BioSQL FeatureFilter into a BioSQL one.
convertTo(FastqVariant) - Method in class org.biojava.bio.program.fastq.Fastq: Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.
convertValueToText(Object, boolean, boolean, boolean, int, boolean) - Method in class org.biojava.bio.gui.FeatureTree: Labels Sequence objects with their name, Annotations with the tag Annotations, Features with the tag Features and other objects with the toString value.
COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
coordinateDisplayOn(boolean) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer: coordinateDisplayOn toggles the display of sequence coordinates.
COPYRIGHT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
cost - Variable in class org.biojava.bibliography.BiblioWebResource: The cost of accessing the resource.
CostMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch: A matrix with the size length(sequence1) times length(sequence2)
Count - Interface in org.biojava.bio.dist: An encapsulation of a count over the Symbols within an alphabet.
CountedBufferedReader - Class in org.biojava.utils.io
CountedBufferedReader(Reader) - Constructor for class org.biojava.utils.io.CountedBufferedReader
countFeatures() - Method in interface org.biojava.bio.seq.FeatureHolder: Count how many features are contained.
countFeatures() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.impl.DummySequence
countFeatures() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.impl.RevCompSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleFeature
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
countFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.MergeFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.NewSimpleAssembly
countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.SimpleAssembly
countFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
countFeatures() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Count how many features are contained.
countFeatures() - Method in class org.biojavax.bio.seq.ThinRichSequence: Count how many features are contained.
COUNTS - Static variable in interface org.biojava.bio.dist.Count: Whenever a component count changes the values that would be returned by getCount, they should fire a ChangeEvent with this object as the type.
countToDistribution(Count) - Static method in class org.biojava.bio.dist.DistributionTools: Make a distribution from a count.
coverage - Variable in class org.biojava.bibliography.BibRef: It defines an extent or scope of the content of the cited resource.
coverage(Location) - Static method in class org.biojava.bio.symbol.LocationTools: Return the number of positions which are covered by a Location
CRC64Checksum - Class in org.biojavax.utils: Utility class that calculates a CRC64 checksum on a stream of bytes.
CRC64Checksum() - Constructor for class org.biojavax.utils.CRC64Checksum
create(File) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory: Creates a new Chromatogram object from the named file.
create(File) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram: Create a new ABIF object from a file.
create(File) - Static method in class org.biojava.bio.program.scf.SCF
create(InputStream) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory: Creates a new Chromatogram object from the supplied stream.
create(InputStream) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram: Create a new ABIF object from a stream of bytes.
create(InputStream, long) - Static method in class org.biojava.bio.program.scf.SCF
CREATE_DATE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
CREATE_DUMMYSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
CREATE_REALSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
CREATE_REL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
createArrayType(String) - Static method in class org.biojava.utils.bytecode.ParametricType: Create a new ParametricType that claims to resolve to an array type.
createBinary(String) - Static method in class org.biojavax.ga.util.GATools: Creates a SymbolList in the GABinary Alphabet
createBioStore() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory: createBioStore creates a BioStore reflecting the current state of the factory and returns a reference to it.
createCode(OutputStream) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
createDistribution(Alphabet) - Method in interface org.biojava.bio.dist.DistributionFactory: Generate a new Distribution as requested.
createDistribution(Alphabet) - Method in class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
createDistribution(Alphabet) - Method in class org.biojava.bio.dist.OrderNDistributionFactory: Creates an OrderNDistribution of the appropriate type.
createDNA(String) - Static method in class org.biojava.bio.seq.DNATools: Return a new DNA SymbolList for dna.
createDNA(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools: Create and return a new DNA SymbolList from the specified FASTQ formatted sequence.
createDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools: Return a new DNA Sequence for dna.
createDNASequence(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools: Create and return a new DNA Sequence from the specified FASTQ formatted sequence.
createDP(MarkovModel) - Method in interface org.biojava.bio.dp.DPFactory
createDP(MarkovModel) - Method in class org.biojava.bio.dp.DPFactory.DefaultFactory
createDummy(String, String) - Static method in class org.biojava.bio.seq.SequenceTools: Create a new Sequence that has no annotation, no features and a zero-length symbol list.
createDummy(Alphabet, int, Symbol, String, String) - Static method in class org.biojava.bio.seq.SequenceTools: Create a new Sequence that contains a single symbol repeated over and over.
createDummySequence(String, Alphabet, int) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB: Deprecated.
createEmblParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.CircularView: Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.FeatureHolder: Create a new Feature, and add it to this FeatureHolder.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.DummySequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.RevCompSequence: createFeature() will call createFeature() on the underlying Sequence.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SubSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.LazyFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext: Create a projected feature with properties matching the template.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Create a new Feature, and add it to this FeatureHolder.
createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.ThinRichSequence: Create a new Feature, and add it to this FeatureHolder.
createFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence: Deprecated.
Please use new 1-arg createFeature instead.
createFeature(Feature, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext: Create a new projected feature.
createFeature(Feature, Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
createFeatureHolder() - Method in class org.biojava.bio.seq.LazyFeatureHolder
createFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler: Create a new template of the appropriate type.
createFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
createField(String, CodeClass, int) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
createGappedDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools: Get a new dna as a GappedSequence
createGappedProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools: Get a new protein as a GappedSequence
createGFFRecord(Feature, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Internal method to create a GFFRecord from an individual Feature.
createImmutableAlignment(Map) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram: A factory method for creating new immutable alignments, particularly for use as base call alignments.
createImmutableSymbolList(Alphabet, List) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram: A factory method for creating new symbol lists with a given alphabet.
createInnerBounds(CircularRendererContext) - Static method in class org.biojava.bio.gui.sequence.GUITools
createList(Object[]) - Static method in class org.biojava.utils.ListTools
createList(List) - Static method in class org.biojava.utils.ListTools
createMatches() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
createMethod(String, CodeClass, CodeClass[], int) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass: Create a new method.
createMethod(String, CodeClass, CodeClass[], String[], int) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass: Create a new method.
createNodeSet() - Method in class org.biojava.utils.automata.FiniteAutomaton
createNodeSet() - Method in interface org.biojava.utils.automata.NfaBuilder
createNodeSet() - Method in class org.biojava.utils.automata.NfaSubModel
createNucleotide(String) - Static method in class org.biojava.bio.seq.NucleotideTools: Return a new Nucleotide SymbolList for nucleotide.
createNucleotideSequence(String, String) - Static method in class org.biojava.bio.seq.NucleotideTools: Return a new Nucleotide Sequence for nucleotide.
createObjectType(String) - Static method in class org.biojava.utils.bytecode.ParametricType: Create a new ParametricType that claims to resolve to an object type.
createOntology(String, String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB: Deprecated.
createOntology(String, String) - Method in interface org.biojava.ontology.OntologyFactory: Creates a new Ontology
createOntologyTerm(Ontology) - Method in class org.biojava.ontology.Ontology.Impl
createOrthologue(int, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Create an orthologue.
createOrthologue(int, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthologue(Taxon, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Create an orthologue.
createOrthologue(Taxon, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthoPair(Orthologue, Orthologue, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Create a curated orthology entry.
createOrthoPair(Orthologue, Orthologue, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Create a computed orthology entry.
createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthoPairSet() - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Create a Homologene Group.
createOrthoPairSet() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOuterBounds(CircularRendererContext, double) - Static method in class org.biojava.bio.gui.sequence.GUITools
createPhred(SymbolList, SymbolList) - Static method in class org.biojava.bio.program.phred.PhredTools: Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.
createPhredSequence(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools: Create and return a new PhredSequence from the specified FASTQ formatted sequence.
createPrimitiveType(String) - Static method in class org.biojava.utils.bytecode.ParametricType: Create a new ParametricType that claims to resolve to a primative type.
createProtease(String, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
createProtease(String, boolean, String, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
createProtease(SymbolList, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
createProtease(SymbolList, boolean, SymbolList, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager: Creates and registers a new Protease.
createProtein(String) - Static method in class org.biojava.bio.seq.ProteinTools: Return a new Protein SymbolList for protein.
createProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools: Return a new PROTEIN Sequence for protein.
createQualityScores(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools: Create and return a new SymbolList of quality scores from the specified FASTQ formatted sequence.
createRecord(GFFDocumentHandler, List, String, String) - Method in class org.biojava.bio.program.gff.GFFParser: Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
createRecord(GFF3DocumentHandler, List, String, String, Ontology, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser: Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.
createRegex(SymbolList) - Static method in class org.biojava.bio.symbol.MotifTools: createRegex creates a regular expression which matches the SymbolList.
createRenderer(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
createRenderer(int) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
createRichSequence(String, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Create a new RichSequence in the specified namespace.
createRichSequence(String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Create a new RichSequence in the default namespace.
createRichSequence(String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Create a new RichSequence in the default namespace.
createRichSequence(Namespace, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Create a new RichSequence in the specified namespace.
createRichSequence(Namespace, String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Create a new RichSequence in the specified namespace.
createRNA(String) - Static method in class org.biojava.bio.seq.RNATools: Return a new RNA SymbolList for rna.
createRNASequence(String, String) - Static method in class org.biojava.bio.seq.RNATools: Return a new RNA Sequence for rna.
createSequence(SymbolList, String, String, Annotation) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
createSequence(SymbolList, String, String, Annotation) - Method in interface org.biojava.bio.seq.SequenceFactory: Deprecated.

Creates a sequence using these parameters.
createSequence(SymbolList, String, String, Annotation) - Static method in class org.biojava.bio.seq.SequenceTools
createSeriesList(String, String, int) - Static method in class org.biojava.utils.ListTools: Create a new SeriesList with the given leader, trailer and size.
createState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine
createSubcontext(String) - Method in class org.biojava.naming.ObdaContext
createSubcontext(String, Attributes) - Method in class org.biojava.naming.ObdaContext
createSubcontext(Name) - Method in class org.biojava.naming.ObdaContext
createSubcontext(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
createSwissprotParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
createSymbol(char, String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager: Deprecated.
Use the two-arg version of this method instead.
createSymbol(char, Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Deprecated.
use the new version, without the token argument
createSymbol(char, Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Deprecated.
use the three-arg version of this method instead.
createSymbol(String) - Static method in class org.biojava.bio.symbol.AlphabetManager: Generate a new AtomicSymbol instance with a name and an Empty Annotation.
createSymbol(String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager: Generate a new AtomicSymbol instance with a name and Annotation.
createSymbol(Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Generates a new Symbol instance that represents the tuple of Symbols in symList.
createSymbol(Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Generates a new Symbol instance that represents the tuple of Symbols in symList.
createSymbolDistribution(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools: Create and return a new array of symbol Distributions from the specified FASTQ formatted sequence.
createTaxon(int, String) - Static method in class org.biojava.bio.program.homologene.HomologeneTools: add a Taxon
createTaxon(String, String) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory: Deprecated.
createTaxon(String, String) - Method in interface org.biojava.bio.taxa.TaxonFactory: Deprecated.

Create a new orphan Taxon with a given scientific and common name.
createTaxon(String, String) - Method in class org.biojava.bio.taxa.WeakTaxonFactory: Deprecated.
createTemplate() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: generates a very basic Template for the feature with SmallAnnotation in the annotation field.
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
createTemplate() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: generates a very basic Template for the feature with SmallAnnotation in the annotation field.
createTerm(String) - Method in class org.biojava.ontology.IntegerOntology
createTerm(String) - Method in interface org.biojava.ontology.Ontology: Create a new term in this ontology.
createTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
createTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Create a new term in this ontology.
createTerm(String, String) - Method in class org.biojava.ontology.IntegerOntology
createTerm(String, String) - Method in interface org.biojava.ontology.Ontology: Create a new term in this ontology.
createTerm(String, String) - Method in class org.biojava.ontology.Ontology.Impl
createTerm(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in class org.biojava.ontology.IntegerOntology
createTerm(String, String, Object[]) - Method in interface org.biojava.ontology.Ontology: Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in class org.biojava.ontology.Ontology.Impl
createTerm(String, String, Object[]) - Method in class org.biojavax.ontology.SimpleComparableOntology: Create a new term in this ontology.
createTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel: Makes a transition between two states legal.
createTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
createTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
createTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.IntegerOntology
createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.ontology.Ontology: Creates a new Triple.
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.Ontology.Impl
createTriple(Term, Term, Term, String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Creates a new Triple.
createType(String) - Static method in class org.biojava.utils.bytecode.ParametricType: Create a new ParametricType that claims nothing.
createType(String, FeatureFilter, Set) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl: Create a new type in this repository.
createType(String, CodeClass[]) - Static method in class org.biojava.utils.bytecode.ParametricType: Create a new ParametricType that claims to be castable to all the classes in a list.
createUnigene(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
createUnigene(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
createUnigene(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
createUnigene(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools: Create a new UnigeneDB instance referred to by a URL.
createURL(Object) - Method in interface org.biojava.utils.net.URLFactory: createURL returns a URL which is relevant to the object in a way specified by the implementation.
createVariable(String, String) - Method in class org.biojava.ontology.IntegerOntology
createVariable(String, String) - Method in interface org.biojava.ontology.Ontology: Create a new term in this ontology that is used as a variable.
createVariable(String, String) - Method in class org.biojava.ontology.Ontology.Impl
createVariable(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Create a new term in this ontology that is used as a variable.
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
criterionAliasMap() - Method in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter: Returns a map of property names (keys) to aliases (values), if the criterion returned by asCriterion() uses aliases at all.
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
CROSS_OVER_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
CrosshairRenderer - Class in org.biojava.bio.gui.sequence: CrosshairRenderer draws a crosshair, optionally with coordinates.
CrosshairRenderer() - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer: Creates a new CrosshairRenderer in light grey with coordinates displayed.
CrosshairRenderer(Paint) - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer: Creates a new CrosshairRenderer of the specified colour, with coordinates displayed.
CrossOverFunction - Interface in org.biojavax.ga.functions: Crosses two chromosomes.
CrossOverFunction.NoCross - Class in org.biojavax.ga.functions: A place holder CrossOverFunction that doesn't perform cross overs
CrossProductTokenization - Class in org.biojava.bio.seq.io: Tokenization for cross-product alphabets.
CrossProductTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
CrossProductTokenization(Alphabet, List) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
CrossRef - Interface in org.biojavax: Represents a cross reference to another database.
CROSSREF - Static variable in interface org.biojavax.bio.seq.RichFeature
CROSSREF - Static variable in interface org.biojavax.DocRef
CrossReferenceResolutionException - Exception in org.biojavax: An exception that indicates that an attempt to resolve a CrossRef has failed.
CrossReferenceResolutionException() - Constructor for exception org.biojavax.CrossReferenceResolutionException: Creates a new instance of CrossReferenceResolutionException
CrossReferenceResolutionException(String) - Constructor for exception org.biojavax.CrossReferenceResolutionException: Creates a new instance of CrossReferenceResolutionException with a message.
CrossReferenceResolutionException(String, Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException: Creates a new instance of CrossReferenceResolutionException with a message and a cause.
CrossReferenceResolutionException(Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException: Creates a new instance of CrossReferenceResolutionException with a cause.
CrossReferenceResolver - Interface in org.biojavax: This interface returns symbols or sequence for a given cross-reference.
crossReferences - Variable in class org.biojava.bibliography.BibRef: It is an array of identifiers, all of them pointing to the same cited source but usually stored in different bibliographic repositories.
crypticVariable - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
cState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM: Gets the c loop state
CURATED - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
CURATED - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
currentCol() - Method in interface org.biojava.bio.dp.onehead.DPCursor: The current column of the matrix.
currentCol() - Method in class org.biojava.bio.dp.onehead.SmallCursor
currentRes() - Method in interface org.biojava.bio.dp.onehead.DPCursor: The current symbol.
CUT_COMPOUND - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme: CUT_COMPOUND a cut type where the enzyme cuts in two positions relative to the recognition site.
CUT_SIMPLE - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme: CUT_SIMPLE a cut type where the enzyme cuts in one position relative to the recognition site.
cutType - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
cys() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Cysteine (C)

D

d() - Static method in class org.biojava.bio.seq.DNATools
d() - Static method in class org.biojava.bio.seq.NucleotideTools
d() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Aspartic Acid
D_MELANOGASTER - Static variable in interface org.biojava.bio.program.homologene.Taxon
D_RERIO - Static variable in interface org.biojava.bio.program.homologene.Taxon
data - Variable in class org.biojava.bio.alignment.FlexibleAlignment
DATA_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.DataBlock: A constant representing the name of Data blocks.
DATA_TYPE_ASCII_ARRAY - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATA_TYPE_DATE - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATA_TYPE_FLOAT - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATA_TYPE_INTEGER - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATA_TYPE_PSTRING - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATA_TYPE_TIME - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATABASE - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser: A name for a comment type.
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
databaseID - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
DatabaseURLGenerator - Interface in org.biojava.bio.program.blast2html: Takes a database ID and some configuration properties ( such as base URL ) and returns either a URL or a full anchor tag.
DataBlock - Class in org.biojavax.bio.phylo.io.nexus: Represents Nexus data blocks.
DataBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.DataBlock: Delegates to NexusBlock.Abstract constructor using DataBlock.DATA_BLOCK as the name.
DataBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus: Builds Nexus characters blocks.
DataBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.DataBlockBuilder
DataBlockListener - Interface in org.biojavax.bio.phylo.io.nexus: Listens to events that represent Nexus data blocks.
DataBlockParser - Class in org.biojavax.bio.phylo.io.nexus: Parses Nexus data blocks.
DataBlockParser(DataBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.DataBlockParser: Delegates to CharactersBlockParser.
dataRecord - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATASOURCE - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
DATASOURCE_SELECTION - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
DataStore - Interface in org.biojava.bio.program.ssaha: A repository that can be searched with a sequence.
DataStoreFactory - Interface in org.biojava.bio.program.ssaha: Builder for a data store.
dataType - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
date - Variable in class org.biojava.bibliography.BibRef: Defines a date associated with an event in the life cycle of the cited resource when this resource became available.
DATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
DATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
DATE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
DATE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
dateFormat - Variable in class org.biojava.ontology.obo.OboFileParser
DB_NUCLEOTIDE - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
DB_PROTEIN - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
DBHelper - Class in org.biojava.bio.seq.db.biosql: Deprecated.
Use hibernate and org.biojavax.bio.db.*
DBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.
DBHelper.BioSequenceStyle - Class in org.biojava.bio.seq.db.biosql: Deprecated.
DBHelper.DeleteStyle - Class in org.biojava.bio.seq.db.biosql: Deprecated.
DBHelper.JoinStyle - Class in org.biojava.bio.seq.db.biosql: Deprecated.
DBREF_DB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBREF_PRIMARY_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBREF_SEC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBREFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBResolver(SequenceDB) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
dbxp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
dbxp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
dbxp - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DBXREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
debug(String) - Method in class org.biojava.bio.alignment.AbstractULAlignment
DEBUG - Static variable in class org.biojava.utils.io.SoftHashMap
DebuggingRichSeqIOListener - Class in org.biojavax.bio.seq.io: This is purely for debugging purposes.
DebuggingRichSeqIOListener(InputStream) - Constructor for class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
declareNamespace(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
declareNamespace(String, String) - Method in interface org.biojava.utils.xml.XMLWriter: Hints that a namespace is going to be used in a sub-tree.
decodeDNAToken(char) - Static method in class org.biojava.bio.program.abi.ABIFParser: Decodes a character into a Symbol in the DNA alphabet.
decorate(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
decorate(Location) - Method in class org.biojava.bio.symbol.BetweenLocation
decorate(Location) - Method in class org.biojava.bio.symbol.CircularLocation
DEF - Static variable in class org.biojava.ontology.obo.OboFileHandler
DEFAULT - Static variable in interface org.biojava.bio.dist.DistributionFactory: The default DistributionFactory object.
DEFAULT - Static variable in class org.biojava.bio.dist.OrderNDistributionFactory: Factory which used DistributionFactory.DEFAULT to create conditioned distributions.
DEFAULT - Static variable in interface org.biojava.bio.dp.DPFactory
DEFAULT - Static variable in class org.biojava.bio.program.phred.PhredFormat
DEFAULT - Static variable in class org.biojava.bio.seq.impl.FeatureImpl: Default implementation of FeatureRealizer, which wraps simple implementations of Feature and StrandedFeature.
DEFAULT - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
DEFAULT - Static variable in class org.biojava.bio.seq.io.FastaFormat: Deprecated.
DEFAULT - Static variable in class org.biojava.bio.seq.io.GAMEFormat
DEFAULT - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
DEFAULT - Static variable in class org.biojava.bio.seq.projection.ProjectionEngine: The standard projection engine object.
DEFAULT - Static variable in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
DEFAULT - Static variable in interface org.biojavax.ga.functions.SelectionFunction: Selects all members of a population for replication
DEFAULT_CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
DEFAULT_DELIMITERS - Static variable in class org.biojava.utils.TypedProperties: the default string of delimiter characters used by getAsStringList()
DEFAULT_FINDER_NAME - Static variable in interface org.biojava.utils.candy.CandyFinder: A default name of this (and any) finder.
DEFAULT_LIMIT - Static variable in class org.biojava.utils.io.SoftHashMap
DEFAULT_MAX_CROSS - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
DEFAULT_MUTATION_PROBS - Static variable in interface org.biojavax.ga.functions.MutationFunction
DEFAULT_TERM_CHAR - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree
DEFAULT_VARIANT - Static variable in class org.biojava.bio.program.fastq.FastqBuilder: Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER.
DefaultDistributionFactory() - Constructor for class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
DefaultFactory(CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.DPFactory.DefaultFactory
DefaultMaskingDetector() - Constructor for class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
DefaultOps - Class in org.biojava.ontology: Default implementation of OntologyOps.
DefaultOps() - Constructor for class org.biojava.ontology.DefaultOps
DefaultURLGeneratorFactory - Class in org.biojava.bio.program.blast2html: A simple default URLGeneratorFactory which returns a single NcbiDatabaseURLGenerator instance.
DefaultURLGeneratorFactory() - Constructor for class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
defineClass(GeneratedCodeClass) - Method in class org.biojava.utils.bytecode.GeneratedClassLoader: Define a class based upon a GeneratedCodeClass.
DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
delegate - Variable in class org.biojava.bio.program.tagvalue.StateMachine
delegate(StAXContentHandler) - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
delegate(StAXContentHandler) - Method in interface org.biojava.utils.stax.DelegationManager
delegates - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
DelegatingTransformer(FilterUtils.FilterTransformer, FilterUtils.FilterTransformer) - Constructor for class org.biojava.bio.seq.FilterUtils.DelegatingTransformer: Create a new DelegatingTransformer that will apply t1 and then t2 if t1 fails.
delegationCache - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
DelegationManager - Interface in org.biojava.bio.seq.io.agave: Interface which exposes delegation services offered by a StAX event source.
DelegationManager - Interface in org.biojava.utils.stax: Interface which exposes delegation services offered by a StAX event source.
DELETE_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.
DELETE_MYSQL4 - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.
DELETE_POSTGRESQL - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.
deleteTerm(Term) - Method in class org.biojava.ontology.IntegerOntology
deleteTerm(Term) - Method in interface org.biojava.ontology.Ontology: Remove a term from an ontology, together with all triples which refer to it.
deleteTerm(Term) - Method in class org.biojava.ontology.Ontology.Impl
deleteTerm(Term) - Method in class org.biojavax.ontology.SimpleComparableOntology: Remove a term from an ontology, together with all triples which refer to it.
DELIMITER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
depth - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
depth - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor: Description of the Field
DEPTH - Static variable in class org.biojava.bio.gui.sequence.AbiTraceRenderer
DEPTH - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer: Constant DEPTH indicating a change to the depth of the renderer.
DEPTH - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer
DESC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
describeSequence(Sequence) - Method in class org.biojava.bio.program.phred.PhredFormat: Return a suitable description line for a Sequence.
describeSequence(Sequence) - Method in class org.biojava.bio.seq.io.FastaFormat: Deprecated.

Return a suitable description line for a Sequence.
description - Variable in class org.biojava.bibliography.BibRef: An account of the content of the cited resource.
description - Variable in class org.biojava.ontology.AbstractTerm
description - Variable in class org.biojava.utils.candy.CandyEntry: A value of this entry.
description(String) - Method in interface org.biojava.bio.program.fastq.ParseListener: Notify this parse listener of a description line.
DESCRIPTION - Static variable in interface org.biojavax.bio.BioEntry
DESCRIPTION - Static variable in interface org.biojavax.Namespace
DESCRIPTION - Static variable in interface org.biojavax.ontology.ComparableOntology
DESCRIPTION - Static variable in interface org.biojavax.ontology.ComparableTerm
DESCRIPTOR - Static variable in interface org.biojavax.ontology.ComparableTriple
destination - Variable in class org.biojava.bio.program.tagvalue.StateMachine.Transition: the terminus of this Transition
destroy() - Method in interface org.biojava.bibliography.BibRefQuery: It frees all resources related to this query collection.
destroy() - Method in interface org.biojava.utils.candy.CandyVocabulary: It frees all resources related to this vocabulary.
destroy() - Static method in class org.biojava.utils.io.FlatFileCache
destroySubcontext(String) - Method in class org.biojava.naming.ObdaContext
destroySubcontext(Name) - Method in class org.biojava.naming.ObdaContext
destroyTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel: Breaks a transition between two states legal.
destroyTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
destroyTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
DfaBuilder - Class in org.biojava.utils.automata
DiagonalAddKernel - Class in org.biojava.stats.svm: Adds a class specific constant to k(x, x).
DiagonalAddKernel() - Constructor for class org.biojava.stats.svm.DiagonalAddKernel
DiagonalCachingKernel - Class in org.biojava.stats.svm: Caches the leading diagonal of a kernel matrix.
DiagonalCachingKernel() - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel: Create a new CachingKernel.
DiagonalCachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel: Creates a new DiagonalCachingKernel that nests k.
diddleQueue() - Method in class org.biojava.utils.IndexedChangeHub
Digest - Class in org.biojava.bio.proteomics: This class contains methods for calculating the results of proteolytic digestion of a protein sequence this class is not designed to be thread safe
Digest() - Constructor for class org.biojava.bio.proteomics.Digest: Creates a new Digest Bean
DIGEST - Static variable in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
DIGEST - Static variable in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
dimensionRatio - Variable in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
disconnect() - Method in interface org.biojava.bibliography.BibRefQuery: It disconnects from the repository.
disconnect() - Method in interface org.biojava.bibliography.BibRefSupport: It closes connection with a utility object.
disconnect() - Method in interface org.biojava.utils.candy.CandyFinder: It closes connection with the finder object.
DISJOINT_FROM - Static variable in class org.biojava.ontology.obo.OboFileHandler
disjunctAdd - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
disjunction - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
DISPLACEMENT - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer: Constant DISPLACEMENT indicating a change to the Y-axis displacement of the features.
displayString() - Method in class org.biojava.utils.ChangeSupport
DistanceBasedTreeMethod - Class in org.biojavax.bio.phylo
DistanceBasedTreeMethod() - Constructor for class org.biojavax.bio.phylo.DistanceBasedTreeMethod
DISTANCES_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.DistancesBlock: A constant representing the name of Distances blocks.
DistancesBlock - Class in org.biojavax.bio.phylo.io.nexus: Represents Nexus distances blocks.
DistancesBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.DistancesBlock: Delegates to NexusBlock.Abstract constructor using DistancesBlock.DISTANCES_BLOCK as the name.
DistancesBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus: Builds Nexus distances blocks.
DistancesBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
DistancesBlockListener - Interface in org.biojavax.bio.phylo.io.nexus: Listens to events that represent Nexus distances blocks.
DistancesBlockParser - Class in org.biojavax.bio.phylo.io.nexus: Parses Nexus distances blocks.
DistancesBlockParser(DistancesBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser: Delegates to NexusBlockParser.Abstract.
DistDataSource - Interface in org.biojava.bio.seq.distributed: Object which contributes data to a DistributedSequenceDB.
distForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
distOverAlignment(Alignment) - Static method in class org.biojava.bio.dist.DistributionTools: Equivalent to distOverAlignment(a, false, 0.0).
distOverAlignment(Alignment, boolean) - Static method in class org.biojava.bio.dist.DistributionTools: Creates an array of distributions, one for each column of the alignment.
distOverAlignment(Alignment, boolean, double) - Static method in class org.biojava.bio.dist.DistributionTools: Creates an array of distributions, one for each column of the alignment.
DistributedSequenceDB - Class in org.biojava.bio.seq.distributed: Sequence database from the meta-DAS system.
DistributedSequenceDB() - Constructor for class org.biojava.bio.seq.distributed.DistributedSequenceDB
Distribution - Interface in org.biojava.bio.dist: An encapsulation of a probability distribution over the Symbols within an alphabet.
DISTRIBUTION - Static variable in interface org.biojava.bio.dp.EmissionState: This signals that the distribution associate with an EmissionState has been altered.
Distribution.NullModelForwarder - Class in org.biojava.bio.dist: Deprecated.
use new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY) instead
DistributionFactory - Interface in org.biojava.bio.dist: A thing that can make Distributions.
DistributionFactory.DefaultDistributionFactory - Class in org.biojava.bio.dist: The default DistributionFactory implementation.
DistributionLogo - Class in org.biojava.bio.gui: The GUI component for rendering a DistributionLogo.
DistributionLogo() - Constructor for class org.biojava.bio.gui.DistributionLogo: Create a new DistributionLogo object.
DistributionTools - Class in org.biojava.bio.dist: A class to hold static methods for calculations and manipulations using Distributions.
DistributionTrainer - Interface in org.biojava.bio.dist: An object that can be used to train a distribution up.
DistributionTrainerContext - Interface in org.biojava.bio.dist: A context within a group of DistributionTrainers can be trained together.
DIVISION - Static variable in interface org.biojavax.bio.BioEntry
DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
DIVISION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DivisionLkpReader - Class in org.biojava.bio.seq.db.emblcd: DivisionLkpReader reads the "division.lkp" file of an EMBL CD-ROM format binary index.
DivisionLkpReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.DivisionLkpReader: Creates a new DivisionLkpReader.
DNA - Static variable in interface org.biojava.bio.chromatogram.Chromatogram: The sequence label for the list of called bases.
DNA - Static variable in class org.biojava.bio.seq.io.FastaAlignmentFormat
DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: DNA indicates that a sequence contains DNA (deoxyribonucleic acid) symbols.
DNAAmbPack - Class in org.biojava.bio.symbol: Packing utility class for DNA.
DNAAmbPack() - Constructor for class org.biojava.bio.symbol.DNAAmbPack
DNAComposition - Class in org.biojava.bio.molbio: Computes composition statistics about a DNA SymbolList.
DNAComposition() - Constructor for class org.biojava.bio.molbio.DNAComposition
DNANoAmbPack - Class in org.biojava.bio.symbol: A Packing implementation which handles the DNA alphabet, without any support for ambiguity symbols.
DNANoAmbPack(byte) - Constructor for class org.biojava.bio.symbol.DNANoAmbPack: Construct a new packing which returns the specified byte value for unknown Symbols (such as ambiguity symbols).
DNANoAmbPack(Symbol) - Constructor for class org.biojava.bio.symbol.DNANoAmbPack: Construct a new packing which translates unknown symbols into the specified symbol.
DNAStyle - Class in org.biojava.bio.gui: A simple implementation of SymbolStyle optimized for DNA.
DNAStyle() - Constructor for class org.biojava.bio.gui.DNAStyle
dnaSymbolFromPhred(Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools: Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
dnaToken(Symbol) - Static method in class org.biojava.bio.seq.DNATools: Get a single-character token for a DNA symbol
DNATools - Class in org.biojava.bio.seq: Useful functionality for processing DNA sequences.
DO_NOTHING - Static variable in class org.biojava.utils.bytecode.CodeUtils
doAnnotation(Sequence) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB: Apply the annotation to a sequence.
docNumber - Variable in class org.biojava.bibliography.BiblioPatent: The document number.
docOffice - Variable in class org.biojava.bibliography.BiblioPatent: Document office.
DocRef - Interface in org.biojavax: Represents a documentary reference.
DocRefAuthor - Interface in org.biojavax: Represents an author of a documentary reference.
DocRefAuthor.Tools - Class in org.biojavax: Useful tools for working with authors.
docType - Variable in class org.biojava.bibliography.BiblioPatent: Document type.
documentEnd() - Method in interface org.biojava.ontology.obo.OboFileEventListener: end of parsing a new OBO file
documentEnd() - Method in class org.biojava.ontology.obo.OboFileHandler
documentStart() - Method in interface org.biojava.ontology.obo.OboFileEventListener: starting to parse a new OBO file
documentStart() - Method in class org.biojava.ontology.obo.OboFileHandler
DOI_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms: Holds a reference to the key that must be used to store DOI references.
doLayer(SequenceRenderContext, FeatureFilter) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
DOMAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
domain1 - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
doPreProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Emit any per-sequence header information.
doProcessFeature(Feature, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Internal method to process an individual Feature.
doProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Internal method to process an individual Sequence.
doRefreshRenderers() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
doRetain() - Method in class org.biojava.bio.program.tagvalue.TagDropper: Find out if known tags are retained or dropped.
doSortPeptides() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
DotState - Interface in org.biojava.bio.dp: A Dot state.
DoubleAlphabet - Class in org.biojava.bio.symbol: An efficient implementation of an Alphabet over the infinite set of double values.
DoubleAlphabet.DoubleRange - Class in org.biojava.bio.symbol: A range of double values.
DoubleAlphabet.DoubleSymbol - Class in org.biojava.bio.symbol: A single double value.
DoubleAlphabet.SubDoubleAlphabet - Class in org.biojava.bio.symbol: A class to represent a contiguous range of double symbols.
DoubleElementHandlerBase - Class in org.biojava.utils.stax: StAX handler for any element which just contains a string representation of a double.
DoubleElementHandlerBase() - Constructor for class org.biojava.utils.stax.DoubleElementHandlerBase
DoubleRange(double, double) - Constructor for class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
Doublet() - Constructor for class org.biojava.utils.ListTools.Doublet
Doublet(Object, Object) - Constructor for class org.biojava.utils.ListTools.Doublet
DoubleTokenization - Class in org.biojava.bio.seq.io
DoubleTokenization() - Constructor for class org.biojava.bio.seq.io.DoubleTokenization
doubleValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable: this method is expected to reverse-translate any symbol in the source alphabet.
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable: this method is expected to reverse-translate any symbol in the source alphabet.
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
dp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
dp - Static variable in class org.biojavax.bio.seq.io.FastaFormat
DP - Class in org.biojava.bio.dp: Objects that can perform dymamic programming operations upon sequences with HMMs.
DP() - Constructor for class org.biojava.bio.dp.DP: This method will result in a DP with no model.
DP(MarkovModel) - Constructor for class org.biojava.bio.dp.DP
dp_ipi - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
dp_uniprot - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
DP.ReverseIterator - Class in org.biojava.bio.dp
DPCompiler - Class in org.biojava.bio.dp.twohead: This is an implementation of CellCalculatorFactoryMaker that compiles the HMM object down to Java byte-code that is equivalent in behaviour to the interpreter.
DPCompiler(boolean) - Constructor for class org.biojava.bio.dp.twohead.DPCompiler
DPCursor - Interface in org.biojava.bio.dp.onehead: Encapsulates the dynamic programmming matrix, and the context within algorithms work.
DPFactory - Interface in org.biojava.bio.dp: The interface for objects that can generate a DP object for a MarkovModel.
DPFactory.DefaultFactory - Class in org.biojava.bio.dp
DPInterpreter - Class in org.biojava.bio.dp.twohead
DPInterpreter(DP) - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter
DPInterpreter.Maker - Class in org.biojava.bio.dp.twohead
DPMatrix - Interface in org.biojava.bio.dp
DR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
DRAW_CALL_A - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating whether to fill in the callboxes for calls of nucleotide A.
DRAW_CALL_C - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating whether to fill in the callboxes for calls of nucleotide C.
DRAW_CALL_G - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating whether to fill in the callboxes for calls of nucleotide G.
DRAW_CALL_OTHER - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating whether to fill in the callboxes for non-base calls (gaps, ambiguities).
DRAW_CALL_SEPARATORS - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating whether to draw vertical lines separating the calls.
DRAW_CALL_T - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating whether to fill in the callboxes for calls of nucleotide T.
DRAW_TRACE_A - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating whether to draw the chromatogram trace for nucleotide A.
DRAW_TRACE_C - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating whether to draw the chromatogram trace for nucleotide C.
DRAW_TRACE_G - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating whether to draw the chromatogram trace for nucleotide G.
DRAW_TRACE_T - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating whether to draw the chromatogram trace for nucleotide T.
drawableCallboxesValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Flag for drawable call boxes.
drawLine(Graphics2D, SequenceRenderContext, int, StrandedFeature.Strand) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer: draws required bar in correct translation frame.
drawTo(Graphics2D) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Draws the chromatogram onto the provided graphics context.
dropBoundaryValues() - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
DROSOPHILA_MELANOGASTER_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools: Drosophila melanogaster codon preferences
dsCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
DummyCrossReferenceResolver - Class in org.biojavax: A simple implementation of CrossReferenceResolver.
DummyCrossReferenceResolver() - Constructor for class org.biojavax.DummyCrossReferenceResolver
DummyRichSequenceHandler - Class in org.biojavax.bio.seq
DummyRichSequenceHandler() - Constructor for class org.biojavax.bio.seq.DummyRichSequenceHandler
DummySequence - Class in org.biojava.bio.seq.impl: A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
DummySequence(String, String) - Constructor for class org.biojava.bio.seq.impl.DummySequence
DummySequenceDB - Class in org.biojava.bio.seq.db: DummySequenceDB is an implementation which contains only a DummySequence.
DummySequenceDB(String) - Constructor for class org.biojava.bio.seq.db.DummySequenceDB
DummySequenceDBInstallation - Class in org.biojava.bio.seq.db: DummySequenceDBInstallation is an implementation which returns the same DummySequenceDB instance regardless of the identifier used to retrieve a database.
DummySequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.DummySequenceDBInstallation
DummySymbolList - Class in org.biojava.bio.symbol: Symbol list which just consists of non-informative symbols.
DummySymbolList(Alphabet, int, Symbol) - Constructor for class org.biojava.bio.symbol.DummySymbolList
DummySymbolList(FiniteAlphabet, int) - Constructor for class org.biojava.bio.symbol.DummySymbolList
dumpBlocks() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Debugging method
duplicate() - Method in class org.biojava.utils.automata.NfaSubModel: Makes a deep clone of this instance.
DuplicateTaxonException - Exception in org.biojava.bio.program.homologene
DuplicateTaxonException() - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
DuplicateTaxonException(String) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
DuplicateTaxonException(Throwable) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
DuplicateTaxonException(Throwable, String) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException

E

e() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Glutamic Acid
EbiDatabaseURLGenerator - Class in org.biojava.bio.program.blast2html: Simple URL generator for EMBL at the EBI.
EbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
EbiFormat - Class in org.biojava.bio.taxa: Deprecated.
replaced by classes in org.biojavax.bio.taxa
EbiFormat() - Constructor for class org.biojava.bio.taxa.EbiFormat: Deprecated.
EC_FROM_STRING - Static variable in class org.biojava.bio.program.formats.FormatTools
EC_PATTERN - Static variable in interface org.biojava.bio.EcNumber: A Pattern that can be used to parse EC strings into the indiidual numbers.
eCache - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
eCache - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor: Description of the Field
ECHIN_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the echinoderm mitochondrial genetic code.
Echo - Class in org.biojava.bio.program.tagvalue: A simple listener that just echoes events back to the console.
Echo() - Constructor for class org.biojava.bio.program.tagvalue.Echo
Echo(PrintStream) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Echo
EcNumber - Interface in org.biojava.bio: An ec (enzyme classification) number.
EcNumber.Impl - Class in org.biojava.bio: A simple implementation of EcNumber.
ECOLI - Static variable in class org.biojava.bio.symbol.CodonPrefTools: Escherichia coli codon preferences
edit(Object, Edit) - Method in interface org.biojava.bio.alignment.EditableAlignment: edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
edit(Object, Edit) - Method in class org.biojava.bio.alignment.FlexibleAlignment
edit(Edit) - Method in class org.biojava.bio.dp.SimpleStatePath
edit(Edit) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
edit(Edit) - Method in class org.biojava.bio.seq.impl.DummySequence
edit(Edit) - Method in class org.biojava.bio.seq.impl.RevCompSequence: edit() will try to edit the underlying Sequence.
edit(Edit) - Method in class org.biojava.bio.seq.impl.SimpleSequence
edit(Edit) - Method in class org.biojava.bio.seq.impl.SubSequence
edit(Edit) - Method in class org.biojava.bio.seq.impl.ViewSequence
edit(Edit) - Method in class org.biojava.bio.seq.NewSimpleAssembly
edit(Edit) - Method in class org.biojava.bio.seq.SimpleAssembly
edit(Edit) - Method in class org.biojava.bio.symbol.AbstractSymbolList
edit(Edit) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
edit(Edit) - Method in class org.biojava.bio.symbol.RelabeledAlignment
edit(Edit) - Method in class org.biojava.bio.symbol.SimpleSymbolList: Apply and edit to the SymbolList as specified by Edit.
edit(Edit) - Method in interface org.biojava.bio.symbol.SymbolList: Apply an edit to the SymbolList as specified by the edit object.
edit(Edit) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList: Apply an edit to the SymbolList as specified by the edit object.
edit(Edit) - Method in class org.biojavax.bio.seq.ThinRichSequence: Apply an edit to the SymbolList as specified by the edit object.
edit(RichSequence, Edit) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler: Apply an edit to the Sequence as specified by the edit object.
edit(RichSequence, Edit) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler: Apply an edit to the Sequence as specified by the edit object.
edit(RichSequence, Edit) - Method in interface org.biojavax.bio.seq.RichSequenceHandler: Apply an edit to the Sequence as specified by the edit object.
Edit - Class in org.biojava.bio.symbol: Encapsulates an edit operation on a SymbolList.
Edit(int, int, SymbolList) - Constructor for class org.biojava.bio.symbol.Edit: Create a new Edit.
Edit(int, int, SymbolList, Map<String, Object>) - Constructor for class org.biojava.bio.symbol.Edit: Create a new Edit with some properties.
Edit(int, Alphabet, Symbol) - Constructor for class org.biojava.bio.symbol.Edit: Convenience construtor for making single residue changes
EDIT - Static variable in interface org.biojava.bio.symbol.SymbolList: Signals that the SymbolList is being edited.
EditableAlignment - Interface in org.biojava.bio.alignment: EditableAlignment is an interface that defines methods for shifting bases within an Alignment.
edition - Variable in class org.biojava.bibliography.BiblioBook: Edition.
editor - Variable in class org.biojava.bibliography.BiblioBook: Editor.
EDITOR_LIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EDITOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
EditScreener(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
EditTranslater(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
elementLength - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
ElementRecognizer - Interface in org.biojava.bio.program.xff: Simple interface for filtering SAX/StAX startElement events.
ElementRecognizer - Interface in org.biojava.bio.seq.io.agave: This class is copied to agave package Simple interface for filtering SAX/StAX startElement events
ElementRecognizer - Interface in org.biojava.bio.seq.io.game: Simple interface for filtering SAX/StAX startElement events
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.program.xff
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.seq.io.agave
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.seq.io.game
ElementRecognizer.ByLocalName - Class in org.biojava.bio.program.xff: Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName - Class in org.biojava.bio.seq.io.agave: Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName - Class in org.biojava.bio.seq.io.game: Filter elements by local name (not recommended).
ElementRecognizer.ByNSName - Class in org.biojava.bio.program.xff: Filter elements by name and namespace.
ElementRecognizer.ByNSName - Class in org.biojava.bio.seq.io.agave: Filter elements by name and namespace.
ElementRecognizer.ByNSName - Class in org.biojava.bio.seq.io.game: Filter elements by name and namespace.
ElementRecognizer.HasAttribute - Class in org.biojava.bio.program.xff: Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute - Class in org.biojava.bio.seq.io.agave: Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute - Class in org.biojava.bio.seq.io.game: Filter elements on the existence of a specified attribute.
EllipticalBeadRenderer - Class in org.biojava.bio.gui.sequence: EllipticalBeadRenderer renders features as simple ellipses.
EllipticalBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.EllipticalBeadRenderer: Creates a new EllipticalBeadRenderer object with the default settings.
EllipticalBeadRenderer(double, double, Paint, Paint, Stroke, double) - Constructor for class org.biojava.bio.gui.sequence.EllipticalBeadRenderer: Creates a new EllipticalBeadRenderer.
email - Variable in class org.biojava.bibliography.BiblioPerson: Their e-mail address.
Embl - Class in org.biojava.bio.program.formats
Embl() - Constructor for class org.biojava.bio.program.formats.Embl
EMBL - Static variable in class org.biojava.bio.program.tagvalue.LineSplitParser: A LineSplitParser pre-configured to process EMBL-style flat files.
EMBL - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: EMBL indicates that the sequence format is EMBL.
EMBL_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: EMBL_AA premade EMBL | AA.
EMBL_AGAVE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
EMBL_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: EMBL_DNA premade EMBL | DNA.
EMBL_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLFormat: The name of the current format
EMBL_GENBANK_FEATURE_TABLE_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
EMBL_PRE87_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLFormat: The name of the Pre-87 format
EMBL_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: EMBL_RNA premade EMBL | RNA.
EMBL_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
Embl2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave: Map EMBL data into AGAVE format
EmblCDROMIndexReader - Class in org.biojava.bio.seq.db.emblcd: EmblCDROMIndexReader is an abstract class whose concrete subclasses read EMBL CD-ROM format indices from an underlying InputStream.
EmblCDROMIndexReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader: Creates a new EmblCDROMIndexReader instance.
EmblCDROMIndexStore - Class in org.biojava.bio.seq.db: EmblCDROMIndexStores implement a read-only IndexStore backed by EMBL CD-ROM format binary indices.
EmblCDROMIndexStore(File, File, File, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.EmblCDROMIndexStore: Creates a new EmblCDROMIndexStore backed by a random access binary index.
EmblCDROMIndexStore(File, File, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.EmblCDROMIndexStore: Creates a new EmblCDROMIndexStore backed by a random access binary index.
EmblCDROMRandomAccess - Class in org.biojava.bio.seq.db.emblcd: EmblCDROMRandomAccess is an abstract class whose concrete subclasses can perform fast lookups in EMBL CD-ROM format index files.
EmblCDROMRandomAccess(File, int, int, long) - Constructor for class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess: Creates a new EmblCDROMRandomAccess object.
EmblFileFormer - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
EmblFileFormer() - Constructor for class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.

Creates a new EmblFileFormer using System.out stream.
EmblFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.

Creates a new EmblFileFormer using the specified stream.
EMBLFormat - Class in org.biojavax.bio.seq.io: Format reader for EMBL files.
EMBLFormat() - Constructor for class org.biojavax.bio.seq.io.EMBLFormat
EMBLFormat.Terms - Class in org.biojavax.bio.seq.io: Implements some EMBL-specific terms.
EmblLikeFormat - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io.EMBLFormat instead
EmblLikeFormat() - Constructor for class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
EmblLikeLocationParser - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
EmblProcessor - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
EmblProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.EmblProcessor: Deprecated.
EmblProcessor.Factory - Class in org.biojava.bio.seq.io: Deprecated.

Factory which wraps SequenceBuilders in an EmblProcessor
EmblReferenceComparator - Class in org.biojava.bio.seq.io
EmblReferenceComparator() - Constructor for class org.biojava.bio.seq.io.EmblReferenceComparator
EMBLXML_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat: The name of this format
EMBLxmlFormat - Class in org.biojavax.bio.seq.io: Format reader for EMBLxml files.
EMBLxmlFormat() - Constructor for class org.biojavax.bio.seq.io.EMBLxmlFormat
EMBLxmlFormat.Terms - Class in org.biojavax.bio.seq.io: Implements some EMBLxml-specific terms.
emissionAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel: Alphabet that is emitted by the emission states.
emissionAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel
emissionAlphabet() - Method in class org.biojava.bio.dp.WMAsMM
EmissionCache - Class in org.biojava.bio.dp.twohead: Cache for columns of emission probabilities in pair-wise alignment algorithms.
EmissionCache(Alphabet, State[], int, ScoreType) - Constructor for class org.biojava.bio.dp.twohead.EmissionCache
emissions - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
emissions - Variable in class org.biojava.bio.dp.twohead.Cell
emissionsNull - Variable in class org.biojava.bio.dp.onehead.SingleDP
emissionsOdds - Variable in class org.biojava.bio.dp.onehead.SingleDP
emissionsProb - Variable in class org.biojava.bio.dp.onehead.SingleDP
EmissionState - Interface in org.biojava.bio.dp: A state in a markov process that has an emission spectrum.
empty - Static variable in interface org.biojava.bio.symbol.Location: The Location which contains no points.
EMPTY - Static variable in interface org.biojava.bio.annodb.AnnotationDB: An AnnotationDB that is always empty.
EMPTY - Static variable in interface org.biojava.bio.CollectionConstraint: EMPTY is a constraint which only accepts the empty set.
EMPTY_ALPHABET - Static variable in interface org.biojava.bio.symbol.Alphabet: A really useful static alphabet that is always empty.
EMPTY_ANNOTATION - Static variable in interface org.biojava.bio.Annotation: A really useful empty and immutable annotation object.
EMPTY_ANNOTATION - Static variable in interface org.biojavax.RichAnnotation
EMPTY_FEATURE_HOLDER - Static variable in interface org.biojava.bio.seq.FeatureHolder
EMPTY_LINE_EOR - Static variable in interface org.biojava.bio.program.tagvalue.TagValueParser: EMPTY_LINE_EOR is a special EOR value which allows an empty line to be used as a record separator.
EMPTY_LIST - Static variable in interface org.biojava.bio.symbol.SymbolList: A useful object that represents an empty symbol list, to avoid returning null.
EMPTY_LIST - Static variable in class org.biojava.utils.bytecode.CodeUtils
EMPTY_LOCATION - Static variable in interface org.biojavax.bio.seq.RichLocation: The empty location matches nothing.
EMPTY_PAIRWISE - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature: Constant EMPTY_PAIRWISE is an empty alignment for situations where there is no available alignment data or the implementation does not want to create one.
EMPTY_POSITION - Static variable in interface org.biojavax.bio.seq.Position: The empty position lies nowhere.
emptyBP - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
emptyBP - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor: Description of the Field
emptyFeature - Variable in class org.biojavax.bio.seq.io.RichSeqIOAdapter: This is a dummy feature.
EmptyFeatureHolder() - Constructor for class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
emptyList(Alphabet) - Static method in class org.biojava.bio.symbol.SymbolListViews: Get a new immutable, empty symbol list with the given alphabet.
EmptyRichAnnotation - Class in org.biojavax: A place holder for a RichAnnotation that prevents null having to be used
EmptyRichAnnotation() - Constructor for class org.biojavax.EmptyRichAnnotation
EmptyRichLocation - Class in org.biojavax.bio.seq: An Empty implementation of RichLocation.
EmptyRichLocation() - Constructor for class org.biojavax.bio.seq.EmptyRichLocation
end - Variable in class org.biojava.utils.automata.FiniteAutomaton
end() - Method in interface org.biojava.bio.search.BioMatcher: Get the last symbol index that matches the pattern.
end() - Method in class org.biojava.bio.search.MaxMismatchMatcher
end() - Method in class org.biojava.utils.regex.Matcher: Returns the index of the last character matched, plus one.
end(int) - Method in class org.biojava.utils.regex.Matcher: Returns the index of the last Symbol, plus one, of the subsequence captured by the given group during the previous match operation.
END_RECORD_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
END_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
END_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
END_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
endBlock() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener: Notifies the parser that a block is ending.
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
endBlock() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser: Notifies the parser that a block is ending.
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
endBlock() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener: Finished reading a block.
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
endBlock() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
endComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
endComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener: Closing a comment tag.
endComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
endComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser: Closing a comment tag.
endComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
endComment() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener: Closing a comment tag.
endComment() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
endDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: end of data for DB
endDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endDocument() - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler: Indicates that the current GFF document has now ended.
endDocument() - Method in class org.biojava.bio.program.gff.GFFFilterer
endDocument() - Method in class org.biojava.bio.program.gff.GFFWriter: Flushes the PrintWriter to make sure that everything is written.
endDocument() - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler: Indicates that the current GFF document has now ended.
endDocument() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
endDocument() - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
endDocument() - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
endElement() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
endElement(String, String, String) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler: Called when the end of an element is reached.
endElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
endElement(String, String, String) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
endElement(String, String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
endElement(String, String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
endElement(String, String, String, StAXContentHandler) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.FeatureHandler: StAX callback for element ends.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler: Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.CharElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.IntElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.LongElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in interface org.biojava.utils.stax.StAXContentHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.StringElementHandlerBase
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler: Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler: when exiting, put the DbXrefElement into the annotation bundle
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMESpanPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler: Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEAspectHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler.SeqRelHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEPropertyHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESpanHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler: Element specific exit handler Subclass to do anything useful.
endFeature() - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
endFeature() - Method in class org.biojava.bio.seq.io.FeatureTableParser: Deprecated.
endFeature() - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
endFeature() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
endFeature() - Method in class org.biojava.bio.seq.io.SeqIOFilter
endFeature() - Method in interface org.biojava.bio.seq.io.SeqIOListener: Mark the end of data associated with one specific feature.
endFeature() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
endFeature() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
endFeature() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Null implementation.
endFeature() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
endFeature() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
endFeature() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Mark the end of data associated with one specific feature.
endFile() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
endFile() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener: Finished reading a file.
endFile() - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
endFile() - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener: Finished reading a file.
endFileComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
endFileComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract: This method will get called when a comment is ended on the file, and not any block within it.
endGroup() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: end of data for group
endGroup() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endHeader() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
endHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
endHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
endHeader() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
endHeader() - Method in class org.biojava.bio.search.FilteringContentHandler
endHeader() - Method in class org.biojava.bio.search.SearchContentAdapter
endHeader() - Method in class org.biojava.bio.search.SearchContentFilter
endHeader() - Method in interface org.biojava.bio.search.SearchContentHandler: The endHeader method indicates the end of a formatted header.
endHeader() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
endHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
endHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
endHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
endHit() - Method in class org.biojava.bio.search.FilteringContentHandler
endHit() - Method in class org.biojava.bio.search.SearchContentAdapter
endHit() - Method in class org.biojava.bio.search.SearchContentFilter
endHit() - Method in interface org.biojava.bio.search.SearchContentHandler: The endHit method indicates the end of a formatted hit.
endHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endIndex - Variable in class org.biojava.ontology.obo.OboFileParser.SOPair
endLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
endLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
endOrthologue() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: end of data for this Orthologue
endOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endOrthoPair() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: end of data for this OrthoPair
endOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endPrefixMapping(String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
endPrefixMapping(String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
endPrefixMapping(String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
endPrefixMapping(String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
endPrefixMapping(String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
endPrefixMapping(String) - Method in interface org.biojava.utils.stax.StAXContentHandler
endPrefixMapping(String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
endRecord() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
endRecord() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
endRecord() - Method in class org.biojava.bio.program.tagvalue.Echo
endRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer
endRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer2
endRecord() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
endRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine
endRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
endRecord() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener: The current record has ended.
endSearch() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
endSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
endSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
endSearch() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
endSearch() - Method in class org.biojava.bio.search.FilteringContentHandler
endSearch() - Method in class org.biojava.bio.search.SearchContentAdapter
endSearch() - Method in class org.biojava.bio.search.SearchContentFilter
endSearch() - Method in interface org.biojava.bio.search.SearchContentHandler: The endSearch method indicates the end of useful search information.
endSearch() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
endSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener: Indicates that a sequence has been searched against a DataStore.
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
endSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.EmblProcessor: Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.OrganismParser: Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
endSequence() - Method in class org.biojava.bio.seq.io.SeqIOFilter
endSequence() - Method in interface org.biojava.bio.seq.io.SeqIOListener: Notify the listener that processing of the sequence is complete.
endSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
endSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
endSequence() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Notify the listener that processing of the sequence is complete.
endSequence() - Method in class org.biojava.bio.seq.io.SwissprotProcessor: Deprecated.
endSequence() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
endSequence() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
endSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Notify the listener that processing of the sequence is complete.
endSubHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
endSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
endSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
endSubHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
endSubHit() - Method in class org.biojava.bio.search.FilteringContentHandler
endSubHit() - Method in class org.biojava.bio.search.SearchContentAdapter
endSubHit() - Method in class org.biojava.bio.search.SearchContentFilter
endSubHit() - Method in interface org.biojava.bio.search.SearchContentHandler: The endSubHit method indicates the end of a formatted subhit.
endSubHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endTag() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
endTag() - Method in class org.biojava.bio.program.tagvalue.Aggregator
endTag() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
endTag() - Method in class org.biojava.bio.program.tagvalue.Echo
endTag() - Method in class org.biojava.bio.program.tagvalue.Indexer
endTag() - Method in class org.biojava.bio.program.tagvalue.Indexer2
endTag() - Method in class org.biojava.bio.program.tagvalue.MultiTagger
endTag() - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
endTag() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
endTag() - Method in class org.biojava.bio.program.tagvalue.StateMachine
endTag() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
endTag() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
endTag() - Method in class org.biojava.bio.program.tagvalue.TagDropper
endTag() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener: End the current tag.
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
endTokenGroup() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener: Closing a line (semi-colon encountered).
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
endTokenGroup() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser: Closing a line (semi-colon encountered).
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
endTokenGroup() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener: Closing a line (semi-colon encountered).
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder
endTokenGroup() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser
endTree() - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
endTree() - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
endTree() - Method in interface org.biojava.utils.stax.StAXContentHandler
endTree() - Method in class org.biojava.utils.stax.StAXContentHandlerBase
enrich(Feature) - Static method in class org.biojavax.bio.seq.RichFeature.Tools: Takes a normal Feature and attempts to convert it into a RichFeature.
enrich(Sequence) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Boldly attempts to convert a Sequence into a RichSequence.
enrich(Location) - Static method in class org.biojavax.bio.seq.RichLocation.Tools: Attempts to convert a plain Location into a RichLocation.
entropy(Distribution, Symbol) - Static method in class org.biojava.bio.gui.DistributionLogo: Calculate the information content of a symbol in bits.
entry - Variable in class org.biojava.utils.candy.CandyEntry: A unique identifier of this entry.
ENTRY_ACCESSION_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_CREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_CREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_DATACLASS_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_NAMESPACE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport: A vocabulary name.
ENTRY_RELCREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_RELUPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_STATUS_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_STATUS_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_SUBACC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_SUBVER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_SUBWGSVER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_TAX_DIVISION_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_UPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_UPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_VERSION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EntryNamIdxReader - Class in org.biojava.bio.seq.db.emblcd: EntryNamIdxReader reads the "entrynam.idx" file of an EMBL CD-ROM format binary index.
EntryNamIdxReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader: Creates a new EntryNamIdxReader.
EntryNamRandomAccess - Class in org.biojava.bio.seq.db.emblcd: EntryNamRandomAccess objects provide random access to records within the "entrynam.idx" file of an EMBL CD-ROM format binary index.
EntryNamRandomAccess(File, int, int, long) - Constructor for class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
entrySet() - Method in class org.biojava.utils.BeanAsMap
entrySet() - Method in class org.biojava.utils.cache.WeakValueHashMap
entrySet() - Method in class org.biojava.utils.io.SoftHashMap
entrySet() - Method in class org.biojava.utils.OverlayMap
entrySet() - Method in class org.biojava.utils.SmallMap
entryStatus - Variable in class org.biojava.bibliography.BibRef: It defines information related to the citation itself rather than to the cited resource.
Enumeration(Object[]) - Constructor for class org.biojava.bio.PropertyConstraint.Enumeration: Creates a new Enumeration using the elements of the specified array as a constraint.
Enumeration(Set) - Constructor for class org.biojava.bio.PropertyConstraint.Enumeration: Creates a new Enumeration using the members of the specified set as a constraint.
enzyme - Variable in class org.biojava.bio.molbio.RestrictionSite.Template: enzyme RestrictionEnzyme field.
Enzyme - Class in org.biojava.bio.program.formats
Enzyme() - Constructor for class org.biojava.bio.program.formats.Enzyme
Enzyme() - Constructor for class org.biojava.bio.program.formats.Ligand.Enzyme
eof() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader: Checks if the end of the file or stream is reached.
eq - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
equals(boolean[], boolean[]) - Static method in class org.biojava.utils.ObjectUtil
equals(boolean, boolean) - Static method in class org.biojava.utils.ObjectUtil
equals(double[], double[]) - Static method in class org.biojava.utils.ObjectUtil
equals(double, double) - Static method in class org.biojava.utils.ObjectUtil
equals(float[], float[]) - Static method in class org.biojava.utils.ObjectUtil
equals(float, float) - Static method in class org.biojava.utils.ObjectUtil
equals(int[], int[]) - Static method in class org.biojava.utils.ObjectUtil
equals(int, int) - Static method in class org.biojava.utils.ObjectUtil
equals(long[], long[]) - Static method in class org.biojava.utils.ObjectUtil
equals(long, long) - Static method in class org.biojava.utils.ObjectUtil
equals(Object) - Method in class org.biojava.bio.AbstractAnnotation
equals(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
equals(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
equals(Object) - Method in class org.biojava.bio.dist.AbstractDistribution
equals(Object) - Method in class org.biojava.bio.dp.SimpleWeightMatrix
equals(Object) - Method in class org.biojava.bio.dp.TrainerTransition: Two transitions are equal if they have the same trainer, from and to states.
equals(Object) - Method in class org.biojava.bio.dp.Transition: Two transitions are equal if they have the same from and to states.
equals(Object) - Method in class org.biojava.bio.EcNumber.Impl
equals(Object) - Method in class org.biojava.bio.gui.sequence.SequencePanel
equals(Object) - Method in class org.biojava.bio.molbio.RestrictionEnzyme
equals(Object) - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
equals(Object) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
equals(Object) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
equals(Object) - Method in class org.biojava.bio.seq.Feature.Template
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.And
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.Not
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.Or
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
equals(Object) - Method in class org.biojava.bio.seq.impl.SimpleFeature
equals(Object) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
equals(Object) - Method in class org.biojava.bio.symbol.AbstractLocation
equals(Object) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
equals(Object) - Method in class org.biojava.bio.symbol.AbstractSymbolList: Provides logical equality for two SymbolLists that share the same list of canonical symbols
equals(Object) - Method in class org.biojava.bio.symbol.CircularLocation
equals(Object) - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
equals(Object) - Method in interface org.biojava.bio.symbol.Location: Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
equals(Object) - Method in interface org.biojava.bio.taxa.Taxon: Deprecated.

Two taxa are equal if they have equivalent children, common and scientific names.
equals(Object) - Method in class org.biojava.ontology.Term.Impl
equals(Object) - Method in interface org.biojava.ontology.Triple: Check to see if an object is an equivalent Triple.
equals(Object) - Method in class org.biojava.ontology.Triple.Impl: Two triples are equal if all their fields are identical.
equals(Object) - Method in class org.biojava.utils.ListTools.Doublet
equals(Object) - Method in class org.biojava.utils.ListTools.Triplet
equals(Object) - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
equals(Object) - Method in class org.biojava.utils.TypedProperties
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
equals(Object) - Method in class org.biojavax.bio.seq.CompoundRichLocation: Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojavax.bio.seq.EmptyRichLocation: Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojavax.bio.seq.RichLocation.Strand: Strands are equal if their numbers and symbols match.
equals(Object) - Method in class org.biojavax.bio.seq.SimplePosition: Two positions are equal if they share all parameters in common, eg. fuzzy start+end, start, end, type.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Features are equal when they have the same rank, parent, type, and source.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Relations are equal if their objects, subjects and terms are equal.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichLocation: Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojavax.bio.SimpleBioEntry: Two bioentries are equal if they share the same namespace, name, accession and version.
equals(Object) - Method in class org.biojavax.bio.SimpleBioEntryRelationship: Relationships are equal if they share the same rank, object, subject and term.
equals(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: NCBITaxon objects are equal if their NCBITaxID fields match.
equals(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName: Two taxon names are equal if their name and class match.
equals(Object) - Method in class org.biojavax.EmptyRichAnnotation
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableOntology: Ontologies are equal if their names are equal.
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm: Two terms are equal if they are in the same ontology and share the same name.
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple: Check to see if an object is an equivalent Triple.
equals(Object) - Method in class org.biojavax.SimpleComment: Two comments are defined as equal if their text values and rankings are identical.
equals(Object) - Method in class org.biojavax.SimpleCrossRef: Equality is defined as having the same database name, accession and version.
equals(Object) - Method in class org.biojavax.SimpleDocRef: Document references are equal if they have the same author and location and title.
equals(Object) - Method in class org.biojavax.SimpleDocRefAuthor: Document references are equal if they have all fields the same.
equals(Object) - Method in class org.biojavax.SimpleNamespace: Namespaces are equal only by name.
equals(Object) - Method in class org.biojavax.SimpleNote: Notes are equal if they have the same rank and term.
equals(Object) - Method in class org.biojavax.SimpleRankedCrossRef: Ranked cross references are the same if they have the same rank and refer to the same cross reference (cross references are equal).
equals(Object) - Method in class org.biojavax.SimpleRankedDocRef: Two ranked document references are equal if they have the same rank and refer to the same location and same document reference.
equals(Object[], Object[]) - Static method in class org.biojava.utils.ObjectUtil
equals(Object, Object) - Static method in class org.biojava.utils.ObjectUtil
equals(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
Equals(Object) - Constructor for class org.biojava.bio.search.FilterTest.Equals
EQUIVALENCE - Static variable in class org.biojava.ontology.OntoTools
EQUIVALENT - Static variable in interface org.biojavax.bio.taxa.NCBITaxon: Use this to define equivalent names for things.
ERROR_FEATURES_PROPERTY - Static variable in class org.biojava.bio.seq.io.SequenceBuilderBase
errorProbabilities(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools: Return the error probabilities from the specified FASTQ formatted sequence.
errorProbabilities(Fastq, double[]) - Static method in class org.biojava.bio.program.fastq.FastqTools: Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.
errorProbability(char) - Method in enum org.biojava.bio.program.fastq.FastqVariant: Convert the specified quality in ASCII format to an error probability.
errorProbability(int) - Method in enum org.biojava.bio.program.fastq.FastqVariant: Calculate the error probability given the specified quality score.
escape(String, boolean) - Static method in class org.biojava.ontology.obo.OboFileParser
escapeChars - Static variable in class org.biojava.ontology.obo.OboFileParser
estimatedSize - Variable in class org.biojava.bibliography.BiblioWebResource: An estomated size in kilobytes.
EUPL_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the euplotid nuclear genetic code.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.CachingKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel: Return the dot product of a, b.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.DiagonalCachingKernel: Returns the kernel product of two Objects.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.LinearKernel: Deprecated.

The linear kernel is equal to the dot product of a and b.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.ListSumKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.NormalizingKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.PolynomialKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.RadialBaseKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.SigmoidKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel: Evaluate the kernel function between two SparseVectors.
evaluate(Object, Object) - Method in interface org.biojava.stats.svm.SVMKernel: Return the dot product of two vectors in an arbitrary feature space.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel: Calculate the dot product between the SuffixTrees a and b.
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
evaluate(BlastLikeSearchFilter.Node) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter: computes the outcome of this filter on the specified node and stores it.
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
Event() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Event
EverythingToXML(PrintWriter) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
EVIDENCE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_ATTRIBUTE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_CATEGORY_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EXACT_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
EXACT_SYNONYM - Static variable in class org.biojava.ontology.Synonym
ExactValue(Object) - Constructor for class org.biojava.bio.PropertyConstraint.ExactValue: Get a PropertyConstraint that matches this object and all those that are equal to it (by the Object.equals() method).
ExceptionFound - Variable in class org.biojava.bio.seq.db.GenbankSequenceDB
exec(String) - Method in class org.biojava.utils.ExecRunner: The exec(String) method runs a process inside of a watched thread.
exec(String[], Reader, Writer, Writer) - Static method in class org.biojava.utils.ProcessTools: Deprecated.

Execute the specified command and wait for it to return.
exec(String[], String[], File, Reader, Writer, Writer, long) - Static method in class org.biojava.utils.ProcessTools: Deprecated.

Execute the specified command and wait for it to return, or kill it if the specified timeout expires first.
exec(String, OutputStream, OutputStream) - Method in class org.biojava.utils.ExecRunner: Convenience method for calling exec with OutputStreams.
exec(String, PrintWriter, PrintWriter) - Method in class org.biojava.utils.ExecRunner: The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread.
exec(String, Reader, Writer, Writer) - Static method in class org.biojava.utils.ProcessTools: Deprecated.

Execute the specified command and wait for it to return.
exec(String, String[]) - Method in class org.biojava.utils.ExecRunner: Sometimes special cases may occur that the arguments of an external program are Strings containing white spaces.
exec(String, String[], File, Reader, Writer, Writer, long) - Static method in class org.biojava.utils.ProcessTools: Deprecated.

Execute the specified command and wait for it to return.
exec(String, String[], OutputStream, OutputStream) - Method in class org.biojava.utils.ExecRunner: Convenience method for calling exec with OutputStreams.
exec(String, String[], PrintWriter, PrintWriter) - Method in class org.biojava.utils.ExecRunner: The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread.
ExecRunner - Class in org.biojava.utils: Makes running external executables easier, optionally under a watched thread.
ExecRunner() - Constructor for class org.biojava.utils.ExecRunner: Basic ExecRunner constructor.
ExecRunner(String) - Constructor for class org.biojava.utils.ExecRunner: ExecRunner constructor which also conveniently runs exec(String).
ExecRunner(String, String[]) - Constructor for class org.biojava.utils.ExecRunner: ExecRunner constructor which also conveniently runs exec(String).
execute() - Method in class org.biojava.utils.process.ExternalProcess: Executes the external process and waits for its termination.
execute(String) - Static method in class org.biojava.utils.process.ExternalProcess: Executes an external program.
execute(String, String, StringWriter, StringWriter) - Static method in class org.biojava.utils.process.ExternalProcess: Executes an external program.
execute(Properties) - Method in class org.biojava.utils.process.ExternalProcess: Executes the external process and waits for its termination.
expandCache(int) - Method in class org.biojava.utils.io.CachingInputStream: Expands the cache to hold some number of additionalBytes.
ExternalProcess - Class in org.biojava.utils.process: Utility class to execute an external process and to handle the STDOUT, STDERR and STDIN streams in multiple threads managed by a thread pool.
ExternalProcess() - Constructor for class org.biojava.utils.process.ExternalProcess: Initializes the external process.
ExternalProcess(ThreadPool) - Constructor for class org.biojava.utils.process.ExternalProcess: Initializes the external process.
extractOverlappingLocation(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Try to determine the minimal location which all features matching a given filter must overlap.
extras - Variable in class org.biojava.utils.candy.CandyEntry: A container for the additional properties represented by this entry.

F

f() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Phenylalanine
factorize(Alphabet, Set) - Static method in class org.biojava.bio.symbol.AlphabetManager: Return a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.EmblProcessor.Factory: Deprecated.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory: Deprecated.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor.Factory: Deprecated.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory: Deprecated.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor.Factory: Deprecated.
Factory(SequenceBuilderFactory, TaxonFactory, TaxonParser, String, String, String) - Constructor for class org.biojava.bio.seq.io.OrganismParser.Factory: Deprecated.
FACTORY - Static variable in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
FACTORY - Static variable in class org.biojava.bio.seq.io.SimpleSequenceBuilder
FACTORY - Static variable in class org.biojava.bio.seq.io.SmartSequenceBuilder
FACTORY - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory: Accessor for the default factory.
FALSE - Static variable in class org.biojava.utils.TriState
FASTA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: FASTA indicates that the alignment format is Fasta.
FASTA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: FASTA indicates that the sequence format is Fasta.
FASTA_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: FASTA_AA premade FASTA | AA;
FASTA_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: FASTA_AA premade FASTA | AA.
FASTA_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: FASTA_DNA premade FASTA | DNA;
FASTA_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: FASTA_DNA premade FASTA | DNA.
FASTA_FORMAT - Static variable in class org.biojavax.bio.seq.io.FastaFormat: The name of this format
FASTA_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: FASTA_RNA premade FASTA | RNA;
FASTA_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: FASTA_RNA premade FASTA | RNA.
FastaAlignmentFormat - Class in org.biojava.bio.seq.io: This class implements the AlignmentFormat interface to read FASTA alignments.
FastaAlignmentFormat() - Constructor for class org.biojava.bio.seq.io.FastaAlignmentFormat
FastaDescriptionLineParser - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io.FastaFormat
FastaDescriptionLineParser(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.FastaDescriptionLineParser: Deprecated.
FastaDescriptionLineParser.Factory - Class in org.biojava.bio.seq.io: Deprecated.

Factory which wraps SequenceBuilders in a FastaDescriptionLineParser
FastaFormat - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io.FastaFormat
FastaFormat - Class in org.biojavax.bio.seq.io: Format object representing FASTA files.
FastaFormat() - Constructor for class org.biojava.bio.seq.io.FastaFormat: Deprecated.
FastaFormat() - Constructor for class org.biojavax.bio.seq.io.FastaFormat
FastaHeader - Class in org.biojavax.bio.seq.io: This class is used by FastaFormat to determine which fields are in the fasta header.
FastaHeader() - Constructor for class org.biojavax.bio.seq.io.FastaHeader
FastaSearchSAXParser - Class in org.biojava.bio.program.sax: FastaSearchSAXParser is a SAX2 compliant parser for '-m 10' format output from the the Fasta search program (see the Fasta documentation for details of this format).
FastaSearchSAXParser() - Constructor for class org.biojava.bio.program.sax.FastaSearchSAXParser: Creates a new FastaSearchSAXParser instance.
FastaSequenceSAXParser - Class in org.biojava.bio.program.sax: A SAX2 parser for dealing with multiple sequences in FASTA format.
FastaSequenceSAXParser() - Constructor for class org.biojava.bio.program.sax.FastaSequenceSAXParser: Initialises internal state Sets namespace prefix to "biojava"
fastq(Fastq) - Method in interface org.biojava.bio.program.fastq.StreamListener: Notify this listener of a FASTQ formatted sequence.
Fastq - Class in org.biojava.bio.program.fastq: FASTQ formatted sequence.
FASTQ_ILLUMINA - org.biojava.bio.program.fastq.FastqVariant: Illumina FASTQ sequence format variant.
FASTQ_SANGER - org.biojava.bio.program.fastq.FastqVariant: Sanger FASTQ sequence format variant.
FASTQ_SOLEXA - org.biojava.bio.program.fastq.FastqVariant: Solexa FASTQ sequence format variant.
FastqBuilder - Class in org.biojava.bio.program.fastq: Fluent builder API for creating FASTQ formatted sequences.
FastqBuilder() - Constructor for class org.biojava.bio.program.fastq.FastqBuilder: Create a new FASTQ formatted sequence builder.
FastqBuilder(Fastq) - Constructor for class org.biojava.bio.program.fastq.FastqBuilder: Create a new FASTQ formatted sequence builder configured from the specified FASTQ formatted sequence.
FastqReader - Interface in org.biojava.bio.program.fastq: Reader for FASTQ formatted sequences.
FastqTools - Class in org.biojava.bio.program.fastq: Utility methods for FASTQ formatted sequences.
FastqVariant - Enum in org.biojava.bio.program.fastq: FASTQ sequence format variant.
FastqWriter - Interface in org.biojava.bio.program.fastq: Writer for FASTQ formatted sequences.
FastXMLWriter - Class in org.biojava.utils.xml: Simple implementation of XMLWriter, optimized for speed.
FastXMLWriter(PrintWriter) - Constructor for class org.biojava.utils.xml.FastXMLWriter
Feature - Interface in org.biojava.bio.seq: A feature within a sequence, or nested within another feature.
FEATURE - Static variable in interface org.biojavax.bio.seq.RichLocation
FEATURE_ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_COLLAPSING - Static variable in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
FEATURE_DESC_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
FEATURE_FLAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
FEATURE_FROM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.FeatureHandler
FEATURE_HEADER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
FEATURE_INTERBP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_INTERVAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_INTERVALS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_ISCOMP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_KEY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_LINE_PREFIX - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
FEATURE_LOC_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
FEATURE_OPERATOR_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_ORIGINAL_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
FEATURE_PARTIAL3_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_PARTIAL5_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_POINT_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_RENDERER - Static variable in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
FEATURE_TABLE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
FEATURE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
FEATURE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
FEATURE_TO_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_VARIATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
Feature.ByLocationComparator - Class in org.biojava.bio.seq: ByLocationComparator compares Features by the minimum base position of their Location.
Feature.Template - Class in org.biojava.bio.seq: Template class for a plain feature.
FeatureBlockSequenceRenderer - Class in org.biojava.bio.gui.sequence: FeatureBlockSequenceRenderer forms a bridge between Sequence rendering and Feature rendering.
FeatureBlockSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer: Creates a new FeatureBlockSequenceRenderer which uses a BasicFeatureRenderer as its renderer.
FeatureBlockSequenceRenderer(FeatureRenderer) - Constructor for class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer: Creates a new FeatureBlockSequenceRenderer which uses the specified FeatureRenderer.
featureData(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser: Deprecated.
featureFilter(FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
FeatureFilter - Interface in org.biojava.bio.seq: A filter for accepting or rejecting a feature.
FeatureFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
FeatureFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
FeatureFilter.And - Class in org.biojava.bio.seq: A filter that returns all features accepted by both child filter.
FeatureFilter.AnnotationContains - Class in org.biojava.bio.seq: Retrieve features that contain a given annotation, and that the set of values contains the value given.
FeatureFilter.ByAncestor - Class in org.biojava.bio.seq: Filter by applying a nested FeatureFilter to all ancestor features.
FeatureFilter.ByAnnotation - Class in org.biojava.bio.seq: Retrieve features that contain a given annotation with a given value.
FeatureFilter.ByAnnotationType - Class in org.biojava.bio.seq: A filter that returns all features that have an annotation bundle that is of a given annotation type.
FeatureFilter.ByChild - Class in org.biojava.bio.seq: Filter by applying a nested FeatureFilter to the child features.
FeatureFilter.ByClass - Class in org.biojava.bio.seq: Filter which accepts only those filters which are an instance of a specific Java class
FeatureFilter.ByComponentName - Class in org.biojava.bio.seq: Accepts features which are ComponentFeatures and have a componentSequenceName property of the specified value.
FeatureFilter.ByDescendant - Class in org.biojava.bio.seq: Filter by applying a nested FeatureFilter to all descendant features.
FeatureFilter.ByFeature - Class in org.biojava.bio.seq: Accept only features which are equal to the specified feature
FeatureFilter.ByPairwiseScore - Class in org.biojava.bio.seq: ByPairwiseScore is used to filter SimilarityPairFeatures by their score.
FeatureFilter.ByParent - Class in org.biojava.bio.seq: Filter by applying a nested FeatureFilter to the parent feature.
FeatureFilter.BySequenceName - Class in org.biojava.bio.seq: Accept features that reside on a sequence with a particular name.
FeatureFilter.BySource - Class in org.biojava.bio.seq: Construct one of these to filter features by source.
FeatureFilter.ByType - Class in org.biojava.bio.seq: Construct one of these to filter features by type.
FeatureFilter.ContainedByLocation - Class in org.biojava.bio.seq: A filter that returns all features contained within a location.
FeatureFilter.FrameFilter - Class in org.biojava.bio.seq: Accept features with a given reading frame.
FeatureFilter.HasAnnotation - Class in org.biojava.bio.seq: Retrieve features that contain a given annotation with any value.
FeatureFilter.Not - Class in org.biojava.bio.seq: A filter that returns all features not accepted by a child filter.
FeatureFilter.OnlyChildren - Class in org.biojava.bio.seq: Accepts features where all immediate children meet the supplied filter.
FeatureFilter.OnlyDescendants - Class in org.biojava.bio.seq: Accepts features where all descendants meet the supplied filter.
FeatureFilter.Or - Class in org.biojava.bio.seq: A filter that returns all features accepted by at least one child filter.
FeatureFilter.OverlapsLocation - Class in org.biojava.bio.seq: A filter that returns all features overlapping a location.
FeatureFilter.ShadowContainedByLocation - Class in org.biojava.bio.seq: A filter that accepts all features whose shadow is contained by a specified Location.
FeatureFilter.ShadowOverlapsLocation - Class in org.biojava.bio.seq: A filter that accepts all features whose shadow overlaps a specified Location.
FeatureFilter.StrandFilter - Class in org.biojava.bio.seq: Accept features with a given strandedness.
FeatureHandler - Class in org.biojava.bio.program.xff: StAX handler for the basic feature type of XFF.
FeatureHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.FeatureHandler: Construct a new Feature handler, passing in an XFF-parsing environment.
FeatureHolder - Interface in org.biojava.bio.seq: The interface for objects that contain features.
FeatureHolder.EmptyFeatureHolder - Class in org.biojava.bio.seq
featureHolderAllocated() - Method in class org.biojava.bio.seq.impl.SimpleFeature: A utility function to find out if the feature holder delegate has been instantiated yet.
featureHolderAllocated() - Method in class org.biojava.bio.seq.impl.SimpleSequence
featureHolderAsSet(FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils: Returns a FeatureHolder as a Set of Features
FeatureHolderUtils - Class in org.biojava.bio.seq: This class intendes to provide some FeatureHolder utilities.
FeatureHolderUtils() - Constructor for class org.biojava.bio.seq.FeatureHolderUtils
FeatureImpl - Class in org.biojava.bio.seq.impl: Wrap up default sets of Feature implementations.
FeatureImpl() - Constructor for class org.biojava.bio.seq.impl.FeatureImpl
FeatureLabelRenderer - Class in org.biojava.bio.gui.sequence
FeatureLabelRenderer() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer
FeatureLabelRenderer(FeatureLabelRenderer.LabelMaker) - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer
FeatureLabelRenderer.AnnotationLabelMaker - Class in org.biojava.bio.gui.sequence
FeatureLabelRenderer.LabelMaker - Interface in org.biojava.bio.gui.sequence
FeatureLabelRenderer.SourceLabelMaker - Class in org.biojava.bio.gui.sequence
FeatureLabelRenderer.TypeLabelMaker - Class in org.biojava.bio.gui.sequence
featureListener - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
featureListener - Variable in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
featureListener - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
featureListener - Variable in class org.biojava.bio.seq.io.game.StAXPropertyHandler
FEATUREQUAL_NAME_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATUREQUAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATUREQUAL_VALUE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATUREQUALS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FeatureRealizer - Interface in org.biojava.bio.seq: Interface for translators which map from Feature.Template instances to real Feature objects.
featureRelationshipSet - Variable in class org.biojavax.bio.seq.RichFeature.Template
FeatureRenderer - Interface in org.biojava.bio.gui.sequence
features - Variable in class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.
features() - Method in interface org.biojava.bio.seq.Feature: Iterate over any child features which are held by this feature.
features() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
features() - Method in interface org.biojava.bio.seq.FeatureHolder: Iterate over the features in no well defined order.
features() - Method in class org.biojava.bio.seq.impl.DummySequence
features() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
features() - Method in class org.biojava.bio.seq.impl.RevCompSequence
features() - Method in class org.biojava.bio.seq.impl.SimpleFeature
features() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
features() - Method in class org.biojava.bio.seq.impl.SimpleSequence
features() - Method in class org.biojava.bio.seq.impl.SubSequence
features() - Method in class org.biojava.bio.seq.impl.ViewSequence
features() - Method in class org.biojava.bio.seq.LazyFeatureHolder
features() - Method in class org.biojava.bio.seq.MergeFeatureHolder: Iterate over all the features in all child FeatureHolders.
features() - Method in class org.biojava.bio.seq.NewSimpleAssembly
features() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
features() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
features() - Method in class org.biojava.bio.seq.SimpleAssembly
features() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
features() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Iterate over any child features which are held by this feature.
features() - Method in class org.biojavax.bio.seq.ThinRichSequence: Iterate over the features in no well defined order.
FEATURES - Static variable in interface org.biojava.bio.seq.FeatureHolder: Signals that features have been added or removed directly within this FeatureHolder.
FEATURES_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FeatureSource - Interface in org.biojava.bio.gui.sequence: A closure that allows AbstractPeptideDigestRenderer implementations to obtain the features of the rendered sequence.
FeatureTableParser - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
featureTemplate - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
featureTemplate - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
FeatureTree - Class in org.biojava.bio.gui: FeatureTree is GUI tree to display the features and annotations of the sequences in a SequenceDB Nested Features are displayed as expandable leaves.
FeatureTree() - Constructor for class org.biojava.bio.gui.FeatureTree: Create a new FeatureTree
FeatureTypes - Class in org.biojava.bio.seq: Registry of known types of features.
FeatureTypes() - Constructor for class org.biojava.bio.seq.FeatureTypes
FeatureTypes.Repository - Interface in org.biojava.bio.seq: A named collection of Types.
FeatureTypes.RepositoryImpl - Class in org.biojava.bio.seq: A simple implementation of a Repository.
FeatureTypes.Type - Interface in org.biojava.bio.seq: A type of feature.
fetch(String) - Method in class org.biojava.bio.seq.db.BioIndex
fetch(String) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
fetch(String) - Method in interface org.biojava.bio.seq.db.IndexStore: Fetch an Index based upon an ID.
fetch(String) - Method in class org.biojava.bio.seq.db.TabIndexStore
FetchURL - Class in org.biojava.bio.seq.db
FetchURL(String, String) - Constructor for class org.biojava.bio.seq.db.FetchURL: Constructs a fetchURL object based on the database name and specified return format of sequence.
FileAsList - Class in org.biojava.utils: FileAsList creates a writable List implementation backed by a random access file.
FileAsList(File, boolean) - Constructor for class org.biojava.utils.FileAsList: Creates a new FileAsList instance from an existing backing file.
FileAsList(File, int) - Constructor for class org.biojava.utils.FileAsList: Creates a new FileAsList and corresponding backing file.
fileCommentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
fileCommentText(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract: This method will get called when comment text is found on the file, and not any block within it.
FileStreamer(SequenceFormat, SymbolTokenization, File) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
FileStreamer(SequenceFormat, SymbolTokenization, List) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
fileToBiojava(int, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Reads a file and returns the corresponding Biojava object.
fileToBiojava(String, String, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Reads a file with the specified format and alphabet
FILL - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer: Constant FILL indicating a change to the fill of the features.
FILL - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
FILL - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer
fillBuffer(StringBuffer, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Simple method that adds spaces onto the buffer passed in.
fillColors - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: The map containing the fill colors for callboxes.
fillPaint(Symbol) - Method in class org.biojava.bio.gui.DNAStyle
fillPaint(Symbol) - Method in class org.biojava.bio.gui.PlainStyle
fillPaint(Symbol) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
fillPaint(Symbol) - Method in interface org.biojava.bio.gui.SymbolStyle: Return the fill paint for a symbol.
fillTemplate(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
fillTemplate(FramedFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
fillTemplate(HomologyFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
fillTemplate(SimilarityPairFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
fillTemplate(RemoteFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
fillTemplate(StrandedFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
filter - Variable in class org.biojava.bio.gui.sequence.FilteringRenderer
filter - Variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer: filter is the filter applied to both FeatureHolders.
filter(AnnotationType) - Method in interface org.biojava.bio.annodb.AnnotationDB: Find all Annotation instances in this DB that are of a particular type.
filter(AnnotationType) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
filter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFEntrySet: Filter this entry set into another set.
filter(OrthologueFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthologueSet
filter(OrthologueFilter) - Method in interface org.biojava.bio.program.homologene.OrthologueSet: Filter the contents of a set.
filter(OrthoPairFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairSet
filter(OrthoPairFilter) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet: filter an OrthoPairSet
filter(OrthoPairSetFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
filter(OrthoPairSetFilter) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Filter the database for a specified group.
filter(OrthoPairSetFilter) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
filter(FeatureFilter) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
filter(FeatureFilter) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB: Deprecated.
filter(FeatureFilter) - Method in interface org.biojava.bio.seq.db.SequenceDB: Query features attached to all sequences in this database.
filter(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
filter(FeatureFilter) - Method in interface org.biojava.bio.seq.FeatureHolder: Query this set of features using a supplied FeatureFilter.
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.DummySequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.RevCompSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleFeature
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SubSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.ViewSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.LazyFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.NewSimpleAssembly
filter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
filter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.SimpleAssembly
filter(FeatureFilter) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
filter(FeatureFilter) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
filter(FeatureFilter) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Query this set of features using a supplied FeatureFilter.
filter(FeatureFilter) - Method in class org.biojavax.bio.seq.ThinRichSequence: Query this set of features using a supplied FeatureFilter.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
filter(FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.FeatureHolder: Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.DummySequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.RevCompSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleFeature
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SubSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.ViewSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.LazyFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.MergeFeatureHolder: When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.NewSimpleAssembly
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.SimpleAssembly
filter(FeatureFilter, boolean) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
filter(FeatureFilter, boolean) - Method in class org.biojavax.bio.seq.ThinRichSequence: Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
FILTER - Static variable in class org.biojava.bio.gui.sequence.FilteringRenderer
FILTER - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer: Constant FILTER indicating a change to the renderer's filter.
FilterByLength(SearchListener, int) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.FilterByLength
FilteringContentHandler - Class in org.biojava.bio.search
FilteringContentHandler(BlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.FilteringContentHandler
FilteringContentHandler(BlastLikeSearchFilter, SearchContentHandler) - Constructor for class org.biojava.bio.search.FilteringContentHandler
FilteringContentHandler.FilterVisitor - Class in org.biojava.bio.search: Visitor class that parses the filter tree
FilteringRenderer - Class in org.biojava.bio.gui.sequence
FilteringRenderer() - Constructor for class org.biojava.bio.gui.sequence.FilteringRenderer
FilteringRenderer(SequenceRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.FilteringRenderer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.program.xff.ElementRecognizer: Recognize an element based upon the start element parameters.
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.seq.io.agave.ElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.seq.io.game.ElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute
FilterTest - Interface in org.biojava.bio.search: Class for implementing tests with BlastLikeSearchFilter objects.
FilterTest.Equals - Class in org.biojava.bio.search: Tests that the value associated with the specified key is equal to the value supplied here by whatever criterion of equality appropriate to those objects.
FilterTest.FindRegex - Class in org.biojava.bio.search: Tests that the value associated with the specified key contains a part matched by the supplied regex.
FilterTest.GreaterThan - Class in org.biojava.bio.search: Tests that the value associated with the specified key is greater than the specified threshold.
FilterTest.LessThan - Class in org.biojava.bio.search: Tests that the value associated with the specified key is less than the specified threshold.
FilterTest.MatchRegex - Class in org.biojava.bio.search: Tests that the value associated with the specified key is matched in its entirety by the supplied regex.
FilterTransformer - Class in org.biojava.bio.seq.filter: Base-class for visitors that re-write a filter tree.
FilterTransformer() - Constructor for class org.biojava.bio.seq.filter.FilterTransformer
FilterUtils - Class in org.biojava.bio.seq: A set of FeatureFilter algebraic operations.
FilterUtils.DelegatingTransformer - Class in org.biojava.bio.seq: An implementation of FilterTransformer that attempts to transform by one transformer, and if that fails, by another.
FilterUtils.FilterTransformer - Interface in org.biojava.bio.seq: An object able to transform some FeatureFilter instances sytematically into others.
FilterVisitor() - Constructor for class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
finalize() - Method in class org.biojava.bio.alignment.SimpleAlignment
finalize() - Method in class org.biojava.bio.seq.io.NameTokenization
finalize() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
finalize() - Method in class org.biojava.bio.symbol.SimpleSymbolList
finalize() - Method in class org.biojava.utils.process.ExternalProcess
find() - Method in interface org.biojava.bio.search.BioMatcher: Attempt to find the next match.
find() - Method in class org.biojava.bio.search.MaxMismatchMatcher
find() - Method in class org.biojava.utils.regex.Matcher: Attempts to find the next subsequence of the input sequence that matches the pattern.
find(int) - Method in class org.biojava.utils.regex.Matcher: Resets this matcher and then attempts to find the next subsequence of the input sequence that matches the pattern, starting at the specified index.
find(String[], String[], Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery: The easiest direct method for querying a repository.
findByAuthor(BiblioProvider, Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery: This is a convenient method for a common query.
findById(String) - Method in interface org.biojava.bibliography.BibRefQuery: This is a convenient method returning just one citation.
findById(String, String[]) - Method in interface org.biojava.bibliography.BibRefQuery: This is a convenient method returning just one citation, perhaps with a limited number of attributes.
findFactory(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools: Find the UnigeneFactory that can accept a URL.
findMatches(SymbolList) - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch: This will return an int[] giving the offsets of the matches in text (ie the location of the first symbol of each match in the text).
findRecord(String) - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess: findRecord performs a binary search within the file for a record specified by an identifier String.
FindRegex(String) - Constructor for class org.biojava.bio.search.FilterTest.FindRegex
findSourceBlock(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Finds the index of the block containing the source coordinate indx.
findSourceGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Finds the index of the Block before the gap at indx within the following gap.
findTaxon(Object[]) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
findUnescaped(String, char) - Static method in class org.biojava.ontology.obo.OboFileParser
findUnescaped(String, char, int, int) - Static method in class org.biojava.ontology.obo.OboFileParser
findUnescaped(String, char, int, int, boolean) - Static method in class org.biojava.ontology.obo.OboFileParser
findViewBlock(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Finds the index of the Block containing indx within the view ranges.
findViewGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Finds the index of the Block before the gap at indx within the view range.
finishedReading() - Method in interface org.biojava.bio.program.abi.ABIFParser.DataAccess: Called when the parser has finished reading.
finishWriting() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.INSDseqFormat: Informs the writer that are done writing.
finishWriting() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat: Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: Informs the writer that are done writing.
FiniteAlphabet - Interface in org.biojava.bio.symbol: An alphabet over a finite set of Symbols.
FiniteAutomaton - Class in org.biojava.utils.automata: Class for modelling finite automata.
fireEndFeature() - Method in class org.biojava.bio.program.xff.FeatureHandler: Fire the endFeature event.
fireHits(int, int, SearchListener) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
fireMouseClicked(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
fireMouseDragged(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
fireMouseMoved(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
fireMousePressed(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
fireMouseReleased(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
firePostChange(Object, ChangeEvent) - Method in interface org.biojava.utils.ChangeHub: invoke the firePostChangeEvent on all ChangeListeners associated with a specific key.
firePostChange(Object, ChangeEvent) - Method in class org.biojava.utils.IndexedChangeHub
firePostChangeEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeSupport: Inform the listeners that a change has taken place using their firePostChangeEvent methods.
firePreChange(Object, ChangeEvent) - Method in interface org.biojava.utils.ChangeHub: invoke the firePreChangeEvent on all ChangeListeners associated with a specific key.
firePreChange(Object, ChangeEvent) - Method in class org.biojava.utils.IndexedChangeHub
firePreChangeEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeSupport: Inform the listeners that a change is about to take place using their firePreChangeEvent methods.
firePropertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.TextLogoPainter
firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.TextLogoPainter
firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.TextLogoPainter
firePropertyChange(String, Object, Object) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(String, Object, Object) - Method in class org.biojava.bio.gui.TextLogoPainter
fireStartFeature() - Method in class org.biojava.bio.program.xff.FeatureHandler: Fire the startFeature event.
firstName - Variable in class org.biojava.bibliography.BiblioPerson: The person's christian name (first name).
firstNonGap() - Method in interface org.biojava.bio.symbol.GappedSymbolList: Return the index of the first Symbol that is not a Gap character.
firstNonGap() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
firstPage - Variable in class org.biojava.bibliography.BiblioArticle: First page of the article.
firstToken(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
fitness(Organism, Population, GeneticAlgorithm) - Method in interface org.biojavax.ga.functions.FitnessFunction: Calculates the fitness of org.
FITNESS_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
FitnessFunction - Interface in org.biojavax.ga.functions: Calculates the fitness of an Organism in a Population of Organisms
fivePrimeBlockIterator() - Method in class org.biojava.bio.symbol.CircularLocation: Iterates over the location blocks in order starting with the most 5'
FixedBaseWidthScaler - Class in org.biojava.bio.chromatogram.graphic: A ChromatogramNonlinearScaler that scales all the base calls in a chromatogram to the same width in pixels, optionally biasing the peak of the call to the center.
FixedBaseWidthScaler(float) - Constructor for class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler: Creates a new scaler that will scale bases to the specified width without attempting to center their peaks.
FixedBaseWidthScaler(float, boolean) - Constructor for class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler: Creates a new scaler that will scale bases to the specified width and may or may not bias the peaks to the center.
FixedSizeCache - Class in org.biojava.utils.cache: Cache which stores up to limit Objects.
FixedSizeCache(int) - Constructor for class org.biojava.utils.cache.FixedSizeCache
FixedSizeMap - Class in org.biojava.utils.cache: A cache that only remembers a given number of keys.
FixedSizeMap(int) - Constructor for class org.biojava.utils.cache.FixedSizeMap
FIXEDWIDTH - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
FLAT_QUERY_ANCHORED - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
FLAT_QUERY_ANCHORED_NO_IDENTITIES - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
FlatFileCache - Class in org.biojava.utils.io: Provides a cache for storing multiple small files in memory.
FlatFileUnigeneFactory - Class in org.biojava.bio.program.unigene: A UnigeneFactory that will use flat-file indexing of the unigene ascii-art files.
FlatFileUnigeneFactory() - Constructor for class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
FlatSequenceDB - Class in org.biojava.bio.seq.db.flat: FlatSequenceDB is an OBDA flatfile sequence databank implementation.
FlatSequenceDB(String, String) - Constructor for class org.biojava.bio.seq.db.flat.FlatSequenceDB
FlatSequenceDBProvider - Class in org.biojava.bio.seq.db.flat: FlatSequenceDBProvider directory-services plugin for flatfile databases.
FlatSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
flatten(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools: Takes a set of locations and returns the set of all members.
flatten(RichLocation) - Static method in class org.biojavax.bio.seq.RichLocation.Tools: Takes a location and returns the set of all members.
flatView(MarkovModel) - Static method in class org.biojava.bio.dp.DP
FlexibleAlignment - Class in org.biojava.bio.alignment: FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment.
FlexibleAlignment(List<AlignmentElement>) - Constructor for class org.biojava.bio.alignment.FlexibleAlignment: construct this object with the reference sequence which can either be a gappedSymbolList or not label in all cases refers to an object that holds the display name (generally just a String). since more than one sequence in an alignment could have the same name this works as long as the labels are different objects even though they may hold the same name.
flip() - Method in class org.biojava.bio.seq.StrandedFeature.Strand: Return a strand that represents flipping this onto the opposite strand.
flip(Location, int) - Static method in class org.biojava.bio.symbol.LocationTools: Flips a location relative to a length.
flip(SymbolList, StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.DNATools: Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
flipLocation(Location, int) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils: Flip a location.
flipStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
fList - Variable in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
FloatElementHandlerBase - Class in org.biojava.utils.stax: StAX handler for any element which just contains a string representation of a float.
FloatElementHandlerBase() - Constructor for class org.biojava.utils.stax.FloatElementHandlerBase
flush() - Method in class org.biojava.utils.RepeatedCharSequence
flushFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
force() - Method in class org.biojava.utils.io.LargeBuffer
forClass(Class) - Static method in class org.biojava.utils.bytecode.IntrospectedCodeClass: Get the CodeClass for a Java Class.
forClass(String) - Static method in class org.biojava.utils.bytecode.IntrospectedCodeClass: Get the CodeClass for a Java class name.
forIndex(int) - Static method in class org.biojava.bio.seq.DNATools: Return the symbol for an index - compatible with index.
forIndex(int) - Static method in class org.biojava.bio.seq.NucleotideTools: Return the symbol for an index - compatible with index.
forIndex(int) - Static method in class org.biojava.bio.seq.RNATools: Return the symbol for an index - compatible with index.
format - Variable in class org.biojava.bibliography.BibRef: It describes the physical or digital manifestation of the cited resource.
Format - Interface in org.biojava.bio.program.formats: A file format supported by the tag-value event-based parsing system.
formatLocation(StringBuffer, Location) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

formatLocation creates a String representation of a Location.
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.SeqFileFormer: Deprecated.

formatLocation creates a String representation of a Location.
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

formatLocation creates a String representation of a Location.
formatLocation(Feature) - Method in interface org.biojava.bio.seq.io.SeqFileFormer: Deprecated.

Formats the location of a feature.
formatLocation(Feature) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Creates a string representation of the location of a feature
formatOutput() - Method in class org.biojava.bio.alignment.AlignmentPair
formatOutput(int) - Method in class org.biojava.bio.alignment.AlignmentPair: This method provides a BLAST-like formated alignment from the given Strings, in which the sequence coordinates and the information "Query" or "Sbjct", respectively is added to each line.
formatPoint(int, int, boolean) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Formats the points from fuzzy locations.
Formats - Class in org.biojava.bio.program.tagvalue: This is intended as a repository for tag-value and AnnotationType information about common file formats.
Formats() - Constructor for class org.biojava.bio.program.tagvalue.Formats
formatToFactory(SequenceFormat, Alphabet) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.
as this essentially duplicates the operation available in the method identifyBuilderFactory.
FormatTools - Class in org.biojava.bio.program.formats
forMethod(Method) - Static method in class org.biojava.utils.bytecode.IntrospectedCodeClass
forName(String) - Static method in class org.biojavax.bio.seq.RichLocation.Strand: Returns the strand object that matches the symbol given.
forSubset - Variable in class org.biojava.bibliography.BiblioCriterion: A name of a repository subset which this criterion is valid/used for.
forSymbol(char) - Static method in class org.biojava.bio.seq.DNATools: Retrieve the symbol for a symbol.
forSymbol(char) - Static method in class org.biojava.bio.seq.NucleotideTools: Retrieve the symbol for a symbol.
forSymbol(char) - Static method in class org.biojava.bio.seq.RNATools: Retrieve the symbol for a symbol.
forValue(int) - Static method in class org.biojavax.bio.seq.RichLocation.Strand: Returns the strand object that matches the number given.
forward(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
FORWARD - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
forward_initialize(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardChangeEvent(ChangeEvent) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder: Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolder
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
forwardRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
forwards(ScoreType) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
forwards(ScoreType) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
forwardsBackwards(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
forwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP: Returns a matrix for the specified States describing all valid Transitions between those States.
forwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP: Compute the log(score) of all transitions between the specified States.
fp - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
Frame - Interface in org.biojava.bio.seq: Title: Frame.
FRAME_0 - Static variable in interface org.biojava.bio.seq.Frame
FRAME_0 - Static variable in interface org.biojava.bio.seq.FramedFeature
FRAME_1 - Static variable in interface org.biojava.bio.seq.Frame
FRAME_1 - Static variable in interface org.biojava.bio.seq.FramedFeature
FRAME_2 - Static variable in interface org.biojava.bio.seq.Frame
FRAME_2 - Static variable in interface org.biojava.bio.seq.FramedFeature
FramedFeature - Interface in org.biojava.bio.seq: Title: FramedFeature.
FramedFeature.ReadingFrame - Class in org.biojava.bio.seq: A singleton to hold the frame information
FramedFeature.Template - Class in org.biojava.bio.seq
FrameFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
FrameFilter(int) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
FrameFilter(FramedFeature.ReadingFrame) - Constructor for class org.biojava.bio.seq.FeatureFilter.FrameFilter: Build a new filter that matches all features of a reading frame.
frequency(int) - Method in class org.biojava.bio.symbol.SuffixTree: Return the number of motifs of a given length encoded in this SuffixTree.
from - Variable in class org.biojava.bio.dp.TrainerTransition
from - Variable in class org.biojava.bio.dp.Transition
FROM_TRACE_SAMPLE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option: Option indicating the lowest (leftmost) trace sample that should be drawn.
fromArray(double[]) - Static method in class org.biojava.bio.symbol.DoubleAlphabet: Retrieve a SymbolList view of an array of doubles.
fromArray(int[]) - Static method in class org.biojava.bio.symbol.IntegerAlphabet: Retrieve a SymbolList view of an array of integers.
fromBook - Variable in class org.biojava.bibliography.BiblioBookArticle: Book this is from.
fromJournal - Variable in class org.biojava.bibliography.BiblioJournalArticle: The journal that this article is in.
FUGU_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools: Takifugu rubripes codon preferences
full - Static variable in interface org.biojava.bio.symbol.Location: The Location which contains all points.
FULL_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
FullHmmerProfileHMM - Class in org.biojava.bio.program.hmmer: This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
fullyLoadRichSequence(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
FundamentalAtomicSymbol - Class in org.biojava.bio.symbol: An atomic symbol consisting only of itself.
FundamentalAtomicSymbol(String, Annotation) - Constructor for class org.biojava.bio.symbol.FundamentalAtomicSymbol
FuzzyLocation - Class in org.biojava.bio.symbol: A 'fuzzy' location a-la Embl fuzzy locations.
FuzzyLocation(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver) - Constructor for class org.biojava.bio.symbol.FuzzyLocation: Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).
FuzzyLocation(int, int, int, int, FuzzyLocation.RangeResolver) - Constructor for class org.biojava.bio.symbol.FuzzyLocation: Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).
FuzzyLocation.RangeResolver - Interface in org.biojava.bio.symbol: Determines how a FuzzyLocation should be treated when used as a normal Location.
FuzzyPointLocation - Class in org.biojava.bio.symbol: FuzzyPointLocation represents two types of EMBL-style partially-defined locations.
FuzzyPointLocation(int, int, FuzzyPointLocation.PointResolver) - Constructor for class org.biojava.bio.symbol.FuzzyPointLocation: Creates a new FuzzyPointLocation object.
FuzzyPointLocation.PointResolver - Interface in org.biojava.bio.symbol: Determines how a FuzzyPointLocation should be treated when used as a normal Location.
FWORM_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the flatworm mitochondrial genetic code.

G

g() - Static method in class org.biojava.bio.seq.DNATools
g() - Static method in class org.biojava.bio.seq.NucleotideTools
g() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Glycine
g() - Static method in class org.biojava.bio.seq.RNATools
GACross - Interface in org.biojavax.ga.functions: Holds the results of a CrossOver event, objects of this type are made by CrossOverFunctions
GACrossResult - Interface in org.biojavax.ga.functions: Holds the results of a CrossOver event, objects of this type are made by CrossOverFunctions
GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler: Description of the Field
GAME_ASPECT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAspectHandler
GAME_ASPECT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler
GAME_DBXREF_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler: Description of the Field
GAME_DBXREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler
GAME_DESCRIPTION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
GAME_FEATURE_SET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler: Description of the Field
GAME_FEATURE_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler: Description of the Field
GAME_FEATURESET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
GAME_FEATURESET_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler
GAME_FEATURESPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
GAME_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEGeneHandler: Description of the Field
GAME_GENE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
GAME_MAP_POS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
GAME_NAME_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMENamePropHandler
GAME_PROPERTY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEPropertyHandler: Description of the Field
GAME_RESIDUES_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
GAME_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqHandler: Description of the Field
GAME_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
GAME_SEQ_REL_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler: Description of the Field
GAME_SEQREL_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler
GAME_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESpanHandler: Description of the Field
GAME_SPAN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESpanPropHandler
GAME_TYPE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMETypePropHandler
GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <annotation> element
GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <annotation> element
GAMEAspectHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <aspect> element
GAMEAspectPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <aspect> element
GAMEDbxrefHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <dbxref> element
GAMEDbxrefPropHandler - Class in org.biojava.bio.seq.io.game: Deals with database crossreferences
GAMEDbxrefPropHandler.DbXrefElement - Class in org.biojava.bio.seq.io.game
GAMEDescriptionPropHandler - Class in org.biojava.bio.seq.io.game: StAX handler for GAME <description> elements.
GAMEDescriptionPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
GAMEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.game: An interface that can be tested for by nested handlers when trying to do a callback.
GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game: Handles the <feature_set> element
GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <feature_set> element this element is used to represent transcripts.
GAMEFeatureSetPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME element
GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game: Handles the <feature_span> element
GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <feature_span> element
GAMEFeatureSpanHandler.SeqRelHandler - Class in org.biojava.bio.seq.io.game12
GAMEFormat - Class in org.biojava.bio.seq.io: A rudimentary read-only GAME 1.2 Format object.
GAMEFormat() - Constructor for class org.biojava.bio.seq.io.GAMEFormat
GAMEGeneHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <annotation> element
GAMEGenePropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <gene> element
GAMEHandler - Class in org.biojava.bio.seq.io.game: Handles the root GAME element
GAMEHandler - Class in org.biojava.bio.seq.io.game12: Handles the root GAME element
GAMEHandler() - Constructor for class org.biojava.bio.seq.io.game.GAMEHandler
GAMEHandler(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.game12.GAMEHandler: Constructor for the GAMEHandler object
GAMEMapPosPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <map_position> element Currently, it just ignores it!
GAMENameCallbackItf - Interface in org.biojava.bio.seq.io.game: An interface that can be tested for by nested handlers when trying to do a callback.
GAMENamePropHandler - Class in org.biojava.bio.seq.io.game: StAX handler for the GAME <name> element.
GAMENamePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMENamePropHandler
GAMEPropertyHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <dbxref> element
GAMEResiduesPropHandler - Class in org.biojava.bio.seq.io.game: StAX handler for GAME <residues> elements.
GAMEResiduesPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
GAMESeqHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <seq> element
GAMESeqPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <seq> element
GAMESeqRelHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <> element
GAMESeqRelPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <aspect> element
GAMESpanHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <> element.
GAMESpanPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <span> element Currently, it just ignores it!
GAMETranscriptCallbackItf - Interface in org.biojava.bio.seq.io.game: An interface that can be tested for by nested handlers when trying to do a callback.
GAMETypePropHandler - Class in org.biojava.bio.seq.io.game: StAX handler for GAME <type> elements.
GAMETypePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMETypePropHandler
GapDistribution - Class in org.biojava.bio.dist: This distribution emits gap symbols.
GapDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.GapDistribution: Get a GapDistribution for an alphabet.
GappedContext() - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
GappedRenderer - Class in org.biojava.bio.gui.sequence: A renderer that will display a gapped sequence as a discontinuous series of regions.
GappedRenderer() - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer
GappedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer
GappedSequence - Interface in org.biojava.bio.seq: Extension of GappedSymbolList which also projects features into the gapped coordinate system.
GappedSymbolList - Interface in org.biojava.bio.symbol: This extends SymbolList with API for manipulating, inserting and deleting gaps.
gappedToLocation(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Translates a Location from the gapped view into the underlying sequence.
gappedView(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools: Create a new gapped sequence for a sequence.
GAPS - Static variable in interface org.biojava.bio.alignment.EditableAlignment
GAStoppingCriteria - Interface in org.biojavax.ga: Used by a GeneticAlgorithm.run() method to determine when the algorithm should stop
GAStoppingCriteria.MaximumGeneration - Class in org.biojavax.ga: Simple Implementation of GAStoppingCriteria, signals a GeneticAlgorithm to stop after n generations
GATools - Class in org.biojavax.ga.util: Utility methods for the GA library
GATools() - Constructor for class org.biojavax.ga.util.GATools
GCG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GCG indicates that the sequence format is GCG.
ge - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
GENBANK - Static variable in class org.biojava.bio.program.tagvalue.LineSplitParser: A LineSplitParser pre-configured to process GENBANK-style flat files.
GENBANK - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GENBANK indicates that the sequence format is GENBANK.
GENBANK_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GENBANK_DNA premade GENBANK | AA.
GENBANK_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GENBANK_DNA premade GENBANK | DNA.
GENBANK_FORMAT - Static variable in class org.biojavax.bio.seq.io.GenbankFormat: The name of this format
GENBANK_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GENBANK_DNA premade GENBANK | RNA.
GenbankFileFormer - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenbankFileFormer() - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.

Creates a new GenbankFileFormer using System.out stream.
GenbankFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.

Creates a new GenbankFileFormer using the specified stream.
GenbankFormat - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io.GenbankFormat
GenbankFormat - Class in org.biojavax.bio.seq.io: Format reader for GenBank files.
GenbankFormat() - Constructor for class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
GenbankFormat() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat
GenbankFormat.Terms - Class in org.biojavax.bio.seq.io: Implements some GenBank-specific terms.
GenbankLocationParser - Class in org.biojavax.bio.seq.io: Parses Genbank location strings into RichLocation objects.
GenbankProcessor - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenbankProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.
GenbankProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.
GenbankProcessor.Factory - Class in org.biojava.bio.seq.io: Deprecated.

Factory which wraps sequence builders in a GenbankProcessor
GenbankRichSequenceDB - Class in org.biojavax.bio.db.ncbi: This class contains functions accessing DNA sequences in Genbank format.
GenbankRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: The default constructor delegates to the parent class.
GenbankSequenceDB - Class in org.biojava.bio.seq.db: This class contains functions accessing DNA sequences in Genbank format.
GenbankSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenbankSequenceDB
GenbankXmlFormat - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io.INSDseqFormat
GenbankXmlFormat() - Constructor for class org.biojava.bio.seq.io.GenbankXmlFormat: Deprecated.
GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
GENELOCATION_NAME_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
GENELOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
GenEmblFeatureComparator - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenEmblPropertyComparator - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
GENENAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
generate() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Generates a comment string based on the current values of the internal fields.
generate(int) - Method in class org.biojava.bio.dp.DP: Generates an alignment from a model.
generateAuthorString(List<DocRefAuthor>, boolean) - Static method in class org.biojavax.DocRefAuthor.Tools: Takes a set of authors and creates a comma-separated string.
generateBackwardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
generateCallboxes() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Precomputes the Rectangle2Ds that are the in-memory representation of the callboxes.
generateChangeSupport() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
generateChangeSupport() - Method in class org.biojava.utils.AbstractChangeable: Called the first time a ChangeSupport object is needed.
generateCrossProductAlphaFromName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager: Generates a new CrossProductAlphabet from the give name.
GeneratedClassLoader - Class in org.biojava.utils.bytecode: A class loader that actually produces real Java classes from GeneratedCodeClass instances.
GeneratedClassLoader() - Constructor for class org.biojava.utils.bytecode.GeneratedClassLoader: Create a new loader with the default parent.
GeneratedClassLoader(ClassLoader) - Constructor for class org.biojava.utils.bytecode.GeneratedClassLoader: Create a new loader with an explicitly set parent class loader.
GeneratedCodeClass - Class in org.biojava.utils.bytecode: A CodeClass implementation that is used to generate new classes.
GeneratedCodeClass(String, Class, Class[], int) - Constructor for class org.biojava.utils.bytecode.GeneratedCodeClass
GeneratedCodeClass(String, CodeClass, CodeClass[], int) - Constructor for class org.biojava.utils.bytecode.GeneratedCodeClass
GeneratedCodeMethod - Class in org.biojava.utils.bytecode: A method that will be generated.
generateDrawableCallboxes(AffineTransform) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Precomputes the callboxes in screen coordinates.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.Annotatable.AnnotationForwarder: Deprecated.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.dist.Distribution.NullModelForwarder: Deprecated.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder: generateEvent generates events in response to layout change and repaint requests.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.MergeAnnotation.PropertyForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.OverlayAnnotation.PropertyForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder: Return the new event to represent the originating event ce.
generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder.Retyper
generateForardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
generateOrderNSequence(String, OrderNDistribution, int) - Static method in class org.biojava.bio.dist.DistributionTools: Deprecated.
use generateSequence() or generateSymbolList() instead.
generateRecord(byte[], Object) - Method in class org.biojava.utils.FileAsList
generateSequence(String, Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools: Produces a sequence by randomly sampling the Distribution.
generateSubpaths() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Precomputes the GeneralPaths used to draw the traces.
generateSymbolList(Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools: Produces a SymbolList by randomly sampling a Distribution.
generateViterbiClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
generatorAt(int) - Method in class org.biojava.utils.bytecode.InstructionVector
GENERIC_PROVIDER - Static variable in interface org.biojava.bibliography.BibRefSupport: A name of a provider type.
GENESYNONYM_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
GeneticAlgorithm - Interface in org.biojavax.ga: The class that runs the cycles of reproduction, evolution and selection, potentially on multiple Populations
GENETICCODE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
GeneticCodes - Class in org.biojava.bio.seq: Collects the references to translation methods in one place.
GENPEPT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GENPEPT indicates that the sequence format is GENPEPT.
GenpeptFormat - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenpeptFormat() - Constructor for class org.biojava.bio.seq.io.GenpeptFormat: Deprecated.
GenpeptRichSequenceDB - Class in org.biojavax.bio.db.ncbi: This class contains functions accessing Peptide sequences in Genpept format.
GenpeptRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: The default constructor delegates to the parent class.
GenpeptSequenceDB - Class in org.biojava.bio.seq.db
GenpeptSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenpeptSequenceDB
get() - Method in interface org.biojava.utils.cache.CacheReference
get() - Method in class org.biojava.utils.io.LargeBuffer
get(int) - Method in class org.biojava.stats.svm.SparseVector: Retrieve the value at dimension dim.
get(int) - Method in class org.biojava.utils.FileAsList
get(int) - Method in class org.biojava.utils.ListTools.Doublet
get(int) - Method in class org.biojava.utils.ListTools.SeriesList
get(int) - Method in class org.biojava.utils.ListTools.Triplet
get(int) - Method in class org.biojava.utils.SingletonList
get(long) - Method in class org.biojava.utils.io.LargeBuffer
get(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable: get the Transition associated with the specified tag.
get(Object) - Method in interface org.biojava.utils.cache.CacheMap: Retrieve the Object associated with the key, or null if either no value has been associated or if the key's value has been cleared by the cache.
get(Object) - Method in class org.biojava.utils.cache.ChangeableCache
get(Object) - Method in class org.biojava.utils.cache.FixedSizeMap
get(Object) - Method in class org.biojava.utils.cache.WeakCacheMap
get(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
get(Object) - Method in class org.biojava.utils.io.SoftHashMap
get(Object) - Method in class org.biojava.utils.OverlayMap
get(Object) - Method in class org.biojava.utils.SmallMap
get(String) - Method in class org.biojava.bio.program.indexdb.BioStore
get(String) - Method in interface org.biojava.bio.program.indexdb.IndexStore: get returns a record specified by a primary identifier.
get(String, String) - Method in class org.biojava.bio.program.indexdb.BioStore
get(String, String) - Method in interface org.biojava.bio.program.indexdb.IndexStore: get returns a list of Records by searching against the primary identifiers if the namespace argument is equal to the primary namespace or otherwise by searching the secondary namespaces.
get_() - Method in class org.biojava.bio.proteomics.StructureTools
get3PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation
get5PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation: The point at which indicates the 5' end of the Location.
getA() - Method in class org.biojava.bio.molbio.DNAComposition: Get the relative compositon of 'A'.
getA() - Method in class org.biojava.utils.ListTools.Doublet
getA() - Method in class org.biojava.utils.ListTools.Triplet
getAbsorptionMax() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property absorptionMax.
getAbsorptionNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property absorptionNote.
getAccession() - Method in interface org.biojava.bio.program.homologene.Orthologue: get the Accession ID associated with this orthologue.
getAccession() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getAccession() - Method in interface org.biojavax.bio.BioEntry: Returns the accession of this bioentry.
getAccession() - Method in class org.biojavax.bio.SimpleBioEntry: Returns the accession of this bioentry.
getAccession() - Method in interface org.biojavax.CrossRef: Returns the accession of the object that the crossref refers to.
getAccession() - Method in class org.biojavax.SimpleCrossRef: Returns the accession of the object that the crossref refers to.
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAccession(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAcronym() - Method in interface org.biojavax.Namespace: If the namespace has an acronym, this will return it.
getAcronym() - Method in class org.biojavax.SimpleNamespace: If the namespace has an acronym, this will return it.
getAddedFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
getAddHandler() - Method in class org.biojava.bio.program.gff.GFFEntrySet: Get the GFFDocumentHandler for adding to this set.
getAdditionalAccessionTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the secondary/tertiary/additional accession term
getAddPos() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier: Retrieve the current value of addPos.
getAddress(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB: Get the URL object for locating sequence object using eutils.
getAddress(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getAddress(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getAddress(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getAddress(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Get the URL object for locating sequence object using eutils.
getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: Get the URL object for locating sequence object using eutils.
getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB: Get the URL object for locating sequence object using eutils.
getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getAdvance() - Method in interface org.biojava.bio.dp.EmissionState: Determine the number of symbols this state advances along one or more symbol lists.
getAdvance() - Method in class org.biojava.bio.dp.SimpleEmissionState
getAE(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
getAlignLength(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAlignLength(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border: Deprecated.
getAlignment() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border: Gets the Alignment - one of LEADING, TRAILING or CENTER.
getAlignment() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.
getAlignment() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getAlignment() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getAlignment() - Method in interface org.biojava.bio.seq.homol.Homology: Retrieve the Alignment that specifies how the homologous regions are aligned.
getAlignment() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature: getAlignment returns the Alignment of two similar features.
getAlignment() - Method in class org.biojava.bio.seq.homol.SimpleHomology: getAlignment returns the alignment, which uses the HomologyFeatures as keys.
getAlignment() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature: getAlignment returns the alignment between the two features.
getAlignment() - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
getAlignment(SymbolList) - Static method in class org.biojava.bio.program.abi.ABITools: View a symbol list over the QUALITY alphabet as an alignment.
getAlignmentNumber() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties: A method that simply returns the number of alignments fetched with this RemoteQBlastOutputProperties object.
getAlignmentOption(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
getAlignmentOption(String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties: Method that returns the value associated with the key given in parameter.
getAlignmentOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
getAlignmentOptions() - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties: Method to get all keys to the information stored in this object.
getAlignmentOutputFormat() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties: Method that returns the alignment output format for this actual RemoteQBlastOutputProperties object
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService: This method extracts the actual Blast report for this request ID.
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService: Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.
getAlignmentStyles() - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler: Returns a fragment of HTML that defines the FONT styles to be used in the alignment markup.
getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAlignUnits(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAll() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster: All sequences that map to this cluster.
getAllAmbiguitySymbol(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Return the ambiguity symbol which matches all symbols in a given alphabet.
getAllBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery: It returns all citations from the current collection as a (possibly big) array.
getAllBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery: It returns all citations from the current collection as a (possibly big) array, perhaps with a limited number of attributes.
getAllBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery: It returns all citations from the current collection as an XML stream.
getAllCharStates() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getAllDataRecords() - Method in class org.biojava.bio.program.abi.ABIFParser: Obtain all data records.
getAllEntries() - Method in interface org.biojava.utils.candy.CandyVocabulary: It returns all available vocabulary entries.
getAllEnzymes() - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getAllEnzymes returns an unmodifable set of all available enzymes.
getAllIDs() - Method in interface org.biojava.bibliography.BibRefQuery: A convenient method returning just identifiers of all current citations.
getAllNames() - Method in interface org.biojava.utils.candy.CandyVocabulary: It return all names (entry identifiers) available in this vocabulary.
getAllNodes(UkkonenSuffixTree.SuffixNode, ArrayList, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getAllProteases() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getAllScientificNames(Connection) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL: Deprecated.

Returns all the scientific names, which are currently stored in the database.
getAllSymbols(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Return a set containing all possible symbols which can be considered members of a given alphabet, including ambiguous symbols.
getAllVocabularies() - Method in interface org.biojava.utils.candy.CandyFinder: It returns all available vocabularies.
getAllVocabularyNames() - Method in interface org.biojava.utils.candy.CandyFinder: It returns names of all vocabularies known to this vocabulary finder.
getAlpha(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getAlpha(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
getAlpha(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
getAlphabet() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
getAlphabet() - Method in class org.biojava.bio.alignment.FlexibleAlignment
getAlphabet() - Method in class org.biojava.bio.alignment.SimpleAlignment
getAlphabet() - Method in class org.biojava.bio.alignment.SubstitutionMatrix: Gives the alphabet used by this matrix.
getAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
getAlphabet() - Method in interface org.biojava.bio.dist.Count: The alphabet from which this Count is over.
getAlphabet() - Method in interface org.biojava.bio.dist.Distribution: The alphabet from which this spectrum emits symbols.
getAlphabet() - Method in class org.biojava.bio.dist.GapDistribution
getAlphabet() - Method in class org.biojava.bio.dist.IndexedCount
getAlphabet() - Method in class org.biojava.bio.dist.PairDistribution
getAlphabet() - Method in class org.biojava.bio.dist.SimpleDistribution
getAlphabet() - Method in class org.biojava.bio.dist.TranslatedDistribution
getAlphabet() - Method in class org.biojava.bio.dist.UniformDistribution
getAlphabet() - Method in class org.biojava.bio.dp.SimpleStatePath
getAlphabet() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
getAlphabet() - Method in interface org.biojava.bio.dp.WeightMatrix: The alphabet for the sequences that this weight matrix models.
getAlphabet() - Method in class org.biojava.bio.gui.SimpleSymbolStyle
getAlphabet() - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
getAlphabet() - Method in interface org.biojava.bio.program.ssaha.DataStore: The alphabet of symbol lists that can be searched against this DataStore.
getAlphabet() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.WebSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
getAlphabet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
getAlphabet() - Method in class org.biojava.bio.seq.impl.DummySequence
getAlphabet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
getAlphabet() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getAlphabet() - Method in class org.biojava.bio.seq.impl.SubSequence
getAlphabet() - Method in class org.biojava.bio.seq.impl.ViewSequence
getAlphabet() - Method in class org.biojava.bio.seq.io.AlternateTokenization
getAlphabet() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolReader: Find the alphabet of all symbols which may be returned by this SymbolReader.
getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolTokenization: The alphabet to which this tokenization applies.
getAlphabet() - Method in class org.biojava.bio.seq.io.WordTokenization
getAlphabet() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools: Gets the protein alphabet
getAlphabet() - Method in class org.biojava.bio.seq.SimpleAssembly
getAlphabet() - Method in interface org.biojava.bio.symbol.AlphabetIndex: Retrieve the alphabet that this indexes.
getAlphabet() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
getAlphabet() - Method in class org.biojava.bio.symbol.DNAAmbPack
getAlphabet() - Method in class org.biojava.bio.symbol.DNANoAmbPack
getAlphabet() - Method in class org.biojava.bio.symbol.DummySymbolList
getAlphabet() - Method in class org.biojava.bio.symbol.PackedSymbolList
getAlphabet() - Method in interface org.biojava.bio.symbol.Packing: The FiniteAlphabet this packing is for.
getAlphabet() - Method in class org.biojava.bio.symbol.RelabeledAlignment
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolList: Get the alphabet of this SymbolList.
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
getAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
getAlphabet() - Method in class org.biojava.bio.symbol.SuffixTree: Return the Alphabet containing all Symbols which might be found in this SuffixTree.
getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolList: The alphabet that this SymbolList is over.
getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
getAlphabet() - Method in class org.biojava.utils.regex.Pattern
getAlphabet() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList: The alphabet that this SymbolList is over.
getAlphabet() - Method in class org.biojavax.bio.seq.ThinRichSequence: The alphabet that this SymbolList is over.
getAlphabet(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

getAlphabet accepts a value which represents a sequence format and returns the relevant FiniteAlphabet object.
getAlphabetIndex(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Get an indexer for a specified alphabet.
getAlphabetIndex(Symbol[]) - Static method in class org.biojava.bio.symbol.AlphabetManager: Get an indexer for an array of symbols.
getAlphabetName() - Method in class org.biojavax.bio.seq.ThinRichSequence
getAlphabets() - Method in interface org.biojava.bio.symbol.Alphabet: Return an ordered List of the alphabets which make up a compound alphabet.
getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SimpleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SingletonAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Gets the components of the Alphabet.
getAlphaStar(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAltIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: This is not supported.
getAmbiguity(Set<Symbol>) - Method in interface org.biojava.bio.symbol.Alphabet: Get a symbol that represents the set of symbols in syms.
getAmbiguityImpl(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet: Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
getAngle(int) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext: Return the angle for an index into a sequence.
getAngle(int) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
getAnnotatedQuerySeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
getAnnotatedSubjectSeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
getAnnotation() - Method in interface org.biojava.bio.Annotatable: Should return the associated annotation object.
getAnnotation() - Method in class org.biojava.bio.dp.SimpleEmissionState
getAnnotation() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.

getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.

getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit: getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult: getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit: getAnnotation returns the Annotation associated with this sub-hit.
getAnnotation() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getAnnotation() - Method in class org.biojava.bio.seq.impl.DummySequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.SubSequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.ViewSequence
getAnnotation() - Method in class org.biojava.bio.seq.io.AlternateTokenization
getAnnotation() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getAnnotation() - Method in class org.biojava.bio.seq.io.WordTokenization
getAnnotation() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getAnnotation() - Method in class org.biojava.bio.seq.SimpleAssembly
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.SimpleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.SingletonAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: The SoftMaskedAlphabet has no annotation
getAnnotation() - Method in class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
getAnnotation() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getAnnotation() - Method in class org.biojava.ontology.OntologyTerm.Impl
getAnnotation() - Method in class org.biojava.ontology.RemoteTerm.Impl
getAnnotation() - Method in class org.biojava.ontology.Term.Impl
getAnnotation() - Method in class org.biojava.ontology.Triple.Impl
getAnnotation() - Method in class org.biojavax.bio.seq.CompoundRichLocation: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.SimpleBioEntry: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTerm: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTriple: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.SimpleCrossRef: Should return the associated annotation object.
getAnnotation(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getAnnotation returns an immutable, static annotation describing the enzyme.
getAnnotations() - Method in class org.biojava.bio.MergeAnnotation: Gets an unmodifiable view of the list of Annotations that are part of the MergeAnnotation.
getAnnotationType() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType: Get the AnnotationType used as a constraint.
getAnnotationType() - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler: Return the AnnotationType built by this handler
getAnnotator() - Method in class org.biojava.bio.program.gff.GFFEntrySet: Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.
getAnnotator(boolean) - Method in class org.biojava.bio.program.gff.GFFEntrySet: Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.
getArg_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getArrowHeadSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getArrowScoop() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getArrowScoop() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getArrowSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getArrowSize() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getArticleAuthors() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the names of the authors which first published an article about the AAindex entry.
getArticleTitle() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the title of the article which describes the AAindex entry.
getAsp_N() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getAttributes(String) - Method in class org.biojava.naming.ObdaContext
getAttributes(String, String[]) - Method in class org.biojava.naming.ObdaContext
getAttributes(Name) - Method in class org.biojava.naming.ObdaContext
getAttributes(Name, String[]) - Method in class org.biojava.naming.ObdaContext
getAuthority() - Method in interface org.biojavax.Namespace: This method will return the authority that governs the namespace.
getAuthority() - Method in class org.biojavax.SimpleNamespace: This method will return the authority that governs the namespace.
getAuthorityId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier: Return the authority id for this identifier.
getAuthorList() - Method in interface org.biojavax.DocRef: Returns the authors of the document reference as a set of DocRefAuthor implementation instances.
getAuthorList() - Method in class org.biojavax.SimpleDocRef: Returns the authors of the document reference as a set of DocRefAuthor implementation instances.
getAuthors() - Method in interface org.biojavax.DocRef: Returns the authors of the document reference.
getAuthors() - Method in class org.biojavax.SimpleDocRef: Returns the authors of the document reference.
getAutomaton() - Method in class org.biojava.utils.automata.FiniteAutomaton
getAutomaton() - Method in interface org.biojava.utils.automata.NfaBuilder
getAutomaton() - Method in class org.biojava.utils.automata.NfaSubModel
getB() - Method in class org.biojava.bio.proteomics.StructureTools
getB() - Method in class org.biojava.utils.ListTools.Doublet
getB() - Method in class org.biojava.utils.ListTools.Triplet
getBackwardTransitions() - Method in class org.biojava.bio.dp.DP
getBackwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
getBasecalls() - Method in class org.biojava.bio.program.abi.ABITrace: Returns an int[] array that represents the basecalls - each int in the array corresponds to an x-coordinate point in the graph that is a peak (a base location).
getBaseCalls() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram: Return the total number of base calls.
getBaseCalls() - Method in interface org.biojava.bio.chromatogram.Chromatogram: Returns an alignment that describes the base calls for this chromatogram.
getBaseColor(Symbol) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Returns the color that will be used to draw the trace for the given DNA symbol.
getBaseFillColor(Symbol) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Returns the color that will be used to fill in the callboxes for calls with the given symbol.
getBases() - Method in class org.biojava.bio.dp.SimpleEmissionState
getBases() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getBases() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getbaseURL() - Method in class org.biojava.bio.seq.db.FetchURL
getBeadDepth() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer: getBeadDepth returns the depth of a single bead produced by this renderer.
getBeadDepth() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer: getBeadDepth returns the depth of a single bead produced by the renderer.
getBeadDepth() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer: getBeadDisplacement returns the displacement of beads from the centre line of the renderer.
getBeadDisplacement() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer: getBeadDisplacement returns the displacement of beads from the centre line of the renderer.
getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
getBeadFill() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer: getBeadFill returns the bead fill paint.
getBeadOutline() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer: getBeadOutline returns the bead outline paint.
getBeadStroke() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer: getBeadStroke returns the bead outline stroke.
getBibRefAsXML(BibRef) - Method in interface org.biojava.bibliography.BibRefQuery: A convenient utility method converting a given citation to its XML representation.
getBibRefCount() - Method in interface org.biojava.bibliography.BibRefQuery: It returns the number of citations in the current collection.
getBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery: It returns an enumeration of all citations from the current collection.
getBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery: It returns an enumeration of all citations from the current collection, perhaps with a limited number of attributes.
getBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery: It returns an enumeration of all citations from the current collection.
getBinaryAlphabet() - Static method in class org.biojavax.ga.util.GATools: Gets a Reference to the FlyWeight GA_Binary Alphabet.
getBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite: Retrieve a single BioEntry by its id.
getBioEntry(String) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
getBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB
getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractBioEntryDB
getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntryIterator() - Method in interface org.biojavax.bio.db.BioEntryDB: Returns a BioEntryIterator over all BioEntrys in the database.
getBioEntrys(Set) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntrys(Set) - Method in interface org.biojavax.bio.db.BioEntryDBLite: Retrieve multiple BioEntry by their ids.
getBioEntrys(Set) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
getBioEntrys(Set) - Method in class org.biojavax.bio.db.HashBioEntryDB
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntrys(Set, BioEntryDB) - Method in interface org.biojavax.bio.db.BioEntryDBLite: Retrieve multiple BioEntry into a specific sequence database.
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.HashBioEntryDB
getBioSequenceStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.

Returns the an object indicating the style of biosequence storage that this database should employ.
getBioSequenceStyle() - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper: Deprecated.
getBlastAdvancedOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties: Simply return the string given as argument via setBlastAdvancedOptions
getBlastDatabase() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties: This method returns the value of the database used for this particular blast run.
getBlastProgram() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties: This method returns the value of the program used for this particular blast run.
getBlockDepth() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
getBlockDepth() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
getBlockListener() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
getBlockListener() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser: Obtain the listener for this parser.
getBlockName() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
getBlockName() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlock: Get the block name.
getBlockName() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract: Obtains the name of this block.
getBlockName() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract
getBlockPainter() - Method in class org.biojava.bio.gui.DistributionLogo
getBlockPainter() - Method in interface org.biojava.bio.gui.LogoContext
getBlockParser(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract
getBlockParser(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener: Gets the parser to use for a given block.
getBlockWidth() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getBlosum100() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM100 amino acid substitution matrix.
getBlosum100_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM100.50 amino acid substitution matrix.
getBlosum30() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM30 amino acid substitution matrix.
getBlosum30_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM30.50 amino acid substitution matrix.
getBlosum35() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM35 amino acid substitution matrix.
getBlosum35_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM35.50 amino acid substitution matrix.
getBlosum40() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM40 amino acid substitution matrix.
getBlosum40_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM40.50 amino acid substitution matrix.
getBlosum45() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM45 amino acid substitution matrix.
getBlosum45_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM45.50 amino acid substitution matrix.
getBlosum50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM50 amino acid substitution matrix.
getBlosum50_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM50.50 amino acid substitution matrix.
getBlosum55() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM55 amino acid substitution matrix.
getBlosum55_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM55.50 amino acid substitution matrix.
getBlosum60() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM60 amino acid substitution matrix.
getBlosum60_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM60.50 amino acid substitution matrix.
getBlosum62() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM62 amino acid substitution matrix.
getBlosum62_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM62.50 amino acid substitution matrix.
getBlosum65() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM65 amino acid substitution matrix.
getBlosum65_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM65.50 amino acid substitution matrix.
getBlosum70() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM70 amino acid substitution matrix.
getBlosum70_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM70.50 amino acid substitution matrix.
getBlosum75() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM75 amino acid substitution matrix.
getBlosum75_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM75.50 amino acid substitution matrix.
getBlosum80() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM80 amino acid substitution matrix.
getBlosum80_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM80.50 amino acid substitution matrix.
getBlosum85() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM85 amino acid substitution matrix.
getBlosum85_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM85.50 amino acid substitution matrix.
getBlosum90() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM90 amino acid substitution matrix.
getBlosum90_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUM90.50 amino acid substitution matrix.
getBlosumn() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUMN amino acid substitution matrix.
getBlosumn_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the BLOSUMN.50 amino acid substitution matrix.
getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.Aggregator
getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.MultiTagger
getBounds() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
getBounds() - Method in interface org.biojava.bio.gui.glyph.Glyph
getBounds() - Method in class org.biojava.bio.gui.glyph.HelixGlyph
getBounds() - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
getBounds() - Method in class org.biojava.bio.gui.glyph.TurnGlyph
getBounds() - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
getBounds() - Method in interface org.biojava.bio.gui.LogoContext
getBuilderFactory(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

getBuilderFactory accepts a value which represents a sequence format and returns the relevant SequenceBuilderFactory object.
getC() - Method in class org.biojava.bio.molbio.DNAComposition: Get the relative compositon of 'C'.
getC() - Method in class org.biojava.bio.proteomics.StructureTools
getC() - Method in class org.biojava.stats.svm.SMOTrainer
getC() - Method in class org.biojava.utils.ListTools.Triplet
getCallboxBounds(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Returns the screen-coordinate bounds of the callbox for a given call.
getCallboxBounds(int, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Returns the bounds of the callbox for a given call.
getCallboxCount() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Returns the number of callboxes, regenerating them if necessary.
getCallContaining(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Synonym for ChromatogramGraphic.getCallContaining(float, boolean) with pointOnScreen=true.
getCallContaining(float, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Same as ChromatogramGraphic.getCallContaining(Point2D, boolean), except that only the x-coordinate of the point is specified.
getCallContaining(Point2D) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Synonym for ChromatogramGraphic.getCallContaining(Point2D, boolean) with pointOnScreen=true.
getCallContaining(Point2D, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Returns the 0-based index of the call containing a given point.
getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn: Get the cardinality constraint used to validate the number of property values.
getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains: Get the cardinality constraint used to validate the number of property values.
getCategory() - Method in class org.biojava.ontology.Synonym
getCell(int[]) - Method in interface org.biojava.bio.dp.DPMatrix
getCell(int[]) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
getCell(int[]) - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
getChainedEvent() - Method in class org.biojava.utils.ChangeEvent: Return the event which caused this to be fired, or null if this change was not caused by another event.
getChange() - Method in class org.biojava.utils.ChangeEvent: Return an object which is to be the new value of some property, or is to be added to a collection.
getChangeEvent() - Method in exception org.biojava.utils.ChangeVetoException: Return the ChangeEvent which is being vetoed.
getChanger() - Method in class org.biojava.bio.AnnotationChanger: getMapper returns the ValueChanger being used to remap the Annotation.
getChanger(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable: Get the Changer currently registered to handle a tag.
getChangeSupport() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
getChangeSupport() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractDistribution
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.TranslatedDistribution
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleEmissionState
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleMarkovModel
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel: getChangeSupport lazily instantiates a helper for change listeners.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster: Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel: getChangeSupport lazily instantiates a helper for change listeners.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.MergeAnnotation
getChangeSupport(ChangeType) - Method in class org.biojava.bio.OverlayAnnotation
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleFeature
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleSequence
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.LazyFeatureHolder
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.NewSimpleAssembly
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.SimpleAssembly
getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.AbstractSymbol
getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.SimpleAlphabet
getChangeSupport(ChangeType) - Method in class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.ontology.AbstractTerm
getChangeSupport(ChangeType) - Method in class org.biojava.ontology.OntologyTerm.Impl
getChangeSupport(ChangeType) - Method in class org.biojava.utils.AbstractChangeable: Called to retrieve the ChangeSupport for this object.
getChangeTable() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
getChangeTypes(Class) - Static method in class org.biojava.utils.ChangeType: Get all ChangeType objects defined within a class.
getChar() - Method in class org.biojava.utils.io.LargeBuffer
getChar(long) - Method in class org.biojava.utils.io.LargeBuffer
getCharacter() - Method in class org.biojava.utils.RepeatedCharSequence
getCharacterOffset() - Method in exception org.biojava.utils.ParserException: Get the character offset in the line where an error was detected.
getCharLabels() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getCharStateLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getCharStateLabelKeywords(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getChild() - Method in class org.biojava.bio.seq.FeatureFilter.Not
getChild() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
getChild(SuffixTree.SuffixNode, int) - Method in class org.biojava.bio.symbol.SuffixTree: Get the n'th child of a node.
getChild(SuffixTree.SuffixNode, Symbol) - Method in class org.biojava.bio.symbol.SuffixTree: Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
getChild1() - Method in class org.biojava.bio.CollectionConstraint.And: Get the first child CollectionConstraint.
getChild1() - Method in class org.biojava.bio.CollectionConstraint.Or: Get the first child CollectionConstraint.
getChild1() - Method in class org.biojava.bio.PropertyConstraint.And: Get the first child PropertyConstraint.
getChild1() - Method in class org.biojava.bio.PropertyConstraint.Or: Get the first child PropertyConstraint.
getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.And
getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.Or
getChild1() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
getChild1() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
getChild2() - Method in class org.biojava.bio.CollectionConstraint.And: Get the seccond child CollectionConstraint.
getChild2() - Method in class org.biojava.bio.CollectionConstraint.Or: Get the seccond child CollectionConstraint.
getChild2() - Method in class org.biojava.bio.PropertyConstraint.And: Get the seccond child PropertyConstraint.
getChild2() - Method in class org.biojava.bio.PropertyConstraint.Or: Get the seccond child PropertyConstraint.
getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.And
getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.Or
getChild2() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
getChild2() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
getChildren() - Method in class org.biojava.bio.taxa.SimpleTaxon: Deprecated.
getChildren() - Method in interface org.biojava.bio.taxa.Taxon: Deprecated.

The children of this Taxon.
getChildren() - Method in class org.biojava.bio.taxa.WeakTaxon: Deprecated.
getChildrenOf(Connection, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL: Deprecated.

Returns all children of the specified taxon.
getChildrenOf(Connection, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL: Deprecated.

Returns the children as a Stack of this given taxon.
getChildrenRaw() - Method in class org.biojava.bio.taxa.WeakTaxon: Deprecated.
getChromatogram() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Accessor for the in-use chromatogram.
getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getChromNum(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getChromosome() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getChromosome(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getChromosomes() - Method in interface org.biojavax.ga.functions.GACross: Gets the chromosomes after the cross
getChromosomes() - Method in interface org.biojavax.ga.functions.GACrossResult: Gets the chromosomes after the cross
getChromosomes() - Method in class org.biojavax.ga.functions.SimpleGACrossResult
getChromosomes() - Method in class org.biojavax.ga.impl.AbstractOrganism
getChromosomes() - Method in interface org.biojavax.ga.Organism: Gets the organisms 'chromosome' sequences
getChymotrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getCircular() - Method in interface org.biojavax.bio.seq.RichSequence: Is the sequence circular?
getCircular() - Method in class org.biojavax.bio.seq.ThinRichSequence: Is the sequence circular?
getCircularLength() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the circular length of this location.
getCircularLength() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: Retrieves the circular length of this location.
getCircularLength() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the circular length of this location.
getCircularLength() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the circular length of this location.
getClasses() - Method in class org.biojava.utils.bytecode.ParametricType
getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifyId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifySystem(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifyType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassLoader(Class) - Static method in class org.biojava.utils.ClassTools: Get the classloader which loaded clazz.
getClassLoader(Object) - Static method in class org.biojava.utils.ClassTools: Get the classloader which loaded the class of obj.
getClassNumber(int) - Method in interface org.biojava.bio.EcNumber: Get the class number associated with the particular level of the ec number.
getClassNumber(int) - Method in class org.biojava.bio.EcNumber.Impl
getCleaveageResidues() - Method in class org.biojava.bio.proteomics.Protease: The list of residues that the protease will cleave at.
getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCloneId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCloneLibrary(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCluster(String) - Method in interface org.biojava.bio.program.unigene.UnigeneDB: Fetch a cluster by its cluster id.
getCNBr() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getCodeClass() - Method in interface org.biojava.utils.bytecode.CodeContext: Get the class for which a method is being generated.
getCodeMethod() - Method in interface org.biojava.utils.bytecode.CodeContext: Get the method which is being generated.
getCodonAlphabet() - Static method in class org.biojava.bio.seq.DNATools: Gets the (DNA x DNA x DNA) Alphabet
getCodonAlphabet() - Static method in class org.biojava.bio.seq.RNATools: Gets the (RNA x RNA x RNA) Alphabet
getCodonPref() - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
getCodonPreference(String) - Static method in class org.biojava.bio.symbol.CodonPrefTools: get the specified codon preference.
getCodonPrefs() - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
getCollapsing() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer: Returns true if this class collapses to zero depth when there are no visible features.
getCollectionConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandler
getCollectionId() - Method in interface org.biojava.bibliography.BibRefQuery: It returns an identification of the current query collection.
getColourClass(String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler: Returns the colour class for the specified colour (in hex).
getColumn(int) - Method in class org.biojava.bio.dp.SimpleWeightMatrix
getColumn(int) - Method in interface org.biojava.bio.dp.WeightMatrix: Retrieve a column as an EmissionState.
getCommands() - Method in class org.biojava.utils.process.ExternalProcess: Gets the command line including the path or name of the external program and its command line arguments.
getComment() - Method in interface org.biojava.bio.AnnotationType: Get the comment for the whole AnnotationType.
getComment() - Method in class org.biojava.bio.AnnotationType.Impl
getComment() - Method in interface org.biojava.bio.program.gff.GFFRecord: The feature comment.
getComment() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getComment() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the user comment for the AAindex entry.
getComment() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
getComment() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event: Getter for property comment.
getComment() - Method in interface org.biojavax.Comment: Returns the comment part of this comment.
getComment() - Method in class org.biojavax.SimpleComment: Returns the comment part of this comment.
getComment(Object) - Method in interface org.biojava.bio.AnnotationType: Get the comment for a particular property.
getComment(Object) - Method in class org.biojava.bio.AnnotationType.Impl
getComments() - Method in class org.biojava.bio.program.scf.SCF: Returns the comments fields as a Properties mapping.
getComments() - Method in interface org.biojavax.bio.BioEntry: Returns a set of all comments associated with this bioentry.
getComments() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock: Returns all comments.
getComments() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock: Returns all comments.
getComments() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock: Returns all comments.
getComments() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock: Returns all comments.
getComments() - Method in class org.biojavax.bio.SimpleBioEntry: Returns a set of all comments associated with this bioentry.
getCommentType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property commentType.
getCommonName() - Method in class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
getCommonName() - Method in interface org.biojava.bio.taxa.Taxon: Deprecated.

The common name of the Taxon.
getComparator() - Method in class org.biojava.utils.FileAsList
getComponentList(boolean) - Method in class org.biojava.bio.symbol.MergeLocation: Gets the component locations that make up this one
getComponentLocation() - Method in interface org.biojava.bio.seq.ComponentFeature: Return a location which identifies a portion of the component sequence which is to be included in the assembly.
getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
getComponentName() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
getComponentSequence() - Method in interface org.biojava.bio.seq.ComponentFeature: Get the sequence object which provides a component of this feature's parent sequence.
getComponentSequenceName() - Method in interface org.biojava.bio.seq.ComponentFeature: Get the name of the component sequence.
getComputationTime() - Method in class org.biojava.bio.alignment.AlignmentPair
getConditionedAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution: Get the conditioned alphabet.
getConditionedAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution: Get the conditioned alphabet.
getConditioningAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution: Get the conditioning alphabet of this distribution.
getConditioningAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution: Get the conditioning alphabet of this distribution.
getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getConfidence(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Composite
getConfigLocator() - Method in interface org.biojava.directory.RegistryConfiguration: getConfigLocator returns a locator for the configuration.
getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Impl
getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Composite
getConfiguration() - Method in interface org.biojava.directory.RegistryConfiguration: getConfiguration returns a mapping of registry database names to collections of tag-value pairs.
getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Impl
getConstant() - Method in class org.biojava.stats.svm.PolynomialKernel
getConstant() - Method in class org.biojava.stats.svm.SigmoidKernel
getConstants() - Method in interface org.biojava.utils.bytecode.CodeContext: Get the constants pool for this context.
getConstraint(Object) - Method in interface org.biojava.bio.AnnotationType: Retrieve the constraint that will be applied to all properties with a given key.
getConstraint(Object) - Method in class org.biojava.bio.AnnotationType.Impl
getConstructor(CodeClass[]) - Method in interface org.biojava.utils.bytecode.CodeClass: Get a constructor by argument list.
getConstructor(CodeClass[]) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
getConstructor(CodeClass[]) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
getContainingClass() - Method in class org.biojava.utils.bytecode.CodeField: Get the class that contains this field.
getContainingClass() - Method in interface org.biojava.utils.bytecode.CodeMethod: The class that contains this method
getContainingClass() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
getContainsTerm() - Static method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Gets the default CONTAINS term used for defining the relationship between features.
getContentHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade: correct this later
getContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
getContext() - Method in class org.biojava.stats.svm.TrainingEvent
getContext(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser: See if empty tags are treated as a continuation of previous tags or as a new tag with the value of the empty string.
getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser: Report whether empty tags will be treated as continuations of the last non -empty tag.
getCoordinates() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot: getCoordinates returns the hotspot coordinates.
getCopyrightTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the copyright term
getCoreOntology() - Static method in class org.biojava.ontology.OntoTools: Get the Ontology that defines our core "central dogma".
getCount() - Method in interface org.biojava.utils.candy.CandyVocabulary: It returns a number of entries contained in this vocabulary.
getCount(Distribution, Symbol) - Method in interface org.biojava.bio.dist.DistributionTrainerContext: Return the number of counts of a particular symbol which will be used to train the specified distribution.
getCount(Distribution, Symbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
getCount(DistributionTrainerContext, AtomicSymbol) - Method in interface org.biojava.bio.dist.DistributionTrainer: Get the current count for this state.
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer: Deprecated.
getCount(AtomicSymbol) - Method in interface org.biojava.bio.dist.Count: Return the counts for a given Symbol.
getCount(AtomicSymbol) - Method in class org.biojava.bio.dist.IndexedCount
getCRC() - Method in interface org.biojavax.DocRef: Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references.
getCRC() - Method in class org.biojavax.SimpleDocRef: Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references.
getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCreateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCreateOnUnderlyingSequence() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getCrossOverFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
getCrossOverFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACross: Returns the collection of cross over locations from the last cross
getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACrossResult: Returns the collection of cross over locations from the last cross
getCrossOverPositions() - Method in class org.biojavax.ga.functions.SimpleGACrossResult
getCrossOverProbs() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
getCrossOverProbs() - Method in interface org.biojavax.ga.functions.CrossOverFunction
getCrossOverProbs() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
getCrossProductAlphabet(List) - Static method in class org.biojava.bio.symbol.AlphabetManager: Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCrossProductAlphabet(List, String) - Static method in class org.biojava.bio.symbol.AlphabetManager: Attempts to create a cross product alphabet and register it under a name.
getCrossProductAlphabet(List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCrossref() - Method in interface org.biojavax.DocRef: The document reference may refer to an object in another database.
getCrossref() - Method in class org.biojavax.SimpleDocRef: The document reference may refer to an object in another database.
getCrossRef() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the crossref associated with this location.
getCrossRef() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: Retrieves the crossref associated with this location.
getCrossRef() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the crossref associated with this location.
getCrossRef() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the crossref associated with this location.
getCrossRef() - Method in interface org.biojavax.RankedCrossRef: Return the cross reference associated with this object.
getCrossRef() - Method in class org.biojavax.SimpleRankedCrossRef: Return the cross reference associated with this object.
getCrossResults() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm: Get a List containing details of all the cross over events during the run.
getCurrentCycle() - Method in interface org.biojava.stats.svm.TrainingContext
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
getCurrentFeature() - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener: Gets the feature currently being created.
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Gets the feature currently being created.
getCurrentScore() - Method in class org.biojava.bio.dp.AbstractTrainer
getCurrentScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getCutoff() - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold
getCuttingSize() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: The cutting size of a restriction enzyme is defined has the number of nucleotides that are directly involved in the recognition sequence.
getCutType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getCutType returns the type of cut produced by the enzyme.
getCycle() - Method in class org.biojava.bio.dp.AbstractTrainer
getCycle() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getDataAccess() - Method in class org.biojava.bio.program.abi.ABIFParser: Returns the accessor for the raw data being parsed by this parser.
getDatabase(String) - Method in class org.biojava.directory.Registry: getDatabase retrieves a database instance known by a name String.
getDataBase() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getDatabaseName() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property databaseName.
getDatabaseURLGenerators() - Method in class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
getDatabaseURLGenerators() - Method in interface org.biojava.bio.program.blast2html.URLGeneratorFactory: Returns a list of 0, 1 or more DatabaseURLGenerator The first is used to link from the id in the summary table, all are used as a list of links in the detail section.
getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms: Getter for the Ensembl-specific 'dataClass' term
getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms: Getter for the Ensembl-specific 'dataClass' term
getDataClassTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the DataClass term
getDataRecord(String, int) - Method in class org.biojava.bio.program.abi.ABIFParser: Get the entry from the file TOC with the given name and tag number.
getDataSource(String, String, String, String) - Static method in class org.biojava.utils.JDBCPooledDataSource
getDataSources() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB: Get the current set of all currently registered data sources.
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
getDataStore(File) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory: Get a pre-built data store associated with a file.
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory
getDataType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
getDataType() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getDateAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the date annotated term
getDateCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the date created term
getDateUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the date updated term
getDayhoff() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the DAYHOFF amino acid substitution matrix.
getDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: retrieve the DB that has just been built
getDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
getDB() - Method in class org.biojava.bio.seq.db.FetchURL
getDbCode() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getDBHelper(Connection) - Static method in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.

Returns a DBHelper implementation suitable for a particular database.
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getDbId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs: return a set of DbId
getDbname() - Method in interface org.biojavax.CrossRef: Returns the name of the database the cross reference refers to.
getDbname() - Method in class org.biojavax.SimpleCrossRef: Returns the name of the database the cross reference refers to.
getDBTaxon(Connection, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL: Deprecated.

Attempts to get a Taxon object corresponding to the specified taxon_id (i.e. the database's internal id for the taxon).
getDbXrefId() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
getDbxrefList(String, int, int) - Method in class org.biojava.ontology.obo.OboFileParser
getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocation
getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getDecorator(Class) - Method in interface org.biojava.bio.symbol.Location: Checks the decorator chain for an instance of decoratorClass and return it if found.
getDecorator(Class) - Method in class org.biojavax.bio.seq.CompoundRichLocation: Checks the decorator chain for an instance of decoratorClass and return it if found.
getDecorator(Class) - Method in class org.biojavax.bio.seq.EmptyRichLocation: Checks the decorator chain for an instance of decoratorClass and return it if found.
getDecorator(Class) - Method in class org.biojavax.bio.seq.SimpleRichLocation: Checks the decorator chain for an instance of decoratorClass and return it if found.
getDefaultChanger() - Method in class org.biojava.bio.program.tagvalue.ValueChanger: Get the changer that will be applied to values of tags with no specific handler registered.
getDefaultConstraint() - Method in interface org.biojava.bio.AnnotationType: Get the CollectionConstraint that will be applied to all properties without an explicit binding.
getDefaultConstraint() - Method in class org.biojava.bio.AnnotationType.Impl
getDefaultCrossReferenceResolver() - Static method in class org.biojavax.RichObjectFactory: Returns the default cross ref resolver object.
getDefaultFactory() - Static method in class org.biojava.ontology.OntoTools
getDefaultFormat() - Method in class org.biojava.bio.program.phred.PhredFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.FastaFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GAMEFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankXmlFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenpeptFormat: Deprecated.
getDefaultFormat() - Method in interface org.biojava.bio.seq.io.SequenceFormat: Deprecated.
new implementations should only write a single format.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.FastaFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.GenbankFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.INSDseqFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultNamespace() - Static method in class org.biojavax.RichObjectFactory: Returns the default namespace object.
getDefaultOntology() - Static method in class org.biojavax.RichObjectFactory: Returns the default ontology object.
getDefaultPaint() - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
getDefaultPositionResolver() - Static method in class org.biojavax.RichObjectFactory: Returns the default position resolver object.
getDefaultRichSequenceHandler() - Static method in class org.biojavax.RichObjectFactory: Returns the default sequence resolver object.
getDefaultSplitter() - Method in class org.biojava.bio.program.tagvalue.ValueChanger: Get the splitter that will be applied to values of tags with no specific handler registered.
getDelegate() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
getDelegate() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
getDelegate() - Method in class org.biojava.bio.program.tagvalue.StateMachine
getDelegate() - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper: get listener to which all calls will be delegated
getDelegate() - Method in class org.biojava.bio.seq.io.SeqIOFilter: Retrieve the delegate that is wrapped.
getDelegate() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter: Retrieve the delegate that is wrapped.
getDelegate() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: The compound alpha that holds the symbols used by this wrapper
getDelegateParser() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getDelete() - Method in class org.biojava.bio.alignment.NeedlemanWunsch: Returns the current expenses of a single delete operation.
getDelete() - Method in class org.biojava.bio.alignment.SmithWaterman
getDelete(int) - Method in class org.biojava.bio.dp.ProfileHMM: Retrieves the delete state for column indx.
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.

Returns the an object indicating the style of deletion that this database should employ.
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper: Deprecated.
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper: Deprecated.
getDepth() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
getDepth() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor: Gets the Depth attribute of the LightPairDPCursor object
getDepth() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor: retrieve the depth of this cursor
getDepth() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
getDepth(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer: getDepth returns the total depth of a list of SequenceRenderers.
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularMLR
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularPaddedRenderer
getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularRenderer: Get the depth needed for this renderer.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer: getDepth calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer: getDepth calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Returns the depth property of this class.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer: getDepth calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer: getDepth calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer: Retrieve the depth of this renderer when rendering src.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
getDepth(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LineInfo
getDepthScaler() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel: Retrieve the current DepthScaler.
getDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix: This gives you the description of this matrix if there is one.
getDescription() - Method in class org.biojava.bio.program.fastq.Fastq: Return the description of this FASTQ formatted sequence.
getDescription() - Method in class org.biojava.bio.program.fastq.FastqBuilder: Return the description for this FASTQ formatted sequence builder.
getDescription() - Method in enum org.biojava.bio.program.fastq.FastqVariant: Return the description of this FASTQ sequence format variant.
getDescription() - Method in class org.biojava.bio.program.homologene.SimilarityType.PlaceHolder
getDescription() - Method in interface org.biojava.bio.program.homologene.Taxon: returns the name of the Taxon
getDescription() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
getDescription() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the description for the AAindex entry.
getDescription() - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
getDescription() - Method in class org.biojava.ontology.IntegerOntology
getDescription() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getDescription() - Method in interface org.biojava.ontology.Ontology: Return a human-readable description of this ontology, or the empty string if none is available
getDescription() - Method in class org.biojava.ontology.Ontology.Impl
getDescription() - Method in class org.biojava.ontology.OntologyTerm.Impl
getDescription() - Method in class org.biojava.ontology.RemoteTerm.Impl
getDescription() - Method in interface org.biojava.ontology.Term: Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojava.ontology.Term.Impl
getDescription() - Method in class org.biojava.ontology.Triple.Impl
getDescription() - Method in interface org.biojava.utils.candy.CandyVocabulary: It returns a description of this vocabulary.
getDescription() - Method in interface org.biojavax.bio.BioEntry: Returns a description of this sequence.
getDescription() - Method in class org.biojavax.bio.SimpleBioEntry: Returns a description of this sequence.
getDescription() - Method in interface org.biojavax.Namespace: Returns a description of this namespace.
getDescription() - Method in interface org.biojavax.ontology.ComparableOntology: Return a human-readable description of this ontology.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableOntology: Return a human-readable description of this ontology.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableTerm: Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableTriple: Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojavax.SimpleNamespace: Returns a description of this namespace.
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getDescription(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getDescriptionNumber() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties: A method that simply returns the number of descriptions fetched with this RemoteQBlastOutputProperties object.
getDescriptor() - Method in interface org.biojava.utils.bytecode.CodeClass
getDescriptor() - Method in interface org.biojava.utils.bytecode.CodeMethod: A human-readable description of the class
getDescriptor() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
getDescriptor() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
getDescriptor() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
getDescriptors() - Method in interface org.biojavax.ontology.ComparableTriple: Returns all descriptors.
getDescriptors() - Method in class org.biojavax.ontology.SimpleComparableTriple: Returns all descriptors.
getDetailsHandler() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler: Return a handler for the XFF details element.
getDFA() - Method in class org.biojava.utils.automata.DfaBuilder
getDimAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector: Retrieve the dimension at a specific index.
getDimensionRatio() - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer: getDimensionRatio returns the maximum ratio of long dimension to short dimension of the bead.
getDimensionsNChar() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock: Get the NCHAR value.
getDimensionsNChar() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock: Get the NCHAR value.
getDimensionsNTax() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock: Get the NTAX value.
getDimensionsNTax() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock: Get the NTAX value.
getDimensionsNTax() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock: Get the NTAX value.
getDinucleotideAlphabet() - Static method in class org.biojava.bio.symbol.CodonPrefTools: returns an RNA dinucleotide alphabet.
getDirection() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel: getDirection returns the direction in which this context expects the sequence to be rendered - HORIZONTAL or VERTICAL.
getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanel: Retrieve the current rendering direction.
getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePoster: Deprecated.

Retrieve the current rendering direction.
getDirection() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext: Gets the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.
getDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getDirection() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getDirection() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel: getDirection returns the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.
getDisplayName() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific
getDisplayName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific or if there are no scientific names at all, the empty string.
getDistanceBetweenFeatures() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
getDistribution() - Method in interface org.biojava.bio.dp.EmissionState: Get the Distribution associated with this state.
getDistribution() - Method in class org.biojava.bio.dp.SimpleEmissionState
getDistribution() - Method in class org.biojava.bio.gui.DistributionLogo: Retrieve the currently rendered dist.
getDistribution() - Method in interface org.biojava.bio.gui.LogoContext
getDistribution() - Method in class org.biojava.bio.molbio.Composition: Returns the distribution backing this class.
getDistribution(Symbol) - Method in interface org.biojava.bio.dist.OrderNDistribution
getDivision() - Method in interface org.biojavax.bio.BioEntry: Returns the division of this bioentry.
getDivision() - Method in class org.biojavax.bio.SimpleBioEntry: Returns the division of this bioentry.
getDNA() - Method in class org.biojava.bio.program.phred.PhredSequence: Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
getDNA() - Static method in class org.biojava.bio.seq.DNATools: Return the DNA alphabet.
getDNAAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence
getDNADistribution(double) - Static method in class org.biojava.bio.seq.DNATools: return a SimpleDistribution of specified GC content.
getDNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools: Creates a DNA symbol tokenizer.
getDNASequence(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools: Get the called DNA sequence from a chromatogram.
getDNAxDNA() - Static method in class org.biojava.bio.seq.DNATools: Gets the (DNA x DNA) Alphabet
getDNAxDNADistribution(double, double) - Static method in class org.biojava.bio.seq.DNATools: return a (DNA x DNA) cross-product Distribution with specified DNA contents in each component Alphabet.
getDocumentReference() - Method in interface org.biojavax.RankedDocRef: Represents a reference to a document.
getDocumentReference() - Method in class org.biojavax.SimpleRankedDocRef: Represents a reference to a document.
getDotStatesIndex() - Method in class org.biojava.bio.dp.DP
getDouble() - Method in class org.biojava.utils.io.LargeBuffer
getDouble(long) - Method in class org.biojava.utils.io.LargeBuffer
getDoubleValue(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
getDoubleValue(Symbol) - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
getDownstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getDownstreamCut returns the cut site within or downstream of the recognition site.
getDownstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getDownstreamEndType returns the double-stranded end type produced by the primary (intra-site or downstream) cut.
getDP() - Method in class org.biojava.bio.dp.AbstractTrainer
getDP() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getDTDHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
getE() - Method in class org.biojava.bio.proteomics.StructureTools
getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getEcNumber(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getEdgeLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getEdgeLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree: Tree navigation methods
getEditDistance() - Method in class org.biojava.bio.alignment.NeedlemanWunsch: This gives the edit distance according to the given parameters of this certain object.
getElementId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getElementId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getElementIds() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getElementIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getElideComments() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Is the format going to emit events when comments data or remarks from bibliographic references are read?
getElideComments() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Is the format going to emit events when comments data or remarks from bibliographic references are read?
getElideFeatures() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Is the format going to emit events when feature data is read?
getElideFeatures() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Is the format going to emit events when feature data is read?
getElideReferences() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Is the format going to emit events when bibliographic reference data is read?
getElideReferences() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Is the format going to emit events when bibliographic reference data is read?
getElideSymbols() - Method in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.

Return a flag indicating if symbol data will be skipped when parsing streams.
getElideSymbols() - Method in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
getElideSymbols() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Is the format going to emit events when sequence data is read?
getElideSymbols() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Is the format going to emit events when sequence data is read?
getEliminateEnd() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getEliminateStart() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getEmail() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService: Get the email for QBlast.
getEmail() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Get the email for Entrez.
getEmblBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Get a default SequenceBuilderFactory for handling EMBL files.
getEMBLTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms: Getter for the EMBL term
getEMBLxmlTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms: Getter for the EMBLxml term
getEmission(Symbol, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP: This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache.
getEmissions(List) - Method in class org.biojava.bio.dp.twohead.EmissionCache
getEmissions(List, boolean) - Method in class org.biojava.bio.dp.twohead.EmissionCache: Retrieve the emission scores from the cache for every EmissionState for the specified symbols.
getEnd() - Method in interface org.biojava.bio.program.gff.GFFRecord: The end of this feature within the source sequence.
getEnd() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getEnd() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getEnd() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getEnd() - Method in class org.biojava.bio.seq.impl.SubSequence
getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
getEnd() - Method in class org.biojava.utils.automata.FiniteAutomaton
getEnd() - Method in interface org.biojava.utils.automata.NfaBuilder
getEnd() - Method in class org.biojava.utils.automata.NfaSubModel
getEnd() - Method in interface org.biojavax.bio.seq.Position: Returns the end of the range of bases this base could lie in.
getEnd() - Method in class org.biojavax.bio.seq.SimplePosition: Returns the end of the range of bases this base could lie in.
getEnd() - Method in interface org.biojavax.RankedDocRef: The end position in the sequence that this reference is referred to from.
getEnd() - Method in class org.biojavax.SimpleRankedDocRef: The end position in the sequence that this reference is referred to from.
getEndLabel() - Method in class org.biojava.utils.bytecode.InstructionVector
getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser: Get the current string indicating that a record has ended.
getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.RegexParser: Get the explicit end-of-record string.
getEntityResolver() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade: This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries.
getEntryByName(String) - Method in interface org.biojava.utils.candy.CandyVocabulary: It returns a selected vocabulary entry.
getEnvironment() - Method in class org.biojava.naming.ObdaContext
getEnvironmentProperties() - Method in class org.biojava.utils.process.ExternalProcess: Gets environment variables for the external process.
getEnzyme() - Method in interface org.biojava.bio.molbio.RestrictionSite: getEnzyme returns the enzyme which cuts at this site.
getEnzyme() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
getEnzyme(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getEnzyme returns an enzyme by name.
getEpsilon() - Method in class org.biojava.stats.svm.SMOTrainer
getEquates() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getErrorHandler() - Method in class org.biojava.bio.program.gff.GFFParser: Find the error handler used by this parser.
getErrorHandler() - Method in class org.biojava.bio.program.gff3.GFF3Parser: Find the error handler used by this parser.
getErrorHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
getErrorHandler() - Method in class org.biojava.utils.process.ExternalProcess: Gets the output error handler which is responsible for the standard error output of the external process.
getErrString() - Method in class org.biojava.utils.ExecRunner: Returns the error string if exec(String) was invoked.
getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return the overall E-value of this hit.
getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return the E-value of this sub-hit.
getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getEvent() - Method in class org.biojava.utils.ChangeListener.ChangeEventRecorder
getEvents() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property events.
getEvidenceAttrTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the evidence attr term
getEvidenceCategoryTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the evidence category term
getEvidenceDateTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the evidence date term
getEvidenceTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the evidence type term
getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getExonIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getExtendedName() - Method in interface org.biojavax.DocRefAuthor: Returns the extended version of the authors name.
getExtendedName() - Method in class org.biojavax.SimpleDocRefAuthor: Returns the extended version of the authors name.
getFactory() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Getter for property factory.
getFactory() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: Getter for property factory.
getFactory(String, FiniteAutomaton) - Method in class org.biojava.utils.automata.ArrayStateMachineToolkit
getFastaBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Get a default SequenceBuilderFactory for handling FASTA files.
getFeature() - Method in interface org.biojava.bio.program.gff.GFFRecord: The feature type filed.
getFeature() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter: Retrieve the current feature.
getFeature() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getFeature() - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
getFeature() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the feature this location is associated with.
getFeature() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the feature this location is associated with.
getFeature() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the feature this location is associated with.
getFeature(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
getFeatureDescTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the FeatureDesc term
getFeatureFilter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Return the current FeatureFilter.
getFeatureFilter() - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandler
getFeatureFilter(int) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Returns the ith FeatureFilter in this renderer.
getFeatureFromOriginal(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence: getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am including this method so that you can get the corresponding feature from the original sequence.
getFeatureHolder() - Method in interface org.biojava.bio.gui.sequence.FeatureSource
getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleFeature: A utility function to retrieve the feature holder delegate, creating it if necessary.
getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getFeatureID(Feature) - Method in class org.biojava.bio.program.xff.BasicXFFHelper
getFeatureID(Feature) - Method in interface org.biojava.bio.program.xff.XFFHelper
getFeatureListener() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler: Return the object which receives startFeature/endFeature notifications.
getFeatureListener() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: Return current feature listener
getFeatureListener() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: Return current feature listener
getFeatureOriginalTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the feature original term
getFeatureRealizer() - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory: Returns the FeatureRealizer set by "setFeatureRealizer".
getFeatureRefTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the feature ref term
getFeatureRelationshipSet() - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder: Returns the set of relationships held in this feature holder.
getFeatureRelationshipSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Returns the set of relationships held in this feature holder.
getFeatureRenderer() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer: getFeatureRenderer returns the currently active renderer.
getFeatures() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext: The features to render.
getFeatures() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel: getFeatures returns all of the Features belonging to the currently rendered Sequence.
getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePanel
getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePoster: Deprecated.
getFeatures() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext: The features to render.
getFeatures() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
getFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getFeatures() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getFeatures() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel: getFeatures returns all of the Features belonging to the currently rendered Sequence.
getFeatures() - Method in interface org.biojava.bio.seq.homol.Homology: Retrieve the set of features that mark homologous regions.
getFeatures() - Method in class org.biojava.bio.seq.homol.SimpleHomology: getFeatures returns the constituent HomologyFeatures which are also used as the keys in the alignment.
getFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
getFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder: Returns the list of features in this featureholder.
getFeatures(String, FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource: Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
getFeatures(FeatureFilter) - Method in interface org.biojava.bio.seq.distributed.DistDataSource: Get all features matching a FeatureFilter provided by this DistDataSource.
getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
getFeatureSet() - Method in interface org.biojavax.bio.seq.RichSequence: The features for this sequence.
getFeatureSet() - Method in class org.biojavax.bio.seq.ThinRichSequence: The features for this sequence.
getFeatureSource() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
getFeatureStatusTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the feature status term
getFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler: Get the template for the feature being constructed.
getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getFeatureType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getFeatureVariationTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the feature variation term
getField() - Method in class org.biojava.utils.ChangeType: Return a Field object where this change type is declared.
getFieldByName(String) - Method in interface org.biojava.utils.bytecode.CodeClass: Get a field by its name.
getFieldByName(String) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
getFieldByName(String) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
getFields() - Method in interface org.biojava.utils.bytecode.CodeClass: Get all fields accessible through this class.
getFields() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
getFields() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
getFile() - Method in interface org.biojava.bio.program.indexdb.Record: getFile returns the random access file in which the record belongs.
getFile() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getFile() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess: getFile returns the File wrapped.
getFile() - Method in interface org.biojava.bio.seq.db.Index: The file to retrieve from.
getFile() - Method in class org.biojava.bio.seq.db.SimpleIndex
getFile() - Method in class org.biojava.utils.io.RAF
getFileIndex(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
getFilePointer() - Method in class org.biojava.utils.io.CountedBufferedReader
getFilePointer() - Method in class org.biojava.utils.io.RandomAccessReader: getFilePointer returns the effective position of the pointer in the underlying RandomAccessFile.
getFiles() - Method in class org.biojava.bio.seq.db.BioIndex
getFiles() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getFiles() - Method in interface org.biojava.bio.seq.db.IndexStore: Retrieve the Set of files that are currently indexed.
getFiles() - Method in class org.biojava.bio.seq.db.TabIndexStore
getFill() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getFill() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
getFill() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
getFill() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
getFillColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer: Get the background color of the label area.
getFillPaint() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph: Returns the paint properties of this glyph.
getFilter() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
getFilter() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getFilter() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer: getFilter returns the current filter.
getFilter() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
getFinderName() - Method in interface org.biojava.utils.candy.CandyFinder: It returns a name of this vocabulary finder.
getFirstIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction: Getter for property firstIntActID.
getFirstOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair: gets the first orthologue in the orthology relationship.
getFirstOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getFitness() - Method in class org.biojavax.ga.impl.AbstractOrganism
getFitness() - Method in interface org.biojavax.ga.Organism: Returns the current fitness of this organism.
getFitnessFunction() - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
getFitnessFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm: Returns the fitness function, i.e. the class that computes the fitness of each organism in a population.
getFitnessFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getFloat() - Method in class org.biojava.utils.io.LargeBuffer
getFloat(long) - Method in class org.biojava.utils.io.LargeBuffer
getFloatOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Helper method for converting a Number-valued option into a float primitive.
getFont() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getFont() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext: Gets the Font attribute of the SequenceRenderContext object
getFont() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getFont() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getFormat() - Method in class org.biojava.bio.seq.db.BioIndex
getFormat() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getFormat() - Method in interface org.biojava.bio.seq.db.IndexStore: Retrieve the format of the index file.
getFormat() - Method in class org.biojava.bio.seq.db.TabIndexStore
getFormat(String) - Static method in class org.biojava.bio.program.formats.FormatTools: Attempt to find aformat for a format identifer string.
getForwarders(ChangeType) - Method in class org.biojava.utils.Unchangeable
getForwardRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getForwardRegex returns a regular expression which matches the forward strand of the recognition site.
getForwardTransitions() - Method in class org.biojava.bio.dp.DP
getForwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
getFrame() - Method in interface org.biojava.bio.program.gff.GFFRecord: The frame of the feature.
getFrame() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
getFrame() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getFrame() - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter: Retrieve the reading frame this filter matches.
getFrame() - Method in interface org.biojava.bio.seq.Frame: A method to get the frame information of the implementing object
getFrame() - Method in class org.biojava.bio.seq.FramedFeature.ReadingFrame
getFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
getFrequency() - Method in interface org.biojava.bio.symbol.CodonPref: returns a Distribution giving the frequency of codons (sums to one over the totality of codons).
getFrequency() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getFrequencyForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref: returns a Distribution giving the frequency of synonymous codons.
getFrequencyForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref
getFrequencyOfNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution: returns the frequency with which synonymous codons start with a specified pair of bases.
getFrom() - Method in exception org.biojava.bio.dp.IllegalTransitionException
getFTIdTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the FTId term
getFullName() - Method in class org.biojava.utils.bytecode.CodeField: Get the fully qualified name of the field.
getFullName() - Method in interface org.biojava.utils.bytecode.CodeMethod: The fully qualified name for this class
getFullName() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
getFuzzyEnd() - Method in interface org.biojavax.bio.seq.Position: Returns true if the position has a fuzzy end.
getFuzzyEnd() - Method in class org.biojavax.bio.seq.SimplePosition: Returns true if the position has a fuzzy end.
getFuzzyStart() - Method in interface org.biojavax.bio.seq.Position: Returns true if the position has a fuzzy start.
getFuzzyStart() - Method in class org.biojavax.bio.seq.SimplePosition: Returns true if the position has a fuzzy start.
getG() - Method in class org.biojava.bio.molbio.DNAComposition: Get the relative compositon of 'G'.
getG() - Method in class org.biojava.bio.proteomics.StructureTools
getGap() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getGapExt() - Method in class org.biojava.bio.alignment.NeedlemanWunsch: Returns the current expenses of any extension of a gap operation.
getGapExt() - Method in class org.biojava.bio.alignment.SmithWaterman
getGapSymbol() - Method in class org.biojava.bio.symbol.AbstractAlphabet
getGapSymbol() - Method in interface org.biojava.bio.symbol.Alphabet: Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
getGapSymbol() - Static method in class org.biojava.bio.symbol.AlphabetManager: Get the special `gap' Symbol.
getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
getGapSymbol(List) - Static method in class org.biojava.bio.symbol.AlphabetManager: Get the gap symbol appropriate to this list of alphabets.
getGenbankBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Get a default SequenceBuilderFactory for handling GenBank files.
getGenBankTerm() - Static method in class org.biojavax.bio.seq.io.GenbankFormat.Terms: Getter for the Genbank term
getGeneNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the GeneName term
getGenerateSequenceHeader() - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Discover if per-sequence header lines will be generated.
getGeneration() - Method in interface org.biojavax.ga.GeneticAlgorithm
getGeneration() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm: The current generation
getGeneSynonymTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the GeneSynonym term
getGeneticCode() - Method in interface org.biojava.bio.symbol.CodonPref: the genetic code that this codon preference is based on.
getGeneticCode() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Returns the genetic code of this taxon, which may be null if not known.
getGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Returns the genetic code of this taxon, which may be null if not known.
getGeneticCode(int) - Static method in class org.biojava.bio.seq.RNATools: Retrieve a TranslationTable by number.
getGeneticCode(String) - Static method in class org.biojava.bio.seq.RNATools: Retrieve a TranslationTable by name.
getGeneticCodeName() - Method in interface org.biojava.bio.symbol.CodonPref: get the name of the genetic code
getGeneticCodeName() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getGeneticCodeNames() - Static method in class org.biojava.bio.seq.RNATools: Retrieve a Set containing the name of each genetic code.
getGenomicTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms: Getter for the Ensembl-specific 'genomic' term
getGenpeptBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Get a default SequenceBuilderFactory for handling Genpept files.
getGlu_C_bicarbonate() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getGlu_C_phosphate() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getGlyphForFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Returns the Glyph object which is assigned to the given feature filter.
getGonnet() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the GONNET amino acid substitution matrix.
getGraphics() - Method in interface org.biojava.bio.gui.LogoContext
getGroupAttributes() - Method in interface org.biojava.bio.program.gff.GFFRecord: A Map containing the group / attribute information.
getGroupAttributes() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getGroupOrder(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getH() - Method in class org.biojava.bio.proteomics.StructureTools
getHandler(String, String) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler: Retrieve a FilterHandler for the specified tag name.
getHandler(SeqSimilarityStAXAdapter) - Method in interface org.biojava.bio.program.ssbind.StAXHandlerFactory: getHandler returns an appropriate StAXContentHandler implementation containing a reference to a parent context.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.agave.StAXHandlerFactory: Return a suitable StAX content handler.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game.StAXHandlerFactory: Return a suitable StAX content handler.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game12.StAXHandlerFactory: Return a suitable StAX content handler.
getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler: get iterator for current stack starting at the position below mine.
getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler: get iterator for current stack starting at the position below mine.
getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: return iterator to callbackStack
getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: return iterator to callbackStack
getHeader() - Method in class org.biojavax.bio.seq.io.FastaFormat
getHeaderDefinitions() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer: Returns the appropriate style and javascript definitions for this renderer.
getHeight() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Returns the height of the whole graphic (in pixels).
getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer: getHeightScaling returns the state of the height scaling policy.
getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer: getHeightScaling returns the state of the height scaling policy.
getHibernateSession() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
getHibernateSession() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
getHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
getHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
getHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult: Return all hits in this sequence similarity search result.
getHits() - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
getHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getHomologeneID() - Method in interface org.biojava.bio.program.homologene.Orthologue: get the Homologene ID.
getHomologeneID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getHomology() - Method in interface org.biojava.bio.seq.homol.HomologyFeature
getHomology() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
getHorizontalScale() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Returns the in-use horizontal scale factor.
getI() - Method in class org.biojava.bio.proteomics.StructureTools
getId() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getId() - Method in class org.biojavax.bio.seq.SimplePosition: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.SimpleBioEntry: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.SimpleBioEntryRelationship: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Gets the Hibernate ID.
getId() - Method in class org.biojavax.ontology.SimpleComparableOntology: Gets the Hibernate ID.
getId() - Method in class org.biojavax.ontology.SimpleComparableTerm: Gets the Hibernate ID.
getId() - Method in class org.biojavax.ontology.SimpleComparableTriple: Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleComment: Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleCrossRef: Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleDocRef: Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleNamespace: Gets the Hibernate ID.
getID() - Method in interface org.biojava.bio.program.indexdb.Record: getID returns the primary identifier of the record.
getID() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getID() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster: The public unigene ID.
getID() - Method in interface org.biojava.bio.seq.db.Index: The ID of the sequence at this position in this file.
getID() - Method in class org.biojava.bio.seq.db.SimpleIndex
getID() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
getID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction: Getter for property ID.
getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getIdAlias(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getIdentifier() - Method in interface org.biojava.utils.lsid.Identifiable: Return the identifier of this object.
getIdentifier() - Method in interface org.biojavax.bio.BioEntry: Returns the identifier of this bioentry.
getIdentifier() - Method in class org.biojavax.bio.SimpleBioEntry: Returns the identifier of this bioentry.
getIdentifier() - Method in interface org.biojavax.ontology.ComparableTerm: Returns the (optional) identifier associated with this term.
getIdentifier() - Method in class org.biojavax.ontology.SimpleComparableTerm: Returns the (optional) identifier associated with this term.
getIdentity() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the IDENTITY amino acid substitution matrix.
getIDMaker() - Method in class org.biojava.bio.seq.db.HashSequenceDB: Retrieve the IDMaker associated with this database.
getIDMaker() - Method in class org.biojavax.bio.db.HashRichSequenceDB: Retrieve the IDMaker associated with this database.
getIDs() - Method in class org.biojava.bio.seq.db.BioIndex
getIDs() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getIDs() - Method in interface org.biojava.bio.seq.db.IndexStore: Retrieve the set of all current IDs.
getIDs() - Method in class org.biojava.bio.seq.db.TabIndexStore
getIfFalse() - Method in class org.biojava.utils.bytecode.IfExpression
getIfInstruction() - Method in class org.biojava.utils.bytecode.IfExpression
getIfTrue() - Method in class org.biojava.utils.bytecode.IfExpression
getImage(int, int) - Method in class org.biojava.bio.program.abi.ABITrace: Returns a BufferedImage that represents the entire trace.
getImageMap() - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer: getImageMap returns the current image map.
getImageMap() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer: getImageMap returns the current image map.
getImageMap() - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer: getImageMap returns the current image map.
getImplementationNames(Class) - Static method in class org.biojava.utils.Services: Return a Set of names of implementations of the given service interface in the classloader from which BioJava was loaded.
getImplementationNames(Class, ClassLoader) - Static method in class org.biojava.utils.Services: Return a List of names of implementations of the given service interface available in a given classloader.
getIndex(double) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext: Calculate the position in the sequence relating to the angle.
getIndex(double) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
getIndexStore() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB: Retrieve the IndexStore.
getInitialContext(Hashtable) - Method in class org.biojava.naming.ObdaInitialContextFactory
getInnerMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
getInnerMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
getInput() - Method in interface org.biojava.utils.process.OutputHandler: Gets the input stream.
getInput() - Method in class org.biojava.utils.process.StreamPipe: Gets the input stream
getInput() - Method in class org.biojava.utils.process.WriterOutputHandler: Gets the input stream.
getInputHandler() - Method in class org.biojava.utils.process.ExternalProcess: Gets the input handler which is responsible for the standard input of the external process.
getInputStream(File) - Method in class org.biojava.utils.io.InputStreamProvider: get an InputStream for the file
getInputStream(String) - Static method in class org.biojava.utils.io.FlatFileCache
getInputStream(String) - Method in class org.biojava.utils.io.InputStreamProvider: get an InputStream for this file
getInputStream(URL) - Method in class org.biojava.utils.io.InputStreamProvider
getINSDseqTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms: Getter for the INSDseq term
getInsert() - Method in class org.biojava.bio.alignment.NeedlemanWunsch: Returns the current expenses of a single insert operation.
getInsert() - Method in class org.biojava.bio.alignment.SmithWaterman
getInsert(int) - Method in class org.biojava.bio.dp.ProfileHMM: Retrieves the insert state at column indx.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.

Returns the id value created during the last insert command.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.HypersonicDBHelper: Deprecated.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper: Deprecated.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper: Deprecated.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper: Deprecated.
getInstance() - Static method in class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity: Retrieve the singleton instance of this class.
getInstance() - Static method in class org.biojava.bio.dist.IgnoreCountsTrainer: Returns the global singleton instance of the IgnoreCountsTrainer.
getInstance() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getInstance() - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory
getInstance() - Static method in class org.biojava.bio.symbol.DoubleAlphabet: Retrieve the single DoubleAlphabet instance.
getInstance() - Static method in class org.biojava.bio.symbol.IntegerAlphabet: Retrieve the single IntegerAlphabet instance.
getInstance() - Static method in class org.biojava.bio.taxa.EbiFormat: Deprecated.
getInstance() - Static method in class org.biojava.naming.ObdaUriParser
getInstance() - Static method in class org.biojava.utils.io.FlatFileCache
getInstance() - Static method in class org.biojava.utils.walker.WalkerFactory
getInstance(Class) - Static method in class org.biojava.utils.walker.WalkerFactory: Make a WalkerFactory that handles a Visitor for a class of type typeClazz.
getInstance(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.
getInstance(FiniteAlphabet, SoftMaskedAlphabet.MaskingDetector) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any Symbol is soft masked or not.
getInt() - Method in class org.biojava.utils.io.LargeBuffer
getInt(long) - Method in class org.biojava.utils.io.LargeBuffer
getIntegerOntology() - Static method in class org.biojava.ontology.OntoTools: Get the Ontology that defines integers.
getInteractions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property interactions.
getInterfaces() - Method in interface org.biojava.utils.bytecode.CodeClass
getInterfaces() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
getInterfaces() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
getInternalSymbolList() - Method in interface org.biojavax.bio.seq.RichSequence: A special function that returns the SymbolList that this RichSequence is based around.
getInternalSymbolList() - Method in class org.biojavax.bio.seq.SimpleRichSequence: A special function that returns the SymbolList that this RichSequence is based around.
getInternalSymbolList() - Method in class org.biojavax.bio.seq.ThinRichSequence: A special function that returns the SymbolList that this RichSequence is based around.
getIntFromSymbolList(SymbolList, int) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools: Retrieves, unwraps, and returns an int from a SymbolList containing IntegerAlphabet.IntegerSymbols.
getIntOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Helper method for converting a Number-valued option into an int primitive.
getInvTransform() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic: Returns a new AffineTransform describing the transformation from output space to chromatogram space.
getIsoelectricPoint(SymbolList) - Static method in class org.biojava.bio.proteomics.IsoelectricPointCalc: Static public method to compute the pI for a polypeptide in denaturating and reduced conditions with both free ends.
getIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property isoforms.
getIsoIDs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform: Getter for property isoIDs.
getIsoschizomers(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getIsoschizomers returns an unmodifable set of the isoschizomers of this enzyme.
getItem() - Method in interface org.biojava.stats.svm.ItemValue
getItem() - Method in class org.biojava.stats.svm.SimpleItemValue
getItems() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getIterator() - Method in class org.biojava.utils.ListTools.Doublet
getIterator() - Method in class org.biojava.utils.ListTools.Triplet
getJName() - Method in interface org.biojava.utils.bytecode.CodeClass
getJName() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
getJName() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
getJoiner() - Method in class org.biojava.bio.program.tagvalue.Aggregator
getJoinStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper: Deprecated.

Returns the an object indicating the style of table joining that this database should employ.
getJoinStyle() - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper: Deprecated.
getJoinTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation: Getter for the "join" term
getJournalReference() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets a reference to the journal which published the article about the AAindex entry.
getKernel() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
getKernel() - Method in interface org.biojava.stats.svm.SVMClassifierModel
getKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
getKernel() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier: Retrieve the currently used kernel
getKernelValue(int, int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getKey() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.HasAnnotation
getKey() - Method in class org.biojava.utils.cache.KeyedWeakReference
getKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
getKeys() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getKeys() - Method in class org.biojava.bio.program.tagvalue.Index2Model
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getKeyword(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getKeywordTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the keyword term
getKineticsNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property kineticsNote.
getKmpNextTable() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch: Returns the table of border lengths
getKMs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property KMs.
getLabel() - Method in interface org.biojava.bio.alignment.AlignmentElement
getLabel() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
getLabel() - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
getLabel() - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
getLabel() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState: return the label of this class.
getLabel() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
getLabel() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
getLabel() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction: Getter for property label.
getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getLabel(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getLabelGlyph(SequenceRenderContext, FontRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
getLabelMaker() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
getLabels() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
getLabels() - Method in interface org.biojava.bio.alignment.Alignment: The list of SymbolLists in the alignment.
getLabels() - Method in class org.biojava.bio.alignment.FlexibleAlignment: getLabels will return a list of labels in left to right order
getLabels() - Method in class org.biojava.bio.alignment.SimpleAlignment
getLabels() - Method in class org.biojava.bio.dp.SimpleStatePath
getLabels() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
getLabels() - Method in class org.biojava.bio.symbol.RelabeledAlignment
getLabelsAt(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
getLambda() - Method in class org.biojava.stats.svm.DiagonalAddKernel: Retrieve the scale factor.
getLast() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder: Get the last complete annotation built.
getLastScore() - Method in class org.biojava.bio.dp.AbstractTrainer
getLastScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getLeader() - Method in class org.biojava.utils.ListTools.SeriesList
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel: getLeadingBorder returns the leading border of the primary sequence.
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel: Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster: Deprecated.

Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.
getLeadingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext: Gets the LeadingBorder attribute of the SequenceRenderContext object.
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel: getLeadingBorder returns the leading border.
getLeadingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getLeftValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Gets the left value.
getLeftValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Gets the left value.
getLength() - Method in interface org.biojava.bio.program.indexdb.Record: getLength returns the length of the record in bytes.
getLength() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getLength() - Method in class org.biojava.bio.search.SeqContentPattern: Get the current length.
getLength() - Method in interface org.biojava.bio.seq.db.Index: The entry can be slurped out of the file by grabbing length bytes from start.
getLength() - Method in class org.biojava.bio.seq.db.SimpleIndex
getLength() - Method in class org.biojava.bio.symbol.CircularLocation
getLength() - Method in class org.biojava.utils.RepeatedCharSequence
getLevel() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: return current stack level.
getLevel() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: return current stack level.
getLimit() - Method in class org.biojava.utils.cache.FixedSizeCache
getLine() - Method in exception org.biojava.utils.ParserException: Get the text of the line where the exception occured.
getLineNumber() - Method in exception org.biojava.utils.ParserException: Get the line number in the stream where this exception occured.
getLines() - Method in class org.biojava.bio.gui.sequence.SequencePoster: Deprecated.

Retrieve the number of lines that the sequence will be rendered over.
getLineWidth() - Method in class org.biojava.bio.program.phred.PhredFormat: Retrive the current line width.
getLineWidth() - Method in class org.biojava.bio.seq.io.FastaFormat: Deprecated.

Retrive the current line width.
getLineWidth() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Retrive the current line width.
getLineWidth() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Retrive the current line width.
getListener() - Method in class org.biojava.bio.program.tagvalue.ParserListener: getListener returns the listener of the pair.
getListener() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState: return the TagValueListener assigned to this State.
getListener() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
getListener(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getListeners(ChangeType) - Method in class org.biojava.utils.Unchangeable
getLITDBEntryNumbers() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the list of literature database identifiers for the AAindex entry.
getLoc() - Method in interface org.biojava.bio.alignment.AlignmentElement
getLoc() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
getLocation() - Method in class org.biojava.bio.program.indexdb.BioStore: getLocation returns the directory where the index is located.
getLocation() - Method in interface org.biojava.bio.seq.Feature: The location of this feature.
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
getLocation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getLocation() - Method in class org.biojava.bio.seq.RemoteFeature.Region: Retrieve the Location of the Region.
getLocation() - Method in class org.biojavax.bio.seq.SimpleRichFeature: The location of this feature.
getLocation() - Method in interface org.biojavax.DocRef: Returns a textual description of the document reference.
getLocation() - Method in interface org.biojavax.RankedDocRef: If this object was constructed using a location instead of two integers, then this method will return that location.
getLocation() - Method in class org.biojavax.SimpleDocRef: Returns a textual description of the document reference.
getLocation() - Method in class org.biojavax.SimpleRankedDocRef
getLocationHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getLocationSequenceTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the location seq term
getLocator() - Method in exception org.biojava.utils.ParserException: Get a locator for the stream which caused this exception.
getLocusID() - Method in interface org.biojava.bio.program.homologene.Orthologue: get the locus ID associated with this orthologue.
getLocusID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getLogoFont() - Method in class org.biojava.bio.gui.TextBlock: Retrieve the current font.
getLogoFont() - Method in class org.biojava.bio.gui.TextLogoPainter: Retrieve the current font.
getLogoPainter() - Method in class org.biojava.bio.gui.DistributionLogo: Retrieve the current logo painter.
getLong() - Method in class org.biojava.utils.io.LargeBuffer
getLong(long) - Method in class org.biojava.utils.io.LargeBuffer
getLSID() - Method in class org.biojava.bio.program.formats.Embl
getLSID() - Method in class org.biojava.bio.program.formats.Enzyme
getLSID() - Method in interface org.biojava.bio.program.formats.Format: Retrieve the LSID associated with this format.
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Compound
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Reaction
getLSID() - Method in class org.biojava.bio.program.formats.Swissprot
getLys_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getMagicalState() - Method in class org.biojava.bio.program.tagvalue.StateMachine
getMagicalState(Alphabet, int) - Static method in class org.biojava.bio.dp.MagicalState
getMapAll() - Method in class org.biojava.bio.molbio.RestrictionMapper: getMapAll returns whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it.
getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMapLocation(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMapper() - Method in class org.biojava.bio.AnnotationRenamer: getMapper returns the TagMapper being used to remap the Annotation.
getMapper() - Method in class org.biojava.bio.program.tagvalue.TagRenamer: Retrieve the mapper used to rename tags
getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMapPosition(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMapType() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getMaskedAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Gets the Alphabet upon which masking is being applied
getMaskingDetector() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Getter for the MaskingDetector
getMass(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc: Get the Mass of this peptide.
getMass(SymbolList, String, boolean) - Static method in class org.biojava.bio.proteomics.MassCalc: getMass calculates the mass of this peptide.
getMatch() - Method in class org.biojava.bio.alignment.NeedlemanWunsch: Returns the current expenses of a single match operation.
getMatch() - Method in class org.biojava.bio.alignment.SmithWaterman
getMatch() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix: Return the MATCH amino acid substitution matrix.
getMatch(int) - Method in class org.biojava.bio.dp.ProfileHMM: Retrieve the match state at column indx.
getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchAlign(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMatchChar() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchDesc(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMatches() - Method in class org.biojava.bio.dp.SimpleEmissionState
getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getMatches() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
getMatches() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getMatches() - Method in interface org.biojava.bio.symbol.Symbol: The alphabet containing the symbols matched by this ambiguity symbol.
getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMatrixData(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getMatrixData(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
getMatrixLabels() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getMatrixLabels() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
getMax() - Method in class org.biojava.bio.alignment.SubstitutionMatrix: The maximum score in this matrix.
getMax() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
getMax() - Method in interface org.biojava.bio.chromatogram.Chromatogram: Gets the max intensity from all the traces.
getMax() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getMax() - Method in class org.biojava.bio.symbol.CircularLocation: This will give you the coordinate of the maximum point contained by this Location.
getMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
getMax() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
getMax() - Method in interface org.biojava.bio.symbol.Location: The maximum position contained.
getMax() - Method in class org.biojava.bio.symbol.PointLocation
getMax() - Method in class org.biojava.bio.symbol.RangeLocation
getMax() - Method in class org.biojavax.bio.seq.EmptyRichLocation: The maximum position contained.
getMax() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: The maximum position contained.
getMax() - Method in class org.biojavax.bio.seq.SimpleRichLocation: The maximum position contained.
getMax(AtomicSymbol) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
getMax(AtomicSymbol) - Method in interface org.biojava.bio.chromatogram.Chromatogram: Gets the max intensity on the trace for the specified nucleotide.
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver: Resolves the maximum possible base for this position.
getMax(Position) - Method in interface org.biojavax.bio.seq.PositionResolver: Resolves the maximum possible base for this position.
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver: Resolves the maximum possible base for this position.
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver: Resolves the maximum possible base for this position.
getMaxCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern: Get the maximum counts required for a symbol.
getMaxCrossOvers() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
getMaxCrossOvers() - Method in interface org.biojavax.ga.functions.CrossOverFunction
getMaxCrossOvers() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
getMaxGenerations() - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
getMaxPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the end position of this location.
getMaxPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: Retrieves the end position of this location.
getMaxPosition() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the end position of this location.
getMaxPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the end position of this location.
getMaxRunTimeExceeded() - Method in class org.biojava.utils.ExecRunner: Returns whether the maximum runtime was exceeded or not.
getMaxRunTimeSecs() - Method in class org.biojava.utils.ExecRunner: Returns the maximum run time in seconds for this object.
getMaxScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore: getMaxScore returns the maximum score accepted.
getMaxSize() - Method in class org.biojava.utils.cache.FixedSizeMap
getMaxValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getMergeAnnotation() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
getMerged() - Method in class org.biojava.bio.annodb.MergingAnnotationDB: Return a list of merged DBs.
getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser: See if tags are being merged.
getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser: Report whether empty tags will be treated as continuations of the last non -empty tag.
getMessage() - Method in class org.biojava.utils.ParseErrorEvent: Find the message about this event
getMetaData() - Method in class org.biojava.bio.program.indexdb.BioStore
getMetaData() - Method in interface org.biojava.bio.program.indexdb.IndexStore: getMetaData returns a data structure which represents an OBDA "config.dat" flatfile indexing configuration file.
getMethod() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory: Get the Method used.
getMethod(String, CodeClass[]) - Method in interface org.biojava.utils.bytecode.CodeClass: Get a method by name and argument list.
getMethod(String, CodeClass[]) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
getMethod(String, CodeClass[]) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
getMethods() - Method in interface org.biojava.utils.bytecode.CodeClass: Get all methods declared by this class and its super classes, removing all super class methods that are over ridden.
getMethods() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
getMethods() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
getMethodsByName(String) - Method in interface org.biojava.utils.bytecode.CodeClass: Get the name of all methods that could be invoked through this class with a given name.
getMethodsByName(String) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
getMethodsByName(String) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
getMin() - Method in class org.biojava.bio.alignment.SubstitutionMatrix: The minimum score of this matrix.
getMin() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getMin() - Method in class org.biojava.bio.symbol.CircularLocation: This will give you the coordinate of the minimum point contained by this Location.
getMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
getMin() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
getMin() - Method in interface org.biojava.bio.symbol.Location: The minimum position contained.
getMin() - Method in class org.biojava.bio.symbol.PointLocation
getMin() - Method in class org.biojava.bio.symbol.RangeLocation
getMin() - Method in class org.biojavax.bio.seq.EmptyRichLocation: The minimum position contained.
getMin() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: The minimum position contained.
getMin() - Method in class org.biojavax.bio.seq.SimpleRichLocation: The minimum position contained.
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver: Resolves the minimum possible base for this position.
getMin(Position) - Method in interface org.biojavax.bio.seq.PositionResolver: Resolves the minimum possible base for this position.
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver: Resolves the minimum possible base for this position.
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver: Resolves the minimum possible base for this position.
getMinCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern: Get the minimum counts required for a symbol.
getMinIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet: get the lowest level of identity observed in this Group
getMinIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
getMinimumLeader(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer: getMinimumLeader returns the maximum value of getMinimumLeader() for a list of SequenceRenderers.
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
getMinimumLeader(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer: Retrieve the minimum leading distance for this renderer when rendering src.
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
getMinimumTrailer(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer: getMinimumTrailer returns the maximum value of getMinimumTrailer() for a list of SequenceRenderers.
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
getMinimumTrailer(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer: Retrieve the minimum trailing distance for this renderer when rendering src.
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
getMinimumWidth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.LabelRenderer: Retrieve the minimum space required to render the label.
getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
getMinPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the start position of this location.
getMinPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: Retrieves the start position of this location.
getMinPosition() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the start position of this location.
getMinPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the start position of this location.
getMinScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore: getMinScore returns the minimum score accepted.
getMinValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getMismatches() - Method in class org.biojava.bio.search.MaxMismatchPattern
getMissing() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
getMissing() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
getMitoGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Returns the mitochondrial genetic code of this taxon, which may be null if not known.
getMitoGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Getter for property mitoGeneticCode.
getModel() - Method in class org.biojava.bio.dp.DP
getModel() - Method in interface org.biojava.bio.dp.ModelInState: The model that is inside this state.
getModel() - Method in class org.biojava.bio.dp.SimpleModelInState
getModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
getModifiable() - Method in class org.biojava.utils.MergingSet
getModifiers() - Method in interface org.biojava.utils.bytecode.CodeClass: Get the modifiers associated with the class.
getModifiers() - Method in class org.biojava.utils.bytecode.CodeField: Get the moddifiers applied to this field.
getModifiers() - Method in interface org.biojava.utils.bytecode.CodeMethod: Get the modifiers, such as PUBLIC, ABSTRACT and so on
getModifiers() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass
getModifiers() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
getModifiers() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass
getMolecularWeight() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property molecularWeight.