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.