Index (biojava-legacy 1.9.5 API)

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

A

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

B

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

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

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

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

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

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

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

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

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

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

C

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

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

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

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

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

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

D

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

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

E

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

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

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

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

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

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

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

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

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

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

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

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

F

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

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

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

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

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

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

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

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

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

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

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

G

g() - Static method in class org.biojava.bio.seq.DNATools

g() - Static method in class org.biojava.bio.seq.NucleotideTools

g() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid Glycine

g() - Static method in class org.biojava.bio.seq.RNATools

GACross - Interface in org.biojavax.ga.functions

Holds the results of a CrossOver event, objects of this type are made by CrossOverFunctions

GACrossResult - Interface in org.biojavax.ga.functions

Holds the results of a CrossOver event, objects of this type are made by CrossOverFunctions

GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler

GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler

Description of the Field

GAME_ASPECT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAspectHandler

GAME_ASPECT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler

GAME_DBXREF_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler

Description of the Field

GAME_DBXREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler

GAME_DESCRIPTION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler

GAME_FEATURE_SET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler

Description of the Field

GAME_FEATURE_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler

Description of the Field

GAME_FEATURESET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler

GAME_FEATURESET_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler

GAME_FEATURESPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler

GAME_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEGeneHandler

Description of the Field

GAME_GENE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEGenePropHandler

GAME_MAP_POS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler

GAME_NAME_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMENamePropHandler

GAME_PROPERTY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEPropertyHandler

Description of the Field

GAME_RESIDUES_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler

GAME_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqHandler

Description of the Field

GAME_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqPropHandler

GAME_SEQ_REL_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler

Description of the Field

GAME_SEQREL_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler

GAME_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESpanHandler

Description of the Field

GAME_SPAN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESpanPropHandler

GAME_TYPE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMETypePropHandler

GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game

Handles the GAME <annotation> element

GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game12

Handles the GAME <annotation> element

GAMEAspectHandler - Class in org.biojava.bio.seq.io.game12

Handles the GAME <aspect> element

GAMEAspectPropHandler - Class in org.biojava.bio.seq.io.game

Handles the GAME <aspect> element

GAMEDbxrefHandler - Class in org.biojava.bio.seq.io.game12

Handles the GAME <dbxref> element

GAMEDbxrefPropHandler - Class in org.biojava.bio.seq.io.game

Deals with database crossreferences

GAMEDbxrefPropHandler.DbXrefElement - Class in org.biojava.bio.seq.io.game

GAMEDescriptionPropHandler - Class in org.biojava.bio.seq.io.game

StAX handler for GAME <description> elements.

GAMEDescriptionPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler

GAMEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.game

An interface that can be tested for by nested handlers when trying to do a callback.

GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game

Handles the <feature_set> element

GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game12

Handles the GAME <feature_set> element this element is used to represent transcripts.

GAMEFeatureSetPropHandler - Class in org.biojava.bio.seq.io.game

Handles the GAME element

GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game

Handles the <feature_span> element

GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game12

Handles the GAME <feature_span> element

GAMEFeatureSpanHandler.SeqRelHandler - Class in org.biojava.bio.seq.io.game12

GAMEFormat - Class in org.biojava.bio.seq.io

A rudimentary read-only GAME 1.2 Format object.

GAMEFormat() - Constructor for class org.biojava.bio.seq.io.GAMEFormat

GAMEGeneHandler - Class in org.biojava.bio.seq.io.game12

Handles the GAME <annotation> element

GAMEGenePropHandler - Class in org.biojava.bio.seq.io.game

Handles the GAME <gene> element

GAMEHandler - Class in org.biojava.bio.seq.io.game

Handles the root GAME element

GAMEHandler - Class in org.biojava.bio.seq.io.game12

Handles the root GAME element

GAMEHandler() - Constructor for class org.biojava.bio.seq.io.game.GAMEHandler

GAMEHandler(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.game12.GAMEHandler

Constructor for the GAMEHandler object

GAMEMapPosPropHandler - Class in org.biojava.bio.seq.io.game

Handles the GAME <map_position> element Currently, it just ignores it!

GAMENameCallbackItf - Interface in org.biojava.bio.seq.io.game

An interface that can be tested for by nested handlers when trying to do a callback.

GAMENamePropHandler - Class in org.biojava.bio.seq.io.game

StAX handler for the GAME <name> element.

GAMENamePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMENamePropHandler

GAMEPropertyHandler - Class in org.biojava.bio.seq.io.game12

Handles the GAME <dbxref> element

GAMEResiduesPropHandler - Class in org.biojava.bio.seq.io.game

StAX handler for GAME <residues> elements.

GAMEResiduesPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler

GAMESeqHandler - Class in org.biojava.bio.seq.io.game12

Handles the GAME <seq> element

GAMESeqPropHandler - Class in org.biojava.bio.seq.io.game

Handles the GAME <seq> element

GAMESeqRelHandler - Class in org.biojava.bio.seq.io.game12

Handles the GAME <> element

GAMESeqRelPropHandler - Class in org.biojava.bio.seq.io.game

Handles the GAME <aspect> element

GAMESpanHandler - Class in org.biojava.bio.seq.io.game12

Handles the GAME <> element.

GAMESpanPropHandler - Class in org.biojava.bio.seq.io.game

Handles the GAME <span> element Currently, it just ignores it!

GAMETranscriptCallbackItf - Interface in org.biojava.bio.seq.io.game

An interface that can be tested for by nested handlers when trying to do a callback.

GAMETypePropHandler - Class in org.biojava.bio.seq.io.game

StAX handler for GAME <type> elements.

GAMETypePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMETypePropHandler

GapDistribution - Class in org.biojava.bio.dist

This distribution emits gap symbols.

GapDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.GapDistribution

Get a GapDistribution for an alphabet.

GappedContext() - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext

GappedRenderer - Class in org.biojava.bio.gui.sequence

A renderer that will display a gapped sequence as a discontinuous series of regions.

GappedRenderer() - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer

GappedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer

GappedSequence - Interface in org.biojava.bio.seq

Extension of GappedSymbolList which also projects features into the gapped coordinate system.

GappedSymbolList - Interface in org.biojava.bio.symbol

This extends SymbolList with API for manipulating, inserting and deleting gaps.

gappedToLocation(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList

Translates a Location from the gapped view into the underlying sequence.

gappedView(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools

Create a new gapped sequence for a sequence.

GAPS - Static variable in interface org.biojava.bio.alignment.EditableAlignment

GAStoppingCriteria - Interface in org.biojavax.ga

Used by a GeneticAlgorithm.run() method to determine when the algorithm should stop

GAStoppingCriteria.MaximumGeneration - Class in org.biojavax.ga

Simple Implementation of GAStoppingCriteria, signals a GeneticAlgorithm to stop after n generations

GATools - Class in org.biojavax.ga.util

Utility methods for the GA library

GATools() - Constructor for class org.biojavax.ga.util.GATools

GCG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

GCG indicates that the sequence format is GCG.

ge - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter

GENBANK - Static variable in class org.biojava.bio.program.tagvalue.LineSplitParser

A LineSplitParser pre-configured to process GENBANK-style flat files.

GENBANK - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

GENBANK indicates that the sequence format is GENBANK.

GENBANK_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

GENBANK_DNA premade GENBANK | AA.

GENBANK_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

GENBANK_DNA premade GENBANK | DNA.

GENBANK_FORMAT - Static variable in class org.biojavax.bio.seq.io.GenbankFormat

The name of this format

GENBANK_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

GENBANK_DNA premade GENBANK | RNA.

GenbankFileFormer - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead

GenbankFileFormer() - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer

Deprecated.

Creates a new GenbankFileFormer using System.out stream.

GenbankFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer

Deprecated.

Creates a new GenbankFileFormer using the specified stream.

GenbankFormat - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io.GenbankFormat

GenbankFormat - Class in org.biojavax.bio.seq.io

Format reader for GenBank files.

GenbankFormat() - Constructor for class org.biojava.bio.seq.io.GenbankFormat

Deprecated.

GenbankFormat() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat

GenbankFormat.Terms - Class in org.biojavax.bio.seq.io

Implements some GenBank-specific terms.

GenbankLocationParser - Class in org.biojavax.bio.seq.io

Parses Genbank location strings into RichLocation objects.

GenbankProcessor - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead

GenbankProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor

Deprecated.

GenbankProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor

Deprecated.

GenbankProcessor.Factory - Class in org.biojava.bio.seq.io

Deprecated.

Factory which wraps sequence builders in a GenbankProcessor

GenbankRichSequenceDB - Class in org.biojavax.bio.db.ncbi

This class contains functions accessing DNA sequences in Genbank format.

GenbankRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

The default constructor delegates to the parent class.

GenbankSequenceDB - Class in org.biojava.bio.seq.db

This class contains functions accessing DNA sequences in Genbank format.

GenbankSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenbankSequenceDB

GenbankXmlFormat - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io.INSDseqFormat

GenbankXmlFormat() - Constructor for class org.biojava.bio.seq.io.GenbankXmlFormat

Deprecated.

GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat

GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat

GENELOCATION_NAME_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat

GENELOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat

GenEmblFeatureComparator - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead

GenEmblPropertyComparator - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead

GENENAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

generate() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Generates a comment string based on the current values of the internal fields.

generate(int) - Method in class org.biojava.bio.dp.DP

Generates an alignment from a model.

generateAuthorString(List<DocRefAuthor>, boolean) - Static method in class org.biojavax.DocRefAuthor.Tools

Takes a set of authors and creates a comma-separated string.

generateBackwardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler

generateCallboxes() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Precomputes the Rectangle2Ds that are the in-memory representation of the callboxes.

generateChangeSupport() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

generateChangeSupport() - Method in class org.biojava.utils.AbstractChangeable

Called the first time a ChangeSupport object is needed.

generateCrossProductAlphaFromName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager

Generates a new CrossProductAlphabet from the give name.

GeneratedClassLoader - Class in org.biojava.utils.bytecode

A class loader that actually produces real Java classes from GeneratedCodeClass instances.

GeneratedClassLoader() - Constructor for class org.biojava.utils.bytecode.GeneratedClassLoader

Create a new loader with the default parent.

GeneratedClassLoader(ClassLoader) - Constructor for class org.biojava.utils.bytecode.GeneratedClassLoader

Create a new loader with an explicitly set parent class loader.

GeneratedCodeClass - Class in org.biojava.utils.bytecode

A CodeClass implementation that is used to generate new classes.

GeneratedCodeClass(String, Class, Class[], int) - Constructor for class org.biojava.utils.bytecode.GeneratedCodeClass

GeneratedCodeClass(String, CodeClass, CodeClass[], int) - Constructor for class org.biojava.utils.bytecode.GeneratedCodeClass

GeneratedCodeMethod - Class in org.biojava.utils.bytecode

A method that will be generated.

generateDrawableCallboxes(AffineTransform) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Precomputes the callboxes in screen coordinates.

generateEvent(ChangeEvent) - Method in class org.biojava.bio.Annotatable.AnnotationForwarder

Deprecated.

generateEvent(ChangeEvent) - Method in class org.biojava.bio.dist.Distribution.NullModelForwarder

Deprecated.

generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder

generateEvent generates events in response to layout change and repaint requests.

generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder

generateEvent(ChangeEvent) - Method in class org.biojava.bio.MergeAnnotation.PropertyForwarder

generateEvent(ChangeEvent) - Method in class org.biojava.bio.OverlayAnnotation.PropertyForwarder

generateEvent(ChangeEvent) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder

generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener

generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater

generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder

Return the new event to represent the originating event ce.

generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder.Retyper

generateForardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler

generateOrderNSequence(String, OrderNDistribution, int) - Static method in class org.biojava.bio.dist.DistributionTools

Deprecated.
use generateSequence() or generateSymbolList() instead.

generateRecord(byte[], Object) - Method in class org.biojava.utils.FileAsList

generateSequence(String, Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools

Produces a sequence by randomly sampling the Distribution.

generateSubpaths() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Precomputes the GeneralPaths used to draw the traces.

generateSymbolList(Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools

Produces a SymbolList by randomly sampling a Distribution.

generateViterbiClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler

generatorAt(int) - Method in class org.biojava.utils.bytecode.InstructionVector

GENERIC_PROVIDER - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a provider type.

GENESYNONYM_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

GeneticAlgorithm - Interface in org.biojavax.ga

The class that runs the cycles of reproduction, evolution and selection, potentially on multiple Populations

GENETICCODE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon

GeneticCodes - Class in org.biojava.bio.seq

Collects the references to translation methods in one place.

GENPEPT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

GENPEPT indicates that the sequence format is GENPEPT.

GenpeptFormat - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead

GenpeptFormat() - Constructor for class org.biojava.bio.seq.io.GenpeptFormat

Deprecated.

GenpeptRichSequenceDB - Class in org.biojavax.bio.db.ncbi

This class contains functions accessing Peptide sequences in Genpept format.

GenpeptRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB

The default constructor delegates to the parent class.

GenpeptSequenceDB - Class in org.biojava.bio.seq.db

GenpeptSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenpeptSequenceDB

get() - Method in interface org.biojava.utils.cache.CacheReference

get() - Method in class org.biojava.utils.io.LargeBuffer

get(int) - Method in class org.biojava.stats.svm.SparseVector

Retrieve the value at dimension dim.

get(int) - Method in class org.biojava.utils.FileAsList

get(int) - Method in class org.biojava.utils.ListTools.Doublet

get(int) - Method in class org.biojava.utils.ListTools.SeriesList

get(int) - Method in class org.biojava.utils.ListTools.Triplet

get(int) - Method in class org.biojava.utils.SingletonList

get(long) - Method in class org.biojava.utils.io.LargeBuffer

get(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable

get the Transition associated with the specified tag.

get(Object) - Method in interface org.biojava.utils.cache.CacheMap

Retrieve the Object associated with the key, or null if either no value has been associated or if the key's value has been cleared by the cache.

get(Object) - Method in class org.biojava.utils.cache.ChangeableCache

get(Object) - Method in class org.biojava.utils.cache.FixedSizeMap

get(Object) - Method in class org.biojava.utils.cache.WeakCacheMap

get(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap

get(Object) - Method in class org.biojava.utils.io.SoftHashMap

get(Object) - Method in class org.biojava.utils.OverlayMap

get(Object) - Method in class org.biojava.utils.SmallMap

get(String) - Method in class org.biojava.bio.program.indexdb.BioStore

get(String) - Method in interface org.biojava.bio.program.indexdb.IndexStore

get returns a record specified by a primary identifier.

get(String, String) - Method in class org.biojava.bio.program.indexdb.BioStore

get(String, String) - Method in interface org.biojava.bio.program.indexdb.IndexStore

get returns a list of Records by searching against the primary identifiers if the namespace argument is equal to the primary namespace or otherwise by searching the secondary namespaces.

get_() - Method in class org.biojava.bio.proteomics.StructureTools

get3PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation

get5PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation

The point at which indicates the 5' end of the Location.

getA() - Method in class org.biojava.bio.molbio.DNAComposition

Get the relative compositon of 'A'.

getA() - Method in class org.biojava.utils.ListTools.Doublet

getA() - Method in class org.biojava.utils.ListTools.Triplet

getAbsorptionMax() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Getter for property absorptionMax.

getAbsorptionNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Getter for property absorptionNote.

getAccession() - Method in interface org.biojava.bio.program.homologene.Orthologue

get the Accession ID associated with this orthologue.

getAccession() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue

getAccession() - Method in interface org.biojavax.bio.BioEntry

Returns the accession of this bioentry.

getAccession() - Method in class org.biojavax.bio.SimpleBioEntry

Returns the accession of this bioentry.

getAccession() - Method in interface org.biojavax.CrossRef

Returns the accession of the object that the crossref refers to.

getAccession() - Method in class org.biojavax.SimpleCrossRef

Returns the accession of the object that the crossref refers to.

getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getAccession(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter

getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getAcronym() - Method in interface org.biojavax.Namespace

If the namespace has an acronym, this will return it.

getAcronym() - Method in class org.biojavax.SimpleNamespace

If the namespace has an acronym, this will return it.

getAddedFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence

getAddHandler() - Method in class org.biojava.bio.program.gff.GFFEntrySet

Get the GFFDocumentHandler for adding to this set.

getAdditionalAccessionTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the secondary/tertiary/additional accession term

getAddPos() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier

Retrieve the current value of addPos.

getAddress(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB

Get the URL object for locating sequence object using eutils.

getAddress(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB

getAddress(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB

getAddress(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB

getAddress(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB

getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

Get the URL object for locating sequence object using eutils.

getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB

Get the URL object for locating sequence object using eutils.

getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB

Get the URL object for locating sequence object using eutils.

getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB

getAdvance() - Method in interface org.biojava.bio.dp.EmissionState

Determine the number of symbols this state advances along one or more symbol lists.

getAdvance() - Method in class org.biojava.bio.dp.SimpleEmissionState

getAE(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment

getAlignLength(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getAlignLength(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border

getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border

Deprecated.

getAlignment() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border

Gets the Alignment - one of LEADING, TRAILING or CENTER.

getAlignment() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit

Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.

getAlignment() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit

Deprecated.

getAlignment() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit

getAlignment() - Method in interface org.biojava.bio.seq.homol.Homology

Retrieve the Alignment that specifies how the homologous regions are aligned.

getAlignment() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature

getAlignment returns the Alignment of two similar features.

getAlignment() - Method in class org.biojava.bio.seq.homol.SimpleHomology

getAlignment returns the alignment, which uses the HomologyFeatures as keys.

getAlignment() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature

getAlignment returns the alignment between the two features.

getAlignment() - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder

getAlignment(SymbolList) - Static method in class org.biojava.bio.program.abi.ABITools

View a symbol list over the QUALITY alphabet as an alignment.

getAlignmentNumber() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties

A method that simply returns the number of alignments fetched with this RemoteQBlastOutputProperties object.

getAlignmentOption(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties

getAlignmentOption(String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties

Method that returns the value associated with the key given in parameter.

getAlignmentOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties

getAlignmentOptions() - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties

Method to get all keys to the information stored in this object.

getAlignmentOutputFormat() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties

Method that returns the alignment output format for this actual RemoteQBlastOutputProperties object

getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService

This method extracts the actual Blast report for this request ID.

getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService

Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.

getAlignmentStyles() - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler

Returns a fragment of HTML that defines the FONT styles to be used in the alignment markup.

getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getAlignUnits(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getAll() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster

All sequences that map to this cluster.

getAllAmbiguitySymbol(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager

Return the ambiguity symbol which matches all symbols in a given alphabet.

getAllBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery

It returns all citations from the current collection as a (possibly big) array.

getAllBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery

It returns all citations from the current collection as a (possibly big) array, perhaps with a limited number of attributes.

getAllBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery

It returns all citations from the current collection as an XML stream.

getAllCharStates() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

getAllDataRecords() - Method in class org.biojava.bio.program.abi.ABIFParser

Obtain all data records.

getAllEntries() - Method in interface org.biojava.utils.candy.CandyVocabulary

It returns all available vocabulary entries.

getAllEnzymes() - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager

getAllEnzymes returns an unmodifable set of all available enzymes.

getAllIDs() - Method in interface org.biojava.bibliography.BibRefQuery

A convenient method returning just identifiers of all current citations.

getAllNames() - Method in interface org.biojava.utils.candy.CandyVocabulary

It return all names (entry identifiers) available in this vocabulary.

getAllNodes(UkkonenSuffixTree.SuffixNode, ArrayList, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree

getAllProteases() - Static method in class org.biojava.bio.proteomics.ProteaseManager

getAllScientificNames(Connection) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL

Deprecated.

Returns all the scientific names, which are currently stored in the database.

getAllSymbols(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager

Return a set containing all possible symbols which can be considered members of a given alphabet, including ambiguous symbols.

getAllVocabularies() - Method in interface org.biojava.utils.candy.CandyFinder

It returns all available vocabularies.

getAllVocabularyNames() - Method in interface org.biojava.utils.candy.CandyFinder

It returns names of all vocabularies known to this vocabulary finder.

getAlpha(int) - Method in class org.biojava.stats.svm.SVMRegressionModel

getAlpha(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel

getAlpha(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel

getAlphabet() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

getAlphabet() - Method in class org.biojava.bio.alignment.FlexibleAlignment

getAlphabet() - Method in class org.biojava.bio.alignment.SimpleAlignment

getAlphabet() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

Gives the alphabet used by this matrix.

getAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution

getAlphabet() - Method in interface org.biojava.bio.dist.Count

The alphabet from which this Count is over.

getAlphabet() - Method in interface org.biojava.bio.dist.Distribution

The alphabet from which this spectrum emits symbols.

getAlphabet() - Method in class org.biojava.bio.dist.GapDistribution

getAlphabet() - Method in class org.biojava.bio.dist.IndexedCount

getAlphabet() - Method in class org.biojava.bio.dist.PairDistribution

getAlphabet() - Method in class org.biojava.bio.dist.SimpleDistribution

getAlphabet() - Method in class org.biojava.bio.dist.TranslatedDistribution

getAlphabet() - Method in class org.biojava.bio.dist.UniformDistribution

getAlphabet() - Method in class org.biojava.bio.dp.SimpleStatePath

getAlphabet() - Method in class org.biojava.bio.dp.SimpleWeightMatrix

getAlphabet() - Method in interface org.biojava.bio.dp.WeightMatrix

The alphabet for the sequences that this weight matrix models.

getAlphabet() - Method in class org.biojava.bio.gui.SimpleSymbolStyle

getAlphabet() - Method in class org.biojava.bio.program.ssaha.CompactedDataStore

getAlphabet() - Method in interface org.biojava.bio.program.ssaha.DataStore

The alphabet of symbol lists that can be searched against this DataStore.

getAlphabet() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB

getAlphabet() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB

getAlphabet() - Method in class org.biojava.bio.seq.db.NCBISequenceDB

getAlphabet() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB

getAlphabet() - Method in class org.biojava.bio.seq.db.WebSequenceDB

getAlphabet() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment

getAlphabet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList

getAlphabet() - Method in class org.biojava.bio.seq.impl.DummySequence

getAlphabet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList

getAlphabet() - Method in class org.biojava.bio.seq.impl.SimpleSequence

getAlphabet() - Method in class org.biojava.bio.seq.impl.SubSequence

getAlphabet() - Method in class org.biojava.bio.seq.impl.ViewSequence

getAlphabet() - Method in class org.biojava.bio.seq.io.AlternateTokenization

getAlphabet() - Method in class org.biojava.bio.seq.io.CharacterTokenization

getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolReader

Find the alphabet of all symbols which may be returned by this SymbolReader.

getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolTokenization

The alphabet to which this tokenization applies.

getAlphabet() - Method in class org.biojava.bio.seq.io.WordTokenization

getAlphabet() - Method in class org.biojava.bio.seq.NewSimpleAssembly

getAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools

Gets the protein alphabet

getAlphabet() - Method in class org.biojava.bio.seq.SimpleAssembly

getAlphabet() - Method in interface org.biojava.bio.symbol.AlphabetIndex

Retrieve the alphabet that this indexes.

getAlphabet() - Method in class org.biojava.bio.symbol.ChunkedSymbolList

getAlphabet() - Method in class org.biojava.bio.symbol.DNAAmbPack

getAlphabet() - Method in class org.biojava.bio.symbol.DNANoAmbPack

getAlphabet() - Method in class org.biojava.bio.symbol.DummySymbolList

getAlphabet() - Method in class org.biojava.bio.symbol.PackedSymbolList

getAlphabet() - Method in interface org.biojava.bio.symbol.Packing

The FiniteAlphabet this packing is for.

getAlphabet() - Method in class org.biojava.bio.symbol.RelabeledAlignment

getAlphabet() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList

getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolList

Get the alphabet of this SymbolList.

getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable

getAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization

getAlphabet() - Method in class org.biojava.bio.symbol.SuffixTree

Return the Alphabet containing all Symbols which might be found in this SuffixTree.

getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolList

The alphabet that this SymbolList is over.

getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable

getAlphabet() - Method in class org.biojava.utils.regex.Pattern

getAlphabet() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

The alphabet that this SymbolList is over.

getAlphabet() - Method in class org.biojavax.bio.seq.ThinRichSequence

The alphabet that this SymbolList is over.

getAlphabet(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.

getAlphabet accepts a value which represents a sequence format and returns the relevant FiniteAlphabet object.

getAlphabetIndex(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager

Get an indexer for a specified alphabet.

getAlphabetIndex(Symbol[]) - Static method in class org.biojava.bio.symbol.AlphabetManager

Get an indexer for an array of symbols.

getAlphabetName() - Method in class org.biojavax.bio.seq.ThinRichSequence

getAlphabets() - Method in interface org.biojava.bio.symbol.Alphabet

Return an ordered List of the alphabets which make up a compound alphabet.

getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet

getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet

getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet

getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet

getAlphabets() - Method in class org.biojava.bio.symbol.SimpleAlphabet

getAlphabets() - Method in class org.biojava.bio.symbol.SingletonAlphabet

getAlphabets() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet

Gets the components of the Alphabet.

getAlphaStar(int) - Method in class org.biojava.stats.svm.SVMRegressionModel

getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getAltIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getAmbiguity(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet

getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet

getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet

getAmbiguity(Set) - Method in class org.biojava.bio.symbol.IntegerAlphabet

getAmbiguity(Set) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet

This is not supported.

getAmbiguity(Set<Symbol>) - Method in interface org.biojava.bio.symbol.Alphabet

Get a symbol that represents the set of symbols in syms.

getAmbiguityImpl(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet

Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.

getAngle(int) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext

Return the angle for an index into a sequence.

getAngle(int) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext

getAnnotatedQuerySeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder

getAnnotatedSubjectSeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder

getAnnotation() - Method in interface org.biojava.bio.Annotatable

Should return the associated annotation object.

getAnnotation() - Method in class org.biojava.bio.dp.SimpleEmissionState

getAnnotation() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl

getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchHit

Deprecated.

getAnnotation returns the Annotation associated with this hit.

getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchResult

Deprecated.

getAnnotation returns the Annotation associated with this hit.

getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit

Deprecated.

getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit

getAnnotation returns the Annotation associated with this hit.

getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult

getAnnotation returns the Annotation associated with this hit.

getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit

getAnnotation returns the Annotation associated with this sub-hit.

getAnnotation() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl

getAnnotation() - Method in class org.biojava.bio.seq.impl.DummySequence

getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleFeature

getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence

getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleSequence

getAnnotation() - Method in class org.biojava.bio.seq.impl.SubSequence

getAnnotation() - Method in class org.biojava.bio.seq.impl.ViewSequence

getAnnotation() - Method in class org.biojava.bio.seq.io.AlternateTokenization

getAnnotation() - Method in class org.biojava.bio.seq.io.CharacterTokenization

getAnnotation() - Method in class org.biojava.bio.seq.io.WordTokenization

getAnnotation() - Method in class org.biojava.bio.seq.NewSimpleAssembly

getAnnotation() - Method in class org.biojava.bio.seq.SimpleAssembly

getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange

getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol

getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet

getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet

getAnnotation() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol

getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet

getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol

getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet

getAnnotation() - Method in class org.biojava.bio.symbol.SimpleAlphabet

getAnnotation() - Method in class org.biojava.bio.symbol.SingletonAlphabet

getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization

getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet

The SoftMaskedAlphabet has no annotation

getAnnotation() - Method in class org.biojava.bio.taxa.AbstractTaxon

Deprecated.

getAnnotation() - Method in class org.biojava.ontology.IntegerOntology.IntTerm

getAnnotation() - Method in class org.biojava.ontology.OntologyTerm.Impl

getAnnotation() - Method in class org.biojava.ontology.RemoteTerm.Impl

getAnnotation() - Method in class org.biojava.ontology.Term.Impl

getAnnotation() - Method in class org.biojava.ontology.Triple.Impl

getAnnotation() - Method in class org.biojavax.bio.seq.CompoundRichLocation

Should return the associated annotation object.

getAnnotation() - Method in class org.biojavax.bio.seq.EmptyRichLocation

Should return the associated annotation object.

getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichFeature

Should return the associated annotation object.

getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichLocation

Should return the associated annotation object.

getAnnotation() - Method in class org.biojavax.bio.SimpleBioEntry

Should return the associated annotation object.

getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTerm

Should return the associated annotation object.

getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTriple

Should return the associated annotation object.

getAnnotation() - Method in class org.biojavax.SimpleCrossRef

Should return the associated annotation object.

getAnnotation(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager

getAnnotation returns an immutable, static annotation describing the enzyme.

getAnnotations() - Method in class org.biojava.bio.MergeAnnotation

Gets an unmodifiable view of the list of Annotations that are part of the MergeAnnotation.

getAnnotationType() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType

Get the AnnotationType used as a constraint.

getAnnotationType() - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler

Return the AnnotationType built by this handler

getAnnotator() - Method in class org.biojava.bio.program.gff.GFFEntrySet

Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.

getAnnotator(boolean) - Method in class org.biojava.bio.program.gff.GFFEntrySet

Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.

getArg_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager

getArrowHeadSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getArrowScoop() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getArrowScoop() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

getArrowSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getArrowSize() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

getArticleAuthors() - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Gets the names of the authors which first published an article about the AAindex entry.

getArticleTitle() - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Gets the title of the article which describes the AAindex entry.

getAsp_N() - Static method in class org.biojava.bio.proteomics.ProteaseManager

getAttributes(String) - Method in class org.biojava.naming.ObdaContext

getAttributes(String, String[]) - Method in class org.biojava.naming.ObdaContext

getAttributes(Name) - Method in class org.biojava.naming.ObdaContext

getAttributes(Name, String[]) - Method in class org.biojava.naming.ObdaContext

getAuthority() - Method in interface org.biojavax.Namespace

This method will return the authority that governs the namespace.

getAuthority() - Method in class org.biojavax.SimpleNamespace

This method will return the authority that governs the namespace.

getAuthorityId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier

Return the authority id for this identifier.

getAuthorList() - Method in interface org.biojavax.DocRef

Returns the authors of the document reference as a set of DocRefAuthor implementation instances.

getAuthorList() - Method in class org.biojavax.SimpleDocRef

Returns the authors of the document reference as a set of DocRefAuthor implementation instances.

getAuthors() - Method in interface org.biojavax.DocRef

Returns the authors of the document reference.

getAuthors() - Method in class org.biojavax.SimpleDocRef

Returns the authors of the document reference.

getAutomaton() - Method in class org.biojava.utils.automata.FiniteAutomaton

getAutomaton() - Method in interface org.biojava.utils.automata.NfaBuilder

getAutomaton() - Method in class org.biojava.utils.automata.NfaSubModel

getB() - Method in class org.biojava.bio.proteomics.StructureTools

getB() - Method in class org.biojava.utils.ListTools.Doublet

getB() - Method in class org.biojava.utils.ListTools.Triplet

getBackwardTransitions() - Method in class org.biojava.bio.dp.DP

getBackwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP

getBasecalls() - Method in class org.biojava.bio.program.abi.ABITrace

Returns an int[] array that represents the basecalls - each int in the array corresponds to an x-coordinate point in the graph that is a peak (a base location).

getBaseCalls() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram

Return the total number of base calls.

getBaseCalls() - Method in interface org.biojava.bio.chromatogram.Chromatogram

Returns an alignment that describes the base calls for this chromatogram.

getBaseColor(Symbol) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Returns the color that will be used to draw the trace for the given DNA symbol.

getBaseFillColor(Symbol) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Returns the color that will be used to fill in the callboxes for calls with the given symbol.

getBases() - Method in class org.biojava.bio.dp.SimpleEmissionState

getBases() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol

getBases() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol

getbaseURL() - Method in class org.biojava.bio.seq.db.FetchURL

getBeadDepth() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getBeadDepth returns the depth of a single bead produced by this renderer.

getBeadDepth() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer

getBeadDepth returns the depth of a single bead produced by the renderer.

getBeadDepth() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getBeadDisplacement returns the displacement of beads from the centre line of the renderer.

getBeadDisplacement() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer

getBeadDisplacement returns the displacement of beads from the centre line of the renderer.

getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

getBeadFill() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getBeadFill returns the bead fill paint.

getBeadOutline() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getBeadOutline returns the bead outline paint.

getBeadStroke() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getBeadStroke returns the bead outline stroke.

getBibRefAsXML(BibRef) - Method in interface org.biojava.bibliography.BibRefQuery

A convenient utility method converting a given citation to its XML representation.

getBibRefCount() - Method in interface org.biojava.bibliography.BibRefQuery

It returns the number of citations in the current collection.

getBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery

It returns an enumeration of all citations from the current collection.

getBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery

It returns an enumeration of all citations from the current collection, perhaps with a limited number of attributes.

getBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery

It returns an enumeration of all citations from the current collection.

getBinaryAlphabet() - Static method in class org.biojavax.ga.util.GATools

Gets a Reference to the FlyWeight GA_Binary Alphabet.

getBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB

getBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite

Retrieve a single BioEntry by its id.

getBioEntry(String) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB

getBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB

getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractBioEntryDB

getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB

getBioEntryIterator() - Method in interface org.biojavax.bio.db.BioEntryDB

Returns a BioEntryIterator over all BioEntrys in the database.

getBioEntrys(Set) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB

getBioEntrys(Set) - Method in interface org.biojavax.bio.db.BioEntryDBLite

Retrieve multiple BioEntry by their ids.

getBioEntrys(Set) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB

getBioEntrys(Set) - Method in class org.biojavax.bio.db.HashBioEntryDB

getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB

getBioEntrys(Set, BioEntryDB) - Method in interface org.biojavax.bio.db.BioEntryDBLite

Retrieve multiple BioEntry into a specific sequence database.

getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB

getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.HashBioEntryDB

getBioSequenceStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper

Deprecated.

Returns the an object indicating the style of biosequence storage that this database should employ.

getBioSequenceStyle() - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper

Deprecated.

getBlastAdvancedOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties

Simply return the string given as argument via setBlastAdvancedOptions

getBlastDatabase() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties

This method returns the value of the database used for this particular blast run.

getBlastProgram() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties

This method returns the value of the program used for this particular blast run.

getBlockDepth() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

getBlockDepth() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

getBlockListener() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract

getBlockListener() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser

Obtain the listener for this parser.

getBlockName() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract

getBlockName() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlock

Get the block name.

getBlockName() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract

Obtains the name of this block.

getBlockName() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract

getBlockPainter() - Method in class org.biojava.bio.gui.DistributionLogo

getBlockPainter() - Method in interface org.biojava.bio.gui.LogoContext

getBlockParser(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract

getBlockParser(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener

Gets the parser to use for a given block.

getBlockWidth() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

getBlosum100() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM100 amino acid substitution matrix.

getBlosum100_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM100.50 amino acid substitution matrix.

getBlosum30() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM30 amino acid substitution matrix.

getBlosum30_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM30.50 amino acid substitution matrix.

getBlosum35() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM35 amino acid substitution matrix.

getBlosum35_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM35.50 amino acid substitution matrix.

getBlosum40() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM40 amino acid substitution matrix.

getBlosum40_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM40.50 amino acid substitution matrix.

getBlosum45() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM45 amino acid substitution matrix.

getBlosum45_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM45.50 amino acid substitution matrix.

getBlosum50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM50 amino acid substitution matrix.

getBlosum50_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM50.50 amino acid substitution matrix.

getBlosum55() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM55 amino acid substitution matrix.

getBlosum55_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM55.50 amino acid substitution matrix.

getBlosum60() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM60 amino acid substitution matrix.

getBlosum60_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM60.50 amino acid substitution matrix.

getBlosum62() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM62 amino acid substitution matrix.

getBlosum62_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM62.50 amino acid substitution matrix.

getBlosum65() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM65 amino acid substitution matrix.

getBlosum65_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM65.50 amino acid substitution matrix.

getBlosum70() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM70 amino acid substitution matrix.

getBlosum70_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM70.50 amino acid substitution matrix.

getBlosum75() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM75 amino acid substitution matrix.

getBlosum75_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM75.50 amino acid substitution matrix.

getBlosum80() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM80 amino acid substitution matrix.

getBlosum80_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM80.50 amino acid substitution matrix.

getBlosum85() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM85 amino acid substitution matrix.

getBlosum85_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM85.50 amino acid substitution matrix.

getBlosum90() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM90 amino acid substitution matrix.

getBlosum90_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM90.50 amino acid substitution matrix.

getBlosumn() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUMN amino acid substitution matrix.

getBlosumn_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUMN.50 amino acid substitution matrix.

getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.Aggregator

getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.MultiTagger

getBounds() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph

getBounds() - Method in interface org.biojava.bio.gui.glyph.Glyph

getBounds() - Method in class org.biojava.bio.gui.glyph.HelixGlyph

getBounds() - Method in class org.biojava.bio.gui.glyph.RectangleGlyph

getBounds() - Method in class org.biojava.bio.gui.glyph.TurnGlyph

getBounds() - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph

getBounds() - Method in interface org.biojava.bio.gui.LogoContext

getBuilderFactory(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.

getBuilderFactory accepts a value which represents a sequence format and returns the relevant SequenceBuilderFactory object.

getC() - Method in class org.biojava.bio.molbio.DNAComposition

Get the relative compositon of 'C'.

getC() - Method in class org.biojava.bio.proteomics.StructureTools

getC() - Method in class org.biojava.stats.svm.SMOTrainer

getC() - Method in class org.biojava.utils.ListTools.Triplet

getCallboxBounds(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Returns the screen-coordinate bounds of the callbox for a given call.

getCallboxBounds(int, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Returns the bounds of the callbox for a given call.

getCallboxCount() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Returns the number of callboxes, regenerating them if necessary.

getCallContaining(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Synonym for ChromatogramGraphic.getCallContaining(float, boolean) with pointOnScreen=true.

getCallContaining(float, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Same as ChromatogramGraphic.getCallContaining(Point2D, boolean), except that only the x-coordinate of the point is specified.

getCallContaining(Point2D) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Synonym for ChromatogramGraphic.getCallContaining(Point2D, boolean) with pointOnScreen=true.

getCallContaining(Point2D, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Returns the 0-based index of the call containing a given point.

getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn

Get the cardinality constraint used to validate the number of property values.

getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains

Get the cardinality constraint used to validate the number of property values.

getCategory() - Method in class org.biojava.ontology.Synonym

getCell(int[]) - Method in interface org.biojava.bio.dp.DPMatrix

getCell(int[]) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix

getCell(int[]) - Method in class org.biojava.bio.dp.twohead.PairDPMatrix

getChainedEvent() - Method in class org.biojava.utils.ChangeEvent

Return the event which caused this to be fired, or null if this change was not caused by another event.

getChange() - Method in class org.biojava.utils.ChangeEvent

Return an object which is to be the new value of some property, or is to be added to a collection.

getChangeEvent() - Method in exception org.biojava.utils.ChangeVetoException

Return the ChangeEvent which is being vetoed.

getChanger() - Method in class org.biojava.bio.AnnotationChanger

getMapper returns the ValueChanger being used to remap the Annotation.

getChanger(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable

Get the Changer currently registered to handle a tag.

getChangeSupport() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB

getChangeSupport() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder

getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractDistribution

getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution

getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.TranslatedDistribution

getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleEmissionState

getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleMarkovModel

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getChangeSupport lazily instantiates a helper for change listeners.

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getChangeSupport lazily instantiates a helper for change listeners.

getChangeSupport(ChangeType) - Method in class org.biojava.bio.MergeAnnotation

getChangeSupport(ChangeType) - Method in class org.biojava.bio.OverlayAnnotation

getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchHit

Deprecated.

getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchResult

Deprecated.

getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchSubHit

Deprecated.

getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit

getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult

getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit

getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper

getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl

getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleFeature

getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleSequence

getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.LazyFeatureHolder

getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.NewSimpleAssembly

getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.SimpleAssembly

getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.AbstractSymbol

getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.SimpleAlphabet

getChangeSupport(ChangeType) - Method in class org.biojava.bio.taxa.AbstractTaxon

Deprecated.

getChangeSupport(ChangeType) - Method in class org.biojava.ontology.AbstractTerm

getChangeSupport(ChangeType) - Method in class org.biojava.ontology.OntologyTerm.Impl

getChangeSupport(ChangeType) - Method in class org.biojava.utils.AbstractChangeable

Called to retrieve the ChangeSupport for this object.

getChangeTable() - Method in class org.biojava.bio.program.tagvalue.ValueChanger

getChangeTypes(Class) - Static method in class org.biojava.utils.ChangeType

Get all ChangeType objects defined within a class.

getChar() - Method in class org.biojava.utils.io.LargeBuffer

getChar(long) - Method in class org.biojava.utils.io.LargeBuffer

getCharacter() - Method in class org.biojava.utils.RepeatedCharSequence

getCharacterOffset() - Method in exception org.biojava.utils.ParserException

Get the character offset in the line where an error was detected.

getCharLabels() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

getCharStateLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

getCharStateLabelKeywords(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

getChild() - Method in class org.biojava.bio.seq.FeatureFilter.Not

getChild() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not

getChild(SuffixTree.SuffixNode, int) - Method in class org.biojava.bio.symbol.SuffixTree

Get the n'th child of a node.

getChild(SuffixTree.SuffixNode, Symbol) - Method in class org.biojava.bio.symbol.SuffixTree

Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.

getChild1() - Method in class org.biojava.bio.CollectionConstraint.And

Get the first child CollectionConstraint.

getChild1() - Method in class org.biojava.bio.CollectionConstraint.Or

Get the first child CollectionConstraint.

getChild1() - Method in class org.biojava.bio.PropertyConstraint.And

Get the first child PropertyConstraint.

getChild1() - Method in class org.biojava.bio.PropertyConstraint.Or

Get the first child PropertyConstraint.

getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.And

getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.Or

getChild1() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And

getChild1() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or

getChild2() - Method in class org.biojava.bio.CollectionConstraint.And

Get the seccond child CollectionConstraint.

getChild2() - Method in class org.biojava.bio.CollectionConstraint.Or

Get the seccond child CollectionConstraint.

getChild2() - Method in class org.biojava.bio.PropertyConstraint.And

Get the seccond child PropertyConstraint.

getChild2() - Method in class org.biojava.bio.PropertyConstraint.Or

Get the seccond child PropertyConstraint.

getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.And

getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.Or

getChild2() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And

getChild2() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or

getChildren() - Method in class org.biojava.bio.taxa.SimpleTaxon

Deprecated.

getChildren() - Method in interface org.biojava.bio.taxa.Taxon

Deprecated.

The children of this Taxon.

getChildren() - Method in class org.biojava.bio.taxa.WeakTaxon

Deprecated.

getChildrenOf(Connection, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL

Deprecated.

Returns all children of the specified taxon.

getChildrenOf(Connection, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL

Deprecated.

Returns the children as a Stack of this given taxon.

getChildrenRaw() - Method in class org.biojava.bio.taxa.WeakTaxon

Deprecated.

getChromatogram() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Accessor for the in-use chromatogram.

getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getChromNum(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getChromosome() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation

getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getChromosome(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getChromosomes() - Method in interface org.biojavax.ga.functions.GACross

Gets the chromosomes after the cross

getChromosomes() - Method in interface org.biojavax.ga.functions.GACrossResult

Gets the chromosomes after the cross

getChromosomes() - Method in class org.biojavax.ga.functions.SimpleGACrossResult

getChromosomes() - Method in class org.biojavax.ga.impl.AbstractOrganism

getChromosomes() - Method in interface org.biojavax.ga.Organism

Gets the organisms 'chromosome' sequences

getChymotrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager

getCircular() - Method in interface org.biojavax.bio.seq.RichSequence

Is the sequence circular?

getCircular() - Method in class org.biojavax.bio.seq.ThinRichSequence

Is the sequence circular?

getCircularLength() - Method in class org.biojavax.bio.seq.EmptyRichLocation

Retrieves the circular length of this location.

getCircularLength() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation

Retrieves the circular length of this location.

getCircularLength() - Method in interface org.biojavax.bio.seq.RichLocation

Retrieves the circular length of this location.

getCircularLength() - Method in class org.biojavax.bio.seq.SimpleRichLocation

Retrieves the circular length of this location.

getClasses() - Method in class org.biojava.utils.bytecode.ParametricType

getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getClassifyId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getClassifySystem(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getClassifyType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getClassLoader(Class) - Static method in class org.biojava.utils.ClassTools

Get the classloader which loaded clazz.

getClassLoader(Object) - Static method in class org.biojava.utils.ClassTools

Get the classloader which loaded the class of obj.

getClassNumber(int) - Method in interface org.biojava.bio.EcNumber

Get the class number associated with the particular level of the ec number.

getClassNumber(int) - Method in class org.biojava.bio.EcNumber.Impl

getCleaveageResidues() - Method in class org.biojava.bio.proteomics.Protease

The list of residues that the protease will cleave at.

getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getCloneId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getCloneLibrary(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getCluster(String) - Method in interface org.biojava.bio.program.unigene.UnigeneDB

Fetch a cluster by its cluster id.

getCNBr() - Static method in class org.biojava.bio.proteomics.ProteaseManager

getCodeClass() - Method in interface org.biojava.utils.bytecode.CodeContext

Get the class for which a method is being generated.

getCodeMethod() - Method in interface org.biojava.utils.bytecode.CodeContext

Get the method which is being generated.

getCodonAlphabet() - Static method in class org.biojava.bio.seq.DNATools

Gets the (DNA x DNA x DNA) Alphabet

getCodonAlphabet() - Static method in class org.biojava.bio.seq.RNATools

Gets the (RNA x RNA x RNA) Alphabet

getCodonPref() - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName

getCodonPreference(String) - Static method in class org.biojava.bio.symbol.CodonPrefTools

get the specified codon preference.

getCodonPrefs() - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll

getCollapsing() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

Returns true if this class collapses to zero depth when there are no visible features.

getCollectionConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandler

getCollectionId() - Method in interface org.biojava.bibliography.BibRefQuery

It returns an identification of the current query collection.

getColourClass(String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler

Returns the colour class for the specified colour (in hex).

getColumn(int) - Method in class org.biojava.bio.dp.SimpleWeightMatrix

getColumn(int) - Method in interface org.biojava.bio.dp.WeightMatrix

Retrieve a column as an EmissionState.

getCommands() - Method in class org.biojava.utils.process.ExternalProcess

Gets the command line including the path or name of the external program and its command line arguments.

getComment() - Method in interface org.biojava.bio.AnnotationType

Get the comment for the whole AnnotationType.

getComment() - Method in class org.biojava.bio.AnnotationType.Impl

getComment() - Method in interface org.biojava.bio.program.gff.GFFRecord

The feature comment.

getComment() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

getComment() - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Gets the user comment for the AAindex entry.

getComment() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector

getComment() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event

Getter for property comment.

getComment() - Method in interface org.biojavax.Comment

Returns the comment part of this comment.

getComment() - Method in class org.biojavax.SimpleComment

Returns the comment part of this comment.

getComment(Object) - Method in interface org.biojava.bio.AnnotationType

Get the comment for a particular property.

getComment(Object) - Method in class org.biojava.bio.AnnotationType.Impl

getComments() - Method in class org.biojava.bio.program.scf.SCF

Returns the comments fields as a Properties mapping.

getComments() - Method in interface org.biojavax.bio.BioEntry

Returns a set of all comments associated with this bioentry.

getComments() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

Returns all comments.

getComments() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock

Returns all comments.

getComments() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock

Returns all comments.

getComments() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock

Returns all comments.

getComments() - Method in class org.biojavax.bio.SimpleBioEntry

Returns a set of all comments associated with this bioentry.

getCommentType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Getter for property commentType.

getCommonName() - Method in class org.biojava.bio.taxa.AbstractTaxon

Deprecated.

getCommonName() - Method in interface org.biojava.bio.taxa.Taxon

Deprecated.

The common name of the Taxon.

getComparator() - Method in class org.biojava.utils.FileAsList

getComponentList(boolean) - Method in class org.biojava.bio.symbol.MergeLocation

Gets the component locations that make up this one

getComponentLocation() - Method in interface org.biojava.bio.seq.ComponentFeature

Return a location which identifies a portion of the component sequence which is to be included in the assembly.

getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList

getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList

getComponentName() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName

getComponentSequence() - Method in interface org.biojava.bio.seq.ComponentFeature

Get the sequence object which provides a component of this feature's parent sequence.

getComponentSequenceName() - Method in interface org.biojava.bio.seq.ComponentFeature

Get the name of the component sequence.

getComputationTime() - Method in class org.biojava.bio.alignment.AlignmentPair

getConditionedAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution

Get the conditioned alphabet.

getConditionedAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution

Get the conditioned alphabet.

getConditioningAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution

Get the conditioning alphabet of this distribution.

getConditioningAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution

Get the conditioning alphabet of this distribution.

getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getConfidence(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Composite

getConfigLocator() - Method in interface org.biojava.directory.RegistryConfiguration

getConfigLocator returns a locator for the configuration.

getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Impl

getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Composite

getConfiguration() - Method in interface org.biojava.directory.RegistryConfiguration

getConfiguration returns a mapping of registry database names to collections of tag-value pairs.

getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Impl

getConstant() - Method in class org.biojava.stats.svm.PolynomialKernel

getConstant() - Method in class org.biojava.stats.svm.SigmoidKernel

getConstants() - Method in interface org.biojava.utils.bytecode.CodeContext

Get the constants pool for this context.

getConstraint(Object) - Method in interface org.biojava.bio.AnnotationType

Retrieve the constraint that will be applied to all properties with a given key.

getConstraint(Object) - Method in class org.biojava.bio.AnnotationType.Impl

getConstructor(CodeClass[]) - Method in interface org.biojava.utils.bytecode.CodeClass

Get a constructor by argument list.

getConstructor(CodeClass[]) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass

getConstructor(CodeClass[]) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass

getContainingClass() - Method in class org.biojava.utils.bytecode.CodeField

Get the class that contains this field.

getContainingClass() - Method in interface org.biojava.utils.bytecode.CodeMethod

The class that contains this method

getContainingClass() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod

getContainsTerm() - Static method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship

Gets the default CONTAINS term used for defining the relationship between features.

getContentHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade

correct this later

getContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder

getContext() - Method in class org.biojava.stats.svm.TrainingEvent

getContext(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser

See if empty tags are treated as a continuation of previous tags or as a new tag with the value of the empty string.

getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser

Report whether empty tags will be treated as continuations of the last non -empty tag.

getCoordinates() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot

getCoordinates returns the hotspot coordinates.

getCopyrightTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the copyright term

getCoreOntology() - Static method in class org.biojava.ontology.OntoTools

Get the Ontology that defines our core "central dogma".

getCount() - Method in interface org.biojava.utils.candy.CandyVocabulary

It returns a number of entries contained in this vocabulary.

getCount(Distribution, Symbol) - Method in interface org.biojava.bio.dist.DistributionTrainerContext

Return the number of counts of a particular symbol which will be used to train the specified distribution.

getCount(Distribution, Symbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext

getCount(DistributionTrainerContext, AtomicSymbol) - Method in interface org.biojava.bio.dist.DistributionTrainer

Get the current count for this state.

getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer

getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer

getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer

Deprecated.

getCount(AtomicSymbol) - Method in interface org.biojava.bio.dist.Count

Return the counts for a given Symbol.

getCount(AtomicSymbol) - Method in class org.biojava.bio.dist.IndexedCount

getCRC() - Method in interface org.biojavax.DocRef

Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references.

getCRC() - Method in class org.biojavax.SimpleDocRef

Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references.

getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getCreateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getCreateOnUnderlyingSequence() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence

getCrossOverFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm

getCrossOverFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm

getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACross

Returns the collection of cross over locations from the last cross

getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACrossResult

Returns the collection of cross over locations from the last cross

getCrossOverPositions() - Method in class org.biojavax.ga.functions.SimpleGACrossResult

getCrossOverProbs() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction

getCrossOverProbs() - Method in interface org.biojavax.ga.functions.CrossOverFunction

getCrossOverProbs() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross

getCrossProductAlphabet(List) - Static method in class org.biojava.bio.symbol.AlphabetManager

Retrieve a CrossProductAlphabet instance over the alphabets in aList.

getCrossProductAlphabet(List, String) - Static method in class org.biojava.bio.symbol.AlphabetManager

Attempts to create a cross product alphabet and register it under a name.

getCrossProductAlphabet(List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager

Retrieve a CrossProductAlphabet instance over the alphabets in aList.

getCrossref() - Method in interface org.biojavax.DocRef

The document reference may refer to an object in another database.

getCrossref() - Method in class org.biojavax.SimpleDocRef

The document reference may refer to an object in another database.

getCrossRef() - Method in class org.biojavax.bio.seq.EmptyRichLocation

Retrieves the crossref associated with this location.

getCrossRef() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation

Retrieves the crossref associated with this location.

getCrossRef() - Method in interface org.biojavax.bio.seq.RichLocation

Retrieves the crossref associated with this location.

getCrossRef() - Method in class org.biojavax.bio.seq.SimpleRichLocation

Retrieves the crossref associated with this location.

getCrossRef() - Method in interface org.biojavax.RankedCrossRef

Return the cross reference associated with this object.

getCrossRef() - Method in class org.biojavax.SimpleRankedCrossRef

Return the cross reference associated with this object.

getCrossResults() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm

Get a List containing details of all the cross over events during the run.

getCurrentCycle() - Method in interface org.biojava.stats.svm.TrainingContext

getCurrentFeature() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener

getCurrentFeature() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter

getCurrentFeature() - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Gets the feature currently being created.

getCurrentFeature() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Gets the feature currently being created.

getCurrentScore() - Method in class org.biojava.bio.dp.AbstractTrainer

getCurrentScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm

getCutoff() - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold

getCuttingSize() - Method in class org.biojava.bio.molbio.RestrictionEnzyme

The cutting size of a restriction enzyme is defined has the number of nucleotides that are directly involved in the recognition sequence.

getCutType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme

getCutType returns the type of cut produced by the enzyme.

getCycle() - Method in class org.biojava.bio.dp.AbstractTrainer

getCycle() - Method in interface org.biojava.bio.dp.TrainingAlgorithm

getDataAccess() - Method in class org.biojava.bio.program.abi.ABIFParser

Returns the accessor for the raw data being parsed by this parser.

getDatabase(String) - Method in class org.biojava.directory.Registry

getDatabase retrieves a database instance known by a name String.

getDataBase() - Method in class org.biojava.bio.seq.db.NCBISequenceDB

getDatabaseName() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Getter for property databaseName.

getDatabaseURLGenerators() - Method in class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory

getDatabaseURLGenerators() - Method in interface org.biojava.bio.program.blast2html.URLGeneratorFactory

Returns a list of 0, 1 or more DatabaseURLGenerator The first is used to link from the id in the summary table, all are used as a list of links in the detail section.

getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms

Getter for the Ensembl-specific 'dataClass' term

getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms

Getter for the Ensembl-specific 'dataClass' term

getDataClassTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the DataClass term

getDataRecord(String, int) - Method in class org.biojava.bio.program.abi.ABIFParser

Get the entry from the file TOC with the given name and tag number.

getDataSource(String, String, String, String) - Static method in class org.biojava.utils.JDBCPooledDataSource

getDataSources() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB

Get the current set of all currently registered data sources.

getDataStore(File) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory

getDataStore(File) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory

Get a pre-built data store associated with a file.

getDataStore(File) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory

getDataStore(File) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory

getDataType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty

getDataType() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

getDateAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the date annotated term

getDateCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the date created term

getDateUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the date updated term

getDayhoff() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the DAYHOFF amino acid substitution matrix.

getDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder

retrieve the DB that has just been built

getDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder

getDB() - Method in class org.biojava.bio.seq.db.FetchURL

getDbCode() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId

getDBHelper(Connection) - Static method in class org.biojava.bio.seq.db.biosql.DBHelper

Deprecated.

Returns a DBHelper implementation suitable for a particular database.

getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion

getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion

getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref

getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getDbId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter

getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition

getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs

return a set of DbId

getDbname() - Method in interface org.biojavax.CrossRef

Returns the name of the database the cross reference refers to.

getDbname() - Method in class org.biojavax.SimpleCrossRef

Returns the name of the database the cross reference refers to.

getDBTaxon(Connection, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL

Deprecated.

Attempts to get a Taxon object corresponding to the specified taxon_id (i.e. the database's internal id for the taxon).

getDbXrefId() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement

getDbxrefList(String, int, int) - Method in class org.biojava.ontology.obo.OboFileParser

getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocation

getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator

getDecorator(Class) - Method in interface org.biojava.bio.symbol.Location

Checks the decorator chain for an instance of decoratorClass and return it if found.

getDecorator(Class) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Checks the decorator chain for an instance of decoratorClass and return it if found.

getDecorator(Class) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Checks the decorator chain for an instance of decoratorClass and return it if found.

getDecorator(Class) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Checks the decorator chain for an instance of decoratorClass and return it if found.

getDefaultChanger() - Method in class org.biojava.bio.program.tagvalue.ValueChanger

Get the changer that will be applied to values of tags with no specific handler registered.

getDefaultConstraint() - Method in interface org.biojava.bio.AnnotationType

Get the CollectionConstraint that will be applied to all properties without an explicit binding.

getDefaultConstraint() - Method in class org.biojava.bio.AnnotationType.Impl

getDefaultCrossReferenceResolver() - Static method in class org.biojavax.RichObjectFactory

Returns the default cross ref resolver object.

getDefaultFactory() - Static method in class org.biojava.ontology.OntoTools

getDefaultFormat() - Method in class org.biojava.bio.program.phred.PhredFormat

Deprecated.

getDefaultFormat() - Method in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.

getDefaultFormat() - Method in class org.biojava.bio.seq.io.FastaFormat

Deprecated.

getDefaultFormat() - Method in class org.biojava.bio.seq.io.GAMEFormat

Deprecated.

getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.

getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankXmlFormat

Deprecated.

getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenpeptFormat

Deprecated.

getDefaultFormat() - Method in interface org.biojava.bio.seq.io.SequenceFormat

Deprecated.
new implementations should only write a single format.

getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLFormat

getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.

getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat

getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.

getDefaultFormat() - Method in class org.biojavax.bio.seq.io.FastaFormat

getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.

getDefaultFormat() - Method in class org.biojavax.bio.seq.io.GenbankFormat

getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.

getDefaultFormat() - Method in class org.biojavax.bio.seq.io.INSDseqFormat

getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.

getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtFormat

getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.

getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat

getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.

getDefaultNamespace() - Static method in class org.biojavax.RichObjectFactory

Returns the default namespace object.

getDefaultOntology() - Static method in class org.biojavax.RichObjectFactory

Returns the default ontology object.

getDefaultPaint() - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer

getDefaultPositionResolver() - Static method in class org.biojavax.RichObjectFactory

Returns the default position resolver object.

getDefaultRichSequenceHandler() - Static method in class org.biojavax.RichObjectFactory

Returns the default sequence resolver object.

getDefaultSplitter() - Method in class org.biojava.bio.program.tagvalue.ValueChanger

Get the splitter that will be applied to values of tags with no specific handler registered.

getDelegate() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper

getDelegate() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper

getDelegate() - Method in class org.biojava.bio.program.tagvalue.StateMachine

getDelegate() - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper

get listener to which all calls will be delegated

getDelegate() - Method in class org.biojava.bio.seq.io.SeqIOFilter

Retrieve the delegate that is wrapped.

getDelegate() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter

Retrieve the delegate that is wrapped.

getDelegate() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet

The compound alpha that holds the symbols used by this wrapper

getDelegateParser() - Method in class org.biojava.bio.program.tagvalue.TagDelegator

getDelete() - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Returns the current expenses of a single delete operation.

getDelete() - Method in class org.biojava.bio.alignment.SmithWaterman

getDelete(int) - Method in class org.biojava.bio.dp.ProfileHMM

Retrieves the delete state for column indx.

getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper

Deprecated.

Returns the an object indicating the style of deletion that this database should employ.

getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper

Deprecated.

getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper

getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper

Deprecated.

getDepth() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor

getDepth() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor

Gets the Depth attribute of the LightPairDPCursor object

getDepth() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor

retrieve the depth of this cursor

getDepth() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

getDepth(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer

getDepth returns the total depth of a list of SequenceRenderers.

getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer

getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer

getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer

getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularMLR

getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularPaddedRenderer

getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularRenderer

Get the depth needed for this renderer.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getDepth calculates the depth required by this renderer to display its beads.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer

getDepth calculates the depth required by this renderer to display its beads.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer

getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

Returns the depth property of this class.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer

getDepth calculates the depth required by this renderer to display its beads.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer

getDepth calculates the depth required by this renderer to display its beads.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer

getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer

Retrieve the depth of this renderer when rendering src.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer

getDepth(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LineInfo

getDepthScaler() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel

Retrieve the current DepthScaler.

getDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

This gives you the description of this matrix if there is one.

getDescription() - Method in class org.biojava.bio.program.fastq.Fastq

Return the description of this FASTQ formatted sequence.

getDescription() - Method in class org.biojava.bio.program.fastq.FastqBuilder

Return the description for this FASTQ formatted sequence builder.

getDescription() - Method in enum org.biojava.bio.program.fastq.FastqVariant

Return the description of this FASTQ sequence format variant.

getDescription() - Method in class org.biojava.bio.program.homologene.SimilarityType.PlaceHolder

getDescription() - Method in interface org.biojava.bio.program.homologene.Taxon

returns the name of the Taxon

getDescription() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub

getDescription() - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Gets the description for the AAindex entry.

getDescription() - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable

getDescription() - Method in class org.biojava.ontology.IntegerOntology

getDescription() - Method in class org.biojava.ontology.IntegerOntology.IntTerm

getDescription() - Method in interface org.biojava.ontology.Ontology

Return a human-readable description of this ontology, or the empty string if none is available

getDescription() - Method in class org.biojava.ontology.Ontology.Impl

getDescription() - Method in class org.biojava.ontology.OntologyTerm.Impl

getDescription() - Method in class org.biojava.ontology.RemoteTerm.Impl

getDescription() - Method in interface org.biojava.ontology.Term

Return a human-readable description of this term, or the empty string if none is available.

getDescription() - Method in class org.biojava.ontology.Term.Impl

getDescription() - Method in class org.biojava.ontology.Triple.Impl

getDescription() - Method in interface org.biojava.utils.candy.CandyVocabulary

It returns a description of this vocabulary.

getDescription() - Method in interface org.biojavax.bio.BioEntry

Returns a description of this sequence.

getDescription() - Method in class org.biojavax.bio.SimpleBioEntry

Returns a description of this sequence.

getDescription() - Method in interface org.biojavax.Namespace

Returns a description of this namespace.

getDescription() - Method in interface org.biojavax.ontology.ComparableOntology

Return a human-readable description of this ontology.

getDescription() - Method in class org.biojavax.ontology.SimpleComparableOntology

Return a human-readable description of this ontology.

getDescription() - Method in class org.biojavax.ontology.SimpleComparableTerm

Return a human-readable description of this term, or the empty string if none is available.

getDescription() - Method in class org.biojavax.ontology.SimpleComparableTriple

Return a human-readable description of this term, or the empty string if none is available.

getDescription() - Method in class org.biojavax.SimpleNamespace

Returns a description of this namespace.

getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getDescription(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter

getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getDescriptionNumber() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties

A method that simply returns the number of descriptions fetched with this RemoteQBlastOutputProperties object.

getDescriptor() - Method in interface org.biojava.utils.bytecode.CodeClass

getDescriptor() - Method in interface org.biojava.utils.bytecode.CodeMethod

A human-readable description of the class

getDescriptor() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass

getDescriptor() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod

getDescriptor() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass

getDescriptors() - Method in interface org.biojavax.ontology.ComparableTriple

Returns all descriptors.

getDescriptors() - Method in class org.biojavax.ontology.SimpleComparableTriple

Returns all descriptors.

getDetailsHandler() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler

Return a handler for the XFF details element.

getDFA() - Method in class org.biojava.utils.automata.DfaBuilder

getDimAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector

Retrieve the dimension at a specific index.

getDimensionRatio() - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer

getDimensionRatio returns the maximum ratio of long dimension to short dimension of the bead.

getDimensionsNChar() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

Get the NCHAR value.

getDimensionsNChar() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock

Get the NCHAR value.

getDimensionsNTax() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

Get the NTAX value.

getDimensionsNTax() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock

Get the NTAX value.

getDimensionsNTax() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock

Get the NTAX value.

getDinucleotideAlphabet() - Static method in class org.biojava.bio.symbol.CodonPrefTools

returns an RNA dinucleotide alphabet.

getDirection() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getDirection returns the direction in which this context expects the sequence to be rendered - HORIZONTAL or VERTICAL.

getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanel

Retrieve the current rendering direction.

getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Retrieve the current rendering direction.

getDirection() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Gets the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.

getDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getDirection() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getDirection() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getDirection returns the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.

getDisplayName() - Method in interface org.biojavax.bio.taxa.NCBITaxon

Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific

getDisplayName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific or if there are no scientific names at all, the empty string.

getDistanceBetweenFeatures() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

getDistribution() - Method in interface org.biojava.bio.dp.EmissionState

Get the Distribution associated with this state.

getDistribution() - Method in class org.biojava.bio.dp.SimpleEmissionState

getDistribution() - Method in class org.biojava.bio.gui.DistributionLogo

Retrieve the currently rendered dist.

getDistribution() - Method in interface org.biojava.bio.gui.LogoContext

getDistribution() - Method in class org.biojava.bio.molbio.Composition

Returns the distribution backing this class.

getDistribution(Symbol) - Method in interface org.biojava.bio.dist.OrderNDistribution

getDivision() - Method in interface org.biojavax.bio.BioEntry

Returns the division of this bioentry.

getDivision() - Method in class org.biojavax.bio.SimpleBioEntry

Returns the division of this bioentry.

getDNA() - Method in class org.biojava.bio.program.phred.PhredSequence

Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList

getDNA() - Static method in class org.biojava.bio.seq.DNATools

Return the DNA alphabet.

getDNAAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence

getDNADistribution(double) - Static method in class org.biojava.bio.seq.DNATools

return a SimpleDistribution of specified GC content.

getDNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Creates a DNA symbol tokenizer.

getDNASequence(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools

Get the called DNA sequence from a chromatogram.

getDNAxDNA() - Static method in class org.biojava.bio.seq.DNATools

Gets the (DNA x DNA) Alphabet

getDNAxDNADistribution(double, double) - Static method in class org.biojava.bio.seq.DNATools

return a (DNA x DNA) cross-product Distribution with specified DNA contents in each component Alphabet.

getDocumentReference() - Method in interface org.biojavax.RankedDocRef

Represents a reference to a document.

getDocumentReference() - Method in class org.biojavax.SimpleRankedDocRef

Represents a reference to a document.

getDotStatesIndex() - Method in class org.biojava.bio.dp.DP

getDouble() - Method in class org.biojava.utils.io.LargeBuffer

getDouble(long) - Method in class org.biojava.utils.io.LargeBuffer

getDoubleValue(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable

getDoubleValue(Symbol) - Method in interface org.biojava.bio.symbol.SymbolPropertyTable

getDownstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme

getDownstreamCut returns the cut site within or downstream of the recognition site.

getDownstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme

getDownstreamEndType returns the double-stranded end type produced by the primary (intra-site or downstream) cut.

getDP() - Method in class org.biojava.bio.dp.AbstractTrainer

getDP() - Method in interface org.biojava.bio.dp.TrainingAlgorithm

getDTDHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade

getE() - Method in class org.biojava.bio.proteomics.StructureTools

getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getEcNumber(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getEdgeLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree

getEdgeLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree

Tree navigation methods

getEditDistance() - Method in class org.biojava.bio.alignment.NeedlemanWunsch

This gives the edit distance according to the given parameters of this certain object.

getElementId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion

getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getElementId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getElementIds() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot

getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getElementIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getElideComments() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Is the format going to emit events when comments data or remarks from bibliographic references are read?

getElideComments() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Is the format going to emit events when comments data or remarks from bibliographic references are read?

getElideFeatures() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Is the format going to emit events when feature data is read?

getElideFeatures() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Is the format going to emit events when feature data is read?

getElideReferences() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Is the format going to emit events when bibliographic reference data is read?

getElideReferences() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Is the format going to emit events when bibliographic reference data is read?

getElideSymbols() - Method in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.

Return a flag indicating if symbol data will be skipped when parsing streams.

getElideSymbols() - Method in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.

getElideSymbols() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Is the format going to emit events when sequence data is read?

getElideSymbols() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Is the format going to emit events when sequence data is read?

getEliminateEnd() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

getEliminateStart() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

getEmail() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService

Get the email for QBlast.

getEmail() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

Get the email for Entrez.

getEmblBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.

Get a default SequenceBuilderFactory for handling EMBL files.

getEMBLTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms

Getter for the EMBL term

getEMBLxmlTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms

Getter for the EMBLxml term

getEmission(Symbol, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP

This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache.

getEmissions(List) - Method in class org.biojava.bio.dp.twohead.EmissionCache

getEmissions(List, boolean) - Method in class org.biojava.bio.dp.twohead.EmissionCache

Retrieve the emission scores from the cache for every EmissionState for the specified symbols.

getEnd() - Method in interface org.biojava.bio.program.gff.GFFRecord

The end of this feature within the source sequence.

getEnd() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

getEnd() - Method in interface org.biojava.bio.program.gff3.GFF3Record

getEnd() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl

getEnd() - Method in class org.biojava.bio.seq.impl.SubSequence

getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion

getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion

getEnd() - Method in class org.biojava.utils.automata.FiniteAutomaton

getEnd() - Method in interface org.biojava.utils.automata.NfaBuilder

getEnd() - Method in class org.biojava.utils.automata.NfaSubModel

getEnd() - Method in interface org.biojavax.bio.seq.Position

Returns the end of the range of bases this base could lie in.

getEnd() - Method in class org.biojavax.bio.seq.SimplePosition

Returns the end of the range of bases this base could lie in.

getEnd() - Method in interface org.biojavax.RankedDocRef

The end position in the sequence that this reference is referred to from.

getEnd() - Method in class org.biojavax.SimpleRankedDocRef

The end position in the sequence that this reference is referred to from.

getEndLabel() - Method in class org.biojava.utils.bytecode.InstructionVector

getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser

Get the current string indicating that a record has ended.

getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.RegexParser

Get the explicit end-of-record string.

getEntityResolver() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade

This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries.

getEntryByName(String) - Method in interface org.biojava.utils.candy.CandyVocabulary

It returns a selected vocabulary entry.

getEnvironment() - Method in class org.biojava.naming.ObdaContext

getEnvironmentProperties() - Method in class org.biojava.utils.process.ExternalProcess

Gets environment variables for the external process.

getEnzyme() - Method in interface org.biojava.bio.molbio.RestrictionSite

getEnzyme returns the enzyme which cuts at this site.

getEnzyme() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite

getEnzyme(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager

getEnzyme returns an enzyme by name.

getEpsilon() - Method in class org.biojava.stats.svm.SMOTrainer

getEquates() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

getErrorHandler() - Method in class org.biojava.bio.program.gff.GFFParser

Find the error handler used by this parser.

getErrorHandler() - Method in class org.biojava.bio.program.gff3.GFF3Parser

Find the error handler used by this parser.

getErrorHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade

getErrorHandler() - Method in class org.biojava.utils.process.ExternalProcess

Gets the output error handler which is responsible for the standard error output of the external process.

getErrString() - Method in class org.biojava.utils.ExecRunner

Returns the error string if exec(String) was invoked.

getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit

Return the overall E-value of this hit.

getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit

Return the E-value of this sub-hit.

getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit

Deprecated.

getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit

Deprecated.

getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit

getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit

getEvent() - Method in class org.biojava.utils.ChangeListener.ChangeEventRecorder

getEvents() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Getter for property events.

getEvidenceAttrTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

Getter for the evidence attr term

getEvidenceCategoryTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

Getter for the evidence category term

getEvidenceDateTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

Getter for the evidence date term

getEvidenceTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

Getter for the evidence type term

getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getExonIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getExtendedName() - Method in interface org.biojavax.DocRefAuthor

Returns the extended version of the authors name.

getExtendedName() - Method in class org.biojavax.SimpleDocRefAuthor

Returns the extended version of the authors name.

getFactory() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

Getter for property factory.

getFactory() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB

Getter for property factory.

getFactory(String, FiniteAutomaton) - Method in class org.biojava.utils.automata.ArrayStateMachineToolkit

getFastaBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.

Get a default SequenceBuilderFactory for handling FASTA files.

getFeature() - Method in interface org.biojava.bio.program.gff.GFFRecord

The feature type filed.

getFeature() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter

Retrieve the current feature.

getFeature() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

getFeature() - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature

getFeature() - Method in class org.biojavax.bio.seq.EmptyRichLocation

Retrieves the feature this location is associated with.

getFeature() - Method in interface org.biojavax.bio.seq.RichLocation

Retrieves the feature this location is associated with.

getFeature() - Method in class org.biojavax.bio.seq.SimpleRichLocation

Retrieves the feature this location is associated with.

getFeature(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade

getFeatureDescTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the FeatureDesc term

getFeatureFilter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF

Return the current FeatureFilter.

getFeatureFilter() - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandler

getFeatureFilter(int) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

Returns the ith FeatureFilter in this renderer.

getFeatureFromOriginal(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence

getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am including this method so that you can get the corresponding feature from the original sequence.

getFeatureHolder() - Method in interface org.biojava.bio.gui.sequence.FeatureSource

getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleFeature

A utility function to retrieve the feature holder delegate, creating it if necessary.

getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleSequence

getFeatureID(Feature) - Method in class org.biojava.bio.program.xff.BasicXFFHelper

getFeatureID(Feature) - Method in interface org.biojava.bio.program.xff.XFFHelper

getFeatureListener() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler

Return the object which receives startFeature/endFeature notifications.

getFeatureListener() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler

Return current feature listener

getFeatureListener() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler

Return current feature listener

getFeatureOriginalTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

Getter for the feature original term

getFeatureRealizer() - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory

Returns the FeatureRealizer set by "setFeatureRealizer".

getFeatureRefTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

Getter for the feature ref term

getFeatureRelationshipSet() - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder

Returns the set of relationships held in this feature holder.

getFeatureRelationshipSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature

Returns the set of relationships held in this feature holder.

getFeatureRenderer() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

getFeatureRenderer returns the currently active renderer.

getFeatures() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext

The features to render.

getFeatures() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getFeatures returns all of the Features belonging to the currently rendered Sequence.

getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePanel

getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

getFeatures() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

The features to render.

getFeatures() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext

getFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getFeatures() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getFeatures() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getFeatures returns all of the Features belonging to the currently rendered Sequence.

getFeatures() - Method in interface org.biojava.bio.seq.homol.Homology

Retrieve the set of features that mark homologous regions.

getFeatures() - Method in class org.biojava.bio.seq.homol.SimpleHomology

getFeatures returns the constituent HomologyFeatures which are also used as the keys in the alignment.

getFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence

getFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder

Returns the list of features in this featureholder.

getFeatures(String, FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource

Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.

getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource

getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource

getFeatures(FeatureFilter) - Method in interface org.biojava.bio.seq.distributed.DistDataSource

Get all features matching a FeatureFilter provided by this DistDataSource.

getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.GFFDataSource

getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource

getFeatureSet() - Method in interface org.biojavax.bio.seq.RichSequence

The features for this sequence.

getFeatureSet() - Method in class org.biojavax.bio.seq.ThinRichSequence

The features for this sequence.

getFeatureSource() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

getFeatureStatusTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

Getter for the feature status term

getFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler

Get the template for the feature being constructed.

getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getFeatureType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getFeatureVariationTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

Getter for the feature variation term

getField() - Method in class org.biojava.utils.ChangeType

Return a Field object where this change type is declared.

getFieldByName(String) - Method in interface org.biojava.utils.bytecode.CodeClass

Get a field by its name.

getFieldByName(String) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass

getFieldByName(String) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass

getFields() - Method in interface org.biojava.utils.bytecode.CodeClass

Get all fields accessible through this class.

getFields() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass

getFields() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass

getFile() - Method in interface org.biojava.bio.program.indexdb.Record

getFile returns the random access file in which the record belongs.

getFile() - Method in class org.biojava.bio.program.indexdb.Record.Impl

getFile() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess

getFile returns the File wrapped.

getFile() - Method in interface org.biojava.bio.seq.db.Index

The file to retrieve from.

getFile() - Method in class org.biojava.bio.seq.db.SimpleIndex

getFile() - Method in class org.biojava.utils.io.RAF

getFileIndex(File) - Method in class org.biojava.bio.seq.db.TabIndexStore

getFilePointer() - Method in class org.biojava.utils.io.CountedBufferedReader

getFilePointer() - Method in class org.biojava.utils.io.RandomAccessReader

getFilePointer returns the effective position of the pointer in the underlying RandomAccessFile.

getFiles() - Method in class org.biojava.bio.seq.db.BioIndex

getFiles() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore

getFiles() - Method in interface org.biojava.bio.seq.db.IndexStore

Retrieve the Set of files that are currently indexed.

getFiles() - Method in class org.biojava.bio.seq.db.TabIndexStore

getFill() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

getFillColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

Get the background color of the label area.

getFillPaint() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph

Returns the paint properties of this glyph.

getFilter() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

getFilter() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getFilter() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

getFilter returns the current filter.

getFilter() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter

getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor

getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByChild

getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant

getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByParent

getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren

getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants

getFinderName() - Method in interface org.biojava.utils.candy.CandyFinder

It returns a name of this vocabulary finder.

getFirstIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction

Getter for property firstIntActID.

getFirstOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair

gets the first orthologue in the orthology relationship.

getFirstOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair

getFitness() - Method in class org.biojavax.ga.impl.AbstractOrganism

getFitness() - Method in interface org.biojavax.ga.Organism

Returns the current fitness of this organism.

getFitnessFunction() - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll

getFitnessFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm

Returns the fitness function, i.e. the class that computes the fitness of each organism in a population.

getFitnessFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm

getFloat() - Method in class org.biojava.utils.io.LargeBuffer

getFloat(long) - Method in class org.biojava.utils.io.LargeBuffer

getFloatOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Helper method for converting a Number-valued option into a float primitive.

getFont() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getFont() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Gets the Font attribute of the SequenceRenderContext object

getFont() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getFont() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getFormat() - Method in class org.biojava.bio.seq.db.BioIndex

getFormat() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore

getFormat() - Method in interface org.biojava.bio.seq.db.IndexStore

Retrieve the format of the index file.

getFormat() - Method in class org.biojava.bio.seq.db.TabIndexStore

getFormat(String) - Static method in class org.biojava.bio.program.formats.FormatTools

Attempt to find aformat for a format identifer string.

getForwarders(ChangeType) - Method in class org.biojava.utils.Unchangeable

getForwardRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme

getForwardRegex returns a regular expression which matches the forward strand of the recognition site.

getForwardTransitions() - Method in class org.biojava.bio.dp.DP

getForwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP

getFrame() - Method in interface org.biojava.bio.program.gff.GFFRecord

The frame of the feature.

getFrame() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter

getFrame() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

getFrame() - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter

Retrieve the reading frame this filter matches.

getFrame() - Method in interface org.biojava.bio.seq.Frame

A method to get the frame information of the implementing object

getFrame() - Method in class org.biojava.bio.seq.FramedFeature.ReadingFrame

getFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature

getFrequency() - Method in interface org.biojava.bio.symbol.CodonPref

returns a Distribution giving the frequency of codons (sums to one over the totality of codons).

getFrequency() - Method in class org.biojava.bio.symbol.SimpleCodonPref

getFrequencyForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref

returns a Distribution giving the frequency of synonymous codons.

getFrequencyForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref

getFrequencyOfNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution

returns the frequency with which synonymous codons start with a specified pair of bases.

getFrom() - Method in exception org.biojava.bio.dp.IllegalTransitionException

getFTIdTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the FTId term

getFullName() - Method in class org.biojava.utils.bytecode.CodeField

Get the fully qualified name of the field.

getFullName() - Method in interface org.biojava.utils.bytecode.CodeMethod

The fully qualified name for this class

getFullName() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod

getFuzzyEnd() - Method in interface org.biojavax.bio.seq.Position

Returns true if the position has a fuzzy end.

getFuzzyEnd() - Method in class org.biojavax.bio.seq.SimplePosition

Returns true if the position has a fuzzy end.

getFuzzyStart() - Method in interface org.biojavax.bio.seq.Position

Returns true if the position has a fuzzy start.

getFuzzyStart() - Method in class org.biojavax.bio.seq.SimplePosition

Returns true if the position has a fuzzy start.

getG() - Method in class org.biojava.bio.molbio.DNAComposition

Get the relative compositon of 'G'.

getG() - Method in class org.biojava.bio.proteomics.StructureTools

getGap() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

getGapExt() - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Returns the current expenses of any extension of a gap operation.

getGapExt() - Method in class org.biojava.bio.alignment.SmithWaterman

getGapSymbol() - Method in class org.biojava.bio.symbol.AbstractAlphabet

getGapSymbol() - Method in interface org.biojava.bio.symbol.Alphabet

Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.

getGapSymbol() - Static method in class org.biojava.bio.symbol.AlphabetManager

Get the special `gap' Symbol.

getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet

getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet

getGapSymbol() - Method in class org.biojava.bio.symbol.IntegerAlphabet

getGapSymbol() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet

getGapSymbol(List) - Static method in class org.biojava.bio.symbol.AlphabetManager

Get the gap symbol appropriate to this list of alphabets.

getGenbankBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.

Get a default SequenceBuilderFactory for handling GenBank files.

getGenBankTerm() - Static method in class org.biojavax.bio.seq.io.GenbankFormat.Terms

Getter for the Genbank term

getGeneNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the GeneName term

getGenerateSequenceHeader() - Method in class org.biojava.bio.program.gff.SequencesAsGFF

Discover if per-sequence header lines will be generated.

getGeneration() - Method in interface org.biojavax.ga.GeneticAlgorithm

getGeneration() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm

The current generation

getGeneSynonymTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the GeneSynonym term

getGeneticCode() - Method in interface org.biojava.bio.symbol.CodonPref

the genetic code that this codon preference is based on.

getGeneticCode() - Method in class org.biojava.bio.symbol.SimpleCodonPref

getGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon

Returns the genetic code of this taxon, which may be null if not known.

getGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Returns the genetic code of this taxon, which may be null if not known.

getGeneticCode(int) - Static method in class org.biojava.bio.seq.RNATools

Retrieve a TranslationTable by number.

getGeneticCode(String) - Static method in class org.biojava.bio.seq.RNATools

Retrieve a TranslationTable by name.

getGeneticCodeName() - Method in interface org.biojava.bio.symbol.CodonPref

get the name of the genetic code

getGeneticCodeName() - Method in class org.biojava.bio.symbol.SimpleCodonPref

getGeneticCodeNames() - Static method in class org.biojava.bio.seq.RNATools

Retrieve a Set containing the name of each genetic code.

getGenomicTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms

Getter for the Ensembl-specific 'genomic' term

getGenpeptBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.

Get a default SequenceBuilderFactory for handling Genpept files.

getGlu_C_bicarbonate() - Static method in class org.biojava.bio.proteomics.ProteaseManager

getGlu_C_phosphate() - Static method in class org.biojava.bio.proteomics.ProteaseManager

getGlyphForFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

Returns the Glyph object which is assigned to the given feature filter.

getGonnet() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the GONNET amino acid substitution matrix.

getGraphics() - Method in interface org.biojava.bio.gui.LogoContext

getGroupAttributes() - Method in interface org.biojava.bio.program.gff.GFFRecord

A Map containing the group / attribute information.

getGroupAttributes() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getGroupOrder(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getH() - Method in class org.biojava.bio.proteomics.StructureTools

getHandler(String, String) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler

Retrieve a FilterHandler for the specified tag name.

getHandler(SeqSimilarityStAXAdapter) - Method in interface org.biojava.bio.program.ssbind.StAXHandlerFactory

getHandler returns an appropriate StAXContentHandler implementation containing a reference to a parent context.

getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.agave.StAXHandlerFactory

Return a suitable StAX content handler.

getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game.StAXHandlerFactory

Return a suitable StAX content handler.

getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game12.StAXHandlerFactory

Return a suitable StAX content handler.

getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler

get iterator for current stack starting at the position below mine.

getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler

get iterator for current stack starting at the position below mine.

getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler

return iterator to callbackStack

getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler

return iterator to callbackStack

getHeader() - Method in class org.biojavax.bio.seq.io.FastaFormat

getHeaderDefinitions() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer

Returns the appropriate style and javascript definitions for this renderer.

getHeight() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Returns the height of the whole graphic (in pixels).

getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer

getHeightScaling returns the state of the height scaling policy.

getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

getHeightScaling returns the state of the height scaling policy.

getHibernateSession() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB

getHibernateSession() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB

getHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node

getHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler

getHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult

Return all hits in this sequence similarity search result.

getHits() - Method in class org.biojava.bio.search.SequenceDBSearchResult

Deprecated.

getHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult

getHomologeneID() - Method in interface org.biojava.bio.program.homologene.Orthologue

get the Homologene ID.

getHomologeneID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue

getHomology() - Method in interface org.biojava.bio.seq.homol.HomologyFeature

getHomology() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature

getHorizontalScale() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Returns the in-use horizontal scale factor.

getI() - Method in class org.biojava.bio.proteomics.StructureTools

getId() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId

getId() - Method in class org.biojavax.bio.seq.SimplePosition

Gets the Hibernate ID.

getId() - Method in class org.biojavax.bio.seq.SimpleRichFeature

Gets the Hibernate ID.

getId() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship

Gets the Hibernate ID.

getId() - Method in class org.biojavax.bio.seq.SimpleRichLocation

Gets the Hibernate ID.

getId() - Method in class org.biojavax.bio.SimpleBioEntry

Gets the Hibernate ID.

getId() - Method in class org.biojavax.bio.SimpleBioEntryRelationship

Gets the Hibernate ID.

getId() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Gets the Hibernate ID.

getId() - Method in class org.biojavax.ontology.SimpleComparableOntology

Gets the Hibernate ID.

getId() - Method in class org.biojavax.ontology.SimpleComparableTerm

Gets the Hibernate ID.

getId() - Method in class org.biojavax.ontology.SimpleComparableTriple

Gets the Hibernate ID.

getId() - Method in class org.biojavax.SimpleComment

Gets the Hibernate ID.

getId() - Method in class org.biojavax.SimpleCrossRef

Gets the Hibernate ID.

getId() - Method in class org.biojavax.SimpleDocRef

Gets the Hibernate ID.

getId() - Method in class org.biojavax.SimpleNamespace

Gets the Hibernate ID.

getID() - Method in interface org.biojava.bio.program.indexdb.Record

getID returns the primary identifier of the record.

getID() - Method in class org.biojava.bio.program.indexdb.Record.Impl

getID() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster

The public unigene ID.

getID() - Method in interface org.biojava.bio.seq.db.Index

The ID of the sequence at this position in this file.

getID() - Method in class org.biojava.bio.seq.db.SimpleIndex

getID() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias

getID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction

Getter for property ID.

getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getIdAlias(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getIdentifier() - Method in interface org.biojava.utils.lsid.Identifiable

Return the identifier of this object.

getIdentifier() - Method in interface org.biojavax.bio.BioEntry

Returns the identifier of this bioentry.

getIdentifier() - Method in class org.biojavax.bio.SimpleBioEntry

Returns the identifier of this bioentry.

getIdentifier() - Method in interface org.biojavax.ontology.ComparableTerm

Returns the (optional) identifier associated with this term.

getIdentifier() - Method in class org.biojavax.ontology.SimpleComparableTerm

Returns the (optional) identifier associated with this term.

getIdentity() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the IDENTITY amino acid substitution matrix.

getIDMaker() - Method in class org.biojava.bio.seq.db.HashSequenceDB

Retrieve the IDMaker associated with this database.

getIDMaker() - Method in class org.biojavax.bio.db.HashRichSequenceDB

Retrieve the IDMaker associated with this database.

getIDs() - Method in class org.biojava.bio.seq.db.BioIndex

getIDs() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore

getIDs() - Method in interface org.biojava.bio.seq.db.IndexStore

Retrieve the set of all current IDs.

getIDs() - Method in class org.biojava.bio.seq.db.TabIndexStore

getIfFalse() - Method in class org.biojava.utils.bytecode.IfExpression

getIfInstruction() - Method in class org.biojava.utils.bytecode.IfExpression

getIfTrue() - Method in class org.biojava.utils.bytecode.IfExpression

getImage(int, int) - Method in class org.biojava.bio.program.abi.ABITrace

Returns a BufferedImage that represents the entire trace.

getImageMap() - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer

getImageMap returns the current image map.

getImageMap() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

getImageMap returns the current image map.

getImageMap() - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer

getImageMap returns the current image map.

getImplementationNames(Class) - Static method in class org.biojava.utils.Services

Return a Set of names of implementations of the given service interface in the classloader from which BioJava was loaded.

getImplementationNames(Class, ClassLoader) - Static method in class org.biojava.utils.Services

Return a List of names of implementations of the given service interface available in a given classloader.

getIndex(double) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext

Calculate the position in the sequence relating to the angle.

getIndex(double) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext

getIndexStore() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB

Retrieve the IndexStore.

getInitialContext(Hashtable) - Method in class org.biojava.naming.ObdaInitialContextFactory

getInnerMax() - Method in class org.biojava.bio.symbol.FuzzyLocation

getInnerMin() - Method in class org.biojava.bio.symbol.FuzzyLocation

getInput() - Method in interface org.biojava.utils.process.OutputHandler

Gets the input stream.

getInput() - Method in class org.biojava.utils.process.StreamPipe

Gets the input stream

getInput() - Method in class org.biojava.utils.process.WriterOutputHandler

Gets the input stream.

getInputHandler() - Method in class org.biojava.utils.process.ExternalProcess

Gets the input handler which is responsible for the standard input of the external process.

getInputStream(File) - Method in class org.biojava.utils.io.InputStreamProvider

get an InputStream for the file

getInputStream(String) - Static method in class org.biojava.utils.io.FlatFileCache

getInputStream(String) - Method in class org.biojava.utils.io.InputStreamProvider

get an InputStream for this file

getInputStream(URL) - Method in class org.biojava.utils.io.InputStreamProvider

getINSDseqTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms

Getter for the INSDseq term

getInsert() - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Returns the current expenses of a single insert operation.

getInsert() - Method in class org.biojava.bio.alignment.SmithWaterman

getInsert(int) - Method in class org.biojava.bio.dp.ProfileHMM

Retrieves the insert state at column indx.

getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.DBHelper

Deprecated.

Returns the id value created during the last insert command.

getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.HypersonicDBHelper

Deprecated.

getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper

Deprecated.

getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper

Deprecated.

getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper

getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper

Deprecated.

getInstance() - Static method in class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity

Retrieve the singleton instance of this class.

getInstance() - Static method in class org.biojava.bio.dist.IgnoreCountsTrainer

Returns the global singleton instance of the IgnoreCountsTrainer.

getInstance() - Static method in class org.biojava.bio.proteomics.ProteaseManager

getInstance() - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory

getInstance() - Static method in class org.biojava.bio.symbol.DoubleAlphabet

Retrieve the single DoubleAlphabet instance.

getInstance() - Static method in class org.biojava.bio.symbol.IntegerAlphabet

Retrieve the single IntegerAlphabet instance.

getInstance() - Static method in class org.biojava.bio.taxa.EbiFormat

Deprecated.

getInstance() - Static method in class org.biojava.naming.ObdaUriParser

getInstance() - Static method in class org.biojava.utils.io.FlatFileCache

getInstance() - Static method in class org.biojava.utils.walker.WalkerFactory

getInstance(Class) - Static method in class org.biojava.utils.walker.WalkerFactory

Make a WalkerFactory that handles a Visitor for a class of type typeClazz.

getInstance(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet

Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.

getInstance(FiniteAlphabet, SoftMaskedAlphabet.MaskingDetector) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet

Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any Symbol is soft masked or not.

getInt() - Method in class org.biojava.utils.io.LargeBuffer

getInt(long) - Method in class org.biojava.utils.io.LargeBuffer

getIntegerOntology() - Static method in class org.biojava.ontology.OntoTools

Get the Ontology that defines integers.

getInteractions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Getter for property interactions.

getInterfaces() - Method in interface org.biojava.utils.bytecode.CodeClass

getInterfaces() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass

getInterfaces() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass

getInternalSymbolList() - Method in interface org.biojavax.bio.seq.RichSequence

A special function that returns the SymbolList that this RichSequence is based around.

getInternalSymbolList() - Method in class org.biojavax.bio.seq.SimpleRichSequence

A special function that returns the SymbolList that this RichSequence is based around.

getInternalSymbolList() - Method in class org.biojavax.bio.seq.ThinRichSequence

A special function that returns the SymbolList that this RichSequence is based around.

getIntFromSymbolList(SymbolList, int) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools

Retrieves, unwraps, and returns an int from a SymbolList containing IntegerAlphabet.IntegerSymbols.

getIntOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Helper method for converting a Number-valued option into an int primitive.

getInvTransform() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

Returns a new AffineTransform describing the transformation from output space to chromatogram space.

getIsoelectricPoint(SymbolList) - Static method in class org.biojava.bio.proteomics.IsoelectricPointCalc

Static public method to compute the pI for a polypeptide in denaturating and reduced conditions with both free ends.

getIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Getter for property isoforms.

getIsoIDs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform

Getter for property isoIDs.

getIsoschizomers(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager

getIsoschizomers returns an unmodifable set of the isoschizomers of this enzyme.

getItem() - Method in interface org.biojava.stats.svm.ItemValue

getItem() - Method in class org.biojava.stats.svm.SimpleItemValue

getItems() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock

getIterator() - Method in class org.biojava.utils.ListTools.Doublet

getIterator() - Method in class org.biojava.utils.ListTools.Triplet

getJName() - Method in interface org.biojava.utils.bytecode.CodeClass

getJName() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass

getJName() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass

getJoiner() - Method in class org.biojava.bio.program.tagvalue.Aggregator

getJoinStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper

Deprecated.

Returns the an object indicating the style of table joining that this database should employ.

getJoinStyle() - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper

Deprecated.

getJoinTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation

Getter for the "join" term

getJournalReference() - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Gets a reference to the journal which published the article about the AAindex entry.

getKernel() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel

getKernel() - Method in interface org.biojava.stats.svm.SVMClassifierModel

getKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel

getKernel() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier

Retrieve the currently used kernel

getKernelValue(int, int) - Method in class org.biojava.stats.svm.SVMRegressionModel

getKey() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker

getKey() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains

getKey() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation

getKey() - Method in class org.biojava.bio.seq.FeatureFilter.HasAnnotation

getKey() - Method in class org.biojava.utils.cache.KeyedWeakReference

getKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model

getKeys() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory

getKeys() - Method in class org.biojava.bio.program.tagvalue.Index2Model

getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getKeyword(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter

getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getKeywordTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms

Getter for the keyword term

getKineticsNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Getter for property kineticsNote.

getKmpNextTable() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch

Returns the table of border lengths

getKMs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Getter for property KMs.

getLabel() - Method in interface org.biojava.bio.alignment.AlignmentElement

getLabel() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement

getLabel() - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer

getLabel() - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer

getLabel() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState

return the label of this class.

getLabel() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State

getLabel() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector

getLabel() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction

Getter for property label.

getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getLabel(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree

getLabelGlyph(SequenceRenderContext, FontRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer

getLabelMaker() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer

getLabels() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

getLabels() - Method in interface org.biojava.bio.alignment.Alignment

The list of SymbolLists in the alignment.

getLabels() - Method in class org.biojava.bio.alignment.FlexibleAlignment

getLabels will return a list of labels in left to right order

getLabels() - Method in class org.biojava.bio.alignment.SimpleAlignment

getLabels() - Method in class org.biojava.bio.dp.SimpleStatePath

getLabels() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment

getLabels() - Method in class org.biojava.bio.symbol.RelabeledAlignment

getLabelsAt(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

getLambda() - Method in class org.biojava.stats.svm.DiagonalAddKernel

Retrieve the scale factor.

getLast() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder

Get the last complete annotation built.

getLastScore() - Method in class org.biojava.bio.dp.AbstractTrainer

getLastScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm

getLeader() - Method in class org.biojava.utils.ListTools.SeriesList

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getLeadingBorder returns the leading border of the primary sequence.

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel

Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.

getLeadingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Gets the LeadingBorder attribute of the SequenceRenderContext object.

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getLeadingBorder returns the leading border.

getLeadingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

getLeftValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon

Gets the left value.

getLeftValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Gets the left value.

getLength() - Method in interface org.biojava.bio.program.indexdb.Record

getLength returns the length of the record in bytes.

getLength() - Method in class org.biojava.bio.program.indexdb.Record.Impl

getLength() - Method in class org.biojava.bio.search.SeqContentPattern

Get the current length.

getLength() - Method in interface org.biojava.bio.seq.db.Index

The entry can be slurped out of the file by grabbing length bytes from start.

getLength() - Method in class org.biojava.bio.seq.db.SimpleIndex

getLength() - Method in class org.biojava.bio.symbol.CircularLocation

getLength() - Method in class org.biojava.utils.RepeatedCharSequence

getLevel() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler

return current stack level.

getLevel() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler

return current stack level.

getLimit() - Method in class org.biojava.utils.cache.FixedSizeCache

getLine() - Method in exception org.biojava.utils.ParserException

Get the text of the line where the exception occured.

getLineNumber() - Method in exception org.biojava.utils.ParserException

Get the line number in the stream where this exception occured.

getLines() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Retrieve the number of lines that the sequence will be rendered over.

getLineWidth() - Method in class org.biojava.bio.program.phred.PhredFormat

Retrive the current line width.

getLineWidth() - Method in class org.biojava.bio.seq.io.FastaFormat

Deprecated.

Retrive the current line width.

getLineWidth() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Retrive the current line width.

getLineWidth() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Retrive the current line width.

getListener() - Method in class org.biojava.bio.program.tagvalue.ParserListener

getListener returns the listener of the pair.

getListener() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState

return the TagValueListener assigned to this State.

getListener() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State

getListener(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator

getListeners(ChangeType) - Method in class org.biojava.utils.Unchangeable

getLITDBEntryNumbers() - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Gets the list of literature database identifiers for the AAindex entry.

getLoc() - Method in interface org.biojava.bio.alignment.AlignmentElement

getLoc() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement

getLocation() - Method in class org.biojava.bio.program.indexdb.BioStore

getLocation returns the directory where the index is located.

getLocation() - Method in interface org.biojava.bio.seq.Feature

The location of this feature.

getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation

getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation

getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation

getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation

getLocation() - Method in class org.biojava.bio.seq.impl.SimpleFeature

getLocation() - Method in class org.biojava.bio.seq.RemoteFeature.Region

Retrieve the Location of the Region.

getLocation() - Method in class org.biojavax.bio.seq.SimpleRichFeature

The location of this feature.

getLocation() - Method in interface org.biojavax.DocRef

Returns a textual description of the document reference.

getLocation() - Method in interface org.biojavax.RankedDocRef

If this object was constructed using a location instead of two integers, then this method will return that location.

getLocation() - Method in class org.biojavax.SimpleDocRef

Returns a textual description of the document reference.

getLocation() - Method in class org.biojavax.SimpleRankedDocRef

getLocationHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler

getLocationSequenceTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms

Getter for the location seq term

getLocator() - Method in exception org.biojava.utils.ParserException

Get a locator for the stream which caused this exception.

getLocusID() - Method in interface org.biojava.bio.program.homologene.Orthologue

get the locus ID associated with this orthologue.

getLocusID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue

getLogoFont() - Method in class org.biojava.bio.gui.TextBlock

Retrieve the current font.

getLogoFont() - Method in class org.biojava.bio.gui.TextLogoPainter

Retrieve the current font.

getLogoPainter() - Method in class org.biojava.bio.gui.DistributionLogo

Retrieve the current logo painter.

getLong() - Method in class org.biojava.utils.io.LargeBuffer

getLong(long) - Method in class org.biojava.utils.io.LargeBuffer

getLSID() - Method in class org.biojava.bio.program.formats.Embl

getLSID() - Method in class org.biojava.bio.program.formats.Enzyme

getLSID() - Method in interface org.biojava.bio.program.formats.Format

Retrieve the LSID associated with this format.

getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Compound

getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme

getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Reaction

getLSID() - Method in class org.biojava.bio.program.formats.Swissprot

getLys_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager

getMagicalState() - Method in class org.biojava.bio.program.tagvalue.StateMachine

getMagicalState(Alphabet, int) - Static method in class org.biojava.bio.dp.MagicalState

getMapAll() - Method in class org.biojava.bio.molbio.RestrictionMapper

getMapAll returns whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it.

getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getMapLocation(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getMapper() - Method in class org.biojava.bio.AnnotationRenamer

getMapper returns the TagMapper being used to remap the Annotation.

getMapper() - Method in class org.biojava.bio.program.tagvalue.TagRenamer

Retrieve the mapper used to rename tags

getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

getMapPosition(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getMapType() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation

getMaskedAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet

Gets the Alphabet upon which masking is being applied

getMaskingDetector() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet

Getter for the MaskingDetector
getMass(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc Get the Mass of this peptide. getMass(SymbolList, String, boolean) - Static method in class org.biojava.bio.proteomics.MassCalc getMass calculates the mass of this peptide. getMatch() - Method in class org.biojava.bio.alignment.NeedlemanWunsch Returns the current expenses of a single match operation. getMatch() - Method in class org.biojava.bio.alignment.SmithWaterman getMatch() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the MATCH amino acid substitution matrix. getMatch(int) - Method in class org.biojava.bio.dp.ProfileHMM Retrieve the match state at column indx. getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getMatchAlign(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getMatchChar() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getMatchDesc(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getMatches() - Method in class org.biojava.bio.dp.SimpleEmissionState getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol getMatches() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol getMatches() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol getMatches() - Method in interface org.biojava.bio.symbol.Symbol The alphabet containing the symbols matched by this ambiguity symbol. getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getMatchRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getMatrixData(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock getMatrixData(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock getMatrixLabels() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock getMatrixLabels() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock getMax() - Method in class org.biojava.bio.alignment.SubstitutionMatrix The maximum score in this matrix. getMax() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram getMax() - Method in interface org.biojava.bio.chromatogram.Chromatogram Gets the max intensity from all the traces. getMax() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator getMax() - Method in class org.biojava.bio.symbol.CircularLocation This will give you the coordinate of the maximum point contained by this Location. getMax() - Method in class org.biojava.bio.symbol.FuzzyLocation getMax() - Method in class org.biojava.bio.symbol.FuzzyPointLocation getMax() - Method in interface org.biojava.bio.symbol.Location The maximum position contained. getMax() - Method in class org.biojava.bio.symbol.PointLocation getMax() - Method in class org.biojava.bio.symbol.RangeLocation getMax() - Method in class org.biojavax.bio.seq.EmptyRichLocation The maximum position contained. getMax() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation The maximum position contained. getMax() - Method in class org.biojavax.bio.seq.SimpleRichLocation The maximum position contained. getMax(AtomicSymbol) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram getMax(AtomicSymbol) - Method in interface org.biojava.bio.chromatogram.Chromatogram Gets the max intensity on the trace for the specified nucleotide. getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver Resolves the maximum possible base for this position. getMax(Position) - Method in interface org.biojavax.bio.seq.PositionResolver Resolves the maximum possible base for this position. getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver Resolves the maximum possible base for this position. getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver Resolves the maximum possible base for this position. getMaxCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern Get the maximum counts required for a symbol. getMaxCrossOvers() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction getMaxCrossOvers() - Method in interface org.biojavax.ga.functions.CrossOverFunction getMaxCrossOvers() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross getMaxGenerations() - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration getMaxPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation Retrieves the end position of this location. getMaxPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation Retrieves the end position of this location. getMaxPosition() - Method in interface org.biojavax.bio.seq.RichLocation Retrieves the end position of this location. getMaxPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation Retrieves the end position of this location. getMaxRunTimeExceeded() - Method in class org.biojava.utils.ExecRunner Returns whether the maximum runtime was exceeded or not. getMaxRunTimeSecs() - Method in class org.biojava.utils.ExecRunner Returns the maximum run time in seconds for this object. getMaxScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore getMaxScore returns the maximum score accepted. getMaxSize() - Method in class org.biojava.utils.cache.FixedSizeMap getMaxValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange getMergeAnnotation() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler getMerged() - Method in class org.biojava.bio.annodb.MergingAnnotationDB Return a list of merged DBs. getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser See if tags are being merged. getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser Report whether empty tags will be treated as continuations of the last non -empty tag. getMessage() - Method in class org.biojava.utils.ParseErrorEvent Find the message about this event getMetaData() - Method in class org.biojava.bio.program.indexdb.BioStore getMetaData() - Method in interface org.biojava.bio.program.indexdb.IndexStore getMetaData returns a data structure which represents an OBDA "config.dat" flatfile indexing configuration file. getMethod() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory Get the Method used. getMethod(String, CodeClass[]) - Method in interface org.biojava.utils.bytecode.CodeClass Get a method by name and argument list. getMethod(String, CodeClass[]) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass getMethod(String, CodeClass[]) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass getMethods() - Method in interface org.biojava.utils.bytecode.CodeClass Get all methods declared by this class and its super classes, removing all super class methods that are over ridden. getMethods() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass getMethods() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass getMethodsByName(String) - Method in interface org.biojava.utils.bytecode.CodeClass Get the name of all methods that could be invoked through this class with a given name. getMethodsByName(String) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass getMethodsByName(String) - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass getMin() - Method in class org.biojava.bio.alignment.SubstitutionMatrix The minimum score of this matrix. getMin() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator getMin() - Method in class org.biojava.bio.symbol.CircularLocation This will give you the coordinate of the minimum point contained by this Location. getMin() - Method in class org.biojava.bio.symbol.FuzzyLocation getMin() - Method in class org.biojava.bio.symbol.FuzzyPointLocation getMin() - Method in interface org.biojava.bio.symbol.Location The minimum position contained. getMin() - Method in class org.biojava.bio.symbol.PointLocation getMin() - Method in class org.biojava.bio.symbol.RangeLocation getMin() - Method in class org.biojavax.bio.seq.EmptyRichLocation The minimum position contained. getMin() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation The minimum position contained. getMin() - Method in class org.biojavax.bio.seq.SimpleRichLocation The minimum position contained. getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver Resolves the minimum possible base for this position. getMin(Position) - Method in interface org.biojavax.bio.seq.PositionResolver Resolves the minimum possible base for this position. getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver Resolves the minimum possible base for this position. getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver Resolves the minimum possible base for this position. getMinCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern Get the minimum counts required for a symbol. getMinIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet get the lowest level of identity observed in this Group getMinIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet getMinimumLeader(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer getMinimumLeader returns the maximum value of getMinimumLeader() for a list of SequenceRenderers. getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer getMinimumLeader(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer Retrieve the minimum leading distance for this renderer when rendering src. getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer getMinimumTrailer(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer getMinimumTrailer returns the maximum value of getMinimumTrailer() for a list of SequenceRenderers. getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer getMinimumTrailer(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer Retrieve the minimum trailing distance for this renderer when rendering src. getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer getMinimumWidth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.LabelRenderer Retrieve the minimum space required to render the label. getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer getMinPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation Retrieves the start position of this location. getMinPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation Retrieves the start position of this location. getMinPosition() - Method in interface org.biojavax.bio.seq.RichLocation Retrieves the start position of this location. getMinPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation Retrieves the start position of this location. getMinScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore getMinScore returns the minimum score accepted. getMinValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange getMismatches() - Method in class org.biojava.bio.search.MaxMismatchPattern getMissing() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock getMissing() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock getMitoGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon Returns the mitochondrial genetic code of this taxon, which may be null if not known. getMitoGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Getter for property mitoGeneticCode. getModel() - Method in class org.biojava.bio.dp.DP getModel() - Method in interface org.biojava.bio.dp.ModelInState The model that is inside this state. getModel() - Method in class org.biojava.bio.dp.SimpleModelInState getModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser getModifiable() - Method in class org.biojava.utils.MergingSet getModifiers() - Method in interface org.biojava.utils.bytecode.CodeClass Get the modifiers associated with the class. getModifiers() - Method in class org.biojava.utils.bytecode.CodeField Get the moddifiers applied to this field. getModifiers() - Method in interface org.biojava.utils.bytecode.CodeMethod Get the modifiers, such as PUBLIC, ABSTRACT and so on getModifiers() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass getModifiers() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod getModifiers() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass getMolecularWeight() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property molecularWeight. getMolecularWeight(SymbolList) - Static method in class org.biojava.bio.proteomics.MassCalc Calculate the molecular weight of a protein, making estimates whenever it is possible like averaging mass values for ambiguity symbols or counting zero when gaps are encountered. getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getMolType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getMolTypeTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms getter for the MolType term getMolWeightError() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property molWeightError. getMolWeightMethod() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property molWeightMethod. getMolWeightRangeEnd() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property molWeightRangeEnd. getMolWeightRangeStart() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property molWeightRangeStart. getMoreSearches() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser getMoreSearches() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder getMoreSearches() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder getMoreSearches() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder getMoreSearches() - Method in class org.biojava.bio.search.SearchContentAdapter getMoreSearches() - Method in class org.biojava.bio.search.SearchContentFilter getMoreSearches() - Method in interface org.biojava.bio.search.SearchContentHandler getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source. getMoreSearches() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger getMotifs() - Method in class org.biojava.bio.program.Meme getMouseEvent() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent Get the mouse event that caused this. getMultiplier() - Method in class org.biojava.stats.svm.PolynomialKernel getMultiplier() - Method in class org.biojava.stats.svm.SigmoidKernel getMutationFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm getMutationFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm getMutationProbs() - Method in class org.biojavax.ga.functions.AbstractMutationFunction getMutationProbs() - Method in interface org.biojavax.ga.functions.MutationFunction getMutationProbs() - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation getMutationSpectrum() - Method in class org.biojavax.ga.functions.AbstractMutationFunction getMutationSpectrum() - Method in interface org.biojavax.ga.functions.MutationFunction getMutationSpectrum() - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation getMyComponents(Name) - Method in class org.biojava.naming.ObdaContext getName() - Method in class org.biojava.bio.alignment.SubstitutionMatrix Every substitution matrix has a name like "BLOSUM30" or "PAM160". getName() - Method in interface org.biojava.bio.annodb.AnnotationDB The name of this AnnotationDB. getName() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB getName() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB getName() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB getName() - Method in class org.biojava.bio.annodb.MergingAnnotationDB getName() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB getName() - Method in class org.biojava.bio.dp.SimpleEmissionState getName() - Method in class org.biojava.bio.molbio.RestrictionEnzyme getName returns the enzyme name. getName() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet retrieves name of this group. getName() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet getName() - Method in class org.biojava.bio.program.indexdb.BioStore The name of this store or null if the name has not been set. getName() - Method in class org.biojava.bio.proteomics.Protease Gets the name of this Protease getName() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider getName() - Method in class org.biojava.bio.seq.db.BioIndex getName() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB Deprecated. getName() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider Deprecated. getName() - Method in class org.biojava.bio.seq.db.CachingSequenceDB getName() - Method in class org.biojava.bio.seq.db.DummySequenceDB getName() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore getName returns the database name as defined within the EMBL CD-ROM index. getName() - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB getName() - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider getName() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB getName() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB getName() - Method in class org.biojava.bio.seq.db.HashSequenceDB getName() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB Get the name of this sequence database. getName() - Method in interface org.biojava.bio.seq.db.IndexStore Retrieve the name of this store. getName() - Method in class org.biojava.bio.seq.db.NCBISequenceDB getName() - Method in interface org.biojava.bio.seq.db.SequenceDBLite Get the name of this sequence database. getName() - Method in class org.biojava.bio.seq.db.SubSequenceDB getName() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB getName() - Method in class org.biojava.bio.seq.db.TabIndexStore getName() - Method in class org.biojava.bio.seq.db.ViewingSequenceDB getName() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB getName() - Method in interface org.biojava.bio.seq.FeatureTypes.Repository The name of this repository. getName() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl getName() - Method in interface org.biojava.bio.seq.FeatureTypes.Type Get the name of this type. getName() - Method in class org.biojava.bio.seq.impl.DummySequence getName() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence getName() - Method in class org.biojava.bio.seq.impl.SimpleSequence getName() - Method in class org.biojava.bio.seq.impl.SubSequence getName() - Method in class org.biojava.bio.seq.impl.ViewSequence getName() - Method in class org.biojava.bio.seq.NewSimpleAssembly getName() - Method in interface org.biojava.bio.seq.Sequence The name of this sequence. getName() - Method in class org.biojava.bio.seq.SimpleAssembly getName() - Method in interface org.biojava.bio.symbol.Alphabet Get the name of the alphabet. getName() - Method in interface org.biojava.bio.symbol.CodonPref get name of object getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet getName() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet getName() - Method in class org.biojava.bio.symbol.SimpleAlphabet getName() - Method in class org.biojava.bio.symbol.SimpleCodonPref getName() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable getName() - Method in class org.biojava.bio.symbol.SingletonAlphabet getName() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet The name of the Alphabet getName() - Method in interface org.biojava.bio.symbol.Symbol The long name for the symbol. getName() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable getName() - Method in class org.biojava.bio.taxa.SimpleTaxonFactory Deprecated. getName() - Method in interface org.biojava.bio.taxa.TaxonFactory Deprecated. Name for this TaxonFactory. getName() - Method in class org.biojava.bio.taxa.WeakTaxonFactory Deprecated. getName() - Method in interface org.biojava.directory.SequenceDBProvider The name of this provider. getName() - Method in class org.biojava.ontology.IntegerOntology getName() - Method in class org.biojava.ontology.IntegerOntology.IntTerm getName() - Method in interface org.biojava.ontology.Ontology Return the name of this ontology getName() - Method in class org.biojava.ontology.Ontology.Impl getName() - Method in class org.biojava.ontology.OntologyTerm.Impl getName() - Method in class org.biojava.ontology.RemoteTerm.Impl getName() - Method in class org.biojava.ontology.Synonym getName() - Method in interface org.biojava.ontology.Term Return the name of this term. getName() - Method in class org.biojava.ontology.Term.Impl getName() - Method in class org.biojava.ontology.Triple.Impl getName() - Method in interface org.biojava.utils.bytecode.CodeClass getName() - Method in class org.biojava.utils.bytecode.CodeField Get the name of the field. getName() - Method in interface org.biojava.utils.bytecode.CodeMethod The name of the method. getName() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass getName() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod getName() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass getName() - Method in class org.biojava.utils.bytecode.LocalVariable getName() - Method in class org.biojava.utils.bytecode.ParametricType Get the name of this type. getName() - Method in interface org.biojava.utils.candy.CandyVocabulary It returns a name of this vocabulary. getName() - Method in class org.biojava.utils.ChangeType Return the name of this change. getName() - Method in class org.biojava.utils.regex.Pattern return the String label associated with this pattern. getName() - Method in interface org.biojavax.bio.BioEntry Returns the name of this bioentry. getName() - Method in interface org.biojavax.bio.db.BioEntryDBLite Get the name of this sequence database. getName() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB getName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName getName() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB getName() - Method in class org.biojavax.bio.db.HashBioEntryDB getName() - Method in class org.biojavax.bio.db.HashRichSequenceDB getName() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB getName() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB getName() - Method in interface org.biojavax.bio.seq.RichFeature Returns the name of this feature. getName() - Method in class org.biojavax.bio.seq.RichLocation.Strand Returns the string symbol of this strand. getName() - Method in class org.biojavax.bio.seq.SimpleRichFeature Returns the name of this feature. getName() - Method in class org.biojavax.bio.SimpleBioEntry Returns the name of this bioentry. getName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName Returns this name. getName() - Method in interface org.biojavax.DocRefAuthor Returns a textual description of the authors name. getName() - Method in class org.biojavax.ga.impl.AbstractOrganism getName() - Method in class org.biojavax.ga.impl.AbstractPopulation getName() - Method in interface org.biojavax.ga.Organism Gets the organisms name getName() - Method in interface org.biojavax.ga.Population getName() - Method in interface org.biojavax.Namespace The name of the namespace is immutable and must be set by the constructor of the instantiating class. getName() - Method in class org.biojavax.ontology.SimpleComparableOntology Return the name of this ontology getName() - Method in class org.biojavax.ontology.SimpleComparableTerm Return the name of this term. getName() - Method in class org.biojavax.ontology.SimpleComparableTriple Return the name of this term. getName() - Method in class org.biojavax.SimpleDocRefAuthor Returns a textual description of the authors name. getName() - Method in class org.biojavax.SimpleNamespace The name of the namespace is immutable and must be set by the constructor of the instantiating class. getNameClass() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName Returns the class of this name. getNameClasses() - Method in interface org.biojavax.bio.taxa.NCBITaxon Returns all the name classes available for a taxon. getNameClasses() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Returns all the name classes available for a taxon. getNamedIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event Getter for property namedIsoforms. getNameHierarchy() - Method in interface org.biojavax.bio.taxa.NCBITaxon Returns the taxonomy hierarchy of this taxon entry in the form: least specific; more specific; ...; most specific. getNameHierarchy() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific. getNameInNamespace() - Method in class org.biojava.naming.ObdaContext getNameParser(String) - Method in class org.biojava.naming.ObdaContext getNameParser(Name) - Method in class org.biojava.naming.ObdaContext getNames() - Static method in class org.biojava.bio.proteomics.ProteaseManager getNames() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform Getter for property names. getNames(String) - Method in interface org.biojavax.bio.taxa.NCBITaxon Returns all the names available for a taxon in a given class. getNames(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Returns all the names available for a taxon in a given class. getNameSet() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon getNamesMap() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon getNamespace() - Method in interface org.biojavax.bio.BioEntry Returns the namespace of this bioentry. getNamespace() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Getter for property namespace. getNamespace() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB Getter for property namespace. getNamespace() - Method in class org.biojavax.bio.SimpleBioEntry Returns the namespace of this bioentry. getNamespaceId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier Return the namespace id for this identifier within the authority. getNameToSymbol() - Method in class org.biojava.bio.seq.io.NameTokenization getNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon Gets the NCBI taxon ID. getNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Gets the NCBI taxon ID. getNCutters(int) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager getNCutters returns an unmodifable set of all enzymes with a cut site of size n. getNegShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier Retrieve the shape used to represent negative points. getNestedKernel() - Method in class org.biojava.stats.svm.NestedKernel Retrieve the currently nested SVMKernel. getNestedValue(NestedValue, String, int) - Method in class org.biojava.ontology.obo.OboFileParser getNewTag(Object) - Method in interface org.biojava.bio.program.tagvalue.PropertyChanger getNewTag returns the tag which substitutes the specified value. getNewTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper getNexusBlock() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract getNexusBlock() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder Obtain the constructed block. getNexusFile() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder Obtain the constructed file. getNodePrefix() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock Returns the node prefix. getNodeRank() - Method in interface org.biojavax.bio.taxa.NCBITaxon Gets the node rank of this taxon. getNodeRank() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Gets the node rank of this taxon. getNodes() - Method in class org.biojava.utils.automata.FiniteAutomaton get all Nodes within this instance. getNodes() - Method in interface org.biojava.utils.automata.NfaBuilder getNodes() - Method in class org.biojava.utils.automata.NfaSubModel getNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution returns Set containing the nonWobbleBases that occur in codons that encode this residue getNormalizingVector() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel Retrive the current normalizing vector. getNotCleaveResidues() - Method in class org.biojava.bio.proteomics.Protease The list of residues that will prevent cleavage if they follow the cleavage residue. getNote() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property note. getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform Getter for property note. getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getNote(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getNote(Note) - Method in class org.biojavax.EmptyRichAnnotation Uses the term and rank to lookup a note in this annotation. getNote(Note) - Method in interface org.biojavax.RichAnnotation Uses the term and rank to lookup a note in this annotation. getNote(Note) - Method in class org.biojavax.SimpleRichAnnotation Uses the term and rank to lookup a note in this annotation. getNoteSet() - Method in class org.biojavax.bio.seq.CompoundRichLocation Returns the set of notes associated with this object. getNoteSet() - Method in class org.biojavax.bio.seq.EmptyRichLocation Returns the set of notes associated with this object. getNoteSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature Returns the set of notes associated with this object. getNoteSet() - Method in class org.biojavax.bio.seq.SimpleRichLocation Returns the set of notes associated with this object. getNoteSet() - Method in class org.biojavax.bio.SimpleBioEntry Returns the set of notes associated with this object. getNoteSet() - Method in class org.biojavax.EmptyRichAnnotation Returns an immutable set of all notes in this annotation. getNoteSet() - Method in interface org.biojavax.RichAnnotatable Returns the set of notes associated with this object. getNoteSet() - Method in interface org.biojavax.RichAnnotation Returns an immutable set of all notes in this annotation. getNoteSet() - Method in class org.biojavax.SimpleCrossRef Returns the set of notes associated with this object. getNoteSet() - Method in class org.biojavax.SimpleRichAnnotation Returns an immutable set of all notes in this annotation. getNuc4_2() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the NUC.4.2 nucleotide substitution matrix. getNuc4_4() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the NUC.4.4 nucleotide substitution matrix. getNucleotide() - Static method in class org.biojava.bio.seq.NucleotideTools Return the Nucleotide alphabet. getNucleotideParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Creates a nucleotide symbol tokenizer. getNullModel() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution getNullModel() - Method in interface org.biojava.bio.dist.Distribution Retrieve the null model Distribution that this Distribution recognizes. getNullModel() - Method in class org.biojava.bio.dist.GapDistribution getNullModel() - Method in class org.biojava.bio.dist.PairDistribution getNullModel() - Method in class org.biojava.bio.dist.SimpleDistribution getNullModel() - Method in class org.biojava.bio.dist.TranslatedDistribution getNullModel() - Method in class org.biojava.bio.dist.UniformDistribution getNullModel(Distribution, Distribution) - Static method in class org.biojava.bio.dist.PairDistribution Get a uniform null model over a PairDistribution over [first,second]. getNullModelWeight() - Method in interface org.biojava.bio.dist.DistributionTrainerContext Return the number of pseudocounts added to the distribution when training. getNullModelWeight() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext getNumber() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode Return a number (usually, but not always, a motif count) associated with this node of the tree. getNumberExperiments() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction Getter for property numberExperiments. getNumCount() - Method in interface org.biojava.utils.candy.CandyFinder It returns the number of available vocabularies. getNumGapsInQuery() - Method in class org.biojava.bio.alignment.AlignmentPair getNumGapsInSubject() - Method in class org.biojava.bio.alignment.AlignmentPair getNumIdenticals() - Method in class org.biojava.bio.alignment.AlignmentPair getNumSimilars() - Method in class org.biojava.bio.alignment.AlignmentPair getObject() - Method in interface org.biojava.ontology.Triple Return the object term of this triple. getObject() - Method in class org.biojava.ontology.Triple.Impl getObject() - Method in interface org.biojavax.bio.BioEntryRelationship Returns the object of this relationship (ie. the BioEntry which this relationship starts from). getObject() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship Returns the object of this relationship (ie. the feature which this relationship starts from). getObject() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship Returns the object of this relationship (ie. the feature which this relationship starts from). getObject() - Method in class org.biojavax.bio.SimpleBioEntryRelationship Returns the object of this relationship (ie. the BioEntry which this relationship starts from). getObject() - Method in class org.biojavax.ontology.SimpleComparableTriple Return the object term of this triple. getObject(Class, Object[]) - Static method in class org.biojavax.RichObjectFactory Delegates to a RichObjectBuilder to construct/retrieve the object, and returns it. getObjectId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier Return the object id of this identifier. getOboFileEventListener() - Method in class org.biojava.ontology.obo.OboFileParser getObsolete() - Method in interface org.biojavax.ontology.ComparableTerm Checks to see if this term is obsolete. getObsolete() - Method in class org.biojavax.ontology.SimpleComparableTerm Checks to see if this term is obsolete. getOffset() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext Get the angle through which the origin of the sequence is rotated through. getOffset() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel getOffset() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext getOffset() - Method in interface org.biojava.bio.program.indexdb.Record getOffset returns the byte offset in the file at which the record begins. getOffset() - Method in class org.biojava.bio.program.indexdb.Record.Impl getOldIDHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler getOntology() - Method in class org.biojava.ontology.IntegerOntology.IntTerm getOntology() - Method in interface org.biojava.ontology.OntologyTerm Get the remote ontology referenced by this term getOntology() - Method in class org.biojava.ontology.OntologyTerm.Impl getOntology() - Method in class org.biojava.ontology.RemoteTerm.Impl getOntology() - Method in interface org.biojava.ontology.Term Return the ontology in which this term exists. getOntology() - Method in class org.biojava.ontology.Term.Impl getOntology() - Method in class org.biojava.ontology.Triple.Impl getOntology() - Method in class org.biojavax.ontology.SimpleComparableTerm Return the ontology in which this term exists. getOntology() - Method in class org.biojavax.ontology.SimpleComparableTriple Return the ontology in which this term exists. getOntology(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB Deprecated. getOps() - Method in class org.biojava.ontology.IntegerOntology getOps() - Method in interface org.biojava.ontology.Ontology Return the associated OntologyOps. getOps() - Method in class org.biojava.ontology.Ontology.Impl getOps() - Method in class org.biojavax.ontology.SimpleComparableOntology Return the associated OntologyOps. getOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Returns the current value for the specified option. getOrCreateTerm(String) - Method in interface org.biojavax.ontology.ComparableOntology Looks for a term with the given name and returns it. getOrCreateTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology Looks for a term with the given name and returns it. getOrCreateTriple(Term, Term, Term) - Method in interface org.biojavax.ontology.ComparableOntology Looks for a triple with the given subject object and predicate and returns it. getOrCreateTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology Looks for a triple with the given subject object and predicate and returns it. getOrder() - Method in class org.biojava.stats.svm.PolynomialKernel getOrderedLocusNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the OrderedLocusName term getOrderTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation Getter for the "order" term getORFNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the ORFName term getOrganelleTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the Organelle term getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getOrganism(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getOrganismByName(String) - Method in class org.biojavax.ga.impl.SimplePopulation getOrganismByName(String) - Method in interface org.biojavax.ga.Population Gets the specified organism getOrganisms() - Method in class org.biojavax.ga.impl.SimplePopulation getOrganisms() - Method in interface org.biojavax.ga.Population Gets the Set of Organisms getOrientation() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation getOrImportTerm(Term) - Method in interface org.biojavax.ontology.ComparableOntology Looks for a term with the same name as the given term and returns it. getOrImportTerm(Term) - Method in class org.biojavax.ontology.SimpleComparableOntology Looks for a term with the same name as the given term and returns it. getOrthologue(String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB Returns an orthologue of specified ID. getOrthologue(String) - Method in interface org.biojava.bio.program.homologene.OrthologueSet getOrthologue(String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB getOrthologue(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet getOrthoPairSets() - Method in interface org.biojava.bio.program.homologene.HomologeneDB Get the HomologeneGroups in this database. getOrthoPairSets() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getOS(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getOtherSeqIdTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms Getter for the INSDseq term getOuterMax() - Method in class org.biojava.bio.symbol.FuzzyLocation getOuterMin() - Method in class org.biojava.bio.symbol.FuzzyLocation getOuterPaint() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph Returns the paint properties of the outer line of this glyph. getOutline() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer getOutline() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer getOutline() - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer getOutline returns the colour used to draw the lines. getOutline() - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer getOutline returns the colour used to draw the lines. getOutline() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer getOutline() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer getOutline() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer getOutline() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer getOutput() - Method in interface org.biojava.utils.process.InputHandler Gets the output stream. getOutput() - Method in class org.biojava.utils.process.ReaderInputHandler Gets the output stream. getOutput() - Method in class org.biojava.utils.process.StreamPipe Gets the output stream. getOutputFormat() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties Simply returns stream output format for the actual RemoteQBlastOutputProperties object getOutputHandler() - Method in class org.biojava.utils.process.ExternalProcess Gets the output handler which is responsible for the standard output of the external process. getOutputOption(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties Method that returns any value associated to any key for this RemoteQBlastOutputProperties object. getOutputOption(String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties Method that returns the value associated with the key given in parameter. getOutputOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties getOutputOptions() - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties Method to get all keys to the information stored in this object. getOutString() - Method in class org.biojava.utils.ExecRunner Returns the output string if exec(String) was invoked. getOverlay() - Method in class org.biojava.bio.OverlayAnnotation Get the map used for the overlay. getOverlayMap() - Method in class org.biojava.utils.OverlayMap Return the object containing the overlay mappings. getPacking(FiniteAlphabet, boolean) - Static method in class org.biojava.bio.symbol.PackingFactory Get the default packing for an alphabet. getPadding() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer Retrieve the current padding. getPaint() - Method in class org.biojava.bio.gui.glyph.RectangleGlyph getPaint() - Method in class org.biojava.bio.gui.glyph.TurnGlyph getPam10() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM10 amino acid substitution matrix. getPam100() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM100 amino acid substitution matrix. getPam110() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM110 amino acid substitution matrix. getPam120() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM120 amino acid substitution matrix. getPam130() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM130 amino acid substitution matrix. getPam140() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM140 amino acid substitution matrix. getPam150() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM150 amino acid substitution matrix. getPam160() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM160 amino acid substitution matrix. getPam170() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM170 amino acid substitution matrix. getPam180() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM180 amino acid substitution matrix. getPam190() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM190 amino acid substitution matrix. getPam20() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM20 amino acid substitution matrix. getPam200() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM200 amino acid substitution matrix. getPam210() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM210 amino acid substitution matrix. getPam220() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM220 amino acid substitution matrix. getPam230() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM230 amino acid substitution matrix. getPam240() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM240 amino acid substitution matrix. getPam250() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM250 amino acid substitution matrix. getPam260() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM260 amino acid substitution matrix. getPam270() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM270 amino acid substitution matrix. getPam280() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM280 amino acid substitution matrix. getPam290() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM290 amino acid substitution matrix. getPam30() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM30 amino acid substitution matrix. getPam300() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM300 amino acid substitution matrix. getPam310() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM310 amino acid substitution matrix. getPam320() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM320 amino acid substitution matrix. getPam330() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM330 amino acid substitution matrix. getPam340() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM340 amino acid substitution matrix. getPam350() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM350 amino acid substitution matrix. getPam360() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM360 amino acid substitution matrix. getPam370() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM370 amino acid substitution matrix. getPam380() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM380 amino acid substitution matrix. getPam390() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM390 amino acid substitution matrix. getPam40() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM40 amino acid substitution matrix. getPam400() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM400 amino acid substitution matrix. getPam410() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM410 amino acid substitution matrix. getPam420() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM420 amino acid substitution matrix. getPam430() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM430 amino acid substitution matrix. getPam440() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM440 amino acid substitution matrix. getPam450() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM450 amino acid substitution matrix. getPam460() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM460 amino acid substitution matrix. getPam470() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM470 amino acid substitution matrix. getPam480() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM480 amino acid substitution matrix. getPam490() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM490 amino acid substitution matrix. getPam50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM50 amino acid substitution matrix. getPam500() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM500 amino acid substitution matrix. getPam60() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM60 amino acid substitution matrix. getPam70() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM70 amino acid substitution matrix. getPam80() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM80 amino acid substitution matrix. getPam90() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return the PAM90 amino acid substitution matrix. getParameterType(int) - Method in interface org.biojava.utils.bytecode.CodeMethod Get the type of the parameter at a given position getParameterType(int) - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod getParent() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB Get the original sequenceDB from this annotated sequenceDB. getParent() - Method in class org.biojava.bio.seq.db.SequenceDBWrapper Return the parent SequenceDB. getParent() - Method in interface org.biojava.bio.seq.Feature Return the FeatureHolder to which this feature has been attached. getParent() - Method in class org.biojava.bio.seq.impl.SimpleFeature getParent() - Method in class org.biojava.bio.seq.projection.ProjectedFeature getParent() - Method in class org.biojava.bio.seq.projection.ReparentContext getParent() - Method in class org.biojava.bio.taxa.SimpleTaxon Deprecated. getParent() - Method in interface org.biojava.bio.taxa.Taxon Deprecated. The parent of this Taxon. getParent() - Method in class org.biojava.bio.taxa.WeakTaxon Deprecated. getParent() - Method in class org.biojavax.bio.seq.SimpleRichFeature Return the FeatureHolder to which this feature has been attached. getParent(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext getParent(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext getParentMap() - Method in class org.biojava.utils.OverlayMap Return the object containing the fallback mappings. getParentNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon Returns the parent NCBI taxon ID, if known. getParentNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Returns the parent NCBI taxon ID, if known. getParents() - Method in interface org.biojava.bio.seq.FeatureTypes.Type Get a set of URIs for parent types. getParser() - Method in class org.biojava.bio.program.tagvalue.ParserListener getParser returns the parser of the pair. getParser(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator getParserListener(TagValueListener) - Method in interface org.biojava.bio.annodb.IndexedAnnotationDB.ParserListenerFactory Get the ParserListener for a TagValueListener. getParserListener(TagValueListener) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Embl getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Enzyme getParserListener(TagValueListener) - Method in interface org.biojava.bio.program.formats.Format Retrieve a ParserListener pair for the format that will pass all events on to a listener. getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Compound getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Enzyme getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Reaction getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Swissprot getParserListenerFactory() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB Get the ParserListenerFactory used by this IndexedAnnotationDB. getPartHandler(XFFFeatureSetHandler) - Method in interface org.biojava.bio.program.xff.XFFPartHandlerFactory Return a suitable StAX content handler. getPath() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent Get the list of SequenceRenderer instances that were passed through to produce this event getPathEnd(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree getPathLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree getPathPrefix() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore getPathPrefix returns the abstract path currently being appended to the raw sequence database filenames extracted from the binary index. getPattern() - Method in class org.biojava.bio.program.tagvalue.RegexParser Get the Pattern currently used to split lines. getPattern() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch getPattern() - Method in class org.biojava.bio.search.MaxMismatchPattern getPatterns(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager getPatterns returns two Pattern objects for an enzyme, one matches the forward strand and one the reverse. getPercentGapsQuery() - Method in class org.biojava.bio.alignment.AlignmentPair getPercentGapsTarget() - Method in class org.biojava.bio.alignment.AlignmentPair getPercentIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPair get percentage identity. getPercentIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair getPercentIdentityQuery() - Method in class org.biojava.bio.alignment.AlignmentPair getPercentIdentitySubject() - Method in class org.biojava.bio.alignment.AlignmentPair getPercentSimilarityQuery() - Method in class org.biojava.bio.alignment.AlignmentPair getPercentSimilaritySubject() - Method in class org.biojava.bio.alignment.AlignmentPair getPhase() - Method in interface org.biojava.bio.program.gff3.GFF3Record getPhase() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl getPHDependence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property PHDependence. getPhredAlphabet() - Static method in class org.biojava.bio.program.phred.PhredTools Retrieves the PHRED alphabet from the AlphabetManager. getPhredSymbol(Symbol, Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets). getPI(SymbolList, boolean, boolean) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc Computes isoelectric point of specified peptide. getPlasmidTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the Plasmid term getPopulation() - Method in interface org.biojavax.ga.GeneticAlgorithm The registered Population getPopulation() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm getPos() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent Get the offset within the sequence - the symbol index. getPos() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition getPosition() - Method in interface org.biojava.bio.molbio.RestrictionSite getPosition returns the common, forward strand cut site. getPosition() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite getPosition1() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation getPosition2() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation getPositions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution getPosShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier Retrieve the shape used to represent positive points. getPredicate() - Method in interface org.biojava.ontology.Triple Return a Term which defines the type of relationship between the subject and object terms. getPredicate() - Method in class org.biojava.ontology.Triple.Impl getPredicate() - Method in class org.biojavax.ontology.SimpleComparableTriple Return a Term which defines the type of relationship between the subject and object terms. getPrevious() - Method in class org.biojava.utils.ChangeEvent Return the old value of a property being changed. getPrimaryKey() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory getPrimaryKey returns the primary identifier namespace. getPrimaryKeyName() - Method in class org.biojava.bio.program.tagvalue.Index2Model Retrieve the tag currently used as primary key. getPrimaryKeyName() - Method in class org.biojava.bio.program.tagvalue.Indexer Retrieve the tag currently used as primary key. getPrintStream() - Method in class org.biojava.bio.seq.io.EmblFileFormer Deprecated. getPrintStream() - Method in class org.biojava.bio.seq.io.GenbankFileFormer Deprecated. getPrintStream() - Method in interface org.biojava.bio.seq.io.SeqFileFormer Deprecated. getPrintStream returns the PrintStream to which an instance will write the formatted data. getPrintStream() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer Deprecated. getPrintStream returns the PrintStream to which an instance of SwissprotFileFormer will write the formatted data. getPrintStream() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat Gets the print stream currently being written to. getPrintStream() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat Gets the print stream currently being written to. getProbabilityAlphabet() - Static method in class org.biojava.bio.program.scf.SCF getProjectAccessionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms Getter for the ProjectAccession term getProjectedFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature getProjectionContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeature getProjectionContext() - Method in interface org.biojava.bio.seq.projection.Projection getPropClass() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty getProperties() - Method in class org.biojava.bio.AbstractAnnotation Implement this to return the Map delegate. getProperties() - Method in class org.biojava.bio.AnnotationChanger getProperties returns the mapped contents of the underlying Annotation as a Map. getProperties() - Method in class org.biojava.bio.AnnotationRenamer getProperties returns the mapped contents of the underlying Annotation as a Map. getProperties() - Method in interface org.biojava.bio.AnnotationType Retrieve the set of properties for which constraints have been explicity specified. getProperties() - Method in class org.biojava.bio.AnnotationType.Impl getProperties() - Method in class org.biojava.bio.BeanAsAnnotation getProperties() - Method in class org.biojava.bio.seq.io.ReferenceAnnotation Deprecated. getProperties() - Method in class org.biojava.bio.SimpleAnnotation Get the property value pairs in this annotation getProperties() - Method in class org.biojava.bio.SmallAnnotation getProperties(Object) - Method in class org.biojavax.EmptyRichAnnotation Find all the Notes with any rank that match the key. getProperties(Object) - Method in interface org.biojavax.RichAnnotation Find all the Notes with any rank that match the key. getProperties(Object) - Method in class org.biojavax.SimpleRichAnnotation Deprecated. getProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation getProperty(Object) - Method in interface org.biojava.bio.Annotation Retrieve the value of a property by key. getProperty(Object) - Method in class org.biojava.bio.MergeAnnotation getProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation getProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation Retrieve the value of a property by key. getProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation Deprecated. getProperty(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade getProperty(Annotation, Object) - Method in class org.biojava.bio.AnnotationType.Abstract getProperty(Annotation, Object) - Method in interface org.biojava.bio.AnnotationType Get the Collection of values associated with an Annotation bundle according to the type we believe it to be. getProperty(Annotation, String) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getProperty(Annotation, String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getProperty(Annotation, String) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter ThomasD made this a bit safer... getProperty(Annotation, String) - Static method in class org.biojava.bio.seq.io.agave.UtilHelper inhibit the getProperty(key) of Annotation from throw exception when key does not exist. getPropertyAsBoolean(String) - Method in class org.biojava.utils.TypedProperties Searches for the property with the specified key in this property list. getPropertyAsDouble(String) - Method in class org.biojava.utils.TypedProperties Searches for the property with the specified key in this property list. getPropertyAsInteger(String) - Method in class org.biojava.utils.TypedProperties Searches for the property with the specified key in this property list. getPropertyAsLong(String) - Method in class org.biojava.utils.TypedProperties Searches for the property with the specified key in this property list. getPropertyAsStringList(String) - Method in class org.biojava.utils.TypedProperties just like getPropertyAsStringList(String key, String delims) but uses ',' (comma), ';' (semicolon) and '\t' (tab) as the possible delimiters. getPropertyAsStringList(String, String) - Method in class org.biojava.utils.TypedProperties Searches for the property with the specified key in this property list. getPropertyClass() - Method in class org.biojava.bio.PropertyConstraint.ByClass Get the Class used as the constraint. getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn Get the PropertyConstraint used to validate each property value. getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains Get the PropertyConstraint used to validate each property value. getPropertyConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandler getProps() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot getPropType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty getProteaseByName(String) - Static method in class org.biojava.bio.proteomics.Protease Retrieves a reference to the named Protease. getProteaseByName(String) - Static method in class org.biojava.bio.proteomics.ProteaseManager Gets a Protease instance by name. getProteaseList() - Static method in class org.biojava.bio.proteomics.Protease Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager. getProteinExistsTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms Getter for the protein exists term getProteinExistsTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms Getter for the protein exists term getProteinParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Creates a protein symbol tokenizer. getProteinTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms Getter for the protein type term getPrototype() - Method in class org.biojava.bio.molbio.RestrictionEnzyme The prototype is a RestrictionEnzyme that represents a set of isoshizomers. getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit Return the overall P-value of this hit. getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit Return the P-value of this sub-hit. getPValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. getPValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit getQcalls() - Method in class org.biojava.bio.program.abi.ABITrace Returns an int[] array that represents the quality - each int in the array corresponds to an quality value 90-255) in the graph at a base location). getQuality() - Method in class org.biojava.bio.program.fastq.Fastq Return the quality scores for this FASTQ formatted sequence. getQuality() - Method in class org.biojava.bio.program.phred.PhredSequence Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99. getQuality() - Method in interface org.biojava.bio.program.phred.Qualitative Retreives the list of quality symbols from the underlying object. getQualityAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence getQualityAt(int) - Method in interface org.biojava.bio.program.phred.Qualitative Retreives the quality symbol for the specified index. getQuery() - Method in class org.biojava.bio.alignment.AlignmentPair Return the query sequence as a gapped sequence. getQueryEnd() - Method in class org.biojava.bio.alignment.AlignmentPair getQueryEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit Return the end position of the last sub-hit in the query sequence. getQueryEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit Return the end position of the sub-hit in the query sequence. getQueryEnd() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. getQueryEnd() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. getQueryEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit getQueryEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit getQueryLength() - Method in class org.biojava.bio.alignment.AlignmentPair getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getQueryRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getQuerySeqHolder() - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory getQuerySeqHolder returns the database of query sequences used to retrieve sequences for creation of the various result objects. getQuerySequence() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult Returns the query sequence which was used to perform the search. getQuerySequence() - Method in class org.biojava.bio.search.SequenceDBSearchResult Deprecated. getQuerySequence() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult getQueryStart() - Method in class org.biojava.bio.alignment.AlignmentPair getQueryStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit Return the start position of the first sub-hit in the query sequence. getQueryStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit Return the start position of the sub-hit in the query sequence. getQueryStart() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. getQueryStart() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. getQueryStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit getQueryStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit getQueryStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit Return the strand of the hit with respect to the query sequence. getQueryStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit Return the strand of the sub-hit with respect to the query sequence. getQueryStrand() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. getQueryStrand() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. getQueryStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit getQueryStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit getRadius() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext Get the current radius at which data should be rendered. getRadius() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel getRadius() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext getRange() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext getRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getRange returns a RangeLocation representing the region of the sequence currently being rendered. getRange() - Method in class org.biojava.bio.gui.sequence.SequencePanel getRange() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper getRange() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. getRange() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext The range of the SymbolList to render. getRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext getRange() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext getRange() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel getRange returns a RangeLocation representing the region of the sequence currently being rendered. getRanges() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout getRanges() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout getRanges() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout getRank() - Method in interface org.biojavax.bio.BioEntryRelationship Returns the rank of this relationship. getRank() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank getRank() - Method in class org.biojavax.bio.seq.EmptyRichLocation Retrieves the rank associated with this location. getRank() - Method in interface org.biojavax.bio.seq.RichFeature Returns the rank of this feature. getRank() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship Gets the rank of this relationship. getRank() - Method in interface org.biojavax.bio.seq.RichLocation Retrieves the rank associated with this location. getRank() - Method in class org.biojavax.bio.seq.SimpleRichFeature Returns the rank of this feature. getRank() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship Gets the rank of this relationship. getRank() - Method in class org.biojavax.bio.seq.SimpleRichLocation Retrieves the rank associated with this location. getRank() - Method in class org.biojavax.bio.SimpleBioEntryRelationship Returns the rank of this relationship. getRank() - Method in interface org.biojavax.Comment Returns the rank of this comment. getRank() - Method in interface org.biojavax.Note Gets the rank that defines this note. getRank() - Method in interface org.biojavax.RankedCrossRef Return the rank associated with the cross reference. getRank() - Method in interface org.biojavax.RankedDocRef The rank of this reference. getRank() - Method in class org.biojavax.SimpleComment Returns the rank of this comment. getRank() - Method in class org.biojavax.SimpleNote Gets the rank that defines this note. getRank() - Method in class org.biojavax.SimpleRankedCrossRef Return the rank associated with the cross reference. getRank() - Method in class org.biojavax.SimpleRankedDocRef The rank of this reference. getRankedCrossRefs() - Method in class org.biojavax.bio.seq.SimpleRichFeature Returns the set of all ranked cross references associated with an object. getRankedCrossRefs() - Method in class org.biojavax.bio.SimpleBioEntry Returns the set of all ranked cross references associated with an object. getRankedCrossRefs() - Method in class org.biojavax.ontology.SimpleComparableTerm Returns the set of all ranked cross references associated with an object. getRankedCrossRefs() - Method in interface org.biojavax.RankedCrossRefable Returns the set of all ranked cross references associated with an object. getRankedDocRefs() - Method in interface org.biojavax.bio.BioEntry Returns a set of all bioentrydocrefs associated with this bioentry. getRankedDocRefs() - Method in class org.biojavax.bio.SimpleBioEntry Returns a set of all bioentrydocrefs associated with this bioentry. getReader() - Method in class org.biojava.bio.program.tagvalue.Indexer Retrieve the reader that can be safely used to index this file. getReader() - Method in class org.biojava.bio.program.tagvalue.Indexer2 Retrieve the reader that can be safely used to index this file. getReader() - Method in class org.biojava.utils.process.ReaderWriterPipe Gets the reader. getReadingFrame() - Method in interface org.biojava.bio.seq.FramedFeature return the reading frame of the feature. getReadingFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature getRealScientificName(Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. This returns the true scientific name of a given taxon, if there is one. getRecognitionSequence(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager getRecognitionSequence returns a string that describes the recognition site of this enzyme. getRecognitionSite() - Method in class org.biojava.bio.molbio.RestrictionEnzyme getRecognitionSite returns the forward strand of the recognition site. getRecordKey(Object[]) - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess getRecordKey returns the field from the record on which the records were sorted in the index. getRecordKey(Object[]) - Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess getRecordKey returns the field from the record on which the records were sorted in the index. getRecordList() - Method in class org.biojava.bio.program.indexdb.BioStore getRecordList returns all the Records in the index. getRecurse() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer getRecurse() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer getRecurse returns the recursion flag of the filter. getRecurse() - Method in class org.biojava.bio.program.gff.SequencesAsGFF Return whether features will be filtered recursively or not. getRecursive() - Method in interface org.biojava.bio.seq.io.agave.DelegationManager getRedoxPotential() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property redoxPotential. getRef() - Method in interface org.biojava.bio.program.homologene.OrthoPair get reference to evidence for orthology. getRef() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair getRegions() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature getRegions() - Method in interface org.biojava.bio.seq.RemoteFeature Retrieve the list of Regions that locate this feature both localy and remotely. getRegistryConfiguration() - Method in class org.biojava.directory.Registry getRegistryConfiguration returns the configuration of the registry. getRegistryPath() - Static method in class org.biojava.directory.SystemRegistry Get the list of places that will be searched for registry files. getRel() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot getRel() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref getRelAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the release annotated term getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getRelatedAnnot(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getRelationships() - Method in interface org.biojavax.bio.BioEntry Returns a set of all relationships associated with this bioentry. getRelationships() - Method in class org.biojavax.bio.SimpleBioEntry Returns a set of all relationships associated with this bioentry. getRelCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the release created term getRelUpdatedRecordVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms Getter for the RelUpdatedRecordVersion term getRelUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the release updated term getRemark() - Method in interface org.biojavax.DocRef If remarks have been made about this document reference, this method will return them. getRemark() - Method in class org.biojavax.SimpleDocRef If remarks have been made about this document reference, this method will return them. getRemoteBioEntry(CrossRef) - Method in class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver Given the CrossRef return the corresponding BioEntry getRemoteBioEntry(CrossRef) - Method in interface org.biojavax.CrossReferenceResolver Given the CrossRef return the corresponding BioEntry getRemoteBioEntry(CrossRef) - Method in class org.biojavax.DummyCrossReferenceResolver Given the CrossRef return the corresponding BioEntry getRemoteFeature() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature getRemoteFeature() - Method in interface org.biojava.bio.seq.RemoteFeature Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly. getRemoteSymbolList(CrossRef, Alphabet) - Method in class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver Given a cross reference, return the corresponding symbol list. getRemoteSymbolList(CrossRef, Alphabet) - Method in interface org.biojavax.CrossReferenceResolver Given a cross reference, return the corresponding symbol list. getRemoteSymbolList(CrossRef, Alphabet) - Method in class org.biojavax.DummyCrossReferenceResolver Given a cross reference, return the corresponding symbol list. getRemoteTerm() - Method in interface org.biojava.ontology.RemoteTerm Return the imported term getRemoteTerm() - Method in class org.biojava.ontology.RemoteTerm.Impl getRemoteTerms() - Method in interface org.biojava.ontology.OntologyOps Get the set of all remote terms. getRenderedWidth() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Returns the width of the graphic as it will be rendered. getRenderedWidth(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Returns the width of the graphic as it would be rendered with the specified horizontal scale. getRenderer() - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer getRenderer() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel getRenderer() - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper getRenderer() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer getRenderer return the current renderer. getRenderer() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getRenderer returns the current PairwiseSequenceRenderer. getRenderer() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper getRenderer() - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper getRenderer() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel getRenderer returns the current SequenceRenderer. getRenderingHints() - Method in class org.biojava.bio.gui.DistributionLogo getRenderingHints() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getRenderingHints returns the RenderingHints currently being used by the Graphics2D instances of delegate renderers. getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePanel getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. getRenderingHints() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel getRenderingHints returns the RenderingHints currently being used by the Graphics2D instances of delegate renderers. getReplace() - Method in class org.biojava.bio.alignment.NeedlemanWunsch Returns the current expenses of a single replace operation. getReplace() - Method in class org.biojava.bio.alignment.SmithWaterman getRepository(String) - Static method in class org.biojava.bio.seq.FeatureTypes Fetch a repository by name. getRepositoryNames() - Static method in class org.biojava.bio.seq.FeatureTypes Find the names of all known repositories. getResidue() - Method in interface org.biojava.bio.symbol.WobbleDistribution returns the residue encoded by this WobbleDistribution getResolver() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature getResolver() - Method in interface org.biojava.bio.seq.RemoteFeature getResolver() - Method in class org.biojava.bio.symbol.FuzzyLocation Retrieve the Location that this decorates. getResolver() - Method in class org.biojava.bio.symbol.FuzzyPointLocation getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getResultType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getRetrievalMode() - Method in class org.biojava.bio.seq.db.FetchURL Get the retrieval mode getRetrievalType() - Method in class org.biojava.bio.seq.db.FetchURL Get the retrieval type getReturnCode() - Method in exception org.biojava.utils.ProcessTimeoutException Get the return code from the dying child process. getReturnFormat() - Method in class org.biojava.bio.seq.db.FetchURL getReturnType() - Method in interface org.biojava.utils.bytecode.CodeMethod Get the return type getReturnType() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod getReverseRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme getReverseRegex returns a regular expression which matches the reverse strand of the recognition site. getReverter() - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext getReverter() - Method in class org.biojava.bio.seq.projection.ReparentContext getReverter() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext getRevisionId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier Return the revision id of this identifier. getRichAnnotation() - Method in class org.biojavax.bio.seq.CompoundRichLocation Return the associated annotation object. getRichAnnotation() - Method in class org.biojavax.bio.seq.EmptyRichLocation Return the associated annotation object. getRichAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichFeature Return the associated annotation object. getRichAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichLocation Return the associated annotation object. getRichAnnotation() - Method in class org.biojavax.bio.SimpleBioEntry Return the associated annotation object. getRichAnnotation() - Method in interface org.biojavax.RichAnnotatable Return the associated annotation object. getRichAnnotation() - Method in class org.biojavax.SimpleCrossRef Return the associated annotation object. getRichLocation() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation getRichLocation() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation getRichSequence(String) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB getRichSequence(String) - Method in class org.biojavax.bio.db.HashRichSequenceDB getRichSequence(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Given the appropriate Genbank ID, return the matching RichSequence object. getRichSequence(String) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB Given the appropriate Genbank ID, return the matching RichSequence object. getRichSequence(String) - Method in interface org.biojavax.bio.db.RichSequenceDBLite Retrieve a single RichSequence by its id. getRichSequence(String, Namespace) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Given the appropriate Genbank ID, return the matching RichSequence object. getRichSequence(String, Namespace) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB Given the appropriate Genbank ID, return the matching RichSequence object. getRichSequenceIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB getRichSequenceIterator() - Method in interface org.biojavax.bio.db.RichSequenceDB Returns a RichSequenceIterator over all sequences in the database. getRichSequences(Set) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB getRichSequences(Set) - Method in class org.biojavax.bio.db.HashRichSequenceDB getRichSequences(Set) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Retrieve rich sequences from a Genbank getRichSequences(Set) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB Retrieve rich sequences from a Genbank getRichSequences(Set) - Method in interface org.biojavax.bio.db.RichSequenceDBLite Retrieve multiple RichSequence by its id. getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.HashRichSequenceDB getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Retrieve rich sequences from a Genbank getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB Retrieve rich sequences from a Genbank getRichSequences(Set, RichSequenceDB) - Method in interface org.biojavax.bio.db.RichSequenceDBLite Retrieve multiple RichSequence into a specific sequence database. getRightValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon Gets the right value. getRightValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Gets the right value. getRNA() - Static method in class org.biojava.bio.seq.RNATools Return the RNA alphabet. getRNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Creates a RNA symbol tokenizer. getRoot() - Method in class org.biojava.bio.symbol.SuffixTree Return the node object which is the root of this suffix tree. getRoot() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree getRoot() - Method in class org.biojava.bio.taxa.SimpleTaxonFactory Deprecated. getRoot() - Method in interface org.biojava.bio.taxa.TaxonFactory Deprecated. Retrieve the root upon which all rooted Taxon that this factory knows about are rooted. getRoot() - Method in class org.biojava.bio.taxa.WeakTaxonFactory Deprecated. getRootType() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString See if the tree is rooted. getS() - Method in class org.biojava.bio.proteomics.StructureTools getSBFactory() - Method in class org.biojava.bio.seq.db.BioIndex getSBFactory() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore getSBFactory() - Method in interface org.biojava.bio.seq.db.IndexStore Retrieve the SequenceBuilderFactory used to build Sequence instances. getSBFactory() - Method in class org.biojava.bio.seq.db.TabIndexStore getScale() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext getScale() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getScale returns the scale in pixels per Symbol. getScale() - Method in class org.biojava.bio.gui.sequence.SequencePanel Retrieve the current scale. getScale() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper getScale() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Retrieve the current scale. getScale() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext Gets the scale as pixels per Symbol getScale() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext getScale() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext getScale() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel getScale returns the scale in pixels per Symbol. getScale(int) - Method in interface org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler Retrieve the scaling factor at a given depth getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler getSchema() - Method in interface org.biojava.bio.annodb.AnnotationDB Get an AnnotationType that accepts all Annotation instances in this DB. getSchema() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB getSchema() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB getSchema() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB getSchema() - Method in class org.biojava.bio.annodb.MergingAnnotationDB getSchema() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB getSchema() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder getSchema() - Method in interface org.biojava.bio.seq.FeatureHolder Return a schema-filter for this FeatureHolder. getSchema() - Method in interface org.biojava.bio.seq.FeatureTypes.Type Get the schema for this type. getSchema() - Method in class org.biojava.bio.seq.impl.DummySequence getSchema() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder getSchema() - Method in class org.biojava.bio.seq.impl.SimpleFeature getSchema() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence getSchema() - Method in class org.biojava.bio.seq.impl.SimpleSequence getSchema() - Method in class org.biojava.bio.seq.impl.SubSequence getSchema() - Method in class org.biojava.bio.seq.impl.ViewSequence getSchema() - Method in class org.biojava.bio.seq.LazyFeatureHolder getSchema() - Method in class org.biojava.bio.seq.MergeFeatureHolder getSchema() - Method in class org.biojava.bio.seq.NewSimpleAssembly getSchema() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder getSchema() - Method in class org.biojava.bio.seq.SimpleAssembly getSchema() - Method in class org.biojava.bio.seq.SimpleFeatureHolder getSchema() - Method in class org.biojavax.bio.seq.SimpleRichFeature Return a schema-filter for this FeatureHolder. getSchema() - Method in class org.biojavax.bio.seq.ThinRichSequence Return a schema-filter for this FeatureHolder. getSchema(String) - Method in class org.biojava.naming.ObdaContext getSchema(Name) - Method in class org.biojava.naming.ObdaContext getSchema(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext getSchemaClassDefinition(String) - Method in class org.biojava.naming.ObdaContext getSchemaClassDefinition(Name) - Method in class org.biojava.naming.ObdaContext getScientificName() - Method in class org.biojava.bio.taxa.AbstractTaxon Deprecated. getScientificName() - Method in interface org.biojava.bio.taxa.Taxon Deprecated. The scientific name of this taxon. getScope() - Method in class org.biojava.ontology.Synonym getScore() - Method in class org.biojava.bio.alignment.SimpleAlignment getScore() - Method in interface org.biojava.bio.dp.DPMatrix getScore() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix getScore() - Method in class org.biojava.bio.dp.SimpleStatePath getScore() - Method in interface org.biojava.bio.dp.StatePath Return the overall score for this state-path and it's emissions. getScore() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix getScore() - Method in interface org.biojava.bio.program.gff.GFFRecord The score of the feature. getScore() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord getScore() - Method in interface org.biojava.bio.program.gff3.GFF3Record getScore() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit Return the overall score of this hit in the units defined by the search algorithm. getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit Return the score of this sub-hit in the units defined by the search algorithm. getScore() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. getScore() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit getScore() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature getScore returns the alignment score. getScore() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature getScore returns the alignment score. getScore() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot getSearchableDBs() - Method in interface org.biojava.bio.search.SeqSimilaritySearcher Return a set of all databases that can be searched with this sequence similarity searcher. getSearchContentHandler() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter getSearchContentHandler gets the handler which will recieve the method calls generated by the adapter. getSearchContentHandler() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter getSearchContentHandler gets the handler which will receive the method calls generated by the adapter. getSearchParameters() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult Returns the search parameters used in the search that produced this search result. getSearchParameters() - Method in class org.biojava.bio.search.SequenceDBSearchResult Deprecated. getSearchParameters() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult getSearchProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node getSearchProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler getSecondaryDirection() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext getSecondaryDirection returns the direction in which the secondary sequence is rendered. getSecondaryDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getSecondaryDirection returns the direction in which this context expects the secondary sequence to be rendered - HORIZONTAL or VERTICAL. getSecondaryDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext getSecondaryFeatures() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext getSecondaryFeatures returns the features on the secondary sequence. getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getSecondaryFeatures returns all of the Features belonging to the currently rendered secondary Sequence. getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext getSecondaryRange() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext getSecondaryRange returns the range of the secondary sequence currently rendered. getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getSecondaryRange returns a RangeLocation representing the region of the secondary sequence currently being rendered. getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext getSecondarySequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getSecondarySequence returns the entire secondary Sequence currently being rendered. getSecondarySymbols() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext getSecondarySymbols returns the symbols of the secondary sequence. getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getSecondarySymbols returns all of the Symbols belonging to the currently rendered secondary Sequence. getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext getSecondarySymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getSecondarySymbolTranslation returns the current translation in Symbols which will be applied when rendering. getSecondIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction Getter for property secondIntActID. getSecondOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair gets the first orthologue in the orthology relationship. getSecondOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair getSelectionFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm getSelectionFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm getSeqCautions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property seqCautions. getSeqDB() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver getSeqDBs() - Method in interface org.biojava.bio.seq.homol.HomologyDB Retrieve the SeqDBs that have been searched against each other. getSeqID() - Method in class org.biojava.bio.seq.RemoteFeature.Region Return the remote Sequence ID if this Region is on another Sequence (isRemote will return true), null otherwise. getSeqIDs() - Method in class org.biojava.bio.program.Meme getSeqIOEvents(Sequence, SeqIOListener) - Method in class org.biojava.bio.seq.io.SeqIOEventEmitter Deprecated. getSeqIOEvents scans a Sequence object and sends events describing its data to the SeqIOListener. getSeqName() - Method in interface org.biojava.bio.program.gff.GFFRecord The sequence name field. getSeqName() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter Retrieve the current sequence name. getSeqName() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord getSequence() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel getSequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getSequence returns the entire Sequence currently being rendered. getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePanel getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. getSequence() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel getSequence returns the entire Sequence currently being rendered. getSequence() - Method in class org.biojava.bio.program.abi.ABITrace Returns the original programatically determined (unedited) sequence as a SymbolList. getSequence() - Method in class org.biojava.bio.program.fastq.Fastq Return the sequence for this FASTQ formatted sequence. getSequence() - Method in class org.biojava.bio.proteomics.Digest getSequence() - Method in interface org.biojava.bio.seq.Feature Return the Sequence object to which this feature is (ultimately) attached. getSequence() - Method in class org.biojava.bio.seq.impl.SimpleFeature getSequence() - Method in class org.biojava.bio.seq.impl.SubSequence Return the parent sequence of which this is a partial view getSequence() - Method in class org.biojava.bio.seq.projection.ProjectedFeature getSequence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution getSequence() - Method in class org.biojavax.bio.seq.SimpleRichFeature Return the Sequence object to which this feature is (ultimately) attached. getSequence(int) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB Deprecated. getSequence(String) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB Deprecated. getSequence(String) - Method in class org.biojava.bio.seq.db.CachingSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB getSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDBLite Retrieve a single sequence by its id. getSequence(String) - Method in class org.biojava.bio.seq.db.SubSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.ViewingSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB Gets a sequence using its unique ID (eg for GenBank this would be the GI number) getSequence(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource Get a Sequence object for an ID. getSequence(String) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB getSequence(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource getSequence(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource getSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB getSequence(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext Get the sequence for a feature. getSequence(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext getSequenceDB() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult Returns the sequence database against which the search was performed. getSequenceDB() - Method in class org.biojava.bio.search.SequenceDBSearchResult Deprecated. getSequenceDB() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult getSequenceDB(String) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation getSequenceDB(String) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation Return the SequenceDB for the given identifier. getSequenceDB(String) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation If the given identifier is known to this sequence db installation because it has been used in a call to addSequenceDB(), then this method returns the SequenceDB associated with this identifier. getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider Deprecated. getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider getSequenceDB(Map) - Method in interface org.biojava.directory.SequenceDBProvider Get a sequence database. getSequenceDBs() - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation getSequenceDBs() - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation Return all sequence dbs available in this sequence db installation. getSequenceDBs() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation Return a newly created set of the SequenceDB objects that were already created through method addSequenceDB(). getSequenceFormat() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory getSequenceFormat returns the current sequence format name. getSequenceFormat() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB getSequenceFormat() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB getSequenceFormat() - Method in class org.biojava.bio.seq.db.NCBISequenceDB getSequenceFormat() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB getSequenceFormat() - Method in class org.biojava.bio.seq.db.WebSequenceDB getSequenceFormat(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. getSequenceFormat accepts a value which represents a sequence format and returns the relevant SequenceFormat object. getSequenceId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getSequenceId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getSequenceID() - Method in interface org.biojava.bio.program.gff3.GFF3Record getSequenceID() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl getSequenceLength() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram Return the sequence length. getSequenceLength() - Method in interface org.biojava.bio.chromatogram.Chromatogram Returns the number of bases called by whatever base-calling software analyzed the chromatogram as loaded. getSequenceLength() - Method in class org.biojava.bio.program.abi.ABITrace Returns the length of the sequence (number of bases) in this trace. getSequenceLength() - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler Gets the sequenceLength attribute of the GAMESeqHandler object getSequenceLength() - Method in class org.biojavax.bio.seq.SimpleRichSequence getSequenceLength() - Method in class org.biojavax.bio.seq.ThinRichSequence getSequenceName() - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName getSequenceName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName getSequenceOffset() - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer getSequenceRef() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform Getter for property sequenceRef. getSequences() - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler getSequences() - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler get all the top level sequences bio_sequence --> SimpleSequence contig --> SimpleAssembly --> SimpleSequence( if only one sequence ) chromosome -> SimpleAssembly -> SimpleSequence( if only one sequence) getSequences(Set) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB Retrieve sequences from a Genbank getSequences(Set, SequenceDB) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB Retrieve sequences from a Genbank getSequenceType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform Getter for property sequenceType. getSeqVersion() - Method in interface org.biojavax.bio.seq.RichSequence The version of the associated symbol list. getSeqVersion() - Method in class org.biojavax.bio.seq.ThinRichSequence The version of the associated symbol list. getShape(int[], int[]) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils getShape(List) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils getShape(List, List) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils getShatter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF Determine if features with non-contiguous locations will be broken into multiple GFF records. getShort() - Method in class org.biojava.utils.io.LargeBuffer getShort(long) - Method in class org.biojava.utils.io.LargeBuffer getSibling() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature getSibling returns the sibling Feature, query for subject and vice versa. getSibling() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature getSibling returns the sibling feature of the pair. getSignificantBits() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram Return the number of significant bits. getSignificantBits() - Method in interface org.biojava.bio.chromatogram.Chromatogram Returns the number of bits of the traces which are significant. getSimilarity() - Method in interface org.biojava.bio.program.homologene.OrthoPair gets the second orthologue in the orthology relationship. getSimilarity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair getSize() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border getSize() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border Deprecated. getSize() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border Gets the current size of the border in pixels. getSleepTime() - Method in class org.biojava.utils.process.ExternalProcess Gets the number of milliseconds the ExternalProcess.execute(Properties) method should pauses after the external process is terminated. getSource() - Method in interface org.biojava.bio.program.gff.GFFRecord The source, or creator of this feature. getSource() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter Retrieve the current source. getSource() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord getSource() - Method in interface org.biojava.bio.program.gff3.GFF3Record getSource() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl getSource() - Method in interface org.biojava.bio.seq.Feature The source of the feature. getSource() - Method in class org.biojava.bio.seq.FeatureFilter.BySource getSource() - Method in class org.biojava.bio.seq.impl.SimpleFeature getSource() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation getSource() - Method in class org.biojava.utils.ChangeForwarder Retrieve the 'source' object for ChangeEvents fired by this forwarder. getSource() - Method in class org.biojavax.bio.seq.SimpleRichFeature The source of the feature. getSourceAlphabet() - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable getSourceAlphabet() - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable getSourceAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable The alphabet of Symbols that can be translated. getSourceFile() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass Get the source file associated with this code class. getSourceHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler getSourceSymbolList() - Method in interface org.biojava.bio.symbol.GappedSymbolList Return the underlying (ungapped) SymbolList. getSourceSymbolList() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList getSourceTerm() - Method in interface org.biojava.bio.seq.Feature An ontology term defining the source of this feature. getSourceTerm() - Method in class org.biojava.bio.seq.impl.SimpleFeature getSourceTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm getSourceTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeature An ontology term defining the source of this feature. getSourceTermName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName getSpacer() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Retrieve the current spacer value getSpeciesForShortName(String) - Static method in class org.biojava.bio.program.unigene.UnigeneTools Converts short species names (like Hs) to long species names (like Homo Sapiens). getSpeciesTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the Species term getSplitOffset() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser Get the current offset at which lines are split. getSplitter(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable Get the Splitter currently registered to handle a tag. getStandardFillPaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle getStandardOutlinePaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle getStart() - Method in interface org.biojava.bio.program.gff.GFFRecord The start of this feature within the source sequence. getStart() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord getStart() - Method in interface org.biojava.bio.program.gff3.GFF3Record getStart() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl getStart() - Method in interface org.biojava.bio.seq.db.Index Skipping this number of bytes through the file should put the file pointer to the first byte of the sequence. getStart() - Method in class org.biojava.bio.seq.db.SimpleIndex getStart() - Method in class org.biojava.bio.seq.impl.SubSequence getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion getStart() - Method in class org.biojava.utils.automata.FiniteAutomaton getStart() - Method in interface org.biojava.utils.automata.NfaBuilder getStart() - Method in class org.biojava.utils.automata.NfaSubModel getStart() - Method in interface org.biojava.utils.automata.StateMachineInstance getStart() - Method in interface org.biojavax.bio.seq.Position Returns the beginning of the range of bases this base could lie in. getStart() - Method in class org.biojavax.bio.seq.SimplePosition Returns the beginning of the range of bases this base could lie in. getStart() - Method in interface org.biojavax.RankedDocRef The start position in the sequence that this reference is referred to from. getStart() - Method in class org.biojavax.SimpleRankedDocRef The start position in the sequence that this reference is referred to from. getStartLabel() - Method in class org.biojava.utils.bytecode.InstructionVector getState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine getStateLabels(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock getStates() - Method in class org.biojava.bio.dp.DP getStatesFormat() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock getStatusDateTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms Getter for the StatusDate term getStatusTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms Getter for the Status term getStAXContentHandler() - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler Return a StAXContentHandler which can deal with any FilterXML construct known to this class. getStoreLocation() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory getStoreLocation returns the directory of the bew index. getStoreName() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory getStoreName returns the name to be given to the new index. getStrainTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the Strain term getStrand() - Method in interface org.biojava.bio.program.gff.GFFRecord The strand of the feature. getStrand() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter getStrand() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord getStrand() - Method in interface org.biojava.bio.program.gff3.GFF3Record getStrand() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl getStrand() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter Retrieve the strand this matches. getStrand() - Method in interface org.biojava.bio.seq.FramedFeature getStrand() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature getStrand() - Method in interface org.biojava.bio.seq.StrandedFeature Retrieve the strand that this feature lies upon. getStrand() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand getStrand() - Method in class org.biojavax.bio.seq.EmptyRichLocation Retrieves the strand associated with this location. getStrand() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation Retrieves the strand associated with this location. getStrand() - Method in interface org.biojavax.bio.seq.RichLocation Retrieves the strand associated with this location. getStrand() - Method in class org.biojavax.bio.seq.SimpleRichFeature Retrieve the strand that this feature lies upon. getStrand() - Method in class org.biojavax.bio.seq.SimpleRichLocation Retrieves the strand associated with this location. getStrandedFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler getStrandedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the Strand term; legal values are "single", "double", and "mixed". getStringSequence() - Method in class org.biojavax.bio.seq.SimpleRichSequence getStructure() - Method in class org.biojava.bio.proteomics.StructureTools getStyle() - Method in class org.biojava.bio.gui.DistributionLogo Retrieve the current style. getStyle() - Method in interface org.biojava.bio.gui.LogoContext getStyle(String, String, String[]) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler Return the styles for the two aligned characters. getStyle(String, String, String[]) - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler Returns the styles for the two aligned characters in the form of predefined font classes. getSubAlphabet(double, double) - Static method in class org.biojava.bio.symbol.DoubleAlphabet getSubAlphabet(int, int) - Static method in class org.biojava.bio.symbol.IntegerAlphabet Construct a finite contiguous subset of the IntegerAlphabet. getSubContext(PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer getSubContext creates a new context which has FeatureHolders filtered using the current filter. getSubHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node getSubHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler getSubHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit Return all sub-hits for this sequence similarity search hit. getSubHits() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. getSubHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit getSubject() - Method in class org.biojava.bio.alignment.AlignmentPair Return the subject sequence as a gapped sequence. getSubject() - Method in interface org.biojava.ontology.Triple Return the subject term of this triple getSubject() - Method in class org.biojava.ontology.Triple.Impl getSubject() - Method in interface org.biojavax.bio.BioEntryRelationship Returns the subject of this relationship (ie. the BioEntry which this relationship targets). getSubject() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship Gets the feature that this relationship refers to. getSubject() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship Gets the feature that this relationship refers to. getSubject() - Method in class org.biojavax.bio.SimpleBioEntryRelationship Returns the subject of this relationship (ie. the BioEntry which this relationship targets). getSubject() - Method in class org.biojavax.ontology.SimpleComparableTriple Return the subject term of this triple getSubjectDBInstallation() - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory getSubjectDBInstallation returns the installation in which all the databases searched may be found. getSubjectEnd() - Method in class org.biojava.bio.alignment.AlignmentPair getSubjectEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit Return the end position of the last sub-hit in the subject sequence. getSubjectEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit Return the start position of the sub-hit in the subject sequence. getSubjectEnd() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. getSubjectEnd() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. getSubjectEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit getSubjectEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit getSubjectID() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit The sequence identifier of this hit within the sequence database against which the search was performed. getSubjectID() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. getSubjectID() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit getSubjectLength() - Method in class org.biojava.bio.alignment.AlignmentPair getSubjectStart() - Method in class org.biojava.bio.alignment.AlignmentPair getSubjectStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit Return the start position of the first sub-hit in the subject sequence. getSubjectStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit Return the start position of the sub-hit in the subject sequence. getSubjectStart() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. getSubjectStart() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. getSubjectStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit getSubjectStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit getSubjectStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit Return the strand of the sub-hit with respect to the subject sequence. getSubjectStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit Return the strand of the sub-hit with respect to the subject sequence. getSubjectStrand() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. getSubjectStrand() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. getSubjectStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit getSubjectStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit getSubMatrix() - Method in class org.biojava.bio.alignment.SmithWaterman getSubmitterAccessionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms Getter for the SubmitterAccession term getSubmitterVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms Getter for the SubmitterVersion term getSubmitterWgsVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms Getter for the SubmitterWgsVersion term getSubSeqStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation getSubstitutionMatrix() - Method in class org.biojava.bio.alignment.AlignmentPair getSubstitutionMatrix(BufferedReader) - Static method in class org.biojava.bio.alignment.SubstitutionMatrix This constructor can be used to guess the alphabet of this substitution matrix. getSubstitutionMatrix(FiniteAlphabet, BufferedReader) - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return a new substitution matrix with the specified alphabet. getSubstitutionMatrix(FiniteAlphabet, BufferedReader, String) - Static method in class org.biojava.bio.alignment.SubstitutionMatrix Return a new substitution matrix with the specified alphabet and name. getSuperClass() - Method in interface org.biojava.utils.bytecode.CodeClass getSuperClass() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass getSuperClass() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass getSuppliers(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager getSuppliers returns a string describing the suppliers of this enzyme according to REBASE encoding for commercial sources or an empty String if the enzyme is not commecially available. getSupportedCriteria() - Method in interface org.biojava.bibliography.BibRefSupport It returns all supported searching and sorting criteria for the whole bibliographic repository. getSupportedCriteria(String) - Method in interface org.biojava.bibliography.BibRefSupport It returns all supported searching and sorting criteria in the given repository subset. getSupportedValues(String, String) - Method in interface org.biojava.bibliography.BibRefSupport It returns a controlled vocabulary containing all possible values of the attribute given in attrName in the context given in resourceType. getSwissprotBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Get a default SequenceBuilderFactory for handling Swissprot files. getSymbol() - Method in exception org.biojava.bio.symbol.IllegalSymbolException Retrieve the symbol that caused this exception, or null. getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet Retrieve the Symbol for a double. getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet getSymbol(double, double) - Method in class org.biojava.bio.symbol.DoubleAlphabet Retrieve the symbol for a range of doubles. getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet Retrieve the Symbol for an int. getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet getSymbol(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet getSymbol(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet getSymbol(List) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet Gets the compound symbol composed of the Symbols in the List. getSymbol(List<Symbol>) - Method in interface org.biojava.bio.symbol.Alphabet Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols. getSymbolArray() - Method in class org.biojava.bio.symbol.SimpleSymbolList Return the Java Symbol[] array that backs this object. getSymbolImpl(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet getSymbolImpl(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet getSymbolImpl(List) - Method in class org.biojava.bio.symbol.SimpleAlphabet getSymbolImpl(List) - Method in class org.biojava.bio.symbol.SingletonAlphabet getSymbolList() - Method in interface org.biojava.bio.alignment.AlignmentElement getSymbolList() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement getSymbolParser() - Method in class org.biojava.bio.seq.db.BioIndex getSymbolParser() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore getSymbolParser() - Method in interface org.biojava.bio.seq.db.IndexStore Retrieve the symbol parser used to turn the sequence characters into Symobl objects. getSymbolParser() - Method in class org.biojava.bio.seq.db.TabIndexStore getSymbolPropertyTable(String) - Static method in class org.biojava.bio.seq.ProteinTools getSymbols() - Method in class org.biojava.bio.dp.SimpleEmissionState getSymbols() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext The SymbolList that is currently rendered by this context. getSymbols() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext getSymbols() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getSymbols returns all of the Symbols belonging to the currently rendered Sequence. getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePanel Retrieve the currently rendered SymbolList getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Retrieve the currently rendered SymbolList getSymbols() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext The SymbolList that is currently rendered by this SequenceRenderContext. getSymbols() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext getSymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext getSymbols() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext getSymbols() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel getSymbols returns all of the Symbols belonging to the currently rendered Sequence. getSymbols() - Method in interface org.biojava.bio.seq.Feature Return a list of symbols that are contained in this feature. getSymbols() - Method in class org.biojava.bio.seq.impl.SimpleFeature getSymbols() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature getSymbols() - Method in class org.biojava.bio.seq.projection.ProjectedFeature getSymbols() - Method in interface org.biojava.bio.seq.StrandedFeature Return a list of symbols that are contained in this feature. getSymbols() - Method in interface org.biojava.bio.symbol.BasisSymbol The list of symbols that this symbol is composed from. getSymbols() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange getSymbols() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol getSymbols() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol getSymbols() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol getSymbols() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock getSymbols() - Method in class org.biojavax.bio.seq.SimpleRichFeature Return a list of symbols that are contained in this feature. getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getSymbolTranslation returns the current translation in Symbols which will be applied when rendering. getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel getSymbolTranslation returns the current translation in Symbols which will be applied when rendering. getSyms() - Method in class org.biojava.bio.symbol.PackedSymbolList Return the long array within which the symbols are bit-packed. getSynonyms() - Method in class org.biojava.ontology.IntegerOntology.IntTerm getSynonyms() - Method in class org.biojava.ontology.OntologyTerm.Impl getSynonyms() - Method in class org.biojava.ontology.RemoteTerm.Impl getSynonyms() - Method in interface org.biojava.ontology.Term Return the synonyms for this term. getSynonyms() - Method in class org.biojava.ontology.Term.Impl getSynonyms() - Method in class org.biojava.ontology.Triple.Impl getSynonyms() - Method in class org.biojavax.ontology.SimpleComparableTerm Return the synonyms for this term. getSynonyms() - Method in class org.biojavax.ontology.SimpleComparableTriple Return the synonyms for this term. getT() - Method in class org.biojava.bio.molbio.DNAComposition Get the relative compositon of 'T'. getT() - Method in class org.biojava.bio.proteomics.StructureTools getTable() - Method in class org.biojava.bio.dist.TranslatedDistribution Retrieve the translation table encapsulating the map from this emission spectrum to the underlying one. getTableNumber() - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable getTag() - Method in class org.biojava.bio.program.tagvalue.TagValue getTagGroup() - Method in class org.biojava.bio.program.tagvalue.RegexParser Get the group number that matches the tag. getTags() - Method in class org.biojava.bio.program.tagvalue.TagDelegator getTags() - Method in class org.biojava.bio.program.tagvalue.TagDropper Get the complete set of tags that are currently recognized. getTAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools Gets the protein alphabet including the translation termination symbols getTarget() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent Get the Object that was the target of the mouse gesture or null if the mouse is not gesturing over any recognizable rendered object. getTarget(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget getTarget(Object) - Method in interface org.biojava.stats.svm.SVMTarget getTargetAlphabet() - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable getTargetAlphabet() - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable getTargetAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable The alphabet of Symbols that will be produced. getTargetOntology() - Method in class org.biojava.ontology.OntologyTerm.Impl getTaxa() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet get the taxa represented in this group getTaxa() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet getTaxLabels() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock Get the TAXLABEL values added so far. getTaxLabels() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock Get the TAXLABEL values added so far. getTaxLabels() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock Get the TAXLABEL values added so far. getTaxon() - Method in interface org.biojava.bio.program.homologene.Orthologue return the Taxon associated with this orthologue getTaxon() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue getTaxon() - Method in interface org.biojavax.bio.BioEntry Gets the taxon associated with this bioentry. getTaxon() - Method in class org.biojavax.bio.SimpleBioEntry Gets the taxon associated with this bioentry. getTaxon(int) - Static method in class org.biojava.bio.program.homologene.HomologeneTools get the Taxon corresponding to this Taxon ID getTaxon(Connection, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Attempts to get a Taxon object corresponding to the specified NCBI taxon ID. getTaxon(Connection, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Attempts to get a Taxon object corresponding to the specified name. getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getTaxonId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getTaxonID() - Method in interface org.biojava.bio.program.homologene.Orthologue a convenience method to return the TaxonID for thsi orhtologue. getTaxonID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue getTaxonID() - Method in interface org.biojava.bio.program.homologene.Taxon returns the taxon ID getTaxonID() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub getTempBuffer() - Method in class org.biojava.ontology.obo.OboFileParser getTemperatureDependence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property temperatureDependence. getTerm() - Method in interface org.biojavax.bio.BioEntryRelationship Returns the term describing the relationship. getTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly getTerm() - Method in class org.biojavax.bio.seq.EmptyRichLocation Retrieves the term associated with this location. getTerm() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship Gets the term that describes this relationship. getTerm() - Method in interface org.biojavax.bio.seq.RichLocation Retrieves the term associated with this location. getTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship Gets the term that describes this relationship. getTerm() - Method in class org.biojavax.bio.seq.SimpleRichLocation Retrieves the term associated with this location. getTerm() - Method in class org.biojavax.bio.SimpleBioEntryRelationship Returns the term describing the relationship. getTerm() - Method in interface org.biojavax.Note Gets the term that defines this note. getTerm() - Method in class org.biojavax.SimpleNote Gets the term that defines this note. getTerm(String) - Method in class org.biojava.ontology.IntegerOntology getTerm(String) - Method in interface org.biojava.ontology.Ontology Fetch the term with the specified name. getTerm(String) - Method in class org.biojava.ontology.Ontology.Impl getTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology Fetch the term with the specified name. getTermMass() - Method in class org.biojava.bio.proteomics.MassCalc getTermMass returns the terminal mass being used by the instance methods. getTerms() - Method in class org.biojava.ontology.IntegerOntology getTerms() - Method in interface org.biojava.ontology.Ontology Return all the terms in this ontology getTerms() - Method in class org.biojava.ontology.Ontology.Impl getTerms() - Method in class org.biojavax.ontology.SimpleComparableOntology Return all the terms in this ontology getTermSet() - Method in interface org.biojavax.ontology.ComparableOntology Returns the set of terms in this ontology. getTermSet() - Method in class org.biojavax.ontology.SimpleComparableOntology Returns the set of terms in this ontology. getTestClass() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass getText() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property text. getTextColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer Get the color of the label text getThis() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod Gets the This attribute of the GeneratedCodeMethod object getThreshold() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel getThreshold() - Method in interface org.biojava.stats.svm.SVMClassifierModel getThreshold() - Method in class org.biojava.stats.svm.SVMRegressionModel getThrownExceptions() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod Gets the ThrownExceptions attribute of the GeneratedCodeMethod object getTickDirection() - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer getTissueTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the Tissue term getTitle() - Method in interface org.biojava.bio.program.homologene.Orthologue return the title used by Genbank for this protein getTitle() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue getTitle() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster The cluster title. getTitle() - Method in interface org.biojavax.DocRef Returns the title of the document reference. getTitle() - Method in class org.biojavax.SimpleDocRef Returns the title of the document reference. getTo() - Method in exception org.biojava.bio.dp.IllegalTransitionException getToken() - Method in class org.biojava.bio.dp.SimpleEmissionState getToken() - Method in class org.biojava.bio.seq.StrandedFeature.Strand Returns the token for strandedness. getTokenization(String) - Method in class org.biojava.bio.symbol.AbstractAlphabet getTokenization(String) - Method in interface org.biojava.bio.symbol.Alphabet Get a SymbolTokenization by name. getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet Creates a new parser (Mark Schreiber 3 May 2001). getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet getTokenization(String) - Method in class org.biojava.bio.symbol.SingletonAlphabet getTokenization(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet getTokenTable() - Method in class org.biojava.bio.seq.io.CharacterTokenization getTokenType() - Method in class org.biojava.bio.seq.io.AlternateTokenization Tokens have fixed size. getTokenType() - Method in class org.biojava.bio.seq.io.CharacterTokenization getTokenType() - Method in interface org.biojava.bio.seq.io.SymbolTokenization Determine the style of tokenization represented by this object. getTokenType() - Method in class org.biojava.bio.seq.io.WordTokenization getTokenType() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization getTool() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService Get the tool identifier for QBlast. getTool() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Get the tool identifier for Entrez. getTopNode() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock Returns the top node of the previously requested graph. getTotalDepth() - Method in class org.biojava.bio.gui.sequence.LineInfo getTotalWeight() - Method in class org.biojavax.ga.util.WeightedSet The total weight that has been added to this Set. getTrace() - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer getTrace(AtomicSymbol) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram getTrace(AtomicSymbol) - Method in interface org.biojava.bio.chromatogram.Chromatogram Returns an array containing the intensities of the sampled waveform representing the chromatogram trace for base nucleotide. getTrace(AtomicSymbol) - Method in class org.biojava.bio.program.abi.ABITrace Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point. getTraceLength() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram getTraceLength() - Method in interface org.biojava.bio.chromatogram.Chromatogram Returns the length of the trace of the Chromatogram. getTraceLength() - Method in class org.biojava.bio.program.abi.ABITrace Returns the length of the trace (number of x-coordinate points in the graph). getTraceOffset(Chromatogram, int) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools Get a specific value from the trace offset sequence in the given chromatogram and extract its int value. getTraceOffsetArray(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools Converts the peak offsets list of the given chromatogram into a new int array. getTraceOffsets(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools Get the peak offsets for the called bases of a chromatogram. getTrackLayout() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper getTrailer() - Method in class org.biojava.utils.ListTools.SeriesList getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getTrailingBorder returns the trailing border of the primary sequence. getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered. getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered. getTrailingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext Gets the TrailingBorder attribute of the SequenceRenderContext object. getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel getTrailingBorder returns the trailing border. getTrailingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer getTrainer(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext Return the Distribution trainer object from the current context. getTrainer(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext getTransform() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Returns a new AffineTransform describing the transformation from chromatogram coordinates to output coordinates. getTransformAndConcat(AffineTransform) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Concatenates the chromatogram-to-output transform to the provided given AffineTransform. getTransformer() - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext getTransformer() - Method in class org.biojava.bio.seq.projection.ReparentContext getTransformer() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext getTransitions() - Method in class org.biojava.utils.automata.FiniteAutomaton retrieve Set of all transitions in instance. getTransitions() - Method in interface org.biojava.utils.automata.NfaBuilder getTransitions() - Method in class org.biojava.utils.automata.NfaSubModel getTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState retrieve the TransitionTable for this State. getTranslation() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext getTranslations() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock Get the translations added so far. getTransposonTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms Getter for the Transposon term getTree(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock Returns a tree for given label getTreeAsWeightedJGraphT(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock Get given (NewickString) tree by label, converts it to weighted graph (JGraphT). getTrees() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock Returns all trees. getTreeString() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString Get the Newick string describing the tree. getTreeText(UndirectedGraph<String, DefaultEdge>, String, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock getTreeText(WeightedGraph<String, DefaultWeightedEdge>, String, String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock getTrimTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser See if tag trimming is enabled. getTrimTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser See if trimming of tags is enabled. getTrimValue() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser See if value trimming is enabled. getTrimValue() - Method in class org.biojava.bio.program.tagvalue.RegexParser See if trimming of values is enabled. getTriples(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology getTriples(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology Return all triples from this ontology which match the supplied pattern. getTriples(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl getTriples(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology Return all triples from this ontology which match the supplied pattern. getTripleSet() - Method in interface org.biojavax.ontology.ComparableOntology Returns the set of triples in this ontology. getTripleSet() - Method in class org.biojavax.ontology.SimpleComparableOntology Returns the set of triples in this ontology. getTrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager getType() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot getType returns the type of hotspot. getType() - Method in class org.biojava.bio.program.formats.Embl getType() - Method in class org.biojava.bio.program.formats.Enzyme getType() - Method in interface org.biojava.bio.program.formats.Format Get the AnnotationType that constrains the events that will be fired. getType() - Method in class org.biojava.bio.program.formats.Ligand.Compound getType() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme getType() - Method in class org.biojava.bio.program.formats.Ligand.Reaction getType() - Method in class org.biojava.bio.program.formats.Swissprot getType() - Method in interface org.biojava.bio.program.gff3.GFF3Record getType() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl getType() - Method in interface org.biojava.bio.seq.Feature The type of the feature. getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByType getType() - Method in class org.biojava.bio.seq.impl.SimpleFeature getType() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias getType() - Method in class org.biojava.utils.bytecode.CodeField Get the type of the field. getType() - Method in class org.biojava.utils.bytecode.LocalVariable getType() - Method in interface org.biojava.utils.bytecode.ParametricCodeGenerator getType() - Method in class org.biojava.utils.ChangeEvent Find the type of this event. getType() - Method in class org.biojava.utils.ChangeForwarder.Retyper getType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event Getter for property type. getType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution getType() - Method in interface org.biojavax.bio.seq.Position Returns the type of this position if it is not a point/single position. getType() - Method in class org.biojavax.bio.seq.SimplePosition Returns the type of this position if it is not a point/single position. getType() - Method in class org.biojavax.bio.seq.SimpleRichFeature The type of the feature. getType(String) - Static method in class org.biojava.bio.seq.FeatureTypes Get a Type by URI. getType(String) - Method in interface org.biojava.bio.seq.FeatureTypes.Repository Find the type for a name. getType(String) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl getType1() - Method in interface org.biojava.utils.bytecode.PParametricCodeGenerator getType2() - Method in interface org.biojava.utils.bytecode.PParametricCodeGenerator getTypeClass() - Method in class org.biojava.utils.walker.WalkerFactory getTypeHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler getTypes() - Method in interface org.biojava.bio.seq.FeatureTypes.Repository Get a set of all type names defined in this repository. getTypes() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl getTypeTerm() - Method in interface org.biojava.bio.seq.Feature An ontology term defining the type of feature. getTypeTerm() - Method in class org.biojava.bio.seq.impl.SimpleFeature getTypeTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm getTypeTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeature An ontology term defining the type of feature. getTypeTermName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName getUngappedLocation() - Method in interface org.biojava.bio.symbol.GappedSymbolList Get a Location that contains exactly those positions that are not gaps. getUngappedLocation() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList getUniProtDBNameTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms Getter for the UniProt combined database term getUniprotKWOnto() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms Getter for the private uniprot ontology. getUniProtTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms Getter for the UniProt term getUniProtXMLTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms Getter for the UniProtXML term getUnique() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster The unique sequence that is used as a representative for this cluster. getUnits() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation getUnprojectedFeatures() - Method in interface org.biojava.bio.seq.projection.ProjectionContext Get the features before projection. getUnprojectedFeatures() - Method in class org.biojava.bio.seq.projection.ReparentContext getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getUpdateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getUpstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme getUpstreamCut returns the cut site upstream of the recognition site. getUpstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme getUpstreamEndType returns the double-stranded end type produced by the secondary (upstream) cut. getUri() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property uri. getURI() - Method in interface org.biojava.bio.seq.FeatureTypes.Type Get the URI for this type. getURI() - Method in interface org.biojavax.Namespace If the namespace has a URI, this will return it. getURI() - Method in class org.biojavax.SimpleNamespace If the namespace has a URI, this will return it. getURL() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot getURL returns the hotspot URL. getURN() - Method in class org.biojava.bio.seq.impl.DummySequence getURN() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence getURN() - Method in class org.biojava.bio.seq.impl.SimpleSequence getURN() - Method in class org.biojava.bio.seq.impl.SubSequence getURN() - Method in class org.biojava.bio.seq.impl.ViewSequence getURN() - Method in class org.biojava.bio.seq.NewSimpleAssembly getURN() - Method in interface org.biojava.bio.seq.Sequence A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. getURN() - Method in class org.biojava.bio.seq.SimpleAssembly getURN() - Method in class org.biojavax.bio.seq.ThinRichSequence A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. getUserObject() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot getUserObject returns the current user object (or null). getValue() - Method in class org.biojava.bio.program.tagvalue.TagValue getValue() - Method in class org.biojava.bio.PropertyConstraint.ExactValue Get the value that all properties must match. getValue() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains getValue() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation getValue() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty getValue() - Method in class org.biojava.bio.seq.StrandedFeature.Strand Returns the integer label for strandedness. getValue() - Method in interface org.biojava.stats.svm.ItemValue getValue() - Method in class org.biojava.stats.svm.SimpleItemValue getValue() - Method in interface org.biojava.utils.walker.Walker If the visitor has a return value, then the result of applying the visitor to the tree can be obtained using this method, otherwise the result will be null. getValue() - Method in interface org.biojavax.Note Gets the value that defines this note. getValue() - Method in class org.biojavax.SimpleNote Gets the value that defines this note. getValue() - Method in class org.biojavax.utils.CRC64Checksum getValueAt(Symbol, Symbol) - Method in class org.biojava.bio.alignment.SubstitutionMatrix There are some substitution matrices containing more columns than lines. getValueAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector Retrieve the value at a specific index. getValueGroup() - Method in class org.biojava.bio.program.tagvalue.RegexParser Get the group number that matches the value. getValues() - Method in class org.biojava.bio.PropertyConstraint.Enumeration getValues returns the set of values which constrain the property. getVariable(int) - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod Gets the Variable attribute of the GeneratedCodeMethod object. getVariable(String) - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod Gets the Variable attribute of the GenerateCodeMethod object by name. getVariableMasses(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc Get all masses including the variable mass. getVariant() - Method in class org.biojava.bio.program.fastq.Fastq Return the FASTQ sequence format variant for this FASTQ formatted sequence. getVariant() - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader getVariant() - Method in class org.biojava.bio.program.fastq.SangerFastqReader getVariant() - Method in class org.biojava.bio.program.fastq.SolexaFastqReader getVector() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector getVector(int) - Method in class org.biojava.stats.svm.SVMRegressionModel getVectorNTISupport() - Method in class org.biojava.bio.seq.io.GenbankFileFormer Deprecated. Is VectorNTI compatable output being produced? getVersion() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId getVersion() - Method in interface org.biojava.utils.candy.CandyVocabulary It returns a vesrion of this vocabulary. getVersion() - Method in interface org.biojavax.bio.BioEntry Gets the version of this bioentry. getVersion() - Method in class org.biojavax.bio.SimpleBioEntry Gets the version of this bioentry. getVersion() - Method in interface org.biojavax.CrossRef Returns the version of the object that the crossref refers to. getVersion() - Method in class org.biojavax.SimpleCrossRef Returns the version of the object that the crossref refers to. getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getVersion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter getVersionLineTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms Getter for the Ensembl-specific 'versionLine' term getVerticalScale() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Returns the in use vertical scale factor. getViewedFeature() - Method in class org.biojava.bio.seq.projection.ProjectedFeature getViewedFeature() - Method in interface org.biojava.bio.seq.projection.Projection getVisibleRange() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. getVisibleRange(SequenceRenderContext, Graphics2D) - Static method in class org.biojava.bio.gui.sequence.GUITools getVisibleSecondarySymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getVisibleSecondarySymbolCount returns the maximum number of secondary Symbols which can be rendered in the visible area (excluding all borders) of the PairwiseSequencePanel at the current scale. getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the PairwiseSequencePanel at the current scale. getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the TranslatedSequencePanel at the current scale. getVMaxes() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Getter for property VMaxes. getVocabularyByName(String) - Method in interface org.biojava.utils.candy.CandyFinder It returns a selected vocabulary. getVocabularyFinder() - Method in interface org.biojava.bibliography.BibRefSupport It returns an object representing a central place where all controlled vocabularies can be received from and shared by all users. getWalker(Visitor) - Method in class org.biojava.utils.walker.WalkerFactory Get a Walker that is customosed to a particular visitor. getWeight(Object) - Method in class org.biojavax.ga.util.WeightedSet Determines the normalized weight for o getWeight(Symbol) - Method in class org.biojava.bio.dist.AbstractDistribution Retrieve the weight for this distribution. getWeight(Symbol) - Method in interface org.biojava.bio.dist.Distribution Return the probability that Symbol s is emitted by this spectrum. getWeight(Symbol) - Method in class org.biojava.bio.dist.GapDistribution getWeight(Symbol) - Method in class org.biojava.bio.dist.PairDistribution getWeight(Symbol) - Method in class org.biojava.bio.dist.TranslatedDistribution getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.AbstractDistribution Override this method to implement getting the weight for an atomic symbol. getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution Get a weight from one of the sub-distributions, conditioned on the first part of the symbol. getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.UniformDistribution getWeightMatrixID() - Method in class org.biojava.bio.dp.WeightMatrixAnnotator Get the value of the weight matrix id. getWeights() - Method in class org.biojava.bio.dist.SimpleDistribution Get the underlying array that stores the weights. getWeights(State) - Method in interface org.biojava.bio.dp.MarkovModel Get a probability Distribution over the transition from 'source'. getWeights(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel getWeights(State) - Method in class org.biojava.bio.dp.WMAsMM getWidth() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Returns the width of the whole graphic (in pixels). getWidth() - Method in class org.biojava.bio.seq.io.AlternateTokenization Get the width of the tokens. getWidth() - Method in class org.biojava.stats.svm.RadialBaseKernel getWobbleDistributionForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref returns a WobbleDistribution for a specified residue. getWobbleDistributionForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref getWobbleFrequency(Symbol) - Method in interface org.biojava.bio.symbol.WobbleDistribution returns the frequency of a specific wobble base in a set of synonymous codons that start with the same two bases. getWorkingDirectory() - Method in class org.biojava.utils.process.ExternalProcess Gets the working directory for the external process. getWrap() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper getWrap() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout getWrap() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout getWrap() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout getWrapIncrement() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout getWrapIncrement() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout getWrapIncrement() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout getWrapped() - Method in class org.biojava.bio.AnnotationChanger getWrapped returns the Annotation being remapped. getWrapped() - Method in class org.biojava.bio.AnnotationRenamer getWrapped returns the Annotation being remapped. getWrapped() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator getWrappedKernel() - Method in class org.biojava.stats.svm.SigmoidKernel getWriter() - Method in class org.biojava.utils.process.ReaderWriterPipe Gets the writer. getXFFEnvironment() - Method in class org.biojava.bio.program.xff.FeatureHandler Return the XFF processing environment passed in when this handler was created. getXrefDb() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement getXrefProps() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref getXrefs() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs return a set of AGAVEXref getXrefs(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter getXrefs(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter getXrefs(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter GFF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants GFF indicates that the sequence format is GFF. GFF3DocumentHandler - Interface in org.biojava.bio.program.gff3 The interface for things that listen to GFF event streams. GFF3Parser - Class in org.biojava.bio.program.gff3 Parse a stream of GFF text into a stream of records and comments. GFF3Parser() - Constructor for class org.biojava.bio.program.gff3.GFF3Parser GFF3Record - Interface in org.biojava.bio.program.gff3 A record in a GFF3 formatted file. GFF3Record.Impl - Class in org.biojava.bio.program.gff3 GFFDataSource - Class in org.biojava.bio.seq.distributed Use a GFFEntrySet as a DataSource for adding annotation to sequences. GFFDataSource(GFFEntrySet) - Constructor for class org.biojava.bio.seq.distributed.GFFDataSource GFFDocumentHandler - Interface in org.biojava.bio.program.gff The interface for things that listen to GFF event streams. GFFEntrySet - Class in org.biojava.bio.program.gff A set of entries and comments as a representation of a GFF file. GFFEntrySet() - Constructor for class org.biojava.bio.program.gff.GFFEntrySet Make an empty GFFEntrySet. GFFErrorHandler - Interface in org.biojava.bio.program.gff Interface which captures any errors which occur when parsing a GFF stream. GFFErrorHandler.AbortErrorHandler - Class in org.biojava.bio.program.gff GFFErrorHandler.SkipRecordErrorHandler - Class in org.biojava.bio.program.gff GFFFilterer - Class in org.biojava.bio.program.gff An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others. GFFFilterer(GFFDocumentHandler, GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFFilterer Create a new GFFFilterer that will forward to handler everything that filter accepts. gffFromSeqDB(SequenceDB) - Static method in class org.biojava.bio.program.gff.GFFTools Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB. gffFromSequence(Sequence) - Static method in class org.biojava.bio.program.gff.GFFTools Creates a GFFEntrySet containing one entry for each feature on a sequence. GFFParser - Class in org.biojava.bio.program.gff Parse a stream of GFF text into a stream of records and comments. GFFParser() - Constructor for class org.biojava.bio.program.gff.GFFParser GFFRecord - Interface in org.biojava.bio.program.gff A single GFF record. GFFRecordFilter - Interface in org.biojava.bio.program.gff A filter that will accept or reject a GFFEntry. GFFRecordFilter.AcceptAll - Class in org.biojava.bio.program.gff Implementation of GFFRecordFilter that accepts everything. GFFRecordFilter.FeatureFilter - Class in org.biojava.bio.program.gff Implementation of GFFRecordFilter that accepts records based upon the feature field. GFFRecordFilter.FrameFilter - Class in org.biojava.bio.program.gff GFFRecordFilter.NotFilter - Class in org.biojava.bio.program.gff GFFRecordFilter.SequenceFilter - Class in org.biojava.bio.program.gff Implementation of GFFRecordFilter that accepts records based upon the sequence name. GFFRecordFilter.SourceFilter - Class in org.biojava.bio.program.gff Implementation of GFFRecordFilter that accepts records based upon the source field. GFFRecordFilter.StrandFilter - Class in org.biojava.bio.program.gff GFFTools - Class in org.biojava.bio.program.gff GFFTools() - Constructor for class org.biojava.bio.program.gff.GFFTools GFFWriter - Class in org.biojava.bio.program.gff Listens to a stream of GFF events and writes the lines to a PrintWriter. GFFWriter(PrintWriter) - Constructor for class org.biojava.bio.program.gff.GFFWriter Create a new GFFWriter that will write to out. GI_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. gList - Variable in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer gln() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Glutamine (Q) GLOBAL - Static variable in class org.biojava.bio.taxa.SimpleTaxonFactory Deprecated. The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects. GLOBAL - Static variable in class org.biojava.bio.taxa.WeakTaxonFactory Deprecated. The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects. glu() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Glutamic Acid (E) GLU_C_BICARB - Static variable in class org.biojava.bio.proteomics.Protease GLU_C_BICARB - Static variable in class org.biojava.bio.proteomics.ProteaseManager GLU_C_PHOS - Static variable in class org.biojava.bio.proteomics.Protease GLU_C_PHOS - Static variable in class org.biojava.bio.proteomics.ProteaseManager gly() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Glycine (G) Glyph - Interface in org.biojava.bio.gui.glyph The Glyph interface for painting a shape within bounds GlyphFeatureRenderer - Class in org.biojava.bio.gui.sequence A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilter GlyphFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.GlyphFeatureRenderer GlyphUtils - Class in org.biojava.bio.gui.glyph Utils class used by Glyph implementors. GOParser - Class in org.biojava.ontology.io Simple parser for the Gene Ontology (GO) flatfile format. GOParser() - Constructor for class org.biojava.ontology.io.GOParser graphicsToSecondarySequence(double) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext graphicsToSecondarySequence converts a graphical position to a sequence coordinate on the secondary sequence. graphicsToSecondarySequence(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel graphicsToSecondarySequence converts a graphical position to a secondary sequence index. graphicsToSecondarySequence(double) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext graphicsToSecondarySequence(Point) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext graphicsToSecondarySequence converts a graphical position to a secondary sequence index. graphicsToSecondarySequence(Point) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel graphicsToSecondarySequence converts a graphical position to a secondary sequence index. graphicsToSecondarySequence(Point) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel graphicsToSequence converts a graphical position to a sequence index. graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePanel graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. graphicsToSequence(double) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext Converts a graphical position into a sequence coordinate. graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel graphicsToSequence converts a graphical position to a sequence index. graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel graphicsToSequence converts a graphical position to a sequence index. graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SequencePanel graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. graphicsToSequence(Point2D) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext Converts a graphical position into a sequence coordinate. graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel graphicsToSequence converts a graphical position to a sequence index. greater(int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment GreaterThan(double) - Constructor for class org.biojava.bio.search.FilterTest.GreaterThan group() - Method in interface org.biojava.bio.search.BioMatcher Get the matching region as a SymbolList. group() - Method in class org.biojava.bio.search.MaxMismatchMatcher group() - Method in class org.biojava.utils.regex.Matcher Returns the input subsequence matched by the previous match. group(int) - Method in class org.biojava.utils.regex.Matcher Returns the input subsequence captured by the given group during the previous match operation. groupCount() - Method in class org.biojava.utils.regex.Matcher Returns the number of capturing groups in this matcher's pattern. groups - Variable in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection growIfNecessary() - Method in class org.biojava.utils.ChangeSupport Grows the internal resources if by adding one more listener they would be full. guessFileType(File) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. because there is no standard file naming convention and guessing by file name is inherantly error prone and bad. guessRecLen(RandomAccessFile) - Method in class org.biojava.bio.seq.db.BioIndex guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.FastaFormat On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. GUITools - Class in org.biojava.bio.gui.sequence GZIP_MAGIC - Static variable in class org.biojava.utils.io.InputStreamProvider The magic number found at the start of a GZIP stream.
H h() - Static method in class org.biojava.bio.seq.DNATools h() - Static method in class org.biojava.bio.seq.NucleotideTools h() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Histidine H_SAPIENS - Static variable in interface org.biojava.bio.program.homologene.Taxon H_VULGARE - Static variable in interface org.biojava.bio.program.homologene.Taxon handleEndElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.HitStAXHandler handleEndElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.HSPStAXHandler handleEndElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler handlesAmbiguity() - Method in class org.biojava.bio.symbol.DNAAmbPack handlesAmbiguity() - Method in class org.biojava.bio.symbol.DNANoAmbPack handlesAmbiguity() - Method in interface org.biojava.bio.symbol.Packing Flag to state if ambiguities are stored. handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.HitStAXHandler handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.HSPStAXHandler handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler hasAnnotation(Object) - Static method in class org.biojava.bio.seq.FilterUtils Match features where the property key has been defined as having some value, regardless of the exact value. HasAnnotation(Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.HasAnnotation Make a new ByAnnotation that will accept features with an annotation bundle containing any value associated with 'key'. HasAttribute(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute hasBoundedMax() - Method in class org.biojava.bio.symbol.FuzzyLocation hasBoundedMax() - Method in class org.biojava.bio.symbol.FuzzyPointLocation hasBoundedMin() - Method in class org.biojava.bio.symbol.FuzzyLocation hasBoundedMin() - Method in class org.biojava.bio.symbol.FuzzyPointLocation hasChangeListeners() - Method in class org.biojava.bio.gui.sequence.SequencePanel hasChangeListeners() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. hasChangeSupport() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB hasChild(int) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode Determine if this node has a child corresponding to a given index number. hasChild(Character) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode Determine if this node has a child corresponding to a given character hasFeatures(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource Find out if this DistDataSource can provide features on a sequence with a particular ID. hasFeatures(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource hasFeatures(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource hasGeneratedClass(String) - Method in class org.biojava.utils.bytecode.GeneratedClassLoader Discover if a class for this name has already been defined by this class loader. HashBioEntryDB - Class in org.biojavax.bio.db An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects. HashBioEntryDB() - Constructor for class org.biojavax.bio.db.HashBioEntryDB Generate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name. HashBioEntryDB(String) - Constructor for class org.biojavax.bio.db.HashBioEntryDB Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name. hashCode() - Method in class org.biojava.bio.AbstractAnnotation hashCode() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn hashCode() - Method in class org.biojava.bio.CollectionConstraint.Contains hashCode() - Method in class org.biojava.bio.dist.AbstractDistribution hashCode() - Method in class org.biojava.bio.dp.SimpleWeightMatrix hashCode() - Method in class org.biojava.bio.dp.TrainerTransition The hash code is model.hashCode() ^ from.hashCode() ^ to.hashCode() hashCode() - Method in class org.biojava.bio.dp.Transition The hash code is from.hashCode() ^ to.hashCode() hashCode() - Method in class org.biojava.bio.EcNumber.Impl hashCode() - Method in class org.biojava.bio.gui.sequence.SequencePanel hashCode() - Method in class org.biojava.bio.molbio.RestrictionEnzyme hashCode() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchResult Deprecated. hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit hashCode() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation hashCode() - Method in class org.biojava.bio.seq.Feature.Template hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.And hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByChild hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByParent hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.BySource hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByType hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.Not hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.Or hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter hashCode() - Method in class org.biojava.bio.seq.impl.SimpleFeature hashCode() - Method in class org.biojava.bio.seq.projection.ProjectedFeature hashCode() - Method in class org.biojava.bio.symbol.AbstractLocation hashCode() - Method in class org.biojava.bio.symbol.AbstractSymbolList hashCode() - Method in class org.biojava.bio.symbol.FuzzyPointLocation hashCode() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol hashCode() - Method in class org.biojava.bio.taxa.AbstractTaxon Deprecated. hashCode() - Method in interface org.biojava.bio.taxa.Taxon Deprecated. The hash-code of a Taxon is equal to the hash-code of it's scientific name. hashCode() - Method in class org.biojava.ontology.Term.Impl hashCode() - Method in interface org.biojava.ontology.Triple The hashcode for a Triple. hashCode() - Method in class org.biojava.ontology.Triple.Impl hashCode() - Method in class org.biojava.utils.ListTools.Doublet hashCode() - Method in class org.biojava.utils.ListTools.Triplet hashCode() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier hashCode() - Method in class org.biojava.utils.TypedProperties hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation hashCode() - Method in class org.biojavax.bio.seq.CompoundRichLocation hashCode() - Method in class org.biojavax.bio.seq.EmptyRichLocation ALWAYS RETURNS 17 hashCode() - Method in class org.biojavax.bio.seq.RichLocation.Strand hashCode() - Method in class org.biojavax.bio.seq.SimpleRichFeature hashCode() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship hashCode() - Method in class org.biojavax.bio.seq.SimpleRichLocation hashCode() - Method in class org.biojavax.bio.SimpleBioEntry hashCode() - Method in class org.biojavax.bio.SimpleBioEntryRelationship hashCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon hashCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName hashCode() - Method in class org.biojavax.EmptyRichAnnotation hashCode() - Method in class org.biojavax.ontology.SimpleComparableOntology hashCode() - Method in class org.biojavax.ontology.SimpleComparableTerm hashCode() - Method in class org.biojavax.ontology.SimpleComparableTriple The hashcode for a Triple. hashCode() - Method in class org.biojavax.SimpleComment hashCode() - Method in class org.biojavax.SimpleCrossRef hashCode() - Method in class org.biojavax.SimpleDocRef hashCode() - Method in class org.biojavax.SimpleDocRefAuthor hashCode() - Method in class org.biojavax.SimpleNamespace hashCode() - Method in class org.biojavax.SimpleNote hashCode() - Method in class org.biojavax.SimpleRankedCrossRef hashCode() - Method in class org.biojavax.SimpleRankedDocRef hashCode(int, boolean) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, boolean[]) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, double) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, double[]) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, float) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, float[]) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, int) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, int[]) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, long) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, long[]) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, Object) - Static method in class org.biojava.utils.ObjectUtil hashCode(int, Object[]) - Static method in class org.biojava.utils.ObjectUtil HashedFastaIterator - Class in org.biojavax.bio.seq.io Iterates over a Fasta file that is kept in memory for optimized access. HashedFastaIterator(BufferedInputStream, Alphabet, Namespace) - Constructor for class org.biojavax.bio.seq.io.HashedFastaIterator HashRichSequenceDB - Class in org.biojavax.bio.db An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects. HashRichSequenceDB() - Constructor for class org.biojavax.bio.db.HashRichSequenceDB Generate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name. HashRichSequenceDB(String) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name. HashRichSequenceDB(IDMaker) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have a null name. HashRichSequenceDB(IDMaker, String) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have the requested name. HashSequenceDB - Class in org.biojava.bio.seq.db An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects. HashSequenceDB() - Constructor for class org.biojava.bio.seq.db.HashSequenceDB Generate a HashSequenceDB object that will use byName to generate ids for sequences and have a null name. HashSequenceDB(String) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB Generate a HashSequenceDB object that will use byName to generate ids and will have the requested name. HashSequenceDB(IDMaker) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have a null name. HashSequenceDB(IDMaker, String) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have the requested name. hasListeners() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer hasListeners() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer hasListeners() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer hasListeners() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel hasListeners returns true if there are active listeners for BioJava events. hasListeners() - Method in class org.biojava.bio.gui.sequence.SequencePanel hasListeners() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel hasListeners returns true if there are active listeners for BioJava events. hasListeners() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder hasListeners() - Method in class org.biojava.utils.AbstractChangeable Discover if we have any listeners registered. hasListeners() - Method in class org.biojava.utils.ChangeSupport Return true if we have any listeners registered at all. hasListeners(String) - Method in class org.biojava.bio.gui.StackedLogoPainter hasListeners(String) - Method in class org.biojava.bio.gui.TextLogoPainter hasListeners(ChangeType) - Method in class org.biojava.utils.AbstractChangeable Discover if we have listeners registered for a particular change type. hasListeners(ChangeType) - Method in class org.biojava.utils.ChangeSupport Return true if we have listeners registered for a particular change type. hasMoreSymbols() - Method in interface org.biojava.bio.seq.io.SymbolReader Determine if there are more symbols left to read in this stream. hasNext() - Method in class org.biojava.bio.alignment.Alignment.SymbolListIterator hasNext() - Method in class org.biojava.bio.dp.DP.ReverseIterator hasNext() - Method in class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor hasNext() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor Are there further Cells to be computed? hasNext() - Method in class org.biojava.bio.dp.twohead.MatrixPairDPCursor hasNext() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor test wether the cursor can be advanced further hasNext() - Method in interface org.biojava.bio.program.homologene.OrthologueSet.Iterator hasNext() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection.Iterator are more OrthoPairSets available? hasNext() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet.Iterator hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet.Iterator hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection.Iterator hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet.Iterator hasNext() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer hasNext() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer hasNext() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer hasNext() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader Checks if there is a further SymbolPropertyTable object. hasNext() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator Checks if there is a further SymbolPropertyTable object. hasNext() - Method in class org.biojava.bio.seq.io.StreamReader hasNext() - Method in interface org.biojava.bio.seq.SequenceIterator Returns whether there are more sequences to iterate over. hasNext() - Method in class org.biojava.utils.MergingIterator hasNext() - Method in interface org.biojavax.bio.BioEntryIterator Returns whether there are more sequences to iterate over. hasNext() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator hasNext() - Method in class org.biojavax.bio.seq.io.RichStreamReader Returns whether there are more sequences to iterate over. hasNext() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator Returns whether there are more sequences to iterate over. hasOffsetData - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord hasOpenSubComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment hasSequence(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource Find out if this DistDataSource provides the sequence information for a sequence ID. hasSequence(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource hasSequence(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource hasWeights() - Method in class org.biojava.bio.dist.SimpleDistribution Indicate whether the weights array has been allocated yet. Havg - Static variable in class org.biojava.bio.proteomics.MassCalc Constant value of Hydrogen average mass HEADER_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HeaderStAXHandler HeaderlessFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat headerLine - Static variable in class org.biojavax.bio.seq.io.EMBLFormat headerLine - Static variable in class org.biojavax.bio.seq.io.GenbankFormat headerLine - Static variable in class org.biojavax.bio.seq.io.UniProtFormat HeaderStAXHandler - Class in org.biojava.bio.program.ssbind HeaderStAXHandler handles the Header element of BioJava BlastLike XML. HeadlessRenderContext - Class in org.biojava.bio.gui.sequence A stand-alone SequenceRenderContext to make it easy to render to an image. HeadlessRenderContext(Sequence, RangeLocation, int) - Constructor for class org.biojava.bio.gui.sequence.HeadlessRenderContext heads() - Method in interface org.biojava.bio.dp.MarkovModel Deprecated. use advance().length heads() - Method in class org.biojava.bio.dp.SimpleMarkovModel heads() - Method in class org.biojava.bio.dp.WMAsMM HEIGHT_IS_AUTHORITATIVE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option Option indicating whether height or vertical scale is the authoritative measure. HEIGHTSCALING - Static variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer Constant HEIGHTSCALING indicating a change to the feature height scaling policy. HelixGlyph - Class in org.biojava.bio.gui.glyph A Glyph that paints a Helix within the bounds HelixGlyph() - Constructor for class org.biojava.bio.gui.glyph.HelixGlyph HelixGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.HelixGlyph HibernateFeatureFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter HIDDEN - Static variable in interface org.biojavax.bio.taxa.NCBITaxon his() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Histidine (H) hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.HitMerger hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.FilterByLength hit(int, int, int, int) - Method in interface org.biojava.bio.program.ssaha.SearchListener There has been a hit between the query sequence and a database sequence. hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper HIT_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HitStAXHandler HitMerger - Class in org.biojava.bio.program.ssaha A listener that merges overlapping hits and culls all hits under a given length. HitMerger(SearchListener, int) - Constructor for class org.biojava.bio.program.ssaha.HitMerger Build a new HitMerger that will pass events on to a delegate. HitStAXHandler - Class in org.biojava.bio.program.ssbind AlignmentStAXHandler handles the Hit element of BioJava BlastLike XML. hmm - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser hmm() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM Gets the inner HmmerProfileHMM state HmmerProfileHMM - Class in org.biojava.bio.program.hmmer This is a class for representing HMMER generated Profile HMM. HmmerProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory, String) - Constructor for class org.biojava.bio.program.hmmer.HmmerProfileHMM HmmerProfileParser - Class in org.biojava.bio.program.hmmer A class for parsing in Hmmer markov models from HMM_ls files generated by HMMER training note that this class is still currently experimental. HmmerProfileParser(String) - Constructor for class org.biojava.bio.program.hmmer.HmmerProfileParser HMMTrainer - Interface in org.biojava.bio.dp interface implemented by objects that train HMMs. Hmono - Static variable in class org.biojava.bio.proteomics.MassCalc Constant value of Hydrogen monoisotopic mass HOMOID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder HomologeneBuilder - Interface in org.biojava.bio.program.homologene an interface for Homologene dataset Builders HomologeneDB - Interface in org.biojava.bio.program.homologene Homologene is a NCBI dataset that curates sets of orthologues from the reference model organisms. HomologeneTools - Class in org.biojava.bio.program.homologene Homologene is a NCBI dataset that curates sets of orthologues from the reference model ogranisms. HomologeneTools() - Constructor for class org.biojava.bio.program.homologene.HomologeneTools homology - Variable in class org.biojava.bio.seq.homol.HomologyFeature.Template Homology - Interface in org.biojava.bio.seq.homol Signifies that two or more features are homologous. HOMOLOGY_FEATURE_TYPE - Static variable in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder HOMOLOGY_FEATURE_TYPE is the type String used by BlastLikeHomologyBuilder when creating HomologyFeatures. HomologyDB - Interface in org.biojava.bio.seq.homol HomologyFeature - Interface in org.biojava.bio.seq.homol HomologyFeature.Template - Class in org.biojava.bio.seq.homol HORIZONTAL_NONLINEAR_SCALER - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option Option specifying the non-linear scaling function to apply, as embodied in a ChromatogramNonlinearScaler object. HotSpot(String, URL, Integer[]) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.HotSpot Creates a new HotSpot with a null user object. HotSpot(String, URL, Integer[], Object) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.HotSpot Creates a new HotSpot. hotSpots() - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide hotSpots() - Method in interface org.biojava.bio.gui.sequence.ImageMap hotSpots iterates over the hotspots in the map hotSpots() - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide hp - Static variable in class org.biojavax.bio.seq.io.FastaFormat HSP_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HSPStAXHandler HSPStAXHandler - Class in org.biojava.bio.program.ssbind HSPStAXHandler handles the HSP element of BioJava BlastLike XML. HSPSUMMARY_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler HSPSummaryStAXHandler - Class in org.biojava.bio.program.ssbind HSPSummaryStAXHandler handles the HSPSummary element of BioJava BlastLike XML. HTML - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat HTMLRenderer - Class in org.biojava.bio.program.blast2html Renders HTML version of blast-like output. HTMLRenderer(PrintWriter, String, int, URLGeneratorFactory, AlignmentMarker, Properties) - Constructor for class org.biojava.bio.program.blast2html.HTMLRenderer Creates an HTMLRenderer, that outputs the HTML to the specified PrintWriter. HYDROPATHICITY - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable HypersonicDBHelper - Class in org.biojava.bio.seq.db.biosql Deprecated. Use hibernate and org.biojavax.bio.db.* HypersonicDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.HypersonicDBHelper Deprecated. I i() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Isoleucine ID_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat ID_KEY - Static variable in class org.biojava.ontology.obo.OboFileHandler ID_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. ID_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat Identifiable - Interface in org.biojava.utils.lsid Marks an implementor as having a LifeScienceIdentifier. identifier - Variable in class org.biojava.bibliography.BibRef It is an unambiguous reference to this citation "within the world". IDENTIFIER - Static variable in interface org.biojavax.bio.BioEntry IDENTIFIER - Static variable in interface org.biojavax.ontology.ComparableTerm identifyFormat(String, String) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. identifyFormat performs a case-insensitive mapping of a pair of common sequence format name (such as 'embl', 'genbank' or 'fasta') and alphabet name (such as 'dna', 'rna', 'protein', 'aa') to an integer. IDMaker - Interface in org.biojava.bio.seq.db Interface for objects that define how to make an ID for a sequence. IDMaker.ByName - Class in org.biojava.bio.seq.db IDMaker.ByURN - Class in org.biojava.bio.seq.db ids() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB ids() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB Deprecated. ids() - Method in class org.biojava.bio.seq.db.CachingSequenceDB ids() - Method in class org.biojava.bio.seq.db.DummySequenceDB ids() - Method in class org.biojava.bio.seq.db.HashSequenceDB ids() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB ids() - Method in interface org.biojava.bio.seq.db.SequenceDB Get an immutable set of all of the IDs in the database. ids() - Method in class org.biojava.bio.seq.db.SubSequenceDB ids() - Method in class org.biojava.bio.seq.db.ViewingSequenceDB ids() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB ids() - Method in interface org.biojavax.bio.db.BioEntryDB Get an immutable set of all of the IDs in the database. ids() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB ids() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB ids() - Method in class org.biojavax.bio.db.HashBioEntryDB ids() - Method in class org.biojavax.bio.db.HashRichSequenceDB ids() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB ids() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB ids(boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource Get the complete set of sequence IDs provided by this DistDataSource. ids(boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource ids(boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource IfExpression - Class in org.biojava.utils.bytecode A CodeGenerator that provides something semanticaly identical to if. IfExpression(byte, CodeGenerator, CodeGenerator) - Constructor for class org.biojava.utils.bytecode.IfExpression IG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants IG indicates that the sequence format is IG. ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor ignorableWhitespace(char[], int, int) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase ignorableWhitespace(char[], int, int) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor ignorableWhitespace(char[], int, int) - Method in interface org.biojava.utils.stax.StAXContentHandler ignorableWhitespace(char[], int, int) - Method in class org.biojava.utils.stax.StAXContentHandlerBase IgnoreCountsTrainer - Class in org.biojava.bio.dist A distribution trainer that just ignores all counts. IgnoreCountsTrainer() - Constructor for class org.biojava.bio.dist.IgnoreCountsTrainer Constructor intended for sub-classes. IgnoreRecordException - Exception in org.biojava.bio.program.gff Ignore this record in the stream. IgnoreRecordException() - Constructor for exception org.biojava.bio.program.gff.IgnoreRecordException ile() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Isoleucine (I) IllegalAlignmentEditException - Exception in org.biojava.bio.alignment The usual reason for throwing an IllegalAlignmentEditException is that you are trying to shift a group of bases in such a way that it would require deleting bases. IllegalAlignmentEditException() - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException Just make the exception. IllegalAlignmentEditException(String) - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException Make the exception with a message. IllegalAlignmentEditException(Throwable) - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException IllegalAlignmentEditException(Throwable, String) - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException IllegalAlphabetException - Exception in org.biojava.bio.symbol The exception to indicate that an invalid alphabet has been used. IllegalAlphabetException() - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException Just make the exception. IllegalAlphabetException(String) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException Make the exception with a message. IllegalAlphabetException(Throwable) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException IllegalAlphabetException(Throwable, String) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException IllegalIDException - Exception in org.biojava.bio.seq.db IllegalIDException() - Constructor for exception org.biojava.bio.seq.db.IllegalIDException IllegalIDException(String) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException IllegalIDException(Throwable) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException IllegalIDException(Throwable, String) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException IllegalOrganismException - Exception in org.biojavax.ga.exception Indicates an invalid organism IllegalOrganismException() - Constructor for exception org.biojavax.ga.exception.IllegalOrganismException IllegalOrganismException(String) - Constructor for exception org.biojavax.ga.exception.IllegalOrganismException IllegalSymbolException - Exception in org.biojava.bio.symbol The exception to indicate that a symbol is not valid within a context. IllegalSymbolException(String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException Make the exception with a message. IllegalSymbolException(Throwable, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException IllegalSymbolException(Throwable, Symbol, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException IllegalSymbolException(Symbol, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException Make the exception with a message and a symbol. IllegalTransitionException - Exception in org.biojava.bio.dp This exception indicates that there is no transition between two states. IllegalTransitionException() - Constructor for exception org.biojava.bio.dp.IllegalTransitionException IllegalTransitionException(State, State) - Constructor for exception org.biojava.bio.dp.IllegalTransitionException IllegalTransitionException(State, State, String) - Constructor for exception org.biojava.bio.dp.IllegalTransitionException IlluminaFastqReader - Class in org.biojava.bio.program.fastq Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences. IlluminaFastqReader() - Constructor for class org.biojava.bio.program.fastq.IlluminaFastqReader IlluminaFastqWriter - Class in org.biojava.bio.program.fastq Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences. IlluminaFastqWriter() - Constructor for class org.biojava.bio.program.fastq.IlluminaFastqWriter ImageMap - Interface in org.biojava.bio.gui.sequence ImageMap represents a collection of image map hotspots. ImageMap.ClientSide - Class in org.biojava.bio.gui.sequence ClientSide represents a client-side style image map. ImageMap.HotSpot - Class in org.biojava.bio.gui.sequence HotSpots represent an image map hotspot. ImageMap.ServerSide - Class in org.biojava.bio.gui.sequence ServerSide represents a server-side style image map. ImageMapRenderer - Interface in org.biojava.bio.gui.sequence ImageMapRenderers create strings representing Features suitable for use in HTML image maps. Impl() - Constructor for class org.biojava.bio.AnnotationType.Impl Create a new Impl with no constraints. Impl() - Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl Impl(int, int, int, int) - Constructor for class org.biojava.bio.EcNumber.Impl Make a new EcNumber.Impl with the data provided. Impl(String, String) - Constructor for class org.biojava.ontology.Ontology.Impl Impl(String, Map) - Constructor for class org.biojava.directory.RegistryConfiguration.Impl Impl(String, RAF, long, int) - Constructor for class org.biojava.bio.program.indexdb.Record.Impl Creates a new Impl record. Impl(CollectionConstraint) - Constructor for class org.biojava.bio.AnnotationType.Impl Create a new Impl with a default collection constraint. Impl(GFF3Record) - Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl Impl(PropertyConstraint, Location) - Constructor for class org.biojava.bio.AnnotationType.Impl Create a new Impl with a default property and cardinality constraint. Impl(Ontology, String) - Constructor for class org.biojava.ontology.Term.Impl Impl(Ontology, String, String) - Constructor for class org.biojava.ontology.Term.Impl Impl(Ontology, String, String) - Constructor for class org.biojava.ontology.Variable.Impl Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.ontology.Term.Impl Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.ontology.Variable.Impl Impl(Ontology, Ontology) - Constructor for class org.biojava.ontology.OntologyTerm.Impl Impl(Ontology, Ontology, Object[]) - Constructor for class org.biojava.ontology.OntologyTerm.Impl Impl(Ontology, Term, String) - Constructor for class org.biojava.ontology.RemoteTerm.Impl Impl(Ontology, Term, String, Object[]) - Constructor for class org.biojava.ontology.RemoteTerm.Impl Impl(Term, Term, Term) - Constructor for class org.biojava.ontology.Triple.Impl Impl(Term, Term, Term, Object[]) - Constructor for class org.biojava.ontology.Triple.Impl Impl(Term, Term, Term, String, String) - Constructor for class org.biojava.ontology.Triple.Impl Impl(Term, Term, Term, String, String, Object[]) - Constructor for class org.biojava.ontology.Triple.Impl importTaxon(Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory Deprecated. importTaxon(Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory Deprecated. Import a Taxon and all its children into the implementation provided by this factory. importTaxon(Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory Deprecated. importTerm(Term, String) - Method in class org.biojava.ontology.IntegerOntology importTerm(Term, String) - Method in class org.biojava.ontology.Ontology.Impl importTerm(Term, String) - Method in interface org.biojava.ontology.Ontology Create a view of a term from another ontology. importTerm(Term, String) - Method in class org.biojavax.ontology.SimpleComparableOntology Create a view of a term from another ontology. in - Variable in class org.biojava.utils.io.CachingInputStream The underlying input stream whose data we're caching IN_RANGE - Static variable in interface org.biojavax.bio.seq.Position A symbol representing a position that occupies a single base somewhere in a range, eg. 5.10 falls on some base between 5 and 10. incCounts(int, int) - Method in class org.biojava.bio.symbol.SuffixTree INCLUDES_PREFIX - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms increaseCount(AtomicSymbol, double) - Method in interface org.biojava.bio.dist.Count Set the probability or odds that Symbol s is emitted by this state. increaseCount(AtomicSymbol, double) - Method in class org.biojava.bio.dist.IndexedCount indent() - Method in class org.biojava.bio.program.xml.BaseXMLWriter indent() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent Add a level of indentation Indent() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter.Indent INDENT - Static variable in class org.biojava.bio.seq.io.agave.AgaveWriter use a two space indent INDETERMINATE - Static variable in class org.biojava.utils.TriState index - Variable in class org.biojava.ontology.obo.OboFileParser.SOPair index(State) - Method in class org.biojava.bio.dp.WMAsMM index(Symbol) - Static method in class org.biojava.bio.seq.DNATools Return an integer index for a symbol - compatible with forIndex. index(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools Return an integer index for a symbol - compatible with forIndex. index(Symbol) - Static method in class org.biojava.bio.seq.RNATools Return an integer index for a symbol - compatible with forIndex. Index - Interface in org.biojava.bio.seq.db This defines an index entry for an individual sequence within a set of indexed files. INDEX - Static variable in interface org.biojava.bio.symbol.AlphabetIndex Indicates that the index is changing, probably due to the underlying alphabet changing. Index2Model - Class in org.biojava.bio.program.tagvalue Index2Model() - Constructor for class org.biojava.bio.program.tagvalue.Index2Model IndexedAnnotationDB - Class in org.biojava.bio.annodb A database of Annotation instances backed by an indexed file set. IndexedAnnotationDB(String, File, Index2Model, List, int, AnnotationType, IndexedAnnotationDB.ParserListenerFactory) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB Create a new IndexedAnnotationDB. IndexedAnnotationDB(BioStore) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB Initialise the db from a store. IndexedAnnotationDB.ParserListenerFactory - Interface in org.biojava.bio.annodb A factory for retrieving parsers and listeners. IndexedAnnotationDB.StaticMethodRPFactory - Class in org.biojava.bio.annodb An implementation of ParserListenerFactory that uses a static method. IndexedChangeHub - Class in org.biojava.utils implements Changeable support with a ChangeHub that stores ChangeListener by key. IndexedChangeHub() - Constructor for class org.biojava.utils.IndexedChangeHub IndexedChangeHub.ListenerMemento - Class in org.biojava.utils IndexedCount - Class in org.biojava.bio.dist An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object. IndexedCount(AlphabetIndex) - Constructor for class org.biojava.bio.dist.IndexedCount Get a new InexedCount for an alphabet indexer. IndexedCount(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.IndexedCount Get a new IdexedCount for an alphabet using the default indexer. IndexedSequenceDB - Class in org.biojava.bio.seq.db This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files. IndexedSequenceDB(IDMaker, IndexStore) - Constructor for class org.biojava.bio.seq.db.IndexedSequenceDB Create an IndexedSequenceDB by specifying both the IDMaker and IndexStore used. IndexedSequenceDB(IndexStore) - Constructor for class org.biojava.bio.seq.db.IndexedSequenceDB Create an IndexedSequenceDB by specifying IndexStore used. indexEmbl(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools indexEmbl indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary. Indexer - Class in org.biojava.bio.program.tagvalue Listens to tag-value events and passes on indexing events to an IndexStore. Indexer(File, IndexStore) - Constructor for class org.biojava.bio.program.tagvalue.Indexer Build a new Indexer. Indexer2 - Class in org.biojava.bio.program.tagvalue Listens to tag-value events and passes on indexing events to an IndexStore. Indexer2(File, IndexStore, Index2Model) - Constructor for class org.biojava.bio.program.tagvalue.Indexer2 Build a new Indexer. indexFasta(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools indexFasta indexes DNA, RNA or protein Fasta format sequence files on primary identifier. indexForSymbol(Symbol) - Method in interface org.biojava.bio.symbol.AlphabetIndex Return the unique index for a symbol. indexGenbank(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools indexGenbank indexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary. IndexStore - Interface in org.biojava.bio.program.indexdb IndexStore is an interface for indexing flatfiles according to the OBDA specification. IndexStore - Interface in org.biojava.bio.seq.db This defines the objects that IndexedSequenceDB uses to store all of the database state, such as name, format, sequence builder and the actual file offsets. indexSwissprot(String, File, File[]) - Static method in class org.biojava.bio.program.indexdb.IndexTools indexSwissprot indexes Swissprot format protein sequence files on ID as primary identifier. IndexTools - Class in org.biojava.bio.program.indexdb IndexTools contains static utility methods for creating flatfile indices according to the OBDA standard. inFeature() - Method in class org.biojava.bio.seq.io.FeatureTableParser Deprecated. InfinitelyAmbiguousSymbolList - Class in org.biojavax.bio.seq A symbol list that is Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything. InfinitelyAmbiguousSymbolList(FiniteAlphabet) - Constructor for class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList Creates a new instance of InfinitelyAmbiguousSymbolList init() - Method in interface org.biojava.utils.xml.Initializable INIT_PROP_LOG - Static variable in interface org.biojava.bibliography.BibRefSupport A property name ("log"). INIT_PROP_SUPPORT - Static variable in interface org.biojava.bibliography.BibRefSupport A property name ("bibrefsupport"). initComponents() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper initialiseProfileHMM(int) - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser Initializable - Interface in org.biojava.utils.xml initialize() - Method in class org.biojava.bio.seq.db.TabIndexStore initialize(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator Initialize the cell at [0][0] to the recursion initial parameters. initializeVariables(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver) - Method in class org.biojava.bio.symbol.FuzzyLocation Refactored initialization code from the constructors. initPopulation() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm Assigns a fitness value to each organism within the population according to the currently set fitness function. input - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader InputHandler - Interface in org.biojava.utils.process Interface to a threadable input handler for an external process. InputStreamProvider - Class in org.biojava.utils.io A class that provides an InputStream from a File. InputStreamProvider() - Constructor for class org.biojava.utils.io.InputStreamProvider INSDSEQ_FORMAT - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat The name of this format INSDSEQ_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat INSDseqFormat - Class in org.biojavax.bio.seq.io Format reader for INSDseq files. INSDseqFormat() - Constructor for class org.biojavax.bio.seq.io.INSDseqFormat INSDseqFormat.Terms - Class in org.biojavax.bio.seq.io Implements some INSDseq-specific terms. INSDSEQS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat insertObject(NexusObject, int) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile Inserts an object at the given position. instance() - Static method in class org.biojava.bio.symbol.AlphabetManager Deprecated. all AlphabetManager methods have become static instance() - Static method in class org.biojava.directory.SystemRegistry Get the singleton Registry instance representing the system-wide default registry. INSTANCE - Static variable in class org.biojava.bio.gui.sequence.LayeredRenderer Static LayeredRenderer INSTANCE used by MultiLineRenderers. INSTANCE - Static variable in class org.biojava.bio.seq.io.GenEmblFeatureComparator Deprecated. INSTANCE - Static variable in class org.biojava.bio.seq.io.GenEmblPropertyComparator Deprecated. INSTANCE - Static variable in class org.biojava.bio.symbol.DoubleAlphabet INSTANCE - Static variable in class org.biojava.bio.symbol.IntegerAlphabet The singleton instance of the IntegerAlphabet class. INSTANCE - Static variable in class org.biojava.utils.xml.XMLBeans instanceOf(Annotation) - Method in class org.biojava.bio.AnnotationType.Abstract instanceOf(Annotation) - Method in interface org.biojava.bio.AnnotationType Validate an Annotation against this AnnotationType. instantiateBean(Element) - Method in class org.biojava.utils.xml.XMLBeans instantiateBean(Element, ClassLoader, Map) - Method in class org.biojava.utils.xml.XMLBeans instantiateDB(URL, HomologeneBuilder) - Static method in class org.biojava.bio.program.homologene.HomologeneTools instantiate a HomologeneDB. instantiateTemplate(Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils This attempts to divine the 'best' template class for a feature and return a new instance readly for pupulating. Instruction - Interface in org.biojava.utils.bytecode Base class for java bytecode instructions. InstructionVector - Class in org.biojava.utils.bytecode A list of Instructions and/or other CodeGenerator objects. InstructionVector() - Constructor for class org.biojava.utils.bytecode.InstructionVector INTEGER - Static variable in class org.biojava.bio.seq.io.SeqIOConstants INTEGER indicates that a sequence contains integer alphabet symbols, such as used to describe sequence quality data. IntegerAlphabet - Class in org.biojava.bio.symbol An efficient implementation of an Alphabet over the infinite set of integer values. IntegerAlphabet.IntegerSymbol - Class in org.biojava.bio.symbol A single int value. IntegerAlphabet.SubIntegerAlphabet - Class in org.biojava.bio.symbol A class to represent a finite contiguous subset of the infinite IntegerAlphabet IntegerOntology - Class in org.biojava.ontology IntegerOntology.IntTerm - Class in org.biojava.ontology IntegerSymbol(int) - Constructor for class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol integerSymbolFromPhred(Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet. IntegerTokenization - Class in org.biojava.bio.seq.io IntegerTokenization() - Constructor for class org.biojava.bio.seq.io.IntegerTokenization IntElementHandlerBase - Class in org.biojava.utils.stax StAX handler for any element which just contains a string representation of an integer. IntElementHandlerBase() - Constructor for class org.biojava.utils.stax.IntElementHandlerBase Interaction() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction INTERACTION - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser A name for a comment type. internalClassify(int) - Method in class org.biojava.stats.svm.SVMRegressionModel intersect(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils Operator: Intersect FeatureHolder1 with FeatureHolder2 intersection(AnnotationType, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools Calculate an AnnotationType that matches all Annotation instances matched by both types. intersection(CollectionConstraint, CollectionConstraint) - Static method in class org.biojava.bio.AnnotationTools Return the CollectionConstraint which accept only collections accepted by both of those specified. intersection(PropertyConstraint, PropertyConstraint) - Static method in class org.biojava.bio.AnnotationTools Calculate the intersection of two PropertyConstraint instances. intersection(Location) - Method in class org.biojava.bio.symbol.AbstractLocation intersection(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator intersection(Location) - Method in class org.biojava.bio.symbol.CircularLocation intersection(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation intersection(Location) - Method in interface org.biojava.bio.symbol.Location Returns a Location that contains all points common to both ranges. intersection(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation Returns a Location that contains all points common to both ranges. intersection(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation Returns a Location that contains all points common to both ranges. intersection(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation Returns a Location that contains all points common to both ranges. intersection(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools Return the intersection of two locations. INTERSECTION_OF - Static variable in class org.biojava.ontology.obo.OboFileHandler IntrospectedCodeClass - Class in org.biojava.utils.bytecode CodeClass instances that represent normal Java Class objects. IntTerm(int) - Constructor for class org.biojava.ontology.IntegerOntology.IntTerm IntTerm(int, Object[]) - Constructor for class org.biojava.ontology.IntegerOntology.IntTerm intValue() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol intValue() - Method in class org.biojava.ontology.IntegerOntology.IntTerm intValue() - Method in class org.biojavax.bio.seq.RichLocation.Strand Returns the numeric value of this strand. iNumberOfColours - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler The number of unique colours. invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler invalidEnd(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler The `end' field of the GFF entry was not a valid value. invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler invalidEnd(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter invalidFrame(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler invalidFrame(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler The `frame' field of the GFF entry was not a valid value. invalidFrame(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler invalidFrame(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter invalidScore(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler invalidScore(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler The `score' field of the GFF entry was not a valid value. invalidScore(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler invalidScore(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter invalidStart(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler invalidStart(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler The `start' field of the GFF entry was not a valid value. invalidStart(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler invalidStart(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler invalidStrand(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler The `strand' field of the GFF entry was not a valid value. invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFWriter InvalidTermException - Exception in org.biojava.ontology Thrown to indicate that an ontology term is not acceptable or appropriate in a given context InvalidTermException() - Constructor for exception org.biojava.ontology.InvalidTermException InvalidTermException(String) - Constructor for exception org.biojava.ontology.InvalidTermException InvalidTermException(String, Throwable) - Constructor for exception org.biojava.ontology.InvalidTermException InvalidTermException(Throwable) - Constructor for exception org.biojava.ontology.InvalidTermException INVERT_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable Translation table name for the invertebrate mitochondrial genetic code. IOExceptionFound - Variable in class org.biojava.bio.seq.db.GenbankSequenceDB IS_A - Static variable in class org.biojava.ontology.obo.OboFileHandler IS_A - Static variable in class org.biojava.ontology.OntoTools IS_OBSOLETE - Static variable in class org.biojava.ontology.obo.OboFileHandler isActive() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel isActive returns true if both the Sequences to be rendered and the PairwiseHomologyRenderer are not null. isActive() - Method in class org.biojava.bio.gui.sequence.SequencePanel isActive() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper isActive() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. isActive() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel isActive returns true if both the Sequence to be rendered and the SequenceRenderer are not null. isArray() - Method in interface org.biojava.utils.bytecode.CodeClass Discover if the class is an array type. isArray() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass isArray() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass isArray() - Method in class org.biojava.utils.bytecode.ParametricType isbn - Variable in class org.biojava.bibliography.BiblioBook ISBN number. isBoundaryEnd(Object) - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder isBoundaryStart(Object) - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder isCaseSensitive() - Method in interface org.biojava.utils.candy.CandyVocabulary It returns true if the vocabulary entries should be considered as case-sensitive. isColoured(String, String) - Method in interface org.biojava.bio.program.blast2html.ColourCommand Returns true if the alignment pair should be coloured else false. isComponentResolvable() - Method in interface org.biojava.bio.seq.ComponentFeature Determine if the sequence references by this ComponentFeature is available in this context. isConsortium() - Method in interface org.biojavax.DocRefAuthor Is this author actually a consortium? isConsortium() - Method in class org.biojavax.SimpleDocRefAuthor Is this author actually a consortium? isContiguous() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator isContiguous() - Method in class org.biojava.bio.symbol.AbstractRangeLocation isContiguous() - Method in class org.biojava.bio.symbol.CircularLocation Delegates to the wrapped location. isContiguous() - Method in class org.biojava.bio.symbol.FuzzyPointLocation isContiguous() - Method in interface org.biojava.bio.symbol.Location Determine if a Location is contiguous. isContiguous() - Method in class org.biojavax.bio.seq.CompoundRichLocation Determine if a Location is contiguous. isContiguous() - Method in class org.biojavax.bio.seq.EmptyRichLocation Determine if a Location is contiguous. isContiguous() - Method in class org.biojavax.bio.seq.SimpleRichLocation Determine if a Location is contiguous. isDeprecated() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass Get the deprecation flag. isDiagonal() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySource isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByType isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter isDisjoint(FeatureFilter) - Method in interface org.biojava.bio.seq.OptimizableFilter Returns true if this filter is disjoint from filt - that is, there is no Feature that is accepted by both filters. isEditor() - Method in interface org.biojavax.DocRefAuthor Is this author actually an editor? isEditor() - Method in class org.biojavax.SimpleDocRefAuthor Is this author actually an editor? isEmpty() - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection isEmpty() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection isEmpty() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection isEmpty() - Method in class org.biojavax.ga.util.WeightedSet isEndoProtease() - Method in class org.biojava.bio.proteomics.Protease isEscapeStarter(char) - Static method in class org.biojava.ontology.obo.OboFileParser isFloatType(CodeClass) - Static method in class org.biojava.utils.bytecode.CodeUtils Returns true if the class is a floating point number. isHaploid() - Method in class org.biojavax.ga.impl.AbstractOrganism isHaploid() - Method in class org.biojavax.ga.impl.SimpleOrganism Simple Organisms are Halpoid isHaploid() - Method in interface org.biojavax.ga.Organism Is the organism Haploid? isIllumina() - Method in enum org.biojava.bio.program.fastq.FastqVariant Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_ILLUMINA. isIntegerType(CodeClass) - Static method in class org.biojava.utils.bytecode.CodeUtils Returns true if the class is an integer number. isInterleaved() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock isInterleaved() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock isLabels() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock isLabels() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock isMasked(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector Default Behaivour is that if the whole token is lower case it is masked. isMasked(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector isMasked(BasisSymbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet Determines if a Symbol is masked. isMatchingType(ChangeType) - Method in class org.biojava.utils.ChangeType Return true iff ct is equal to this type or any of it's supertypes (including ChangeType.UNKNOWN). isMaxFuzzy() - Method in class org.biojava.bio.symbol.FuzzyLocation isMinFuzzy() - Method in class org.biojava.bio.symbol.FuzzyLocation isMultiSource(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools Returns false if all the locations in the set are from the same strand of the same sequence. isMyChangeEvent(ChangeEvent, IndexedChangeHub.ListenerMemento) - Method in class org.biojava.utils.IndexedChangeHub isNewTag() - Method in class org.biojava.bio.program.tagvalue.TagValue isObject() - Method in class org.biojava.utils.bytecode.ParametricType IsoelectricPointCalc - Class in org.biojava.bio.proteomics Class that computes isoelectric point for denaturated proteins. IsoelectricPointCalc() - Constructor for class org.biojava.bio.proteomics.IsoelectricPointCalc IsoelectricPointCalc.ChargeCalculator - Class in org.biojava.bio.proteomics Isoform() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform Creates a new instance. isOppositeStrand() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext isOrganismsDiffer() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction Getter for property organismsDiffer. isPalindromic() - Method in class org.biojava.bio.molbio.RestrictionEnzyme isPalindromic returns true if the recognition site is palindromic. isParseable(String) - Static method in class org.biojavax.bio.seq.io.UniProtCommentParser Returns true if the comment may be parseable (starts with -! isParseable(Comment) - Static method in class org.biojavax.bio.seq.io.UniProtCommentParser Returns true if the comment may be parseable (starts with -! isPrimitive() - Method in interface org.biojava.utils.bytecode.CodeClass Discover if the class represents a primitive type. isPrimitive() - Method in class org.biojava.utils.bytecode.GeneratedCodeClass isPrimitive() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass isPrimitive() - Method in class org.biojava.utils.bytecode.ParametricType Discover if this type must resolve to a primative. isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySource isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByType isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter isProperSubset(FeatureFilter) - Method in interface org.biojava.bio.seq.OptimizableFilter Returns true if this filter is a proper subset of sup - that is, for every feature that matches this, it also matches sup. isPrototype() - Method in class org.biojava.bio.molbio.RestrictionEnzyme isQuote(char) - Static method in class org.biojava.ontology.obo.OboFileParser isReady() - Method in interface org.biojava.bibliography.BibRefQuery It checks if the repository is available. isReady() - Method in interface org.biojava.bibliography.BibRefSupport It checks if a utility object is available. isReady() - Method in interface org.biojava.utils.candy.CandyFinder It checks if a vocabulary finder object is available. isReady(String, long) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService This method is used only for the executeBlastSearch method to check for completion of request using the NCBI specified RTOE variable isReady(String, long) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService Simple method to check if the specified request has been completed by the service used. isRemote() - Method in class org.biojava.bio.seq.RemoteFeature.Region Return whether this Region is remote or local. isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML isRequired(String) - Method in interface org.biojava.bio.symbol.CodonPrefFilter indicates if the current CodonPref is to be accepted isRespectCase() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock isSane() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block isSane() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList isSanger() - Method in enum org.biojava.bio.program.fastq.FastqVariant Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SANGER. isScaleByInformation() - Method in class org.biojava.bio.gui.DistributionLogo isShowAccession() - Method in class org.biojavax.bio.seq.io.FastaHeader isShowDescription() - Method in class org.biojavax.bio.seq.io.FastaHeader isShowIdentifier() - Method in class org.biojavax.bio.seq.io.FastaHeader isShowName() - Method in class org.biojavax.bio.seq.io.FastaHeader isShowNamespace() - Method in class org.biojavax.bio.seq.io.FastaHeader isShowVersion() - Method in class org.biojavax.bio.seq.io.FastaHeader issn - Variable in class org.biojava.bibliography.BiblioJournal A standard number for journals. isSolexa() - Method in enum org.biojava.bio.program.fastq.FastqVariant Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SOLEXA. isStarred() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString Tests whether this tree has a star before it's name. isStrict() - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter Determine if this writer is in strict mode. isStrict() - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter Determine if this writer is in strict mode. isSubTypeOf(FeatureTypes.Type, FeatureTypes.Type) - Static method in class org.biojava.bio.seq.FeatureTypes Work out if one type is a sub-type of another. issue - Variable in class org.biojava.bibliography.BiblioJournalArticle The issue of the journal. issueSupplement - Variable in class org.biojava.bibliography.BiblioJournalArticle Suplement. isTaxonHidden() - Method in interface org.biojavax.bio.taxa.NCBITaxon used in getNameHierarchy() to determine whether this taxonomy level is displayed isTaxonHidden() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific. isTerminal() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode Determine is this node is terminal (has no children). isTerminal() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode Determine is this node is terminal (has no children). isTokens() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock isTrainingComplete(TrainingAlgorithm) - Method in interface org.biojava.bio.dp.StoppingCriteria Decide if the training has completed. isTransposed() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature isUnchanging(ChangeType) - Method in class org.biojava.utils.AbstractChangeable isUnchanging(ChangeType) - Method in interface org.biojava.utils.Changeable A particular ChangeType can never be raised by this Changeable. isUnchanging(ChangeType) - Method in class org.biojava.utils.ChangeSupport isUnchanging(ChangeType) - Method in class org.biojava.utils.Unchangeable isUnchanging(ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList A particular ChangeType can never be raised by this Changeable. isUnchanging(ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross isUnchanging(ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation itemAlphas() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel itemAlphas() - Method in interface org.biojava.stats.svm.SVMClassifierModel items() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel items() - Method in class org.biojava.stats.svm.SimpleSVMTarget items() - Method in interface org.biojava.stats.svm.SVMClassifierModel items() - Method in interface org.biojava.stats.svm.SVMTarget itemTargets() - Method in class org.biojava.stats.svm.SimpleSVMTarget itemTargets() - Method in interface org.biojava.stats.svm.SVMTarget ItemValue - Interface in org.biojava.stats.svm A simple Object-double tuple. iterator() - Method in interface org.biojava.bio.annodb.AnnotationDB Loop over each Annotation in this db. iterator() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB iterator() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB iterator() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB iterator() - Method in class org.biojava.bio.annodb.MergingAnnotationDB iterator() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB iterator() - Method in class org.biojava.bio.dp.SimpleStatePath iterator() - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection iterator() - Method in interface org.biojava.bio.program.homologene.OrthologueSet Return an iterator to the contents of the set. iterator() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection iterator() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet returns an iterator to the members of this set iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet iterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment iterator() - Method in class org.biojava.bio.seq.impl.DummySequence iterator() - Method in class org.biojava.bio.seq.impl.SimpleSequence iterator() - Method in class org.biojava.bio.seq.impl.SubSequence iterator() - Method in class org.biojava.bio.seq.impl.ViewSequence iterator() - Method in class org.biojava.bio.seq.NewSimpleAssembly iterator() - Method in class org.biojava.bio.seq.SimpleAssembly iterator() - Method in class org.biojava.bio.symbol.AbstractSymbolList iterator() - Method in interface org.biojava.bio.symbol.FiniteAlphabet Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet. iterator() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet iterator() - Method in class org.biojava.bio.symbol.RelabeledAlignment iterator() - Method in class org.biojava.bio.symbol.SimpleAlphabet iterator() - Method in class org.biojava.bio.symbol.SingletonAlphabet iterator() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet iterator() - Method in interface org.biojava.bio.symbol.SymbolList An Iterator over all Symbols in this SymbolList. iterator() - Method in class org.biojava.utils.FileAsList iterator() - Method in class org.biojava.utils.MergingSet iterator() - Method in class org.biojava.utils.SmallSet iterator() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList An Iterator over all Symbols in this SymbolList. iterator() - Method in class org.biojavax.bio.seq.ThinRichSequence An Iterator over all Symbols in this SymbolList. iterator() - Method in class org.biojavax.ga.util.WeightedSet Returns an unmodifiable iterator over the keys of the set. iterator(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler An Iterator over all Symbols in this SymbolList. iterator(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler An Iterator over all Symbols in this SymbolList. iterator(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler An Iterator over all Symbols in this SymbolList. J JDBCConnectionPool - Class in org.biojava.utils Really simple connection pool for JDBC databases. JDBCConnectionPool(String) - Constructor for class org.biojava.utils.JDBCConnectionPool JDBCConnectionPool(String, String, String) - Constructor for class org.biojava.utils.JDBCConnectionPool JDBCPooledDataSource - Class in org.biojava.utils Returns a DataSource that implements connection pooling Uses Jakarta Commons DBCP and Pool packages. JDBCPooledDataSource() - Constructor for class org.biojava.utils.JDBCPooledDataSource JOIN_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper Deprecated. JOIN_ORACLE8 - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper Deprecated. joinCommands(Object[]) - Static method in class org.biojava.utils.process.ExternalProcess Joins a command list to a single command string. jointDistOverAlignment(Alignment, boolean, double, int[]) - Static method in class org.biojava.bio.dist.DistributionTools Creates a joint distribution. JOURNAL_ABBREV - Static variable in interface org.biojava.bibliography.BibRefSupport A vocabulary name. JOURNAL_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. JOURNAL_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. JOURNAL_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat JOURNAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat JOURNAL_TITLES - Static variable in interface org.biojava.bibliography.BibRefSupport A vocabulary name. jState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM Gets the J loop state JukesCantor(String, String) - Static method in class org.biojavax.bio.phylo.MultipleHitCorrection jumpTo(UkkonenSuffixTree.SuffixNode, CharSequence, int, int) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree Just like walkTo, but faster when used during tree construction, as it assumes that a mismatch can only occurs with the last character of the target string. K k() - Static method in class org.biojava.bio.seq.DNATools k() - Static method in class org.biojava.bio.seq.NucleotideTools k() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Lysine kernel - Static variable in class org.biojava.stats.svm.SparseVector KEY_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat KEY_QUERY_ID - Static variable in interface org.biojava.bio.search.BlastLikeSearchFilter KeyedWeakReference - Class in org.biojava.utils.cache Subclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has been enqueued. KeyedWeakReference(Object, Object) - Constructor for class org.biojava.utils.cache.KeyedWeakReference KeyedWeakReference(Object, Object, ReferenceQueue) - Constructor for class org.biojava.utils.cache.KeyedWeakReference keys() - Method in class org.biojava.bio.AbstractAnnotation keys() - Method in interface org.biojava.bio.Annotation Get a set of key objects. keys() - Method in class org.biojava.bio.MergeAnnotation keys() - Method in class org.biojava.bio.OverlayAnnotation Return a Set containing all key objects visible in this annotation. keys() - Method in class org.biojavax.EmptyRichAnnotation Get a set of key objects. keys() - Method in class org.biojavax.SimpleRichAnnotation Get a set of key objects. KEYS - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory KEYS is the key used to identify the secondary namespaces in the OBDA config.dat files. keySet() - Method in class org.biojava.utils.OverlayMap keySet() - Method in class org.biojava.utils.SmallMap KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat keywords - Variable in class org.biojava.bibliography.BiblioSubject The keywords are usually (but not limited to) one word long. KEYWORDS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat KEYWORDS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. KEYWORDS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat KimuraTwoParameter(String, String) - Static method in class org.biojavax.bio.phylo.MultipleHitCorrection KLDistance(Distribution, Distribution, double) - Static method in class org.biojava.bio.dist.DistributionTools A method to calculate the Kullback-Liebler Distance (relative entropy). KnuthMorrisPrattSearch - Class in org.biojava.bio.search An object to find exact subsequences within a sequence. KnuthMorrisPrattSearch(SymbolList) - Constructor for class org.biojava.bio.search.KnuthMorrisPrattSearch Constructs a KMP matcher to find exact occurances of pattern in text using the Knuth-Morris-Pratt algorithm. L l() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Leucine L_ESCULENTUM - Static variable in interface org.biojava.bio.program.homologene.Taxon label - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement Label - Class in org.biojava.utils.bytecode A Label used to mark a position in byte code. Label() - Constructor for class org.biojava.utils.bytecode.Label Label(String) - Constructor for class org.biojava.utils.bytecode.Label LABEL - Static variable in class org.biojava.bio.gui.sequence.AlignmentRenderer LABEL - Static variable in class org.biojava.bio.gui.sequence.SimpleLabelRenderer LABEL_MAKER - Static variable in class org.biojava.bio.gui.sequence.FeatureLabelRenderer LabelledSequenceRenderer - Class in org.biojava.bio.gui.sequence Renderer which draws a track of sequence with a textual label. LabelledSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer Creates new LabelledSequenceRenderer with default width and depth; LabelledSequenceRenderer(double, double) - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer Creates new LabelledSequenceRenderer with the specified width and depth. LabelledSequenceRenderer(String, SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer LabelledVector(SparseVector, double) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector LabelledVector(SparseVector, double, String) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector labelOrder - Variable in class org.biojava.bio.alignment.FlexibleAlignment LabelRenderer - Interface in org.biojava.bio.gui.sequence The interface for things that can render labels for a line of information about a sequence. LabelRenderer.RenderNothing - Class in org.biojava.bio.gui.sequence labelsAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment labelsAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment labelsAt(int) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment Returns a list labels, of all seqs that cover that column labelsInRange(Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment labelsInRange(Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment labelsInRange(Location) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment Returns list of all the labels that intersect that range LANE - Static variable in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer language - Variable in class org.biojava.bibliography.BiblioDescription It defines a language used for BiblioDescription.theAbstract and BiblioDescription.tableOfContents. language - Variable in class org.biojava.bibliography.BibRef It defines a language of the intellectual contents of the cited resource. LANGUAGES - Static variable in interface org.biojava.bibliography.BibRefSupport A vocabulary name. LargeBuffer - Class in org.biojava.utils.io Wrapper arround MappedByteBuffers to allow long-indexed access to files larger than 2 gigs. LargeBuffer(FileChannel, FileChannel.MapMode, long, long) - Constructor for class org.biojava.utils.io.LargeBuffer lastCol() - Method in interface org.biojava.bio.dp.onehead.DPCursor The previous column. lastCol() - Method in class org.biojava.bio.dp.onehead.SmallCursor lastModifiedDate - Variable in class org.biojava.bibliography.BiblioEntryStatus It defines when the citation record was added or last modified. lastNonGap() - Method in interface org.biojava.bio.symbol.GappedSymbolList Return the index of the last Symbol that is not a Gap character. lastNonGap() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList lastPage - Variable in class org.biojava.bibliography.BiblioArticle Last page of the article. lastRes() - Method in interface org.biojava.bio.dp.onehead.DPCursor The previous symbol. layer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer LayeredRenderer - Class in org.biojava.bio.gui.sequence LayeredRenderer handles the lane offsets for MultiLineRenders. LayeredRenderer() - Constructor for class org.biojava.bio.gui.sequence.LayeredRenderer LAYOUT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext LazyFeatureHolder - Class in org.biojava.bio.seq Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand. LazyFeatureHolder() - Constructor for class org.biojava.bio.seq.LazyFeatureHolder Construct a LazyFeatureHolder with the schema of its contained featureholder LazyFeatureHolder(FeatureFilter) - Constructor for class org.biojava.bio.seq.LazyFeatureHolder Construct a LazyFeatureHolder with the specified schema LazyFilteredAnnotationDB - Class in org.biojava.bio.annodb An implementation of AnnotationDB that lazily applies a filter. LazyFilteredAnnotationDB(String, AnnotationDB, AnnotationType) - Constructor for class org.biojava.bio.annodb.LazyFilteredAnnotationDB Create a new DB by wrapping another with a schema. LazyFilterFeatureHolder - Class in org.biojava.bio.seq.impl FeatureHolder which lazily applies a specified filter to another FeatureHolder. LazyFilterFeatureHolder(FeatureHolder, FeatureFilter) - Constructor for class org.biojava.bio.seq.impl.LazyFilterFeatureHolder LazySearchedAnnotationDB - Class in org.biojava.bio.annodb An implementation of AnnotationDB that does a JIT search on another set. LazySearchedAnnotationDB(String, AnnotationDB, AnnotationType) - Constructor for class org.biojava.bio.annodb.LazySearchedAnnotationDB Create a new DB from an old one by applying a schema. le - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter leaf - Static variable in interface org.biojava.bio.seq.FeatureFilter A filter which accepts features with no children leaf() - Static method in class org.biojava.bio.seq.FilterUtils Return a filter which matches features with zero children. leftIndent(String, int) - Static method in class org.biojavax.utils.StringTools Takes an input string and appends spaces to the left. leftMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment leftMost and rightMost return labels. leftPad(String, char, int) - Static method in class org.biojavax.utils.StringTools Pads a string to be a certain width by prepending given symbols. leftPad(String, int) - Static method in class org.biojavax.utils.StringTools Pads a string to be a certain width by prepending spaces. LeftRightLocationComparator() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator LEFTVALUE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon length - Variable in class org.biojava.bio.symbol.Edit length() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment length() - Method in class org.biojava.bio.alignment.FlexibleAlignment length() - Method in class org.biojava.bio.alignment.SimpleAlignment length() - Method in interface org.biojava.bio.dp.onehead.DPCursor The length of the sequence. length() - Method in class org.biojava.bio.dp.onehead.SmallCursor length() - Method in class org.biojava.bio.dp.SimpleStatePath length() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment length() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList length() - Method in class org.biojava.bio.seq.impl.DummySequence length() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList length() - Method in class org.biojava.bio.seq.impl.SimpleSequence length() - Method in class org.biojava.bio.seq.impl.SubSequence length() - Method in class org.biojava.bio.seq.impl.ViewSequence length() - Method in class org.biojava.bio.seq.io.SymbolListCharSequence length() - Method in class org.biojava.bio.seq.NewSimpleAssembly length() - Method in class org.biojava.bio.seq.SimpleAssembly length() - Method in class org.biojava.bio.symbol.ChunkedSymbolList length() - Method in class org.biojava.bio.symbol.DummySymbolList length() - Method in class org.biojava.bio.symbol.PackedSymbolList length() - Method in class org.biojava.bio.symbol.RelabeledAlignment length() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList length() - Method in class org.biojava.bio.symbol.SimpleSymbolList Get the length of this SymbolList. length() - Method in interface org.biojava.bio.symbol.SymbolList The number of symbols in this SymbolList. length() - Method in class org.biojava.utils.io.RandomAccessReader length returns the length of the underlying RandomAccessFile. length() - Method in class org.biojava.utils.RepeatedCharSequence length() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList The number of symbols in this SymbolList. length() - Method in class org.biojavax.bio.seq.SimpleRichSequence The number of symbols in this SymbolList. length() - Method in class org.biojavax.bio.seq.ThinRichSequence The number of symbols in this SymbolList. LENGTH_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat lesser(int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment LessThan(double) - Constructor for class org.biojava.bio.search.FilterTest.LessThan leu() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Leucine (L) LIBRARY_ANNOTATION - Static variable in class org.biojava.bio.program.unigene.UnigeneTools Annotation schema for all Unigene libraries. LifeScienceIdentifier - Class in org.biojava.utils.lsid Life Science Identifier (LSID). LifeScienceIdentifierParseException - Exception in org.biojava.utils.lsid Exception thrown in the event of an error in parsing a LSID-formatted string. LifeScienceIdentifierParseException() - Constructor for exception org.biojava.utils.lsid.LifeScienceIdentifierParseException Construct a new parse exception with no message. LifeScienceIdentifierParseException(String) - Constructor for exception org.biojava.utils.lsid.LifeScienceIdentifierParseException Construct a new parse exception with the specified error message. Ligand - Class in org.biojava.bio.program.formats Ligand.Compound - Class in org.biojava.bio.program.formats Ligand.Enzyme - Class in org.biojava.bio.program.formats Ligand.Reaction - Class in org.biojava.bio.program.formats LightPairDPCursor - Class in org.biojava.bio.dp.twohead A LIGHT implementation of PairDPCursor. LightPairDPCursor(SymbolList, SymbolList, int, int, int, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.LightPairDPCursor Constructor for the LightPairDPCursor object line - Variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer line is the line to be drawn for each feature. line - Variable in class org.biojava.ontology.obo.OboFileParser LINEAGE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat LINEAGE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat LinearKernel - Class in org.biojava.stats.svm Deprecated. Just use SparseVector.kernel instead... LinearKernel() - Constructor for class org.biojava.stats.svm.LinearKernel Deprecated. LineInfo - Class in org.biojava.bio.gui.sequence Encapsulates the rendering info for a single line of the display. LineInfo() - Constructor for class org.biojava.bio.gui.sequence.LineInfo lineIterator() - Method in class org.biojava.bio.program.gff.GFFEntrySet Loop over all lines in the set. linenum - Variable in class org.biojava.ontology.obo.OboFileParser LineSplitParser - Class in org.biojava.bio.program.tagvalue A parser that splits a line into tag/value at a given column number. LineSplitParser() - Constructor for class org.biojava.bio.program.tagvalue.LineSplitParser LineSplitParser(LineSplitParser) - Constructor for class org.biojava.bio.program.tagvalue.LineSplitParser lineWidth - Variable in class org.biojava.bio.seq.io.FastaFormat Deprecated. The line width for output. list(String) - Method in class org.biojava.naming.ObdaContext list(Name) - Method in class org.biojava.naming.ObdaContext listBindings(String) - Method in class org.biojava.naming.ObdaContext listBindings(Name) - Method in class org.biojava.naming.ObdaContext listener - Variable in class org.biojava.utils.IndexedChangeHub.ListenerMemento ListenerMemento(ChangeType, Reference) - Constructor for class org.biojava.utils.IndexedChangeHub.ListenerMemento listIntersection(List<String>, List<String>) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment ListSumKernel - Class in org.biojava.stats.svm This kernel computes the sum of the dot products between items of two lists at corresponding indexes. ListSumKernel() - Constructor for class org.biojava.stats.svm.ListSumKernel ListTools - Class in org.biojava.utils ListTools() - Constructor for class org.biojava.utils.ListTools ListTools.Doublet - Class in org.biojava.utils ListTools.Mapper - Interface in org.biojava.utils Maps one object to another. ListTools.SeriesList - Class in org.biojava.utils A list that represents a series of values. ListTools.Triplet - Class in org.biojava.utils load(File) - Method in class org.biojava.bio.program.abi.ABIFChromatogram load(File) - Method in class org.biojava.bio.program.scf.SCF load(InputStream) - Method in class org.biojava.bio.program.abi.ABIFChromatogram load(InputStream, long) - Method in class org.biojava.bio.program.scf.SCF load(Class, String) - Method in class org.biojava.utils.TypedProperties Reads a property list (key and element pairs) from the given file which is interpreted as a resource of the given class. load(String) - Method in class org.biojava.utils.TypedProperties Reads a property list (key and element pairs) from the file with the given file name. loadAlphabets(InputSource) - Static method in class org.biojava.bio.symbol.AlphabetManager Load additional Alphabets, defined in XML format, into the AlphabetManager's registry. loadEnzymeFile(InputStream, boolean) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager loadEnzymeFile loads a new REBASE file (or any file using REBASE format #31). loadUnigene(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory loadUnigene(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory loadUnigene(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory loadUnigene(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools Load a UnigeneDB instance referred to by a URL. loc - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement LOC_ELEMENT_ACC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat LOC_ELEMENT_COMPL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat LOC_ELEMENT_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat LOC_ELEMENT_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat LOC_FUZZY_END_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms LOC_FUZZY_START_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms LocalVariable - Class in org.biojava.utils.bytecode A local variable. LocalVariable(CodeClass) - Constructor for class org.biojava.utils.bytecode.LocalVariable Create a new local variable that will store values of a given type. LocalVariable(CodeClass, String) - Constructor for class org.biojava.utils.bytecode.LocalVariable Create a new local variable with a type and a name. location - Variable in class org.biojava.bio.seq.Feature.Template Location - Interface in org.biojava.bio.symbol A set of integers, often used to represent positions on biological sequences. LOCATION - Static variable in interface org.biojava.bio.alignment.EditableAlignment LOCATION - Static variable in interface org.biojava.bio.seq.Feature The location of this feature is being altered. LOCATION - Static variable in interface org.biojavax.bio.seq.RichFeature LOCATION - Static variable in interface org.biojavax.RankedDocRef LOCATION_BEGIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat LOCATION_COMPL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat LOCATION_ELEMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat LOCATION_END_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat LOCATION_POSITION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat LOCATION_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat LOCATION_SEQ_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat LOCATION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat LocationHandlerBase - Class in org.biojava.bio.program.xff Handler to the XFF location type. LocationHandlerBase() - Constructor for class org.biojava.bio.program.xff.LocationHandlerBase locationToGapped(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList Translate a Location onto the gapped view, splitting blocks if necessary LocationTools - Class in org.biojava.bio.symbol Tools class containing a number of operators for working with Location objects. LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat locInAlignment(Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment The location of an individual SymbolList relative to overall Alignment locInAlignment(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment The location of an individual SymbolList relative to overall Alignment locInAlignment(Object) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment The location of an individual SymbolList relative to overall Alignment locInSeq(Object, Location) - Method in class org.biojava.bio.alignment.FlexibleAlignment lock() - Method in class org.biojava.utils.automata.PatternBlitz lockModel() - Method in class org.biojava.bio.dp.DP LOCUS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat LOCUSID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder LOG_TO_OUT - Static variable in interface org.biojava.utils.ChangeListener Convenience implementation that echoes all events to out. log2(double) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileHMM log2(double) - Static method in class org.biojava.bio.program.hmmer.ProfileEmissionState LoggingListener(PrintStream) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener Create a LoggingListener that will log all events to 'out'. LoggingListener(PrintStream, String) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener Create a LoggingListener that will log all events to 'out' with a prefix. LogoContext - Interface in org.biojava.bio.gui LogoPainter - Interface in org.biojava.bio.gui The interface for something that will draw the sequence logo for a state. logProb(Symbol) - Method in class org.biojava.bio.program.hmmer.ProfileEmissionState LongElementHandlerBase - Class in org.biojava.utils.stax StAX handler for any element which just contains a string representation of a long. LongElementHandlerBase() - Constructor for class org.biojava.utils.stax.LongElementHandlerBase lookingAt() - Method in class org.biojava.utils.regex.Matcher Attempts to match the input SymbolList, starting at the beginning, against the pattern. lookup(String) - Static method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option Looks up an Option instance based on its string description. lookup(String) - Method in class org.biojava.naming.ObdaContext lookup(Name) - Method in class org.biojava.naming.ObdaContext lookupLink(String) - Method in class org.biojava.naming.ObdaContext lookupLink(Name) - Method in class org.biojava.naming.ObdaContext lowercaseName() - Method in enum org.biojava.bio.program.fastq.FastqVariant Return the name of this FASTQ sequence format variant in lowercase-with-dashes style. lp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat lp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat lp_ipi - Static variable in class org.biojavax.bio.seq.io.UniProtFormat lp_uniprot - Static variable in class org.biojavax.bio.seq.io.UniProtFormat lpPre87 - Static variable in class org.biojavax.bio.seq.io.EMBLFormat LSID_EMBL_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants LSID_EMBL_AA sequence format LSID for EMBL AA. LSID_EMBL_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants LSID_EMBL_DNA sequence format LSID for EMBL DNA. LSID_EMBL_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants LSID_EMBL_RNA sequence format LSID for EMBL RNA. LSID_FASTA_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants LSID_FASTA_AA sequence format LSID for Fasta AA. LSID_FASTA_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants LSID_FASTA_DNA sequence format LSID for Fasta DNA. LSID_FASTA_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants LSID_FASTA_RNA sequence format LSID for Fasta RNA. LSID_GENBANK_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants LSID_GENBANK_AA sequence format LSID for Genbank AA. LSID_GENBANK_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants LSID_GENBANK_DNA sequence format LSID for Genbank DNA. LSID_GENBANK_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants LSID_GENBANK_RNA sequence format LSID for Genbank RNA. LSID_SWISSPROT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants LSID_SWISSPROT sequence format LSID for Swissprot. lys() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Lysine (K) LYS_C - Static variable in class org.biojava.bio.proteomics.Protease LYS_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager M m() - Static method in class org.biojava.bio.seq.DNATools m() - Static method in class org.biojava.bio.seq.NucleotideTools m() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Methionine M_MUSCULUS - Static variable in interface org.biojava.bio.program.homologene.Taxon M_TRUNCULATA - Static variable in interface org.biojava.bio.program.homologene.Taxon MAGICAL_STATE - Static variable in class org.biojava.bio.program.tagvalue.StateMachine magicalState() - Method in interface org.biojava.bio.dp.MarkovModel The MagicalState for this model. magicalState() - Method in class org.biojava.bio.dp.SimpleMarkovModel magicalState() - Method in class org.biojava.bio.dp.WMAsMM MagicalState - Class in org.biojava.bio.dp Start/end state for HMMs. main(String[]) - Static method in class org.biojava.App main(String[]) - Static method in class org.biojava.bio.search.KnuthMorrisPrattSearch Demo and Test method main(String[]) - Static method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation Test this class main(String[]) - Static method in class org.biojava.bio.seq.io.MSFAlignmentFormat used to quick test the code main(String[]) - Static method in class org.biojava.stats.svm.tools.ClassifierExample Entry point for the application. main(String[]) - Static method in class org.biojava.stats.svm.tools.Classify main(String[]) - Static method in class org.biojava.stats.svm.tools.Train main(String[]) - Static method in class org.biojava.stats.svm.tools.TrainRegression main(String[]) - Static method in class org.biojava.utils.ExecRunner This is for unit testing of the class. main(String[]) - Static method in class org.biojava.utils.io.UncompressInputStream main(String[]) - Static method in class org.biojava.utils.JDBCPooledDataSource main(String[]) - Static method in class org.biojava.utils.process.ExternalProcess Runs an external program from the command line. main(String[]) - Static method in class org.biojava.utils.xml.AppBeanRunner make(DP) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker make(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler make(DP) - Method in class org.biojava.bio.dp.twohead.DPInterpreter.Maker make(SymbolReader) - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory Method to create a Sequence with a SymbolReader. make_aaload() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the aaload instruction. make_aastore() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the aastore instruction. make_aconst_null() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the aconst_null instruction. make_add(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_aload(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode make_and(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_areturn() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the areturn instruction. make_array_load(ParametricType) - Static method in class org.biojava.utils.bytecode.ByteCode Load an element of a parametric type to an array. make_arraylength() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the arraylength instruction. make_arrayStore(ParametricType) - Static method in class org.biojava.utils.bytecode.ByteCode Store an element of a parametric type to an array. make_astore(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode make_athrow() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the athrow instruction. make_baload() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the baload instruction. make_bastore() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the bastore instruction. make_breakpoint() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the breakpoint instruction. make_caload() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the caload instruction. make_cast(ParametricType, ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_castore() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the castore instruction. make_checkcast(CodeClass) - Static method in class org.biojava.utils.bytecode.ByteCode make_cmpg(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_cmpl(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_d2f() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the d2f instruction. make_d2i() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the d2i instruction. make_d2l() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the d2l instruction. make_dadd() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dadd instruction. make_daload() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the daload instruction. make_dastore() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dastore instruction. make_dcmpg() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dcmpg instruction. make_dcmpl() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dcmpl instruction. make_dconst(double) - Static method in class org.biojava.utils.bytecode.ByteCode make_ddiv() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ddiv instruction. make_div(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_dload(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode make_dmul() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dmul instruction. make_dneg() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dneg instruction. make_drem() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the drem instruction. make_dreturn() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dreturn instruction. make_dstore(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode make_dsub() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dsub instruction. make_dup() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dup instruction. make_dup(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_dup_x1() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dup_x1 instruction. make_dup_x2() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dup_x2 instruction. make_dup2() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dup2 instruction. make_dup2_x1() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dup2_x1 instruction. make_dup2_x2() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the dup2_x2 instruction. make_f2d() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the f2d instruction. make_f2i() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the f2i instruction. make_f2l() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the f2l instruction. make_fadd() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the fadd instruction. make_faload() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the faload instruction. make_fastore() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the fastore instruction. make_fcmpg() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the fcmpg instruction. make_fcmpl() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the fcmpl instruction. make_fconst(float) - Static method in class org.biojava.utils.bytecode.ByteCode make_fdiv() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the fdiv instruction. make_fload(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode make_fmul() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the fmul instruction. make_fneg() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the fneg instruction. make_frem() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the frem instruction. make_freturn() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the freturn instruction. make_fstore(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode make_fsub() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the fsub instruction. make_getfield(CodeField) - Static method in class org.biojava.utils.bytecode.ByteCode make_getstatic(CodeField) - Static method in class org.biojava.utils.bytecode.ByteCode make_goto(Label) - Static method in class org.biojava.utils.bytecode.ByteCode make_i2b() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the i2b instruction. make_i2c() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the i2c instruction. make_i2d() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the i2d instruction. make_i2f() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the i2f instruction. make_i2l() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the i2l instruction. make_i2s() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the i2s instruction. make_iadd() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the iadd instruction. make_iaload() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the iaload instruction. make_iand() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the iand instruction. make_iastore() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the iastore instruction. make_iconst(int) - Static method in class org.biojava.utils.bytecode.ByteCode make_idiv() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the idiv instruction. make_if(byte, Label) - Static method in class org.biojava.utils.bytecode.ByteCode Make an if Instruction for the opcode and label. make_if_acmpeq(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the if_acmpeq instruction. make_if_acmpne(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the if_acmpne instruction. make_if_icmpeq(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the if_icmpeq instruction. make_if_icmpge(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the if_icmpge instruction. make_if_icmpgt(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the if_icmpgt instruction. make_if_icmple(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the if_icmple instruction. make_if_icmplt(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the if_icmplt instruction. make_if_icmpne(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the if_icmpne instruction. make_ifeq(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ifeq instruction. make_ifge(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ifge instruction. make_ifgt(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ifgt instruction. make_ifle(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ifle instruction. make_iflt(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the iflt instruction. make_ifne(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ifne instruction. make_ifnonnull(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ifnonnull instruction. make_ifnull(Label) - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ifnull instruction. make_iload(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode make_impdep1() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the impdep1 instruction. make_impdep2() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the impdep2 instruction. make_imul() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the imul instruction. make_ineg() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ineg instruction. make_instanceof(CodeClass) - Static method in class org.biojava.utils.bytecode.ByteCode make_invoke(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode Make an invoke opcode that is suited to the method. make_invokeinterface(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode make_invokespecial(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode make_invokestatic(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode make_invokevirtual(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode make_invokevirtual_quick_w() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the invokevirtual_quick_w instruction. make_ior() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ior instruction. make_irem() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the irem instruction. make_ireturn() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ireturn instruction. make_ishl() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ishl instruction. make_ishr() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ishr instruction. make_istore(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode make_isub() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the isub instruction. make_iushr() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the iushr instruction. make_ixor() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ixor instruction. make_jsr(Label) - Static method in class org.biojava.utils.bytecode.ByteCode make_l2d() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the l2d instruction. make_l2f() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the l2f instruction. make_l2i() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the l2i instruction. make_ladd() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ladd instruction. make_laload() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the laload instruction. make_land() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the land instruction. make_lastore() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lastore instruction. make_lcmp() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lcmp instruction. make_lconst(long) - Static method in class org.biojava.utils.bytecode.ByteCode make_ldiv() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the ldiv instruction. make_lload(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode make_lmul() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lmul instruction. make_lneg() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lneg instruction. make_load(ParametricType, LocalVariable) - Method in class org.biojava.utils.bytecode.ByteCode Load an item of a parametric type from a local variable. make_lor() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lor instruction. make_lrem() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lrem instruction. make_lreturn() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lreturn instruction. make_lshl() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lshl instruction. make_lshr() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lshr instruction. make_lstore(LocalVariable) - Static method in class org.biojava.utils.bytecode.ByteCode make_lsub() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lsub instruction. make_lushr() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lushr instruction. make_lxor() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the lxor instruction. make_markLabel(Label) - Static method in class org.biojava.utils.bytecode.ByteCode make_monitorenter() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the monitorenter instruction. make_monitorexit() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the monitorexit instruction. make_mul(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_neg(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_new(CodeClass) - Static method in class org.biojava.utils.bytecode.ByteCode make_newarray(CodeClass) - Static method in class org.biojava.utils.bytecode.ByteCode make_newraray(ParametricType) - Static method in class org.biojava.utils.bytecode.ByteCode make_nop() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the nop instruction. make_or(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_pop() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the pop instruction. make_pop2() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the pop2 instruction. make_putfield(CodeField) - Static method in class org.biojava.utils.bytecode.ByteCode make_putstatic(CodeField) - Static method in class org.biojava.utils.bytecode.ByteCode make_rem(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_return() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the return instruction. make_return(CodeClass) - Static method in class org.biojava.utils.bytecode.ByteCode Creates the return Instruction suitable for a given class or type. make_return(CodeMethod) - Static method in class org.biojava.utils.bytecode.ByteCode A convenient one-stop method to get a return statement suitable for a method. make_return(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode Make a return statement for the parametric type. make_saload() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the saload instruction. make_sastore() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the sastore instruction. make_save(ParametricType, LocalVariable) - Method in class org.biojava.utils.bytecode.ByteCode Store an item of a parametric type to a local variable. make_sconst(String) - Static method in class org.biojava.utils.bytecode.ByteCode make_shiftLeft(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_shiftRight(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_shiftRightLogical(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_sub(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode make_swap() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the swap instruction. make_synchronizedBlock(CodeGenerator) - Static method in class org.biojava.utils.bytecode.ByteCode Synchronize the processing of an entire block of code on the object on the top of the stack. make_synchronizedBlock(LocalVariable, CodeGenerator) - Static method in class org.biojava.utils.bytecode.ByteCode Synchronize the processing of an entire block of code on a local variable. make_wide() - Static method in class org.biojava.utils.bytecode.ByteCode Return the Instruction object for the wide instruction. make_xor(ParametricType) - Method in class org.biojava.utils.bytecode.ByteCode makeAnnotation(Map) - Static method in class org.biojava.bio.program.ssbind.AnnotationFactory makeAnnotation creates the annotation. makeBatchRequest(URL, Set) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank. makeBatchRequest(URL, Set) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank. makeBatchRequest(URL, Set) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank. makeCircularLocation(int, int, int) - Static method in class org.biojava.bio.symbol.LocationTools A simple method to generate a RangeLocation wrapped in a CircularLocation. makeConfigFile(File) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory makeConfigFile returns a file which represents an OBDA "config.dat" in the specified index directory. makeContext(SequenceRenderContext, RangeLocation) - Method in class org.biojava.bio.gui.sequence.GappedRenderer makeEmptyFeature() - Static method in class org.biojavax.bio.seq.RichFeature.Tools A way to make a dummy feature makeFactory(FiniteAlphabet) - Static method in class org.biojava.utils.regex.PatternFactory Returns a factory for Patterns in the specified Alphabet. makeHandler(String, String) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory makeHandler(String, String) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory makeHandler(String, String, XMLFilterHandler) - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandlerFactory makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker makeLabel(Feature) - Method in interface org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker makeLocation(int, int) - Static method in class org.biojava.bio.symbol.LocationTools Return a contiguous Location from min to max. makeName(String, MarkovModel) - Static method in class org.biojava.bio.dp.twohead.DPCompiler makeNewBlock() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder makeNewBlock() - Method in class org.biojavax.bio.phylo.io.nexus.DataBlockBuilder makeNewInsertState(String, Annotation, int[], Distribution) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM makeNewMatchState(String, Annotation, int[], Distribution) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM makePrimaryKeyFile(File, String) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory makePrimaryKeyFile returns a file which represents an OBDA "key_<primary namespace>.key" primary key file on the specified index directory. makeProjectionSet(FeatureHolder) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder Called internally to construct a lightweight projected view of a set of features makeQueryViewSequence(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory Maker() - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter.Maker makeReference(Object) - Method in interface org.biojava.utils.cache.Cache Construct a temporary reference to an object. makeReference(Object) - Method in class org.biojava.utils.cache.FixedSizeCache makeReference(Object) - Method in class org.biojava.utils.cache.SoftReferenceCache makeRichSequence() - Method in interface org.biojavax.bio.seq.io.RichSequenceBuilder Build a RichSequence. makeRichSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Build a RichSequence. makeSearchResult() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder makeSearchResult() - Method in interface org.biojava.bio.search.SearchBuilder The makeSearchResult method returns a SeqSimilaritySearchResult instance created from accumulated data. makeSecondaryFile(File, String) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory makeSecondaryFile returns a file which represents an OBDA "id_<secondary namespace>.index" secondary key file on the specified. makeSequence() - Method in interface org.biojava.bio.seq.io.SequenceBuilder Return the Sequence object which has been constructed by this builder. makeSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase makeSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter makeSequence() - Method in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder create the sequence makeSequence() - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder makeSequence() - Method in class org.biojava.bio.seq.io.SimpleSequenceBuilder makeSequence() - Method in class org.biojava.bio.seq.io.SmartSequenceBuilder makeSequence() - Method in interface org.biojavax.bio.seq.io.RichSequenceBuilder Return the Sequence object which has been constructed by this builder. makeSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Return the Sequence object which has been constructed by this builder. makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.EmblProcessor.Factory Deprecated. makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory Deprecated. makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.GenbankProcessor.Factory Deprecated. makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.OrganismParser.Factory Deprecated. makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory Deprecated. makeSequenceBuilder() - Method in interface org.biojava.bio.seq.io.SequenceBuilderFactory makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.SwissprotProcessor.Factory Deprecated. makeSequenceBuilder() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory makeSequenceBuilder(String) - Method in class org.biojava.bio.seq.io.GenbankProcessor.Factory Deprecated. makeSequenceBuilder(String) - Method in class org.biojava.bio.seq.io.SwissprotProcessor.Factory Deprecated. makeSubjectViewSequence(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory makeSymbolList() - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory Converts accumulated Symbols to a SymbolList makeSymbolList(Symbol[], int, Alphabet) - Method in class org.biojava.bio.symbol.PackedSymbolListFactory Makes a packed SymbolList out of a list of Symbols. makeSymbolList(Symbol[], int, Alphabet) - Method in class org.biojava.bio.symbol.SimpleSymbolListFactory Create a factory for SimpleSymbolLists. makeSymbolList(Symbol[], int, Alphabet) - Method in interface org.biojava.bio.symbol.SymbolListFactory makes a SymbolList containing size Symbols from a Symbol array. makeTemplate() - Method in interface org.biojava.bio.seq.Feature Create a new Template that could be used to generate a feature identical to this one. makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleFeature makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature makeTemplate() - Method in class org.biojava.bio.seq.projection.ProjectedFeature makeTemplate() - Method in class org.biojavax.bio.seq.SimpleRichFeature Create a new Template that could be used to generate a feature identical to this one. makeTemplate(Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils MAN_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools Homo sapiens codon preferences mAnnotFilter - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter The AnnotationMap to use for getting AGAVE XML attributes from a Sequence Annotation. ManyToOneTranslationTable - Interface in org.biojava.bio.symbol A translation table that will handle the many-to-one mappings that you see, for example, with genetic codes. map(Object) - Method in class org.biojava.bio.symbol.RelabeledAlignment map(Object) - Method in interface org.biojava.utils.ListTools.Mapper Map the object. map(Set<String>) - Method in class org.biojava.bio.symbol.RelabeledAlignment mapList(List, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools mapLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext mapMap(Map, ListTools.Mapper, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools MappedDataStoreFactory - Class in org.biojava.bio.program.ssaha Builder for a data store that is backed by a java.nio.MappedByteBuffer. MappedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.MappedDataStoreFactory mapSet(Set, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools mark(int) - Method in class org.biojava.utils.io.CountedBufferedReader markLabel(Label) - Method in interface org.biojava.utils.bytecode.CodeContext Mark a label at the current point in the stream. MarkLabel - Class in org.biojava.utils.bytecode A CodeGenerator that just marks a label that can be used for jumps. MarkLabel(Label) - Constructor for class org.biojava.utils.bytecode.MarkLabel MarkovModel - Interface in org.biojava.bio.dp A markov model. markSupported() - Method in class org.biojava.utils.io.CountedBufferedReader markSupported() - Method in class org.biojava.utils.io.UncompressInputStream This stream does not support mark/reset on the stream. mask(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector Masks a token by making it lowercase mask(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector Present the token for a Symbol as it would appear if masked maskSequence(Sequence, RangeLocation) - Static method in class org.biojava.bio.seq.SequenceTools Mask of a sequence. MASS_SPECTROMETRY - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser A name for a comment type. MassCalc - Class in org.biojava.bio.proteomics MassCalc calculates the mass of peptides which for our purposes are SymbolLists which contain Symbolsfrom the protein Alphabet. MassCalc(String, boolean) - Constructor for class org.biojava.bio.proteomics.MassCalc Creates a new MassCalc. matcher(SymbolList) - Method in interface org.biojava.bio.search.BioPattern Get a matcher that will use these parameters to search a SymbolList. matcher(SymbolList) - Method in class org.biojava.bio.search.MaxMismatchPattern matcher(SymbolList) - Method in class org.biojava.bio.search.SeqContentPattern matcher(SymbolList) - Method in class org.biojava.utils.regex.Pattern Creates a matcher that will match the given input against this pattern. Matcher - Class in org.biojava.utils.regex This class is analogous to java.util.Matcher except that it works on SymbolLists instead of Strings. matches() - Method in class org.biojava.utils.regex.Matcher Attempts to match the entire input sequence against the pattern. matchingTypes() - Method in class org.biojava.utils.ChangeType Return an iterator which contains this type, and all supertypes. MatchRegex(String) - Constructor for class org.biojava.bio.search.FilterTest.MatchRegex mathExp(double) - Method in class org.biojava.bio.dp.BaumWelchTrainer MatrixPairDPCursor - Class in org.biojava.bio.dp.twohead MatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.MatrixPairDPCursor max - Variable in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener MAX_CROSSES - Static variable in interface org.biojavax.ga.functions.CrossOverFunction MaximalResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.MaximalResolver MaximumGeneration(int) - Constructor for class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration Public Constructer maximumQualityScore() - Method in enum org.biojava.bio.program.fastq.FastqVariant Return the maximum quality score for this FASTQ sequence format variant. maxIndex() - Method in class org.biojava.stats.svm.SparseVector maxLength() - Method in class org.biojava.bio.symbol.SuffixTree Return the length of the longest motif represented in this SuffixTree MaxMismatchMatcher - Class in org.biojava.bio.search A BioMatcher class returned by MaxMismatchPattern.matcher() that implements searching of a SymbolList. MaxMismatchPattern - Class in org.biojava.bio.search This class permits searching a SymbolList with another SymbolList while permitting a specified number of mismatches. MaxMismatchPattern() - Constructor for class org.biojava.bio.search.MaxMismatchPattern MaxMismatchPattern(SymbolList, int) - Constructor for class org.biojava.bio.search.MaxMismatchPattern MEDLINE_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms Holds a reference to the key that must be used to store Medline references. MEDLINE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. MEDLINE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat members - Variable in class org.biojavax.bio.seq.CompoundRichLocation Meme - Class in org.biojava.bio.program The results of a meme run. Meme(InputStream, SymbolTokenization) - Constructor for class org.biojava.bio.program.Meme merge(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools Takes a set of locations and tries to merge all pairs where the union operation results in a simple rich location, not a compound one. merge(Set, Set) - Static method in class org.biojava.utils.MergingSet MergeAnnotation - Class in org.biojava.bio Merged view onto a list of underlying Annotation objects. MergeAnnotation() - Constructor for class org.biojava.bio.MergeAnnotation MergeAnnotation.PropertyForwarder - Class in org.biojava.bio Listener used to forward changes for any of the underlying annotations to listeners on this annotation. MergeFeatureHolder - Class in org.biojava.bio.seq FeatureHolder which exposes all the features in a set of sub-FeatureHolders. MergeFeatureHolder() - Constructor for class org.biojava.bio.seq.MergeFeatureHolder Create a new, empty, MergeFeatureHolder. MergeLocation - Class in org.biojava.bio.symbol Produced by LocationTools as a result of union operations. mergeLocations(List) - Static method in class org.biojava.bio.symbol.MergeLocation Static Factory method for getting an instance of a MergeLocation mergeLocations(Location, Location) - Static method in class org.biojava.bio.symbol.MergeLocation MergingAnnotationDB - Class in org.biojava.bio.annodb An AnnotationDB that provides a merged view of a list of underlying DBs. MergingAnnotationDB(String) - Constructor for class org.biojava.bio.annodb.MergingAnnotationDB Create a new MergingAnnotationDB with a name and no DBs to merge. MergingAnnotationDB(String, List) - Constructor for class org.biojava.bio.annodb.MergingAnnotationDB Create a new MergingAnnotationDB with a name and a list of DBs to merge. MergingIterator - Class in org.biojava.utils MergingIterator(Iterator) - Constructor for class org.biojava.utils.MergingIterator MergingSet - Class in org.biojava.utils MergingSet() - Constructor for class org.biojava.utils.MergingSet MergingSet(Set) - Constructor for class org.biojava.utils.MergingSet met() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Methionine (M) META_DATA_TYPE - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory AnnotationType that all meta-data files should fit. mFilter - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter writes PCDATA replacing XML characters with escape entities midInitials - Variable in class org.biojava.bibliography.BiblioPerson Any middle innitials. min - Variable in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener min(int, int, int) - Static method in class org.biojava.bio.alignment.NeedlemanWunsch This just computes the minimum of three integer values. mIndent - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent Base indent mIndent - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter indent MinimalResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.MinimalResolver minimumQualityScore() - Method in enum org.biojava.bio.program.fastq.FastqVariant Return the minimum quality score for this FASTQ sequence format variant. mismatchCount() - Method in class org.biojava.bio.search.MaxMismatchMatcher Returns number of mismatches MITOGENETICCODE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon mListeners - Variable in class org.biojava.bio.seq.io.FastaFormat Deprecated. model - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix model() - Method in interface org.biojava.bio.dp.DPMatrix model() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix model() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix ModelInState - Interface in org.biojava.bio.dp A state that contains an entire sub-model. ModelTrainer - Interface in org.biojava.bio.dp Encapsulates the training of an entire model. modifiableMerge() - Static method in class org.biojava.utils.MergingSet modifiableMerge(Set) - Static method in class org.biojava.utils.MergingSet MODIFY - Static variable in interface org.biojava.bio.program.homologene.OrthologueSet MODIFY - Static variable in interface org.biojava.bio.program.homologene.OrthoPairSet modifyAttributes(String, int, Attributes) - Method in class org.biojava.naming.ObdaContext modifyAttributes(String, ModificationItem[]) - Method in class org.biojava.naming.ObdaContext modifyAttributes(Name, int, Attributes) - Method in class org.biojava.naming.ObdaContext modifyAttributes(Name, ModificationItem[]) - Method in class org.biojava.naming.ObdaContext modulateCircularIndex(int, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base. modulateCircularLocation(int, int, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools Takes a start and end position on a circular location of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence. modulateCircularLocationPair(Location, Location, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools Takes two circular locations of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence. MOLD_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable Translation table name for the mold mitochondrial genetic code. MOLTYPE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat MONO_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable MotifTools - Class in org.biojava.bio.symbol MotifTools contains utility methods for sequence motifs. MotifTools() - Constructor for class org.biojava.bio.symbol.MotifTools MOUSE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools Mus musculus codon preferences mouseClicked(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener mouseDragged(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerMotionListener mouseMoved(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerMotionListener mousePressed(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener mouseReleased(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener mOut - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter Write to XML document MP(TaxaBlock, CharactersBlock) - Static method in class org.biojavax.bio.phylo.ParsimonyTreeMethod MSF - Static variable in class org.biojava.bio.seq.io.AlignIOConstants MSF indicates that the alignment format is MSF. MSF_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants MSF_AA premade MSF | AA; MSF_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants MSF_DNA premade MSF | DNA; MSF_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants MSF_DNA premade MSF | RNA; MSFAlignmentFormat - Class in org.biojava.bio.seq.io MSFAlignmentFormat() - Constructor for class org.biojava.bio.seq.io.MSFAlignmentFormat MultiLineRenderer - Class in org.biojava.bio.gui.sequence MultiLineRenderer is a SequenceRenderer which collects a number of other SequenceRenderers each of which render their own view of a Sequence. MultiLineRenderer() - Constructor for class org.biojava.bio.gui.sequence.MultiLineRenderer MULTIPLE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder MULTIPLE - Static variable in interface org.biojava.bio.program.homologene.SimilarityType MultipleHitCorrection - Class in org.biojavax.bio.phylo MultipleHitCorrection() - Constructor for class org.biojavax.bio.phylo.MultipleHitCorrection MultipleScalar(SuffixTreeKernel.DepthScaler, SuffixTreeKernel.DepthScaler) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar MultiSourceCompoundRichLocation - Class in org.biojavax.bio.seq An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences. MultiSourceCompoundRichLocation(Collection) - Constructor for class org.biojavax.bio.seq.MultiSourceCompoundRichLocation Constructs a MultiSourceCompoundRichLocation from the given set of members, with the default term of "join". MultiSourceCompoundRichLocation(ComparableTerm, Collection) - Constructor for class org.biojavax.bio.seq.MultiSourceCompoundRichLocation Constructs a MultiSourceCompoundRichLocation from the given set of members. MultiTagger - Class in org.biojava.bio.program.tagvalue Partician multiple values for a tag into their own tag groups. MultiTagger(TagValueListener, BoundaryFinder) - Constructor for class org.biojava.bio.program.tagvalue.MultiTagger mutate(SymbolList) - Method in interface org.biojavax.ga.functions.MutationFunction Produces a new SymbolList by mutation. mutate(SymbolList) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation mutate(SymbolList) - Method in class org.biojavax.ga.functions.SimpleMutationFunction mutate(SymbolList) - Method in class org.biojavax.ga.functions.SwapMutationFunction MUTATION_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm MUTATION_PROBS - Static variable in interface org.biojavax.ga.functions.MutationFunction MUTATION_SPECTRUM - Static variable in interface org.biojavax.ga.functions.MutationFunction MutationFunction - Interface in org.biojavax.ga.functions A class that mutates a SymbolList MutationFunction.NoMutation - Class in org.biojavax.ga.functions Place Holder class that doesn't mutate its SymbolLists mutuallyExclusiveWith - Variable in class org.biojava.bibliography.BiblioCriterion A list of other criteria names that this criterion is mutually exclusive with. mWriteDocType - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter write DOCTYPE if true myLocalName - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler MySQLDBHelper - Class in org.biojava.bio.seq.db.biosql Deprecated. Use hibernate and org.biojavax.bio.db.* MySQLDBHelper(Connection) - Constructor for class org.biojava.bio.seq.db.biosql.MySQLDBHelper Deprecated. N n() - Static method in class org.biojava.bio.seq.DNATools n() - Static method in class org.biojava.bio.seq.NucleotideTools n() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Asparagine n() - Static method in class org.biojava.bio.seq.RNATools name - Variable in class org.biojava.bibliography.BiblioCriterion Each Criterion is identified by its name. name - Variable in class org.biojava.bibliography.BiblioJournal A journal title. name - Variable in class org.biojava.bibliography.BiblioOrganisation The name of the organisation. name - Variable in class org.biojava.bibliography.BiblioService The name of a bibliographic service. name - Variable in class org.biojava.bio.molbio.RestrictionEnzyme name - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase name - Variable in class org.biojava.utils.bytecode.Label NAME - Static variable in class org.biojava.ontology.obo.OboFileHandler NAME - Static variable in interface org.biojavax.bio.seq.RichFeature NAME - Static variable in interface org.biojavax.ga.Organism NAME - Static variable in interface org.biojavax.ga.Population NAME - Static variable in interface org.biojavax.Namespace NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat NAME_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat names - Variable in class org.biojavax.bio.taxa.SimpleNCBITaxon names() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB Returns the set of unique table names. names() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB Returns the set of unique table names. NAMES - Static variable in interface org.biojavax.bio.taxa.NCBITaxon NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEGenePropHandler NameSetStringValue(String) - Method in interface org.biojava.bio.seq.io.game.GAMENameCallbackItf Callback implemented by nesting class to allow nested class to pass string to nesting class for handling. NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMESeqPropHandler Namespace - Interface in org.biojavax The namespace of an entry in a database schema. NAMESPACE - Static variable in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter NameTokenization - Class in org.biojava.bio.seq.io Simple implementation of SymbolTokenization which uses the `name' field of the symbols. NameTokenization(FiniteAlphabet) - Constructor for class org.biojava.bio.seq.io.NameTokenization Construct a new NameTokenization, defaulting to case-insensitive. NameTokenization(FiniteAlphabet, boolean) - Constructor for class org.biojava.bio.seq.io.NameTokenization NARROW_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler NARROW_SYNONYM - Static variable in class org.biojava.ontology.Synonym NATURAL_ORDER - Static variable in interface org.biojava.bio.program.gff.GFFRecord Comparator which defines a useful sort order for GFF records. naturalOrder - Static variable in interface org.biojava.bio.symbol.Location Comparator which orders Locations naturally. Navg - Static variable in class org.biojava.bio.proteomics.MassCalc Constant value of Nitrogen average mass NBRF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants NBRF indicates that the sequence format is NBRF. NCBI_TAXON_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms NcbiDatabaseURLGenerator - Class in org.biojava.bio.program.blast2html Simple URL generator for Entrez at the NCBI. NcbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator NCBIids(Connection) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Returns a Set of all NCBI-Taxon-IDs which are currently stored in the database. NCBISequenceDB - Class in org.biojava.bio.seq.db NCBISequenceDB() - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB Default constructor, querys the Genbank nucleotide database on "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi" and retrieves sequences in FastaFormat. NCBISequenceDB(String, String, String, SequenceFormat) - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB Parameterized constructor NCBISequenceDB(String, SequenceFormat) - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB Parameterized constructor NCBITaxon - Interface in org.biojavax.bio.taxa Represents an NCBI Taxon entry, a combination of the taxon and taxon_name tables in BioSQL. NCBITaxonomyLoader - Interface in org.biojavax.bio.taxa.io Implementors are able to load taxonomy files and generate sets of NCBITaxon objects that represent them. NeedlemanWunsch - Class in org.biojava.bio.alignment Needleman and Wunsch defined the problem of global sequence alignments, from the first till the last symbol of a sequence. NeedlemanWunsch(short, short, short, short, short, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.NeedlemanWunsch Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix. needSlots() - Method in class org.biojava.utils.bytecode.LocalVariable NEGATIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature Flag to indicate that a feature is on the negative strand. NEGATIVE_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand The negative strand is represented by the symbol '-' and has the number -1. NeighborJoining(TaxaBlock, CharactersBlock) - Static method in class org.biojavax.bio.phylo.DistanceBasedTreeMethod NestedKernel - Class in org.biojava.stats.svm Encapsulates a kernel that wraps another kernel up. NestedKernel() - Constructor for class org.biojava.stats.svm.NestedKernel Create a new NestedKernel. NestedKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NestedKernel Create a new NestedKernel that wraps k. NEW_LINE - Static variable in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat New-line symbol. NewAssembledSymbolList - Class in org.biojava.bio.seq.impl Support class for applications which need to patch together sections of sequence into a single SymbolList. NewAssembledSymbolList() - Constructor for class org.biojava.bio.seq.impl.NewAssembledSymbolList NewickTreeString() - Constructor for class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString newInstance(Constructor, Object[]) - Method in interface org.biojava.bio.seq.projection.ProjectionEngine.Instantiator newInstance(Location) - Method in class org.biojava.bio.symbol.AbstractLocation newInstance(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator newInstance(Location) - Method in interface org.biojava.bio.symbol.Location Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc. newInstance(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc. newInstance(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc. newInstance(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc. newKey(String, String) - Method in interface org.biojava.ontology.obo.OboFileEventListener found a new key in the file newKey(String, String) - Method in class org.biojava.ontology.obo.OboFileHandler newMessage(Class, String, String, String, String) - Static method in exception org.biojava.bio.seq.io.ParseException Make a new error message. newOboFileHeader() - Method in interface org.biojava.ontology.obo.OboFileEventListener parsed a new OBO file header newOboFileHeader() - Method in class org.biojava.ontology.obo.OboFileHandler NewSimpleAssembly - Class in org.biojava.bio.seq A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects. NewSimpleAssembly(int, String, String) - Constructor for class org.biojava.bio.seq.NewSimpleAssembly Construct a new SimpleAssembly using the DNA alphabet. NewSimpleAssembly(String, String) - Constructor for class org.biojava.bio.seq.NewSimpleAssembly Construct a new NewSimpleAssembly using the DNA alphabet. newStanza(String) - Method in interface org.biojava.ontology.obo.OboFileEventListener parsed a new stanza in the file newStanza(String) - Method in class org.biojava.ontology.obo.OboFileHandler newSynonym(Synonym) - Method in interface org.biojava.ontology.obo.OboFileEventListener a new synonym has been found newSynonym(Synonym) - Method in class org.biojava.ontology.obo.OboFileHandler next() - Method in class org.biojava.bio.alignment.Alignment.SymbolListIterator next() - Method in class org.biojava.bio.dp.DP.ReverseIterator next() - Method in class org.biojava.utils.MergingIterator next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor Description of the Method next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.MatrixPairDPCursor next(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.PairDPCursor retrieve the next block of cells nextBioEntry() - Method in interface org.biojavax.bio.BioEntryIterator nextBioEntry() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator nextBioEntry() - Method in class org.biojavax.bio.seq.io.RichStreamReader nextBioEntry() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator nextOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthologueSet.Iterator nextOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet.Iterator nextOrthoPair() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet.Iterator nextOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet.Iterator nextRequest() - Method in class org.biojava.utils.SimpleThreadPool nextRequest gets the next Runnable from the queue. nextRichSequence() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator nextRichSequence() - Method in class org.biojavax.bio.seq.io.RichStreamReader nextRichSequence() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator nextRichSequence() - Method in interface org.biojavax.bio.seq.RichSequenceIterator nextSequence() - Method in class org.biojava.bio.seq.io.StreamReader Pull the next sequence out of the stream. nextSequence() - Method in interface org.biojava.bio.seq.SequenceIterator Returns the next sequence in the iterator. nextSequence() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator nextSequence() - Method in class org.biojavax.bio.seq.io.RichStreamReader Returns the next sequence in the iterator. nextSequence() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator Returns the next sequence in the iterator. nextSet() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection.Iterator returns the next OrthoPairSet nextSet() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection.Iterator nextTable() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader Returns the next SymbolPropertyTable object. nextTable() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator Returns the next SymbolPropertyTable object. nextWord(SymbolList, int, int, int, Packing) - Static method in class org.biojava.bio.symbol.PackingFactory NexusBlock - Interface in org.biojavax.bio.phylo.io.nexus Represents a Nexus block. NexusBlock.Abstract - Class in org.biojavax.bio.phylo.io.nexus NexusBlockBuilder - Interface in org.biojavax.bio.phylo.io.nexus Builds a Nexus block from listening to events. NexusBlockBuilder.Abstract - Class in org.biojavax.bio.phylo.io.nexus This abstract version knows how to build and add comments. NexusBlockListener - Interface in org.biojavax.bio.phylo.io.nexus Listens to events from NexusBlockParser objects to create objects. NexusBlockParser - Interface in org.biojavax.bio.phylo.io.nexus Parses Nexus blocks. NexusBlockParser.Abstract - Class in org.biojavax.bio.phylo.io.nexus All block parsers should derive from this abstract parser. NexusComment - Class in org.biojavax.bio.phylo.io.nexus Represents a Nexus comment, possibly nested. NexusComment() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusComment NexusFile - Class in org.biojavax.bio.phylo.io.nexus Represents Nexus files. NexusFile() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusFile NexusFileBuilder - Class in org.biojavax.bio.phylo.io.nexus Builds a Nexus file by listening to events. NexusFileBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder NexusFileFormat - Class in org.biojavax.bio.phylo.io.nexus Reads/writes Nexus files and fires events at a NexusFileListener object. NexusFileListener - Interface in org.biojavax.bio.phylo.io.nexus Listens to events fired by the Nexus parser. NexusFileListener.Abstract - Class in org.biojavax.bio.phylo.io.nexus Example abstract implementation which all others should extend. NexusObject - Interface in org.biojavax.bio.phylo.io.nexus Represents general info about nexus objects. Nfa - Class in org.biojava.utils.automata Class for modelling non-deterministic finite automata. Nfa(String, FiniteAlphabet) - Constructor for class org.biojava.utils.automata.Nfa NfaBuilder - Interface in org.biojava.utils.automata NfaSubModel - Class in org.biojava.utils.automata This class caches a reference to all objects that it directs its delegate to make. NIODataStoreFactory - Class in org.biojava.bio.program.ssaha Builder for a datastore that has no practical file size limit. NIODataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.NIODataStoreFactory nl() - Method in class org.biojava.bio.program.xml.BaseXMLWriter Nmono - Static variable in class org.biojava.bio.proteomics.MassCalc Constant value of Nitrogen monoisotopic mass NO_CROSS - Static variable in interface org.biojavax.ga.functions.CrossOverFunction NO_FRAME - Static variable in interface org.biojava.bio.program.gff.GFFRecord Deprecated. Use GFFTools.NO_FRAME instead NO_FRAME - Static variable in class org.biojava.bio.program.gff.GFFTools Flag to indicate that there is no frame info. NO_MUTATION - Static variable in interface org.biojavax.ga.functions.MutationFunction NO_SCORE - Static variable in interface org.biojava.bio.program.gff.GFFRecord Deprecated. Use GFFTools.NO_SCORE instead NO_SCORE - Static variable in class org.biojava.bio.program.gff.GFFTools Flag to indicate that there is no score info. NoCross() - Constructor for class org.biojavax.ga.functions.CrossOverFunction.NoCross NODERANK - Static variable in interface org.biojavax.bio.taxa.NCBITaxon nodes - Variable in class org.biojava.utils.automata.FiniteAutomaton NoMutation() - Constructor for class org.biojavax.ga.functions.MutationFunction.NoMutation none - Static variable in interface org.biojava.bio.seq.FeatureFilter No features are selected by this filter. none - Static variable in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter No features are selected by this filter. none() - Static method in class org.biojava.bio.seq.FilterUtils Return a filter which matches no features. NONE - Static variable in interface org.biojava.bio.AnnotationType The type that accepts no annotations at all and is the subtype of all other annotations. NONE - Static variable in class org.biojava.bio.CardinalityConstraint This cardinality contains no intengers, not even zero. NONE - Static variable in interface org.biojava.bio.CollectionConstraint NONE is a constraint which accepts no value for a property under any condition. NONE - Static variable in interface org.biojava.bio.PropertyConstraint NONE is a constraint which accepts no value for a property under any condition. NONE - Static variable in class org.biojava.ontology.OntoTools nonRemoveIterator(Iterator) - Static method in class org.biojava.utils.ListTools normalizeMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix With this method you can get a “normalized” SubstitutionMatrix object; however, since this implementation uses an short matrix, the normalized matrix will be scaled by ten. NormalizingKernel - Class in org.biojava.stats.svm Performs a normalization on the results of a nested kernel. NormalizingKernel() - Constructor for class org.biojava.stats.svm.NormalizingKernel NormalizingKernel(List) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel Generate a normalizing kernel defined by the SparseVectors in vectors. NormalizingKernel(SparseVector) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel Generate a normalizing kernel with the normalizing vector s. NormalizingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NormalizingKernel normalLengthVector(SparseVector, double) - Static method in class org.biojava.stats.svm.SparseVector not - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter not(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils Construct a new filter which is the negation of filter. not(FeatureFilter.Not, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer not(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils Operator: FeatureHolder 1 NOT FeatureHolder2 Not(OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Not Not(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Not Not(OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not Not(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.Not Not(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Not Not(BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not Note - Interface in org.biojavax Note is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank. NOTE - Static variable in interface org.biojavax.bio.seq.RichLocation NOTE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat NotFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter NotFilter(GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter notifyExit() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.ExitNotification notifyHit(String, int, int, boolean) - Method in interface org.biojava.utils.automata.PatternListener notifyOnExit - Variable in class org.biojava.bio.program.tagvalue.StateMachine.Transition should the State listener be notified that this transition is leaving the state. notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.program.phred.PhredFormat Passes the event on to all the listeners registered for ParseErrorEvents. notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents. notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblProcessor Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents. notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents. notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents. notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankProcessor Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents. notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.SwissprotProcessor Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents. nState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM Gets the n loop state nucleotideToken(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools Get a single-character token for a Nucleotide symbol NucleotideTools - Class in org.biojava.bio.seq Useful functionality for processing nucleotide sequences. NULL_MAPPER - Static variable in class org.biojava.utils.ListTools NULL_MODEL - Static variable in interface org.biojava.bio.dist.Distribution Whenever the null model distribution changes the values that would be returned by getWeight, either by being edited or by being replaced, a ChangeEvent with this object as the type should be thrown. NULL_MODEL - Static variable in interface org.biojava.bio.dp.ScoreType NullModel() - Constructor for class org.biojava.bio.dp.ScoreType.NullModel nullModelForwarder - Variable in class org.biojava.bio.dist.AbstractDistribution Forwarder for modifications to the null model. NullModelForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.dist.Distribution.NullModelForwarder Deprecated. Create a new forwarder. NullModelScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler numberOfElements - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord numericalEntity(char) - Method in class org.biojava.utils.xml.FastXMLWriter numericalEntity(char) - Method in class org.biojava.utils.xml.PrettyXMLWriter numParameters() - Method in interface org.biojava.utils.bytecode.CodeMethod Get the number of parameters taken by this method numParameters() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod numStates - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor numStates - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor Description of the Field numTables() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB Returns the number of symbol property tables in the database. numTables() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB Returns the number of symbol property tables in the database. O o() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Pyrrolysine O_SATIVA - Static variable in interface org.biojava.bio.program.homologene.Taxon Oavg - Static variable in class org.biojava.bio.proteomics.MassCalc Constant value of Oxygen average mass OBDA_SEARCH_ENV - Static variable in class org.biojava.directory.SystemRegistry ObdaContext - Class in org.biojava.naming ObdaInitialContextFactory - Class in org.biojava.naming ObdaInitialContextFactory() - Constructor for class org.biojava.naming.ObdaInitialContextFactory OBDARegistryParser - Class in org.biojava.directory This class encapsulates all the parsing of the OBDA registry configuration file. OBDARegistryParser() - Constructor for class org.biojava.directory.OBDARegistryParser ObdaUriParser - Class in org.biojava.naming Singleton class for parsers that understand OBDA URIs. objectIterator() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile Iterate over all objects in the file in order. ObjectUtil - Class in org.biojava.utils utility methods for implementing the equals() and hashCode() methods of Objects. ObjectUtil() - Constructor for class org.biojava.utils.ObjectUtil OboFileEventListener - Interface in org.biojava.ontology.obo an interface for events that occur during parsing of .obo files OboFileHandler - Class in org.biojava.ontology.obo A file handler for .obo files OboFileHandler(Ontology) - Constructor for class org.biojava.ontology.obo.OboFileHandler OboFileParser - Class in org.biojava.ontology.obo A class to parse the content of an OBO file. OboFileParser() - Constructor for class org.biojava.ontology.obo.OboFileParser OboFileParser.SOPair - Class in org.biojava.ontology.obo OboParser - Class in org.biojava.ontology.io Parses an OBO file. OboParser() - Constructor for class org.biojava.ontology.io.OboParser OBSOLETE - Static variable in interface org.biojavax.ontology.ComparableTerm oColourClassMap - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler Stores mapping from a Colour to a FONT Class. oColourMap - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler Map between Char and the Colour class. oColourSet - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler Store the unique colours for markup. Odds() - Constructor for class org.biojava.bio.dp.ScoreType.Odds ODDS - Static variable in interface org.biojava.bio.dp.ScoreType OFFSET - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer offsetData - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord OffsetRulerRenderer - Class in org.biojava.bio.gui.sequence OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence. OffsetRulerRenderer() - Constructor for class org.biojava.bio.gui.sequence.OffsetRulerRenderer OffsetRulerRenderer(int, int) - Constructor for class org.biojava.bio.gui.sequence.OffsetRulerRenderer OFFSETS - Static variable in interface org.biojava.bio.chromatogram.Chromatogram The sequence label for the trace offsets of the called bases. Omono - Static variable in class org.biojava.bio.proteomics.MassCalc Constant value of Oxygen monoisotopic mass one() - Static method in class org.biojavax.ga.util.GATools ONE - Static variable in class org.biojava.bio.CardinalityConstraint The property should have exactly one value. ONE_OR_MORE - Static variable in class org.biojava.bio.CardinalityConstraint The property should have one or more values. onlyChildren(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils Construct a filter which matches features whose children all match the specified filter. onlyChildren(FeatureFilter.OnlyChildren, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer OnlyChildren(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.OnlyChildren onlyDescendants(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils Construct a filter which matches features whose decendants all match the specified filter. onlyDescendants(FeatureFilter.OnlyDescendants, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer OnlyDescendants(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.OnlyDescendants Ontology - Interface in org.biojava.ontology An ontology. ONTOLOGY - Static variable in class org.biojava.ontology.obo.OboFileHandler ONTOLOGY - Static variable in interface org.biojava.ontology.Term ChangeType which indicates that this term's ontology has been altered Ontology.Impl - Class in org.biojava.ontology A basic in-memory implementation of an ontology OntologyException - Exception in org.biojava.ontology Thrown to indicate an error in an Ontology object OntologyException() - Constructor for exception org.biojava.ontology.OntologyException OntologyException(String) - Constructor for exception org.biojava.ontology.OntologyException OntologyException(String, Throwable) - Constructor for exception org.biojava.ontology.OntologyException OntologyException(Throwable) - Constructor for exception org.biojava.ontology.OntologyException OntologyFactory - Interface in org.biojava.ontology A factory for Ontology instances. OntologyOps - Interface in org.biojava.ontology This is an interface for optimizing ontology operators. OntologyTerm - Interface in org.biojava.ontology A term in an ontology which identifies another ontology. OntologyTerm.Impl - Class in org.biojava.ontology Simple in-memory implementation of a remote ontology term. OntoTools - Class in org.biojava.ontology Tools for manipulating ontologies. op_aaload - Static variable in class org.biojava.utils.bytecode.ByteCode op_aastore - Static variable in class org.biojava.utils.bytecode.ByteCode op_aconst_null - Static variable in class org.biojava.utils.bytecode.ByteCode op_aload - Static variable in class org.biojava.utils.bytecode.ByteCode op_aload_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_aload_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_aload_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_aload_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_anewarray - Static variable in class org.biojava.utils.bytecode.ByteCode op_anewarray_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_areturn - Static variable in class org.biojava.utils.bytecode.ByteCode op_arraylength - Static variable in class org.biojava.utils.bytecode.ByteCode op_astore - Static variable in class org.biojava.utils.bytecode.ByteCode op_astore_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_astore_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_astore_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_astore_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_athrow - Static variable in class org.biojava.utils.bytecode.ByteCode op_baload - Static variable in class org.biojava.utils.bytecode.ByteCode op_bastore - Static variable in class org.biojava.utils.bytecode.ByteCode op_bipush - Static variable in class org.biojava.utils.bytecode.ByteCode op_breakpoint - Static variable in class org.biojava.utils.bytecode.ByteCode op_caload - Static variable in class org.biojava.utils.bytecode.ByteCode op_castore - Static variable in class org.biojava.utils.bytecode.ByteCode op_checkcast - Static variable in class org.biojava.utils.bytecode.ByteCode op_checkcast_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_d2f - Static variable in class org.biojava.utils.bytecode.ByteCode op_d2i - Static variable in class org.biojava.utils.bytecode.ByteCode op_d2l - Static variable in class org.biojava.utils.bytecode.ByteCode op_dadd - Static variable in class org.biojava.utils.bytecode.ByteCode op_daload - Static variable in class org.biojava.utils.bytecode.ByteCode op_dastore - Static variable in class org.biojava.utils.bytecode.ByteCode op_dcmpg - Static variable in class org.biojava.utils.bytecode.ByteCode op_dcmpl - Static variable in class org.biojava.utils.bytecode.ByteCode op_dconst_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dconst_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_ddiv - Static variable in class org.biojava.utils.bytecode.ByteCode op_dload - Static variable in class org.biojava.utils.bytecode.ByteCode op_dload_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dload_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dload_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dload_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dmul - Static variable in class org.biojava.utils.bytecode.ByteCode op_dneg - Static variable in class org.biojava.utils.bytecode.ByteCode op_drem - Static variable in class org.biojava.utils.bytecode.ByteCode op_dreturn - Static variable in class org.biojava.utils.bytecode.ByteCode op_dstore - Static variable in class org.biojava.utils.bytecode.ByteCode op_dstore_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dstore_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dstore_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dstore_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dsub - Static variable in class org.biojava.utils.bytecode.ByteCode op_dup - Static variable in class org.biojava.utils.bytecode.ByteCode op_dup_x1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dup_x2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dup2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dup2_x1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_dup2_x2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_f2d - Static variable in class org.biojava.utils.bytecode.ByteCode op_f2i - Static variable in class org.biojava.utils.bytecode.ByteCode op_f2l - Static variable in class org.biojava.utils.bytecode.ByteCode op_fadd - Static variable in class org.biojava.utils.bytecode.ByteCode op_faload - Static variable in class org.biojava.utils.bytecode.ByteCode op_fastore - Static variable in class org.biojava.utils.bytecode.ByteCode op_fcmpg - Static variable in class org.biojava.utils.bytecode.ByteCode op_fcmpl - Static variable in class org.biojava.utils.bytecode.ByteCode op_fconst_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fconst_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fconst_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fdiv - Static variable in class org.biojava.utils.bytecode.ByteCode op_fload - Static variable in class org.biojava.utils.bytecode.ByteCode op_fload_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fload_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fload_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fload_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fmul - Static variable in class org.biojava.utils.bytecode.ByteCode op_fneg - Static variable in class org.biojava.utils.bytecode.ByteCode op_frem - Static variable in class org.biojava.utils.bytecode.ByteCode op_freturn - Static variable in class org.biojava.utils.bytecode.ByteCode op_fstore - Static variable in class org.biojava.utils.bytecode.ByteCode op_fstore_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fstore_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fstore_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fstore_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_fsub - Static variable in class org.biojava.utils.bytecode.ByteCode op_getfield - Static variable in class org.biojava.utils.bytecode.ByteCode op_getfield_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_getfield_quick_w - Static variable in class org.biojava.utils.bytecode.ByteCode op_getfield2_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_getstatic - Static variable in class org.biojava.utils.bytecode.ByteCode op_getstatic_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_getstatic2_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_goto - Static variable in class org.biojava.utils.bytecode.ByteCode op_goto_w - Static variable in class org.biojava.utils.bytecode.ByteCode op_i2b - Static variable in class org.biojava.utils.bytecode.ByteCode op_i2c - Static variable in class org.biojava.utils.bytecode.ByteCode op_i2d - Static variable in class org.biojava.utils.bytecode.ByteCode op_i2f - Static variable in class org.biojava.utils.bytecode.ByteCode op_i2l - Static variable in class org.biojava.utils.bytecode.ByteCode op_i2s - Static variable in class org.biojava.utils.bytecode.ByteCode op_iadd - Static variable in class org.biojava.utils.bytecode.ByteCode op_iaload - Static variable in class org.biojava.utils.bytecode.ByteCode op_iand - Static variable in class org.biojava.utils.bytecode.ByteCode op_iastore - Static variable in class org.biojava.utils.bytecode.ByteCode op_iconst_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_iconst_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_iconst_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_iconst_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_iconst_4 - Static variable in class org.biojava.utils.bytecode.ByteCode op_iconst_5 - Static variable in class org.biojava.utils.bytecode.ByteCode op_iconst_m1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_idiv - Static variable in class org.biojava.utils.bytecode.ByteCode op_if_acmpeq - Static variable in class org.biojava.utils.bytecode.ByteCode op_if_acmpne - Static variable in class org.biojava.utils.bytecode.ByteCode op_if_icmpeq - Static variable in class org.biojava.utils.bytecode.ByteCode op_if_icmpge - Static variable in class org.biojava.utils.bytecode.ByteCode op_if_icmpgt - Static variable in class org.biojava.utils.bytecode.ByteCode op_if_icmple - Static variable in class org.biojava.utils.bytecode.ByteCode op_if_icmplt - Static variable in class org.biojava.utils.bytecode.ByteCode op_if_icmpne - Static variable in class org.biojava.utils.bytecode.ByteCode op_ifeq - Static variable in class org.biojava.utils.bytecode.ByteCode op_ifge - Static variable in class org.biojava.utils.bytecode.ByteCode op_ifgt - Static variable in class org.biojava.utils.bytecode.ByteCode op_ifle - Static variable in class org.biojava.utils.bytecode.ByteCode op_iflt - Static variable in class org.biojava.utils.bytecode.ByteCode op_ifne - Static variable in class org.biojava.utils.bytecode.ByteCode op_ifnonnull - Static variable in class org.biojava.utils.bytecode.ByteCode op_ifnull - Static variable in class org.biojava.utils.bytecode.ByteCode op_iinc - Static variable in class org.biojava.utils.bytecode.ByteCode op_iload - Static variable in class org.biojava.utils.bytecode.ByteCode op_iload_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_iload_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_iload_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_iload_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_impdep1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_impdep2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_imul - Static variable in class org.biojava.utils.bytecode.ByteCode op_ineg - Static variable in class org.biojava.utils.bytecode.ByteCode op_instanceof - Static variable in class org.biojava.utils.bytecode.ByteCode op_instanceof_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokeinterface - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokeinterface_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokenonvirtual_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokespecial - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokestatic - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokestatic_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokesuper_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokevirtual - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokevirtual_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokevirtual_quick_w - Static variable in class org.biojava.utils.bytecode.ByteCode op_invokevirtualobject_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_ior - Static variable in class org.biojava.utils.bytecode.ByteCode op_irem - Static variable in class org.biojava.utils.bytecode.ByteCode op_ireturn - Static variable in class org.biojava.utils.bytecode.ByteCode op_ishl - Static variable in class org.biojava.utils.bytecode.ByteCode op_ishr - Static variable in class org.biojava.utils.bytecode.ByteCode op_istore - Static variable in class org.biojava.utils.bytecode.ByteCode op_istore_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_istore_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_istore_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_istore_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_isub - Static variable in class org.biojava.utils.bytecode.ByteCode op_iushr - Static variable in class org.biojava.utils.bytecode.ByteCode op_ixor - Static variable in class org.biojava.utils.bytecode.ByteCode op_jsr - Static variable in class org.biojava.utils.bytecode.ByteCode op_jsr_w - Static variable in class org.biojava.utils.bytecode.ByteCode op_l2d - Static variable in class org.biojava.utils.bytecode.ByteCode op_l2f - Static variable in class org.biojava.utils.bytecode.ByteCode op_l2i - Static variable in class org.biojava.utils.bytecode.ByteCode op_ladd - Static variable in class org.biojava.utils.bytecode.ByteCode op_laload - Static variable in class org.biojava.utils.bytecode.ByteCode op_land - Static variable in class org.biojava.utils.bytecode.ByteCode op_lastore - Static variable in class org.biojava.utils.bytecode.ByteCode op_lcmp - Static variable in class org.biojava.utils.bytecode.ByteCode op_lconst_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_lconst_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_ldc - Static variable in class org.biojava.utils.bytecode.ByteCode op_ldc_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_ldc_w - Static variable in class org.biojava.utils.bytecode.ByteCode op_ldc_w_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_ldc2_w - Static variable in class org.biojava.utils.bytecode.ByteCode op_ldc2_w_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_ldiv - Static variable in class org.biojava.utils.bytecode.ByteCode op_lload - Static variable in class org.biojava.utils.bytecode.ByteCode op_lload_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_lload_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_lload_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_lload_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_lmul - Static variable in class org.biojava.utils.bytecode.ByteCode op_lneg - Static variable in class org.biojava.utils.bytecode.ByteCode op_lookupswitch - Static variable in class org.biojava.utils.bytecode.ByteCode op_lor - Static variable in class org.biojava.utils.bytecode.ByteCode op_lrem - Static variable in class org.biojava.utils.bytecode.ByteCode op_lreturn - Static variable in class org.biojava.utils.bytecode.ByteCode op_lshl - Static variable in class org.biojava.utils.bytecode.ByteCode op_lshr - Static variable in class org.biojava.utils.bytecode.ByteCode op_lstore - Static variable in class org.biojava.utils.bytecode.ByteCode op_lstore_0 - Static variable in class org.biojava.utils.bytecode.ByteCode op_lstore_1 - Static variable in class org.biojava.utils.bytecode.ByteCode op_lstore_2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_lstore_3 - Static variable in class org.biojava.utils.bytecode.ByteCode op_lsub - Static variable in class org.biojava.utils.bytecode.ByteCode op_lushr - Static variable in class org.biojava.utils.bytecode.ByteCode op_lxor - Static variable in class org.biojava.utils.bytecode.ByteCode op_monitorenter - Static variable in class org.biojava.utils.bytecode.ByteCode op_monitorexit - Static variable in class org.biojava.utils.bytecode.ByteCode op_multianewarray - Static variable in class org.biojava.utils.bytecode.ByteCode op_multianewarray_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_new - Static variable in class org.biojava.utils.bytecode.ByteCode op_new_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_newarray - Static variable in class org.biojava.utils.bytecode.ByteCode op_nop - Static variable in class org.biojava.utils.bytecode.ByteCode op_pop - Static variable in class org.biojava.utils.bytecode.ByteCode op_pop2 - Static variable in class org.biojava.utils.bytecode.ByteCode op_putfield - Static variable in class org.biojava.utils.bytecode.ByteCode op_putfield_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_putfield_quick_w - Static variable in class org.biojava.utils.bytecode.ByteCode op_putfield2_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_putstatic - Static variable in class org.biojava.utils.bytecode.ByteCode op_putstatic_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_putstatic2_quick - Static variable in class org.biojava.utils.bytecode.ByteCode op_ret - Static variable in class org.biojava.utils.bytecode.ByteCode op_return - Static variable in class org.biojava.utils.bytecode.ByteCode op_saload - Static variable in class org.biojava.utils.bytecode.ByteCode op_sastore - Static variable in class org.biojava.utils.bytecode.ByteCode op_sipush - Static variable in class org.biojava.utils.bytecode.ByteCode op_swap - Static variable in class org.biojava.utils.bytecode.ByteCode op_tableswitch - Static variable in class org.biojava.utils.bytecode.ByteCode op_wide - Static variable in class org.biojava.utils.bytecode.ByteCode open() - Method in interface org.biojava.utils.bytecode.CodeContext Open the context for writing. open(File) - Static method in class org.biojava.bio.seq.db.TabIndexStore Open an existing index store. openSubComment() - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment openTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter openTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter openTag(String) - Method in interface org.biojava.utils.xml.XMLWriter Open a new unqualified XML tag. openTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter openTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter Open a new namespace-qualified XML tag. OptimizableFilter - Interface in org.biojava.bio.seq The interface for filters that can potentialy optimize themselves, and compare themselves with other filters. optimize(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with fewer terms. optionIsTrue(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Helper method for converting a Boolean-valued option into a boolean primitive. options - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic The map containing the ChromatogramGraphic.Options and values for this instance. or - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter or(FeatureFilter.Or, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer or(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils Construct a new filter which matches the intersection of two filters. or(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils Construct a new filter which matches the union of two filters. Or(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.Or Create a new Or from two child constraints. Or(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Or Or(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Or Or(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or Or(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.Or Create a new Or from two child constraints. Or(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.Or Or(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Or Or(BioSQLFeatureFilter, BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or OracleDBHelper - Class in org.biojava.bio.seq.db.biosql Deprecated. Use hibernate and org.biojavax.bio.db.* OracleDBHelper(Connection) - Constructor for class org.biojava.bio.seq.db.biosql.OracleDBHelper Deprecated. OrderCrossover - Class in org.biojavax.ga.functions This does a 2-point-crossover on two chromosomes keeping the Symbols in each chromosome constant. OrderCrossover() - Constructor for class org.biojavax.ga.functions.OrderCrossover Sets the maximal number of crossover points to two and the crossover probability to 0.5 and initializes this object. orderedLables(Comparator<String>) - Method in class org.biojava.bio.alignment.AbstractULAlignment OrderNDistribution - Interface in org.biojava.bio.dist Provides an N'th order distribution. OrderNDistributionFactory - Class in org.biojava.bio.dist Default factory for Order-N distributions. OrderNDistributionFactory(DistributionFactory) - Constructor for class org.biojava.bio.dist.OrderNDistributionFactory Construct a new OrderNDistributionFactory with a specified factory for conditioned distributions. orderNSymbolList(SymbolList, int) - Static method in class org.biojava.bio.symbol.SymbolListViews An n-th order view of another SymbolList. ORDLOCNAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms ORFNAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms org.biojava - package org.biojava org.biojava.bibliography - package org.biojava.bibliography The data structures and interfaces included in this package define an interoperable framework for bibliographic searches. org.biojava.bio - package org.biojava.bio The core classes that will be used throughout the bio packages. org.biojava.bio.alignment - package org.biojava.bio.alignment Classes to generate and describe sequence alignments. org.biojava.bio.annodb - package org.biojava.bio.annodb Databases of generic structured data (annotation) objects. org.biojava.bio.chromatogram - package org.biojava.bio.chromatogram Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment. org.biojava.bio.chromatogram.graphic - package org.biojava.bio.chromatogram.graphic Tools for displaying chromatograms. org.biojava.bio.dist - package org.biojava.bio.dist Probability distributions over Alphabets. org.biojava.bio.dp - package org.biojava.bio.dp HMM and Dynamic Programming Algorithms. org.biojava.bio.dp.onehead - package org.biojava.bio.dp.onehead org.biojava.bio.dp.twohead - package org.biojava.bio.dp.twohead org.biojava.bio.gui - package org.biojava.bio.gui Graphical interfaces for biojava objects. org.biojava.bio.gui.glyph - package org.biojava.bio.gui.glyph Glyphs implementations that draw shapes into SequenceRenderers org.biojava.bio.gui.sequence - package org.biojava.bio.gui.sequence Graphical displays of biological sequences and associated annotations. org.biojava.bio.gui.sequence.tracklayout - package org.biojava.bio.gui.sequence.tracklayout Classes for the handling of the layout of a WrappedSequencePanel. org.biojava.bio.molbio - package org.biojava.bio.molbio The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR. org.biojava.bio.program - package org.biojava.bio.program Java wrappers for interacting with external bioinformatics tools. org.biojava.bio.program.abi - package org.biojava.bio.program.abi ABI Trace Handling. org.biojava.bio.program.blast2html - package org.biojava.bio.program.blast2html Code for generating HTML reports from blast output org.biojava.bio.program.fastq - package org.biojava.bio.program.fastq FASTQ and variants sequence format I/O. org.biojava.bio.program.formats - package org.biojava.bio.program.formats Experimental parsers using the tagvalue framework. org.biojava.bio.program.gff - package org.biojava.bio.program.gff GFF manipulation. org.biojava.bio.program.gff3 - package org.biojava.bio.program.gff3 Support for reading and writing GFF3. org.biojava.bio.program.hmmer - package org.biojava.bio.program.hmmer Tools for working with profile Hidden Markov Models from the HMMer package. org.biojava.bio.program.homologene - package org.biojava.bio.program.homologene Support classes for Homologene data. org.biojava.bio.program.indexdb - package org.biojava.bio.program.indexdb A flat-file ascii index of ascii flat files as per the OBDA specification. org.biojava.bio.program.phred - package org.biojava.bio.program.phred Parser for Phred output org.biojava.bio.program.sax - package org.biojava.bio.program.sax Parsers which offer XML representations of the output from common bioinformatics tools. org.biojava.bio.program.sax.blastxml - package org.biojava.bio.program.sax.blastxml Parsers for the XML output from NCBI blast. org.biojava.bio.program.scf - package org.biojava.bio.program.scf Support for the SCF chromatogram format. org.biojava.bio.program.ssaha - package org.biojava.bio.program.ssaha SSAHA sequence searching API. org.biojava.bio.program.ssbind - package org.biojava.bio.program.ssbind Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. org.biojava.bio.program.tagvalue - package org.biojava.bio.program.tagvalue Process files as streams of records, each with tags with values. org.biojava.bio.program.unigene - package org.biojava.bio.program.unigene Objects for representing Unigene clusters. org.biojava.bio.program.xff - package org.biojava.bio.program.xff Event-driven parsing system for the Extensible Feature Format (XFF). org.biojava.bio.program.xml - package org.biojava.bio.program.xml Utility classes for the org.biojava.bio.program.sax package. org.biojava.bio.proteomics - package org.biojava.bio.proteomics Utilities to aid in performing various physical analysis of proteins. org.biojava.bio.proteomics.aaindex - package org.biojava.bio.proteomics.aaindex Classes and interfaces to load Amino Acid Index database files. org.biojava.bio.search - package org.biojava.bio.search Interfaces and classes for representing sequence similarity search results. org.biojava.bio.seq - package org.biojava.bio.seq Classes and interfaces for defining biological sequences and informatics objects. org.biojava.bio.seq.db - package org.biojava.bio.seq.db Collections of biological sequence data. org.biojava.bio.seq.db.biofetch - package org.biojava.bio.seq.db.biofetch Client for the OBDA BioFetch protocol. org.biojava.bio.seq.db.biosql - package org.biojava.bio.seq.db.biosql General purpose Sequence storage in a relational database. org.biojava.bio.seq.db.emblcd - package org.biojava.bio.seq.db.emblcd Readers for the EMBL CD-ROM format binary index files used by EMBOSS and Staden packages. org.biojava.bio.seq.db.flat - package org.biojava.bio.seq.db.flat Support for OBDA flatfile databases. org.biojava.bio.seq.distributed - package org.biojava.bio.seq.distributed Sequences and SequenceDBs which are composed from data taken from a number of data sources. org.biojava.bio.seq.filter - package org.biojava.bio.seq.filter org.biojava.bio.seq.homol - package org.biojava.bio.seq.homol The classes and interfaces for defining sequence similarity and honology. org.biojava.bio.seq.impl - package org.biojava.bio.seq.impl Standard in-memory implementations of Sequence and Feature. org.biojava.bio.seq.io - package org.biojava.bio.seq.io Classes and interfaces for processing and producing flat-file representations of sequences. org.biojava.bio.seq.io.agave - package org.biojava.bio.seq.io.agave Classes for converting between AGAVE XML and BioJava objects. org.biojava.bio.seq.io.filterxml - package org.biojava.bio.seq.io.filterxml Tools for reading and writing an XML representation of BioJava's FeatureFilter language. org.biojava.bio.seq.io.game - package org.biojava.bio.seq.io.game Event-driven parsing system for the Gene Annotation Markup Elements (GAME). org.biojava.bio.seq.io.game12 - package org.biojava.bio.seq.io.game12 Event-driven parsing system for the Gene Annotation Markup Elements (GAME). org.biojava.bio.seq.projection - package org.biojava.bio.seq.projection Code for projecting Feature objects and systematically altering their properties. org.biojava.bio.symbol - package org.biojava.bio.symbol Representation of the Symbols that make up a sequence, and locations within them. org.biojava.bio.taxa - package org.biojava.bio.taxa Taxonomy object for representing species information. org.biojava.directory - package org.biojava.directory Open Bio Sequence Database Access (OBDA) registry support. org.biojava.naming - package org.biojava.naming org.biojava.ontology - package org.biojava.ontology A general-purpose API for ontologies. org.biojava.ontology.io - package org.biojava.ontology.io Tools for loading and saving ontologies. org.biojava.ontology.obo - package org.biojava.ontology.obo org.biojava.stats.svm - package org.biojava.stats.svm Support Vector Machine classification and regression. org.biojava.stats.svm.tools - package org.biojava.stats.svm.tools Tools for use of the SVM package. org.biojava.utils - package org.biojava.utils Miscellaneous utility classes used by other BioJava components. org.biojava.utils.automata - package org.biojava.utils.automata org.biojava.utils.bytecode - package org.biojava.utils.bytecode A Java object-model for a Java Bytecode Macro-Assembler. org.biojava.utils.cache - package org.biojava.utils.cache A simple cache system with pluggable caching behaviours. org.biojava.utils.candy - package org.biojava.utils.candy The data structures and interfaces included in this package define an interoperable framework for simple controlled vocabularies. org.biojava.utils.io - package org.biojava.utils.io I/O utility classes. org.biojava.utils.lsid - package org.biojava.utils.lsid Life Science Identifier (LSID) package. org.biojava.utils.math - package org.biojava.utils.math Mathematical utility classes. org.biojava.utils.net - package org.biojava.utils.net Network programming utility classes. org.biojava.utils.process - package org.biojava.utils.process Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads. org.biojava.utils.regex - package org.biojava.utils.regex This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets. org.biojava.utils.stax - package org.biojava.utils.stax The Stack API for XML (StAX). org.biojava.utils.walker - package org.biojava.utils.walker org.biojava.utils.xml - package org.biojava.utils.xml Utility classes for handling and generating XML documents. org.biojavax - package org.biojavax The Biojava extensions packages, classes that extend the core biojava functionality org.biojavax.bio - package org.biojavax.bio Classes to represent biological entities and their relationships. org.biojavax.bio.alignment - package org.biojavax.bio.alignment This package contains the interfaces that need to be implemented by discrete alignment services. org.biojavax.bio.alignment.blast - package org.biojavax.bio.alignment.blast This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services through the WWW. org.biojavax.bio.db - package org.biojavax.bio.db Interactions between biojavax objects and a DB. org.biojavax.bio.db.biosql - package org.biojavax.bio.db.biosql Interface between biojava and biosql databases org.biojavax.bio.db.ncbi - package org.biojavax.bio.db.ncbi Interfaces to NCBI data. org.biojavax.bio.phylo - package org.biojavax.bio.phylo Classes to support phlylogeny objects. org.biojavax.bio.phylo.io.nexus - package org.biojavax.bio.phylo.io.nexus Classes to support the I/O of Nexus files. org.biojavax.bio.phylo.io.phylip - package org.biojavax.bio.phylo.io.phylip Classes to support the reading and writing of PHYLIP format. org.biojavax.bio.seq - package org.biojavax.bio.seq Rich implementations of Sequences, Locations and Features. org.biojavax.bio.seq.io - package org.biojavax.bio.seq.io Classes to support the I/O of RichSequence and Bioentry objects. org.biojavax.bio.taxa - package org.biojavax.bio.taxa Objects that model the NCBI taxonomy schema as described in the BioSQL schema. org.biojavax.bio.taxa.io - package org.biojavax.bio.taxa.io org.biojavax.ga - package org.biojavax.ga Classes to provide a genetic algorithm framework org.biojavax.ga.exception - package org.biojavax.ga.exception Exceptions related to the GA framework org.biojavax.ga.functions - package org.biojavax.ga.functions GA functions org.biojavax.ga.impl - package org.biojavax.ga.impl Default implementations and abstract classes. org.biojavax.ga.util - package org.biojavax.ga.util Utility functions and helper classes org.biojavax.ontology - package org.biojavax.ontology Extensions to the biojava ontology model that represent BioSQL ontology. org.biojavax.utils - package org.biojavax.utils Utility classes that are used by biojavax objects but could have wider utility to other applications. ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat Organism - Interface in org.biojavax.ga A GA 'organism' contains one or more Chromosomes ORGANISM_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. ORGANISM_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat ORGANISM_XREF_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. OrganismParser - Class in org.biojava.bio.seq.io Deprecated. Use org.biojavax.bio.taxa framework instead OrganismParser(SequenceBuilder, TaxonFactory, TaxonParser, String, String, String) - Constructor for class org.biojava.bio.seq.io.OrganismParser Deprecated. OrganismParser.Factory - Class in org.biojava.bio.seq.io Deprecated. Factory which wraps SequenceBuilders in an OrganismParser. organisms() - Method in class org.biojavax.ga.impl.SimplePopulation organisms() - Method in interface org.biojavax.ga.Population ORGANISMS - Static variable in interface org.biojavax.ga.Population origSeq - Variable in class org.biojava.bio.seq.impl.RevCompSequence Orthologue - Interface in org.biojava.bio.program.homologene this entry contains data about the orthologue. OrthologueFilter - Interface in org.biojava.bio.program.homologene OrthologueFilter.AcceptAll - Class in org.biojava.bio.program.homologene OrthologueFilter.And - Class in org.biojava.bio.program.homologene OrthologueFilter.ByAccession - Class in org.biojava.bio.program.homologene OrthologueFilter.ByHomologeneID - Class in org.biojava.bio.program.homologene OrthologueFilter.ByLocusID - Class in org.biojava.bio.program.homologene OrthologueFilter.ByTaxon - Class in org.biojava.bio.program.homologene OrthologueFilter.ByTaxonID - Class in org.biojava.bio.program.homologene OrthologueFilter.ByTitle - Class in org.biojava.bio.program.homologene OrthologueFilter.Not - Class in org.biojava.bio.program.homologene OrthologueFilter.Or - Class in org.biojava.bio.program.homologene OrthologueFilter.Xor - Class in org.biojava.bio.program.homologene OrthologueSet - Interface in org.biojava.bio.program.homologene Interface for classes that store and manipulate orthologues. OrthologueSet.Iterator - Interface in org.biojava.bio.program.homologene An iterator for the contents of an OrthologueSet. OrthoPair - Interface in org.biojava.bio.program.homologene Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues. OrthoPairCollection - Interface in org.biojava.bio.program.homologene Interface for a Set of OrthoPairSets OrthoPairCollection.Iterator - Interface in org.biojava.bio.program.homologene Iterator for a OrthoPairCollection OrthoPairFilter - Interface in org.biojava.bio.program.homologene OrthoPairFilter.AcceptAll - Class in org.biojava.bio.program.homologene OrthoPairFilter.And - Class in org.biojava.bio.program.homologene OrthoPairFilter.ByMaxIdentity - Class in org.biojava.bio.program.homologene OrthoPairFilter.ByMinIdentity - Class in org.biojava.bio.program.homologene OrthoPairFilter.ByRef - Class in org.biojava.bio.program.homologene OrthoPairFilter.BySimilarityType - Class in org.biojava.bio.program.homologene OrthoPairFilter.Not - Class in org.biojava.bio.program.homologene OrthoPairFilter.Or - Class in org.biojava.bio.program.homologene OrthoPairFilter.Xor - Class in org.biojava.bio.program.homologene OrthoPairSet - Interface in org.biojava.bio.program.homologene represents the Homologene Group. OrthoPairSet.Iterator - Interface in org.biojava.bio.program.homologene OrthoPairSetFilter - Interface in org.biojava.bio.program.homologene OrthoPairSetFilter.AcceptAll - Class in org.biojava.bio.program.homologene OrthoPairSetFilter.AllPairsInCollection - Class in org.biojava.bio.program.homologene all OrthoPairs must meet the requirement defined by filter. OrthoPairSetFilter.And - Class in org.biojava.bio.program.homologene OrthoPairSetFilter.ByMinIdentity - Class in org.biojava.bio.program.homologene OrthoPairSetFilter.ByTaxon - Class in org.biojava.bio.program.homologene OrthoPairSetFilter.Not - Class in org.biojava.bio.program.homologene OrthoPairSetFilter.Or - Class in org.biojava.bio.program.homologene OrthoPairSetFilter.SomePairsInCollection - Class in org.biojava.bio.program.homologene at least one OrthoPair must meet the requirement defined by filter. OrthoPairSetFilter.Xor - Class in org.biojava.bio.program.homologene OTHER_SEQID_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat OTHER_SEQIDS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat outline - Variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer outline is the line colour. OUTLINE - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer Constant OUTLINE indicating a change to the outline paint of the features. OUTLINE - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer OUTLINE - Static variable in class org.biojava.bio.gui.sequence.CrosshairRenderer Constant OUTLINE indicating a change to the crosshair paint. OUTLINE - Static variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer Constant OUTLINE indicating a change to the fill of the features. OUTLINE - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer outlinePaint(Symbol) - Method in class org.biojava.bio.gui.DNAStyle outlinePaint(Symbol) - Method in class org.biojava.bio.gui.PlainStyle outlinePaint(Symbol) - Method in class org.biojava.bio.gui.SimpleSymbolStyle outlinePaint(Symbol) - Method in interface org.biojava.bio.gui.SymbolStyle Return the outline paint for a symbol. OutputHandler - Interface in org.biojava.utils.process Interface to a threadable output handler for an external process. OVERHANG_3PRIME - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme OVERHANG_3PRIME the sticky end type created by enzymes which leave a 3' overhang (e.g. a stretch of single-stranded DNA with a free 3' end). OVERHANG_5PRIME - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme OVERHANG_5PRIME the sticky end type created by enzymes which leave a 5' overhang (e.g. a stretch of single-stranded DNA with a free 5' end). overlaps(Location) - Method in class org.biojava.bio.symbol.AbstractLocation overlaps(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator overlaps(Location) - Method in class org.biojava.bio.symbol.CircularLocation overlaps(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation overlaps(Location) - Method in interface org.biojava.bio.symbol.Location Checks if these two locations overlap, using this location's concept of overlapping. overlaps(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation Checks if these two locations overlap, using this location's concept of overlapping. overlaps(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation Checks if these two locations overlap, using this location's concept of overlapping. overlaps(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation Checks if these two locations overlap, using this location's concept of overlapping. overlaps(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools Determines whether the locations overlap or not. overlapsLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils Construct a filter which matches features with locations contained by or overlapping the specified Location. OverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.OverlapsLocation Creates a filter that returns everything overlapping loc. overlapsOrigin() - Method in class org.biojava.bio.symbol.CircularLocation Does the Location overlap the origin (position 1) of the sequence? OverlapsRichLocation(RichLocation) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation Creates a filter that returns everything overlapping loc. OverlayAnnotation - Class in org.biojava.bio Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation. OverlayAnnotation(Annotation) - Constructor for class org.biojava.bio.OverlayAnnotation Construct an annotation which can overlay new key-value pairs onto an underlying annotation. OverlayAnnotation.PropertyForwarder - Class in org.biojava.bio Forwards change events from the underlying Annotation to this one. OverlayMap - Class in org.biojava.utils Overlap one map onto another. OverlayMap(Map) - Constructor for class org.biojava.utils.OverlayMap Build a new map with default key-value pairs. OverlayMap(Map, Map) - Constructor for class org.biojava.utils.OverlayMap Build a new map with default key-value pairs. OverlayMarker - Interface in org.biojava.bio.gui.sequence This is a dummy interface to permit identification of renderers whose output is to be overlaid along the lines of the Marker Interface pattern. OverlayRendererWrapper - Class in org.biojava.bio.gui.sequence This class wraps SequenceRenderer classes to present an Overlay Marker interface that will indicate to LayeredRenderer that subsequent renderers should overdraw the same space as the wrapped renderer. OverlayRendererWrapper() - Constructor for class org.biojava.bio.gui.sequence.OverlayRendererWrapper OverlayRendererWrapper(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.OverlayRendererWrapper P p() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Proline pack(Symbol) - Method in class org.biojava.bio.symbol.DNAAmbPack pack(Symbol) - Method in class org.biojava.bio.symbol.DNANoAmbPack pack(Symbol) - Method in interface org.biojava.bio.symbol.Packing Return a byte representing the packing of a symbol. PACKED - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory Accessor for a factory that produces builders that compress the SymbolList of a RichSequence. PackedSymbolList - Class in org.biojava.bio.symbol A SymbolList that stores symbols as bit-patterns in an array of longs. PackedSymbolList(Packing, long[], int) - Constructor for class org.biojava.bio.symbol.PackedSymbolList Create a new PackedSymbolList directly from a bit pattern. PackedSymbolList(Packing, Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.PackedSymbolList Create a new PackedSymbolList from an array of Symbols. PackedSymbolList(Packing, SymbolList) - Constructor for class org.biojava.bio.symbol.PackedSymbolList Create a new PackedSymbolList as a packed copy of another symbol list. PackedSymbolListFactory - Class in org.biojava.bio.symbol This class makes PackedSymbolLists. PackedSymbolListFactory() - Constructor for class org.biojava.bio.symbol.PackedSymbolListFactory Create a factory for PackedSymbolLists. PackedSymbolListFactory(boolean) - Constructor for class org.biojava.bio.symbol.PackedSymbolListFactory Deprecated. the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately. Packing - Interface in org.biojava.bio.symbol An encapsulation of the way symbols map to bit-patterns. PackingFactory - Class in org.biojava.bio.symbol A factory that is used to maintain associations between alphabets and preferred bit-packings for them. PackingFactory() - Constructor for class org.biojava.bio.symbol.PackingFactory PADDING - Static variable in class org.biojava.bio.gui.sequence.PaddingRenderer Event type for when the size of the padding changes. PaddingRenderer - Class in org.biojava.bio.gui.sequence A renderer that adds padding before and after a delegate renderer. PaddingRenderer() - Constructor for class org.biojava.bio.gui.sequence.PaddingRenderer Build a new PaddingRenderer with zero padding. PaddingRenderer(SequenceRenderer, double) - Constructor for class org.biojava.bio.gui.sequence.PaddingRenderer Build a new PaddingRenderer that wraps renderer and has padding depth padding. paint(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper paint(Graphics2D, List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularMLR paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularPaddedRenderer paint(Graphics2D, CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularRenderer Paint this renderer. paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer paint renders the feature as a simple line. paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer paint applies all renderers in the order in which they were added. paint(Graphics2D, PairwiseRenderContext) - Method in interface org.biojava.bio.gui.sequence.PairwiseSequenceRenderer paints some or all of the information about the sequence pair. paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer paint(Graphics2D, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox. paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in interface org.biojava.bio.gui.sequence.LabelRenderer Render a label for the information for sp to g. paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in interface org.biojava.bio.gui.BlockPainter paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in class org.biojava.bio.gui.PlainBlock paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in class org.biojava.bio.gui.TextBlock paintComponent(Graphics) - Method in class org.biojava.bio.gui.DistributionLogo Transforms the graphics context so that it is in bits space, and then requests the logo painter to fill the area. paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanel Paint this component. paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Paint this component. paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel paintComponent paints this component. paintComponent(Graphics) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier Renders this component to display the points, and if present, the support vector machine. paintLogo(LogoContext) - Method in class org.biojava.bio.gui.BarLogoPainter paintLogo(LogoContext) - Method in interface org.biojava.bio.gui.LogoPainter Render the state from sl onto the graphics object g. paintLogo(LogoContext) - Method in class org.biojava.bio.gui.StackedLogoPainter paintLogo(LogoContext) - Method in class org.biojava.bio.gui.TextLogoPainter PairDistribution - Class in org.biojava.bio.dist Class for pairing up two independant distributions. PairDistribution(Distribution, Distribution) - Constructor for class org.biojava.bio.dist.PairDistribution Create a new PairDistribution that represents the product of two other distributions. PairDPCursor - Interface in org.biojava.bio.dp.twohead A cursor over a DP matrix. PairDPMatrix - Class in org.biojava.bio.dp.twohead Storage structure for intermediate values from a pairwise dynamic programming run. PairDPMatrix(DP, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.twohead.PairDPMatrix PAIRWISE - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat pairwiseAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.AlignmentAlgorithm Performs a pairwise sequence alignment of the two given sequences. pairwiseAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.NeedlemanWunsch Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm. pairwiseAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.SmithWaterman Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment. PairwiseDiagonalRenderer - Class in org.biojava.bio.gui.sequence PairwiseDiagonalRenderer renders a region of similarity between two sequences as a straight line. PairwiseDiagonalRenderer() - Constructor for class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer Creates a new PairwiseDiagonalRenderer which will draw black lines. PairwiseDiagonalRenderer(Paint) - Constructor for class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer Creates a new PairwiseDiagonalRenderer which will draw lines using the specified Paint. PairwiseDP - Class in org.biojava.bio.dp.twohead Algorithms for dynamic programming (alignments) between pairs of SymbolLists. PairwiseDP(MarkovModel, CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.twohead.PairwiseDP PairwiseFilteringRenderer - Class in org.biojava.bio.gui.sequence PairwiseFilteringRenderer wraps a PairwiseSequenceRenderer and filters the PairwiseRenderContexts passed to it. PairwiseFilteringRenderer(PairwiseSequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer Creates a new PairwiseFilteringRenderer which uses a filter which accepts all features. PairwiseFilteringRenderer(PairwiseSequenceRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer Creates a new PairwiseFilteringRenderer. PairwiseOverlayRenderer - Class in org.biojava.bio.gui.sequence PairwiseOverlayRenderer allows a list of other PairwiseSequenceRenderers to superimpose their output. PairwiseOverlayRenderer() - Constructor for class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer Creates a new, empty PairwiseOverlayRenderer. PairwiseRenderContext - Interface in org.biojava.bio.gui.sequence PairwiseRenderContext encapsulates information required for the rendering of a pair of sequences. PairwiseRendererForwarder(PairwiseSequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder Creates a new PairwiseRendererForwarder. PairwiseSequencePanel - Class in org.biojava.bio.gui.sequence A PairwiseSequencePanel is a panel that displays a pair of sequences; one sequence (the primary) may be either left-to-right (HORIZONTAL) or from top-to-bottom (VERTICAL). PairwiseSequencePanel() - Constructor for class org.biojava.bio.gui.sequence.PairwiseSequencePanel Creates a new PairwiseSequencePanel with the default settings (primary sequence direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, secondary symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font). PairwiseSequenceRenderer - Interface in org.biojava.bio.gui.sequence PairwiseSequenceRenderers render information about the relationship between two sequences. PairwiseSequenceRenderer.PairwiseRendererForwarder - Class in org.biojava.bio.gui.sequence PairwiseRendererForwarder forward events to other renderers. PARAMETER - Static variable in interface org.biojava.bio.dp.MarkovModel Signals that one or more parameters have altered. ParametricCodeGenerator - Interface in org.biojava.utils.bytecode ParametricType - Class in org.biojava.utils.bytecode A template type. parent - Variable in class org.biojava.bio.taxa.SimpleTaxon Deprecated. parent - Variable in class org.biojava.bio.taxa.WeakTaxon Deprecated. parent() - Method in interface org.biojava.utils.automata.StateMachineInstance PARENT - Static variable in interface org.biojavax.bio.seq.RichFeature PARENT - Static variable in interface org.biojavax.bio.taxa.NCBITaxon parse(BufferedReader, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFParser Informs handler of each line of gff read from bReader. parse(BufferedReader, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.GFFParser Informs handler of each line of GFF read from bReader parse(BufferedReader, GFF3DocumentHandler, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser Informs handler of each line of gff read from bReader. parse(BufferedReader, GFF3DocumentHandler, Ontology, String) - Method in class org.biojava.bio.program.gff3.GFF3Parser Informs handler of each line of GFF read from bReader parse(BufferedReader, OntologyFactory) - Method in class org.biojava.ontology.io.TabDelimParser Parse an ontology from a reader. parse(File) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileParser Returns a profile HMM representing the core HMMER hmm parse(Object) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser parse(Object) - Method in class org.biojava.bio.program.tagvalue.RegexParser parse(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueParser parse(Readable, ParseListener) - Method in interface org.biojava.bio.program.fastq.FastqReader Parse the specified readable. parse(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade parse(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser parse(String) - Method in class org.biojava.naming.ObdaUriParser parse(TaxonFactory, String) - Method in class org.biojava.bio.taxa.EbiFormat Deprecated. parse(TaxonFactory, String) - Method in interface org.biojava.bio.taxa.TaxonParser Deprecated. Convert a stringified Taxon into a Taxon instance. parse(PHYLIPFileListener, BufferedReader) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat parse(InputSource) - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser parse initiates the parsing operation. parse(InputSource) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade parse(InputSource) - Method in class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser Describe 'parse' method here. parse(InputSource) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser parse(InputSource) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser Describe 'parse' method here. parse(InputSource) - Method in class org.biojava.bio.program.sax.PdbSAXParser Describe 'parse' method here. parse(InputSource) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser Describe 'parse' method here. parseAttribute(String) - Method in class org.biojava.bio.program.gff.GFFParser Parse attValList into a Map of attributes and value lists. parseAttribute(String, Annotation, Ontology, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser Parse attValList into a Map of attributes and value lists. parseAuthorString(String) - Static method in class org.biojavax.DocRefAuthor.Tools Takes a list of authors and returns a set of DocRefAuthor objects. parseComment(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Parses the comment string from the given comment and populates the internal fields appropriately. parseComment(Comment) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Parses the comment string from the given comment and populates the internal fields appropriately. ParseErrorEvent - Class in org.biojava.utils Event which signals a bad line when parsing a record. ParseErrorEvent(Object) - Constructor for class org.biojava.utils.ParseErrorEvent Construct a ParseErrorEvent with no other information. ParseErrorEvent(Object, String) - Constructor for class org.biojava.utils.ParseErrorEvent Construct a ParseErrorEvent with a message. ParseErrorListener - Interface in org.biojava.utils Listener for a ParseErrorEvent. ParseErrorSource - Interface in org.biojava.utils Source for a ParseErrorEvent. parseExample(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light ParseException - Exception in org.biojava.bio.seq.io ParseException should be thrown to indicate that there was a problem with parsing sequence information. ParseException() - Constructor for exception org.biojava.bio.seq.io.ParseException ParseException(String) - Constructor for exception org.biojava.bio.seq.io.ParseException ParseException(Throwable) - Constructor for exception org.biojava.bio.seq.io.ParseException ParseException(Throwable, String) - Constructor for exception org.biojava.bio.seq.io.ParseException parseFastqVariant(String) - Static method in enum org.biojava.bio.program.fastq.FastqVariant Return the FASTQ sequence format variant with the specified name, if any. parseFile(NexusFileListener, File) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat Parse a file and send events to the given listener. parseFile(PHYLIPFileListener, File) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat parseFull(File) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileParser Returns the full markov model - including the core model + J,C,N loop states. parseGO(BufferedReader, String, String, OntologyFactory) - Method in class org.biojava.ontology.io.GOParser parseInputStream(NexusFileListener, InputStream) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat Parse a stream and send events to the given listener. parseInputStream(PHYLIPFileListener, InputStream) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat ParseListener - Interface in org.biojava.bio.program.fastq Low-level event based parser callback. parseLocation(String) - Static method in class org.biojavax.bio.seq.io.UniProtLocationParser Parses a location. parseLocation(String, Feature.Template) - Method in class org.biojava.bio.seq.io.EmblLikeLocationParser Deprecated. parseLocation creates a Location from the String and returns a stranded location. parseLocation(Namespace, String, String) - Static method in class org.biojavax.bio.seq.io.GenbankLocationParser Parses a location. parseModel(File) - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser parseOBO(BufferedReader) - Method in class org.biojava.ontology.obo.OboFileParser parse an ontology file parseOBO(BufferedReader, String, String) - Method in class org.biojava.ontology.io.OboParser Parse a OBO file and return its content as a BioJava Ontology object Parser - Class in org.biojava.bio.program.tagvalue Encapsulate the parsing of lines from a buffered reader into tag-value events. Parser() - Constructor for class org.biojava.bio.program.tagvalue.Parser Parser(File) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser Parser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser parseReader(NexusFileListener, Reader) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat Parse a reader and send events to the given listener. parseReader(PHYLIPFileListener, Reader) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat parseRecord(byte[]) - Method in class org.biojava.utils.FileAsList parseRegistry(BufferedReader, String) - Static method in class org.biojava.directory.OBDARegistryParser parseRegistry parses an Open Bioinformatics Database Access (OBDA) configuration file. ParserException - Exception in org.biojava.utils Exception thrown when an error occurs in document parsing. ParserException(String) - Constructor for exception org.biojava.utils.ParserException ParserException(String, String) - Constructor for exception org.biojava.utils.ParserException ParserException(String, String, int) - Constructor for exception org.biojava.utils.ParserException ParserException(String, String, int, String) - Constructor for exception org.biojava.utils.ParserException ParserException(String, String, int, String, int) - Constructor for exception org.biojava.utils.ParserException ParserException(String, Throwable) - Constructor for exception org.biojava.utils.ParserException ParserException(Throwable) - Constructor for exception org.biojava.utils.ParserException ParserException(Throwable, String) - Constructor for exception org.biojava.utils.ParserException Deprecated. use new ParserException(detail, t) ParserException(Throwable, String, String) - Constructor for exception org.biojava.utils.ParserException ParserException(Throwable, String, String, int) - Constructor for exception org.biojava.utils.ParserException ParserException(Throwable, String, String, int, String) - Constructor for exception org.biojava.utils.ParserException ParserException(Throwable, String, String, int, String, int) - Constructor for exception org.biojava.utils.ParserException ParserListener - Class in org.biojava.bio.program.tagvalue ParserListener is an immutable pairing of a parser and listener. ParserListener(TagValueParser, TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.ParserListener Creates a new ParserListener instance. PARSERS - Static variable in interface org.biojava.bio.symbol.Alphabet This signals that the available parsers have changed. parseStrand(String) - Static method in class org.biojava.bio.seq.StrandParser parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.AlternateTokenization Will throw an exception. parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.CharacterTokenization parseStream(SeqIOListener) - Method in interface org.biojava.bio.seq.io.SymbolTokenization Return an object which can parse an arbitrary character stream into symbols. parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.WordTokenization parseStream(SeqIOListener) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization The current implementation only supports character parsing. parseString(String) - Method in class org.biojava.bio.seq.io.WordTokenization parseToken(String) - Method in class org.biojava.bio.seq.io.AlternateTokenization Will throw an exception. parseToken(String) - Method in class org.biojava.bio.seq.io.CharacterTokenization parseToken(String) - Method in class org.biojava.bio.seq.io.CrossProductTokenization parseToken(String) - Method in class org.biojava.bio.seq.io.DoubleTokenization parseToken(String) - Method in class org.biojava.bio.seq.io.IntegerTokenization parseToken(String) - Method in class org.biojava.bio.seq.io.NameTokenization parseToken(String) - Method in class org.biojava.bio.seq.io.SubIntegerTokenization parseToken(String) - Method in interface org.biojava.bio.seq.io.SymbolTokenization Returns the symbol for a single token. parseToken(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract parseToken(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser Notifies the parser of the next token. parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract parseToken(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener Encountered a token. parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockParser parseToken(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser parseTokenChar(char) - Method in class org.biojava.bio.seq.io.CharacterTokenization parseXML(InputStream) - Method in class org.biojava.bio.dist.XMLDistributionReader Reads an XML representation of a Distribution from a file. parseXref(String, int, int) - Method in class org.biojava.ontology.obo.OboFileParser ParsimonyTreeMethod - Class in org.biojavax.bio.phylo ParsimonyTreeMethod() - Constructor for class org.biojavax.bio.phylo.ParsimonyTreeMethod PART_OF - Static variable in class org.biojava.ontology.OntoTools PARTIAL_ORDER - Static variable in class org.biojava.ontology.OntoTools PATENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat pattern() - Method in class org.biojava.utils.regex.Matcher Returns the Pattern object that compiled this Matcher. Pattern - Class in org.biojava.utils.regex A class analogous to java.util.regex.Pattern but for SymbolLists. patternAsString() - Method in class org.biojava.utils.regex.Pattern returns the Pattern to be matched as a String. PatternBlitz - Class in org.biojava.utils.automata PatternBlitz(FiniteAlphabet, StateMachineToolkit) - Constructor for class org.biojava.utils.automata.PatternBlitz patternExpanded() - Method in class org.biojava.utils.regex.Pattern returns the actual String used to construct the regex with all ambiguities expanded. PatternFactory - Class in org.biojava.utils.regex A class that creates Patterns for regex matching on SymbolLists of a specific Alphabet. PatternListener - Interface in org.biojava.utils.automata PatternMaker - Class in org.biojava.utils.automata pcs - Variable in class org.biojava.bio.gui.sequence.SequencePanel.Border pcs - Variable in class org.biojava.bio.gui.sequence.SequencePoster.Border Deprecated. PDB - Static variable in class org.biojava.bio.seq.io.SeqIOConstants PDB indicates that the sequence format is PDB. PdbSAXParser - Class in org.biojava.bio.program.sax A SAX2 parser for dealing with native PDB files. PdbSAXParser() - Constructor for class org.biojava.bio.program.sax.PdbSAXParser Sets namespace prefix to "biojava" PdbToXMLConverter - Class in org.biojava.bio.program A class that converts Protein Data Bank (PDB) to XML that will validate against the biojava:MacromolecularStructure DTD. PdbToXMLConverter(String) - Constructor for class org.biojava.bio.program.PdbToXMLConverter Creates a new BlastToXMLConverter instance. PEPTIDE_FEATURE_TYPE - Static variable in class org.biojava.bio.proteomics.Digest PeptideDigestRenderer - Class in org.biojava.bio.gui.sequence A concrete AbstractPeptideDigestRenderer. PeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer PeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer PeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer PERCENTIDENTITY - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross performCrossOver(SymbolList, SymbolList) - Method in interface org.biojavax.ga.functions.CrossOverFunction Performs a cross between the pair of chromosomes performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.OrderCrossover performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.SimpleCrossOverFunction PERSON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat pFromQuality(double) - Static method in class org.biojava.bio.program.phred.PhredTools Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10) pFromQuality(int) - Static method in class org.biojava.bio.program.phred.PhredTools Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10) pFromQuality(IntegerAlphabet.IntegerSymbol) - Static method in class org.biojava.bio.program.phred.PhredTools Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10) phe() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Phenylalanine (F) PHRED - Static variable in class org.biojava.bio.seq.io.SeqIOConstants PHRED indicates that the sequence format is PHRED. phredAlignmentToDistArray(Alignment) - Static method in class org.biojava.bio.program.phred.PhredTools converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment. PhredFormat - Class in org.biojava.bio.program.phred Format object representing Phred Quality files. PhredFormat() - Constructor for class org.biojava.bio.program.phred.PhredFormat PhredSequence - Class in org.biojava.bio.program.phred PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores. PhredSequence(SymbolList, String, String, Annotation) - Constructor for class org.biojava.bio.program.phred.PhredSequence Constructs a new PhredSequence. phredToDistArray(PhredSequence) - Static method in class org.biojava.bio.program.phred.PhredTools Converts a Phred sequence to an array of distributions. PhredTools - Class in org.biojava.bio.program.phred PhredTools contains static methods for working with phred quality data. PhredTools() - Constructor for class org.biojava.bio.program.phred.PhredTools PHYLIPFileBuilder - Class in org.biojavax.bio.phylo.io.phylip Builds a PHYLIP file by listening to events. PHYLIPFileBuilder() - Constructor for class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder PHYLIPFileFormat - Class in org.biojavax.bio.phylo.io.phylip Reads PHYLIP interleaved alignment files and fires events at a PHYLIPFileListener object. PHYLIPFileListener - Interface in org.biojavax.bio.phylo.io.phylip Listens to events fired by the PHYLIP parser. PK - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable PK_Cterm - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable PK_Nterm - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable PlainBlock - Class in org.biojava.bio.gui A painter that just draws a block (or bar). PlainBlock() - Constructor for class org.biojava.bio.gui.PlainBlock PlainStyle - Class in org.biojava.bio.gui A simple implementation of SymbolStyle that just uses a single paint for outlines and a single paint for filling. PlainStyle() - Constructor for class org.biojava.bio.gui.PlainStyle PlainStyle(Paint, Paint) - Constructor for class org.biojava.bio.gui.PlainStyle PLASMID_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms point - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer point is the current location (in sequence coordinates) of the crosshair in the X and Y sequences. PointClassifier() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier Make a new PointClassifier. PointLocation - Class in org.biojava.bio.symbol A location representing a single point. PointLocation(int) - Constructor for class org.biojava.bio.symbol.PointLocation POLY - Static variable in interface org.biojava.bio.gui.sequence.ImageMap POLY indicates a polygonal image map hotspot. polyKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier PolynomialKernel - Class in org.biojava.stats.svm This kernel computes all possible products of order features in feature space. PolynomialKernel() - Constructor for class org.biojava.stats.svm.PolynomialKernel PolynomialKernel(SVMKernel, double, double, double) - Constructor for class org.biojava.stats.svm.PolynomialKernel POMBE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools Schizosaccharomyces pombe codon preferences pop() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler pop a StAXContentHandler off the stack. pop() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler pop a StAXContentHandler off the stack. populate(Feature.Template, Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils This attempts to populate the fields of a template using the publically accessible information in a feature. population - Variable in class org.biojavax.ga.impl.AbstractGeneticAlgorithm Population - Interface in org.biojavax.ga A collection of GA organisms POPULATION - Static variable in interface org.biojavax.ga.GeneticAlgorithm pos - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor pos - Variable in class org.biojava.bio.symbol.Edit posInSeq(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment get the position in the sequence corresponding to the postion within the alignment position() - Method in class org.biojava.utils.io.LargeBuffer position(long) - Method in class org.biojava.utils.io.LargeBuffer Position - Interface in org.biojavax.bio.seq Holds info about base positions. PositionResolver - Interface in org.biojavax.bio.seq Resolves a position that is fuzzy or covers a range of bases by converting it to a single base. PositionResolver.AverageResolver - Class in org.biojavax.bio.seq The minimal resolver returns the base which provides the average range, halfway between maximal and minimal. PositionResolver.MaximalResolver - Class in org.biojavax.bio.seq The maximal resolver returns the base which provides the largest possible range. PositionResolver.MinimalResolver - Class in org.biojavax.bio.seq The minimal resolver returns the base which provides the smallest possible range. POSITIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature Flag to indicate that a feature is on the positive strand. POSITIVE_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand The positive strand is represented by the symbol '+' and has the number 1. posmax(Position, Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation posmin(Position, Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation postalAddress - Variable in class org.biojava.bibliography.BiblioPerson Their postal address. postChange(ChangeEvent) - Method in class org.biojava.bio.symbol.SimpleSymbolList postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeAdapter postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.AlwaysVetoListener postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.LoggingListener postChange(ChangeEvent) - Method in interface org.biojava.utils.ChangeListener Called when a change has just taken place. PostgreSQLDBHelper - Class in org.biojava.bio.seq.db.biosql PostgreSQLDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper PParametricCodeGenerator - Interface in org.biojava.utils.bytecode preChange(ChangeEvent) - Method in class org.biojava.bio.symbol.SimpleSymbolList On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeAdapter preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.AlwaysVetoListener preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.ChangeEventRecorder preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.LoggingListener preChange(ChangeEvent) - Method in interface org.biojava.utils.ChangeListener Called before a change takes place. press() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor press() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor Returns the minimal context of the DP matrix necessary to compute the value of a single point in that matrix. press() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor press out a new correctly sized cell array PrettyXMLWriter - Class in org.biojava.utils.xml Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter. PrettyXMLWriter(PrintWriter) - Constructor for class org.biojava.utils.xml.PrettyXMLWriter PRIMARY_KEY_NAME - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory PRIMARY_KEY_NAME is the key used to identify the primary namespace in the OBDA config.dat files. PRIME - Static variable in class org.biojava.utils.ObjectUtil the current hashCode is always first multiplied with this prime before the hashCode value for a particular field is added. primeWord(SymbolList, int, Packing) - Static method in class org.biojava.bio.symbol.PackingFactory print(String) - Method in class org.biojava.utils.xml.FastXMLWriter print(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter print(String) - Method in interface org.biojava.utils.xml.XMLWriter Prints some textual content in an element. printAttributeValue(String) - Method in class org.biojava.utils.xml.FastXMLWriter printAttributeValue(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter printChars(String) - Method in class org.biojava.utils.xml.FastXMLWriter printChars(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter printCostMatrix(int[][], char[], char[]) - Static method in class org.biojava.bio.alignment.NeedlemanWunsch Prints a String representation of the CostMatrix for the given Alignment on the screen. println(String) - Method in class org.biojava.utils.xml.FastXMLWriter println(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter println(String) - Method in interface org.biojava.utils.xml.XMLWriter Prints some textual content, terminated with a newline character. printMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix Just to perform some test. printOutSequenceHeaderLine(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer Deprecated. Prints out sequence header with only length data. printRaw(String) - Method in class org.biojava.utils.xml.FastXMLWriter printRaw(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter printRaw(String) - Method in interface org.biojava.utils.xml.XMLWriter Send raw data to the stream. printRemoteBlastInfo() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService A simple method to check the availability of the QBlast service printTree() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree priority - Variable in class org.biojava.utils.SimpleThreadPool pro() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Proline (P) PROB_NUC_A - Static variable in class org.biojava.bio.program.scf.SCF Base call alignment sequence label for the probability that call should be A. PROB_NUC_C - Static variable in class org.biojava.bio.program.scf.SCF Base call alignment sequence label for the probability that call should be C. PROB_NUC_G - Static variable in class org.biojava.bio.program.scf.SCF Base call alignment sequence label for the probability that call should be G. PROB_NUC_T - Static variable in class org.biojava.bio.program.scf.SCF Base call alignment sequence label for the probability that call should be T. PROB_OVERCALL - Static variable in class org.biojava.bio.program.scf.SCF Base call alignment sequence label for the overcall probability. PROB_SUBSTITUTION - Static variable in class org.biojava.bio.program.scf.SCF Base call alignment sequence label for the substitution probability. PROB_UNDERCALL - Static variable in class org.biojava.bio.program.scf.SCF Base call alignment sequence label for the undercall probability. Probability() - Constructor for class org.biojava.bio.dp.ScoreType.Probability PROBABILITY - Static variable in interface org.biojava.bio.dp.ScoreType processDB(SequenceDB, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF Process all Sequences within a SequenceDB, informing handler of any suitable features. processFeatureFilter(FeatureFilter) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB processHeader(String, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat Parse the Header information from the Fasta Description line processingInstruction(String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter processingInstruction(String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor processingInstruction(String, String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler processingInstruction(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase processingInstruction(String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor processingInstruction(String, String) - Method in interface org.biojava.utils.stax.StAXContentHandler processingInstruction(String, String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase processMouseEvent(List, MouseEvent, List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer processMouseEvent processes any MouseEvents directed to the renderer. processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer processMouseEvent acts on a mouse gesture. processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer processMouseEvent produces a SequenceViewerEvent in response to a mouse gesture. processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in interface org.biojava.bio.gui.sequence.PairwiseSequenceRenderer processMouseEvent produces a SequenceViewerEvent in response to a mouse gesture. processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.RulerRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer Produce a SequenceViewerEvent in response to a mouse gesture. processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.StopRenderer processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer processMouseEvent defines the behaviour on revieving a mouse event. processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer processSequence(Sequence, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF Process an individual Sequence, informing handler of any suitable features. processSequenceLine(String, StreamParser) - Method in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. Dispatch symbol data from SQ-block line of an EMBL-like file. ProcessTimeoutException - Exception in org.biojava.utils Exception which is thrown if a child process managed by ProcessTools exceeds a specified time limit. ProcessTimeoutException(int) - Constructor for exception org.biojava.utils.ProcessTimeoutException ProcessTimeoutException(int, String) - Constructor for exception org.biojava.utils.ProcessTimeoutException ProcessTools - Class in org.biojava.utils Deprecated. preferable to use org.biojava.utils.ExecRunner or the org.biojava.utils.process package. ProfileEmissionState - Class in org.biojava.bio.program.hmmer A state in a HMMer model. ProfileEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.program.hmmer.ProfileEmissionState ProfileHMM - Class in org.biojava.bio.dp ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory) - Constructor for class org.biojava.bio.dp.ProfileHMM Deprecated. ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory, String) - Constructor for class org.biojava.bio.dp.ProfileHMM Create a new ProfileHMM. PROJ_ACC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat projectChildFeatures(Feature, FeatureHolder) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext projectChildFeatures(Feature, FeatureHolder) - Method in interface org.biojava.bio.seq.projection.ProjectionContext Project all features that are children of feature so that they become children of parent. projectChildFeatures(Feature, FeatureHolder) - Method in class org.biojava.bio.seq.projection.ReparentContext ProjectedFeature - Class in org.biojava.bio.seq.projection Internal class used by ProjectionEngine to wrap Feature objects. ProjectedFeature(Feature, ProjectionContext) - Constructor for class org.biojava.bio.seq.projection.ProjectedFeature ProjectedFeatureHolder - Class in org.biojava.bio.seq.projection Helper class for projecting Feature objects into an alternative coordinate system. ProjectedFeatureHolder(ProjectionContext) - Constructor for class org.biojava.bio.seq.projection.ProjectedFeatureHolder projectFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext projectFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext Project a single feature. projectFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext Create a single projected feature using the rules of this ProjectedFeatureHolder. projectFeature(Feature, ProjectionContext) - Method in class org.biojava.bio.seq.projection.ProjectionEngine Return a projection of Feature f into the system defined by a given ProjectionContext. projectFeatures(FeatureHolder) - Method in interface org.biojava.bio.seq.projection.ProjectionContext Project all of the features in a FeatureHolder. projectFeatures(FeatureHolder) - Method in class org.biojava.bio.seq.projection.ReparentContext projectFilter(FeatureFilter) - Method in interface org.biojava.bio.seq.projection.ProjectionContext Transform a filter on unprojected features so that it applies to projected features. projectFilter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ReparentContext Projection - Interface in org.biojava.bio.seq.projection Interface implemented by all projected feature objects. ProjectionContext - Interface in org.biojava.bio.seq.projection Interface that defines the projection between original features and projected features. ProjectionEngine - Class in org.biojava.bio.seq.projection Factory for proxy objects which project BioJava features into alternate coordinate systems. ProjectionEngine.Instantiator - Interface in org.biojava.bio.seq.projection Internal helper class. ProjectionEngine.TemplateProjector - Interface in org.biojava.bio.seq.projection This is an interface for things that project feature templates. ProjectionUtils - Class in org.biojava.bio.seq.projection Some common things you want to do while projecting features. ProjectionUtils() - Constructor for class org.biojava.bio.seq.projection.ProjectionUtils projectLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext projectLocation(Location) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext projectLocation(Location) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext projectStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext PROP_CASE_SENSITIVE - Static variable in interface org.biojava.utils.candy.CandyVocabulary A property name. PROP_CRITERIONS - Static variable in interface org.biojava.bibliography.BibRefQuery A property name specifying a list of searching and ordering criteria names (type of the property value should be String[]). PROP_ENTRY_COUNT - Static variable in interface org.biojava.utils.candy.CandyVocabulary A property name. PROP_EXCLUDED_ATTRS - Static variable in interface org.biojava.bibliography.BibRefQuery A property name specifying a list of excluded attribute names (the type of the property value should be String[]). PROP_VOCAB_DESC - Static variable in interface org.biojava.utils.candy.CandyVocabulary A property name. PROP_VOCAB_NAME - Static variable in interface org.biojava.utils.candy.CandyVocabulary A property name. PROP_VOCAB_VERSION - Static variable in interface org.biojava.utils.candy.CandyVocabulary A property name. PROP_VOCABULARY - Static variable in interface org.biojava.utils.candy.CandyFinder A property name. PROP_VOCABULARY - Static variable in interface org.biojava.utils.candy.CandyVocabulary A property name. PROPDETAIL_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.PropDetailHandler PropDetailHandler - Class in org.biojava.bio.program.xff StAX handler for xff:prop detail elements. PropDetailHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.PropDetailHandler properties - Variable in class org.biojava.bibliography.BiblioEntryStatus The dynamic properties may be used to add features related to the citation itself. properties - Variable in class org.biojava.bibliography.BiblioJournal Additional properties used when the explicit attributes are not sufficient. properties - Variable in class org.biojava.bibliography.BiblioProvider Additional properties used when the explicit attributes of the sub-classes are not sufficient. properties - Variable in class org.biojava.bibliography.BiblioScope It may contain additional properties related to the extend or scope of the cited resource. properties - Variable in class org.biojava.bibliography.BibRef Additional attributes of this citation. propertiesAllocated() - Method in class org.biojava.bio.AbstractAnnotation A convenience method to see if we have allocated the properties Map. propertiesAllocated() - Method in class org.biojava.bio.AnnotationChanger propertiesAllocated is a convenience method to see if we have allocated the properties Map. propertiesAllocated() - Method in class org.biojava.bio.AnnotationRenamer propertiesAllocated Javadoc FIXME - this overrides a protected method and I'm not sure why (KJ). propertiesAllocated() - Method in class org.biojava.bio.BeanAsAnnotation propertiesAllocated() - Method in class org.biojava.bio.seq.io.ReferenceAnnotation Deprecated. propertiesAllocated() - Method in class org.biojava.bio.SimpleAnnotation Test to see if any properties have been allocated propertiesAllocated() - Method in class org.biojava.bio.SmallAnnotation PROPERTY - Static variable in interface org.biojava.bio.Annotation This type symbolizes that one or more properties have changed. PROPERTY_DATA_KEY - Static variable in interface org.biojava.bio.seq.Feature This is used as a key in the Annotation where it identifies internal data. PROPERTY_DESCRIPTIONLINE - Static variable in class org.biojava.bio.program.phred.PhredFormat Constant string which is the property key used to notify listeners of the description lines of Phred sequences. PROPERTY_DESCRIPTIONLINE - Static variable in class org.biojava.bio.seq.io.FastaFormat Deprecated. Constant string which is the property key used to notify listeners of the description lines of FASTA sequences. PROPERTY_EMBL_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.EmblProcessor Deprecated. PROPERTY_GENBANK_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.GenbankProcessor Deprecated. PROPERTY_GFF_SCORE - Static variable in class org.biojava.bio.program.gff.GFFEntrySet PROPERTY_NCBI_TAXON - Static variable in class org.biojava.bio.taxa.EbiFormat Deprecated. PROPERTY_ORGANISM - Static variable in class org.biojava.bio.seq.io.OrganismParser Deprecated. PROPERTY_SWISSPROT_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor Deprecated. PROPERTY_SWISSPROT_COMMENT - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor Deprecated. PROPERTY_SWISSPROT_FEATUREATTRIBUTE - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor Deprecated. PROPERTY_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat PROPERTY_TAXON_NAMES - Static variable in class org.biojava.bio.taxa.EbiFormat Deprecated. PROPERTY_XFF_ID - Static variable in class org.biojava.bio.program.xff.XFFFeatureSetHandler PropertyChanger - Interface in org.biojava.bio.program.tagvalue Interface for objects that change tag names or properties systematically. PropertyConstraint - Interface in org.biojava.bio PropertyConstraints describes a constraint applied to the members of an annotation bundle. PropertyConstraint.And - Class in org.biojava.bio A property constraint that accpepts items iff they are accepted by both child constraints. PropertyConstraint.ByAnnotationType - Class in org.biojava.bio ByAnnotationType accepts a property value if it belongs to type defined by AnnotationType. PropertyConstraint.ByClass - Class in org.biojava.bio ByClass accepts a property value if it is an instance of a specific Java class. PropertyConstraint.Enumeration - Class in org.biojava.bio Enumeration accepts a property if it is present in the specified set of values. PropertyConstraint.ExactValue - Class in org.biojava.bio Matches properties if they have exactly this one value. PropertyConstraint.Or - Class in org.biojava.bio A property constraint that accepts items iff they are accepted by either child constraints. PropertyForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.MergeAnnotation.PropertyForwarder Create a new forwarder on behalf of a source using the change support. PropertyForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.OverlayAnnotation.PropertyForwarder Forward on behalf of source using the change support provided. PropertyWriter - Class in org.biojava.bio.program.xff PropertyWriter() - Constructor for class org.biojava.bio.program.xff.PropertyWriter ProportionalSelection - Class in org.biojavax.ga.functions A Selection function that determines the proportion of individuals in a new population proportionally to their fitness. ProportionalSelection() - Constructor for class org.biojavax.ga.functions.ProportionalSelection props - Variable in class org.biojava.bio.symbol.Edit Protease - Class in org.biojava.bio.proteomics The protease class stores parameters needed by Digest to digest a protein sequence. Protease(String, boolean) - Constructor for class org.biojava.bio.proteomics.Protease Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) Protease(String, boolean, String) - Constructor for class org.biojava.bio.proteomics.Protease Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) Protease(SymbolList, boolean, SymbolList) - Constructor for class org.biojava.bio.proteomics.Protease Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) Protease(SymbolList, boolean, SymbolList, String) - Constructor for class org.biojava.bio.proteomics.Protease ProteaseManager - Class in org.biojava.bio.proteomics Registry and utility methods for Proteases. ProteaseManager() - Constructor for class org.biojava.bio.proteomics.ProteaseManager PROTEIN - Static variable in class org.biojava.bio.seq.io.FastaAlignmentFormat PROTEIN_ALPHABET - Static variable in class org.biojava.bio.proteomics.aaindex.AAindex The alphabet of the symbol property table, that is protein. PROTEIN_EXIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat PROTEIN_EXISTS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat PROTEIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat PROTEIN_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat ProteinRefSeqFileFormer - Class in org.biojava.bio.seq.io Deprecated. Use org.biojavax.bio.seq.io framework instead ProteinRefSeqFileFormer() - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqFileFormer Deprecated. ProteinRefSeqFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqFileFormer Deprecated. ProteinRefSeqProcessor - Class in org.biojava.bio.seq.io Deprecated. Use org.biojavax.bio.seq.io framework instead ProteinRefSeqProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqProcessor Deprecated. ProteinRefSeqProcessor.Factory - Class in org.biojava.bio.seq.io Deprecated. Factory which wraps sequence builders in a ProteinRefSeqProcessor ProteinTools - Class in org.biojava.bio.seq The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet. PROVIDER_ORGANISATION - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a provider type. PROVIDER_PERSON - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a provider type. PROVIDER_SERVICE - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a provider type. ProviderNotFoundException - Exception in org.biojava.directory ProviderNotFoundException is thrown when a sequence database provider can not be located. ProviderNotFoundException() - Constructor for exception org.biojava.directory.ProviderNotFoundException Creates a ProviderNotFoundException with no detail message. ProviderNotFoundException(String) - Constructor for exception org.biojava.directory.ProviderNotFoundException Creates a ProviderNotFoundException with the specified detail message. PTM - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser A name for a comment type. ptr - Variable in class org.biojava.utils.io.CachingInputStream The 0-based index into cache of the _next_ byte to return. publisher - Variable in class org.biojava.bibliography.BibRef A publisher is responsible for making the resource available. PUBMED_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms Holds a reference to the key that must be used to store PubMed references. PUBMED_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. PUBMED_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat PUBMED_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat push(StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler Push StAXContentHandler object onto stack push(StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler Push StAXContentHandler object onto stack pushParser(TagValueParser, TagValueListener) - Method in interface org.biojava.bio.program.tagvalue.TagValueContext Push a parser and listener pair onto the parser stack. put(byte) - Method in class org.biojava.utils.io.LargeBuffer put(int, double) - Method in class org.biojava.stats.svm.SparseVector Set the value at a particular dimension. put(long, byte) - Method in class org.biojava.utils.io.LargeBuffer put(Object, Object) - Method in class org.biojava.utils.BeanAsMap put(Object, Object) - Method in interface org.biojava.utils.cache.CacheMap Associate a value with a key. put(Object, Object) - Method in class org.biojava.utils.cache.ChangeableCache put(Object, Object) - Method in class org.biojava.utils.cache.FixedSizeMap put(Object, Object) - Method in class org.biojava.utils.cache.WeakCacheMap put(Object, Object) - Method in class org.biojava.utils.cache.WeakValueHashMap put(Object, Object) - Method in class org.biojava.utils.io.SoftHashMap Here we put the key, value pair into the HashMap using a SoftValue object. put(Object, Object) - Method in class org.biojava.utils.OverlayMap put(Object, Object) - Method in class org.biojava.utils.SmallMap put(Object, StateMachine.Transition) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable set a Transition within this TransitionTable (2-argument form) put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML put(CodonPref) - Method in interface org.biojava.bio.symbol.CodonPrefFilter handles storage of a CodonPref object putChar(char) - Method in class org.biojava.utils.io.LargeBuffer putChar(long, char) - Method in class org.biojava.utils.io.LargeBuffer putComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList putComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList putComponent(Location, SymbolList) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList putConnection(Connection) - Method in class org.biojava.utils.JDBCConnectionPool putDouble(double) - Method in class org.biojava.utils.io.LargeBuffer putDouble(long, double) - Method in class org.biojava.utils.io.LargeBuffer putFloat(float) - Method in class org.biojava.utils.io.LargeBuffer putFloat(long, float) - Method in class org.biojava.utils.io.LargeBuffer putInt(int) - Method in class org.biojava.utils.io.LargeBuffer putInt(long, int) - Method in class org.biojava.utils.io.LargeBuffer putLong(long) - Method in class org.biojava.utils.io.LargeBuffer putLong(long, long) - Method in class org.biojava.utils.io.LargeBuffer putShort(long, short) - Method in class org.biojava.utils.io.LargeBuffer putShort(short) - Method in class org.biojava.utils.io.LargeBuffer putStatement(Statement) - Method in class org.biojava.utils.JDBCConnectionPool putTaxon(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Adds a Taxon (along with its parents) to the database. putTokenization(String, SymbolTokenization) - Method in class org.biojava.bio.symbol.AbstractAlphabet Assigns a symbol parser to a String object. pyl() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Pyrrolysine (O) Q q() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Glutamine QUALIFIER - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty QUALIFIER_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat QUALIFIER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat Qualitative - Interface in org.biojava.bio.program.phred Qualitative is an interface for classes wanting to hold quality data in symbolic form such as Phred scores. QualitativeAlignment - Interface in org.biojava.bio.alignment quality(int) - Method in enum org.biojava.bio.program.fastq.FastqVariant Convert the specified quality score to a quality in ASCII format. quality(String) - Method in interface org.biojava.bio.program.fastq.ParseListener Notify this listener of a quality line. QUALITY - Static variable in class org.biojava.bio.program.abi.ABITools The quality alphabet. qualityAt(Object, int) - Method in interface org.biojava.bio.alignment.QualitativeAlignment Returns a quality score for label/position qualityFromP(double) - Static method in class org.biojava.bio.program.phred.PhredTools The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ) where P_e is the probability that the base call is an error. qualityScore(char) - Method in enum org.biojava.bio.program.fastq.FastqVariant Convert the specified quality in ASCII format to a quality score. qualityScore(double) - Method in enum org.biojava.bio.program.fastq.FastqVariant Convert the specified error probability to a quality score. qualityScores(Fastq) - Static method in class org.biojava.bio.program.fastq.FastqTools Return the quality scores from the specified FASTQ formatted sequence. qualityScores(Fastq, int[]) - Static method in class org.biojava.bio.program.fastq.FastqTools Copy the quality scores from the specified FASTQ formatted sequence into the specified int array. query(String, Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery It queries the current collection using a query language. QUERY_ANCHORED - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat QUERY_ANCHORED_NO_IDENTITIES - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat QUERY_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion A query criterion. QUERY_LABEL - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit This object is used as the label for the query sequence in the alignment of the query sequence with this sub-hit sequence. QUERY_LABEL - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature Constant QUERY_LABEL is the alignment label used for all query sequences. querySeqHolder - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory queryViewCache - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory R r() - Static method in class org.biojava.bio.seq.DNATools r() - Static method in class org.biojava.bio.seq.NucleotideTools r() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Arginine R_NORVEGICUS - Static variable in interface org.biojava.bio.program.homologene.Taxon RadialBaseKernel - Class in org.biojava.stats.svm This kernel computes the radial base kernel that corresponds to a gausian distribution. RadialBaseKernel() - Constructor for class org.biojava.stats.svm.RadialBaseKernel RadialBaseKernel(SVMKernel, double) - Constructor for class org.biojava.stats.svm.RadialBaseKernel RAF - Class in org.biojava.utils.io RAF(File, String) - Constructor for class org.biojava.utils.io.RAF RAF(String, String) - Constructor for class org.biojava.utils.io.RAF raIndexFile - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess RandomAccessReader - Class in org.biojava.utils.io RandomAccessReader extends Reader to provide a means to create buffered Readers from RandomAccessFiles. RandomAccessReader(RandomAccessFile) - Constructor for class org.biojava.utils.io.RandomAccessReader Creates a new RandomAccessReader wrapping the RandomAccessFile and using a default-sized buffer (8192 bytes). RandomAccessReader(RandomAccessFile, int) - Constructor for class org.biojava.utils.io.RandomAccessReader Creates a new RandomAccessReader wrapping the RandomAccessFile and using a buffer of the specified size. randomizeDistribution(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools Randomizes the weights of a Distribution. RangeLocation - Class in org.biojava.bio.symbol A simple implementation of Location that contains all points between getMin and getMax inclusive. RangeLocation(int, int) - Constructor for class org.biojava.bio.symbol.RangeLocation Construct a new RangeLocation from min to max. RANK - Static variable in interface org.biojavax.bio.BioEntryRelationship RANK - Static variable in interface org.biojavax.bio.seq.RichFeature RANK - Static variable in interface org.biojavax.bio.seq.RichFeatureRelationship RANK - Static variable in interface org.biojavax.bio.seq.RichLocation RANK - Static variable in interface org.biojavax.Comment RANK - Static variable in interface org.biojavax.Note RANK - Static variable in interface org.biojavax.RankedCrossRef RANK - Static variable in interface org.biojavax.RankedDocRef RankedCrossRef - Interface in org.biojavax Allows cross-references to other databases to be ranked. RANKEDCROSSREF - Static variable in interface org.biojavax.bio.BioEntry RANKEDCROSSREF - Static variable in interface org.biojavax.ontology.ComparableTerm RankedCrossRefable - Interface in org.biojavax Defines an object as being able to have ranked cross references associated with it. rankedCrossRefs - Variable in class org.biojavax.bio.seq.RichFeature.Template RankedDocRef - Interface in org.biojavax Represents a documentary reference. RANKEDDOCREF - Static variable in interface org.biojavax.bio.BioEntry RAT_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools Rattus norvegicus codon preferences RATIO - Static variable in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer Constant RATIO indicating a change to the minimum allowed ratio of long axis to short axis of the features. RAW - Static variable in class org.biojava.bio.seq.io.AlignIOConstants RAW indicates that the alignment format is raw (symbols only). RAW - Static variable in class org.biojava.bio.seq.io.SeqIOConstants RAW indicates that the sequence format is raw (symbols only). RAW_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants RAW_AA premade RAW | AA. RAW_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants RAW_DNA premade RAW | DNA. RAW_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants RAW_RNA premade RAW | RNA. rawGet(int) - Method in class org.biojava.utils.FileAsList rawGet reads the record at the specified index as a raw byte array. rbfKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier RC_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat RC_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat RC_PLASMID_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat RC_SPECIES_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat RC_STRAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat RC_TISSUE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat RC_TRANSP_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat Reaction() - Constructor for class org.biojava.bio.program.formats.Ligand.Reaction read() - Method in class org.biojava.utils.io.CachingInputStream read() - Method in class org.biojava.utils.io.CountedBufferedReader read() - Method in class org.biojava.utils.io.RandomAccessReader read reads one byte from the underlying RandomAccessFile. read() - Method in class org.biojava.utils.io.UncompressInputStream read() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener read(byte[], int, int) - Method in class org.biojava.utils.io.CachingInputStream read(byte[], int, int) - Method in class org.biojava.utils.io.UncompressInputStream read(char[]) - Method in class org.biojava.utils.io.CountedBufferedReader read(char[], int, int) - Method in class org.biojava.utils.io.CountedBufferedReader read(char[], int, int) - Method in class org.biojava.utils.io.RandomAccessReader read reads from the underlying RandomAccessFile into an array. read(BufferedReader) - Method in interface org.biojava.bio.seq.io.AlignmentFormat Read in an alignment from a buffered reader object read(BufferedReader) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat Reads an alignment in FASTA format. read(BufferedReader) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat Reads an MSF Alignment File read(BufferedReader, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.Parser read(File) - Method in interface org.biojava.bio.program.fastq.FastqReader Read zero or more FASTQ formatted sequences from the specified file. read(InputStream) - Method in interface org.biojava.bio.program.fastq.FastqReader Read zero or more FASTQ formatted sequences from the specified input stream. read(URL) - Method in interface org.biojava.bio.program.fastq.FastqReader Read zero or more FASTQ formatted sequences from the specified url. readableFileNames - Static variable in class org.biojavax.bio.seq.io.EMBLFormat readableFiles - Static variable in class org.biojavax.bio.seq.io.FastaFormat readableFiles - Static variable in class org.biojavax.bio.seq.io.GenbankFormat readColourMap() - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler Read the the properties file that specifies the character/colour mapping. readColourMapFromProperties(String) - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler Setup styles from java property file. readDBDate() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader readDBDate reads the date from the index header. readDBName() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader readDBName returns the database name from the index header. readDBRelease() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader readDBRelease returns the database release from the index header. readEmbl(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Iterate over the sequences in an EMBL-format stream. readEMBL(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Read a EMBL file using a custom type of SymbolList. readEMBLDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an EMBL-format stream of DNA sequences. readEmblNucleotide(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Iterate over the sequences in an EMBL-format stream. readEMBLProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an EMBL-format stream of Protein sequences. readEmblRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Iterate over the sequences in an EMBL-format stream, but for RNA. readEMBLRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an EMBL-format stream of RNA sequences. readEMBLxml(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Read a EMBLxml file using a custom type of SymbolList. readEMBLxmlDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an EMBLxml-format stream of DNA sequences. readEMBLxmlProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an EMBLxml-format stream of Protein sequences. readEMBLxmlRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an EMBLxml-format stream of RNA sequences. ReaderInputHandler - Class in org.biojava.utils.process Reader input handler that reads the input for an external process from a reader. ReaderInputHandler(Reader, String) - Constructor for class org.biojava.utils.process.ReaderInputHandler Initializes the reader input handler. ReaderWriterPipe - Class in org.biojava.utils.process A multi threaded class which pipes the contents of an input reader to an output writer. ReaderWriterPipe(Reader, Writer, String) - Constructor for class org.biojava.utils.process.ReaderWriterPipe Initializes the reader writer pipe. readFasta(BufferedReader, SymbolTokenization) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Read a fasta file. readFasta(BufferedReader, SymbolTokenization, SequenceBuilderFactory) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Read a fasta file using a custom type of SymbolList. readFasta(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Read a fasta file building a custom type of RichSequence . readFasta(BufferedReader, SymbolTokenization, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Read a fasta file. readFasta(InputStream, Alphabet) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Create a sequence database from a fasta file provided as an input stream. readFastaDNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Iterate over the sequences in an FASTA-format stream of DNA sequences. readFastaDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an FASTA-format stream of DNA sequences. readFastaProtein(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Iterate over the sequences in an FASTA-format stream of Protein sequences. readFastaProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an FASTA-format stream of Protein sequences. readFastaRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Iterate over the sequences in an FASTA-format stream of RNA sequences. readFastaRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an FASTA-format stream of RNA sequences. readFile(File, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Guess which format a file is then attempt to read it. readFile(File, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Guess which format a file is then attempt to read it. readFileLength() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader readFileLength returns the file length in bytes (stored within the file's header by the indexing program). readFromXML(InputStream) - Static method in class org.biojava.bio.dist.DistributionTools Read a distribution from XML. readFromXML(InputStream) - Static method in class org.biojava.bio.symbol.CodonPrefTools readFromXML(InputStream, String) - Static method in class org.biojava.bio.symbol.CodonPrefTools reads a specified CodonPref from an file. readFromXML(InputStream, CodonPrefFilter) - Static method in class org.biojava.bio.symbol.CodonPrefTools read an CodonPref XML stream and handle it with a CodonPrefFilter object. readGenbank(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Iterate over the sequences in an Genbank-format stream. readGenbank(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Read a GenBank file using a custom type of SymbolList. readGenbankDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an GenBank-format stream of DNA sequences. readGenbankProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an GenBank-format stream of Protein sequences. readGenbankRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an GenBank-format stream of RNA sequences. readGenbankXml(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Iterate over the sequences in an GenbankXML-format stream. readGenpept(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Iterate over the sequences in an Genpept-format stream. readGFF(BufferedReader) - Static method in class org.biojava.bio.program.gff.GFFTools Read all GFF entries from a buffered reader. readGFF(BufferedReader, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools Read all GFF entries matching a filter from a buffered reader. readGFF(File) - Static method in class org.biojava.bio.program.gff.GFFTools Reads a GFFEntrySet from a file with no filtering. readGFF(File, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools Reads a GFFEntrySet from a file with the specified filter. readGFF(String) - Static method in class org.biojava.bio.program.gff.GFFTools Deprecated. use: readGff(File) readGFF(String, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools Deprecated. use: readGff(File,GFFRecordFilter) readHashedFastaDNA(BufferedInputStream, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an FASTA-format stream of DNA sequences. readingFrame - Variable in class org.biojava.bio.seq.FramedFeature.Template readINSDseq(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Read a INSDseq file using a custom type of SymbolList. readINSDseqDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an INSDseq-format stream of DNA sequences. readINSDseqProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an INSDseq-format stream of Protein sequences. readINSDseqRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an INSDseq-format stream of RNA sequences. readLine() - Method in class org.biojava.utils.io.CountedBufferedReader readMatrix(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel readModel(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel readModelFile(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light readName(BufferedReader) - Method in interface org.biojavax.bio.taxa.io.NCBITaxonomyLoader Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already. readName(BufferedReader) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already. readNode(BufferedReader) - Method in interface org.biojavax.bio.taxa.io.NCBITaxonomyLoader Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object. readNode(BufferedReader) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object. readPhredQuality(BufferedReader) - Static method in class org.biojava.bio.program.phred.PhredTools Constructs a StreamReader to read in Phred quality data in FASTA format. readPhredSequence(BufferedReader) - Static method in class org.biojava.bio.program.phred.PhredTools Calls SeqIOTools.readFastaDNA(br), added here for convinience. readQuotedString(String, int, int, char, boolean, boolean) - Method in class org.biojava.ontology.obo.OboFileParser readRawRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader readRawRecord returns the raw bytes of a single record from the index. readRecord() - Method in class org.biojava.bio.seq.db.emblcd.AcnumHitReader readRecord creates an array of Objects from the raw byte array of a single record. readRecord() - Method in class org.biojava.bio.seq.db.emblcd.AcnumTrgReader readRecord creates an array of Objects from the raw byte array of a single record. readRecord() - Method in class org.biojava.bio.seq.db.emblcd.DivisionLkpReader readRecord creates an array of Objects from the raw byte array of a single record. readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader readRecord returns an array of objects parsed from a single record. readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess readRecord returns an array of objects parsed from a single record. readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader readRecord creates an array of Objects from the raw byte array of a single record. readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess readRecord creates an array of Objects from the raw byte array of a single record. readRecordCount() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader readRecordCount returns the number of records in the file. readRecordLength() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader readRecordLength returns the record length (bytes). readResolve() - Method in class org.biojava.bio.proteomics.Protease Prevent duplication of the object during Serialization readResolve() - Method in class org.biojava.bio.symbol.AbstractAlphabet To prevent duplication of a what should be a single instance of an existing alphabet. readResolve() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet To prevent duplication of a what should be a single instance of an existing alphabet. readResolve() - Method in class org.biojava.utils.StaticMemberPlaceHolder readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.GenbankFormat Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.INSDseqFormat Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtFormat Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.program.phred.PhredFormat readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.FastaFormat Deprecated. Reads information from a flatfile to a SeqIOListener using a SymbolTokenizer to convert sequence strings to Symbol objects. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GAMEFormat this version only reads annotations (no symbols) readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GenbankFormat Deprecated. Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GenbankXmlFormat Deprecated. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in interface org.biojava.bio.seq.io.SequenceFormat Read a sequence and pass data on to a SeqIOListener. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.EMBLFormat Read a sequence and pass data on to a SeqIOListener. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat Read a sequence and pass data on to a SeqIOListener. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.FastaFormat Read a sequence and pass data on to a SeqIOListener. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.GenbankFormat Read a sequence and pass data on to a SeqIOListener. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.INSDseqFormat Read a sequence and pass data on to a SeqIOListener. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.UniProtFormat Read a sequence and pass data on to a SeqIOListener. readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat Read a sequence and pass data on to a SeqIOListener. readStream(BufferedInputStream, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Guess which format a stream is then attempt to read it. readStream(BufferedInputStream, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Guess which format a stream is then attempt to read it. readSwissprot(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Iterate over the sequences in an Swissprot-format stream. readSymbol() - Method in interface org.biojava.bio.seq.io.SymbolReader Return a single symbol from the stream. readSymbols(Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SymbolReader Read one or more symbols from the stream. readUniProt(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Read a UniProt file using a custom type of SymbolList. readUniProt(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an UniProt-format stream of RNA sequences. readUniProtXML(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Read a UniProt XML file using a custom type of SymbolList. readUniProtXML(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Iterate over the sequences in an UniProt XML-format stream of RNA sequences. readXFF(File, String) - Static method in class org.biojava.bio.program.xff.XFFTools readXFF(File, String, FiniteAlphabet) - Static method in class org.biojava.bio.program.xff.XFFTools readXMLChunk(BufferedReader, DefaultHandler, String) - Static method in class org.biojavax.utils.XMLTools Attempts to read XML file in chunks, passing each chunk to a SAX parser. ready() - Method in class org.biojava.utils.io.CountedBufferedReader realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly realizeFeature(FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.RealizingFeatureHolder Realize a feature template. realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.FeatureRealizer Install a feature on the specified sequence. realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer realizeSubFeatures(Feature) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler recursively attach children features to parent RealizingFeatureHolder - Interface in org.biojava.bio.seq Interface for FeatureHolder objects which know how to instantiate new child Features. reapGarbageListeners() - Method in class org.biojava.utils.ChangeSupport Remove all references to listeners which have been cleared by the garbage collector. REBASE_DATA_KEY - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager REBASE_DATA_KEY the ResourceBundle key which specifies the location of the REBASE flat file. REBASE_TAG_COMM - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager REBASE_TAG_COMM the REBASE tag containing the commercial suppliers. REBASE_TAG_ISZR - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager REBASE_TAG_ISZR the REBASE tag containing the enzyme isoschizomers. REBASE_TAG_METH - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager REBASE_TAG_METH the REBASE tag containing the methylation site. REBASE_TAG_NAME - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager REBASE_TAG_NAME the REBASE tag containing the enzyme name. REBASE_TAG_ORGN - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager REBASE_TAG_ORGN the REBASE tag containing the organism. REBASE_TAG_REFS - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager REBASE_TAG_REFS the REBASE tag containing the references. REBASE_TAG_SITE - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager REBASE_TAG_SITE the REBASE tag containing the enzyme site. REBASE_TAG_SRCE - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager REBASE_TAG_SRCE the REBASE tag containing the source. rebind(String, Object) - Method in class org.biojava.naming.ObdaContext rebind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext rebind(Name, Object) - Method in class org.biojava.naming.ObdaContext rebind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext recBytes - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess receiveSequence(String) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder receiveSequence(String) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener Receive sequence data for the current sequence. Record - Interface in org.biojava.bio.program.indexdb Record represents a record within an indexed flat file databank as defined by the OBDA standard. Record.Impl - Class in org.biojava.bio.program.indexdb Impl is the default implementation of Record. recordEmittedSymbol(State, Symbol, double) - Method in interface org.biojava.bio.dp.HMMTrainer record that the specified symbol was emitted from the specified state. recordEmittedSymbol(State, Symbol, double) - Method in class org.biojava.bio.dp.SimpleHMMTrainer recordLength - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord recordLine(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler A record line has been encountered. recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFFilterer Only forward the GFFRecords that match a filter. recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFWriter Prints record to the PrintWriter. recordLine(GFF3Record) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler A record line has been encountered. recordTransition(State, State, double) - Method in interface org.biojava.bio.dp.HMMTrainer record that a transition was observed between the specified states. recordTransition(State, State, double) - Method in class org.biojava.bio.dp.SimpleHMMTrainer recParser - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader recParser - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess A recParser for implementing readRecord() specific to each concrete subclass. rect - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer rect - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer RECT - Static variable in interface org.biojava.bio.gui.sequence.ImageMap RECT indicates a rectangular image map hotspot. RectangleGlyph - Class in org.biojava.bio.gui.glyph A Glyph that paints a rectangle shape within the bounds. RectangleGlyph() - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph RectangleGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph RectangleGlyph(Paint) - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph RectangularBeadRenderer - Class in org.biojava.bio.gui.sequence RectangularBeadRenderer renders features as simple rectangles. RectangularBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.RectangularBeadRenderer Creates a new RectangularBeadRenderer with the default settings. RectangularBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.RectangularBeadRenderer Creates a new RectangularBeadRenderer. RectangularImapRenderer - Class in org.biojava.bio.gui.sequence RectangularImapRenderer is a decorator for RectangularBeadRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the RectangularBeadRenderer. RectangularImapRenderer(RectangularBeadRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.RectangularImapRenderer Creates a new RectangularImapRenderer. recurse - Variable in class org.biojava.bio.gui.sequence.FilteringRenderer recurse - Variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer recurse indicates whether the filter should recurse through any subfeatures. RECURSE - Static variable in class org.biojava.bio.gui.sequence.FilteringRenderer RECURSE - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer Constant RECURSE indicating a change to the renderer's filter recursion flag. REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. REF_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat REF_POS_BEGIN_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat REF_POS_END_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat REF_XREF_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. REFERENCE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder REFERENCE_LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat REFERENCE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat REFERENCE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat ReferenceAnnotation - Class in org.biojava.bio.seq.io Deprecated. Use org.biojavax.bio.seq.io framework instead ReferenceAnnotation() - Constructor for class org.biojava.bio.seq.io.ReferenceAnnotation Deprecated. REFERENCES_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat REFLEXIVE - Static variable in class org.biojava.ontology.OntoTools refp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat refRange - Static variable in class org.biojavax.bio.seq.io.GenbankFormat refreshSequencePanels() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper REFSEQ - Static variable in class org.biojava.bio.seq.io.SeqIOConstants REFSEQ indicates that the sequence format is REFSEQ. REFSEQ_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants REFSEQ_AA premade REFSEQ | AA. REFSEQ_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants REFSEQ_DNA premade REFSEQ | DNA. REFSEQ_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants REFSEQ_RNA premade REFSEQ | RNA. RegexChanger - Class in org.biojava.bio.program.tagvalue A ValueChanger.Changer that returns a specific match value using a regex Pattern. RegexChanger(Pattern, int) - Constructor for class org.biojava.bio.program.tagvalue.RegexChanger Create a new RegexChanger with a pattern. RegexException - Exception in org.biojava.utils.regex An exception thrown by classes of this package. RegexException(String) - Constructor for exception org.biojava.utils.regex.RegexException RegexException(Throwable) - Constructor for exception org.biojava.utils.regex.RegexException RegexException(Throwable, String) - Constructor for exception org.biojava.utils.regex.RegexException RegexFieldFinder - Class in org.biojava.bio.program.tagvalue RegexFieldFinder(TagValueListener, Pattern, String[], boolean) - Constructor for class org.biojava.bio.program.tagvalue.RegexFieldFinder Creates a new RegexFiledFinder. RegexParser - Class in org.biojava.bio.program.tagvalue A TagValueParser that splits a line based upon a regular expression. RegexParser() - Constructor for class org.biojava.bio.program.tagvalue.RegexParser Create a new RegexParser with all boolean values set to false. RegexSplitter - Class in org.biojava.bio.program.tagvalue A ValueChanger.Splitter that splits a line of text using a regular expression, returning one value per match. RegexSplitter(Pattern, int) - Constructor for class org.biojava.bio.program.tagvalue.RegexSplitter Create a new RegexSplitter with a pattern. Region(Location, String, boolean) - Constructor for class org.biojava.bio.seq.RemoteFeature.Region Create a new Region. regions - Variable in class org.biojava.bio.seq.RemoteFeature.Template register(RestrictionEnzyme, Set) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager register regisiters a new RestrictionEnzyme with the manager. registerAlphabet(String[], Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager Register and Alphabet by more than one name. registerAlphabet(String, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager Register an alphabet by name. registerCollectionHandlerFactory(String, String, XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler Register a factory used to create handlers for the specified tag in an XML AnnotationType registerDistribution(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext Register a distribution object with this context. registerDistribution(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext registered(String) - Static method in class org.biojava.bio.proteomics.ProteaseManager Has a Protease been registered with that name? registered(String) - Static method in class org.biojava.bio.symbol.AlphabetManager Has an Alphabet been registered by that name registerFactory(UnigeneFactory) - Static method in class org.biojava.bio.program.unigene.UnigeneTools Register a UnigeneFactory. registerFormat(Class) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Register a new format with IOTools for auto-guessing. registerHandlerFactory(String, String, XMLFilterHandler.FilterHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler Register a factory used to create handlers for the specified tag name registerModel(MarkovModel) - Method in interface org.biojava.bio.dp.ModelTrainer Registers an HMM with this trainer. registerModel(MarkovModel) - Method in class org.biojava.bio.dp.SimpleModelTrainer registerParametricType(ParametricType, CodeClass) - Method in interface org.biojava.utils.bytecode.CodeContext Register a concrete type for a parametric type. registerPropertyHandlerFactory(String, String, XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler Register a factory used to create handlers for the specified tag in an XML AnnotationType registerProtease(Protease) - Static method in class org.biojava.bio.proteomics.ProteaseManager Registers a protease and ensures its flyweight status registerTrainer(Distribution, DistributionTrainer) - Method in interface org.biojava.bio.dist.DistributionTrainerContext Register a Distribution and an associated DistributionTrainer object. registerTrainer(Distribution, DistributionTrainer) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractDistribution Register an IgnoreCountsTrainer instance as the trainer for this distribution. registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution registerWithTrainer(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.Distribution Register this distribution with a training context. registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.GapDistribution registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.PairDistribution registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution Register an SimpleDistribution.Trainer instance as the trainer for this distribution. registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.TranslatedDistribution registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UniformDistribution registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UntrainableDistribution registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dist.PairDistribution Register this paired distribution with a model trainer. registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.SimpleEmissionState registerWithTrainer(ModelTrainer) - Method in interface org.biojava.bio.dp.Trainable Perform any registration that is necessary with mt. registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.WMAsMM registrations() - Static method in class org.biojava.bio.symbol.AlphabetManager A set of names under which Alphabets have been registered. Registry - Class in org.biojava.directory Registry is a factory which gets implementations of the BioJava SequenceDBLite interface. Registry(RegistryConfiguration) - Constructor for class org.biojava.directory.Registry Creates a new OBDA Registry with the specified configuration. RegistryConfiguration - Interface in org.biojava.directory The BioDirectory Registry is a simple system for specifying where to find services which provide sequence databases. RegistryConfiguration.Composite - Class in org.biojava.directory A RegistryConfiguration that allows you to treat other configurations as providing important or default configuration information. RegistryConfiguration.Impl - Class in org.biojava.directory A simple implementation of RegistryConfiguration backed by a Map. RegistryException - Exception in org.biojava.directory A RegistryException thrown when the registry cannot find an implementation of a requested SequenceDB. RegistryException() - Constructor for exception org.biojava.directory.RegistryException Creates a new RegistryException with no detail message. RegistryException(String) - Constructor for exception org.biojava.directory.RegistryException Creates a new RegistryException with the specified detail message. RegistryException(String, Throwable) - Constructor for exception org.biojava.directory.RegistryException RegistryException(Throwable) - Constructor for exception org.biojava.directory.RegistryException Creates a new RegistryException with no detail message, wrapping another Throwable. RegistryException(Throwable, String) - Constructor for exception org.biojava.directory.RegistryException Deprecated. use new RegistryException(message, cause) REL_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler RelabeledAlignment - Class in org.biojava.bio.symbol An alignment that relabels another alignment. RelabeledAlignment(Alignment) - Constructor for class org.biojava.bio.symbol.RelabeledAlignment RELATED_SYNONYM - Static variable in class org.biojava.ontology.Synonym RELATION - Static variable in class org.biojava.ontology.OntoTools RELATION - Static variable in interface org.biojavax.bio.seq.RichFeature RELATIONS - Static variable in interface org.biojavax.bio.BioEntry RELATIONSHIP - Static variable in class org.biojava.ontology.obo.OboFileHandler REMARK - Static variable in interface org.biojavax.DocRef REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat RemoteFeature - Interface in org.biojava.bio.seq A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence. RemoteFeature.Region - Class in org.biojava.bio.seq A tuple of Location and sequence ID. RemoteFeature.Resolver - Interface in org.biojava.bio.seq The interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature. RemoteFeature.Template - Class in org.biojava.bio.seq RemotePairwiseAlignmentOutputProperties - Interface in org.biojavax.bio.alignment RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object. RemotePairwiseAlignmentProperties - Interface in org.biojavax.bio.alignment RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties. RemotePairwiseAlignmentService - Interface in org.biojavax.bio.alignment This interface specifies minimal information needed to execute a pairwise alignment on a remote service. RemoteQBlastAlignmentProperties - Class in org.biojavax.bio.alignment.blast This class implements RemotePairwiseAlignmentProperties by specifying several convenient methods used to wrap the addition of Blast alignment parameters. RemoteQBlastAlignmentProperties() - Constructor for class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties RemoteQBlastOutputFormat - Enum in org.biojavax.bio.alignment.blast The RemoteQBlastOutputFormat enum acts like static fields for specifiying various values for certain output options. RemoteQBlastOutputProperties - Class in org.biojavax.bio.alignment.blast The actual implementation of the RemotePairwiseAlignmentOutputProperties interface for the QBlast service. RemoteQBlastOutputProperties() - Constructor for class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties This constructor build the parameters for the default output of the GET command sent to the QBlast service. RemoteQBlastService - Class in org.biojavax.bio.alignment.blast RemoteQBlastService - A simple way of submitting BLAST request to the QBlast service at NCBI. RemoteQBlastService() - Constructor for class org.biojavax.bio.alignment.blast.RemoteQBlastService The constructor for a QBlast service request. RemoteTerm - Interface in org.biojava.ontology A term in another ontology. RemoteTerm.Impl - Class in org.biojava.ontology Simple in-memory implementation of a remote ontology term. remove() - Method in class org.biojava.bio.alignment.Alignment.SymbolListIterator remove() - Method in class org.biojava.bio.dp.DP.ReverseIterator remove() - Method in class org.biojava.utils.MergingIterator remove(int) - Method in class org.biojava.utils.bytecode.InstructionVector remove(Object) - Method in interface org.biojava.utils.cache.CacheMap Explicitly remove an object. remove(Object) - Method in class org.biojava.utils.cache.FixedSizeMap remove(Object) - Method in class org.biojava.utils.cache.WeakCacheMap remove(Object) - Method in class org.biojava.utils.io.SoftHashMap remove(Object) - Method in class org.biojava.utils.MergingSet remove(Object) - Method in class org.biojavax.ga.util.WeightedSet REMOVE_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment removeAllItems() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock removeAllOrganisms() - Method in class org.biojavax.ga.impl.AbstractPopulation removeAllOrganisms() - Method in interface org.biojavax.ga.Population Removes all the Organisms in this Population removeAllOrganismsImpl() - Method in class org.biojavax.ga.impl.AbstractPopulation removeAllOrganismsImpl() - Method in class org.biojavax.ga.impl.SimplePopulation removeAllSymbols() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock removeAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation Remove an Annotation from the list. removeAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB Remove a DB from this view. removeBioEntry(String) - Method in class org.biojavax.bio.db.AbstractBioEntryDB removeBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB removeBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite Remove the BioEntry associated with an ID from the database. removeBioEntry(String) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB removeBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB removeChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext Remove a ChangeListener from a projected feature. removeChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel removeChangeListener removes a listener. removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel removeChangeListener removes a listener. removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature removeChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable removeChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable Deprecated. use removeChangeListener(cl, ChangeType.UNKNOWN) removeChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport Remove a listener that was interested in all types of changes. removeChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable removeChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList Remove a listener that was interested in all types of changes. removeChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross removeChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel removeChangeListener removes a listener. removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel removeChangeListener removes a listener. removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable removeChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable Remove a listener that was interested in a specific types of changes. removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport Remove a listener that was interested in a specific types of changes. removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList Remove a listener that was interested in a specific types of changes. removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation removeCharLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock removeCharState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory Deprecated. removeChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory Deprecated. Remove a Taxon as a child to this one. removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory Deprecated. removeComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock Removes a comment. removeComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock Removes a comment. removeComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock Removes a comment. removeComment(NexusComment) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock Removes a comment. removeComment(Comment) - Method in interface org.biojavax.bio.BioEntry Removes a comment instance from this bioentry. removeComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry Removes a comment instance from this bioentry. removeComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList removeComponent(Location) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList removeDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB Remove a distributed data source. removeDelegateRenderer(OptimizableFilter) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer removeDelegateRenderer removes any association of the given OptimizableFilter with a BeadFeatureRenderer. removeDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple Removes a descriptor. removeDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple Removes a descriptor. removeEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper removeEnzyme removes an enzyme from those to be searched for in the Sequence. removeEquate(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock removeFeature(Feature) - Method in class org.biojava.bio.seq.AbstractFeatureHolder removeFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder removeFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder Remove a feature from this FeatureHolder. removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence Remove a feature attached to this sequence. removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence Remove a feature from this sequence. removeFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder removeFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder removeFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext Remove the dying child. removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder removeFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature Remove a feature from this FeatureHolder. removeFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence Remove a feature from this FeatureHolder. removeFeature(Feature, Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext Remove the dying child. removeFeature(Feature, Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext removeFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder Remove a FeatureHolder from the set of FeatureHolders which are merged. removeFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder Removes a relationship from this feature holder. removeFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature Removes a relationship from this feature holder. removeFilterWithGlyph(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer removeForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable removeFromEnvironment(String) - Method in class org.biojava.naming.ObdaContext removeGap(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList Remove a single gap at position pos in this GappedSymbolList. removeGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList removeGaps(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList Remove some gaps at position pos in this GappedSymbolList. removeGaps(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList removeGaps(GappedSymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment because there is a bug in GappedSymbolList removeGeneticCodeID(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Deletes the genetic code annotation from the taxon in the database. removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget removeItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel removeItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget removeItem(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock removeKey(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory removeKey removes the specified key. removeKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model Remove a key. removeLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer Remove a piece of text from the label removeLeftValue(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Deletes the left value from the specified taxon in the database. removeListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub remove a ChangeListener associated with given key. removeListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub removeMitochondrialGeneticCodeID(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Deletes the so called mitochondrial genetic code annotation from the given taxon. removeName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon Removes the name from the given name class. removeName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Removes the name from the given name class. removeName(Connection, DBHelper, Taxon, String, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Deletes the specified name from of the taxon from the database. removeNote(Note) - Method in class org.biojavax.EmptyRichAnnotation Removes a note from this annotation. removeNote(Note) - Method in interface org.biojavax.RichAnnotation Removes a note from this annotation. removeNote(Note) - Method in class org.biojavax.SimpleRichAnnotation Removes a note from this annotation. removeObject(NexusObject) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFile Removes an object from the file. removeOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation removeOrganism(Organism) - Method in interface org.biojavax.ga.Population Kills off the organism removeOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation removeOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation removeOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation removeOrganisms(Set) - Method in interface org.biojavax.ga.Population Removes all the Organisms in orgs removeOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation removeOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population Removes all the Organisms in orgs removeOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet Remove an orthologue from the set. removeOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet removeOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet removes a specified OrthoPair relationship from this group. removeOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat Removes a parse error listener from the list of listeners if it is included. removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. Removes a parse error listener from the list of listeners if it is included. removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor Deprecated. Removes a parse error listener from the list of listeners if it is included. removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat Deprecated. Removes a parse error listener from the list of listeners if it is included. removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat Deprecated. Removes a parse error listener from the list of listeners if it is included. removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor Deprecated. Removes a parse error listener from the list of listeners if it is included. removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor Deprecated. Removes a parse error listener from the list of listeners if it is included. removeParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource Removes a parse error listener from the list of listeners. removeProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation removeProperty(Object) - Method in interface org.biojava.bio.Annotation Delete a property. removeProperty(Object) - Method in class org.biojava.bio.MergeAnnotation removeProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation removeProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation Delete a property. removeProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation Deprecated. removeProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract removeProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType Remove a value from the specified property slot. removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border Deprecated. removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter removeRank(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Removes the rank persistently from the taxon in the database. removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature Removes a ranked cross reference from the existing set. removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry Removes a ranked cross reference from the existing set. removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm Removes a ranked cross reference from the existing set. removeRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable Removes a ranked cross reference from the existing set. removeRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry Removes a ranked docref instance from this bioentry. removeRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry Removes a ranked docref instance from this bioentry. removeRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry Removes a relation instance from this bioentry. removeRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry Removes a relation instance from this bioentry. removeRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR removeRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer removeRenderer removes a renderer. removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer removeRenderer removes a renderer. removeRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes Remove a repository from FeaturTypes. removeRichSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB removeRichSequence(String) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB removeRichSequence(String) - Method in interface org.biojavax.bio.db.RichSequenceDBLite Remove the RichSequence associated with an ID from the database. removeRightValue(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Deletes the right value from the specified taxon in the database. removeSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer Remove a secondary key. removeSequence(Object) - Method in interface org.biojava.bio.alignment.ARAlignment removeSequence(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment removeSequence(String) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB removeSequence(String) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB removeSequence(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB Deprecated. removeSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB removeSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB removeSequence always throws a ChangeVetoException as this implementation is immutable. removeSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB removeSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDBLite Remove the sequence associated with an ID from the database. removeSequence(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB Not supported, you can't remove a sequence from a WebDB! removeSequence(String) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB removeSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB removeSequence(String) - Method in class org.biojavax.bio.db.HashRichSequenceDB removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel removeSequenceViewerListener removes a listener for mouse click SequenceViewerEvents. removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel removeSequenceViewerListener removes a listener for mouse click SequenceViewerEvents. removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel addSequenceViewerMotionListener removes a listener for mouse motion SequenceViewerEvents. removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel addSequenceViewerMotionListener removes a listener for mouse motion SequenceViewerEvents. removeSet(Set) - Method in class org.biojava.utils.MergingSet removeState(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock removeState(State) - Method in interface org.biojava.bio.dp.MarkovModel Remove a state from the model. removeState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel removeState(State) - Method in class org.biojava.bio.dp.WMAsMM removeSymbol(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock removeSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet Remove a symbol from this alphabet. removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet SoftMaskedAlphabets cannot remove Symbols. removeSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm removeSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl removeSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl removeSynonym(Object) - Method in class org.biojava.ontology.Term.Impl removeSynonym(Object) - Method in interface org.biojava.ontology.Term Remove a synonym for this term. removeSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl removeSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm Remove a synonym for this term. removeSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple Remove a synonym for this term. removeTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper Remove a tag so that it will not be retained. removeTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock Removes the given TAXLABEL. removeTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock Removes the given TAXLABEL. removeTaxLabel(String) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock Removes the given TAXLABEL. removeTaxon(Connection, int, DBHelper) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the removed taxon. removeTaxon(Connection, DBHelper, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Deletes a taxon specified by one of it's names with all it's different names, annotations and sequences from the database. removeTranslation(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock Removes the given translation. removeTree(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock Removes a tree. removeVariableModifications(char) - Method in class org.biojava.bio.proteomics.MassCalc Remove all variable modifications assocaited with this residue. removeVariableModifications(Symbol) - Method in class org.biojava.bio.proteomics.MassCalc Remove all variable modifications assocaited with this residue. rename(String, String) - Method in class org.biojava.naming.ObdaContext rename(Name, Name) - Method in class org.biojava.naming.ObdaContext render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph render(Graphics2D) - Method in interface org.biojava.bio.gui.glyph.Glyph render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.HelixGlyph render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.TurnGlyph render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph RENDER_NOTHING - Static variable in interface org.biojava.bio.gui.sequence.LabelRenderer renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer renderBead should be overridden by the concrete BeadRenderer. renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer renderBead should implement rendering for this bead type only. renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer renderBead renders features as simple ellipse. renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer renderBead renders features as simple rectangle. renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer renderBead renders features as a rectangle with rounded corners. RENDERER - Static variable in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer RENDERER - Static variable in class org.biojava.bio.gui.sequence.OverlayRendererWrapper RENDERER - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer Constant RENDERER indicating a change to the renderer. RENDERER - Static variable in class org.biojava.bio.gui.sequence.PairwiseSequencePanel Constant RENDERER is a ChangeType which indicates a change to the renderer, requiring a layout update. RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequencePanel RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequenceRendererWrapper RENDERER - Static variable in class org.biojava.bio.gui.sequence.TranslatedSequencePanel Constant RENDERER is a ChangeType which indicates a change to the renderer, requiring a layout update. RendererForwarder(SequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder renderers - Variable in class org.biojava.bio.gui.sequence.MultiLineRenderer RENDERERS - Static variable in class org.biojava.bio.gui.sequence.MultiLineRenderer RENDERERS - Static variable in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer Constant RENDERERS indicating a change to the renderers handled by the overlay. RENDERERS - Static variable in class org.biojava.bio.gui.sequence.StackedFeatureRenderer renderFeature(Graphics2D, Feature, CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer renderFeature draws a feature using the supplied graphics context. renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer renderImageMap writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer. renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.ImageMapRenderer renderImageMap renders the Feature as set of image map hotspots. renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer renderImageMap writes a set of image map coordinates corresponding to the rectangle drawn by the renderer. renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer renderImageMap writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer. renderLocation(Graphics2D, SequenceRenderContext, Location) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer Render another "exon" in the correct translation frame. RenderNothing() - Constructor for class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing renumber(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList Renumber the view indexes from block, adding delta to each offset. REPAINT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext ReparentContext - Class in org.biojava.bio.seq.projection A good base class to implement ProjectionContext from. ReparentContext(FeatureHolder, FeatureHolder) - Constructor for class org.biojava.bio.seq.projection.ReparentContext repeatDescription(String) - Method in interface org.biojava.bio.program.fastq.ParseListener Notify this parse listener of a repeat description line. RepeatedCharSequence - Class in org.biojava.utils RepeatedCharSequence() - Constructor for class org.biojava.utils.RepeatedCharSequence RepeatedCharSequence(int, char) - Constructor for class org.biojava.utils.RepeatedCharSequence replacement - Variable in class org.biojava.bio.symbol.Edit replicate(String) - Method in class org.biojavax.ga.impl.SimpleOrganism replicate(String) - Method in interface org.biojavax.ga.Organism Creates a replica of this Organism with a new name. reportDna(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf reportDna(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler reportDna(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf reportDna(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler reportExon(RangeLocation, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler reportExon(RangeLocation, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf Allows nesting class that manages a transcript template to gain information about its extent from nested elements that represent exons. reportFeature(Location) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf Allows nesting class that manages a gene template to gain information about its extent from nested elements. reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler reportFeature(Location) - Method in interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler reportFeature(Location) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler reportFeature(Location) - Method in interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf Allows nesting class that manages a gene template to gain information about its extent from nested elements. reportMatch(SymbolList, Pattern, int, int) - Method in interface org.biojava.utils.regex.Search.Listener reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVECallbackItf reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf REPOSITORY_SUBSETS - Static variable in interface org.biojava.bibliography.BibRefSupport A vocabulary name. RepositoryImpl(String) - Constructor for class org.biojava.bio.seq.FeatureTypes.RepositoryImpl Create a named repository. repositorySubset - Variable in class org.biojava.bibliography.BiblioEntryStatus Some bibliographic repositories consist of several, or even many, databases. requestsQueued() - Method in class org.biojava.utils.SimpleThreadPool requestsQueued returns the number of Runnables currently queued. reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer reset() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer reset() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter reset() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter resets the internal state of this filter including any cached evaluations. reset() - Method in class org.biojava.utils.io.CountedBufferedReader reset() - Method in class org.biojava.utils.regex.Matcher Resets this matcher. reset() - Method in class org.biojavax.utils.CRC64Checksum reset(SymbolList) - Method in class org.biojava.utils.regex.Matcher Resets this matcher with a new input SymbolList. resetRange() - Method in class org.biojava.bio.alignment.FlexibleAlignment check that begining is at 1 otherwise shift everything over resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder Allowed to be called by DATA subclass. resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract This function is called when the parser is reset before starting a new block. resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockParser resetStatus() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockParser resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel resizeAndValidate sets the minimum, preferred and maximum sizes of the component according to the current visible symbol count. resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePanel resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel resizeAndValidate sets the minimum, preferred and maximum sizes of the component according to the current leading and trailing borders, renderer depth and visible symbol count. resolve(RemoteFeature) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver resolve(RemoteFeature) - Method in interface org.biojava.bio.seq.RemoteFeature.Resolver Resolve rFeat. resolve(FuzzyPointLocation) - Method in interface org.biojava.bio.symbol.FuzzyPointLocation.PointResolver Return the actual point that the specified location should claim to occupy. RESOLVE_AVERAGE - Static variable in class org.biojava.bio.symbol.FuzzyLocation Use the arithmetic mean of the `inner' and `outer' values, unless the outer value is unbounded. RESOLVE_AVERAGE - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation RESOLVE_INNER - Static variable in class org.biojava.bio.symbol.FuzzyLocation Always use the `inner' values. RESOLVE_MAX - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation RESOLVE_MIN - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation RESOLVE_OUTER - Static variable in class org.biojava.bio.symbol.FuzzyLocation Use the `outer' values, unless they are unbounded in which case the `inner' values are used. resolveAlphabet(String) - Static method in class org.biojava.bio.program.ssbind.AlphabetResolver resolveAlphabet returns an appropriate Alphabet for an arbitrary identifier. resolveClass(CodeClass) - Method in class org.biojava.utils.bytecode.ConstantPool resolveCommands(String, Properties) - Static method in class org.biojava.utils.process.ExternalProcess Resolves the given command line by replacing all placeholder of the format %NAME% with the values from the given properties for the corresponding keys of the format NAME. resolveDouble(double) - Method in class org.biojava.utils.bytecode.ConstantPool resolveEntity(String, String) - Method in class org.biojava.utils.xml.ResourceEntityResolver resolveField(CodeField) - Method in class org.biojava.utils.bytecode.ConstantPool resolveFloat(float) - Method in class org.biojava.utils.bytecode.ConstantPool resolveInt(int) - Method in class org.biojava.ontology.IntegerOntology resolveInt(int) - Method in class org.biojava.utils.bytecode.ConstantPool resolveInterfaceMethod(CodeMethod) - Method in class org.biojava.utils.bytecode.ConstantPool resolveLocal(LocalVariable) - Method in interface org.biojava.utils.bytecode.CodeContext Resolve a local variable to the local variable slot assigned to it. resolveLong(long) - Method in class org.biojava.utils.bytecode.ConstantPool resolveMax(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver Delegate for the getMax() method. resolveMethod(CodeMethod) - Method in class org.biojava.utils.bytecode.ConstantPool resolveMin(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver Delegate for the getMin() method. resolveNameAndType(String, String) - Method in class org.biojava.utils.bytecode.ConstantPool resolveParametricType(ParametricType) - Method in interface org.biojava.utils.bytecode.CodeContext Resolve a parametric type to a concrete class. resolver - Variable in class org.biojava.bio.seq.RemoteFeature.Template resolveString(String) - Method in class org.biojava.utils.bytecode.ConstantPool resolveUtf8(String) - Method in class org.biojava.utils.bytecode.ConstantPool RESOURCE_TYPES - Static variable in interface org.biojava.bibliography.BibRefSupport A vocabulary name. ResourceEntityResolver - Class in org.biojava.utils.xml SAX EntityResolve which looks up system IDs as resources from a Java ClassLoader. ResourceEntityResolver(String) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver Construct a resolver which searches for resources in the specified path relative to the current classloader. ResourceEntityResolver(String[]) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver Construct a resolver which searches for resources in the specified list of directories relative to the current classloader. ResourceEntityResolver(String[], ClassLoader) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver Construct a resolver which searches for resources in the specified list of directories relative to the supplied classloader. ResourceEntityResolver(String, ClassLoader) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver Construct a resolver which searches for resources in the specified path relative to the supplied classloader. RestrictionEnzyme - Class in org.biojava.bio.molbio RestrictionEnzyme represents a restriction enzyme according to the REBASE standard. RestrictionEnzyme(String, SymbolList, int, int) - Constructor for class org.biojava.bio.molbio.RestrictionEnzyme Creates a new RestrictionEnzyme which cuts within or downstream of the recognition site. RestrictionEnzyme(String, SymbolList, int, int, int, int) - Constructor for class org.biojava.bio.molbio.RestrictionEnzyme Creates a new RestrictionEnzyme of the unusual type which cuts both upstream and downstream of its recognition site. RestrictionEnzymeManager - Class in org.biojava.bio.molbio RestrictionEnzymeManager manages collections of static RestrictionEnzyme instances. RestrictionMapper - Class in org.biojava.bio.molbio RestrictionMapper is a class for annotating Sequences with Features which represent restriction sites. RestrictionMapper(ExecutorService) - Constructor for class org.biojava.bio.molbio.RestrictionMapper Creates a new RestrictionMapper which will use the specified ExecutorService. RestrictionMapper(ThreadPool) - Constructor for class org.biojava.bio.molbio.RestrictionMapper Creates a new RestrictionMapper which will use the specified ThreadPool. RestrictionSite - Interface in org.biojava.bio.molbio RestrictionSite represents the recognition site of a restriction enzyme. RestrictionSite.Template - Class in org.biojava.bio.molbio Template for construction of RestrictionSites. RESULT_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty retainAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet returnData(Object) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler provides a standardised way of returning an object that represents the result of parsing the child element Retyper(Object, ChangeSupport, ChangeType) - Constructor for class org.biojava.utils.ChangeForwarder.Retyper Create a new Retyper for forwarding events. RevCompSequence - Class in org.biojava.bio.seq.impl A reverse complement view onto Sequence interface. RevCompSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.RevCompSequence URN, Name and Annotation are copied as is from the original Sequence, unless you use the the other contructor that sets these. RevCompSequence(Sequence, String, String, Annotation) - Constructor for class org.biojava.bio.seq.impl.RevCompSequence reverse(int[]) - Static method in class org.biojava.bio.chromatogram.AbstractChromatogram Utility method for reversing an int[] array. reverse(SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews A reversed view onto a SymbolList. reverseComplement() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram reverseComplement() - Method in interface org.biojava.bio.chromatogram.Chromatogram Returns a new Chromatogram representing the reverse complement of this one. reverseComplement(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools Reverse-complement a sequence, and flip all of its features. reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools Retrieve a reverse-complement view of list. reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools Retrieve a reverse-complement view of list. reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools Retrieve a reverse-complement view of list. reverseComplementBaseCallList(Object) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram Return a symbol list containing the reverse complement of the base call data for the given label. reverseComplementBaseCallList(String) - Method in class org.biojava.bio.program.scf.SCF Overrides AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object) to support the 7 quality values from the SCF. reverseComplementBaseCalls() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram Returns a new base call alignment that is the reverse complement of one in this chromatogram. reverseComplementInstance() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram Returns a new instance of this AbstractChromatogram subclass for use in AbstractChromatogram.reverseComplement(). reverseComplementInstance() - Method in class org.biojava.bio.chromatogram.SimpleChromatogram reverseComplementInstance() - Method in class org.biojava.bio.program.abi.ABIFChromatogram reverseComplementInstance() - Method in class org.biojava.bio.program.scf.SCF ReverseIterator(SymbolList) - Constructor for class org.biojava.bio.dp.DP.ReverseIterator reverseRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme ReversibleTranslationTable - Interface in org.biojava.bio.symbol A translation table that can also translate from the target to source alphabet. revertFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext revertFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext Unproject a feature. revertFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext revertFilter(FeatureFilter) - Method in interface org.biojava.bio.seq.projection.ProjectionContext Transform a filter on projected features so that it applies to unprojected features. revertFilter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ReparentContext revertLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext revertLocation(Location) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext revertLocation(Location, int, boolean) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils Revert a location, translating and flipping as required. revertStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext revertTemplate(Feature.Template, ProjectionContext) - Method in class org.biojava.bio.seq.projection.ProjectionEngine Revert a template so that it can be used on the original feature-space. revertTemplate(ProjectionContext, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionEngine.TemplateProjector RichAnnotatable - Interface in org.biojavax Annotatable objects that can have rich annotations. RichAnnotation - Interface in org.biojavax An annotation collection which stores annotations as Note objects. RichFeature - Interface in org.biojavax.bio.seq Represents a feature that can be given name and rank and be moved from one sequence to another. RichFeature.Template - Class in org.biojavax.bio.seq Added-value extension of Feature.Template including bits we're interested in, eg. featureRelationshipSet for relationships with other features, and rankedCrossRefs for lookups into other databases. RichFeature.Tools - Class in org.biojavax.bio.seq Some useful tools for working with features. RichFeatureRelationship - Interface in org.biojavax.bio.seq Represents the relation between two features. RichFeatureRelationshipHolder - Interface in org.biojavax.bio.seq Holds feature relationships. RichLocation - Interface in org.biojavax.bio.seq Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases. RichLocation.Strand - Class in org.biojavax.bio.seq This class represents a strand on which a location may lie. RichLocation.Tools - Class in org.biojavax.bio.seq Some useful tools for working with Locations. RichObjectBuilder - Interface in org.biojavax This interface allows a class to generate Rich objects based on a class name and some parameters. RichObjectFactory - Class in org.biojavax Runs a service that builds rich objects, and provides some default values for things like default ontology, default namespace, etc. RichSeqIOAdapter - Class in org.biojavax.bio.seq.io This class implements all methods of RichSeqIOListener and takes no action. RichSeqIOAdapter() - Constructor for class org.biojavax.bio.seq.io.RichSeqIOAdapter Creates a new instance of RichSeqIOAdapter RichSeqIOListener - Interface in org.biojavax.bio.seq.io An interface for classes that listen to BioEntry or RichSequence I/O streams. RichSequence - Interface in org.biojavax.bio.seq A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence. RichSequence.IOTools - Class in org.biojavax.bio.seq A set of convenience methods for handling common file formats. RichSequence.IOTools.SingleRichSeqIterator - Class in org.biojavax.bio.seq Used to iterate over a single rich sequence RichSequence.Terms - Class in org.biojavax.bio.seq Stores a number of useful terms used across many sequence formats for consistency's sake. RichSequence.Tools - Class in org.biojavax.bio.seq Some useful tools for working with RichSequence objects. RichSequenceBuilder - Interface in org.biojavax.bio.seq.io An interface for objects that can build RichSequences. RichSequenceBuilderFactory - Interface in org.biojavax.bio.seq.io Simple factory for constructing new RichSequenceBuilder objects. RichSequenceDB - Interface in org.biojavax.bio.db A database of RichSequences with accessible keys and iterators over all sequences. RichSequenceDBLite - Interface in org.biojavax.bio.db A database of RichSequences. RichSequenceFormat - Interface in org.biojavax.bio.seq.io Allows a file format to be read/written as RichSequences. RichSequenceFormat.BasicFormat - Class in org.biojavax.bio.seq.io Provides a basic format with simple things like line-widths precoded. RichSequenceFormat.HeaderlessFormat - Class in org.biojavax.bio.seq.io Provides the basic implementation required for simple header/footer-less files such as Genbank. RichSequenceHandler - Interface in org.biojavax.bio.seq An interface for classes that know how to handle subsequence operations. RichSequenceIterator - Interface in org.biojavax.bio.seq Essentially the same as SequenceIterator. RichStreamReader - Class in org.biojavax.bio.seq.io Parses a stream into sequences. RichStreamReader(BufferedReader, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Constructor for class org.biojavax.bio.seq.io.RichStreamReader Creates a new stream reader on the given reader, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace. RichStreamReader(InputStream, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Constructor for class org.biojavax.bio.seq.io.RichStreamReader Creates a new stream reader on the given input stream, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace. RichStreamWriter - Class in org.biojavax.bio.seq.io Writes all of the sequences from a SequenceIterator to a stream with a particular format. RichStreamWriter(OutputStream, RichSequenceFormat) - Constructor for class org.biojavax.bio.seq.io.RichStreamWriter Generate a new RichStreamWriter to the stream os and using format. rightMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment rightPad(String, char, int) - Static method in class org.biojavax.utils.StringTools Pads a string to be a certain width by appending given symbols. rightPad(String, int) - Static method in class org.biojavax.utils.StringTools Pads a string to be a certain width by appending spaces. rights - Variable in class org.biojava.bibliography.BibRef It specifies information about rights over the cited resource. RIGHTVALUE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants RNA indicates that a sequence contains RNA (ribonucleic acid) symbols. RNATools - Class in org.biojava.bio.seq Useful functionality for processing DNA and RNA sequences. ROLE_ATTR_QUERYABLE - Static variable in interface org.biojava.bibliography.BibRefSupport A role of an attribute. ROLE_ATTR_RETRIEVABLE - Static variable in interface org.biojava.bibliography.BibRefSupport A role of an attribute. rollback() - Method in class org.biojava.bio.seq.db.BioIndex rollback() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore rollback rolls back changes made since the last commit. rollback() - Method in interface org.biojava.bio.seq.db.IndexStore Discard all uncommited changes. rollback() - Method in class org.biojava.bio.seq.db.TabIndexStore rollback() - Method in interface org.biojava.utils.Commitable rollback reverses pending changes to restore initial (or prior commit) state. rollback() - Method in class org.biojava.utils.FileAsList RoundRectangularBeadRenderer - Class in org.biojava.bio.gui.sequence RoundRectangularBeadRenderer renders features as rectangles with rounded corners. RoundRectangularBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer Creates a new RoundRectangularBeadRenderer object with the default settings. RoundRectangularBeadRenderer(double, double, Paint, Paint, Stroke, double, double) - Constructor for class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer Creates a new RoundRectangularBeadRenderer. RP_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat RP_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat rpp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat rppat - Static variable in class org.biojavax.bio.seq.io.UniProtFormat rppat - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat RulerRenderer - Class in org.biojava.bio.gui.sequence RulerRenderer renders numerical scales in sequence coordinates. RulerRenderer() - Constructor for class org.biojava.bio.gui.sequence.RulerRenderer Creates a new RulerRenderer with the default setting of ticks pointing downwards. RulerRenderer(int) - Constructor for class org.biojava.bio.gui.sequence.RulerRenderer Creates a new RulerRenderer with the specified tick direction. run() - Method in class org.biojava.utils.process.ReaderInputHandler run() - Method in class org.biojava.utils.process.ReaderWriterPipe run() - Method in class org.biojava.utils.process.SimpleInputHandler run() - Method in class org.biojava.utils.process.StreamPipe run(GAStoppingCriteria) - Method in interface org.biojavax.ga.GeneticAlgorithm Iterates the Algorithm until the stopping criteria are met. run(GAStoppingCriteria) - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm S s() - Static method in class org.biojava.bio.seq.DNATools s() - Static method in class org.biojava.bio.seq.NucleotideTools s() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Serine S_SCROFA - Static variable in interface org.biojava.bio.program.homologene.Taxon sample() - Method in class org.biojavax.ga.util.WeightedSet Randomly samples an Object from the Set according to its weight. sampleSymbol() - Method in class org.biojava.bio.dist.AbstractDistribution sampleSymbol() - Method in interface org.biojava.bio.dist.Distribution Sample a symbol from this state's probability distribution. sampleSymbol() - Method in class org.biojava.bio.dist.GapDistribution sampleSymbol() - Method in class org.biojava.bio.dist.PairDistribution sampleSymbol() - Method in class org.biojava.bio.dist.TranslatedDistribution SangerFastqReader - Class in org.biojava.bio.program.fastq Reader for FastqVariant.FASTQ_SANGER formatted sequences. SangerFastqReader() - Constructor for class org.biojava.bio.program.fastq.SangerFastqReader SangerFastqWriter - Class in org.biojava.bio.program.fastq Writer for FastqVariant.FASTQ_SANGER formatted sequences. SangerFastqWriter() - Constructor for class org.biojava.bio.program.fastq.SangerFastqWriter SAX2StAXAdaptor - Class in org.biojava.bio.seq.io.agave Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services. SAX2StAXAdaptor - Class in org.biojava.utils.stax Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services. SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor Construct a new SAX Content handler which wraps a StAX handler. SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.utils.stax.SAX2StAXAdaptor Construct a new SAX Content handler which wraps a StAX handler. sb - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader scale(Chromatogram, int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity scale(Chromatogram, int) - Method in interface org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler Returns the remapped coordinate for the provided trace sample index of the given chromatogram. scale(Chromatogram, int) - Method in class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler scaleHeight - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer SCENE_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable Translation table name for the scenedesmus obliquus mitochondrial genetic code. SCF - Class in org.biojava.bio.program.scf A Chromatogram as loaded from an SCF v2 or v3 file. SCF() - Constructor for class org.biojava.bio.program.scf.SCF Creates a new, completely empty SCF. SCF_MAGIC - Static variable in class org.biojava.bio.chromatogram.ChromatogramFactory The magic number for SCF files. SCHEMA - Static variable in interface org.biojava.bio.seq.FeatureHolder Signals that the schema of this FeatureHolder has changed. SCI_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty SCIENTIFIC - Static variable in interface org.biojavax.bio.taxa.NCBITaxon Use this to define scientific names for things. SCIENTIFIC_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms SCINAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat SCOOP - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer score - Variable in class org.biojava.bio.dp.BackPointer The score of this element of the DP matrix. score - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix score - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template score of the search which produced the alignment. scores - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix scores - Variable in class org.biojava.bio.dp.twohead.Cell SCORES - Static variable in interface org.biojava.bio.dp.StatePath Alignment label for the likelyhood at each step. ScoreType - Interface in org.biojava.bio.dp This class computes the score that is used to be used in a DP optimisation. ScoreType.NullModel - Class in org.biojava.bio.dp In this class, calculateScore returns the probability of a Symbol being emitted by the null model. ScoreType.Odds - Class in org.biojava.bio.dp In this class, calculateScore returns the odds ratio of a symbol being emitted. ScoreType.Probability - Class in org.biojava.bio.dp In this class, calculateScore returns the probability of a Symbol being emitted. scoreWeightMatrix(WeightMatrix, SymbolList, int) - Static method in class org.biojava.bio.dp.DP Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix. scoreWeightMatrix(WeightMatrix, SymbolList, ScoreType, int) - Static method in class org.biojava.bio.dp.DP Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType. search(Object) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory Deprecated. search(Object) - Method in interface org.biojava.bio.taxa.TaxonFactory Deprecated. Retrieve a Taxon that matches some ID. search(Object) - Method in class org.biojava.bio.taxa.WeakTaxonFactory Deprecated. search(String, String, Object[], SearchControls) - Method in class org.biojava.naming.ObdaContext search(String, String, SearchControls) - Method in class org.biojava.naming.ObdaContext search(String, Attributes) - Method in class org.biojava.naming.ObdaContext search(String, Attributes, String[]) - Method in class org.biojava.naming.ObdaContext search(String, SymbolList, SearchListener) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore search(String, SymbolList, SearchListener) - Method in interface org.biojava.bio.program.ssaha.DataStore Search the DataStore with a symbol list. search(Name, String, Object[], SearchControls) - Method in class org.biojava.naming.ObdaContext search(Name, String, SearchControls) - Method in class org.biojava.naming.ObdaContext search(Name, Attributes) - Method in class org.biojava.naming.ObdaContext search(Name, Attributes, String[]) - Method in class org.biojava.naming.ObdaContext search(AnnotationType) - Method in interface org.biojava.bio.annodb.AnnotationDB Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType. search(AnnotationType) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB search(AnnotationType) - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB search(AnnotationType) - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB search(AnnotationType) - Method in class org.biojava.bio.annodb.MergingAnnotationDB search(AnnotationType) - Method in class org.biojava.bio.annodb.SimpleAnnotationDB search(SymbolList) - Method in class org.biojava.utils.automata.PatternBlitz search(SymbolList) - Method in class org.biojava.utils.regex.Search search the Sequence with the patterns already registered with this object. search(SymbolList, int, int) - Method in class org.biojava.utils.regex.Search search part of the SymbolList with the patterns already registered with this object. search(SymbolList, SequenceDB, Map) - Method in interface org.biojava.bio.search.SeqSimilaritySearcher Using this sequence similarity searcher, search with the given sequence against the given sequence database. Search - Class in org.biojava.utils.regex A utility class to make searching a Sequence with many regex patterns easier. Search(FiniteAlphabet) - Constructor for class org.biojava.utils.regex.Search Search.Listener - Interface in org.biojava.utils.regex Interface for a class that will recieve match information from this class. searchAnnotation(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type. SearchBuilder - Interface in org.biojava.bio.search The SearchBuilder interface is to be used by objects which accumulate state via a SearchContentHandler and then construct a SeqSimilaritySearchResult object. SearchContentAdapter - Class in org.biojava.bio.search An adapter for SearchContentHandler. SearchContentAdapter() - Constructor for class org.biojava.bio.search.SearchContentAdapter SearchContentFilter - Class in org.biojava.bio.search Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain. SearchContentFilter(SearchContentHandler) - Constructor for class org.biojava.bio.search.SearchContentFilter SearchContentHandler - Interface in org.biojava.bio.search SearchContentHandler is a notification interface for objects which listen to search stream parsers. SearchContentHandlerDebugger - Class in org.biojava.bio.search This class prints to a PrintStream calls to the SearchContentHandler interface in human readable form. SearchContentHandlerDebugger() - Constructor for class org.biojava.bio.search.SearchContentHandlerDebugger Create an instance that dumps to System.out. SearchContentHandlerDebugger(PrintStream) - Constructor for class org.biojava.bio.search.SearchContentHandlerDebugger SearchException - Exception in org.biojava.bio.program.ssaha There has been some failure that prevents a search from completing. SearchException(String) - Constructor for exception org.biojava.bio.program.ssaha.SearchException SearchException(String, Throwable) - Constructor for exception org.biojava.bio.program.ssaha.SearchException SearchException(Throwable) - Constructor for exception org.biojava.bio.program.ssaha.SearchException SearchListener - Interface in org.biojava.bio.program.ssaha The interface used to inform interested parties that some sequence has been searched and something found. SearchListener.Echo - Class in org.biojava.bio.program.ssaha A SearchListener that prints events out to a PrintStream. SearchListener.FilterByLength - Class in org.biojava.bio.program.ssaha A simple listener that filters out all hits that are too short. SearchListener.Tee - Class in org.biojava.bio.program.ssaha A SearchListener that passes events on to two delegate listeners. SearchListener.Wrapper - Class in org.biojava.bio.program.ssaha A simple wrapper implementation. sec() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Selenocysteine (U) SEC_ACC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat SECONDARY_ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat SECONDARY_ACCESSIONS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat secondarySequenceToGraphics(int) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext secondarySequenceToGraphics converts a sequence coordinate on the secondary sequence to a graphical position. secondarySequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel secondarySequenceToGraphics converts a sequence index to a graphical position. secondarySequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext SecondaryStructureFeatureRenderer - Class in org.biojava.bio.gui.sequence A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands). SecondaryStructureFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer sectp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat seek(long) - Method in class org.biojava.utils.io.CachingInputStream seek(long) - Method in class org.biojava.utils.io.RandomAccessReader seek moves the pointer to the specified position. seek(long) - Method in interface org.biojava.utils.io.Seekable Moves the pointer in the inputstream such that the byte starting at pos are returned by the next read. Seekable - Interface in org.biojava.utils.io This interface provides a collective name for IO classes that implement a seek function (e.g., RandomAccessFile). select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.ProportionalSelection select(Population, GeneticAlgorithm) - Method in interface org.biojavax.ga.functions.SelectionFunction Selects a Population of Organisms for replication based on their fitness. select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold Selects individuals whose fitness (as determined by the FitnessFunction) is more than the cutoff. select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.TournamentSelection Standard call to select organisms, will select a number of Organisms corresponding to 75 % of the population. SelectAll() - Constructor for class org.biojavax.ga.functions.SelectionFunction.SelectAll SELECTION_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm SelectionFunction - Interface in org.biojavax.ga.functions Selects Organisms for Replication and returns the offspring. SelectionFunction.SelectAll - Class in org.biojavax.ga.functions SelectionFunction.Threshold - Class in org.biojavax.ga.functions Selects individuals who's fitness exceeds a threshold value. SelectionScalar(BitSet) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar Make a new SelectionScalar that masks in different depths. selectNIndividuals(Population, GeneticAlgorithm, int) - Method in class org.biojavax.ga.functions.TournamentSelection This method selects n Organism from the population it is given, using the tournament selection method sendAlignmentRequest(int, RemotePairwiseAlignmentProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a GenBank GID. sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a string representing the sequence. sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object sendAlignmentRequest(RichSequence, RemotePairwiseAlignmentProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a RichSequence. sendAlignmentRequest(RichSequence, RemotePairwiseAlignmentProperties) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object SEPARATED - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization SEPARATOR_COLOR - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option Option indicating the color that the call separators should be. SEPARATOR_STROKE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option Option providing the the stroke to use for drawing call separators. SEPARATOR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. seq - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement seq - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase SeqCaution() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution Creates a new instance. SeqContentPattern - Class in org.biojava.bio.search A pattern that can be used to find regions with given sequence content. SeqContentPattern(FiniteAlphabet) - Constructor for class org.biojava.bio.search.SeqContentPattern Create a new SeqContentPattern over an alphabet. SeqFileFormer - Interface in org.biojava.bio.seq.io Deprecated. Use org.biojavax.bio.seq.io framework instead SeqIOAdapter - Class in org.biojava.bio.seq.io Adapter class for SeqIOListener that has empty methods. SeqIOAdapter() - Constructor for class org.biojava.bio.seq.io.SeqIOAdapter SeqIOConstants - Class in org.biojava.bio.seq.io SeqIOConstants contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing sequences. SeqIOConstants() - Constructor for class org.biojava.bio.seq.io.SeqIOConstants SeqIOEventEmitter - Class in org.biojava.bio.seq.io Deprecated. Use org.biojavax.bio.seq.io framework instead SeqIOEventEmitter(Comparator, Comparator) - Constructor for class org.biojava.bio.seq.io.SeqIOEventEmitter Deprecated. SeqIOFilter - Class in org.biojava.bio.seq.io Base-class for listeners that pass filtered events onto another listener. SeqIOFilter(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.SeqIOFilter Create a new SeqIOFilter that will forward events on to another listener. SeqIOListener - Interface in org.biojava.bio.seq.io Notification interface for objects which listen to a sequence stream parser. SeqIOTools - Class in org.biojava.bio.seq.io Deprecated. use org.biojavax.bio.seq.RichSequence.IOTools seqNameForID(int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore seqNameForID(int) - Method in interface org.biojava.bio.program.ssaha.DataStore Resolve an ID to a sequence name. seqPanels - Variable in class org.biojava.bio.gui.sequence.SequencePanelWrapper seqs - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor SeqSimilarityAdapter - Class in org.biojava.bio.program.ssbind A SeqSimilarityAdapter converts SAX events into method calls on a SearchContentHandler implementation. SeqSimilarityAdapter() - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityAdapter SeqSimilaritySearcher - Interface in org.biojava.bio.search Objects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP. SeqSimilaritySearchHit - Interface in org.biojava.bio.search Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search. SeqSimilaritySearchHit.ByScoreComparator - Class in org.biojava.bio.search ByScoreComparator compares SeqSimilaritySearchHits by their score. SeqSimilaritySearchHit.BySubHitCountComparator - Class in org.biojava.bio.search BySubHitCountComparator compares SeqSimilaritySearchHits by their number of sub-hits. SeqSimilaritySearchResult - Interface in org.biojava.bio.search Objects of this type represent one particular result of a sequence similarity search. SeqSimilaritySearchSubHit - Interface in org.biojava.bio.search Objects of this type represent one particular sub-hit (one concrete sequence stretch within a sequence and associated information) from a sequence similarity search hit. SeqSimilaritySearchSubHit.ByScoreComparator - Class in org.biojava.bio.search ByScoreComparator compares SeqSimilaritySearchSubHits by their score. SeqSimilaritySearchSubHit.BySubjectStartComparator - Class in org.biojava.bio.search BySubjectStartComparator compares SeqSimilaritySearchSubHits by their start position on the subject sequence. SeqSimilarityStAXAdapter - Class in org.biojava.bio.program.ssbind SeqSimilarityStAXAdapter is a handler for XML conforming to the BioJava BlastLike DTD. SeqSimilarityStAXAdapter() - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter SeqSimilarityStAXHandler - Class in org.biojava.bio.program.ssbind SeqSimilarityStAXHandler is a base class for creating modular StAX handlers which send callbacks to a SeqSimilarityStAXAdapter. SeqSimilarityStAXHandler(SeqSimilarityStAXAdapter) - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler Creates a new SeqSimilarityStAXHandler which simply maintains a list of StAXHandlerBindings and delegates to any suitable StAXContentHandler bound by one of them. seqString() - Method in class org.biojava.bio.dp.SimpleStatePath seqString() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment seqString() - Method in class org.biojava.bio.seq.impl.DummySequence seqString() - Method in class org.biojava.bio.seq.impl.SimpleSequence seqString() - Method in class org.biojava.bio.seq.impl.SubSequence seqString() - Method in class org.biojava.bio.seq.impl.ViewSequence seqString() - Method in class org.biojava.bio.seq.NewSimpleAssembly seqString() - Method in class org.biojava.bio.seq.SimpleAssembly seqString() - Method in class org.biojava.bio.symbol.AbstractSymbolList seqString() - Method in class org.biojava.bio.symbol.RelabeledAlignment seqString() - Method in interface org.biojava.bio.symbol.SymbolList Stringify this symbol list. seqString() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList Stringify this symbol list. seqString() - Method in class org.biojavax.bio.seq.ThinRichSequence Stringify this symbol list. seqString(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler Stringify this Sequences. seqString(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler Stringify this Sequences. seqString(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler Stringify this Sequences. sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler sequence(String) - Method in interface org.biojava.bio.program.fastq.ParseListener Notify this parse listener of a sequence line. Sequence - Interface in org.biojava.bio.seq A biological sequence. SEQUENCE - Static variable in interface org.biojava.bio.dp.StatePath Alignment label for the emitted sequence. SEQUENCE - Static variable in class org.biojava.bio.program.abi.ABITools Alignment label for the DNA sequence row. SEQUENCE_CAUTION - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser A name for a comment type. SEQUENCE_CHECKSUM_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat SEQUENCE_FORMAT - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory SEQUENCE_FORMAT is the key used to identify the format of the indexed sequence files represented by the store in the OBDA config.dat files. SEQUENCE_LENGTH_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat SEQUENCE_LENGTH_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat SEQUENCE_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat SEQUENCE_MODIFIED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat SEQUENCE_TOPOLOGY_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat SEQUENCE_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat SEQUENCE_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat SEQUENCE_VERSION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat SequenceAlignmentSAXParser - Class in org.biojava.bio.program.sax A SAX2 parser for dealing with a sequence alignments. SequenceAlignmentSAXParser() - Constructor for class org.biojava.bio.program.sax.SequenceAlignmentSAXParser Initialises internal state Sets namespace prefix to "biojava" sequenceAndQualityLengthsMatch() - Method in class org.biojava.bio.program.fastq.FastqBuilder Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length. SequenceAnnotator - Interface in org.biojava.bio.seq An object which adds some additional information to a Sequence. SequenceBuilder - Interface in org.biojava.bio.seq.io Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object. SequenceBuilderBase - Class in org.biojava.bio.seq.io Basic SequenceBuilder implementation which accumulates all notified information. SequenceBuilderBase() - Constructor for class org.biojava.bio.seq.io.SequenceBuilderBase SequenceBuilderFactory - Interface in org.biojava.bio.seq.io Simple factory for constructing new SequenceBuilder objects. SequenceBuilderFilter - Class in org.biojava.bio.seq.io Base-class for builders that pass filtered events onto another builder. SequenceBuilderFilter(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SequenceBuilderFilter Create a new SeqIOFilter that will forward events on to another listener. SequenceContentHandlerBase - Class in org.biojava.bio.seq.io.game StAX handler for elements containing sequence SequenceContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.game.SequenceContentHandlerBase SequenceDB - Interface in org.biojava.bio.seq.db A database of sequences with accessible keys and iterators over all sequences. SequenceDBDataSource - Class in org.biojava.bio.seq.distributed Turn an entire SequenceDB instance into a DistDataSource. SequenceDBDataSource(SequenceDB) - Constructor for class org.biojava.bio.seq.distributed.SequenceDBDataSource SequenceDBInstallation - Interface in org.biojava.bio.seq.db A SequenceDBInstallation has the functionality of a factory for SequenceDB objects and additionally manages the SequenceDB objects created by itself such that the minimum number of SequenceDB objects is created by a particular SequenceDBInstallation object. SequenceDBLite - Interface in org.biojava.bio.seq.db A database of sequences. SequenceDBProvider - Interface in org.biojava.directory Interfaces for named resources that can provide sequences via a database given some configuration information as defined by the OBDA standard. SequenceDBSearchHit - Class in org.biojava.bio.search Deprecated. SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical. SequenceDBSearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List) - Constructor for class org.biojava.bio.search.SequenceDBSearchHit Deprecated. Creates a new SequenceDBSearchHit object. SequenceDBSearchResult - Class in org.biojava.bio.search Deprecated. SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical. SequenceDBSearchResult(Sequence, SequenceDB, Map, List, Annotation) - Constructor for class org.biojava.bio.search.SequenceDBSearchResult Deprecated. Creates a new SequenceDBSearchResult. SequenceDBSearchSubHit - Class in org.biojava.bio.search Deprecated. SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical. SequenceDBSearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation) - Constructor for class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. Creates a new SequenceDBSearchSubHit object. SequenceDBSequenceBuilder - Class in org.biojava.bio.seq.io This SequenceBuilder has a variety of modes of operation. SequenceDBSequenceBuilder(SequenceDB, int) - Constructor for class org.biojava.bio.seq.io.SequenceDBSequenceBuilder constructor SequenceDBStreamer(SequenceDB) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer SequenceDBWrapper - Class in org.biojava.bio.seq.db An abstract implementation of SequenceDB that wraps up another database. SequenceDBWrapper(SequenceDB) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper SequenceDBWrapper.SequencesForwarder - Class in org.biojava.bio.seq.db sequenceExtentOfPixels(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer SequenceFactory - Interface in org.biojava.bio.seq Deprecated. use org.biojavax.bio.seq.io.RichSequenceBuilder or use org.biojavax.bio.seq.io.SequenceBuilder SequenceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter SequenceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter SequenceFormat - Interface in org.biojava.bio.seq.io Defines what a sequence format does. SequenceHandler - Interface in org.biojava.bio.seq.io.agave mark interface sequenceIterator() - Method in class org.biojava.bio.seq.db.AbstractSequenceDB sequenceIterator() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB sequenceIterator() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB Deprecated. sequenceIterator() - Method in class org.biojava.bio.seq.db.DummySequenceDB sequenceIterator() - Method in class org.biojava.bio.seq.db.HashSequenceDB sequenceIterator() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB sequenceIterator() - Method in interface org.biojava.bio.seq.db.SequenceDB Returns a SequenceIterator over all sequences in the database. sequenceIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB sequenceIterator() - Method in interface org.biojavax.bio.db.RichSequenceDB Returns a SequenceIterator over all sequences in the database. SequenceIterator - Interface in org.biojava.bio.seq An iterator over a bag of sequences. SequencePanel - Class in org.biojava.bio.gui.sequence A panel that displays a Sequence. SequencePanel() - Constructor for class org.biojava.bio.gui.sequence.SequencePanel Create a new SequencePanel. SequencePanel.Border - Class in org.biojava.bio.gui.sequence SequencePanelWrapper - Class in org.biojava.bio.gui.sequence Handles multiple SequencePanels and Ranges so that a Sequence can be wrapped over more than one line on screen. SequencePanelWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequencePanelWrapper Creates a new instance of WrappedSequencePanel SequencePoster - Class in org.biojava.bio.gui.sequence Deprecated. This doesn't handle loads of stuff. Use SequencePoster. SequencePoster() - Constructor for class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Create a new SeqeuncePanel. SequencePoster.Border - Class in org.biojava.bio.gui.sequence Deprecated. SequenceRenderContext - Interface in org.biojava.bio.gui.sequence A context within which sequence information may be rendered. SequenceRenderContext.Border - Class in org.biojava.bio.gui.sequence The metric object for the 'border' area - the area between the extent of the rendered area and the beginning or end of the sequence. SequenceRenderer - Interface in org.biojava.bio.gui.sequence The interface for things that can render a line of information about a sequence. SequenceRenderer.RendererForwarder - Class in org.biojava.bio.gui.sequence SequenceRendererWrapper - Class in org.biojava.bio.gui.sequence An implementation of SequenceRenderer that delegates rendering to another renderer. SequenceRendererWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper Create a new renderer with no wrapped renderer. SequenceRendererWrapper(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper Create a new wrapper with a wrapped renderer SEQUENCES - Static variable in interface org.biojava.bio.seq.db.SequenceDBLite Signals that sequences are being added to or remove from the database. SequencesAsGFF - Class in org.biojava.bio.program.gff Turns a sequence database into a GFF event stream. SequencesAsGFF() - Constructor for class org.biojava.bio.program.gff.SequencesAsGFF SequencesForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder SequenceStreamer - Interface in org.biojava.bio.program.ssaha SequenceStreamer.FileStreamer - Class in org.biojava.bio.program.ssaha SequenceStreamer.SequenceDBStreamer - Class in org.biojava.bio.program.ssaha sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel sequenceToGraphics converts a sequence index to a graphical position. sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. sequenceToGraphics(int) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext Converts a sequence index into a graphical coordinate. sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel sequenceToGraphics converts a sequence index to a graphical position. SequenceTools - Class in org.biojava.bio.seq Methods for manipulating sequences. SequenceViewerEvent - Class in org.biojava.bio.gui.sequence An event indicating that a mouse gesture was recognised within a widget that renders sequences. SequenceViewerEvent(Object, Object, int, MouseEvent, List) - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerEvent Construct a SequenceViewerEvent with the given source, target, mouseEvent and path. SequenceViewerListener - Interface in org.biojava.bio.gui.sequence SequenceViewerMotionListener - Interface in org.biojava.bio.gui.sequence SequenceViewerMotionSupport - Class in org.biojava.bio.gui.sequence SequenceViewerMotionSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport SequenceViewerSupport - Class in org.biojava.bio.gui.sequence SequenceViewerSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerSupport SEQVERSION - Static variable in interface org.biojavax.bio.BioEntry ser() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Serine (S) serialize(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat Deprecated. serialize(Taxon) - Method in interface org.biojava.bio.taxa.TaxonParser Deprecated. Convert a Taxon into a stringified representation. serializeSource(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat Deprecated. serializeXRef(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat Deprecated. serialVersionUID - Static variable in class org.biojava.bio.dp.SimpleMarkovModel serialVersionUID - Static variable in class org.biojava.bio.symbol.AbstractAlphabet serialVersionUID - Static variable in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties serialVersionUID - Static variable in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties series - Variable in class org.biojava.bibliography.BiblioBook Book series. ServerSide() - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ServerSide Creates a new ServerSide image map. Services - Class in org.biojava.utils Utility methods for handling META-INF/services files Services() - Constructor for class org.biojava.utils.Services set(int, Object) - Method in class org.biojava.utils.FileAsList This always returns null, not the previous object. set(Object, Object) - Method in class org.biojava.utils.ListTools.Doublet set(Object, Object, Object) - Method in class org.biojava.utils.ListTools.Triplet setA(Object) - Method in class org.biojava.utils.ListTools.Doublet setA(Object) - Method in class org.biojava.utils.ListTools.Triplet setAbsorptionMax(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property absorptionMax. setAbsorptionNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property absorptionNote. setAccession(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setAccession(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setAccession(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener the accession of the record being read. setAccession(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener the accession of the record being read. setAcronym(String) - Method in interface org.biojavax.Namespace Sets an optional acronym for the namespace. setAcronym(String) - Method in class org.biojavax.SimpleNamespace Sets an optional acronym for the namespace. setAddPos(boolean) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier Set a flag so that newly added points will be in the positive class or negative class, depending on wether addPos is true or false respectively. setAdvance(int[]) - Method in interface org.biojava.bio.dp.EmissionState Set the advance array. setAdvance(int[]) - Method in class org.biojava.bio.dp.SimpleEmissionState setAdvancedOptions(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties This method is to be used if a request is to use non-default values at submission. setAlignementOption(String, String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties setAlignementOption(String, String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties Method to set the value for a specific alignment parameter using a key to store in a map. setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border Deprecated. setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border Sets the Alignment attribute of the Border object. setAlignment(Alignment) - Method in class org.biojava.bio.seq.homol.SimpleHomology setAlignment sets the alignment which describes the homology. setAlignmentNumber(int) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties A method to set the number of alignments to fetch to the GET command. setAlignmentOutputFormat(RemoteQBlastOutputFormat) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties This method is use to set the alignment output format to get from the QBlast service setAlpha(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel setAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel setAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel setAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel setAlphabetName(String) - Method in class org.biojavax.bio.seq.SimpleRichSequence setAlphabetName(String) - Method in class org.biojavax.bio.seq.ThinRichSequence setAlphaStar(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel setAnnotation(Annotation) - Method in class org.biojava.bio.dp.SimpleEmissionState setAnnotation(Annotation) - Method in class org.biojava.ontology.Term.Impl setApplicationClass(Class, Class) - Static method in class org.biojavax.RichObjectFactory Allow application to override the default biojava class created in getObject - subclass restriction is checked in the builder. setArrowHeadSize(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer setArticleAuthors(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex Sets the names of the authors which first published an article about the AAindex entry. setArticleTitle(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex Sets the title of the article which describes the AAindex entry. setAuthority(String) - Method in interface org.biojavax.Namespace This method sets the authority that governs the namespace. setAuthority(String) - Method in class org.biojavax.SimpleNamespace This method sets the authority that governs the namespace. setB(Object) - Method in class org.biojava.utils.ListTools.Doublet setB(Object) - Method in class org.biojava.utils.ListTools.Triplet setBaseCallAlignment(Alignment) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram Provides the list of base calls. setBaseColor(Symbol, Color) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Maps a color to a DNA symbol. setBeadDepth(double) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer setBeadDepth sets the depth of a single bead produced by this renderer. setBeadDisplacement(double) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer setBeadDisplacement sets the displacement of beads from the centre line of the renderer. setBeadFill(Paint) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer setBeadFill sets the bead fill paint. setBeadOutline(Paint) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer setBeadOutline sets the bead outline paint. setBeadStroke(Stroke) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer setBeadStroke sets the bead outline stroke. setBits(int) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram Sets the number of significant bits in the trace samples. setBlastDatabase(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties This method set the database to be use with blastall setBlastProgram(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties This method set the program to be use with blastall. setBlockDepth(double) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer setBlockDepth(double) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer setBlockPainter(BlockPainter) - Method in class org.biojava.bio.gui.DistributionLogo setBlockParser(String, NexusBlockParser) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract setBlockParser(String, NexusBlockParser) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener Sets the parser to use for a given block. setBlockWidth(double) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer setBooleanValue(boolean) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase Override this method to do something useful with the boolean we collect. setBoundaryFinder(BoundaryFinder) - Method in class org.biojava.bio.program.tagvalue.Aggregator setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph setBounds(Rectangle2D.Float) - Method in interface org.biojava.bio.gui.glyph.Glyph setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.HelixGlyph setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.TurnGlyph setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph setByteValue(byte) - Method in class org.biojava.utils.stax.ByteElementHandlerBase Override this method to do something useful with the byte we collect. setC(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer setC(double) - Method in class org.biojava.stats.svm.SMOTrainer setC(Object) - Method in class org.biojava.utils.ListTools.Triplet setCategory(String) - Method in class org.biojava.ontology.Synonym setChanger(Object, ChangeTable.Changer) - Method in class org.biojava.bio.program.tagvalue.ChangeTable Set the Changer to be used for all values of a particular tag. setChangeTable(ChangeTable) - Method in class org.biojava.bio.program.tagvalue.ValueChanger setCharacter(char) - Method in class org.biojava.utils.RepeatedCharSequence setCharStateLabel(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setCharStateLabel(String, String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setCharStateLabel(String, String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setCharValue(char) - Method in class org.biojava.utils.stax.CharElementHandlerBase Override this method to do something useful with the char we collect. setChildrenRaw(Set) - Method in class org.biojava.bio.taxa.WeakTaxon Deprecated. setChromatogram(Chromatogram) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Sets the chromatogram to draw. setChromImpl(SymbolList[]) - Method in class org.biojavax.ga.impl.AbstractOrganism setChromImpl(SymbolList[]) - Method in class org.biojavax.ga.impl.SimpleOrganism setChromosome(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation setChromosomes(SymbolList[]) - Method in class org.biojavax.ga.impl.AbstractOrganism setChromosomes(SymbolList[]) - Method in interface org.biojavax.ga.Organism Sets the organisms 'chromosome' sequences. setCircular(boolean) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setCircular(boolean) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setCircular(boolean) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Defined this sequence being parser as circular. setCircular(boolean) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Defined this sequence being parser as circular. setCircular(boolean) - Method in interface org.biojavax.bio.seq.RichSequence Circularises the Sequence. setCircular(boolean) - Method in class org.biojavax.bio.seq.ThinRichSequence Circularises the Sequence. setCircularLength(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation Sets the circular length of this location. setCircularLength(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation Sets the circular length of this location. setCircularLength(int) - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation Sets the circular length of this location. setCircularLength(int) - Method in interface org.biojavax.bio.seq.RichLocation Sets the circular length of this location. setCircularLength(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation Sets the circular length of this location. setCodeGenerator(CodeMethod, CodeGenerator) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass setCollapsing(boolean) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer Specifies if the renderer should collapse to zero depth when no features are visible (default true). setCommands(String) - Method in class org.biojava.utils.process.ExternalProcess Sets the command line including the path or name of the external program and its command line arguments. setComment(Object, String) - Method in class org.biojava.bio.AnnotationType.Impl setComment(Object, String) - Method in interface org.biojava.bio.AnnotationType Set the comment for a particular property. setComment(String) - Method in class org.biojava.bio.AnnotationType.Impl setComment(String) - Method in interface org.biojava.bio.AnnotationType Set the comment for the whole AnnotationType. setComment(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord Set the comment to comment. setComment(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex Sets the user comment for the AAindex entry. setComment(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setComment(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setComment(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener about a comment in the record being read. setComment(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener about a comment in the record being read. setComment(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event Setter for property comment. setComment(String) - Method in class org.biojavax.SimpleComment setCommentType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property commentType. setCommonName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon Deprecated. setCommonName(String) - Method in interface org.biojava.bio.taxa.Taxon Deprecated. Set the new common name of this Taxon. setCommonName(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. With this method the common name of the given taxon can be changed or created, if there was none before. setConstant(double) - Method in class org.biojava.stats.svm.PolynomialKernel setConstant(double) - Method in class org.biojava.stats.svm.SigmoidKernel setConstraint(Object, CollectionConstraint) - Method in class org.biojava.bio.AnnotationType.Impl setConstraint(Object, CollectionConstraint) - Method in interface org.biojava.bio.AnnotationType Specifies the constraint to apply to the specified property. setConstraints(Object, PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract setConstraints(Object, PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType Set the constraints associated with a property. setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser sets the ContentHandler for this object setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade this sets the ContentHandler that receives SAX events from the internal Blast XML parser which is the actual ContentHandler. setContinueOnEmptyTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser Choose whether to treat empty tags as a continuation of previous tags or as a new tag with the value of the empty string. setContinueOnEmptyTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser Decide whether to treat empty tags as continuations of the previous non -empty tag. setCount(AtomicSymbol, double) - Method in interface org.biojava.bio.dist.Count Set the count for the Symbol s. setCount(AtomicSymbol, double) - Method in class org.biojava.bio.dist.IndexedCount setCounts(Count) - Method in interface org.biojava.bio.dist.Count Set the counts in this Counts to be equal to the counts in c. setCounts(Count) - Method in class org.biojava.bio.dist.IndexedCount setCreateOnUnderlyingSequence(boolean) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence setCrossOverFunction(CrossOverFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm Changes the CrossOverFunction used to CrossOver Chromosomes setCrossOverFunction(CrossOverFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm setCrossOverProbs(double[]) - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction setCrossOverProbs(double[]) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross setCrossOverProbs(double[]) - Method in interface org.biojavax.ga.functions.CrossOverFunction Sets the probability of crossing at each base. setCrossref(CrossRef) - Method in interface org.biojavax.DocRef The document reference may refer to an object in another database. setCrossref(CrossRef) - Method in class org.biojavax.SimpleDocRef The document reference may refer to an object in another database. setCrossRef(CrossRef) - Method in class org.biojavax.bio.seq.SimpleRichLocation setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.CompoundRichLocation Sets the cross ref resolver to use when retrieving remote symbols. setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.EmptyRichLocation Sets the cross ref resolver to use when retrieving remote symbols. setCrossRefResolver(CrossReferenceResolver) - Method in interface org.biojavax.bio.seq.RichLocation Sets the cross ref resolver to use when retrieving remote symbols. setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.SimpleRichLocation Sets the cross ref resolver to use when retrieving remote symbols. setCurrentSequenceName(String) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder setCurrentSequenceName(String) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener Set the name of the sequence which is about to be received. setDatabase(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB setDatabaseID(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser setDatabaseID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder setDatabaseID(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory setDatabaseID(String) - Method in class org.biojava.bio.search.FilteringContentHandler setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentAdapter setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentFilter setDatabaseID(String) - Method in interface org.biojava.bio.search.SearchContentHandler setDatabaseID identifies the database searched by a name, ID or URN. setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger setDatabaseName(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property databaseName. setDataType(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setDataType(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setDataType(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setDbCode(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref setDefaultBlockParsers() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder setDefaultBlockParsers() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract setDefaultBlockParsers() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener Causes the default block parsers to be assigned. setDefaultChanger(ChangeTable.Changer) - Method in class org.biojava.bio.program.tagvalue.ValueChanger The changer that will be applied to the values of tags not registered explicitly to any changer or splitter instance. setDefaultConstraint(CollectionConstraint) - Method in class org.biojava.bio.AnnotationType.Impl setDefaultConstraint(CollectionConstraint) - Method in interface org.biojava.bio.AnnotationType Specifies the default constraint to apply to properties where no other constraint is specified. setDefaultConstraints(PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract setDefaultConstraints(PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType Set the constraints that will apply to all properties without an explicitly defined set of constraints. setDefaultCrossReferenceResolver(CrossReferenceResolver) - Static method in class org.biojavax.RichObjectFactory Sets the default crossref resolver to use when resolving remote entries. setDefaultNamespaceName(String) - Static method in class org.biojavax.RichObjectFactory Sets the default namespace name to use when loading sequences. setDefaultOntologyName(String) - Static method in class org.biojavax.RichObjectFactory Sets the default ontology name to use when loading sequences. setDefaultPaint(Paint) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer setDefaultPositionResolver(PositionResolver) - Static method in class org.biojavax.RichObjectFactory Sets the default position resolver to use when creating new rich feature locations. setDefaultRichSequenceHandler(RichSequenceHandler) - Static method in class org.biojavax.RichObjectFactory Sets the default sequence handler to use when performing sequence manipulation. setDefaultSplitter(ChangeTable.Splitter) - Method in class org.biojava.bio.program.tagvalue.ValueChanger The splitter that will be applied to the values of tags not registered explicitly to any changer or splitter instance. setDefaultTransitions(StateMachine.TransitionTable) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState specify fallback TransitionTable for this State setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.StateMachine TagValueWrapper interface setDelegate(TagValueListener) - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper set listener to which all calls will be delegated setDelegateParser(TagValueParser) - Method in class org.biojava.bio.program.tagvalue.TagDelegator setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer setDelegateRenderer associates an OptimizableFilter with a BeadFeatureRenderer. setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer setDelegateRenderer associates an OptimizableFilter with a BeadFeatureRenderer. setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer setDelegateRenderer for the specified filter. setDelete(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch Sets the penalty for a delete operation to the specified value. setDelete(short) - Method in class org.biojava.bio.alignment.SmithWaterman Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a delete operation to the specified value. setDeprecated(boolean) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass Set the deprecation flag. setDepth(double) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer setDepth(double) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer setDepth(double) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer setDepth(SequenceRenderer, double) - Method in class org.biojava.bio.gui.sequence.LineInfo setDepthScaler(SuffixTreeKernel.DepthScaler) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel Change the current DepthScaler to depthScaler. setDescription(String) - Method in class org.biojava.bio.alignment.SubstitutionMatrix Sets the description to the given value. setDescription(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex Sets the description for the AAindex entry. setDescription(String) - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable setDescription(String) - Method in class org.biojava.ontology.AbstractTerm setDescription(String) - Method in class org.biojava.ontology.IntegerOntology.IntTerm setDescription(String) - Method in class org.biojava.ontology.IntegerOntology setDescription(String) - Method in class org.biojava.ontology.Ontology.Impl setDescription(String) - Method in interface org.biojava.ontology.Ontology set the description of this ontology setDescription(String) - Method in class org.biojava.ontology.OntologyTerm.Impl setDescription(String) - Method in interface org.biojava.ontology.Term set the description of the term; setDescription(String) - Method in class org.biojava.ontology.Triple.Impl setDescription(String) - Method in interface org.biojavax.bio.BioEntry Sets the description for this bioentry. setDescription(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setDescription(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setDescription(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener the description of the record being read. setDescription(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener the description of the record being read. setDescription(String) - Method in class org.biojavax.bio.SimpleBioEntry Sets the description for this bioentry. setDescription(String) - Method in interface org.biojavax.Namespace This method sets a description for the namespace. setDescription(String) - Method in interface org.biojavax.ontology.ComparableOntology Sets a human-readable description of this ontology. setDescription(String) - Method in interface org.biojavax.ontology.ComparableTerm Sets the description associated with this term. setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableOntology Sets a human-readable description of this ontology. setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableTerm Sets the description associated with this term. setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableTriple set the description of the term; setDescription(String) - Method in class org.biojavax.SimpleNamespace This method sets a description for the namespace. setDescriptionNumber(int) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties A method to set the number of descriptions to fetch to the GET command. setDescriptors(Set) - Method in interface org.biojavax.ontology.ComparableTriple Clears the current set of descriptors and replaces it with the content of the set passed. setDescriptors(Set) - Method in class org.biojavax.ontology.SimpleComparableTriple Clears the current set of descriptors and replaces it with the content of the set passed. setDiagonal(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock setDiagonal(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder setDiagonal(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener setDimensionRatio(double) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer setDimensionRatio sets the minimum ratio of long dimension to short dimension of the bead. setDimensionsNChar(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock Set the NCHAR value. setDimensionsNChar(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setDimensionsNChar(int) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener Set the NCHAR value. setDimensionsNChar(int) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock Set the NCHAR value. setDimensionsNChar(int) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder setDimensionsNChar(int) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener Set the NCHAR value. setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock Set the NTAX value. setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setDimensionsNTax(int) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener Set the NTAX value. setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock Set the NTAX value. setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder setDimensionsNTax(int) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener Set the NTAX value. setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock Set the NTAX value. setDimensionsNTax(int) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder setDimensionsNTax(int) - Method in interface org.biojavax.bio.phylo.io.nexus.TaxaBlockListener Set the DIMENSIONS NTAX value. setDirection(int) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph This method allows you to decide in which direction the arrow has to point. setDirection(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel setDirection sets the direction in which this context will render the sequence - HORIZONTAL or VERTICAL. setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel Set the direction that this SequencePanel renders in. setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Set the direction that this SequencePoster renders in. setDirection(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel setDirection sets the direction in which this context will render sequences - HORIZONTAL or VERTICAL. setDistanceBetweenFeatures(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer setDistribution(Distribution) - Method in interface org.biojava.bio.dp.EmissionState Set the Distribution associated with this state. setDistribution(Distribution) - Method in class org.biojava.bio.dp.SimpleEmissionState setDistribution(Distribution) - Method in class org.biojava.bio.gui.DistributionLogo Set the dist to render. setDistribution(Symbol, Distribution) - Method in interface org.biojava.bio.dist.OrderNDistribution Set the distribution assocated with a symbol. setDivision(String) - Method in interface org.biojavax.bio.BioEntry Sets the division of this bioentry. setDivision(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setDivision(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setDivision(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener the division of the record being read. setDivision(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener the division of the record being read. setDivision(String) - Method in class org.biojavax.bio.SimpleBioEntry Sets the division of this bioentry. setDocumentLocator(Locator) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter setDocumentLocator(Locator) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor setDocumentLocator(Locator) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler setDocumentLocator(Locator) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase setDocumentLocator(Locator) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor setDocumentLocator(Locator) - Method in interface org.biojava.utils.stax.StAXContentHandler setDocumentLocator(Locator) - Method in class org.biojava.utils.stax.StAXContentHandlerBase setDoubleProperty(Symbol, String) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable setDoubleValue(double) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase Override this method to do something useful with the double we collect. setDTDHandler(DTDHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade setElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion setElideComments(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat Use this method to toggle reading of comments data. setElideComments(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat Use this method to toggle reading of comments data. setElideFeatures(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat Use this method to toggle reading of feature data. setElideFeatures(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat Use this method to toggle reading of feature data. setElideReferences(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat Use this method to toggle reading of bibliographic reference data. setElideReferences(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat Use this method to toggle reading of bibliographic reference data. setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. Specifies whether the symbols (SQ) part of the entry should be ignored. setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.GenbankFormat Deprecated. Use this method to toggle reading of sequence data. setElideSymbols(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat Use this method to toggle reading of sequence data. setElideSymbols(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat Use this method to toggle reading of sequence data. setEliminateEnd(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setEliminateEnd(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setEliminateEnd(int) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setEliminateStart(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setEliminateStart(int) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setEliminateStart(int) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setEmail(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService Set the email for QBlast. setEmail(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Set the email for Entrez. setEnd(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord Set the end coordinate to end. setEnd(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl setEnd(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion setEnd(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser Set the string indicating that a record has ended. setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.RegexParser Set the explicit end-of-record string. setEntityResolver(EntityResolver) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries. setEnvironmentProperties(String[]) - Method in class org.biojava.utils.process.ExternalProcess Sets environment variables for the external process. setEpsilon(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer setEpsilon(double) - Method in class org.biojava.stats.svm.SMOTrainer setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff.GFFParser Set the error handler used by this parser. setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff3.GFF3Parser Set the error handler used by this parser. setErrorHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess Sets the output error handler which is responsible for the standard error output of the external process. setErrorHandler(ErrorHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade setEvents(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property events. setExceptionOnNullDelegate(boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener determines if an exception is thrown when an event arrives without the delegate being set. setFactory(RichSequenceBuilderFactory) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Setter for property factory. setFactory(RichSequenceBuilderFactory) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB Setter for property factory. setFallback(StateMachine.TransitionTable) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable set the specified TransitionTable to be looked looked up if the Transition cannot be found in this one. setFeature(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter Set the feature to feature. setFeature(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord Set the feature type to type. setFeature(String, boolean) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade by default, we set the parser to non-validating. setFeature(RichFeature) - Method in class org.biojavax.bio.seq.CompoundRichLocation Sets the feature this location is associated with. setFeature(RichFeature) - Method in class org.biojavax.bio.seq.EmptyRichLocation Sets the feature this location is associated with. setFeature(RichFeature) - Method in interface org.biojavax.bio.seq.RichLocation Sets the feature this location is associated with. setFeature(RichFeature) - Method in class org.biojavax.bio.seq.SimpleRichLocation Sets the feature this location is associated with. setFeatureFilter(FeatureFilter) - Method in class org.biojava.bio.program.gff.SequencesAsGFF Replace the current FeatureFilter with filter. setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler Set the object which receives startFeature/endFeature notifications. setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler setFeatureProperty(Object, Object) - Method in class org.biojava.bio.program.xff.FeatureHandler Set a property. setFeatureRealizer(FeatureRealizer) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory Set the FeatureRealizer used by new sequences created by this factory. setFeatureRelationshipSet(Set<RichFeatureRelationship>) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder Clears the relations from this feature holder and replaces them with a new set. setFeatureRelationshipSet(Set<RichFeatureRelationship>) - Method in class org.biojavax.bio.seq.SimpleRichFeature Clears the relations from this feature holder and replaces them with a new set. setFeatureRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer setFeatureRenderer sets the renderer to be used. setFeatureSet(Set<Feature>) - Method in interface org.biojavax.bio.seq.RichSequence Sets the features of this sequence. setFeatureSet(Set<Feature>) - Method in class org.biojavax.bio.seq.ThinRichSequence Sets the features of this sequence. setFeatureSource(FeatureSource) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer setFill(Paint) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer setFill(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer setFill(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer setFill(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer setFill(Paint) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer setFill(Paint) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer setFillColor(Color) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer Set the background color of the label area. setFillPaint(Paint) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph Allows you to set the paint properties of this glyph. setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle setFilter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer setFilter sets the filter. setFirstIntActID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction Setter for property firstIntActID. setFitness(double[]) - Method in class org.biojavax.ga.impl.AbstractOrganism setFitness(double[]) - Method in interface org.biojavax.ga.Organism This method allows to set the fitness of this organism to the specified value. setFitnessFunction(FitnessFunction) - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll setFitnessFunction(FitnessFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm The fitness function that will be used to compute the fitness of each organism. setFitnessFunction(FitnessFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm setFloatValue(float) - Method in class org.biojava.utils.stax.FloatElementHandlerBase Override this method to do something useful with the float we collect. setFont(Font) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper setFrame(int) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter setFrame(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord Set the frame to frame. setGap(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setGap(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setGap(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setGapExt(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch Sets the penalty for an extension of any gap (insert or delete) to the specified value. setGapExt(short) - Method in class org.biojava.bio.alignment.SmithWaterman Overrides the method inherited from the NeedlemanWunsch and sets the penalty for an extension of any gap (insert or delete) to the specified value. setGenerateSequenceHeader(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF Specify whether a per-sequence header line, giving the length of the sequence, should be generated. setGeneticCode(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon Sets the genetic code of this taxon, which may be null, which will unset it. setGeneticCode(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Sets the genetic code of this taxon, which may be null, which will unset it. setGeneticCodeID(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Updates the taxon in the database and sets its genetic code id to the specified value. setGlyphForFilter(FeatureFilter, Glyph) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer Allows setting another Glyph object to be painted for the given FeatureFilter. setGroupAttributes(Map) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord Replace the group-attribute Map with ga. setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler Sets the element name that the class responds to. setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler Sets the element name that the class responds to. setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler Sets the element name that the class responds to. setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler Sets the element name that the class responds to. setHeader(FastaHeader) - Method in class org.biojavax.bio.seq.io.FastaFormat setHeight(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Sets the height (in pixels). setHeightScaling(boolean) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer setHeightScaling sets the height scaling policy. setHeightScaling(boolean) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer setHeightScaling sets the height scaling policy. setHorizontalScale(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Sets the horizontal scale (proportional). setId(Integer) - Method in class org.biojavax.bio.seq.SimplePosition Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichFeature Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichLocation Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.bio.SimpleBioEntry Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.bio.SimpleBioEntryRelationship Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableOntology Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableTerm Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableTriple Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.SimpleComment Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.SimpleCrossRef Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.SimpleDocRef Sets the Hibernate ID. setId(Integer) - Method in class org.biojavax.SimpleNamespace Sets the Hibernate ID. setId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId setID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction Setter for property ID. setIdentifier(String) - Method in interface org.biojavax.bio.BioEntry Sets the identifier of this bioentry. setIdentifier(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setIdentifier(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setIdentifier(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener the identifier of the record being read. setIdentifier(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener the identifier of the record being read. setIdentifier(String) - Method in class org.biojavax.bio.SimpleBioEntry Sets the identifier of this bioentry. setIdentifier(String) - Method in interface org.biojavax.ontology.ComparableTerm Sets the (optional) identifier associated with this term. setIdentifier(String) - Method in class org.biojavax.ontology.SimpleComparableTerm Sets the (optional) identifier associated with this term. setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer setImageMap sets the current image map. setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer setImageMap sets the current image map. setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer setImageMap sets the current image map. setInput(InputStream) - Method in interface org.biojava.utils.process.OutputHandler Sets the input stream. setInput(InputStream) - Method in class org.biojava.utils.process.StreamPipe Sets the input stream setInput(InputStream) - Method in class org.biojava.utils.process.WriterOutputHandler Sets the input stream. setInputHandler(InputHandler) - Method in class org.biojava.utils.process.ExternalProcess Sets the input handler which is responsible for the standard input of the external process. setInsert(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch Sets the penalty for an insert operation to the specified value. setInsert(short) - Method in class org.biojava.bio.alignment.SmithWaterman Overrides the method inherited from the NeedlemanWunsch and sets the penalty for an insert operation to the specified value. setInteractions(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property interactions. setInterleaved(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setInterleaved(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setInterleaved(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setInterleaved(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock setInterleaved(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder setInterleaved(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener setIntValue(int) - Method in class org.biojava.utils.stax.IntElementHandlerBase Override this method to do something useful with the int we collect. setIsoforms(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property isoforms. setIsoIDs(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform Setter for property isoIDs. setIsStrict(boolean) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter Selects strict mode. setIsStrict(boolean) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter Selects strict mode. setJoiner(String) - Method in class org.biojava.bio.program.tagvalue.Aggregator setJournalReference(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex Sets a reference to the journal which published the article about the AAindex entry. setKernel(SVMKernel) - Method in class org.biojava.stats.svm.SVMRegressionModel setKernel(SVMKernel) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier Set the kernel used for classification. setKey(Object) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker setKineticsNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property kineticsNote. setKMs(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property KMs. setLabel(String) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer setLabel(String) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer setLabel(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction Setter for property label. setLabelMaker(FeatureLabelRenderer.LabelMaker) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer setLabels(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setLabels(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setLabels(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setLabels(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock setLabels(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder setLabels(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener setLambda(double) - Method in class org.biojava.stats.svm.DiagonalAddKernel Set the scale factor. setLeadingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer setLeftValue(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon Sets the left value. setLeftValue(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Sets the left value. setLeftValue(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Updates the taxon and sets the left value to the specified value. setLength(int) - Method in class org.biojava.bio.search.SeqContentPattern Set the pattern length. setLength(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList setLength(int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList setLength(int) - Method in class org.biojava.utils.RepeatedCharSequence setLimit(int) - Method in class org.biojava.utils.cache.FixedSizeCache setLines(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Set the absolute number of lines that the sequence will be rendered on. setLineWidth(int) - Method in class org.biojava.bio.program.phred.PhredFormat Set the line width. setLineWidth(int) - Method in class org.biojava.bio.seq.io.FastaFormat Deprecated. Set the line width. setLineWidth(int) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat Set the line width. setLineWidth(int) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat Set the line width. setListener(Object, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator setListener(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState set a TagValueListener for this State. setListener(PatternListener) - Method in class org.biojava.utils.automata.PatternBlitz setListener(PatternListener) - Method in interface org.biojava.utils.automata.StateMachineFactory setListener(Search.Listener) - Method in class org.biojava.utils.regex.Search setLITDBEntryNumbers(String[]) - Method in class org.biojava.bio.proteomics.aaindex.AAindex Sets the list of literature database identifiers for the AAindex entry. setLoc(Location) - Method in interface org.biojava.bio.alignment.AlignmentElement setLoc(Location) - Method in class org.biojava.bio.alignment.SimpleAlignmentElement setLocation(Location) - Method in interface org.biojava.bio.seq.Feature The new location for this feature. setLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleFeature setLocation(Location) - Method in class org.biojavax.bio.seq.SimpleRichFeature The new location for this feature. setLocation(RichLocation) - Method in interface org.biojavax.RankedDocRef Set the location of this reference. setLocation(RichLocation) - Method in class org.biojavax.SimpleRankedDocRef Set the location of this reference. setLocationValue(Location) - Method in class org.biojava.bio.program.xff.LocationHandlerBase Override this method to do something useful with the location we collect. setLogoFont(Font) - Method in class org.biojava.bio.gui.TextBlock Set the current logo font. setLogoFont(Font) - Method in class org.biojava.bio.gui.TextLogoPainter Set the current logo font. setLogoPainter(LogoPainter) - Method in class org.biojava.bio.gui.DistributionLogo Set the logo painter. setLongValue(long) - Method in class org.biojava.utils.stax.LongElementHandlerBase Override this method to do something useful with the long we collect. setLRUCacheSize(int) - Static method in class org.biojavax.RichObjectFactory Sets the size of the LRU cache. setLRUCacheSize(Class, int) - Static method in class org.biojavax.RichObjectFactory Sets the size of the LRU cache. setMapAll(boolean) - Method in class org.biojava.bio.molbio.RestrictionMapper setMapAll sets whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it. setMapType(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation setMatch(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch Sets the penalty for a match operation to the specified value. setMatch(short) - Method in class org.biojava.bio.alignment.SmithWaterman Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a match operation to the specified value. setMatchChar(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setMatchChar(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setMatchChar(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setMaxCounts(AtomicSymbol, int) - Method in class org.biojava.bio.search.SeqContentPattern Set the maximum counts required for a symbol. setMaxCrossOvers(int) - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction setMaxCrossOvers(int) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross setMaxCrossOvers(int) - Method in interface org.biojavax.ga.functions.CrossOverFunction Sets an upper limit on the number of crosses. setMaxMissedCleavages(int) - Method in class org.biojava.bio.proteomics.Digest Sets the maximum number of partial digest products to be annotated. setMaxPosition(Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation setMaxRunTimeSecs(int) - Method in class org.biojava.utils.ExecRunner Sets the maximum run time in seconds. setMergeAnnotation(Annotation) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler setMergeSameTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser Enable or disable treating runs of identical tags as a single tag start event with multiple values or each as a separate tag start, value, and tag end. setMergeSameTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser Decide if multiple examples of a single tag should be merged into a single start/endTag pair with multiple values, or multiple start/endTag pairs each with a single value. setMinCounts(AtomicSymbol, int) - Method in class org.biojava.bio.search.SeqContentPattern Set the minimum counts required for a symbol. setMinPosition(Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation setMismatches(int) - Method in class org.biojava.bio.search.MaxMismatchPattern setMissing(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setMissing(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setMissing(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setMissing(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock setMissing(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder setMissing(String) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener setMitochondrialGeneticCodeID(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Updates the given taxon and sets it's so called mitochondrial genetic code id to the specified value. setMitoGeneticCode(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon Sets the mitochondrial genetic code of this taxon, which may be null, which will unset it. setMitoGeneticCode(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Sets the mitochondrial genetic code of this taxon, which may be null, which will unset it. setModel(MarkovModel) - Method in class org.biojava.bio.dp.DP setModeLazy() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter setModeLazy() - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser Setting the mode to lazy means that, if the program is recognised, e.g. setModeStrict() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter setModeStrict() - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser This is the default, parsing will be attempted only if both the program e.g. setMolecularWeight(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property molecularWeight. setMolWeightError(Integer) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property molWeightError. setMolWeightMethod(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property molWeightMethod. setMolWeightRangeEnd(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property molWeightRangeEnd. setMolWeightRangeStart(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property molWeightRangeStart. setMoreSearches(boolean) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentAdapter setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentFilter setMoreSearches(boolean) - Method in interface org.biojava.bio.search.SearchContentHandler setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results. setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger setMultiplier(double) - Method in class org.biojava.stats.svm.PolynomialKernel setMultiplier(double) - Method in class org.biojava.stats.svm.SigmoidKernel setMutationFunction(MutationFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm Sets the current MutationFunction setMutationFunction(MutationFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm setMutationProbs(double[]) - Method in class org.biojavax.ga.functions.AbstractMutationFunction setMutationProbs(double[]) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation setMutationProbs(double[]) - Method in interface org.biojavax.ga.functions.MutationFunction Set the probability of a mutation occuring at a certain position Position 0 in the array corresponds to the probability of the first residue of seq mutating. setMutationSpectrum(OrderNDistribution) - Method in class org.biojavax.ga.functions.AbstractMutationFunction setMutationSpectrum(OrderNDistribution) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation setMutationSpectrum(OrderNDistribution) - Method in interface org.biojavax.ga.functions.MutationFunction Sets the Distribution of Symbols that will be selected from when a mutation occurs. setName(String) - Method in class org.biojava.bio.dp.SimpleEmissionState setName(String) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet set the name of this group. setName(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet setName(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence Assign a name to this sequence setName(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer Deprecated. setName(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer Deprecated. setName(String) - Method in class org.biojava.bio.seq.io.SeqIOAdapter setName(String) - Method in class org.biojava.bio.seq.io.SeqIOFilter setName(String) - Method in interface org.biojava.bio.seq.io.SeqIOListener Notify the listener that the current sequence is generally known by a particular name. setName(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase setName(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter setName(String) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer Deprecated. The name is printed out as part of the identifier line. setName(String) - Method in class org.biojava.bio.symbol.SimpleAlphabet Assign a name to the alphabet setName(String) - Method in class org.biojava.ontology.IntegerOntology setName(String) - Method in class org.biojava.ontology.Ontology.Impl setName(String) - Method in interface org.biojava.ontology.Ontology Set the name for this ontology setName(String) - Method in class org.biojava.ontology.Synonym setName(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setName(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setName(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Notify the listener that the current sequence is generally known by a particular name. setName(String) - Method in interface org.biojavax.bio.seq.RichFeature Sets the name of this feature. setName(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature Sets the name of this feature. setName(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName Changes the name. setName(String) - Method in class org.biojavax.ga.impl.AbstractOrganism setName(String) - Method in class org.biojavax.ga.impl.AbstractPopulation setName(String) - Method in interface org.biojavax.ga.Organism Sets the organisms name setName(String) - Method in interface org.biojavax.ga.Population Sets the name of the population setName(String) - Method in class org.biojavax.ontology.SimpleComparableOntology setNameClass(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName Changes the class of this name. setNamedIsoforms(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event Setter for property namedIsoforms. setNames(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform Setter for property names. setNamespace(Namespace) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Setter for property namespace. setNamespace(Namespace) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB Setter for property namespace. setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setNamespace(Namespace) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener the namespace of the record being read. setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener the namespace of the record being read. setNegShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier Set the Shape to represent the negative points. setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.CachingKernel setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.DiagonalCachingKernel Set the kernel to nest. setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.NestedKernel Set the SVMKernel to nest to k. setNewTag(Object, Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper setNewTag. setNodePrefix(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock Sets the node prefix of intermediate nodes for returned graphs. setNodeRank(String) - Method in interface org.biojavax.bio.taxa.NCBITaxon Sets the node rank of this taxon. setNodeRank(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Setter for property nodeRank. setNormalizingVector(SparseVector) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel Set the normalizing vector. setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform Setter for property note. setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property note. setNoteSet(Set) - Method in class org.biojavax.bio.seq.CompoundRichLocation Clears the notes associated with this object and replaces them with the contents of this set. setNoteSet(Set) - Method in class org.biojavax.bio.seq.EmptyRichLocation Clears the notes associated with this object and replaces them with the contents of this set. setNoteSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature Clears the notes associated with this object and replaces them with the contents of this set. setNoteSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichLocation Clears the notes associated with this object and replaces them with the contents of this set. setNoteSet(Set) - Method in class org.biojavax.EmptyRichAnnotation Clears the notes from this annotation and replaces them with those from the given set. setNoteSet(Set) - Method in class org.biojavax.SimpleCrossRef Clears the notes associated with this object and replaces them with the contents of this set. setNoteSet(Set<Note>) - Method in class org.biojavax.bio.SimpleBioEntry Clears the notes associated with this object and replaces them with the contents of this set. setNoteSet(Set<Note>) - Method in interface org.biojavax.RichAnnotatable Clears the notes associated with this object and replaces them with the contents of this set. setNoteSet(Set<Note>) - Method in interface org.biojavax.RichAnnotation Clears the notes from this annotation and replaces them with those from the given set. setNoteSet(Set<Note>) - Method in class org.biojavax.SimpleRichAnnotation Clears the notes from this annotation and replaces them with those from the given set. setNullModel(Distribution) - Method in class org.biojava.bio.dist.AbstractDistribution setNullModel(Distribution) - Method in interface org.biojava.bio.dist.Distribution Set the null model Distribution that this Distribution recognizes. setNullModel(Distribution) - Method in class org.biojava.bio.dist.GapDistribution setNullModel(Distribution) - Method in class org.biojava.bio.dist.PairDistribution setNullModel(Distribution) - Method in class org.biojava.bio.dist.TranslatedDistribution setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.AbstractDistribution Implement this to set the null model. setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.SimpleDistribution setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.UniformDistribution Assign a background distribution. setNullModelWeight(double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext Set the number of pseudocounts to add when training the distribution. setNullModelWeight(double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext setNumber(float) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode Set the number associated with this node. setNumberExperiments(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction Setter for property numberExperiments. setObsolete(Boolean) - Method in interface org.biojavax.ontology.ComparableTerm Sets the obsolescence flag associated with this term. setObsolete(Boolean) - Method in class org.biojavax.ontology.SimpleComparableTerm Sets the obsolescence flag associated with this term. setOffset(double) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel setOption(ChromatogramGraphic.Option, Object) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Sets a new value for the specified option. setOrder(double) - Method in class org.biojava.stats.svm.PolynomialKernel setOrganismsDiffer(boolean) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction Setter for property organismsDiffer. setOrientation(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation setOuterPaint(Paint) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph Allows setting the paint properties of the outer line of this glyph to the given value. setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer setOutline sets the the colour used to draw the lines. setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer setOutline sets the the colour used to draw the lines. setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle setOutput(OutputStream) - Method in interface org.biojava.utils.process.InputHandler Sets the output stream. setOutput(OutputStream) - Method in class org.biojava.utils.process.ReaderInputHandler Sets the output stream. setOutput(OutputStream) - Method in class org.biojava.utils.process.StreamPipe Sets the output stream setOutputFormat(RemoteQBlastOutputFormat) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties This method is use to set the stream output format to get from the QBlast service setOutputHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess Sets the output handler which is responsible for the standard output of the external process. setOutputOption(String, String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties setOutputOption(String, String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties Method to set the value for a specific output parameter using a key to store in a map. setPadding(double) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer Set the padding. setPaint(Paint) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph Allows you to set the paint properties of this glyph, i.e., its color. setPaint(Paint) - Method in class org.biojava.bio.gui.glyph.TurnGlyph Allows you to set the paint properties of this glyph, i.e., its color. setParent(Connection, Taxon, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. This updates the taxonomic tree in the database and sets the parent of the given child taxon to the parent taxon. setParent(FeatureHolder) - Method in interface org.biojavax.bio.seq.RichFeature Sets the parent of this feature. setParent(FeatureHolder) - Method in class org.biojavax.bio.seq.SimpleRichFeature Sets the parent of this feature. setParentNCBITaxID(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon Sets the parent NCBI taxon ID. setParentNCBITaxID(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Sets the parent NCBI taxon ID. setParserListener(Object, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator setPathPrefix(File) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore setPathPrefix sets the abstract path to be appended to sequence database filenames retrieved from the binary index. setPattern(Pattern) - Method in class org.biojava.bio.program.tagvalue.RegexParser Set the Pattern used to split lines. setPattern(SymbolList) - Method in class org.biojava.bio.search.MaxMismatchPattern setPhase(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl setPHDependence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property PHDependence. setPopulation(Population) - Method in interface org.biojavax.ga.GeneticAlgorithm Sets the Population of Organisms to the Algorithm. setPopulation(Population) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm setPos(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition setPositionResolver(PositionResolver) - Method in class org.biojavax.bio.seq.EmptyRichLocation Sets the resolver to use when working out actual base coordinates from fuzzy positions. setPositionResolver(PositionResolver) - Method in interface org.biojavax.bio.seq.RichLocation Sets the resolver to use when working out actual base coordinates from fuzzy positions. setPositionResolver(PositionResolver) - Method in class org.biojavax.bio.seq.SimpleRichLocation Sets the resolver to use when working out actual base coordinates from fuzzy positions. setPositions(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution setPosShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier Set the Shape to represent the positive points. setPrimaryKey(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory setPrimaryKey sets the primary identifier namespace. setPrimaryKeyName(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model Set the tag to use as a primary key in the index. setPrimaryKeyName(String) - Method in class org.biojava.bio.program.tagvalue.Indexer Set the tag to use as a primary key in the index. setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.EmblFileFormer Deprecated. setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFileFormer Deprecated. setPrintStream(PrintStream) - Method in interface org.biojava.bio.seq.io.SeqFileFormer Deprecated. setPrintStream informs an instance which PrintStream to use. setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer Deprecated. setPrintStream informs an instance which PrintStream to use. setPrintStream(PrintStream) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat Sets the stream to write to. setPrintStream(PrintStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat Sets the stream to write to. setPrintWriter(PrintWriter) - Method in class org.biojava.bio.program.blast2html.HTMLRenderer Set the PrintWriter to output the HTML to. setProfileHMM() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser setProperty(Object, Object) - Method in class org.biojava.bio.AbstractAnnotation setProperty(Object, Object) - Method in interface org.biojava.bio.Annotation Set the value of a property. setProperty(Object, Object) - Method in class org.biojava.bio.MergeAnnotation setProperty(Object, Object) - Method in class org.biojava.bio.OverlayAnnotation setProperty(Object, Object) - Method in class org.biojavax.EmptyRichAnnotation Set the value of a property. setProperty(Object, Object) - Method in class org.biojavax.SimpleRichAnnotation Deprecated. setProperty(String, Object) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade setProperty(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler setProperty(String, String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler setProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract setProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType Set the property in an annotation bundle according to the type we believe it should be. setProtease(Protease) - Method in class org.biojava.bio.proteomics.Digest setProtype(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionEnzyme Set the prototype of this RestrictionEnzyme. setQueryID(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser setQueryID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder setQueryID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder setQueryID(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder setQueryID(String) - Method in class org.biojava.bio.search.FilteringContentHandler setQueryID(String) - Method in class org.biojava.bio.search.SearchContentAdapter setQueryID(String) - Method in class org.biojava.bio.search.SearchContentFilter setQueryID(String) - Method in interface org.biojava.bio.search.SearchContentHandler setQueryID identifies the query sequence by a name, ID or URN. setQueryID(String) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger setQuerySeq(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser Deprecated. use setQueryID instead. setQuerySeqHolder(SequenceDB) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder setQuerySeqHolder sets the query sequence holder to a specific database. setQuerySeqHolder(SequenceDB) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory setQuerySeqHolder sets the query sequence holder to a specific database. setRadius(double) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanel setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout setRange(RangeLocation) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout setRank(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation Sets the rank for this location. setRank(int) - Method in interface org.biojavax.bio.seq.RichFeature Sets the rank of this feature. setRank(int) - Method in interface org.biojavax.bio.seq.RichFeatureRelationship Sets the rank of this relationship. setRank(int) - Method in interface org.biojavax.bio.seq.RichLocation Sets the rank for this location. setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichFeature Sets the rank of this feature. setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship Sets the rank of this relationship. setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation Sets the rank for this location. setRank(int) - Method in interface org.biojavax.Comment Sets the rank of this comment. setRank(int) - Method in interface org.biojavax.Note Sets the rank for this note. setRank(int) - Method in interface org.biojavax.RankedCrossRef Set the rank associated with the cross reference. setRank(int) - Method in interface org.biojavax.RankedDocRef Set the rank of this reference. setRank(int) - Method in class org.biojavax.SimpleComment Sets the rank of this comment. setRank(int) - Method in class org.biojavax.SimpleNote Sets the rank for this note. setRank(int) - Method in class org.biojavax.SimpleRankedCrossRef Set the rank associated with the cross reference. setRank(int) - Method in class org.biojavax.SimpleRankedDocRef Set the rank of this reference. setRank(Integer) - Method in interface org.biojavax.bio.BioEntryRelationship Sets the rank of this relationship. setRank(Integer) - Method in class org.biojavax.bio.SimpleBioEntryRelationship Sets the rank of this relationship. setRank(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Updates a taxon and sets it's rank to the specified String. setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener about a cross reference. setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener about a cross reference. setRankedCrossRefs(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature Sets the ranked cross references associated with an object. setRankedCrossRefs(Set) - Method in class org.biojavax.ontology.SimpleComparableTerm Sets the ranked cross references associated with an object. setRankedCrossRefs(Set<RankedCrossRef>) - Method in class org.biojavax.bio.SimpleBioEntry setRankedCrossRefs(Set<RankedCrossRef>) - Method in interface org.biojavax.RankedCrossRefable Sets the ranked cross references associated with an object. setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener about a literature reference in the record being read. setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener about a literature reference in the record being read. setReader(Reader) - Method in class org.biojava.utils.process.ReaderWriterPipe Sets the reader. setRecurse(boolean) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer setRecurse(boolean) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer setRecurse sets the recursion flag on the filter. setRecurse(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF Set whether features will be filtered recursively to recurse. setRecursive(boolean) - Method in interface org.biojava.bio.seq.io.agave.DelegationManager setRedoxPotential(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property redoxPotential. setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry. setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry. setRemark(String) - Method in interface org.biojavax.DocRef Set the remarks for this document reference using this method. setRemark(String) - Method in class org.biojavax.SimpleDocRef Set the remarks for this document reference using this method. setRenderer(CircularFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer setRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel setRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer setRenderer sets the renderer. setRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel setRenderer sets the current PairwiseSequenceRenderer. setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer Set the child renderer responsible for drawing the contents of this track setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanel setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel setRenderer sets the current SequenceRenderer. setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.DistributionLogo setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel setRenderingHints sets the RenderingHints which will be used by the Graphics2D instances of delegate renderers. setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePanel Use this to switch on effects like Anti-aliasing etc setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Use this to switch on effects like Anti-aliasing etc setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel setRenderingHints sets the RenderingHints which will be used by the Graphics2D instances of delegate renderers. setReplace(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch Sets the penalty for a replace operation to the specified value. setReplace(short) - Method in class org.biojava.bio.alignment.SmithWaterman Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a replace operation to the specified value. setRespectCase(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setRespectCase(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setRespectCase(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setRetain(boolean) - Method in class org.biojava.bio.program.tagvalue.TagDropper Set wether known tags are to be retained or dropped. setRichObjectBuilder(RichObjectBuilder) - Static method in class org.biojavax.RichObjectFactory Sets the builder to use when instantiating new Rich objects. setRightValue(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon Sets the right value. setRightValue(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Sets the right value. setRightValue(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Updates the taxon in the database and sets the right value to the specified value. setRootType(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString Make the tree (un)rooted. setScale(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel setScale sets the scale in pixels per Symbol. setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePanel Set the scale. setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Set the scale. setScale(double) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel setScale sets the scale in pixels per Symbol. setScaleByInformation(boolean) - Method in class org.biojava.bio.gui.DistributionLogo setScientificName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon Deprecated. setScientificName(String) - Method in interface org.biojava.bio.taxa.Taxon Deprecated. Change the scientific name of this species. setScientificName(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. This changes the scientific name of the given taxon and stores the new name persistent in the database. setScope(int) - Method in class org.biojava.ontology.Synonym setScore(double) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix setScore(double) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord Set the score to score. setScore(double) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl setScore(int) - Method in class org.biojava.bio.alignment.SimpleAlignment setScore(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter setSearchContentHandler sets the handler which will recieve the method calls generated by the adapter. setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter setSearchContentHandler sets the handler which will recieve the method calls generated by the adapter. setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.search.FilteringContentHandler setSecondarySequence(Sequence) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel setSecondarySequence sets the secondary Sequence to be rendered. setSecondarySymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel setSecondarySymbolTranslation sets the translation in Symbols which will be applied when rendering. setSecondIntActID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction Setter for property secondIntActID. setSelectionFunction(SelectionFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm Changes the SelectionFunction used to select candidates for the next generation setSelectionFunction(SelectionFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm setSelectionPressure(int) - Method in class org.biojavax.ga.functions.TournamentSelection sets the parameter controlling selection pressure setSeqCautions(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property seqCautions. setSeqID(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser Deprecated. setSeqName(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter Set the sequence name to seqName. setSeqName(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord Set the sequence name to seqName. setSequence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel setSequence sets the Sequence to be rendered. setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Set the SymboList to be rendered. setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout setSequence(Sequence) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout setSequence(Sequence) - Method in class org.biojava.bio.proteomics.Digest setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.SequencePanel Set the SymboList to be rendered. setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel setSequence sets the Sequence to be rendered. setSequenceCount(int) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder setSequenceCount(int) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener Set the number of sequences in the alignment. setSequenceDB(SequenceDB) - Method in class org.biojava.bio.gui.FeatureTree Use this method to provide the sequences for the tree to work with. setSequenceFormat(SequenceFormat) - Method in class org.biojava.bio.seq.db.NCBISequenceDB setSequenceFormat(LifeScienceIdentifier) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory setSequenceFormat sets the sequence format name which will be indicated in the index. setSequenceID(String) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl setSequenceLength(int) - Method in class org.biojavax.bio.seq.SimpleRichSequence setSequenceLength(int) - Method in class org.biojavax.bio.seq.ThinRichSequence setSequenceOffset(int) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer setSequenceRef(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform Setter for property sequenceRef. setSequenceType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform Setter for property sequenceType. setSeqVersion(Double) - Method in interface org.biojavax.bio.seq.RichSequence Sets the version of the associated symbol list. setSeqVersion(Double) - Method in class org.biojavax.bio.seq.ThinRichSequence Sets the version of the associated symbol list. setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setSeqVersion(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener the version of the sequence of the record being read. setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener the version of the sequence of the record being read. setShatter(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF Specify whether features with non-contiguous locations should be broken up such that a GFF feature line is emitted for each contiguous block. setShowAccession(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader setShowDescription(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader setShowIdentifier(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader setShowName(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader setShowNamespace(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader setShowVersion(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader Determines if the version number of a sequence should be displayed. setSibling(SimilarityPairFeature) - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature setSibling sets the sibling feature of the pair. setSibling(SimilarityPairFeature) - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature setSignificantBits(int) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram Sets the number of significant bits in the data. setSitesCount(int) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder setSitesCount(int) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener Set the number of sites in the alignment setSize(double) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border Sets the size of the border in number of pixels. setSleepTime(int) - Method in class org.biojava.utils.process.ExternalProcess Sets the number of milliseconds the ExternalProcess.execute(Properties) method should pauses after the external process is terminated. setSource(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter Set the source to source. setSource(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord Set the feature source to source. setSource(String) - Method in interface org.biojava.bio.seq.Feature Change the source of the Feature. setSource(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature setSource(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation setSource(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature Change the source of the Feature. setSource(Term) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl setSourceFile(String) - Method in class org.biojava.utils.bytecode.GeneratedCodeClass Set the source file associated with this code class. setSourceTerm(Term) - Method in interface org.biojava.bio.seq.Feature Set the source ontology-term for this feature. setSourceTerm(Term) - Method in class org.biojava.bio.seq.impl.SimpleFeature setSourceTerm(Term) - Method in class org.biojavax.bio.seq.SimpleRichFeature Set the source ontology-term for this feature. setSpacer(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. Set the number of pixels to leave blank between each block of sequence information. setSplitOffset(int) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser Set the offset to split lines at. setSplitter(Object, ChangeTable.Splitter) - Method in class org.biojava.bio.program.tagvalue.ChangeTable Set the Splitter to be used for all values of a particular tag. setStarred(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString Sets whether this tree has a star before it's name. setStart(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord Set the start coordinate to start. setStart(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion setStatesFormat(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setStatesFormat(String) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setStatesFormat(String) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setStoreLocation(File) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory setStoreLocation sets the directory of the new index. setStoreName(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory setStoreName sets the name to be given to the new index. setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord Set the strand to strand. setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature setStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.StrandedFeature Set the strand that this feature lies upon. setStrand(StrandedFeature.Strand) - Method in class org.biojavax.bio.seq.SimpleRichFeature Set the strand that this feature lies upon. setStrand(RichLocation.Strand) - Method in class org.biojavax.bio.seq.SimpleRichLocation setStreamParser(StreamParser) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase assign a StreamParser object to instance. setStringSequence(String) - Method in class org.biojavax.bio.seq.SimpleRichSequence setStringValue(String) - Method in class org.biojava.bio.program.xff.PropDetailHandler setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMENamePropHandler setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMETypePropHandler setStringValue(String) - Method in class org.biojava.utils.stax.StringElementHandlerBase Override this method to do something useful with the string we collect. setStyle(SymbolStyle) - Method in class org.biojava.bio.gui.DistributionLogo Set the symbol style. setSubjectDB(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser Deprecated. use setDatabaseID instead. setSubjectDBInstallation(SequenceDBInstallation) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder setSubjectDBInstallation sets the subject database holder to a specific installation. setSubjectDBInstallation(SequenceDBInstallation) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory setSubjectDBInstallation sets the subject database holder to a specific installation. setSubMatrix(SubstitutionMatrix) - Method in class org.biojava.bio.alignment.SmithWaterman setSubSeqStart(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation setSubstitutionMatrix(SubstitutionMatrix) - Method in class org.biojava.bio.alignment.NeedlemanWunsch Sets the substitution matrix to be used to the specified one. setSymbolList(SymbolList) - Method in class org.biojava.bio.molbio.Composition Set the SymbolList to calculation the composition of. setSymbolLists(SymbolList, SymbolList) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram Set the DNA and OFFSETS symbol lists for the basecall alignment. setSymbolModification(char, double) - Method in class org.biojava.bio.proteomics.MassCalc Use this to set a post translational modification for the Symbol represented by this character. setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel setSymbolTranslation sets the translation in Symbols which will be applied when rendering. setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel setSymbolTranslation sets the translation in Symbols which will be applied when rendering. setSynonyms(Set<Object>) - Method in class org.biojava.ontology.Term.Impl setTableNumber(int) - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable setTagGroup(int) - Method in class org.biojava.bio.program.tagvalue.RegexParser Set the group number that will match the tag. setTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget setTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget setTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget setTaxon(NCBITaxon) - Method in interface org.biojavax.bio.BioEntry Sets the taxon for this bioentry. setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setTaxon(NCBITaxon) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener the Taxon of the record being read. setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener the Taxon of the record being read. setTaxon(NCBITaxon) - Method in class org.biojavax.bio.SimpleBioEntry Sets the taxon for this bioentry. setTaxonHidden(boolean) - Method in interface org.biojavax.bio.taxa.NCBITaxon determines whether this taxonomy level is displayed in etNameHierarchy() setTaxonHidden(boolean) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon setTemperatureDependence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property temperatureDependence. setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.CompoundRichLocation Sets the term for this location. setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.EmptyRichLocation Sets the term for this location. setTerm(ComparableTerm) - Method in interface org.biojavax.bio.seq.RichLocation Sets the term for this location. setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.SimpleRichLocation Sets the term for this location. setTerm(ComparableTerm) - Method in interface org.biojavax.Note Sets the term for this note. setTerm(ComparableTerm) - Method in class org.biojavax.SimpleNote Sets the term for this note. setTermSet(Set) - Method in interface org.biojavax.ontology.ComparableOntology Clears out all the terms and populates the ontology with the contents of the set passed. setTermSet(Set) - Method in class org.biojavax.ontology.SimpleComparableOntology Clears out all the terms and populates the ontology with the contents of the set passed. setText(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property text. setTextColor(Color) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer Set the color of the label text setThreshold() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel setThreshold(double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel setThreshold(double) - Method in interface org.biojava.stats.svm.SVMClassifierModel setThreshold(double) - Method in class org.biojava.stats.svm.SVMRegressionModel setTickDirection(int) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer setTitle(String) - Method in interface org.biojava.bio.program.homologene.Orthologue setTitle(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthologue setTokens(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setTokens(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setTokens(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setTool(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService Set the tool identifier for QBlast. setTool(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB Set the tool identifier for Entrez. setTrace(ABITrace) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer setTrace(AtomicSymbol, int[], int) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram Provides the trace samples for a particular nucleotide. setTraceValues(AtomicSymbol, int[], int) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram Sets the trace array for one of the DNA nucleotides. setTrackLayout(TrackLayout) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper setTrailingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer setTransition(Object, StateMachine.State) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState set a Transition for this State setting notifyOnExit to false. setTransition(Object, StateMachine.State, boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState set a Transition for this State setTransition(Object, StateMachine.State, boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable set a Transition within this TransitionTable (3-argument form) setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable Alter the translation mapping. setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable Alter the translation mapping. setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable Alter the translation mapping. setTransposed(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock setTransposed(boolean) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder setTransposed(boolean) - Method in interface org.biojavax.bio.phylo.io.nexus.CharactersBlockListener setTreeString(String) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString Set the Newick string describing the tree. setTriangle(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock setTriangle(String) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder setTriangle(String) - Method in interface org.biojavax.bio.phylo.io.nexus.DistancesBlockListener setTrimTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser Enable or disable trimming of tags. setTrimTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser Enable trimming of the tag using String.trim(). setTrimValue(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser Enable or disable trimming of values. setTrimValue(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser Enable trimming of the value using String.trim(). setTripleSet(Set) - Method in interface org.biojavax.ontology.ComparableOntology Clears out all the triples and populates the ontology with the contents of the set passed. setTripleSet(Set) - Method in class org.biojavax.ontology.SimpleComparableOntology Clears out all the triples and populates the ontology with the contents of the set passed. setType(String) - Method in interface org.biojava.bio.seq.Feature Change the type of this feature. setType(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature setType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event Setter for property type. setType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution setType(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature Change the type of this feature. setType(AnnotationType) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType setType(Term) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl setTypeTerm(Term) - Method in interface org.biojava.bio.seq.Feature Set the type ontology-term for this feature. setTypeTerm(Term) - Method in class org.biojava.bio.seq.impl.SimpleFeature setTypeTerm(Term) - Method in class org.biojavax.bio.seq.SimpleRichFeature Set the type ontology-term for this feature. setUnits(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation setUri(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property uri. setURI(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer Deprecated. setURI(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer Deprecated. setURI(String) - Method in class org.biojava.bio.seq.io.SeqIOAdapter setURI(String) - Method in class org.biojava.bio.seq.io.SeqIOFilter setURI(String) - Method in interface org.biojava.bio.seq.io.SeqIOListener Notify the listener of a URI identifying the current sequence. setURI(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase setURI(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter setURI(String) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer Deprecated. Null implementation. setURI(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setURI(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setURI(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Deprecated. There is no clear mapping between URI and BioSQL. This method is no longer used or supported in biojavax. Don't use it. Calling it may result in exceptions. Use instead setName(String name), setAccession(String accession), setVersion(int version) etc as appropriate. setURI(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Notify the listener of a URI identifying the current sequence. setURI(URI) - Method in interface org.biojavax.Namespace Sets an optional URI for the namespace. setURI(URI) - Method in class org.biojavax.SimpleNamespace Sets an optional URI for the namespace. setURN(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence Provide the URN for this sequence setUserObject(Object) - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot setUserObject sets the user object. setValue(double) - Method in interface org.biojava.stats.svm.ItemValue setValue(double) - Method in class org.biojava.stats.svm.SimpleItemValue setValue(String) - Method in interface org.biojavax.Note Sets the value for this note, or null for no value. setValue(String) - Method in class org.biojavax.SimpleNote Sets the value for this note, or null for no value. setValueGroup(int) - Method in class org.biojava.bio.program.tagvalue.RegexParser Set the group number that will match the value. setVectorNTISupport(boolean) - Method in class org.biojava.bio.seq.io.GenbankFileFormer Deprecated. VectorNTI requires GenBank format to be a little more specific than required by the GenBank definition. setVersion(int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener setVersion(int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter setVersion(int) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener Call back method so the event emitter can tell the listener the version of the record being read. setVersion(int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Call back method so the event emitter can tell the listener the version of the record being read. setVersion(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId setVerticalScale(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Sets the vertical scale (proportional). setVMaxes(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser Setter for property VMaxes. setWeight(Object, double) - Method in class org.biojavax.ga.util.WeightedSet Sets the weight of an Object. setWeight(Symbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution Set the weight of a given symbol in this distribution. setWeight(Symbol, double) - Method in interface org.biojava.bio.dist.Distribution Set the probability or odds that Symbol s is emitted by this state. setWeight(Symbol, double) - Method in class org.biojava.bio.dist.GapDistribution setWeight(Symbol, double) - Method in class org.biojava.bio.dist.PairDistribution setWeight(Symbol, double) - Method in class org.biojava.bio.dist.TranslatedDistribution setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution Implement this to actually set the weight. setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution Set a weight in one of the conditioned distributions. setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.UniformDistribution setWeightMatrixID(String) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator Set the weight matrix id. setWeights(State, Distribution) - Method in interface org.biojava.bio.dp.MarkovModel Set the probability distribution over the transitions from 'source'. setWeights(State, Distribution) - Method in class org.biojava.bio.dp.SimpleMarkovModel Use this methods to customize the transition probabilities. setWeights(State, Distribution) - Method in class org.biojava.bio.dp.WMAsMM setWidth(double) - Method in class org.biojava.stats.svm.RadialBaseKernel setWidth(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Sets the width of the whole graphic (in pixels). setWorkingDirectory(File) - Method in class org.biojava.utils.process.ExternalProcess Sets the working directory for the external process. setWrap(int) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper setWrap(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout setWrap(int) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout setWrap(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout setWrapIncrement(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout setWrapIncrement(int) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout setWrapIncrement(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout setWrappedKernel(SVMKernel) - Method in class org.biojava.stats.svm.SigmoidKernel setWriteDocType(boolean) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter Set flag that determines if XML DOCTYPE is written or not. setWriter(Writer) - Method in class org.biojava.utils.process.ReaderWriterPipe Sets the writer. shadow(Location) - Static method in class org.biojava.bio.symbol.LocationTools Return a contiguous location running from the minimum to the maximum points of the specified location. shadowContainedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils Construct a filter which matches features with locations where the interval between the min and max positions are contained by the specified Location. ShadowContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation Creates a filter that returns everything contained within loc. shadowOverlapsLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils Construct a filter which matches features with locations where the interval between the min and max positions are contained by or overlap the specified Location. ShadowOverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation Creates a filter that returns everything overlapping loc. shannonEntropy(Distribution, double) - Static method in class org.biojava.bio.dist.DistributionTools A method to calculate the Shannon Entropy for a Distribution. shift(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment moves the whole sequence shiftAll(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment shiftAtAlignmentLoc(Object, Location, int) - Method in interface org.biojava.bio.alignment.EditableAlignment loc in this case is the Alignment Location shiftAtAlignmentLoc(Object, Location, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment loc in this case is the Alignment Location shiftAtSequenceLoc(Object, Location, int) - Method in interface org.biojava.bio.alignment.EditableAlignment loc in this case is the SymbolList Location shiftAtSequenceLoc(Object, Location, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment loc in this case is the SymbolList Location SHORT_MAX_VALUE - Static variable in class org.biojava.bio.program.scf.SCF Represents the maximum unsigned value of a short for wrapping purposes SHOW_ALL - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler Return default styles SHOW_DIFF - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler As NORMAL except only return if the two colour classes for query and subject are the different SHOW_SAME - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler Only return if the two colour classes for query and subject are the same sibling - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template sibling SimilarityPairFeature field. SIBLING - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature The sibling of this feature has altered. SigmoidKernel - Class in org.biojava.stats.svm This kernel implements a three layer neural net. SigmoidKernel() - Constructor for class org.biojava.stats.svm.SigmoidKernel sign(double) - Static method in class org.biojava.stats.svm.tools.Classify similarEntries() - Method in class org.biojava.bio.proteomics.aaindex.AAindex Returns a map with the names of similar AAindex entries and its correlation coefficients. SIMILARITY_PAIR_FEATURE_TYPE - Static variable in class org.biojava.bio.program.ssbind.SimilarityPairBuilder Constant SIMILARITY_PAIR_FEATURE_TYPE the type String used by SimilarityPairBuilder when creating SimilarityPairFeatures. SimilarityPairBuilder - Class in org.biojava.bio.program.ssbind SimilarityPairBuilder annotates query and subject Sequence with SimilarityPairFeatures created from SAX events supplied via a SeqSimilarityAdapter. SimilarityPairBuilder() - Constructor for class org.biojava.bio.program.ssbind.SimilarityPairBuilder SimilarityPairFeature - Interface in org.biojava.bio.seq.homol SimilarityPairFeature describes a pairwise similarity between two nucleotide sequences (as it extends StrandedFeature). SimilarityPairFeature.EmptyPairwiseAlignment - Class in org.biojava.bio.seq.homol EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists. SimilarityPairFeature.Template - Class in org.biojava.bio.seq.homol Template for construction of SimilarityPairFeatures. SimilarityType - Interface in org.biojava.bio.program.homologene Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues. SIMILARITYTYPE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder SimilarityType.PlaceHolder - Class in org.biojava.bio.program.homologene SIMPLE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter SimpleAlignment - Class in org.biojava.bio.alignment A simple implementation of an Alignment. SimpleAlignment(Map<String, SymbolList>) - Constructor for class org.biojava.bio.alignment.SimpleAlignment Generate an alignment from a list of SymbolLists. SimpleAlignmentElement - Class in org.biojava.bio.alignment SimpleSimpleAlignment is a simple implementation of AlignmentElement. SimpleAlignmentElement(String, SymbolList, Location) - Constructor for class org.biojava.bio.alignment.SimpleAlignmentElement SimpleAlignmentStyler - Class in org.biojava.bio.program.blast2html Simple implementation for specifying markup styles. SimpleAlignmentStyler(int) - Constructor for class org.biojava.bio.program.blast2html.SimpleAlignmentStyler Creates a new SimpleAlignmentStyler instance. SimpleAlphabet - Class in org.biojava.bio.symbol A simple no-frills implementation of the FiniteAlphabet interface. SimpleAlphabet() - Constructor for class org.biojava.bio.symbol.SimpleAlphabet SimpleAlphabet(String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet SimpleAlphabet(Set) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet SimpleAlphabet(Set, String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet SimpleAnnotation - Class in org.biojava.bio A no-frills implementation of Annotation that is just a wrapper around a LinkedHashMap. SimpleAnnotation() - Constructor for class org.biojava.bio.SimpleAnnotation Create a new, empty SimpleAnnotation instance. SimpleAnnotation(Map) - Constructor for class org.biojava.bio.SimpleAnnotation Create a new SimpleAnnotation using the values in a Map. SimpleAnnotation(Annotation) - Constructor for class org.biojava.bio.SimpleAnnotation Create a new SimpleAnnotation by copying the properties from another one. SimpleAnnotationDB - Class in org.biojava.bio.annodb A no-frills implementation of AnnotationDB. SimpleAnnotationDB(String, Set, AnnotationType) - Constructor for class org.biojava.bio.annodb.SimpleAnnotationDB Create a no-frills AnnotationDB instancec. SimpleAnnotFilter - Class in org.biojava.bio.seq.io.agave Basic implementation of AGAVEAnnotFilter SimpleAssembly - Class in org.biojava.bio.seq A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects. SimpleAssembly(int, String, String) - Constructor for class org.biojava.bio.seq.SimpleAssembly Construct a new SimpleAssembly using the DNA alphabet. SimpleAssembly(String, String) - Constructor for class org.biojava.bio.seq.SimpleAssembly Construct a new SimpleAssembly using the DNA alphabet. SimpleAssemblyBuilder - Class in org.biojava.bio.seq.io Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly. SimpleAssemblyBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleAssemblyBuilder SimpleAtomicSymbol - Class in org.biojava.bio.symbol A basic implementation of AtomicSymbol. SimpleAtomicSymbol(Annotation, List) - Constructor for class org.biojava.bio.symbol.SimpleAtomicSymbol SimpleBioEntry - Class in org.biojavax.bio Reference implementation of a BioEntry object which has no features or sequence. SimpleBioEntry() - Constructor for class org.biojavax.bio.SimpleBioEntry SimpleBioEntry(Namespace, String, String, int) - Constructor for class org.biojavax.bio.SimpleBioEntry Creates a new bioentry representing the sequence in the given namespace with the given name, accession and version. SimpleBioEntryRelationship - Class in org.biojavax.bio Represents a relationship between two bioentries that is described by a term and given a rank. SimpleBioEntryRelationship() - Constructor for class org.biojavax.bio.SimpleBioEntryRelationship SimpleBioEntryRelationship(BioEntry, BioEntry, ComparableTerm, Integer) - Constructor for class org.biojavax.bio.SimpleBioEntryRelationship Creates a new instance of SimpleBioEntryRelationship. SimpleChromatogram - Class in org.biojava.bio.chromatogram A basic chromatogram implementation which provides public mutators for setting the various attributes of the chromatogram. SimpleChromatogram() - Constructor for class org.biojava.bio.chromatogram.SimpleChromatogram Creates a new instance of SimpleChromatogram. SimpleCodonPref - Class in org.biojava.bio.symbol a simple no-frills implementation of the CodonPref object that encapsulates codon preference data. SimpleCodonPref(String, Distribution, String) - Constructor for class org.biojava.bio.symbol.SimpleCodonPref SimpleComment - Class in org.biojavax An implementaion of Comment. SimpleComment() - Constructor for class org.biojavax.SimpleComment SimpleComment(String, int) - Constructor for class org.biojavax.SimpleComment Constructs a new, immutable comment, given some text and a rank. SimpleComparableOntology - Class in org.biojavax.ontology Represents an ontology that can be compared to other ontologies. SimpleComparableOntology() - Constructor for class org.biojavax.ontology.SimpleComparableOntology SimpleComparableOntology(String) - Constructor for class org.biojavax.ontology.SimpleComparableOntology Creates a new instance of SimpleComparableOntology with the given, immutable, non-nullable name. SimpleComparableTerm - Class in org.biojavax.ontology A Term object that can be compared and thus sorted. SimpleComparableTerm() - Constructor for class org.biojavax.ontology.SimpleComparableTerm SimpleComparableTriple - Class in org.biojavax.ontology Basic comparable triple, BioSQL style. SimpleComparableTriple() - Constructor for class org.biojavax.ontology.SimpleComparableTriple SimpleCrossOverFunction - Class in org.biojavax.ga.functions Simple Implementation of the CrossOverFunction interface SimpleCrossOverFunction() - Constructor for class org.biojavax.ga.functions.SimpleCrossOverFunction SimpleCrossRef - Class in org.biojavax A basic CrossRef implementation. SimpleCrossRef() - Constructor for class org.biojavax.SimpleCrossRef SimpleCrossRef(String, String, int) - Constructor for class org.biojavax.SimpleCrossRef Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version. SimpleCrossRef(String, String, Integer) - Constructor for class org.biojavax.SimpleCrossRef Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version. SimpleDistribution - Class in org.biojava.bio.dist A simple implementation of a distribution, which works with any finite alphabet. SimpleDistribution(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistribution make an instance of SimpleDistribution with weights identical to the specified Distribution. SimpleDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.SimpleDistribution make an instance of SimpleDistribution for the specified Alphabet. SimpleDistribution.Trainer - Class in org.biojava.bio.dist A simple implementation of a trainer for this class. SimpleDistributionTrainer - Class in org.biojava.bio.dist Deprecated. Distribution impls should be providing custom trainers. SimpleDistributionTrainer(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainer Deprecated. SimpleDistributionTrainerContext - Class in org.biojava.bio.dist A no-frills implementation of DistributionTrainerContext. SimpleDistributionTrainerContext() - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainerContext Create a new context with no initial distributions or trainers. SimpleDocRef - Class in org.biojavax A basic DocRef implementation. SimpleDocRef() - Constructor for class org.biojavax.SimpleDocRef SimpleDocRef(String, String) - Constructor for class org.biojavax.SimpleDocRef Creates a new document reference from the given immutable authors and location and title. SimpleDocRef(String, String, String) - Constructor for class org.biojavax.SimpleDocRef Creates a new document reference from the given immutable authors and location and title. SimpleDocRef(String, String, String, String, String, Integer) - Constructor for class org.biojavax.SimpleDocRef Construct a doc ref with populated cross ref. SimpleDocRef(List<DocRefAuthor>, String) - Constructor for class org.biojavax.SimpleDocRef Creates a new document reference from the given immutable authors and location and title. SimpleDocRef(List<DocRefAuthor>, String, String) - Constructor for class org.biojavax.SimpleDocRef Creates a new document reference from the given immutable authors and location and title. SimpleDocRef(List, String, String, String, String, Integer) - Constructor for class org.biojavax.SimpleDocRef Construct a doc ref with populated cross ref. SimpleDocRefAuthor - Class in org.biojavax Represents an author of a documentary reference. SimpleDocRefAuthor(String) - Constructor for class org.biojavax.SimpleDocRefAuthor Constructs a new author instance from a string. SimpleDocRefAuthor(String, boolean, boolean) - Constructor for class org.biojavax.SimpleDocRefAuthor Constructs a new author instance. SimpleDotState - Class in org.biojava.bio.dp A Dot state that you can make and use. SimpleDotState(char, String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState Deprecated. token is ignored since 1.2. Use the 2-arg constructor instead. SimpleDotState(String) - Constructor for class org.biojava.bio.dp.SimpleDotState SimpleDotState(String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState Construct a new state with the specified name and annotation SimpleEmissionState - Class in org.biojava.bio.dp SimpleEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.dp.SimpleEmissionState SimpleFeature - Class in org.biojava.bio.seq.impl A no-frills implementation of a feature. SimpleFeature(Sequence, FeatureHolder, Feature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFeature Create a SimpleFeature on the given sequence. SimpleFeatureHolder - Class in org.biojava.bio.seq A no-frills implementation of FeatureHolder. SimpleFeatureHolder() - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder Construct a new SimpleFeatureHolder with a non-informative schema. SimpleFeatureHolder(FeatureFilter) - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder Construct a new SimpleFeatureHolder with the specified schema. SimpleFeatureRealizer - Class in org.biojava.bio.seq FeatureRealizer which uses a lookup table to map template classes to implementations. SimpleFeatureRealizer() - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer SimpleFeatureRealizer(FeatureRealizer) - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer SimpleFramedFeature - Class in org.biojava.bio.seq.impl Title: SimpleFramedFeature. SimpleFramedFeature(Sequence, FeatureHolder, FramedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFramedFeature SimpleGACrossResult - Class in org.biojavax.ga.functions Simple implementation of the GACross interface. SimpleGACrossResult(PointLocation[], SymbolList[]) - Constructor for class org.biojavax.ga.functions.SimpleGACrossResult SimpleGappedSequence - Class in org.biojava.bio.seq.impl Simple implementation of GappedSequence. SimpleGappedSequence(GappedSequence) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence SimpleGappedSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence SimpleGappedSequence(Alphabet) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence SimpleGappedSequence.GappedContext - Class in org.biojava.bio.seq.impl SimpleGappedSymbolList - Class in org.biojava.bio.symbol This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps. SimpleGappedSymbolList(Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList SimpleGappedSymbolList(GappedSymbolList) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList Create a new SimpleGappedSymbolList that will view source, inheriting all existing gaps. SimpleGappedSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList Create a new SimpleGappedSymbolList that will view source. SimpleGappedSymbolList.Block - Class in org.biojava.bio.symbol An aligned block. SimpleGeneticAlgorithm - Class in org.biojavax.ga.impl A simple implementation of the GeneticAlgorithm interface it is not intended that this class be overidden, hence it is final. SimpleGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.SimpleGeneticAlgorithm SimpleGeneticAlgorithm(Population, MutationFunction, CrossOverFunction, SelectionFunction) - Constructor for class org.biojavax.ga.impl.SimpleGeneticAlgorithm SimpleGeneticCodeTable - Class in org.biojava.bio.symbol A genetic code translation table representing a translation table in the DDBJ/EMBL/GenBank Feature Table (appendix V). SimpleGeneticCodeTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleGeneticCodeTable Creates a new instance of SimpleGeneticCodeTable SimpleGFFRecord - Class in org.biojava.bio.program.gff A no-frills implementation of a GFFRecord. SimpleGFFRecord() - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord Create a new SimpleGFFRecord with values set to null or zero SimpleGFFRecord(String, String, String, int, int, double, StrandedFeature.Strand, int, String, Map) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord SimpleGFFRecord(GFFRecord) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord Create a new SimpleGFFRecord from GFFRecord object SimpleHMMTrainer - Class in org.biojava.bio.dp SimpleHMMTrainer(MarkovModel) - Constructor for class org.biojava.bio.dp.SimpleHMMTrainer SimpleHomologeneBuilder - Class in org.biojava.bio.program.homologene A simple no-frills implementation of the HomologeneBuilder interface. SimpleHomologeneBuilder() - Constructor for class org.biojava.bio.program.homologene.SimpleHomologeneBuilder SimpleHomologeneDB - Class in org.biojava.bio.program.homologene SimpleHomologeneDB() - Constructor for class org.biojava.bio.program.homologene.SimpleHomologeneDB SimpleHomology - Class in org.biojava.bio.seq.homol A no-frills implementation of Homology. SimpleHomology() - Constructor for class org.biojava.bio.seq.homol.SimpleHomology Creates a new empty SimpleHomology containing no Alignment and no FeatureHolder. SimpleHomologyFeature - Class in org.biojava.bio.seq.impl SimpleHomologyFeature(Sequence, FeatureHolder, HomologyFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleHomologyFeature SimpleIndex - Class in org.biojava.bio.seq.db This is a no-frills implementation of the Index interface. SimpleIndex(File, long, int, String) - Constructor for class org.biojava.bio.seq.db.SimpleIndex Build the index using the given file, start and id SimpleInputHandler - Class in org.biojava.utils.process Simple input handler that reads the input for an external process from an input stream. SimpleInputHandler(InputStream, String) - Constructor for class org.biojava.utils.process.SimpleInputHandler Initializes the simple input handler. SimpleItemValue - Class in org.biojava.stats.svm A no-frills implementation of ItemValue. SimpleItemValue(Object, double) - Constructor for class org.biojava.stats.svm.SimpleItemValue SimpleLabelRenderer - Class in org.biojava.bio.gui.sequence SimpleLabelRenderer() - Constructor for class org.biojava.bio.gui.sequence.SimpleLabelRenderer SimpleManyToOneTranslationTable - Class in org.biojava.bio.symbol A no-frills implementation of a translation table that maps between two alphabets. SimpleManyToOneTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleManyToOneTranslationTable Construct a new translation table. SimpleMarkovModel - Class in org.biojava.bio.dp SimpleMarkovModel(int, Alphabet) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel Deprecated. SimpleMarkovModel(int, Alphabet, String) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel SimpleModelInState - Class in org.biojava.bio.dp SimpleModelInState(MarkovModel, String) - Constructor for class org.biojava.bio.dp.SimpleModelInState SimpleModelTrainer - Class in org.biojava.bio.dp SimpleModelTrainer() - Constructor for class org.biojava.bio.dp.SimpleModelTrainer SimpleMutationFunction - Class in org.biojavax.ga.functions Simple no frills Implementation of the MutationFunction interface SimpleMutationFunction() - Constructor for class org.biojavax.ga.functions.SimpleMutationFunction SimpleNamespace - Class in org.biojavax A basic Namespace implemenation. SimpleNamespace() - Constructor for class org.biojavax.SimpleNamespace SimpleNamespace(String) - Constructor for class org.biojavax.SimpleNamespace Creates a new instance of SimpleNamespace with the given name, which cannot be null. SimpleNCBITaxon - Class in org.biojavax.bio.taxa Reference implementation of NCBITaxon. SimpleNCBITaxon() - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon SimpleNCBITaxon(int) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon Creates a new instance of SimpleNCBITaxon based on the given taxon ID. SimpleNCBITaxon(Integer) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon Creates a new instance of SimpleNCBITaxon based on the given taxon ID. SimpleNCBITaxonName - Class in org.biojavax.bio.taxa Represents a name class plus name combination for an NCBITaxon object. SimpleNCBITaxonName() - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxonName SimpleNCBITaxonName(String, String) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxonName Creates a new taxon name based on the given class and name, both of which cannot be null. SimpleNCBITaxonomyLoader - Class in org.biojavax.bio.taxa.io Loads NCBI taxon information from names.dmp and nodes.dmp, which are two of the files in the archive downloadable at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ . SimpleNCBITaxonomyLoader() - Constructor for class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader SimpleNote - Class in org.biojavax Simple implementation of Note. SimpleNote() - Constructor for class org.biojavax.SimpleNote SimpleNote(ComparableTerm, String, int) - Constructor for class org.biojavax.SimpleNote Creates a new instance of SimpleNote with a given term, value and rank. SimpleOrganism - Class in org.biojavax.ga.impl A Simple Haploid Organism implementation SimpleOrganism() - Constructor for class org.biojavax.ga.impl.SimpleOrganism SimpleOrganism(String) - Constructor for class org.biojavax.ga.impl.SimpleOrganism SimpleOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.SimpleOrganism SimpleOrthologue - Class in org.biojava.bio.program.homologene this entry contains data about the orthologue. SimpleOrthologue(int, String, String, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologue this constructor does the Taxon lookup for you too SimpleOrthologue(Taxon, String, String, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologue SimpleOrthologueSet - Class in org.biojava.bio.program.homologene SimpleOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologueSet SimpleOrthologueSet.Iterator - Class in org.biojava.bio.program.homologene SimpleOrthoPair - Class in org.biojava.bio.program.homologene A no-frills implementation of the OrthoPair interface SimpleOrthoPair(Orthologue, Orthologue, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPair constructor for the curated form of an orthology relationship SimpleOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPair constructor for the computed form of an orthology relationship. SimpleOrthoPairCollection - Class in org.biojava.bio.program.homologene SimpleOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPairCollection SimpleOrthoPairCollection.Iterator - Class in org.biojava.bio.program.homologene SimpleOrthoPairSet - Class in org.biojava.bio.program.homologene a no-frills implementation of a Homologene Group SimpleOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPairSet SimpleOrthoPairSet.Iterator - Class in org.biojava.bio.program.homologene SimpleOutputHandler - Class in org.biojava.utils.process Simple output handler that pipes the output of an external process to an output stream. SimpleOutputHandler(OutputStream, String) - Constructor for class org.biojava.utils.process.SimpleOutputHandler Initializes the simple output handler. SimplePopulation - Class in org.biojavax.ga.impl Simple concrete implementation of the Population interface SimplePopulation() - Constructor for class org.biojavax.ga.impl.SimplePopulation SimplePopulation(String) - Constructor for class org.biojavax.ga.impl.SimplePopulation SimplePosition - Class in org.biojavax.bio.seq A simple implementation of the Position interface. SimplePosition() - Constructor for class org.biojavax.bio.seq.SimplePosition SimplePosition(boolean, boolean, int) - Constructor for class org.biojavax.bio.seq.SimplePosition Constructs a point position, with optionally fuzzy start and end. SimplePosition(boolean, boolean, int, int, String) - Constructor for class org.biojavax.bio.seq.SimplePosition Constructs a range position, with optionally fuzzy start and end. SimplePosition(int) - Constructor for class org.biojavax.bio.seq.SimplePosition Constructs a point position, with no fuzzy start or end. SimplePosition(int, int) - Constructor for class org.biojavax.bio.seq.SimplePosition Constructs a range position, with no fuzzy start or end. SimpleRankedCrossRef - Class in org.biojavax Simple implementation of RankedCrossRef. SimpleRankedCrossRef() - Constructor for class org.biojavax.SimpleRankedCrossRef SimpleRankedCrossRef(CrossRef, int) - Constructor for class org.biojavax.SimpleRankedCrossRef Constructs a new crossref with a rank. SimpleRankedDocRef - Class in org.biojavax Represents a documentary reference. SimpleRankedDocRef() - Constructor for class org.biojavax.SimpleRankedDocRef SimpleRankedDocRef(DocRef, Integer, Integer, int) - Constructor for class org.biojavax.SimpleRankedDocRef Constructs a new docref for a given location. SimpleRankedDocRef(DocRef, RichLocation, int) - Constructor for class org.biojavax.SimpleRankedDocRef Constructs a new docref for a given location. SimpleRemoteFeature - Class in org.biojava.bio.seq.impl A no-frills implementation of a remote feature. SimpleRemoteFeature(Sequence, FeatureHolder, RemoteFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature SimpleRemoteFeature.DBResolver - Class in org.biojava.bio.seq.impl SimpleRestrictionSite - Class in org.biojava.bio.seq.impl SimpleRestrictionSite represents the recognition site of a restriction enzyme. SimpleRestrictionSite(Sequence, FeatureHolder, RestrictionSite.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleRestrictionSite Creates a new SimpleRestrictionSite. SimpleReversibleTranslationTable - Class in org.biojava.bio.symbol A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet. SimpleReversibleTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleReversibleTranslationTable Construct a new translation table. SimpleRichAnnotation - Class in org.biojavax Simple annotation wrapper. SimpleRichAnnotation() - Constructor for class org.biojavax.SimpleRichAnnotation Creates a new, empty instance of SimpleRichAnnotation SimpleRichFeature - Class in org.biojavax.bio.seq A simple implementation of RichFeature. SimpleRichFeature() - Constructor for class org.biojavax.bio.seq.SimpleRichFeature SimpleRichFeature(FeatureHolder, Feature.Template) - Constructor for class org.biojavax.bio.seq.SimpleRichFeature Creates a new instance of SimpleRichFeature based on a template. SimpleRichFeatureRelationship - Class in org.biojavax.bio.seq Represents a relationship between two features that is described by a term. SimpleRichFeatureRelationship() - Constructor for class org.biojavax.bio.seq.SimpleRichFeatureRelationship SimpleRichFeatureRelationship(RichFeature, RichFeature, ComparableTerm, int) - Constructor for class org.biojavax.bio.seq.SimpleRichFeatureRelationship Creates a new instance of SimpleRichFeatureRelationship. SimpleRichLocation - Class in org.biojavax.bio.seq A simple implementation of RichLocation. SimpleRichLocation() - Constructor for class org.biojavax.bio.seq.SimpleRichLocation SimpleRichLocation(Position, int) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation Creates a new instance of SimpleRichSequenceLocation that points to a single position on the positive strand. SimpleRichLocation(Position, int, RichLocation.Strand) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation Creates a new instance of SimpleRichSequenceLocation that points to a single position. SimpleRichLocation(Position, int, RichLocation.Strand, CrossRef) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation Creates a new instance of SimpleRichSequenceLocation that points to a single position on another sequence. SimpleRichLocation(Position, Position, int) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation Creates a new instance of SimpleRichSequenceLocation that points to a range position on the positive strand. SimpleRichLocation(Position, Position, int, RichLocation.Strand) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation Creates a new instance of SimpleRichSequenceLocation that points to a range position. SimpleRichLocation(Position, Position, int, RichLocation.Strand, CrossRef) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation Creates a new instance of SimpleRichSequenceLocation that points to a range position on another sequence. SimpleRichObjectBuilder - Class in org.biojavax Creates objects and returns them, and stores them in an internal map of singletons for reference. SimpleRichObjectBuilder() - Constructor for class org.biojavax.SimpleRichObjectBuilder SimpleRichSequence - Class in org.biojavax.bio.seq A simple implementation of RichSequence. SimpleRichSequence() - Constructor for class org.biojavax.bio.seq.SimpleRichSequence SimpleRichSequence(Namespace, String, String, int, SymbolList, Double) - Constructor for class org.biojavax.bio.seq.SimpleRichSequence Creates a new instance of SimpleRichSequence. SimpleRichSequenceBuilder - Class in org.biojavax.bio.seq.io Constructs BioEntry objects by listening to events. SimpleRichSequenceBuilder() - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Creates a new instance of SimpleRichSequenceBuilder using a SimpleSymbolListFactory with a threshold of zero. SimpleRichSequenceBuilder(SymbolListFactory) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Creates a new instance of SimpleRichSequenceBuilder with the desired symbollistfactory and threshold of zero. SimpleRichSequenceBuilder(SymbolListFactory, int) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Creates a new instance of SimpleRichSequenceBuilder with the desired symbollistfactory and threshold. SimpleRichSequenceBuilderFactory - Class in org.biojavax.bio.seq.io Generates RichSequenceBuilder objects. SimpleRichSequenceBuilderFactory() - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory Creates a new instance of SimpleRichSequenceBuilderFactory SimpleRichSequenceBuilderFactory(SymbolListFactory) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory Creates a new instance of SimpleRichSequenceBuilderFactory SimpleRichSequenceBuilderFactory(SymbolListFactory, int) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory Creates a new instance of SimpleRichSequenceBuilderFactory that uses a specified factory for SymbolLists longer than a specified length. SimpleSeqSimilaritySearchHit - Class in org.biojava.bio.search SimpleSeqSimilaritySearchHit objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object. SimpleSeqSimilaritySearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchHit Creates a new SimpleSeqSimilaritySearchHit object. SimpleSeqSimilaritySearchResult - Class in org.biojava.bio.search SimpleSeqSimilaritySearchResult objects represent a result of a search of a SymbolList against the sequences within a SequenceDB object. SimpleSeqSimilaritySearchResult(Sequence, SequenceDB, Map, List, Annotation) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchResult Creates a new SimpleSeqSimilaritySearchResult. SimpleSeqSimilaritySearchSubHit - Class in org.biojava.bio.search SimpleSeqSimilaritySearchSubHit objects represent sub-hits which make up a hit. SimpleSeqSimilaritySearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit Creates a new SimpleSeqSimilaritySearchSubHit object. SimpleSequence - Class in org.biojava.bio.seq.impl A basic implementation of the Sequence interface. SimpleSequence(SymbolList, String, String, Annotation) - Constructor for class org.biojava.bio.seq.impl.SimpleSequence Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed. SimpleSequence(SymbolList, String, String, Annotation, FeatureRealizer) - Constructor for class org.biojava.bio.seq.impl.SimpleSequence Create a SimpleSequence using a specified FeatureRealizer. SimpleSequenceBuilder - Class in org.biojava.bio.seq.io Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence. SimpleSequenceBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleSequenceBuilder SimpleSequenceDBInstallation - Class in org.biojava.bio.seq.db This class is an implementation of interface SequenceDBInstallation that manages a set of SequenceDB objects. SimpleSequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.SimpleSequenceDBInstallation create an initially empty SimpleSequenceDBInstallation SimpleSequenceFactory - Class in org.biojava.bio.seq.impl A no-frills implementation of SequenceFactory that produces SimpleSequence objects. SimpleSequenceFactory() - Constructor for class org.biojava.bio.seq.impl.SimpleSequenceFactory SimpleSimilarityPairFeature - Class in org.biojava.bio.seq.impl SimpleSimilarityPairFeature represents a similarity between a query sequence and a subject sequence as produced by a search program. SimpleSimilarityPairFeature(Sequence, FeatureHolder, SimilarityPairFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature Creates a new SimpleSimilarityPairFeature. SimpleStateListener() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener SimpleStatePath - Class in org.biojava.bio.dp A no-frills implementation of StatePath. SimpleStatePath(double, SymbolList, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.SimpleStatePath SimpleStrandedFeature - Class in org.biojava.bio.seq.impl A no-frills implementation of StrandedFeature. SimpleStrandedFeature(Sequence, FeatureHolder, StrandedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleStrandedFeature SimpleSVMClassifierModel - Class in org.biojava.stats.svm A no-frills implementation of an SVM classifier model. SimpleSVMClassifierModel(SVMKernel) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel SimpleSVMClassifierModel(SVMKernel, Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel SimpleSVMClassifierModel(SVMKernel, SVMTarget) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel SimpleSVMTarget - Class in org.biojava.stats.svm No-frills implementation of SVMTarget. SimpleSVMTarget() - Constructor for class org.biojava.stats.svm.SimpleSVMTarget SimpleSVMTarget(Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMTarget SimpleSymbolList - Class in org.biojava.bio.symbol Basic implementation of SymbolList. SimpleSymbolList(SymbolTokenization, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList Construct a SymbolList from a string. SimpleSymbolList(Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList Construct an empty SimpleSymbolList. SimpleSymbolList(Alphabet, List) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList Construct a SymbolList containing the symbols in the specified list. SimpleSymbolList(Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList Construct a SimpleSymbolList given the Symbol array that backs it. SimpleSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList Construct a copy of an existing SymbolList. SimpleSymbolListFactory - Class in org.biojava.bio.symbol This class makes SimpleSymbolLists. SimpleSymbolListFactory() - Constructor for class org.biojava.bio.symbol.SimpleSymbolListFactory SimpleSymbolPropertyTable - Class in org.biojava.bio.symbol Class that implements the SymbolPropertyTable interface SimpleSymbolPropertyTable(Alphabet, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolPropertyTable SimpleSymbolPropertyTableDB - Class in org.biojava.bio.proteomics.aaindex A simple implementation of a symbol property table database. SimpleSymbolPropertyTableDB() - Constructor for class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB Initializes the database. SimpleSymbolPropertyTableDB(SymbolPropertyTableIterator) - Constructor for class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB Initializes the database by copying all symbol property tables from a given iterator into the database. SimpleSymbolStyle - Class in org.biojava.bio.gui A no-frills implementation of SymbolStyle. SimpleSymbolStyle(FiniteAlphabet) - Constructor for class org.biojava.bio.gui.SimpleSymbolStyle SimpleTagValueWrapper - Class in org.biojava.bio.program.tagvalue Helper class to wrap one TagValueListener inside another one. SimpleTagValueWrapper() - Constructor for class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper SimpleTagValueWrapper(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper Build a SimpleTagValueWrapper that will forward everything to a delegate. SimpleTaxon - Class in org.biojava.bio.taxa Deprecated. replaced by classes in org.biojavax.bio.taxa SimpleTaxon() - Constructor for class org.biojava.bio.taxa.SimpleTaxon Deprecated. SimpleTaxon(String, String) - Constructor for class org.biojava.bio.taxa.SimpleTaxon Deprecated. Create a new instance with no parent, no children and given scientific and common names. SimpleTaxonFactory - Class in org.biojava.bio.taxa Deprecated. replaced by classes in org.biojavax.bio.taxa SimpleTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.SimpleTaxonFactory Deprecated. SimpleThreadPool - Class in org.biojava.utils SimpleThreadPool is a basic implementation of ThreadPool for use where we don't wish to introduce a dependency on a 3rd-party pool. SimpleThreadPool() - Constructor for class org.biojava.utils.SimpleThreadPool Creates a new SimpleThreadPool containing 4 non-daemon threads and starts them. SimpleThreadPool(int, boolean) - Constructor for class org.biojava.utils.SimpleThreadPool Creates a new SimpleThreadPool containing the specified number of threads and starts them. SimpleThreadPool(int, boolean, int) - Constructor for class org.biojava.utils.SimpleThreadPool Creates a new SimpleThreadPool containing the specified number of threads and starts them. SimpleTrackLayout - Class in org.biojava.bio.gui.sequence.tracklayout A TrackLayout implenentation that wraps the sequence smoothly after a set number of residues SimpleTrackLayout() - Constructor for class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout SimpleTrackLayout(Sequence, int) - Constructor for class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout SimpleTranslationTable - Class in org.biojava.bio.symbol A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet. SimpleTranslationTable(FiniteAlphabet, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable Create a new translation table that will translate symbols from source to target. SimpleTranslationTable(FiniteAlphabet, Alphabet, Map) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable Create a new translation table that will translate symbols from source to target. SimpleWeightMatrix - Class in org.biojava.bio.dp SimpleWeightMatrix(Distribution[]) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix SimpleWeightMatrix(Alphabet, int, DistributionFactory) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix SimpleXMLEmitter - Class in org.biojava.bio.program.xml A simple XML DocumentHandler that processes SAX2 events to create a sensibly formatted XML as it parsed without populating objects with data. SimpleXMLEmitter() - Constructor for class org.biojava.bio.program.xml.SimpleXMLEmitter SimpleXMLEmitter(boolean) - Constructor for class org.biojava.bio.program.xml.SimpleXMLEmitter SingleDP - Class in org.biojava.bio.dp.onehead An implementation of DP that aligns a single sequence against a single model. SingleDP(MarkovModel) - Constructor for class org.biojava.bio.dp.onehead.SingleDP SingleDPMatrix - Class in org.biojava.bio.dp.onehead The dynamic programming matrix for a single sequence. SingleDPMatrix(DP, SymbolList) - Constructor for class org.biojava.bio.dp.onehead.SingleDPMatrix SingleRichSeqIterator(Sequence) - Constructor for class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator Creates an iterator over a single sequence. singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.AbstractTrainer singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchSampler singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchTrainer singleSequenceIteration(ModelTrainer, SymbolList, ScoreType) - Method in class org.biojava.bio.dp.BaumWelchSampler SingletonAlphabet - Class in org.biojava.bio.symbol An alphabet that contains a single atomic symbol. SingletonAlphabet(AtomicSymbol) - Constructor for class org.biojava.bio.symbol.SingletonAlphabet SingletonList - Class in org.biojava.utils SingletonList(Object) - Constructor for class org.biojava.utils.SingletonList site - Variable in class org.biojava.bio.molbio.RestrictionEnzyme SITE_FEATURE_SOURCE - Static variable in class org.biojava.bio.molbio.RestrictionMapper SITE_FEATURE_SOURCE the source String used by RestrictionMapper when creating restriction site Features. SITE_FEATURE_TYPE - Static variable in class org.biojava.bio.molbio.RestrictionMapper SITE_FEATURE_TYPE the type String used by RestrictionMapper when creating restriction site Features. SixFrameRenderer - Class in org.biojava.bio.gui.sequence Class that handles drawing in six frames for other classes. SixFrameRenderer() - Constructor for class org.biojava.bio.gui.sequence.SixFrameRenderer SixFrameZiggyRenderer - Class in org.biojava.bio.gui.sequence A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data. SixFrameZiggyRenderer(SixFrameRenderer) - Constructor for class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer size - Variable in class org.biojavax.bio.seq.CompoundRichLocation size() - Method in interface org.biojava.bio.annodb.AnnotationDB The number of Annotation instances in the DB. size() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB size() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB size() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB size() - Method in class org.biojava.bio.annodb.MergingAnnotationDB size() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB size() - Method in class org.biojava.bio.program.gff.GFFEntrySet Return how many lines are in this set. size() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet returns an iterator to the contents of the set. /** no. of entries in this Homologene group size() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet size() - Method in interface org.biojava.bio.symbol.FiniteAlphabet The number of symbols in the alphabet. size() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet size() - Method in class org.biojava.bio.symbol.SimpleAlphabet size() - Method in class org.biojava.bio.symbol.SingletonAlphabet size() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet size() - Method in class org.biojava.stats.svm.SparseVector The number of used dimensions. size() - Method in class org.biojava.stats.svm.SVMRegressionModel size() - Method in class org.biojava.utils.BeanAsMap size() - Method in class org.biojava.utils.bytecode.InstructionVector size() - Method in class org.biojava.utils.FileAsList size() - Method in class org.biojava.utils.io.FlatFileCache size() - Method in class org.biojava.utils.io.SoftHashMap size() - Method in class org.biojava.utils.ListTools.Doublet size() - Method in class org.biojava.utils.ListTools.SeriesList size() - Method in class org.biojava.utils.ListTools.Triplet size() - Method in class org.biojava.utils.MergingSet size() - Method in class org.biojava.utils.SingletonList size() - Method in class org.biojava.utils.SmallMap size() - Method in class org.biojava.utils.SmallSet size() - Method in class org.biojavax.ga.impl.SimplePopulation size() - Method in interface org.biojavax.ga.Population Gets the Size of the population size() - Method in class org.biojavax.ga.util.WeightedSet SIZE - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer SIZE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. SIZE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. skip(long) - Method in class org.biojava.utils.io.CachingInputStream skip(long) - Method in class org.biojava.utils.io.CountedBufferedReader skip(long) - Method in class org.biojava.utils.io.UncompressInputStream SKIP_RECORD - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler skippedEntity(String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter skippedEntity(String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor skippedEntity(String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler skippedEntity(String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase skippedEntity(String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor skippedEntity(String) - Method in interface org.biojava.utils.stax.StAXContentHandler skippedEntity(String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase SkipRecordErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler SLEEP_TIME - Static variable in class org.biojava.utils.process.ExternalProcess Number of milliseconds the execute method should pauses after the external process has finished the execution. SmallAnnotation - Class in org.biojava.bio Annotation that is optimized for memory usage. SmallAnnotation() - Constructor for class org.biojava.bio.SmallAnnotation Return a new SmallAnnotation optimised for small sets of properties. SmallAnnotation(Map) - Constructor for class org.biojava.bio.SmallAnnotation Return a new SmallAnnotation that copies all values from a Map. SmallAnnotation(Annotation) - Constructor for class org.biojava.bio.SmallAnnotation Return a new SmallAnnotation that copies all values from another annoation. SmallCursor - Class in org.biojava.bio.dp.onehead Constant-memory implementation of single-head DP cursor. SmallCursor(State[], SymbolList, Iterator) - Constructor for class org.biojava.bio.dp.onehead.SmallCursor SmallMap - Class in org.biojava.utils Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability. SmallMap() - Constructor for class org.biojava.utils.SmallMap SmallMap(int) - Constructor for class org.biojava.utils.SmallMap SmallMap(Map) - Constructor for class org.biojava.utils.SmallMap SmallSet - Class in org.biojava.utils Lightweight implementation of Set which uses little memory to store a small number of items, at the expense of scalability. SmallSet() - Constructor for class org.biojava.utils.SmallSet SmallSet(int) - Constructor for class org.biojava.utils.SmallSet SmallSet(Collection) - Constructor for class org.biojava.utils.SmallSet SmartSequenceBuilder - Class in org.biojava.bio.seq.io Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence. sMatrix - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor SmithWaterman - Class in org.biojava.bio.alignment Smith and Waterman developed an efficient dynamic programming algorithm to perform local sequence alignments, which returns the most conserved region of two sequences (longest common substring with modifications). SmithWaterman() - Constructor for class org.biojava.bio.alignment.SmithWaterman Default constructor. SmithWaterman(short, short, short, short, short, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.SmithWaterman Constructs the new SmithWaterman alignment object. SMORegressionTrainer - Class in org.biojava.stats.svm Train a regression support vector machine using the Sequential Minimal Optimization algorithm. SMORegressionTrainer() - Constructor for class org.biojava.stats.svm.SMORegressionTrainer SMOTrainer - Class in org.biojava.stats.svm Train a support vector machine using the Sequential Minimal Optimization algorithm. SMOTrainer() - Constructor for class org.biojava.stats.svm.SMOTrainer SoftHashMap - Class in org.biojava.utils.io A in memory cache using soft references. SoftHashMap() - Constructor for class org.biojava.utils.io.SoftHashMap SoftHashMap(int) - Constructor for class org.biojava.utils.io.SoftHashMap SoftMaskedAlphabet - Class in org.biojava.bio.symbol Soft masking is usually displayed by making the masked regions somehow different from the non masked regions. SoftMaskedAlphabet.CaseSensitiveTokenization - Class in org.biojava.bio.symbol This SymbolTokenizer works with a delegate to softmask symbol tokenization as appropriate. SoftMaskedAlphabet.MaskingDetector - Interface in org.biojava.bio.symbol Implementations will define how soft masking looks. SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector - Class in org.biojava.bio.symbol SoftReferenceCache - Class in org.biojava.utils.cache Cache which is cleared according to memory pressure. SoftReferenceCache() - Constructor for class org.biojava.utils.cache.SoftReferenceCache SolexaFastqReader - Class in org.biojava.bio.program.fastq Reader for FastqVariant.FASTQ_SOLEXA formatted sequences. SolexaFastqReader() - Constructor for class org.biojava.bio.program.fastq.SolexaFastqReader SolexaFastqWriter - Class in org.biojava.bio.program.fastq Writer for FastqVariant.FASTQ_SOLEXA formatted sequences. SolexaFastqWriter() - Constructor for class org.biojava.bio.program.fastq.SolexaFastqWriter solve(double, double, double, ComputeObject) - Static method in class org.biojava.utils.math.BinarySearch method that will attempt solving the equation. SomePairsInCollection(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection SOPair(String, int) - Constructor for class org.biojava.ontology.obo.OboFileParser.SOPair SOPair(String, int, int) - Constructor for class org.biojava.ontology.obo.OboFileParser.SOPair sort() - Method in class org.biojavax.bio.seq.CompoundRichLocation Sorts the member locations of a compound location. sort() - Method in class org.biojavax.bio.seq.EmptyRichLocation Sorts the member locations of a compound location. sort() - Method in interface org.biojavax.bio.seq.RichLocation Sorts the member locations of a compound location. sort() - Method in class org.biojavax.bio.seq.SimpleRichLocation Sorts the member locations of a compound location. sort(String[], Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery It sorts the current collection and returns another collection which is a sorted copy of the current collection. SORT_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion A sort criterion. sortPeptidesIntoLanes() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer source - Variable in class org.biojava.bio.seq.Feature.Template SOURCE - Static variable in interface org.biojava.bio.seq.Feature The source of this feature has altered SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat sourceEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block SourceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter SourceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter SourceLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker sourceStart - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block sourceTerm - Variable in class org.biojava.bio.seq.Feature.Template SOURCETERM - Static variable in interface org.biojava.bio.seq.Feature The ontological source of this feature has altered SOURCETERM - Static variable in interface org.biojavax.bio.seq.RichFeature sourceToView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList Coordinate conversion from source to view. sourceToView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList sourceToView(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList Coordinate conversion from source to view. SparseVector - Class in org.biojava.stats.svm An implementation of a sparse vector. SparseVector() - Constructor for class org.biojava.stats.svm.SparseVector SparseVector(int) - Constructor for class org.biojava.stats.svm.SparseVector SparseVector.NormalizingKernel - Class in org.biojava.stats.svm A version of the standard dot-product kernel that scales each column independently. spatialLocation - Variable in class org.biojava.bibliography.BiblioScope It defines a spatial location of the cited resource. SPECIES_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms split(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Splitter Produce a list of values from an old value. split(Object) - Method in class org.biojava.bio.program.tagvalue.RegexSplitter splitString(String) - Method in class org.biojava.bio.seq.io.WordTokenization SQLUnigeneFactory - Class in org.biojava.bio.program.unigene An implementatoin of UnigeneFactory that manages it's data in an SQL database. SQLUnigeneFactory() - Constructor for class org.biojava.bio.program.unigene.SQLUnigeneFactory ssContext - Variable in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler stackDelta() - Method in interface org.biojava.utils.bytecode.CodeGenerator Return the change in the stack dept this generator will cause. stackDelta() - Method in class org.biojava.utils.bytecode.IfExpression stackDelta() - Method in class org.biojava.utils.bytecode.InstructionVector stackDelta() - Method in class org.biojava.utils.bytecode.Label stackDelta() - Method in class org.biojava.utils.bytecode.MarkLabel stackDepth() - Method in interface org.biojava.utils.bytecode.CodeGenerator Return the total depth of the stack required by this CodeGenerator. stackDepth() - Method in class org.biojava.utils.bytecode.IfExpression stackDepth() - Method in class org.biojava.utils.bytecode.InstructionVector stackDepth() - Method in class org.biojava.utils.bytecode.Label stackDepth() - Method in class org.biojava.utils.bytecode.MarkLabel StackedFeatureRenderer - Class in org.biojava.bio.gui.sequence Allows you to stack multiple feature renderers up (for example a label renderer and a beaded renderer) and have them treated as a single renderer for layout. StackedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.StackedFeatureRenderer StackedLogoPainter - Class in org.biojava.bio.gui A logo painter that paints in stacked areas. StackedLogoPainter() - Constructor for class org.biojava.bio.gui.StackedLogoPainter stackLevel - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler stackLevel - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler standardMutationDistribution(FiniteAlphabet) - Static method in class org.biojavax.ga.util.GATools Makes a mutation Distribution where the probability of a Symbol being mutated to itself is zero and the probability of it being changed to any other Symbol in the Alphabet a is 1.0 / (a.size() - 1.0) start - Variable in class org.biojava.utils.automata.FiniteAutomaton start() - Method in interface org.biojava.bio.search.BioMatcher Get the first symbol index that matches the pattern. start() - Method in class org.biojava.bio.search.MaxMismatchMatcher start() - Method in class org.biojava.utils.regex.Matcher Returns the start index of the previous match. start(int) - Method in class org.biojava.utils.regex.Matcher Returns the start index of the subsequence captured by the given group during the previous match operation. start(String[]) - Method in interface org.biojava.utils.xml.AppEntry START_RECORD_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat startBlock(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract startBlock(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener Notifies the parser that a new block is starting. startBlock(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract startBlock(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser Notifies the parser that a new block is starting. startBlock(String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract startBlock(String) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener About to start a new block. startBlockObject() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder startBlockObject() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder startBlockObject() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract Tell the builder to start a new block object. startBlockObject() - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder startBlockObject() - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder startCycle() - Method in interface org.biojava.bio.dp.HMMTrainer called to put the trainer into an initial state for a new round of training. startCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer startDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder indicates start of data for a HomologeneDB startDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder startDocument() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter startDocument() - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor startDocument() - Method in class org.biojava.utils.stax.SAX2StAXAdaptor startDocument(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler Indicates that a new GFF document has been started. startDocument(String) - Method in class org.biojava.bio.program.gff.GFFFilterer startDocument(String) - Method in class org.biojava.bio.program.gff.GFFWriter startDocument(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler Indicates that a new GFF document has been started. startedActivity(Object) - Method in interface org.biojava.utils.ActivityListener Notification that an activity has started. startElement(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter startElement(String, String, String, Attributes) - Method in class org.biojava.bio.dist.XMLDistributionReader Required by SAXParser to be public. startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler This is called when an element is entered. startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter startElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor startElement(String, String, String, Attributes) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor startElement(String, String, String, Attributes, DelegationManager) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler Handles basic entry processing for all feature handlers. startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler Override this to do any processing required but call this prior to returning. startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser we override the superclass startElement method so we can determine the the start tag type and use it to set up delegation for the superclass. startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.FeatureHandler StAX callback for element starts. startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.LocationHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.PropDetailHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMENamePropHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMETypePropHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler Handles basic entry processing for all feature handlers. startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler Override this to do any processing required but call this prior to returning. startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler Handles basic entry processing for all feature handlers. startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.ByteElementHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.CharElementHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.FloatElementHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.IntElementHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.LongElementHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in interface org.biojava.utils.stax.StAXContentHandler startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StAXContentHandlerBase startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StringElementHandlerBase startElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVECdsHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler currently we do not handler >computation< as subtag of sciobj yet startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler Element-specific handler. startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler Element-specific handler. startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEGenePropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMESeqPropHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler Element-specific handler. startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler Element-specific handler. startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEGeneHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEHandler Description of the Method startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler Element-specific handler. startElementHandler(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler startElementHandler(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEHandler startFeature(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser Deprecated. startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.EmblFileFormer Deprecated. startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.GenbankFileFormer Deprecated. startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer Deprecated. startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SeqIOAdapter startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SeqIOFilter startFeature(Feature.Template) - Method in interface org.biojava.bio.seq.io.SeqIOListener Notify the listener that a new feature object is starting. startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer Deprecated. Null implementation. startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Notify the listener that a new feature object is starting. startFile() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder startFile() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener About to start a new file. startFile() - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder startFile() - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener About to start a new file. startGroup() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder indicates start of data for a OrthoPairSet startGroup() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder startHeader() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser startHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder startHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder startHeader() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder startHeader() - Method in class org.biojava.bio.search.FilteringContentHandler startHeader() - Method in class org.biojava.bio.search.SearchContentAdapter startHeader() - Method in class org.biojava.bio.search.SearchContentFilter startHeader() - Method in interface org.biojava.bio.search.SearchContentHandler The startHeader method indicates the start of a formatted header. startHeader() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger startHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser startHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder startHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder startHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder startHit() - Method in class org.biojava.bio.search.FilteringContentHandler startHit() - Method in class org.biojava.bio.search.SearchContentAdapter startHit() - Method in class org.biojava.bio.search.SearchContentFilter startHit() - Method in interface org.biojava.bio.search.SearchContentHandler The startHit method indicates the start of a formatted hit. startHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger startInstance(int, int) - Method in interface org.biojava.utils.automata.StateMachineFactory Return a StateMachineInstance if the Symbol represented by the symbol index is valid as the initial symbol of the pattern. startLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler startLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler startOrthologue() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder indicates start of data for an orthologue startOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder startOrthoPair() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder indicates start of data for an OrthoPair startOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder startPrefixMapping(String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter startPrefixMapping(String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor startPrefixMapping(String, String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler startPrefixMapping(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase startPrefixMapping(String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor startPrefixMapping(String, String) - Method in interface org.biojava.utils.stax.StAXContentHandler startPrefixMapping(String, String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase startRecord() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper startRecord() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder startRecord() - Method in class org.biojava.bio.program.tagvalue.Echo startRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer startRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer2 startRecord() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper startRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener startRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine startRecord() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener A new record is about to start. startSearch() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser startSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder startSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder startSearch() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder startSearch() - Method in class org.biojava.bio.search.FilteringContentHandler startSearch() - Method in class org.biojava.bio.search.SearchContentAdapter startSearch() - Method in class org.biojava.bio.search.SearchContentFilter startSearch() - Method in interface org.biojava.bio.search.SearchContentHandler The startSearch method indicates the start of useful search information. startSearch() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger startSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo startSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener Indicates that a sequence is about to be searched against a DataStore. startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper startSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer Deprecated. startSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer Deprecated. startSequence() - Method in class org.biojava.bio.seq.io.SeqIOAdapter startSequence() - Method in class org.biojava.bio.seq.io.SeqIOFilter startSequence() - Method in interface org.biojava.bio.seq.io.SeqIOListener Start the processing of a sequence. startSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase startSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter startSequence() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer Deprecated. Start the processing of a sequence. startSequence() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener startSequence() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter startSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder Start the processing of a sequence. startSubHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser startSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder startSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder startSubHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder startSubHit() - Method in class org.biojava.bio.search.FilteringContentHandler startSubHit() - Method in class org.biojava.bio.search.SearchContentAdapter startSubHit() - Method in class org.biojava.bio.search.SearchContentFilter startSubHit() - Method in interface org.biojava.bio.search.SearchContentHandler The startSubHit method indicates the start of a formatted subhit. startSubHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger startTag(Object) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Aggregator startTag(Object) - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Echo startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Indexer startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Indexer2 startTag(Object) - Method in class org.biojava.bio.program.tagvalue.MultiTagger startTag(Object) - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder startTag(Object) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper startTag(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener startTag(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine TagValueListener interface startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagRenamer startTag(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueListener Start a new tag. startTag(Object) - Method in class org.biojava.bio.program.tagvalue.ValueChanger startThreads() - Method in class org.biojava.utils.SimpleThreadPool startThreads() - Method in interface org.biojava.utils.ThreadPool startThreads starts all the threads running and opens the pool to requests. startTree() - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler startTree() - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase startTree() - Method in interface org.biojava.utils.stax.StAXContentHandler startTree() - Method in class org.biojava.utils.stax.StAXContentHandlerBase startZiggy(StrandedFeature.Strand) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer Used to initialise the spliced transcript renderer for a CDS feature where the ends of the feature define the frame of the feature. startZiggy(StrandedFeature.Strand, int) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer This method is called to initialise the renderer for a spliced transcript. state - Variable in class org.biojava.bio.dp.BackPointer The state with which this backpointer is associated. State - Interface in org.biojava.bio.dp A state in a markov process. stateAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel FiniteAlphabet of the states. stateAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel stateAlphabet() - Method in class org.biojava.bio.dp.WMAsMM stateList(MarkovModel) - Method in class org.biojava.bio.dp.DP StateMachine - Class in org.biojava.bio.program.tagvalue This class implements a state machine for parsing events from the Parser class. StateMachine() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine StateMachine.BasicState - Class in org.biojava.bio.program.tagvalue Implementation of a State in a state machine StateMachine.ExitNotification - Interface in org.biojava.bio.program.tagvalue Interface implemented by State listeners that want notification when a transition leaves the State. StateMachine.SimpleStateListener - Class in org.biojava.bio.program.tagvalue a basic listener for a State. StateMachine.State - Interface in org.biojava.bio.program.tagvalue Interface for a State within this StateMachine StateMachine.Transition - Class in org.biojava.bio.program.tagvalue class to represent a State Transition StateMachine.TransitionTable - Class in org.biojava.bio.program.tagvalue Table of Transition destination States and their corresponding Tags. StateMachineFactory - Interface in org.biojava.utils.automata Class that produces StateMachineInstance objects. StateMachineInstance - Interface in org.biojava.utils.automata StatePath - Interface in org.biojava.bio.dp Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods. states - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix states() - Method in interface org.biojava.bio.dp.DPMatrix states() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix states() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix STATES - Static variable in interface org.biojava.bio.dp.StatePath Alignment label for the state path. StaticMemberPlaceHolder - Class in org.biojava.utils StaticMemberPlaceHolder() - Constructor for class org.biojava.utils.StaticMemberPlaceHolder StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.utils.StaticMemberPlaceHolder StaticMethodRPFactory(Method) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory Create a new StaticMethodRPFactory for a method. STATUS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat StAXContentHandler - Interface in org.biojava.bio.seq.io.agave Interface for StAX content handlers. StAXContentHandler - Interface in org.biojava.utils.stax Interface for StAX content handlers. StAXContentHandlerBase - Class in org.biojava.bio.seq.io.agave Simple implementation of the StAXContentHandler interface, with empty implementations for all the methods. StAXContentHandlerBase - Class in org.biojava.utils.stax Simple implementation of the StAXContentHandler interface, with empty implementations for all the methods. StAXContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.agave.StAXContentHandlerBase StAXContentHandlerBase() - Constructor for class org.biojava.utils.stax.StAXContentHandlerBase staxenv - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler staxenv - Variable in class org.biojava.bio.seq.io.agave.StAXPropertyHandler staxenv - Variable in class org.biojava.bio.seq.io.game.StAXPropertyHandler staxenv - Variable in class org.biojava.bio.seq.io.game12.StAXFeatureHandler Nesting class that provides callback interfaces to nested class StAXFeatureHandler - Class in org.biojava.bio.seq.io.agave StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. StAXFeatureHandler - Class in org.biojava.bio.seq.io.game StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. StAXFeatureHandler - Class in org.biojava.bio.seq.io.game12 StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. StAXFeatureHandler() - Constructor for class org.biojava.bio.seq.io.game.StAXFeatureHandler StAXHandlerBinding - Class in org.biojava.bio.program.ssbind StAXHandlerBindings associates an ElementRecognizer with a factory which creates StAXContentHandlers for elements which it the ElementRecognizer accepts. StAXHandlerFactory - Interface in org.biojava.bio.program.ssbind StAXHandlerFactory is an interface for factories producing StAXContentHandlers which are used by the SeqSimilarityStAXAdapter. StAXHandlerFactory - Interface in org.biojava.bio.seq.io.agave Factory for StAX content handlers. StAXHandlerFactory - Interface in org.biojava.bio.seq.io.game Factory for StAX content handlers. StAXHandlerFactory - Interface in org.biojava.bio.seq.io.game12 Factory for StAX content handlers. StAXPropertyHandler - Class in org.biojava.bio.seq.io.agave StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. StAXPropertyHandler - Class in org.biojava.bio.seq.io.game StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. stop(GeneticAlgorithm) - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration Stops the Algorithm if the iterations are >= maxGenerations stop(GeneticAlgorithm) - Method in interface org.biojavax.ga.GAStoppingCriteria Determines if an Algorithm should stop spawning new generations StoppingCriteria - Interface in org.biojava.bio.dp A callback that is invoked during the training of an HMM. StopRenderer - Class in org.biojava.bio.gui.sequence Compute sites of stop codons. StopRenderer(SixFrameRenderer, int, StrandedFeature.Strand) - Constructor for class org.biojava.bio.gui.sequence.StopRenderer stopThreads() - Method in class org.biojava.utils.SimpleThreadPool Waits for all working threads to return and then stops them. stopThreads() - Method in interface org.biojava.utils.ThreadPool stopThreads causes all running threads to stop when their current task is complete. store(Index) - Method in class org.biojava.bio.seq.db.BioIndex store(Index) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore store adds an Index to the store. store(Index) - Method in interface org.biojava.bio.seq.db.IndexStore Add the Index to the store. store(Index) - Method in class org.biojava.bio.seq.db.TabIndexStore STORE_NAME - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory STORE_NAME is the key used to identify the arbitrary name of the store in the OBDA config.dat files. str - Variable in class org.biojava.ontology.obo.OboFileParser.SOPair STRAIN_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms strand - Variable in class org.biojava.bio.seq.StrandedFeature.Template STRAND - Static variable in interface org.biojava.bio.seq.StrandedFeature The strand of this feature is being altered. STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. STRANDED_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat StrandedFeature - Interface in org.biojava.bio.seq Adds the concept of 'strand' to features. STRANDEDFEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.StrandedFeatureHandler StrandedFeature.Strand - Class in org.biojava.bio.seq Class to represent the 'strandedness' of a feature. StrandedFeature.Template - Class in org.biojava.bio.seq Template class for parameterizing the creation of a new StrandedFeature. StrandedFeatureHandler - Class in org.biojava.bio.program.xff StAX handler for XFF strandedFeature type. StrandedFeatureHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.StrandedFeatureHandler StrandFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.seq.FeatureFilter.StrandFilter Build a new filter that matches all features of a given strand. StrandParser - Class in org.biojava.bio.seq Process strings and return strand objects. StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser stream(Readable, StreamListener) - Method in interface org.biojava.bio.program.fastq.FastqReader Stream the specified readable. StreamListener - Interface in org.biojava.bio.program.fastq Event based parser callback. streamNext(SeqIOListener) - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer streamNext(SeqIOListener) - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer streamNext(SeqIOListener) - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer StreamParser - Interface in org.biojava.bio.seq.io Parse a stream of characters into BioJava symbols. StreamPipe - Class in org.biojava.utils.process A multi threaded class which pipes the contents of an input stream to an output stream. StreamPipe(InputStream, OutputStream, String) - Constructor for class org.biojava.utils.process.StreamPipe Initializes the stream pipe. StreamReader - Class in org.biojava.bio.seq.io Parses a stream into sequences. StreamReader(BufferedReader, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader StreamReader(InputStream, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader streamRecords(GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFEntrySet Write all records in this set out to a handler. StreamWriter - Class in org.biojava.bio.seq.io Writes all of the sequences from a SequenceIterator to a stream with a particular format. StreamWriter(OutputStream, SequenceFormat) - Constructor for class org.biojava.bio.seq.io.StreamWriter Generate a new StreamWriter to the stream os and using format. STRING_TO_INT - Static variable in class org.biojava.bio.program.tagvalue.ChangeTable StringElementHandlerBase - Class in org.biojava.utils.stax StAX handler for any element which just contains a string. StringElementHandlerBase() - Constructor for class org.biojava.utils.stax.StringElementHandlerBase stringifyAttributes(Map) - Static method in class org.biojava.bio.program.gff.SimpleGFFRecord Create a String representation of attMap. stringnifyDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix Converts the description of the matrix to a String. stringnifyMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix Creates a String representation of this matrix. stringToClob(Connection, ResultSet, int, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper Deprecated. StringTools - Class in org.biojavax.utils Utility class for formatting strings into regular-sized blocks. STROKE - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer Constant STROKE indicating a change to the outline stroke of the features. StructureTools - Class in org.biojava.bio.proteomics Simple access to protein seccondary structure assignments. StructureTools() - Constructor for class org.biojava.bio.proteomics.StructureTools subAlignment(Set<String>, int, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment Retreives a subAlignment subAlignment(Set<String>, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment Retrieves a subalignment specified by the location. subAlignment(Set<String>, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment subAlignment(Set<String>, Location) - Method in interface org.biojava.bio.alignment.Alignment Make a view onto this alignment. subAlignment(Set<String>, Location) - Method in class org.biojava.bio.alignment.SimpleAlignment subAlignment(Set<String>, Location) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment subAlignment(Set<String>, Location) - Method in class org.biojava.bio.symbol.RelabeledAlignment subAlignment(Set, Location) - Method in class org.biojava.bio.dp.SimpleStatePath SubCircularRendererContext - Class in org.biojava.bio.gui.sequence A renderer context that allows some or all properties of another context to be over-ridden. SubCircularRendererContext(CircularRendererContext, SymbolList, FeatureHolder, double) - Constructor for class org.biojava.bio.gui.sequence.SubCircularRendererContext Create a new sub context. subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.And subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.Contains subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.Or subConstraintOf(CollectionConstraint) - Method in interface org.biojava.bio.CollectionConstraint subConstraintOf returns true if the constraint is a sub-constraint. subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.And subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ByClass subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.Enumeration subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ExactValue subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.Or subConstraintOf(PropertyConstraint) - Method in interface org.biojava.bio.PropertyConstraint subConstraintOf returns true if the constraint is a sub-constraint. subContext() - Method in interface org.biojava.utils.bytecode.CodeContext Open a sub context. subFeatures - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler SubIntegerTokenization - Class in org.biojava.bio.seq.io SubIntegerTokenization(IntegerAlphabet.SubIntegerAlphabet) - Constructor for class org.biojava.bio.seq.io.SubIntegerTokenization subject - Variable in class org.biojava.bibliography.BibRef It defines the topic of the content of the cited resource. SUBJECT_HEADINGS - Static variable in interface org.biojava.bibliography.BibRefSupport A vocabulary name. SUBJECT_LABEL - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature Constant SUBJECT_LABEL is the alignment label used for all subject sequences. subjectDBs - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory subjectHeadings - Variable in class org.biojava.bibliography.BiblioSubject The subject headings usually come from standard lists such as Sears List of Subject Headings, or Library of Congress Subject Headings (LCSH). subjectHeadingsSource - Variable in class org.biojava.bibliography.BiblioSubject The source of subject headings. subjectViewCache - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory subList(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath subList(int, int) - Method in class org.biojava.bio.seq.CircularView Over rides ViewSequence. subList(int, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment subList(int, int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList subList(int, int) - Method in class org.biojava.bio.seq.impl.DummySequence subList(int, int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList subList(int, int) - Method in class org.biojava.bio.seq.impl.SimpleSequence subList(int, int) - Method in class org.biojava.bio.seq.impl.SubSequence subList(int, int) - Method in class org.biojava.bio.seq.impl.ViewSequence subList(int, int) - Method in class org.biojava.bio.seq.NewSimpleAssembly subList(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly subList(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList subList(int, int) - Method in class org.biojava.bio.symbol.ChunkedSymbolList subList(int, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment subList(int, int) - Method in class org.biojava.bio.symbol.SimpleSymbolList create a subList of the original, this will be a view until either the original symbolList or the sublist is edited subList(int, int) - Method in interface org.biojava.bio.symbol.SymbolList Return a new SymbolList for the symbols start to end inclusive. subList(int, int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList Return a new SymbolList for the symbols start to end inclusive. subList(int, int) - Method in class org.biojavax.bio.seq.ThinRichSequence Return a new SymbolList for the symbols start to end inclusive. subList(SymbolList, int, int) - Static method in class org.biojava.bio.symbol.SymbolListViews View a portion of a SymbolList. subList(RichSequence, int, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler Return a new SymbolList for the symbols start to end inclusive. subList(RichSequence, int, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler Return a new SymbolList for the symbols start to end inclusive. subList(RichSequence, int, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler Return a new SymbolList for the symbols start to end inclusive. subMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch A matrix with the size length(alphabet) times length(alphabet) SubPairwiseRenderContext - Class in org.biojava.bio.gui.sequence SubPairwiseRenderContext is a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own. SubPairwiseRenderContext(PairwiseRenderContext, SymbolList, SymbolList, FeatureHolder, FeatureHolder, RangeLocation, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubPairwiseRenderContext Creates a new SubPairwiseRenderContext. SUBPATH_LENGTH - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option To improve performance, the drawing objects for the chromatogram traces are precomputed. subpathsValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic Flag for subpaths. subSequence(int, int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence subSequence(int, int) - Method in class org.biojava.utils.RepeatedCharSequence subSequence(Sequence, int, int) - Static method in class org.biojava.bio.seq.SequenceTools Extract a sub-sequence from a sequence. subSequence(Sequence, int, int, String) - Static method in class org.biojava.bio.seq.SequenceTools Extract a sub-sequence from a sequence. subSequence(Sequence, int, int, String, StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.SequenceTools Extract a sub-sequence from a sequence. subSequence(RichSequence, int, int, Namespace, String, String, String, int, Double) - Static method in class org.biojavax.bio.seq.RichSequence.Tools Creates a new sequence from a subregion of another sequence. SubSequence - Class in org.biojava.bio.seq.impl View a sub-section of a given sequence object, including all the features intersecting that region. SubSequence(Sequence, int, int) - Constructor for class org.biojava.bio.seq.impl.SubSequence Construct a new SubSequence of the specified sequence. SubSequence(Sequence, int, int, String) - Constructor for class org.biojava.bio.seq.impl.SubSequence Construct a new SubSequence of the specified sequence. SubSequence.SubProjectedFeatureContext - Class in org.biojava.bio.seq.impl TargetContext that implements the mapping between the parent sequence and this sub-sequence. SubSequenceDB - Class in org.biojava.bio.seq.db SubSequenceDB(SequenceDB, Set) - Constructor for class org.biojava.bio.seq.db.SubSequenceDB SubSequenceRenderContext - Class in org.biojava.bio.gui.sequence Allows a new renderer to "wrap" another one, replacing one or more values. SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation, int) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext SUBSET - Static variable in class org.biojava.ontology.obo.OboFileHandler SubstitutionMatrix - Class in org.biojava.bio.alignment This object is able to read a substitution matrix file and constructs a short matrix in memory. SubstitutionMatrix(File) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix This constructor can be used to guess the alphabet of this substitution matrix. SubstitutionMatrix(FiniteAlphabet, short, short) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters. SubstitutionMatrix(FiniteAlphabet, File) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix This constructs a SubstitutionMatrix object that contains two Map data structures having BioJava symbols as keys and the value being the index of the matrix containing the substitution score. SubstitutionMatrix(FiniteAlphabet, String, String) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file. subStr(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath subStr(int, int) - Method in class org.biojava.bio.seq.CircularView Over rides ViewSequence. subStr(int, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment subStr(int, int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList subStr(int, int) - Method in class org.biojava.bio.seq.impl.DummySequence subStr(int, int) - Method in class org.biojava.bio.seq.impl.SimpleSequence subStr(int, int) - Method in class org.biojava.bio.seq.impl.SubSequence subStr(int, int) - Method in class org.biojava.bio.seq.impl.ViewSequence subStr(int, int) - Method in class org.biojava.bio.seq.NewSimpleAssembly subStr(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly subStr(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList subStr(int, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment subStr(int, int) - Method in interface org.biojava.bio.symbol.SymbolList Return a region of this symbol list as a String. subStr(int, int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList Return a region of this symbol list as a String. subStr(int, int) - Method in class org.biojavax.bio.seq.ThinRichSequence Return a region of this symbol list as a String. subStr(RichSequence, int, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler Return a region of this sequence as a String. subStr(RichSequence, int, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler Return a region of this sequence as a String. subStr(RichSequence, int, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler Return a region of this sequence as a String. subStringExists(String) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree subtract(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools Subtract one location from another. subTypeOf(AnnotationType) - Method in class org.biojava.bio.AnnotationType.Abstract subTypeOf(AnnotationType) - Method in interface org.biojava.bio.AnnotationType See if an AnnotationType is a specialisation of this type. SubULAlignment(Set<String>, Location) - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment SuffixNode() - Constructor for class org.biojava.bio.symbol.SuffixTree.SuffixNode SuffixNode() - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode SuffixTree - Class in org.biojava.bio.symbol Suffix tree implementation. SuffixTree(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SuffixTree Construct a new SuffixTree to contain motifs over the specified alphabet. SuffixTree.SuffixNode - Class in org.biojava.bio.symbol A node in the suffix tree. SuffixTreeKernel - Class in org.biojava.stats.svm.tools Computes the dot-product of two suffix-trees as the sum of the products of the counts of all nodes they have in common. SuffixTreeKernel() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel SuffixTreeKernel.DepthScaler - Interface in org.biojava.stats.svm.tools Encapsulates the scale factor to apply at a given depth. SuffixTreeKernel.MultipleScalar - Class in org.biojava.stats.svm.tools Scale using a multiple of two DepthScalers. SuffixTreeKernel.NullModelScaler - Class in org.biojava.stats.svm.tools Scales by 4^depth - equivalent to dividing by a probablistic flatt prior null model SuffixTreeKernel.SelectionScalar - Class in org.biojava.stats.svm.tools Scale using a BitSet to allow/disallow depths. SuffixTreeKernel.UniformScaler - Class in org.biojava.stats.svm.tools Scale all depths by 1.0 SUPPORT - Static variable in class org.biojava.bio.program.abi.ABITools Alignment label for the support row. surname - Variable in class org.biojava.bibliography.BiblioPerson The person's sirname (family name). SVM_Light - Class in org.biojava.stats.svm.tools SVM_Light() - Constructor for class org.biojava.stats.svm.tools.SVM_Light SVM_Light.LabelledVector - Class in org.biojava.stats.svm.tools SVMClassifierModel - Interface in org.biojava.stats.svm An SVM classifier model. SVMKernel - Interface in org.biojava.stats.svm Kernel for support vector machines and related methods. SVMRegressionModel - Class in org.biojava.stats.svm SVMRegressionModel() - Constructor for class org.biojava.stats.svm.SVMRegressionModel SVMRegressionModel(int) - Constructor for class org.biojava.stats.svm.SVMRegressionModel SVMTarget - Interface in org.biojava.stats.svm An SVM classifier model. SwapMutationFunction - Class in org.biojavax.ga.functions This class does a sort of mutation by exchanging two positions on the chromosome. SwapMutationFunction(double[]) - Constructor for class org.biojavax.ga.functions.SwapMutationFunction Sets the mutation probabilities to the designated values. Swissprot - Class in org.biojava.bio.program.formats Swissprot() - Constructor for class org.biojava.bio.program.formats.Swissprot SWISSPROT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants SWISSPROT indicates that the sequence format is SWISSPROT. SWISSPROT_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats SwissprotFileFormer - Class in org.biojava.bio.seq.io Deprecated. Use org.biojavax.bio.seq.io framework instead SwissprotFileFormer() - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer Deprecated. Creates a new SwissprotFileFormer using System.out stream. SwissprotFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer Deprecated. Creates a new SwissprotFileFormer using the specified stream. SwissprotProcessor - Class in org.biojava.bio.seq.io Deprecated. Use org.biojavax.bio.seq.io framework instead SwissprotProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor Deprecated. SwissprotProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor Deprecated. Constructor that sets the source of the feature to theSource. SwissprotProcessor.Factory - Class in org.biojava.bio.seq.io Deprecated. Factory which wraps SequenceBuilders in a SwissprotProcessor SwissprotSequenceDB - Class in org.biojava.bio.seq.db This class contains functions accessing sequences in swiss-prot. SwissprotSequenceDB() - Constructor for class org.biojava.bio.seq.db.SwissprotSequenceDB Symbol - Interface in org.biojava.bio.symbol A single symbol. symbolAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment symbolAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment this will return the ambiguity symbol associated with all symbols in that column symbolAt(int) - Method in class org.biojava.bio.alignment.SimpleAlignment symbolAt(int) - Method in class org.biojava.bio.dp.SimpleStatePath symbolAt(int) - Method in class org.biojava.bio.seq.CircularView Over rides ViewSequence. symbolAt(int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment symbolAt(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList symbolAt(int) - Method in class org.biojava.bio.seq.impl.DummySequence symbolAt(int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList symbolAt(int) - Method in class org.biojava.bio.seq.impl.SimpleSequence symbolAt(int) - Method in class org.biojava.bio.seq.impl.SubSequence symbolAt(int) - Method in class org.biojava.bio.seq.impl.ViewSequence symbolAt(int) - Method in class org.biojava.bio.seq.NewSimpleAssembly symbolAt(int) - Method in class org.biojava.bio.seq.SimpleAssembly symbolAt(int) - Method in class org.biojava.bio.symbol.ChunkedSymbolList symbolAt(int) - Method in class org.biojava.bio.symbol.DummySymbolList symbolAt(int) - Method in class org.biojava.bio.symbol.PackedSymbolList symbolAt(int) - Method in class org.biojava.bio.symbol.RelabeledAlignment symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleSymbolList Find a symbol at a specified offset in the SymbolList. symbolAt(int) - Method in interface org.biojava.bio.symbol.SymbolList Return the symbol at index, counting from 1. symbolAt(int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList Return the symbol at index, counting from 1. symbolAt(int) - Method in class org.biojavax.bio.seq.ThinRichSequence Return the symbol at index, counting from 1. symbolAt(String, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment symbolAt(String, int) - Method in interface org.biojava.bio.alignment.Alignment Retrieve a symbol by label and column. symbolAt(String, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment This gets the symbol for an individual sequence at position in the overall alignment If the sequence is not aligned at that location it returns null symbolAt(String, int) - Method in class org.biojava.bio.alignment.SimpleAlignment symbolAt(String, int) - Method in class org.biojava.bio.dp.SimpleStatePath symbolAt(String, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment symbolAt(String, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment symbolAt(RichSequence, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler Return the symbol at index, counting from 1. symbolAt(RichSequence, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler Return the symbol at index, counting from 1. symbolAt(RichSequence, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler Return the symbol at index, counting from 1. symbolForIndex(int) - Method in interface org.biojava.bio.symbol.AlphabetIndex Retrieve the symbol for an index. symbolForLifeScienceID(LifeScienceIdentifier) - Static method in class org.biojava.bio.symbol.AlphabetManager Retreives the Symbol for the LSID symbolForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager Deprecated. use symbolForLifeScienceID() instead SymbolList - Interface in org.biojava.bio.symbol A sequence of symbols that belong to an alphabet. SymbolListCharSequence - Class in org.biojava.bio.seq.io SymbolListCharSequence is a CharSequence implementation which wraps a SymbolList. SymbolListCharSequence(SymbolList) - Constructor for class org.biojava.bio.seq.io.SymbolListCharSequence Creates a new SymbolListCharSequence wrapping a SymbolList. SymbolListFactory - Interface in org.biojava.bio.symbol This interface exists to hide implementational details of SymbolLists when making chunked symbol lists. symbolListForLabel(String) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment symbolListForLabel(String) - Method in interface org.biojava.bio.alignment.Alignment Retrieve a single row of the alignment by label. symbolListForLabel(String) - Method in class org.biojava.bio.alignment.FlexibleAlignment symbolListForLabel(String) - Method in class org.biojava.bio.alignment.SimpleAlignment symbolListForLabel(String) - Method in class org.biojava.bio.dp.SimpleStatePath symbolListForLabel(String) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment symbolListForLabel(String) - Method in class org.biojava.bio.symbol.RelabeledAlignment symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment symbolListIterator() - Method in interface org.biojava.bio.alignment.Alignment Creates an Iterator over the SymbolLists in the alignment. symbolListIterator() - Method in class org.biojava.bio.alignment.SimpleAlignment symbolListIterator() - Method in class org.biojava.bio.dp.SimpleStatePath symbolListIterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment symbolListIterator() - Method in class org.biojava.bio.symbol.RelabeledAlignment SymbolListIterator(Alignment) - Constructor for class org.biojava.bio.alignment.Alignment.SymbolListIterator Creates a SymbolListIterator for a given alignment object. SymbolListViews - Class in org.biojava.bio.symbol Tools class for constructing views of SymbolList objects. SymbolPropertyTable - Interface in org.biojava.bio.symbol class for maintaining properties associated with a symbol SymbolPropertyTableDB - Interface in org.biojava.bio.proteomics.aaindex Database of SymbolPropertyTable objects. SymbolPropertyTableIterator - Interface in org.biojava.bio.proteomics.aaindex Iterator over SymbolPropertyTable objects. SymbolReader - Interface in org.biojava.bio.seq.io Encapsulate a stream of Symbols being parsed from some input stream. symbols(SymbolList) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator symbols(SymbolList) - Method in class org.biojava.bio.symbol.AbstractRangeLocation symbols(SymbolList) - Method in class org.biojava.bio.symbol.CircularLocation symbols(SymbolList) - Method in class org.biojava.bio.symbol.FuzzyPointLocation symbols(SymbolList) - Method in interface org.biojava.bio.symbol.Location Return the symbols in a sequence that fall within this range. symbols(SymbolList) - Method in class org.biojavax.bio.seq.CompoundRichLocation Return the symbols in a sequence that fall within this range. symbols(SymbolList) - Method in class org.biojavax.bio.seq.EmptyRichLocation Return the symbols in a sequence that fall within this range. symbols(SymbolList) - Method in class org.biojavax.bio.seq.SimpleRichLocation Return the symbols in a sequence that fall within this range. SYMBOLS - Static variable in interface org.biojava.bio.symbol.Alphabet This ChangeType indicates that some symbols have been added or removed from the alphabet. SymbolSequenceRenderer - Class in org.biojava.bio.gui.sequence SymbolSequenceRenderer renders symbols of a SymbolList. SymbolSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.SymbolSequenceRenderer SymbolStyle - Interface in org.biojava.bio.gui The interface for things that say how to paint a symbol. SymbolTokenization - Interface in org.biojava.bio.seq.io Encapsulate a mapping between BioJava Symbol objects and some string representation. SymbolTokenization.TokenType - Class in org.biojava.bio.seq.io symList - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix symList() - Method in interface org.biojava.bio.dp.DPMatrix symList() - Method in interface org.biojava.bio.dp.onehead.DPCursor The symbol list being looped over. symList() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix symList() - Method in class org.biojava.bio.dp.onehead.SmallCursor symList() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix SYMLISTVERSION - Static variable in interface org.biojavax.bio.seq.RichSequence SYMMETRIC - Static variable in class org.biojava.ontology.OntoTools Synonym - Class in org.biojava.ontology Synonym() - Constructor for class org.biojava.ontology.Synonym SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler SYNONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon Use this to define common names for things. SYNONYM_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms SystemRegistry - Class in org.biojava.directory A registry that loads up the standard biodirectory files. SystemRegistry() - Constructor for class org.biojava.directory.SystemRegistry T t() - Static method in class org.biojava.bio.seq.DNATools t() - Static method in class org.biojava.bio.seq.NucleotideTools t() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Threonine T_AESTIVUM - Static variable in interface org.biojava.bio.program.homologene.Taxon TabDelimParser - Class in org.biojava.ontology.io Parse tab-delimited ontology files into Ontology objects. TabDelimParser() - Constructor for class org.biojava.ontology.io.TabDelimParser TabIndexStore - Class in org.biojava.bio.seq.db Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets. TabIndexStore(File, File, String, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.TabIndexStore Create a new TabIndexStore. table(String) - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB Returns the table with the specified name. table(String) - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB Returns the table with the specified name. tableIterator() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB Returns an iterator over SymbolPropertyTable objects. tableIterator() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB Returns an iterator over SymbolPropertyTable objects. tableOfContents - Variable in class org.biojava.bibliography.BiblioDescription It is a table of contents of the cited resource. tableOfContentsType - Variable in class org.biojava.bibliography.BiblioDescription It specifies how BiblioDescription.tableOfContents is coded. TABULAR - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat TagDelegator - Class in org.biojava.bio.program.tagvalue Pushes a new parser and listener, or delegate to a listener depending on the tag. TagDelegator() - Constructor for class org.biojava.bio.program.tagvalue.TagDelegator TagDelegator(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.TagDelegator TagDropper - Class in org.biojava.bio.program.tagvalue Silently drop all tags except those specified, and pass the rest onto a delegate. TagDropper() - Constructor for class org.biojava.bio.program.tagvalue.TagDropper TagDropper(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.TagDropper Create a new TagDropper that will pass on all retained tags and values to tvl. TaggedDataRecord(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord Creates a new TaggedDataRecord from the next 28 bytes of din. TagMapper - Class in org.biojava.bio.program.tagvalue TagMapper maps arbitrary object keys to new keys. TagMapper() - Constructor for class org.biojava.bio.program.tagvalue.TagMapper Creates a new, empty TagMapper. tagName - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord tagNumber - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord TagRenamer - Class in org.biojava.bio.program.tagvalue Rename tags using a TagMapper. TagRenamer(TagValueListener, PropertyChanger) - Constructor for class org.biojava.bio.program.tagvalue.TagRenamer Build a new TagRenamer with a delegate and mapper. TagValue - Class in org.biojava.bio.program.tagvalue Utility class for representing tag-value pairs for TagValueParser implementors. TagValue(Object, Object, boolean) - Constructor for class org.biojava.bio.program.tagvalue.TagValue Build a new TagValue with a tag, a value and a flag indicating if this is a new example of this tag or a continuation of an old example. TagValueContext - Interface in org.biojava.bio.program.tagvalue Communication interface between Parser and a TagValueListener that allows listeners to request that a parser/listener pair be pushed onto the stack to handle the current tag. TagValueListener - Interface in org.biojava.bio.program.tagvalue An object that wishes to be informed of events during the parsing of a file. TagValueParser - Interface in org.biojava.bio.program.tagvalue Tokenize single records (lines of text, objects) into a tag and a value. TagValueWrapper - Interface in org.biojava.bio.program.tagvalue Interface for TagValueListeners that wrap other TagValueListeners takeConnection() - Method in class org.biojava.utils.JDBCConnectionPool takeStatement() - Method in class org.biojava.utils.JDBCConnectionPool tanh(double) - Method in class org.biojava.stats.svm.SigmoidKernel taxa - Static variable in interface org.biojava.bio.program.homologene.Taxon TAXA_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.TaxaBlock A constant representing the name of Taxa blocks. TaxaBlock - Class in org.biojavax.bio.phylo.io.nexus Represents Nexus taxa blocks. TaxaBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.TaxaBlock Delegates to NexusBlock.Abstract constructor using TaxaBlock.TAXA_BLOCK as the name. TaxaBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus Builds Nexus taxa blocks. TaxaBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder TaxaBlockListener - Interface in org.biojavax.bio.phylo.io.nexus Listens to events that represent Nexus taxa blocks. TaxaBlockParser - Class in org.biojavax.bio.phylo.io.nexus Parses Nexus taxa blocks. TaxaBlockParser(TaxaBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.TaxaBlockParser Delegates to NexusBlockParser.Abstract. TAXID_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat Taxon - Interface in org.biojava.bio.program.homologene Taxon - Interface in org.biojava.bio.taxa Deprecated. replaced by classes in org.biojavax.bio.taxa TAXON - Static variable in interface org.biojavax.bio.BioEntry TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat Taxon.TaxonStub - Class in org.biojava.bio.program.homologene TaxonFactory - Interface in org.biojava.bio.taxa Deprecated. replaced by classes in org.biojavax.bio.taxa TAXONID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder TAXONOMY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat TaxonParser - Interface in org.biojava.bio.taxa Deprecated. replaced by classes in org.biojavax.bio.taxa TaxonSQL - Class in org.biojava.bio.seq.db.biosql Deprecated. Use hibernate and org.biojavax.bio.db.* TaxonSQL() - Constructor for class org.biojava.bio.seq.db.biosql.TaxonSQL Deprecated. Tee(SearchListener, SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Tee tempBuffer - Variable in class org.biojava.ontology.obo.OboFileParser Template() - Constructor for class org.biojava.bio.molbio.RestrictionSite.Template Template() - Constructor for class org.biojava.bio.seq.ComponentFeature.Template Template() - Constructor for class org.biojava.bio.seq.Feature.Template Template() - Constructor for class org.biojava.bio.seq.FramedFeature.Template Template() - Constructor for class org.biojava.bio.seq.homol.HomologyFeature.Template Template() - Constructor for class org.biojava.bio.seq.homol.SimilarityPairFeature.Template Template() - Constructor for class org.biojava.bio.seq.RemoteFeature.Template Template() - Constructor for class org.biojava.bio.seq.StrandedFeature.Template Template() - Constructor for class org.biojavax.bio.seq.RichFeature.Template Template(Feature.Template) - Constructor for class org.biojava.bio.seq.RemoteFeature.Template Creates a RemoteFeature.Template that has the same values as the template passed in. TemplateUtils - Class in org.biojava.bio.seq.impl Common things you may want to do with feature templates. temporalPeriod - Variable in class org.biojava.bibliography.BiblioScope It defines temporal period of the cited resource. ter() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the termination (*) placeholder term - Variable in class org.biojavax.bio.seq.SimpleRichLocation Term - Interface in org.biojava.ontology A term in an ontology. TERM - Static variable in class org.biojava.ontology.obo.OboFileHandler TERM - Static variable in interface org.biojava.ontology.Ontology TERM - Static variable in interface org.biojavax.bio.seq.RichLocation TERM - Static variable in interface org.biojavax.Note TERM - Static variable in interface org.biojavax.ontology.ComparableOntology Term.Impl - Class in org.biojava.ontology Simple in-memory implementation of an ontology term. Terms() - Constructor for class org.biojavax.bio.seq.io.EMBLFormat.Terms Terms() - Constructor for class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms Terms() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat.Terms Terms() - Constructor for class org.biojavax.bio.seq.io.INSDseqFormat.Terms Terms() - Constructor for class org.biojavax.bio.seq.io.UniProtFormat.Terms Terms() - Constructor for class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms Terms() - Constructor for class org.biojavax.bio.seq.RichSequence.Terms TEXT - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat TEXT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat TextBlock - Class in org.biojava.bio.gui A BlockPainter that renders letters in proportion to the size of the signal. TextBlock() - Constructor for class org.biojava.bio.gui.TextBlock TextLogoPainter - Class in org.biojava.bio.gui A logo painter that paints in stacked letters. TextLogoPainter() - Constructor for class org.biojava.bio.gui.TextLogoPainter theAbstract - Variable in class org.biojava.bibliography.BiblioDescription It is an abstract of the cited resource. ThinRichSequence - Class in org.biojavax.bio.seq A simple implementation of RichSequence. ThinRichSequence() - Constructor for class org.biojavax.bio.seq.ThinRichSequence ThinRichSequence(Namespace, String, String, int, Alphabet, Double) - Constructor for class org.biojavax.bio.seq.ThinRichSequence Creates a new instance of ThinRichSequence. thr() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Threonine (T) THREAD_POOL_SIZE - Static variable in class org.biojava.utils.process.ExternalProcess Size of the thread pool for the static execute methods. threadPool() - Method in class org.biojava.utils.process.ExternalProcess Gets the thread pool which is used for the input and output handlers. ThreadPool - Interface in org.biojava.utils ThreadPool specifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava. threads - Variable in class org.biojava.utils.SimpleThreadPool threadsAlive() - Method in class org.biojava.utils.SimpleThreadPool threadsAlive returns the number of threads currently alive. threadsIdle() - Method in class org.biojava.utils.SimpleThreadPool threadsIdle returns the number of threads currently waiting for work. threadsWorking() - Method in class org.biojava.utils.SimpleThreadPool threadsWorking returns the number of threads currently performing work. Threshold(double) - Constructor for class org.biojavax.ga.functions.SelectionFunction.Threshold THRESHOLD - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory Accessor for a factory that produces builders that compress the SymbolList of a RichSequence when the length of the SymbolList exceeds THRESHOLD. THRESHOLD_VALUE - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory The value that will be used as a threshold for the THRESHOLD builder. TickFeatureRenderer - Class in org.biojava.bio.gui.sequence TickFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.TickFeatureRenderer TICKS - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer TICKS_DOWN - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer TICKS_DOWN - Static variable in class org.biojava.bio.gui.sequence.RulerRenderer TICKS_DOWN indicates that the ticks will point downwards from a baseline. TICKS_UP - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer TICKS_UP - Static variable in class org.biojava.bio.gui.sequence.RulerRenderer TICKS_UP indicates that the ticks will point upwards from a baseline. TISSUE_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms title - Variable in class org.biojava.bibliography.BibRef A title given to the cited resource (a name by which the resource is formally known). TITLE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. TITLE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat to - Variable in class org.biojava.bio.dp.TrainerTransition to - Variable in class org.biojava.bio.dp.Transition TO_A_LEAF - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree TO_TRACE_SAMPLE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option Option indicating the highest (rightmost) trace sample that should be drawn. toArray() - Method in class org.biojavax.ga.util.WeightedSet toggleSelectionStatus() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.AlternateTokenization tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.CharacterTokenization tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.CrossProductTokenization tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.DoubleTokenization tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.IntegerTokenization tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.NameTokenization tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.SubIntegerTokenization tokenizeSymbol(Symbol) - Method in interface org.biojava.bio.seq.io.SymbolTokenization Return a token representing a single symbol. tokenizeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.AlternateTokenization tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.CharacterTokenization tokenizeSymbolList(SymbolList) - Method in interface org.biojava.bio.seq.io.SymbolTokenization Return a string representation of a list of symbols. tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.WordTokenization tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization toLink(String, Properties) - Method in interface org.biojava.bio.program.blast2html.DatabaseURLGenerator Returns a full retrieve item anchor for the given database id. toLink(String, Properties) - Method in class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator toLink(String, Properties) - Method in class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator toList() - Method in class org.biojava.bio.dp.SimpleStatePath toList() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment toList() - Method in class org.biojava.bio.seq.impl.DummySequence toList() - Method in class org.biojava.bio.seq.impl.SimpleSequence toList() - Method in class org.biojava.bio.seq.impl.SubSequence toList() - Method in class org.biojava.bio.seq.impl.ViewSequence toList() - Method in class org.biojava.bio.seq.NewSimpleAssembly toList() - Method in class org.biojava.bio.seq.SimpleAssembly toList() - Method in class org.biojava.bio.symbol.AbstractSymbolList toList() - Method in class org.biojava.bio.symbol.RelabeledAlignment toList() - Method in interface org.biojava.bio.symbol.SymbolList Returns a List of symbols. toList() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList Returns a List of symbols. toList() - Method in class org.biojavax.bio.seq.ThinRichSequence Returns a List of symbols. toList(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler Returns a List of symbols. toList(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler Returns a List of symbols. toList(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler Returns a List of symbols. Tools() - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools top_level - Static variable in interface org.biojava.bio.seq.FeatureFilter A filter which accepts only top-level Features. topLevel() - Static method in class org.biojava.bio.seq.FilterUtils Return a filter which matches all top-level features. TOPOLOGY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat toProtein(SymbolList) - Static method in class org.biojava.bio.seq.DNATools Convenience method that directly converts a DNA sequence to RNA then to protein. toProtein(SymbolList, int, int) - Static method in class org.biojava.bio.seq.DNATools Convenience method to translate a region of a DNA sequence directly into protein. toRNA(SymbolList) - Static method in class org.biojava.bio.seq.DNATools Converts a SymbolList from the DNA Alphabet to the RNA Alphabet. toString() - Method in class org.biojava.bio.AbstractAnnotation toString() - Method in class org.biojava.bio.alignment.SubstitutionMatrix Overrides the inherited method. toString() - Method in class org.biojava.bio.AnnotationType.Abstract toString() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option toString() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn toString() - Method in class org.biojava.bio.CollectionConstraint.And toString() - Method in class org.biojava.bio.CollectionConstraint.Contains toString() - Method in class org.biojava.bio.CollectionConstraint.Or toString() - Method in class org.biojava.bio.dp.SimpleMarkovModel toString() - Method in class org.biojava.bio.EcNumber.Impl toString() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide toString() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer toString() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent toString() - Method in class org.biojava.bio.molbio.RestrictionEnzyme toString() - Method in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord A very verbose toString that dumps all of the data in this record in a human-readable format. toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByNSName toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute toString() - Method in class org.biojava.bio.PropertyConstraint.And toString() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType toString() - Method in class org.biojava.bio.PropertyConstraint.ByClass toString() - Method in class org.biojava.bio.PropertyConstraint.Enumeration toString() - Method in class org.biojava.bio.PropertyConstraint.ExactValue toString() - Method in class org.biojava.bio.PropertyConstraint.Or toString() - Method in class org.biojava.bio.search.SequenceDBSearchHit Deprecated. toString() - Method in class org.biojava.bio.search.SequenceDBSearchResult Deprecated. toString() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit Deprecated. toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit toString() - Method in class org.biojava.bio.seq.db.biosql.DBHelper.BioSequenceStyle Deprecated. toString() - Method in class org.biojava.bio.seq.db.biosql.DBHelper.DeleteStyle Deprecated. toString() - Method in class org.biojava.bio.seq.db.biosql.DBHelper.JoinStyle Deprecated. toString() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation toString() - Method in class org.biojava.bio.seq.Feature.Template toString() - Method in class org.biojava.bio.seq.FeatureFilter.And toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore toString() - Method in class org.biojava.bio.seq.FeatureFilter.BySource toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByType toString() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation toString() - Method in class org.biojava.bio.seq.FeatureFilter.Not toString() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren toString() - Method in class org.biojava.bio.seq.FeatureFilter.Or toString() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation toString() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation toString() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation toString() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter toString() - Method in class org.biojava.bio.seq.FramedFeature.ReadingFrame toString() - Method in class org.biojava.bio.seq.homol.SimpleHomology toString() - Method in class org.biojava.bio.seq.impl.SimpleFeature toString() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature toString() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature toString() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite toString() - Method in class org.biojava.bio.seq.impl.SimpleSequence toString() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature toString() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion toString() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot toString() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent Return the current indent toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref return the agave xml representation of this instance toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs the agave xml representation of xrefs toString() - Method in class org.biojava.bio.seq.io.SymbolListCharSequence toString() - Method in class org.biojava.bio.seq.io.SymbolTokenization.TokenType toString() - Method in class org.biojava.bio.seq.StrandedFeature.Strand toString() - Method in class org.biojava.bio.symbol.AbstractAlphabet toString() - Method in class org.biojava.bio.symbol.AbstractSymbol toString() - Method in class org.biojava.bio.symbol.AbstractSymbolList toString() - Method in class org.biojava.bio.symbol.CircularLocation toString() - Method in class org.biojava.bio.symbol.FuzzyLocation toString() - Method in class org.biojava.bio.symbol.FuzzyPointLocation toString() - Method in class org.biojava.bio.symbol.PointLocation toString() - Method in class org.biojava.bio.symbol.RangeLocation toString() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block toString() - Method in class org.biojava.bio.taxa.AbstractTaxon Deprecated. toString() - Method in class org.biojava.ontology.Ontology.Impl toString() - Method in class org.biojava.ontology.OntologyTerm.Impl toString() - Method in class org.biojava.ontology.RemoteTerm.Impl toString() - Method in class org.biojava.ontology.Synonym toString() - Method in class org.biojava.ontology.Term.Impl toString() - Method in class org.biojava.ontology.Triple.Impl toString() - Method in class org.biojava.stats.svm.CachingKernel toString() - Method in class org.biojava.stats.svm.DiagonalAddKernel toString() - Method in class org.biojava.stats.svm.DiagonalCachingKernel toString() - Method in class org.biojava.stats.svm.ListSumKernel toString() - Method in class org.biojava.stats.svm.NormalizingKernel toString() - Method in class org.biojava.stats.svm.PolynomialKernel toString() - Method in class org.biojava.stats.svm.RadialBaseKernel toString() - Method in class org.biojava.stats.svm.SigmoidKernel toString() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel toString() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel toString() - Method in class org.biojava.utils.automata.FiniteAutomaton dumps internal data of Nodes and Transitions that describe this FiniteAutomaton. toString() - Method in interface org.biojava.utils.automata.NfaBuilder toString() - Method in class org.biojava.utils.automata.NfaSubModel toString() - Method in class org.biojava.utils.bytecode.CodeField toString() - Method in class org.biojava.utils.bytecode.IntrospectedCodeClass toString() - Method in class org.biojava.utils.bytecode.Label toString() - Method in class org.biojava.utils.bytecode.LocalVariable toString() - Method in class org.biojava.utils.bytecode.ParametricType toString() - Method in class org.biojava.utils.candy.CandyEntry It prints the entry contents. toString() - Method in class org.biojava.utils.ChangeEvent toString() - Method in class org.biojava.utils.ChangeType Return a string representation of this change. toString() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier toString() - Method in class org.biojava.utils.ParseErrorEvent toString() - Method in exception org.biojava.utils.ParserException Represent this exception as a string. toString() - Method in class org.biojava.utils.RepeatedCharSequence toString() - Method in class org.biojava.utils.TypedProperties toString() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter toString() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation toString() - Method in class org.biojavax.bio.seq.CompoundRichLocation Form: "start..end" or just "point" for point locations toString() - Method in class org.biojavax.bio.seq.EmptyRichLocation ALWAYS RETURNS "empty" toString() - Method in class org.biojavax.bio.seq.RichLocation.Strand Form: "symbol" (eg. +,-,?) toString() - Method in class org.biojavax.bio.seq.SimplePosition toString() - Method in class org.biojavax.bio.seq.SimpleRichFeature Form: "(#rank) parent:type,source(location)" toString() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship Form: "(#rank) term(object,subject)" toString() - Method in class org.biojavax.bio.seq.SimpleRichLocation Form: "start..end" or just "point" for point locations toString() - Method in class org.biojavax.bio.SimpleBioEntry Form: namespace:name/accession.version toString() - Method in class org.biojavax.bio.SimpleBioEntryRelationship Form is "(#rank) term(object,subject)" toString() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon Form: "taxid:[name,name...]" toString() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName Form: "class:name" toString() - Method in class org.biojavax.ontology.SimpleComparableOntology Form: "name" toString() - Method in class org.biojavax.ontology.SimpleComparableTerm Form: "ontology:name [obsolete]" where [obsolete] is optional toString() - Method in class org.biojavax.ontology.SimpleComparableTriple Form: "ontology:predicate(subject,object)" toString() - Method in class org.biojavax.SimpleComment Form: "(#rank) comment" toString() - Method in class org.biojavax.SimpleCrossRef Form: "dbname:accession.version" toString() - Method in class org.biojavax.SimpleDocRef Form: "authors; location" toString() - Method in class org.biojavax.SimpleDocRefAuthor Form: "name (consortium) (ed.)" where sections in brackets are optional. toString() - Method in class org.biojavax.SimpleNamespace Form: "name" toString() - Method in class org.biojavax.SimpleNote Form: "(#rank) term: value" toString() - Method in class org.biojavax.SimpleRankedCrossRef Form: "(#rank) crossref" toString() - Method in class org.biojavax.SimpleRankedDocRef Form: "(#rank) docref" toString() - Method in class org.biojavax.SimpleRichAnnotation Form: list of "[note]" values separated by commas toString() - Method in class org.biojavax.utils.CRC64Checksum Returns a zero-padded 16 character wide string containing the current value of this checksum in uppercase hexadecimal format. toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref return the agave xml representation of this instance toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs totalBits(Distribution) - Static method in class org.biojava.bio.gui.DistributionLogo Retrieve the maximal number of bits possible for this type of dist. totalEntropy(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools Calculates the total Entropy for a Distribution. totalInformation(Distribution) - Static method in class org.biojava.bio.gui.DistributionLogo Calculates the total information of the dist in bits. totalSize - Variable in class org.biojava.ontology.obo.OboFileParser toURL(String, Properties) - Method in interface org.biojava.bio.program.blast2html.DatabaseURLGenerator Returns a string representation of a URL to the specified ID. toURL(String, Properties) - Method in class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator toURL(String, Properties) - Method in class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator TournamentSelection - Class in org.biojavax.ga.functions Tournament Selection chooses the best organisms from n random subsets of a given population. TournamentSelection() - Constructor for class org.biojavax.ga.functions.TournamentSelection Default constructor: sets the selection pressure to the value of 10. TPA_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat TRACE - Static variable in class org.biojava.bio.gui.sequence.AbiTraceRenderer TRACE_STROKE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option Option providing the the stroke to use for drawing the chromatogram traces. TrackLayout - Interface in org.biojava.bio.gui.sequence.tracklayout An interface for the handling of the layout of a WrappedSequencePanel. train() - Method in interface org.biojava.bio.dist.DistributionTrainerContext Trains the Distribution, given a null model. train() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext train(double, double) - Method in interface org.biojava.bio.dp.TransitionTrainer Trains the transition, given an expected probability, and a weight for that probability. train(DistributionTrainerContext, double) - Method in interface org.biojava.bio.dist.DistributionTrainer Trains the Distribution, given a null model. train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer Deprecated. train(SequenceDB, double, StoppingCriteria) - Method in class org.biojava.bio.dp.AbstractTrainer Trains the sequences in db until stopper says to finnish. train(SequenceDB, double, StoppingCriteria) - Method in interface org.biojava.bio.dp.TrainingAlgorithm Trains the sequences in db untill stopper says to finnish. Train - Class in org.biojava.stats.svm.tools Train() - Constructor for class org.biojava.stats.svm.tools.Train Trainable - Interface in org.biojava.bio.dp Flags an object as being able to register itself with a model trainer. trainer - Variable in class org.biojava.bio.dp.TrainerTransition trainer - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier Trainer() - Constructor for class org.biojava.bio.dist.SimpleDistribution.Trainer Create a new trainer. TrainerTransition - Class in org.biojava.bio.dp This is a small and ugly class for storing a trainer and a transition. TrainerTransition(TransitionTrainer, State, State) - Constructor for class org.biojava.bio.dp.TrainerTransition trainImpl(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer TrainingAlgorithm - Interface in org.biojava.bio.dp trainingComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener TrainingContext - Interface in org.biojava.stats.svm trainingCycleComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener TrainingEvent - Class in org.biojava.stats.svm TrainingEvent(TrainingContext) - Constructor for class org.biojava.stats.svm.TrainingEvent TrainingListener - Interface in org.biojava.stats.svm trainModel(SVMRegressionModel, double[]) - Method in class org.biojava.stats.svm.SMORegressionTrainer trainModel(SVMTarget, SVMKernel, TrainingListener) - Method in class org.biojava.stats.svm.SMOTrainer TrainRegression - Class in org.biojava.stats.svm.tools TrainRegression() - Constructor for class org.biojava.stats.svm.tools.TrainRegression transcribe(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes Transcribe DNA into RNA. transcribe(SymbolList) - Static method in class org.biojava.bio.seq.RNATools Deprecated. The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour. transcribeToRNA(SymbolList) - Static method in class org.biojava.bio.seq.DNATools Transcribes DNA to RNA. transcriptionTable() - Static method in class org.biojava.bio.seq.RNATools Get a translation table for converting DNA to RNA. transform(FeatureFilter) - Method in class org.biojava.bio.seq.FilterUtils.DelegatingTransformer transform(FeatureFilter) - Method in interface org.biojava.bio.seq.FilterUtils.FilterTransformer Transform a filter, or return null if it can not be transformed. transformFilter(FeatureFilter, FilterUtils.FilterTransformer) - Static method in class org.biojava.bio.seq.FilterUtils This is a general framework method for transforming one filter into another. transformLocation(Location, int, boolean) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils Transform a location, translating and flipping as required. transit(int) - Method in interface org.biojava.utils.automata.StateMachineInstance invoke transition from current state indicated by Symbol represented by symbol index. transit(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState Find the destination State when the specified tag is encountered. transit(Object) - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State Transition - Class in org.biojava.bio.dp This is a small and ugly class for storing a transition. Transition(State, State) - Constructor for class org.biojava.bio.dp.Transition transitions - Variable in class org.biojava.utils.automata.FiniteAutomaton transitionsFrom(State) - Method in interface org.biojava.bio.dp.MarkovModel Returns the FiniteAlphabet of all states that have a transition from 'source'. transitionsFrom(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel transitionsFrom(State) - Method in class org.biojava.bio.dp.WMAsMM transitionsTo(State) - Method in interface org.biojava.bio.dp.MarkovModel Returns the FiniteAlphabet of all states that have a transition to 'dest'. transitionsTo(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel transitionsTo(State) - Method in class org.biojava.bio.dp.WMAsMM TransitionTable() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable TransitionTrainer - Interface in org.biojava.bio.dp An object that can be used to train the transitions within a MarkovModel. TRANSITIVE - Static variable in class org.biojava.ontology.OntoTools translate(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator translate(int) - Method in class org.biojava.bio.symbol.FuzzyLocation translate(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation translate(int) - Method in interface org.biojava.bio.symbol.Location Create a location that is a translation of this location. translate(int) - Method in class org.biojava.bio.symbol.PointLocation translate(int) - Method in class org.biojava.bio.symbol.RangeLocation translate(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation Create a location that is a translation of this location. translate(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation Create a location that is a translation of this location. translate(int) - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation Create a location that is a translation of this location. translate(int) - Method in interface org.biojavax.bio.seq.Position Takes this position and returns a copy translated by 'distance' bases. translate(int) - Method in class org.biojavax.bio.seq.SimplePosition Takes this position and returns a copy translated by 'distance' bases. translate(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation Create a location that is a translation of this location. translate(Symbol) - Method in interface org.biojava.bio.symbol.TranslationTable Translate a single symbol from source alphabet to the target alphabet. translate(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes Translate RNA into protein (with termination symbols). translate(SymbolList) - Static method in class org.biojava.bio.seq.RNATools Translate RNA into protein (with termination symbols). translate(SymbolList, TranslationTable) - Static method in class org.biojava.bio.symbol.SymbolListViews Provides a 'translated' view of an underlying SymbolList. translateCUD(InputStream, OutputStream) - Static method in class org.biojava.bio.symbol.CodonPrefTools reads in a file in Codon Usage Database format and translate it into our XML format These can be obtained from the Codon Usage Database. TranslatedDistribution - Class in org.biojava.bio.dist A translated view of some underlying distribution. TranslatedDistribution(ReversibleTranslationTable, Distribution, DistributionFactory) - Constructor for class org.biojava.bio.dist.TranslatedDistribution Create a new TranslatedDistribution. TranslatedSequencePanel - Class in org.biojava.bio.gui.sequence TranslatedSequencePanel is a panel that displays a Sequence. TranslatedSequencePanel() - Constructor for class org.biojava.bio.gui.sequence.TranslatedSequencePanel Creates a new TranslatedSequencePanel with the default settings (direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font). TranslateFlipContext - Class in org.biojava.bio.seq.projection A ProjectionContext that translates and optionaly flips features. TranslateFlipContext(FeatureHolder, FeatureHolder, int) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext Create a new TranslateFlipContext with translation only. TranslateFlipContext(FeatureHolder, FeatureHolder, int, boolean) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext Create a new TranslateFlipContext with explicit translation and flip. TranslateFlipContext(FeatureHolder, FeatureHolder, int, int) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext Create a new TranslateFlipContext that flips all featurs arround min and max. TRANSLATION - Static variable in class org.biojava.bio.gui.sequence.PairwiseSequencePanel Constant TRANSLATION is a ChangeType which indicates a change to the translation, requiring a paint update. TRANSLATION - Static variable in class org.biojava.bio.gui.sequence.TranslatedSequencePanel Constant TRANSLATION is a ChangeType which indicates a change to the translation, requiring a paint update. TranslationTable - Interface in org.biojava.bio.symbol Encapsulates the mapping from a source to a destination alphabet. TRANSPOSON_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms transScore(State, State, Symbol, Symbol) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM TREES_BLOCK - Static variable in class org.biojavax.bio.phylo.io.nexus.TreesBlock A constant representing the name of Trees blocks. TreesBlock - Class in org.biojavax.bio.phylo.io.nexus Represents Nexus trees blocks. TreesBlock() - Constructor for class org.biojavax.bio.phylo.io.nexus.TreesBlock Delegates to NexusBlock.Abstract constructor using TreesBlock.TREES_BLOCK as the name. TreesBlock.NewickTreeString - Class in org.biojavax.bio.phylo.io.nexus A simple representation of a Newick tree as a single string. TreesBlockBuilder - Class in org.biojavax.bio.phylo.io.nexus Builds Nexus taxa blocks. TreesBlockBuilder() - Constructor for class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder TreesBlockListener - Interface in org.biojavax.bio.phylo.io.nexus Listens to events that represent Nexus trees blocks. TreesBlockParser - Class in org.biojavax.bio.phylo.io.nexus Parses Nexus taxa blocks. TreesBlockParser(TreesBlockListener) - Constructor for class org.biojavax.bio.phylo.io.nexus.TreesBlockParser Delegates to NexusBlockParser.Abstract. TREMA_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable Translation table name for the trematode mitochondrial genetic code. Triple - Interface in org.biojava.ontology A triple in an ontology. TRIPLE - Static variable in interface org.biojava.ontology.Ontology TRIPLE - Static variable in interface org.biojavax.ontology.ComparableOntology Triple.Impl - Class in org.biojava.ontology Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple Triplet() - Constructor for class org.biojava.utils.ListTools.Triplet Triplet(Object, Object, Object) - Constructor for class org.biojava.utils.ListTools.Triplet TriState - Class in org.biojava.utils Class that represents the tristate values possible in a logical operation: true, false and indeterminate. trp() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Tryptophan (W) TRUE - Static variable in class org.biojava.utils.TriState TRYPSIN - Static variable in class org.biojava.bio.proteomics.Protease TRYPSIN - Static variable in class org.biojava.bio.proteomics.ProteaseManager TurnGlyph - Class in org.biojava.bio.gui.glyph A Glyph that paints a wide 'H' line within the bounds TurnGlyph() - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph TurnGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph TurnGlyph(Paint, Stroke) - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph TWIN - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder TWIN - Static variable in interface org.biojava.bio.program.homologene.SimilarityType TwoHeadedArrowGlyph - Class in org.biojava.bio.gui.glyph A Glyph that paints a two headed arrow within the bounds TwoHeadedArrowGlyph() - Constructor for class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph TwoHeadedArrowGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph type - Variable in class org.biojava.bibliography.BiblioCriterion The criteria can be used for defining rules for matching (type BiblioCriterion.QUERY_CRITERION), or for ordering (type BiblioCriterion.SORT_CRITERION). type - Variable in class org.biojava.bibliography.BibRef It defines the nature or genre of the cited resource. type - Variable in class org.biojava.bio.seq.Feature.Template type - Variable in class org.biojava.utils.IndexedChangeHub.ListenerMemento TYPE - Static variable in interface org.biojava.bio.seq.Feature The type of this feature has altered. TYPE_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a bibliographic resource type. TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat TYPE_BOOK - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a bibliographic resource type. TYPE_BOOK_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a bibliographic resource type. TYPE_BOOLEAN - Static variable in class org.biojava.utils.bytecode.CodeUtils TYPE_BYTE - Static variable in class org.biojava.utils.bytecode.CodeUtils TYPE_CHAR - Static variable in class org.biojava.utils.bytecode.CodeUtils TYPE_DOUBLE - Static variable in class org.biojava.utils.bytecode.CodeUtils TYPE_FLOAT - Static variable in class org.biojava.utils.bytecode.CodeUtils TYPE_INT - Static variable in class org.biojava.utils.bytecode.CodeUtils TYPE_JOURNAL_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a bibliographic resource type. TYPE_LONG - Static variable in class org.biojava.utils.bytecode.CodeUtils TYPE_OBJECT - Static variable in class org.biojava.utils.bytecode.CodeUtils TYPE_PATENT - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a bibliographic resource type. TYPE_PROCEEDING - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a bibliographic resource type. TYPE_SHORT - Static variable in class org.biojava.utils.bytecode.CodeUtils TYPE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. TYPE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. TYPE_TECH_REPORT - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a bibliographic resource type. TYPE_THESIS - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a bibliographic resource type. TYPE_VOID - Static variable in class org.biojava.utils.bytecode.CodeUtils TYPE_WEB_RESOURCE - Static variable in interface org.biojava.bibliography.BibRefSupport A name of a bibliographic resource type. TYPEDEF - Static variable in class org.biojava.ontology.obo.OboFileHandler TypedProperties - Class in org.biojava.utils a sub-class of java.util.Properties that provides the same constructors, adds two convenient load methods to load the properties from files and, most importantly, adds getPropertyAsXXX() methods to get a property as an object of type XXX. TypedProperties() - Constructor for class org.biojava.utils.TypedProperties Creates an empty property list with no default values. TypedProperties(Properties) - Constructor for class org.biojava.utils.TypedProperties Creates an empty property list with the specified defaults. TypeLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker typeTerm - Variable in class org.biojava.bio.seq.Feature.Template TYPETERM - Static variable in interface org.biojava.bio.seq.Feature The ontological type of this feature has altered. TYPETERM - Static variable in interface org.biojavax.bio.seq.RichFeature tyr() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Tyrosine (Y) U u() - Static method in class org.biojava.bio.seq.NucleotideTools u() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Selenocysteine u() - Static method in class org.biojava.bio.seq.RNATools UkkonenSuffixTree - Class in org.biojava.bio.symbol A suffix tree is an efficient method for encoding the frequencies of motifs in a sequence. UkkonenSuffixTree() - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree Initializes a new UkkonenSuffixTree instance. UkkonenSuffixTree(String) - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree UkkonenSuffixTree(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree UkkonenSuffixTree.SuffixNode - Class in org.biojava.bio.symbol end Tree modification methods unbind(String) - Method in class org.biojava.naming.ObdaContext unbind(Name) - Method in class org.biojava.naming.ObdaContext Unchangeable - Class in org.biojava.utils This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. Unchangeable() - Constructor for class org.biojava.utils.Unchangeable UNCLASSIFIED - Static variable in interface org.biojava.bio.EcNumber Constant that represents EC number components that are as yet unclassified. uncompress(String, FileOutputStream) - Static method in class org.biojava.utils.io.UncompressInputStream UncompressInputStream - Class in org.biojava.utils.io This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant). UncompressInputStream(InputStream) - Constructor for class org.biojava.utils.io.UncompressInputStream UNDEFINED - Static variable in interface org.biojava.bio.EcNumber Constant that represents EC number components that are not defined. UnequalLengthAlignment - Interface in org.biojava.bio.alignment UnequalLengthAlignment has the following behavior. unescape(String) - Method in class org.biojava.ontology.obo.OboFileParser unescape(String, char, int, boolean) - Method in class org.biojava.ontology.obo.OboFileParser unescape(String, char, int, int, boolean) - Method in class org.biojava.ontology.obo.OboFileParser unescapeChars - Static variable in class org.biojava.ontology.obo.OboFileParser UniformDistribution - Class in org.biojava.bio.dist An implementation of an uniform distribution UniformDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.UniformDistribution Create a new UniformDistribution. uniformMutationDistribution(FiniteAlphabet) - Static method in class org.biojavax.ga.util.GATools Makes a 1st order distribution which is infact uniform (equivalent to a uniform zero order distribution). UniformScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler UNIGENE_ANNOTATION - Static variable in class org.biojava.bio.program.unigene.UnigeneTools Annotation schema for all UnigeneCluster instances. UnigeneCluster - Interface in org.biojava.bio.program.unigene A single unigene cluster. UnigeneDB - Interface in org.biojava.bio.program.unigene A database of Unigene clusters. UnigeneFactory - Interface in org.biojava.bio.program.unigene Objects that can be used to produce a UnigeneDB instance given a URL. UnigeneTools - Class in org.biojava.bio.program.unigene Usefull tools for working with Unigene. UnigeneTools() - Constructor for class org.biojava.bio.program.unigene.UnigeneTools unIndent() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent Remove a level of indentation union(Collection) - Static method in class org.biojava.bio.symbol.LocationTools The n-way union of a Collection of locations. union(BibRefQuery[], Hashtable) - Method in interface org.biojava.bibliography.BibRefSupport It merges all given collections together. union(AnnotationType, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools Create an AnnotationType that matches all Anntotations that are accepted by two others. union(CollectionConstraint, CollectionConstraint) - Static method in class org.biojava.bio.AnnotationTools Calculate a CollectionConstaint that will accept all items accepted by either constraint. union(PropertyConstraint, PropertyConstraint) - Static method in class org.biojava.bio.AnnotationTools Create a PropertyConstraint that matches all Objects that are accepted by two others. union(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils Operator: Union of FeatureHolder1 and FeatureHolder2 union(Location) - Method in class org.biojava.bio.symbol.AbstractLocation union(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator union(Location) - Method in class org.biojava.bio.symbol.CircularLocation union(Location) - Method in interface org.biojava.bio.symbol.Location Return a Location containing all points in either ranges. union(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation Return a Location containing all points in either ranges. union(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation Return a Location containing all points in either ranges. union(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation Return a Location containing all points in either ranges. union(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools Return the union of two locations. UNIPROT_FORMAT - Static variable in class org.biojavax.bio.seq.io.UniProtFormat The name of this format UniProtCommentParser - Class in org.biojavax.bio.seq.io UniProtCommentParser() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser Creates a new instance of UniProtCommentParser. UniProtCommentParser.Event - Class in org.biojavax.bio.seq.io A class to describe events for alternative product comments. UniProtCommentParser.Interaction - Class in org.biojavax.bio.seq.io A class to describe protein-protein interactions. UniProtCommentParser.Isoform - Class in org.biojavax.bio.seq.io A class to describe isoforms for alternative product comments. UniProtCommentParser.SeqCaution - Class in org.biojavax.bio.seq.io A class to describe seq caution entries. UniProtFormat - Class in org.biojavax.bio.seq.io Format reader for UniProt files. UniProtFormat() - Constructor for class org.biojavax.bio.seq.io.UniProtFormat UniProtFormat.Terms - Class in org.biojavax.bio.seq.io Implements some UniProt-specific terms. UniProtLocationParser - Class in org.biojavax.bio.seq.io Parses UniProt location strings into RichLocation objects. UNIPROTXML_FORMAT - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat The name of this format UniProtXMLFormat - Class in org.biojavax.bio.seq.io Format reader for UniProtXML files. UniProtXMLFormat() - Constructor for class org.biojavax.bio.seq.io.UniProtXMLFormat UniProtXMLFormat.Terms - Class in org.biojavax.bio.seq.io Implements some UniProtXML-specific terms. UNIVERSAL - Static variable in interface org.biojava.bio.symbol.TranslationTable Translation table name for the universal genetic code. UNKNOWN - Static variable in class org.biojava.bio.seq.io.AlignIOConstants UNKNOWN indicates that the alignment format is unknown. UNKNOWN - Static variable in class org.biojava.bio.seq.io.SeqIOConstants UNKNOWN indicates that the sequence format is unknown. UNKNOWN - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization UNKNOWN - Static variable in interface org.biojava.bio.seq.StrandedFeature Flag to indicate that a feature has an unknown strand. UNKNOWN - Static variable in class org.biojava.utils.ChangeType Constant ChangeType field which indicates that a change has occured which can't otherwise be represented. UNKNOWN_BLOCK - Static variable in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser The name for an unknown block parser. UNKNOWN_SCOPE - Static variable in class org.biojava.ontology.Synonym UNKNOWN_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand The unknown strand is represented by the symbol '?' UnknownDBHelper - Class in org.biojava.bio.seq.db.biosql Deprecated. Use hibernate and org.biojavax.bio.db.* UnknownDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.UnknownDBHelper Deprecated. unlockModel() - Method in class org.biojava.bio.dp.DP unmask(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector Un-masks the token by making it upper case. unmask(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector Present the token for a Symbol as it would appear if it wasn't softmasked unpack(byte) - Method in class org.biojava.bio.symbol.DNAAmbPack unpack(byte) - Method in class org.biojava.bio.symbol.DNANoAmbPack unpack(byte) - Method in interface org.biojava.bio.symbol.Packing Return the symbol for a packing. unregisterFactory(UnigeneFactory) - Static method in class org.biojava.bio.program.unigene.UnigeneTools Register a UnigeneFactory. UnsupportedChromatogramFormatException - Exception in org.biojava.bio.chromatogram Exception indicating that some provided data does not represent a supported chromatogram format. UnsupportedChromatogramFormatException() - Constructor for exception org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException Create a new UnsupportedChromatogramFormatException. UnsupportedChromatogramFormatException(String) - Constructor for exception org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException Create a new UnsupportedChromatogramFormatException with a message. UntrainableDistribution - Class in org.biojava.bio.dist A distribution which does not interact with the training framework. UntrainableDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.UntrainableDistribution Construct a new untrainable distribution over the specified alphabet. untranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet. untranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable untranslate(Symbol) - Method in interface org.biojava.bio.symbol.ManyToOneTranslationTable Translate a single symbol from target alphabet to the source alphabet. untranslate(Symbol) - Method in interface org.biojava.bio.symbol.ReversibleTranslationTable Translate a single symbol from target alphabet to the source alphabet. update() - Method in class org.biojava.bio.dp.DP update() - Method in class org.biojava.bio.dp.onehead.SingleDP update() - Method in class org.biojava.bio.dp.twohead.PairwiseDP update(byte[], int, int) - Method in class org.biojavax.utils.CRC64Checksum update(int) - Method in class org.biojavax.utils.CRC64Checksum update(String) - Method in class org.biojavax.utils.CRC64Checksum UPDATE_DATE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat UPDATE_REL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat Upgma(TaxaBlock, CharactersBlock) - Static method in class org.biojavax.bio.phylo.DistanceBasedTreeMethod uri - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase URI - Static variable in interface org.biojavax.Namespace URI_PREFIX - Static variable in class org.biojava.bio.seq.FeatureTypes The standard prefix for all type URIs url - Variable in class org.biojava.bibliography.BiblioWebResource The URL of the resource. urlBatchSequences - Static variable in class org.biojava.bio.seq.db.GenbankSequenceDB urlBatchSequences - Static variable in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB urlBatchSequences - Static variable in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB URLFactory - Interface in org.biojava.utils.net URLFactory defines a means of obtaining a URL associated with an object. URLGeneratorFactory - Interface in org.biojava.bio.program.blast2html Interface for a factory method to return a list of 0, 1 or more DatabaseURLGenerator instances. usCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme USE_CUSTOM_STROKE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option Option indicating whether to use custom strokes when drawing traces and separators. USE_PER_SHAPE_TRANSFORM - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option Option indicating whether to apply scaling and translation transforms to each shape individually or to apply a single transform to the graphics context. UserDefinedTrackLayout - Class in org.biojava.bio.gui.sequence.tracklayout An implementation of TrackLayout that that wraps a sequence over an arbitrary set of ranges UserDefinedTrackLayout(RangeLocation[]) - Constructor for class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout useSuppliedSymListFactory() - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory Call this to convert from default SymbolList implementation to user-supplied implementation. UtilHelper - Class in org.biojava.bio.seq.io.agave Just make the property follow the common case UtilHelper() - Constructor for class org.biojava.bio.seq.io.agave.UtilHelper V v() - Static method in class org.biojava.bio.seq.DNATools v() - Static method in class org.biojava.bio.seq.NucleotideTools v() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Valine val() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Valine (V) validate(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet validate(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet. validate(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet validate(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet validate(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet validate(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.And validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Contains validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Or validateAddValue(Collection, Object) - Method in interface org.biojava.bio.CollectionConstraint Return true iff the Collection formed by adding newValue to current would be accepted by this constraint. validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.And validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Contains validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Or validateRemoveValue(Collection, Object) - Method in interface org.biojava.bio.CollectionConstraint Return true iff the Collection formed by removing newValue from current would be accepted by this constraint. validLen - Variable in class org.biojava.utils.io.CachingInputStream A count of the number of bytes in CachingInputStream.cache that contain data read from the stream. value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Aggregator value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Echo value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Indexer value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Indexer2 value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.MultiTagger value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper value(TagValueContext, Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueListener A value has been seen. value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.ValueChanger VALUE - Static variable in interface org.biojavax.Note VALUE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat ValueChanger - Class in org.biojava.bio.program.tagvalue Intercept the values associated with some tags and change them systematically. ValueChanger(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.ValueChanger ValueChanger(TagValueListener, ChangeTable) - Constructor for class org.biojava.bio.program.tagvalue.ValueChanger Create a new changer that will pass the modified event stream to a delegate. valueOf(String) - Static method in class org.biojava.bio.EcNumber.Impl Process a string into an EcNumber. valueOf(String) - Static method in enum org.biojava.bio.program.fastq.FastqVariant Returns the enum constant of this type with the specified name. valueOf(String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier Create a new LifeScienceIdentifier parsed from the properly formatted string lsid. valueOf(String) - Static method in enum org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat Returns the enum constant of this type with the specified name. valueOf(String, String, String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier Create a new LifeScienceIdentifier from the specified parameters. valueOf(String, String, String, String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier Create a new LifeScienceIdentifier from the specified parameters. values() - Static method in enum org.biojava.bio.program.fastq.FastqVariant Returns an array containing the constants of this enum type, in the order they are declared. values() - Static method in enum org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat Returns an array containing the constants of this enum type, in the order they are declared. VALUES - Static variable in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer Variable - Interface in org.biojava.ontology Variable.Impl - Class in org.biojava.ontology vectorToString(SparseVector) - Static method in class org.biojava.stats.svm.tools.SVM_Light VERSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. VERSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat Deprecated. VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat VERT_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable Translation table name for the vertebrate mitochondrial genetic code. view(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly. view(Sequence, String) - Static method in class org.biojava.bio.seq.SequenceTools Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly. view(Sequence, FeatureRealizer) - Static method in class org.biojava.bio.seq.SequenceTools Creates a new Sequence with the data of the old but with a different FeatureRealizer that will be applied to new Features. viewEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block ViewingSequenceDB - Class in org.biojava.bio.seq.db SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database. ViewingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.ViewingSequenceDB Create a new ViewingSequenceDB that views the sequences in parent. ViewSequence - Class in org.biojava.bio.seq.impl A view onto another Sequence object. ViewSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.ViewSequence Construct a view onto an existing sequence which takes on that sequence's name. ViewSequence(Sequence, String) - Constructor for class org.biojava.bio.seq.impl.ViewSequence Construct a view onto an existing sequence and give it a new name. ViewSequence(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.impl.ViewSequence Construct a view onto a sequence, using a specific FeatureRealizer. ViewSequenceFactory - Class in org.biojava.bio.program.ssbind ViewSequenceFactory is a base class for creating search handlers which create and cache views on the query and subject sequences. ViewSequenceFactory() - Constructor for class org.biojava.bio.program.ssbind.ViewSequenceFactory viewStart - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block viewToSource(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList Coordinate conversion from view to source. viewToSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList viewToSource(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList Coordinate conversion from view to source. visitFilter(FeatureFilter, Visitor) - Static method in class org.biojava.bio.seq.FilterUtils Applies a visitor to a filter, and returns the visitor's result or null. Visitor - Interface in org.biojava.utils.walker Things that will be shown filters. viterbi(ScoreType, BackPointer) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory viterbi(ScoreType, BackPointer) - Method in class org.biojava.bio.dp.twohead.DPInterpreter viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP volume - Variable in class org.biojava.bibliography.BiblioBook Book volume. volume - Variable in class org.biojava.bibliography.BiblioJournalArticle The journal volume. vp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat vp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat W w() - Static method in class org.biojava.bio.seq.DNATools w() - Static method in class org.biojava.bio.seq.NucleotideTools w() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Tryptophan waitForThreads() - Method in class org.biojava.utils.SimpleThreadPool waitForThreads() - Method in interface org.biojava.utils.ThreadPool waitForThreads temporarily closes the pool to new requests until such time as the current request queue has been emptied and all running tasks completed. walk(Object, Visitor) - Method in interface org.biojava.utils.walker.Walker This walks the feature tree, showing the visitor each filter in the expression. Walker - Interface in org.biojava.utils.walker Objects that can walk over a filter expression, showing each element to a visitor. WalkerFactory - Class in org.biojava.utils.walker walkTo(UkkonenSuffixTree.SuffixNode, String, int, int) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree This method is used to walk down the tree, from a given node. wantsBracketsAndBraces() - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser wantsBracketsAndBraces() - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser wantsBracketsAndBraces() - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract wantsBracketsAndBraces() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockParser Does the listener want to know about brackets and braces as separate tokens? wantsBracketsAndBraces() - Method in class org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract wantsBracketsAndBraces() - Method in interface org.biojavax.bio.phylo.io.nexus.NexusFileListener Does the listener want to know about brackets and braces as separate tokens? wasEmpty() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer Returns true if no HitSummary and no Hit elements were encountered WeakCacheMap - Class in org.biojava.utils.cache A cache which retains weak references to objects WeakCacheMap() - Constructor for class org.biojava.utils.cache.WeakCacheMap WeakTaxon - Class in org.biojava.bio.taxa Deprecated. replaced by classes in org.biojavax.bio.taxa WeakTaxon() - Constructor for class org.biojava.bio.taxa.WeakTaxon Deprecated. WeakTaxon(String, String) - Constructor for class org.biojava.bio.taxa.WeakTaxon Deprecated. WeakTaxonFactory - Class in org.biojava.bio.taxa Deprecated. replaced by classes in org.biojavax.bio.taxa WeakTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.WeakTaxonFactory Deprecated. WeakValueHashMap - Class in org.biojava.utils.cache Map implementation which keeps weak references to values. WeakValueHashMap() - Constructor for class org.biojava.utils.cache.WeakValueHashMap WebSequenceDB - Class in org.biojava.bio.seq.db Functions for access to a web based database that returns sequences in a variety of formats. WebSequenceDB() - Constructor for class org.biojava.bio.seq.db.WebSequenceDB WeightedSet - Class in org.biojavax.ga.util Inspred by the BioJava Distribution objects the WeightedSet is a map from a Key to a Weight. WeightedSet() - Constructor for class org.biojavax.ga.util.WeightedSet weightForwarder - Variable in class org.biojava.bio.dist.AbstractOrderNDistribution The listener that will forward events from the underlying distributions to listeners for this distribution. WeightMatrix - Interface in org.biojava.bio.dp A log odds weight matrix. WeightMatrixAnnotator - Class in org.biojava.bio.dp Annotates a sequence with hits to a weight-matrix. WeightMatrixAnnotator(WeightMatrix, double) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator Create a new annotator that uses PROBABILITY score type. WeightMatrixAnnotator(WeightMatrix, ScoreType, double) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator Create a new annotator that uses a specific score type. WeightMatrixAnnotator(WeightMatrix, ScoreType, double, String) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix. WEIGHTS - Static variable in interface org.biojava.bio.dist.Distribution Whenever a distribution changes the values that would be returned by getWeight, they should fire a ChangeEvent with this object as the type. WIDTH_IS_AUTHORITATIVE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option Option indicating whether width or horizontal scale is the authoritative measure. windowedSymbolList(SymbolList, int) - Static method in class org.biojava.bio.symbol.SymbolListViews A view of windows onto another SymbolList. withDescription(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder Return this FASTQ formatted sequence builder configured with the specified description. withQuality(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder Return this FASTQ formatted sequence builder configured with the specified quality scores. withSequence(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder Return this FASTQ formatted sequence builder configured with the specified sequence. withVariant(FastqVariant) - Method in class org.biojava.bio.program.fastq.FastqBuilder Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant. WMAsMM - Class in org.biojava.bio.dp Wraps a weight matrix up so that it appears to be a very simple HMM. WMAsMM(WeightMatrix) - Constructor for class org.biojava.bio.dp.WMAsMM WobbleDistribution - Interface in org.biojava.bio.symbol an object to return statistics about the frequency of the wobble base in a set of synonymous codons. wordsForType(CodeClass) - Static method in class org.biojava.utils.bytecode.CodeUtils Number of words needed for local variables of this type. wordSize() - Method in class org.biojava.bio.symbol.DNAAmbPack wordSize() - Method in class org.biojava.bio.symbol.DNANoAmbPack wordSize() - Method in interface org.biojava.bio.symbol.Packing The number of bits required to pack a symbol. WordTokenization - Class in org.biojava.bio.seq.io Base class for tokenizations which accept whitespace-separated `words'. WordTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.WordTokenization wordWrap(String, String, int) - Static method in class org.biojavax.utils.StringTools Word-wraps a string into an array of lines of no more than the given width. WORM_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools Caenorhabditis elegans codon preferences Wrapper(SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Wrapper write(File, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter Write the specified FASTQ formatted sequences to the specified file. write(File, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter Write the specified FASTQ formatted sequences to the specified file. write(OutputStream, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter Write the specified FASTQ formatted sequences to the specified output stream. write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat Writes out the alignment to an FASTA file. write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat write(OutputStream, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter Write the specified FASTQ formatted sequences to the specified output stream. write(Sequence) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter Writing Sequence. writeAnnotations(FeatureHolder) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter writeAnnotationType(AnnotationType, XMLWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter Write an AnnotationType to the specified XMLWriter. writeAssembly(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter writeBioSequence(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter writeBlockContents(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock writeBlockContents(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock writeBlockContents(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract Implement this to write out block contents, not including the BEGIN and END tags. writeBlockContents(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock writeBlockContents(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock writeByte(byte) - Method in interface org.biojava.utils.bytecode.CodeContext Write a single byte to the context. writeClassification(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter writeCode(CodeContext) - Method in interface org.biojava.utils.bytecode.CodeGenerator Write the byte or bytes for this CodeGenerator to a CodeContext. writeCode(CodeContext) - Method in class org.biojava.utils.bytecode.IfExpression writeCode(CodeContext) - Method in class org.biojava.utils.bytecode.InstructionVector writeCode(CodeContext) - Method in class org.biojava.utils.bytecode.Label writeCode(CodeContext) - Method in class org.biojava.utils.bytecode.MarkLabel writeCollectionConstraint(CollectionConstraint, XMLWriter, XMLAnnotationTypeWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLCollectionConstraintWriter writeCompResult(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter writeConstantPool(DataOutput) - Method in class org.biojava.utils.bytecode.ConstantPool writeContig(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter writeDetails(XMLWriter, Feature) - Method in class org.biojava.bio.program.xff.BasicXFFHelper writeDetails(XMLWriter, Feature) - Method in class org.biojava.bio.program.xff.PropertyWriter writeDetails(XMLWriter, Feature) - Method in interface org.biojava.bio.program.xff.XFFHelper writeDistribution(Distribution, OutputStream) - Method in class org.biojava.bio.dist.XMLDistributionWriter Writes an OrderNDistribution or simple Distribution to an XML file. writeDna(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat writeDna(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat writeEmbl(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Writes a single Sequence to an OutputStream in EMBL format. writeEmbl(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Writes a stream of Sequences to an OutputStream in EMBL format. writeEMBL(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes sequences from a SequenceIterator to an OutputStream in EMBL Format. writeEMBL(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes a single Sequence to an OutputStream in EMBL format. writeEMBLxml(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes sequences from a SequenceIterator to an OutputStream in EMBLxml Format. writeEMBLxml(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes a single Sequence to an OutputStream in EMBLxml format. writeEmptyElement(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter writeEmptyElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter writeFasta(OutputStream, SequenceDB) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Write a sequenceDB to an output stream in fasta format. writeFasta(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Writes a single Sequence to an OutputStream in Fasta format. writeFasta(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Writes sequences from a SequenceIterator to an OutputStream in Fasta Format. writeFasta(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes Sequences from a SequenceIterator to an OutputStream in Fasta Format. writeFasta(OutputStream, SequenceIterator, Namespace, FastaHeader) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes Sequences from a SequenceIterator to an OutputStream in Fasta Format. writeFasta(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes a single Sequence to an OutputStream in Fasta format. writeFasta(OutputStream, Sequence, Namespace, FastaHeader) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes a single Sequence to an OutputStream in Fasta format. writeFeatureSet(FeatureHolder, XMLWriter) - Method in class org.biojava.bio.program.xff.XFFWriter writeFile(File, Alignment) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat Writes the given Alignment in PHYLIP format to a file. writeFile(File, NexusFile) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat Writes the given Nexus output to a file. writeFilter(FeatureFilter, XMLWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter Write a FeatureFilter to the supplied XMLWriter writeFilter(FeatureFilter, XMLWriter, XMLFilterWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterWriter.FilterWriter writeFooter() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter Write </sciobj> writeGenbank(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Writes a single Sequence to an OutputStream in Genbank format. writeGenbank(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Writes a stream of Sequences to an OutputStream in Genbank format. writeGenbank(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes sequences from a SequenceIterator to an OutputStream in GenBank Format. writeGenbank(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes a single Sequence to an OutputStream in GenBank format. writeGene(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter writeGenpept(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Writes a single Sequence to an OutputStream in Genpept format. writeGenpept(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Writes a stream of Sequences to an OutputStream in Genpept format. writeGFF(File, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools Writes a GFFEntrySet to a file. writeGFF(PrintWriter, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools Writes a GFFEntrySet to a PrintWriter. writeGFF(String, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools Writes a GFFEntrySet to a file. writeHeader() - Method in class org.biojava.bio.program.xml.BaseXMLWriter writeHeader() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter Write <sciobj> writeIndent() - Method in class org.biojava.utils.xml.PrettyXMLWriter writeINSDseq(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes sequences from a SequenceIterator to an OutputStream in INSDseq Format. writeINSDseq(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes a single Sequence to an OutputStream in INSDseq format. writeKeyValueLine(String, String, int, int, PrintStream) - Static method in class org.biojavax.utils.StringTools Writes some text to the output stream in the following format: key text continuation of text where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth, and the text is split over multiple lines at the nearest occurrence of whitespace. writeKeyValueLine(String, String, int, int, String, PrintStream) - Static method in class org.biojavax.utils.StringTools Writes some text to the output stream in the following format: key text continuation of text where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth, and the text is split over multiple lines at the nearest occurrence of separator sep. writeKeyValueLine(String, String, int, int, String, String, PrintStream) - Static method in class org.biojavax.utils.StringTools Writes some text to the output stream in the following format: key text wrappedKey continuation of text where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth, and the text is split over multiple lines at the nearest occurrence of separator sep. writeLabel(Label) - Method in interface org.biojava.utils.bytecode.CodeContext Write the offset of a Label to the context. writeLocation(RichLocation) - Static method in class org.biojavax.bio.seq.io.GenbankLocationParser Writes a location in Genbank format. writeLocation(RichLocation) - Static method in class org.biojavax.bio.seq.io.UniProtLocationParser Writes a location in UniProt format. writeMatrix(WeightMatrix, PrintStream) - Static method in class org.biojava.bio.dp.XmlMarkovModel writeModel(MarkovModel, PrintStream) - Static method in class org.biojava.bio.dp.XmlMarkovModel writeModelFile(SVMClassifierModel, String) - Static method in class org.biojava.stats.svm.tools.SVM_Light writeObject(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract writeObject(Writer) - Method in class org.biojavax.bio.phylo.io.nexus.NexusComment writeObject(Writer) - Method in interface org.biojavax.bio.phylo.io.nexus.NexusObject Writes this object to the given writer. writePCData(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter writePhredQuality(OutputStream, OutputStream, SequenceDB) - Static method in class org.biojava.bio.program.phred.PhredTools Writes Phred quality data in a Fasta type format. writePropertyConstraint(PropertyConstraint, XMLWriter, XMLAnnotationTypeWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLPropertyConstraintWriter writeProtein(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat writeProtein(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat writeRecord(RAF, long, int, String, Map) - Method in class org.biojava.bio.program.indexdb.BioStore writeRecord(RAF, long, int, String, Map) - Method in interface org.biojava.bio.program.indexdb.IndexStore writeRecord creates and writes a new Record WriterOutputHandler - Class in org.biojava.utils.process Simple output handler that writes the output of an external process to an writer. WriterOutputHandler(Writer, String) - Constructor for class org.biojava.utils.process.WriterOutputHandler Initializes the writer output handler. writeSeqFeature(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter Write SeqFeature XML writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.program.phred.PhredFormat This method will print symbols to the line width followed by a new line etc. writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter Write sequence into AGAVE XML format. writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat Deprecated. Writes a Sequence or RichSequence to a PrintStream in FASTA format. writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GAMEFormat writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat Deprecated. writeSequence(Sequence, PrintStream) - Method in interface org.biojava.bio.seq.io.SequenceFormat writeSequence writes a sequence to the specified PrintStream, using the default format. writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat writeSequence writes a sequence to the specified PrintStream, using the default format. writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat writeSequence writes a sequence to the specified PrintStream, using the default format. writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.FastaFormat writeSequence writes a sequence to the specified PrintStream, using the default format. writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat writeSequence writes a sequence to the specified PrintStream, using the default format. writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat writeSequence writes a sequence to the specified PrintStream, using the default format. writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat writeSequence writes a sequence to the specified PrintStream, using the default format. writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat writeSequence writes a sequence to the specified PrintStream, using the default format. writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.program.phred.PhredFormat Deprecated. use writeSequence(Sequence seq, PrintStream os) writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.EmblLikeFormat Deprecated. use writeSequence(Sequence seq, PrintStream os) writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat Deprecated. use writeSequence(Sequence seq, PrintStream os) writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.GAMEFormat writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat Deprecated. use writeSequence(Sequence seq, PrintStream os) writeSequence(Sequence, String, PrintStream) - Method in interface org.biojava.bio.seq.io.SequenceFormat Deprecated. use writeSequence(Sequence seq, PrintStream os) writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat writeSequence writes a sequence to the specified PrintStream, using the specified format. writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat writeSequence writes a sequence to the specified PrintStream, using the specified format. writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.FastaFormat writeSequence writes a sequence to the specified PrintStream, using the specified format. writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat writeSequence writes a sequence to the specified PrintStream, using the specified format. writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat writeSequence writes a sequence to the specified PrintStream, using the specified format. writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat writeSequence writes a sequence to the specified PrintStream, using the specified format. writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat writeSequence writes a sequence to the specified PrintStream, using the specified format. writeSequence(Sequence, String, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat As per EMBLFormat.writeSequence(Sequence, Namespace), except that it also takes a format parameter. writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.GenbankFormat Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.INSDseqFormat Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. writeSequence(Sequence, Namespace) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtFormat Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. writeSequenceMap(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter group sequence_map by getSource() writeSequenceMap2(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter Write SequenceMap XML writeShort(int) - Method in interface org.biojava.utils.bytecode.CodeContext Write a short (2 bytes) to the context. writeStream(OutputStream, Alignment) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat Writes the given Alignment in PHYLIP format to a stream. writeStream(OutputStream, NexusFile) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat Writes the given Nexus output to a stream. writeStream(SequenceIterator) - Method in class org.biojava.bio.seq.io.StreamWriter Write each of the sequences in ss to the stream in the given format. writeStream(SequenceIterator, Namespace) - Method in class org.biojavax.bio.seq.io.RichStreamWriter Write each of the sequences in ss to the stream in the given format. writeSwissprot(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Writes a single Sequence to an OutputStream in SwissProt format. writeSwissprot(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools Deprecated. Writes a stream of Sequences to an OutputStream in SwissProt format. writeToken(Writer, String) - Method in class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract Writes a token and correctly substitutes all symbols in it. writeToXML(Distribution, OutputStream) - Static method in class org.biojava.bio.dist.DistributionTools Writes a Distribution to XML that can be read with the readFromXML method. writeToXML(CodonPref, PrintWriter) - Static method in class org.biojava.bio.symbol.CodonPrefTools write out a specified CodonPref object in XML format. writeTranscript(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter writeUniProt(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes sequences from a SequenceIterator to an OutputStream in UniProt Format. writeUniProt(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes a single Sequence to an OutputStream in UniProt format. writeUniProtXML(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes sequences from a SequenceIterator to an OutputStream in UniProt XML Format. writeUniProtXML(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools Writes a single Sequence to an OutputStream in UniProt XML format. writeWriter(Writer, Alignment) - Static method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat Writes the given Alignment in PHYLIP format to a writer. writeWriter(Writer, NexusFile) - Static method in class org.biojavax.bio.phylo.io.nexus.NexusFileFormat Writes the given Nexus output to a writer. writeXFF(File, FeatureHolder) - Static method in class org.biojava.bio.program.xff.XFFTools writeXFF(PrintWriter, FeatureHolder) - Static method in class org.biojava.bio.program.xff.XFFTools writeXML(XMLWriter) - Method in interface org.biojava.utils.xml.XMLWritable X X_LAEVIS - Static variable in interface org.biojava.bio.program.homologene.Taxon XFF_BIOJAVA_NS - Static variable in class org.biojava.bio.program.xff.XFFTools XFF_NS - Static variable in class org.biojava.bio.program.xff.XFFTools XFFFeatureSetHandler - Class in org.biojava.bio.program.xff StAX handler which converts and stream of parse events for an XFF featureSet element into BioJava SeqIO events. XFFFeatureSetHandler() - Constructor for class org.biojava.bio.program.xff.XFFFeatureSetHandler Construct a new XFFFeatureSetHandler with the default set of handlers. XFFHelper - Interface in org.biojava.bio.program.xff XFFPartHandlerFactory - Interface in org.biojava.bio.program.xff Factory for StAX content handlers. XFFTools - Class in org.biojava.bio.program.xff Common functionality for manipulating XFF. XFFTools() - Constructor for class org.biojava.bio.program.xff.XFFTools XFFWriter - Class in org.biojava.bio.program.xff Simple XFF writing code, ripped off from Dazzle 0.08. XFFWriter() - Constructor for class org.biojava.bio.program.xff.XFFWriter XFFWriter(XFFHelper) - Constructor for class org.biojava.bio.program.xff.XFFWriter xHair - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer xHair is the vertical line positioned along the X-axis. XML - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat XML_ANNOTATIONTYPE_NS - Static variable in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter XML namespace string used to the AnnotationType representation XML_FILTER_NS - Static variable in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter XMLAnnotationTypeHandler - Class in org.biojava.bio.seq.io.filterxml StAX handler for parsing AnnotationTypes in FilterXML documents. XMLAnnotationTypeHandler() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler Construct a new XMLAnnotationTypeHandler which can parse the builtin PropertyConstraints. XMLAnnotationTypeHandler.CollectionConstraintHandler - Interface in org.biojava.bio.seq.io.filterxml Handler for an individual CollectionConstraint in an AnnotationType. XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml Handler Factory for a CollectionConstraint in an AnnotationType. XMLAnnotationTypeHandler.PropertyConstraintHandler - Interface in org.biojava.bio.seq.io.filterxml Handler for an individual PropertyConstraint in an AnnotationType. XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml Handler Factory for a PropertyConstraint in an AnnotationType. XMLAnnotationTypeWriter - Class in org.biojava.bio.seq.io.filterxml Main class for writing AnnotationTypes as XML. XMLAnnotationTypeWriter() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter Construct a new AnnotationTypeWriter which knows about the builtin types of PropertyConstraint XMLAnnotationTypeWriter.XMLCollectionConstraintWriter - Interface in org.biojava.bio.seq.io.filterxml Writer for types of CollectionConstraint. XMLAnnotationTypeWriter.XMLPropertyConstraintWriter - Interface in org.biojava.bio.seq.io.filterxml Writer for types of PropertyConstraint. XMLBeans - Class in org.biojava.utils.xml Construct java beans from XML elements XMLBeans() - Constructor for class org.biojava.utils.xml.XMLBeans XMLDistributionReader - Class in org.biojava.bio.dist A SAX parser that reads an XML representation of a Distribution from a file and recreates it as a Distribution Object. XMLDistributionReader() - Constructor for class org.biojava.bio.dist.XMLDistributionReader XMLDistributionWriter - Class in org.biojava.bio.dist Writes an OrderNDistribution or simple Distribution to an XML file. XMLDistributionWriter() - Constructor for class org.biojava.bio.dist.XMLDistributionWriter XMLFilterHandler - Class in org.biojava.bio.seq.io.filterxml Factory producing content handlers for parsing FilterXML elements. XMLFilterHandler() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLFilterHandler Construct a new XMLFilterHandler which can parse the builtin types of FeatureFilter. XMLFilterHandler.FilterHandler - Interface in org.biojava.bio.seq.io.filterxml StAXContentHandler for a particular type of FeatureFilter. XMLFilterHandler.FilterHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml Factory of StAXContentHandlers for a particular type of FeatureFilter. XMLFilterWriter - Class in org.biojava.bio.seq.io.filterxml Write FeatureFilters in XML format. XMLFilterWriter() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLFilterWriter Construct a new XMLFilterWriter which can serialize the buildin types of FeatureFilter. XMLFilterWriter.FilterWriter - Interface in org.biojava.bio.seq.io.filterxml Interface for an object which can write a FeatureFilter as XML. XmlMarkovModel - Class in org.biojava.bio.dp XmlMarkovModel() - Constructor for class org.biojava.bio.dp.XmlMarkovModel xmlSchema - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat xmlSchema - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat xmlSchema - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat XMLTools - Class in org.biojavax.utils Utility class for reading chunks of XML files and feeding them to SAX. XMLWritable - Interface in org.biojava.utils.xml Object which knows how to represent itself as an XML element. XMLWriter - Interface in org.biojava.utils.xml Simple interface for building XML documents. Xor(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Xor Xor(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Xor Xor(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor XREF_ANALOG - Static variable in class org.biojava.ontology.obo.OboFileHandler XREF_DBNAME_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat XREF_ID_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat XREF_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty XREF_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat Y y() - Static method in class org.biojava.bio.seq.DNATools y() - Static method in class org.biojava.bio.seq.NucleotideTools y() - Static method in class org.biojava.bio.seq.ProteinTools Returns the AtomicSymbol for the amino acid Tyrosine YEAST_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable Translation table name for the yeast mitochondrial genetic code. yHair - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer yHair is the horizontal line positioned along the Y-axis. Z Z_MAYS - Static variable in interface org.biojava.bio.program.homologene.Taxon zero() - Static method in class org.biojavax.ga.util.GATools ZERO - Static variable in class org.biojava.bio.CardinalityConstraint The property should have zero values. ZERO_OR_ONE - Static variable in class org.biojava.bio.CardinalityConstraint The property should have zero or one values. zeroCol - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor zeroCol - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor Description of the Field zeroCounts() - Method in interface org.biojava.bio.dist.Count Reset all the counts to zero. zeroCounts() - Method in class org.biojava.bio.dist.IndexedCount ZiggyFeatureRenderer - Class in org.biojava.bio.gui.sequence A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags. ZiggyFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer ZiggyImapRenderer - Class in org.biojava.bio.gui.sequence ZiggyImapRenderer is a decorator for ZiggyFeatureRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the ZiggyFeatureRenderer. ZiggyImapRenderer(ZiggyFeatureRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.ZiggyImapRenderer Creates a new ZiggyImapRenderer. _ _0 - Static variable in class org.biojava.bio.program.abi.ABITools The poorly supported symbol. _1 - Static variable in class org.biojava.bio.program.abi.ABITools The well supported symbol. _addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB _addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer _addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer _removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer _removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer _setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanel _setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster Deprecated. 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