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

## A

AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `AA` indicates that a sequence contains AA (amino acid) symbols.
ABIFChromatogram - class org.biojava.bio.program.abi.ABIFChromatogram.
  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 org.biojava.bio.program.abi.ABIFChromatogram.Parser.
  An extension of `ABIFParser` that reads the particular fields from the ABIF that contain the chromatogram data and initializes the fields in its enclosing `ABIFChromatogram` instance.
ABIFChromatogram.Parser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
ABIFChromatogram.Parser(File) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
ABIFParser - class org.biojava.bio.program.abi.ABIFParser.
  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 org.biojava.bio.program.abi.ABIFParser.DataAccess.
  Concatenation of the `Seekable` and `DataInput` interfaces.
ABIFParser.TaggedDataRecord - class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord.
  An aggregate immutable type for an ABIF tagged data record.
ABIFParser.TaggedDataRecord(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
  Creates a new TaggedDataRecord from the next 28 bytes of `din`.
ABITools - class org.biojava.bio.program.abi.ABITools.
  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 org.biojava.bio.program.abi.ABITrace.
  Title: ABITrace
  ABITrace is a class for managing ABI file information, it is capable of opening an ABI file and storing the most important fields, which can be recalled as simple java types.
ABITrace(File) - Constructor for class org.biojava.bio.program.abi.ABITrace
  The File constructor opens a local ABI file and parses the content.
ABITrace(URL) - Constructor for class org.biojava.bio.program.abi.ABITrace
  The URL constructor opens an ABI file from any URL.
ABITrace(byte[]) - Constructor for class org.biojava.bio.program.abi.ABITrace
  The `byte[]` constructor parses an ABI file represented as a byte array.
ABI_MAGIC - Static variable in class org.biojava.bio.chromatogram.ChromatogramFactory
  The magic number for ABIF files
ABORT_PARSING - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
ACCEPT_ALL - Static variable in interface org.biojava.bio.program.gff.GFFRecordFilter
  A GFFRecordFilter that accepts everything.
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
ADD_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
ADVANCE - Static variable in interface org.biojava.bio.dp.EmissionState
  This signals that the advance array has been altered.
AGAVEAltIdsPropHandler - class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler.
  Deals with alternate sequence IDs
AGAVEAnnotFilter - interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter.
  This interface defines mapping from BioJava into AGAVE format.
AGAVEAnnotFilterFactory - interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory.
AGAVEAnnotationsHandler - class org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler.
AGAVEAssemblyHandler - class org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler.
AGAVEBioSeqCallbackItf - interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf.
  An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEBioSeqHandler - class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler.
  Handles the AGAVE <bio_sequence> element
AGAVEBioSequenceHandler - class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler.
  Handles the AGAVE <bio_sequence> element
AGAVECallbackItf - interface org.biojava.bio.seq.io.agave.AGAVECallbackItf.
  An interface that can be tested for by nested handlers when trying to do a callback.
AGAVECdsHandler - class org.biojava.bio.seq.io.agave.AGAVECdsHandler.
  Handles the AGAVE <cds> element
AGAVEChromosomeCallbackItf - interface org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf.
  An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEChromosomeHandler - class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler.
  Handles the AGAVE <chromosome> element
AGAVEClassificationHandler - class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler.
AGAVECompResultHandler - class org.biojava.bio.seq.io.agave.AGAVECompResultHandler.
AGAVEComputationHandler - class org.biojava.bio.seq.io.agave.AGAVEComputationHandler.
AGAVEContigCallbackItf - interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf.
  An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEContigHandler - class org.biojava.bio.seq.io.agave.AGAVEContigHandler.
  Handles the AGAVE <contig> element
AGAVEDbId - class org.biojava.bio.seq.io.agave.AGAVEDbId.
  * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEDbId() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEDbId
AGAVEDbIdCallbackItf - interface org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf.
  this is the interface implemented by several classes
AGAVEDbIdPropCallbackItf - interface org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf.
AGAVEDbIdPropHandler - class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler.
  Deals with database crossreferences
AGAVEDescPropHandler - class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler.
  Deals with database crossreferences
AGAVEElementIdPropHandler - class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler.
AGAVEEvidenceCallbackItf - interface org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf.
AGAVEEvidenceHandler - class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler.
AGAVEExonsPropHandler - class org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler.
AGAVEFeatureCallbackItf - interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf.
  An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEFragmentOrderHandler - class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler.
AGAVEFragmentOrientationHandler - class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler.
AGAVEGeneHandler - class org.biojava.bio.seq.io.agave.AGAVEGeneHandler.
AGAVEHandler - class org.biojava.bio.seq.io.agave.AGAVEHandler.
  Handles the root AGAVE element modified for agave format
AGAVEHandler() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEHandler
AGAVEIdAlias - class org.biojava.bio.seq.io.agave.AGAVEIdAlias.
  * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEIdAliasCallbackItf - interface org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf.
AGAVEIdAliasPropHandler - class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler.
AGAVEKeywordPropHandler - class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler.
  Deals with AGAVE keywords
AGAVEMapLocation - class org.biojava.bio.seq.io.agave.AGAVEMapLocation.
  * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEMapLocation() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapLocation
AGAVEMapLocationPropHandler - class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler.
AGAVEMapPosition - class org.biojava.bio.seq.io.agave.AGAVEMapPosition.
  * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEMapPosition() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapPosition
AGAVEMapPositionPropHandler - class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler.
AGAVEMatchAlignPropHandler - class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler.
  Deals with match_align
AGAVEMatchDescPropHandler - class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler.
  Deals with match_desc
AGAVEMatchRegion - class org.biojava.bio.seq.io.agave.AGAVEMatchRegion.
  * match_region * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEMatchRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
AGAVEMatchRegionPropHandler - class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler.
  Deals with match_region
AGAVEMrnaHandler - class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler.
  Handles the AGAVE <mrna> element
AGAVENotePropHandler - class org.biojava.bio.seq.io.agave.AGAVENotePropHandler.
  Deals with note
AGAVEPredictedProteinHandler - class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler.
  Handles the AGAVE <predicted_protein> element
AGAVEProperty - class org.biojava.bio.seq.io.agave.AGAVEProperty.
AGAVEProperty(String, String, String, String) - Constructor for class org.biojava.bio.seq.io.agave.AGAVEProperty
AGAVEQualifierPropHandler - class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler.
AGAVEQueryRegion - class org.biojava.bio.seq.io.agave.AGAVEQueryRegion.
  * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEQueryRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
AGAVEQueryRegionPropHandler - class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler.
AGAVERelatedAnnot - class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot.
  * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVERelatedAnnot() - Constructor for class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
  construct..
AGAVERelatedAnnotPropHandler - class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler.
AGAVEResultGroupHandler - class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler.
AGAVEResultPropertyPropHandler - class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler.
AGAVESciPropertyPropHandler - class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler.
  sci_property
AGAVESeqFeatureHandler - class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler.
  seq_feature
AGAVESeqLocationPropHandler - class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler.
  seq_location
AGAVESeqMapHandler - class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler.
  sequence_map
AGAVESeqPropHandler - class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler.
  * Deals with sequence code * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVETranscriptHandler - class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler.
  transcript
AGAVEUnorderedFragmentsHandler - class org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler.
  unordered_fragments
AGAVEViewPropHandler - class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler.
  Moves view attributes into annotation properties.
AGAVEXref - class org.biojava.bio.seq.io.agave.AGAVEXref.
  xref
AGAVEXref() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXref
AGAVEXrefCallbackItf - interface org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf.
AGAVEXrefPropHandler - class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler.
  handle AGAVE xref
AGAVEXrefPropPropHandler - class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler.
  xref_property
AGAVEXrefs - class org.biojava.bio.seq.io.agave.AGAVEXrefs.
  * xrefs * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEXrefs() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXrefs
AGAVEXrefsPropHandler - class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler.
  Deals with database crossreferences (xrefs)
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_SEQUENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
AGAVE_BIO_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
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_COMPUTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
AGAVE_COMP_RESULT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
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_XREFS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
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
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
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
ALT_YEAST_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the alternative yeast nuclear genetic code.
ALWAYS_VETO - Static variable in interface org.biojava.utils.ChangeListener
  Convenience implementation which vetoes every change of which it is notified.
AMBIGUOUS - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `AMBIGUOUS` indicates that a sequence contains ambiguity symbols.
ANNOTATE_EXISTING - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
ANNOTATION - Static variable in interface org.biojava.bio.Annotatable
  Signals that the associated Annotation has altered in some way.
ANNOTATIONS - Static variable in class org.biojava.bio.program.das.DASSequence
  Change type which indicates that the set of annotation servers used by this DASSequence has been changed.
ANNOTATOR - Static variable in class org.biojava.bio.program.das.ReferenceServer
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.
ARAlignment - interface org.biojava.bio.alignment.ARAlignment.
  ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
ARCHITECTURE - Static variable in interface org.biojava.bio.dp.MarkovModel
  Signals that the architecture of the model is changing.
ARG_C - Static variable in class org.biojava.bio.proteomics.Protease
ARG_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager
ASCID_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the ascidian mitochondrial genetic code.
ASP_N - Static variable in class org.biojava.bio.proteomics.Protease
ASP_N - Static variable in class org.biojava.bio.proteomics.ProteaseManager
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.
AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
AVG_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
AbiTraceRenderer - class org.biojava.bio.gui.sequence.AbiTraceRenderer.
  Renders an ABI trace file as a chromatogram graph.
AbiTraceRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbiTraceRenderer
AbstractAlignmentStyler - class org.biojava.bio.program.blast2html.AbstractAlignmentStyler.
  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 org.biojava.bio.symbol.AbstractAlphabet.
  An abstract implementation of `Alphabet`.
AbstractAlphabet() - Constructor for class org.biojava.bio.symbol.AbstractAlphabet
AbstractAnnotation - class org.biojava.bio.AbstractAnnotation.
  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
AbstractAnnotation(Annotation) - Constructor for class org.biojava.bio.AbstractAnnotation
AbstractAnnotation(Map) - Constructor for class org.biojava.bio.AbstractAnnotation
AbstractBeadRenderer - class org.biojava.bio.gui.sequence.AbstractBeadRenderer.
  `AbstractBeadRenderer` is a an abstract base class for the creation of `FeatureRenderer`s which use a 'string of beads' metaphor for displaying features.
AbstractBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Creates a new `AbstractBeadRenderer` with no delegates.
AbstractBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Creates a new `AbstractBeadRenderer` object.
AbstractChangeable - class org.biojava.utils.AbstractChangeable.
  Useful base-class for objects implementing Changeable
AbstractChangeable() - Constructor for class org.biojava.utils.AbstractChangeable
AbstractChromatogram - class org.biojava.bio.chromatogram.AbstractChromatogram.
  A basic, abstract implementation of `Chromatogram`.
AbstractChromatogram() - Constructor for class org.biojava.bio.chromatogram.AbstractChromatogram
AbstractDistribution - class org.biojava.bio.dist.AbstractDistribution.
  An abstract implementation of Distribution.
AbstractDistribution() - Constructor for class org.biojava.bio.dist.AbstractDistribution
AbstractFeatureHolder - class org.biojava.bio.seq.AbstractFeatureHolder.
  An abstract implementation of FeatureHolder.
AbstractFeatureHolder() - Constructor for class org.biojava.bio.seq.AbstractFeatureHolder
AbstractLocation - class org.biojava.bio.symbol.AbstractLocation.
  An abstract implementation of `Location`.
AbstractLocation() - Constructor for class org.biojava.bio.symbol.AbstractLocation
AbstractLocationDecorator - class org.biojava.bio.symbol.AbstractLocationDecorator.
  Abstract `Location` decorator (wrapper).
AbstractLocationDecorator(Location) - Constructor for class org.biojava.bio.symbol.AbstractLocationDecorator
  Construct a new decorator wrapping the specified Location.
AbstractMatrixPairDPCursor - class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor.
AbstractMatrixPairDPCursor(SymbolList, SymbolList, int, int, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
AbstractOrderNDistribution - class org.biojava.bio.dist.AbstractOrderNDistribution.
  Simple base class for OrderNDistributions
AbstractOrderNDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.AbstractOrderNDistribution
  Construct a new NthOrderDistribution.
AbstractRangeLocation - class org.biojava.bio.symbol.AbstractRangeLocation.
  Base class for simple contiguous Location implementations.
AbstractRangeLocation() - Constructor for class org.biojava.bio.symbol.AbstractRangeLocation
AbstractSVMClassifierModel - class org.biojava.stats.svm.AbstractSVMClassifierModel.
  Abstract implementation of SVMClassifierModel.
AbstractSVMClassifierModel() - Constructor for class org.biojava.stats.svm.AbstractSVMClassifierModel
AbstractSVMTarget - class org.biojava.stats.svm.AbstractSVMTarget.
  An abstract implementation of an SVMModel.
AbstractSVMTarget() - Constructor for class org.biojava.stats.svm.AbstractSVMTarget
AbstractSequenceDB - class org.biojava.bio.seq.db.AbstractSequenceDB.
  An abstract implementation of SequenceDB that provides the sequenceIterator method.
AbstractSequenceDB() - Constructor for class org.biojava.bio.seq.db.AbstractSequenceDB
AbstractSymbol - class org.biojava.bio.symbol.AbstractSymbol.
  The base-class for Symbol implementations.
AbstractSymbol() - Constructor for class org.biojava.bio.symbol.AbstractSymbol
AbstractSymbolList - class org.biojava.bio.symbol.AbstractSymbolList.
  Abstract helper implementation of the SymbolList core interface.
AbstractSymbolList() - Constructor for class org.biojava.bio.symbol.AbstractSymbolList
AbstractSymbolList.EditScreener - class org.biojava.bio.symbol.AbstractSymbolList.EditScreener.
  This adapter screens all edit events to see if they overlap with a window of interest.
AbstractSymbolList.EditScreener(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
AbstractSymbolList.EditTranslater - class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater.
  This translates edit events that fall within a window into window co-ordinates.
AbstractSymbolList.EditTranslater(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
AbstractTaxon - class org.biojava.bio.taxa.AbstractTaxon.
  An abstract implementation of Taxon.
AbstractTaxon() - Constructor for class org.biojava.bio.taxa.AbstractTaxon
AbstractTaxon(String, String) - Constructor for class org.biojava.bio.taxa.AbstractTaxon
AbstractTrainer - class org.biojava.bio.dp.AbstractTrainer.
  An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.
AbstractTrainer(DP) - Constructor for class org.biojava.bio.dp.AbstractTrainer
AbstractTrainer() - Constructor for class org.biojava.bio.dp.AbstractTrainer
AbstractULAlignment - class org.biojava.bio.alignment.AbstractULAlignment.
AbstractULAlignment() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment
AbstractULAlignment.LeftRightLocationComparator - class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator.
  Orders by location left to right.
AbstractULAlignment.LeftRightLocationComparator() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
AbstractULAlignment.SubULAlignment - class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment.
AbstractULAlignment.SubULAlignment(Set, Location) - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
AcnumHitReader - class org.biojava.bio.seq.db.emblcd.AcnumHitReader.
  `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 org.biojava.bio.seq.db.emblcd.AcnumTrgReader.
  `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`.
ActivityListener - interface org.biojava.utils.ActivityListener.
  Interface for object which monitor long-running activities.
Agave2AgaveAnnotFilter - class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter.
  Dumping the data from biojava with source of agave into agave format
AgaveWriter - class org.biojava.bio.seq.io.agave.AgaveWriter.
  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 org.biojava.bio.seq.io.agave.AgaveWriter.Indent.
  Implements indenting for elements.
AgaveWriter.Indent() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
AlignIOConstants - class org.biojava.bio.seq.io.AlignIOConstants.
  `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 - interface org.biojava.bio.symbol.Alignment.
  An alignment containing multiple SymbolLists.
Alignment.SymbolListIterator - class org.biojava.bio.symbol.Alignment.SymbolListIterator.
  Iterator implementation looping over symbol lists in an alignment using the labels.
Alignment.SymbolListIterator(Alignment) - Constructor for class org.biojava.bio.symbol.Alignment.SymbolListIterator
AlignmentElement - interface org.biojava.bio.alignment.AlignmentElement.
  AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.
AlignmentFormat - interface org.biojava.bio.seq.io.AlignmentFormat.
AlignmentMarker - class org.biojava.bio.program.blast2html.AlignmentMarker.
  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.
AlignmentRenderer - class org.biojava.bio.gui.sequence.AlignmentRenderer.
AlignmentRenderer() - Constructor for class org.biojava.bio.gui.sequence.AlignmentRenderer
AlignmentStAXHandler - class org.biojava.bio.program.ssbind.AlignmentStAXHandler.
  `AlignmentStAXHandler` handles the BlastLikeAlignment element of BioJava BlastLike XML.
Alphabet - interface org.biojava.bio.symbol.Alphabet.
  The set of AtomicSymbols which can be concatenated together to make a SymbolList.
AlphabetIndex - interface org.biojava.bio.symbol.AlphabetIndex.
  Map between Symbols and index numbers.
AlphabetManager - class org.biojava.bio.symbol.AlphabetManager.
  Utility methods for working with Alphabets.
AlphabetManager() - Constructor for class org.biojava.bio.symbol.AlphabetManager
AlphabetResolver - class org.biojava.bio.program.ssbind.AlphabetResolver.
  `AlphabetResolver`s 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
Annotatable - interface org.biojava.bio.Annotatable.
  Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder - class org.biojava.bio.Annotatable.AnnotationForwarder.
  A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
Annotatable.AnnotationForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.Annotatable.AnnotationForwarder
AnnotatedSequenceDB - class org.biojava.bio.seq.db.AnnotatedSequenceDB.
  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
Annotation - interface org.biojava.bio.Annotation.
  Arbitrary annotation associated with one or more objects.
AnnotationBuilder - class org.biojava.bio.program.tagvalue.AnnotationBuilder.
  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 org.biojava.bio.AnnotationChanger.
  `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.
AnnotationFactory - class org.biojava.bio.program.ssbind.AnnotationFactory.
  `AnnotationFactory` is a utility class for making `Annotation`s from `Map`s.
AnnotationFactory() - Constructor for class org.biojava.bio.program.ssbind.AnnotationFactory
AnnotationRenamer - class org.biojava.bio.AnnotationRenamer.
  `AnnotationRenamer` remaps the keys of an `Annotation` to new keys specified by a `TagMapper`.
AnnotationRenamer(Annotation, TagMapper) - Constructor for class org.biojava.bio.AnnotationRenamer
  Creates a new `AnnotationRenamer` using the specified `TagMapper` to remap its keys.
AnnotationTools - class org.biojava.bio.AnnotationTools.
  `AnnotationTools` is a set of static utility methods for manipulating `Annotation`s and `AnnotationType`s.
AnnotationTools() - Constructor for class org.biojava.bio.AnnotationTools
AnnotationType - interface org.biojava.bio.AnnotationType.
  A set of constraints on the data contained in an `Annotation`.
AnnotationType.Abstract - class org.biojava.bio.AnnotationType.Abstract.
  An abstract base class useful for implementing AnnotationType instances.
AnnotationType.Abstract() - Constructor for class org.biojava.bio.AnnotationType.Abstract
AnnotationType.Impl - class org.biojava.bio.AnnotationType.Impl.
  An implementation of `AnnotationType`.
AnnotationType.Impl() - Constructor for class org.biojava.bio.AnnotationType.Impl
  Create a new Impl with no constraints.
AnnotationType.Impl(PropertyConstraint, Location) - Constructor for class org.biojava.bio.AnnotationType.Impl
  Create a new Impl with a default property and cardinality constraint.
AnnotationType.Impl(CollectionConstraint) - Constructor for class org.biojava.bio.AnnotationType.Impl
  Create a new Impl with a default collection constraint.
AppBeanRunner - class org.biojava.utils.xml.AppBeanRunner.
  Create a bean from an XML file, then attempt to enter it.
AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner
AppEntry - interface org.biojava.utils.xml.AppEntry.
AppException - exception org.biojava.utils.xml.AppException.
AppException(String) - Constructor for class org.biojava.utils.xml.AppException
AssembledSymbolList - class org.biojava.bio.seq.impl.AssembledSymbolList.
  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
AtomicSymbol - interface org.biojava.bio.symbol.AtomicSymbol.
  A symbol that is not ambiguous.
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.RNATools
abbreviation - Variable in class org.biojava.bibliography.BiblioJournal
  An abbreviation of the journal title.
abstractType - Variable in class org.biojava.bibliography.BiblioDescription
  It specifies how `BiblioDescription.theAbstract` is coded.
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.CollectionConstraint
  `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.PropertyConstraint
  `accept` returns true if the value fulfills the constraint.
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(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFRecordFilter
  Return whether or not to accept record.
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 interface org.biojava.bio.seq.FeatureFilter
  This method determines whether a feature is to be accepted.
activityFailed(Object, Exception) - Method in interface org.biojava.utils.ActivityListener
  Notification of errors behind the scenes.
activityProgress(Object, int, int) - Static method in class org.biojava.bio.program.das.DAS
activityProgress(Object, int, int) - Method in interface org.biojava.utils.ActivityListener
  Estimated progress of an activity.
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(Object) - Method in class org.biojava.utils.FileAsList
add(Object) - Method in class org.biojava.utils.SmallSet
addActivityListener(ActivityListener) - Static method in class org.biojava.bio.program.das.DAS
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 the list to be merged.
addAnnotationSource(URL) - Method in class org.biojava.bio.program.das.DASSequence
addBottomConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
  Add a configuration as the most default place to look.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `addChangeListener` adds a listener for all types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `addChangeListener` adds a listener for specific types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `addChangeListener` adds a listener for all types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `addChangeListener` adds a listener for specific types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.program.das.ReferenceServer
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
addChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.SubSequence
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.SubSequence
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
addChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Delegate for addChangeListener
addChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
addChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport
  Add a listener that will be informed of all changes.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport
  Add a listener that will be informed of changes of a given type (and it's subtypes)
addChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable
  Add a listener that will be informed of all changes.
addChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable
  Add a listener that will be informed of changes of a given type.
addChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
addChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
  Add a taxon as a child to a parent.
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
addCluster(UnigeneCluster) - Method in interface org.biojava.bio.program.unigene.UnigeneDB
  Add a cluster to a database.
addComponentFeature(String, ComponentFeature) - Method in class org.biojava.bio.seq.ragbag.RagbagComponentDirectory.EmptyComponentDirectory
addComponentFeature(String, ComponentFeature) - Method in interface org.biojava.bio.seq.ragbag.RagbagComponentDirectory
  Add specified component feature to the directory
addComponentFeature(String, ComponentFeature) - Method in class org.biojava.bio.seq.ragbag.RagbagHashedComponentDirectory
  Add specified component feature to the directory
addComponentSequence(ComponentFeature.Template) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
  Registers that sym was counted in this state.
addCount(Distribution, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  Registers that sym was counted in this state.
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
addCount(Distribution, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
addCount(State, State, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
  Add 'count' to the transition from->to.
addDasURL(URL) - Method in class org.biojava.bio.program.das.DAS
addDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
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
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`.
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
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
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
  Null implementation
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
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
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.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.
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
addHotSpot(ImageMap.HotSpot) - Method in interface org.biojava.bio.gui.sequence.ImageMap
  `addHotSpot` adds a hotspot to the map.
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 interface org.biojava.stats.svm.SVMClassifierModel
addItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
addItemAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
addItemTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
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
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
addNeg(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  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
  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
  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
  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
  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
  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.
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
addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
addPropertyChangeListener(String, 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.TextLogoPainter
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
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
addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
  `addRenderer` adds a renderer as a new track.
addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
  `addRenderer` adds a renderer.
addRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
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.
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.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.
addSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
  Add a secondary key.
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.program.das.DASSequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.DummySequenceDB
addSequence(String, Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
  Add a sequence under a particular id.
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.db.biofetch.BioFetchSequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
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.distributed.DistributedSequenceDB
addSequence(String, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
  Add a sequence into the tree.
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(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.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
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblProcessor
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankProcessor
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.OrganismParser
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
  Notify the listener of a sequence-wide property.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `addSequenceViewerListener` adds a listener for mouse click `SequenceViewerEvent`s.
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
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 `SequenceViewerEvent`s.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `addSequenceViewerMotionListener` adds a listener for mouse motion `SequenceViewerEvent`s.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
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 `SequenceViewerEvent`s.
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
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.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.
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.
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.ChunkedSymbolListBuilder
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
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
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
  Prints out the sequences properties in order.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
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.
addTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
  Add a tag to retain.
addTopConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
  Add a configuration as the most authoritative place to look.
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, double, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
addVector(Object) - 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
affiliation - Variable in class org.biojava.bibliography.BiblioPerson
alignment - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
  `alignment` `Alignment` field.
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(List, SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews
  View a SymbolList over a cross-product Alphabet as an Alignment.
alignmentRange - Variable in class org.biojava.bio.alignment.FlexibleAlignment
all - Static variable in interface org.biojava.bio.seq.FeatureFilter
  All features are selected by this filter.
all() - Static method in class org.biojava.bio.seq.FilterUtils
allEntryPointsDB() - Method in class org.biojava.bio.program.das.DASSequenceDB
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`.
alph - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
alphabet - Variable in class org.biojava.bio.alignment.AbstractULAlignment
alphabetForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Retrieve the alphabet for a specific name.
alphabets() - Static method in class org.biojava.bio.symbol.AlphabetManager
  Get an iterator over all alphabets known.
and(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
and(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils
annot - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
annotate(Sequence) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
annotate(Sequence) - Method in class org.biojava.bio.molbio.RestrictionMapper
  `annotate` adds `Feature`s which represent restriction sites.
annotate(Sequence) - Method in interface org.biojava.bio.seq.SequenceAnnotator
  Return an annotated version of a sequence.
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
annotation - Variable in class org.biojava.bio.seq.Feature.Template
annotation - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
annotationForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
annotationForwarder - Variable in class org.biojava.bio.program.das.DASSequence
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.SimpleAssembly
annotationForwarder - Variable in class org.biojava.bio.seq.SubSequence
annotationForwarder - Variable in class org.biojava.bio.symbol.AbstractSymbol
annotationForwarder - Variable in class org.biojava.bio.symbol.SimpleAlphabet
applicants - Variable in class org.biojava.bibliography.BiblioPatent
arcHeight - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
arcWidth - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
areDisjoint(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Determines is 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 distributions
areEmissionSpectraEqual(Distribution[], Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
  Compares the emission spectra of two distribution arrays
areEqual(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
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.
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
  Return a `Map` view onto this annotation.
asMap() - Method in class org.biojava.bio.OverlayAnnotation
  Return a `Map` view onto this annotation.
attribute(String, String) - Method in class org.biojava.utils.xml.FastXMLWriter
attribute(String, String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
attribute(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.
attribute(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
  Add an un-qualified attribute to an element.
authors - Variable in class org.biojava.bibliography.BibRef
  The authors and contributors are responsible for creating the contents of the cited resource.
average(Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
  Averages two or more distributions.

## B

BLEPH_MNUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the blepharisma macronuclear genetic code.
BLUNT - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
  `BLUNT` the end type created by enzymes which leave a blunt end.
BOTH_FORWARD_COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
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
BackMatrixPairDPCursor - class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor.
BackMatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
BackPointer - class org.biojava.bio.dp.BackPointer.
  A backpointer.
BackPointer(State, BackPointer, double) - Constructor for class org.biojava.bio.dp.BackPointer
BackPointer(State) - Constructor for class org.biojava.bio.dp.BackPointer
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat
  This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat
  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 org.biojava.bio.gui.BarLogoPainter.
  A logo painter that paints in bars.
BarLogoPainter() - Constructor for class org.biojava.bio.gui.BarLogoPainter
BaseXMLWriter - class org.biojava.bio.program.xml.BaseXMLWriter.
  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 org.biojava.bio.gui.sequence.BasicFeatureRenderer.
BasicFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.BasicFeatureRenderer
BasicXFFHelper - class org.biojava.bio.program.xff.BasicXFFHelper.
BasicXFFHelper() - Constructor for class org.biojava.bio.program.xff.BasicXFFHelper
BasisSymbol - interface org.biojava.bio.symbol.BasisSymbol.
  A symbol that can be represented as a string of Symbols.
BaumWelchSampler - class org.biojava.bio.dp.BaumWelchSampler.
  Train a hidden markov model using a sampling algorithm.
BaumWelchSampler(DP) - Constructor for class org.biojava.bio.dp.BaumWelchSampler
BaumWelchTrainer - class org.biojava.bio.dp.BaumWelchTrainer.
  Train a hidden markov model using maximum likelihood.
BaumWelchTrainer(DP) - Constructor for class org.biojava.bio.dp.BaumWelchTrainer
BeadFeatureRenderer - interface org.biojava.bio.gui.sequence.BeadFeatureRenderer.
  `BeadFeatureRenderer`s use a 'string of beads' metaphor for displaying features.
BeanAsAnnotation - class org.biojava.bio.BeanAsAnnotation.
  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 org.biojava.utils.BeanAsMap.
BeanAsMap(Object) - Constructor for class org.biojava.utils.BeanAsMap
BetweenLocation - class org.biojava.bio.symbol.BetweenLocation.
  Between view onto an underlying Location instance.
BetweenLocation(Location) - Constructor for class org.biojava.bio.symbol.BetweenLocation
BibRef - class org.biojava.bibliography.BibRef.
  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
BibRefQuery - interface org.biojava.bibliography.BibRefQuery.
  The interface BibRefQuery is a fundamental part of the Bibliographic Query Service.
BibRefSupport - interface org.biojava.bibliography.BibRefSupport.
  This interface defines supporting utilities for working with bibliographic repositories.
BiblioArticle - class org.biojava.bibliography.BiblioArticle.
  It represents an article.
BiblioArticle() - Constructor for class org.biojava.bibliography.BiblioArticle
BiblioBook - class org.biojava.bibliography.BiblioBook.
  It represents a book.
BiblioBook() - Constructor for class org.biojava.bibliography.BiblioBook
BiblioBookArticle - class org.biojava.bibliography.BiblioBookArticle.
  It represents a book article.
BiblioBookArticle() - Constructor for class org.biojava.bibliography.BiblioBookArticle
BiblioCriterion - class org.biojava.bibliography.BiblioCriterion.
  The criteria define how the matching or ordering should be done during queries.
BiblioCriterion() - Constructor for class org.biojava.bibliography.BiblioCriterion
BiblioDescription - class org.biojava.bibliography.BiblioDescription.
  It represents an account of the content of the cited resource.
BiblioDescription() - Constructor for class org.biojava.bibliography.BiblioDescription
BiblioEntryStatus - class org.biojava.bibliography.BiblioEntryStatus.
  It defines information related to the citation itself rather than to the cited resource.
BiblioEntryStatus() - Constructor for class org.biojava.bibliography.BiblioEntryStatus
BiblioJournal - class org.biojava.bibliography.BiblioJournal.
  A class describing journals.
BiblioJournal() - Constructor for class org.biojava.bibliography.BiblioJournal
BiblioJournalArticle - class org.biojava.bibliography.BiblioJournalArticle.
  It represents a journal article.
BiblioJournalArticle() - Constructor for class org.biojava.bibliography.BiblioJournalArticle
BiblioOrganisation - class org.biojava.bibliography.BiblioOrganisation.
  It represents an organisation dealing with the bibliographic resources.
BiblioOrganisation() - Constructor for class org.biojava.bibliography.BiblioOrganisation
BiblioPatent - class org.biojava.bibliography.BiblioPatent.
  It represents a patent.
BiblioPatent() - Constructor for class org.biojava.bibliography.BiblioPatent
BiblioPerson - class org.biojava.bibliography.BiblioPerson.
  It represents a person dealing with the bibliographic resources.
BiblioPerson() - Constructor for class org.biojava.bibliography.BiblioPerson
BiblioProceeding - class org.biojava.bibliography.BiblioProceeding.
  It represents a conference proceeding.
BiblioProceeding() - Constructor for class org.biojava.bibliography.BiblioProceeding
BiblioProvider - class org.biojava.bibliography.BiblioProvider.
  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 org.biojava.bibliography.BiblioScope.
  It represent an extent or scope of the content of the cited resource.
BiblioScope() - Constructor for class org.biojava.bibliography.BiblioScope
BiblioService - class org.biojava.bibliography.BiblioService.
  It represents a service dealing with the bibliographic resources.
BiblioService() - Constructor for class org.biojava.bibliography.BiblioService
BiblioSubject - class org.biojava.bibliography.BiblioSubject.
  It represents the topic of the content of the cited resource.
BiblioSubject() - Constructor for class org.biojava.bibliography.BiblioSubject
BiblioTechReport - class org.biojava.bibliography.BiblioTechReport.
  It represents a technical report.
BiblioTechReport() - Constructor for class org.biojava.bibliography.BiblioTechReport
BiblioThesis - class org.biojava.bibliography.BiblioThesis.
  It represents a thesis.
BiblioThesis() - Constructor for class org.biojava.bibliography.BiblioThesis
BiblioWebResource - class org.biojava.bibliography.BiblioWebResource.
  It represents a WWW resource.
BiblioWebResource() - Constructor for class org.biojava.bibliography.BiblioWebResource
BinarySearch - class org.biojava.utils.math.BinarySearch.
  solves y = f(x) = 0 by binary search.
BinarySearch() - Constructor for class org.biojava.utils.math.BinarySearch
BioError - error org.biojava.bio.BioError.
  A nestable biological error.
BioError(String) - Constructor for class org.biojava.bio.BioError
  Create a new BioError with a message.
BioError(Throwable) - Constructor for class org.biojava.bio.BioError
  Create a new BioError with a cause.
BioError(Throwable, String) - Constructor for class org.biojava.bio.BioError
  Create a new BioError with a cause and a message.
BioError() - Constructor for class org.biojava.bio.BioError
  Create a new BioError.
BioException - exception org.biojava.bio.BioException.
  A nestable biological exception.
BioException(String) - Constructor for class org.biojava.bio.BioException
  Create a new BioException with a message.
BioException(Throwable) - Constructor for class org.biojava.bio.BioException
  Create a new BioException with a cause.
BioException(Throwable, String) - Constructor for class org.biojava.bio.BioException
  Create a new BioException with a cause and a message.
BioException() - Constructor for class org.biojava.bio.BioException
  Create a new BioException.
BioFetchSequenceDB - class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB.
  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 org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider.
  Directory-services plugin for biofetch databases.
BioFetchSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
BioIndex - class org.biojava.bio.seq.db.BioIndex.
  The original object for indexing sequence files.
BioIndex(File, String, int) - Constructor for class org.biojava.bio.seq.db.BioIndex
BioIndex(File) - Constructor for class org.biojava.bio.seq.db.BioIndex
  Load an existing index file.
BioRuntimeException - exception org.biojava.bio.BioRuntimeException.
  A nestable biological exception.
BioRuntimeException(String) - Constructor for class org.biojava.bio.BioRuntimeException
  Create a new BioRuntimeException with a message.
BioRuntimeException(Throwable) - Constructor for class org.biojava.bio.BioRuntimeException
  Create a new BioRuntimeException with a cause.
BioRuntimeException(Throwable, String) - Constructor for class org.biojava.bio.BioRuntimeException
  Create a new BioRuntimeException with a cause and a message.
BioRuntimeException() - Constructor for class org.biojava.bio.BioRuntimeException
  Create a new BioRuntimeException.
BioSQLSequenceDB - class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.
  SequenceDB keyed off a BioSQL database.
BioSQLSequenceDB(String, String, String, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Connect to a BioSQL database.
BioSQLSequenceDBProvider - class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider.
BioSQLSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
BioStore - class org.biojava.bio.program.indexdb.BioStore.
  `BioStore`s represent directory and file structures which index flat files according to the OBDA specification.
BioStore(File, boolean) - Constructor for class org.biojava.bio.program.indexdb.BioStore
  Creates a new `BioStore` flatfile index at the specified location with the specified caching behaviour.
BioStoreFactory - class org.biojava.bio.program.indexdb.BioStoreFactory.
  `BioStoreFactory` creates `BioStore` instances.
BioStoreFactory() - Constructor for class org.biojava.bio.program.indexdb.BioStoreFactory
  Creates a new `BioStoreFactory`.
Blast2HTMLHandler - class org.biojava.bio.program.blast2html.Blast2HTMLHandler.
  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 org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder.
  `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 org.biojava.bio.program.sax.BlastLikeSAXParser.
  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 org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.
  `BlastLikeSearchBuilder` will create `SeqSimilaritySearchResult`s 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.
BlastLikeToXMLConverter - class org.biojava.bio.program.BlastLikeToXMLConverter.
  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 org.biojava.bio.program.sax.blastxml.BlastXMLParser.
  This class parses NCBI Blast XML output.
BlastXMLParser() - Constructor for class org.biojava.bio.program.sax.blastxml.BlastXMLParser
BlockIterator() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Get list of the un-gapped region of the SymbolList.
BlockPainter - interface org.biojava.bio.gui.BlockPainter.
BooleanElementHandlerBase - class org.biojava.utils.stax.BooleanElementHandlerBase.
  StAX handler for any element which just contains a string representation of an boolean.
BooleanElementHandlerBase() - Constructor for class org.biojava.utils.stax.BooleanElementHandlerBase
BumpedRenderer - class org.biojava.bio.gui.sequence.BumpedRenderer.
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
ByteElementHandlerBase - class org.biojava.utils.stax.ByteElementHandlerBase.
  StAX handler for any element which just contains a string representation of a byte.
ByteElementHandlerBase() - Constructor for class org.biojava.utils.stax.ByteElementHandlerBase
b() - Static method in class org.biojava.bio.seq.NucleotideTools
bPointers - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
bPointers - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
back - Variable in class org.biojava.bio.dp.BackPointer
backPointers - Variable in class org.biojava.bio.dp.twohead.Cell
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
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP
backwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
backwards(ScoreType) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
backwards(ScoreType) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
beadDepth - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
beadDisplacement - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
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
binary(long) - Static method in class org.biojava.bio.symbol.PackingFactory
binary(int) - Static method in class org.biojava.bio.symbol.PackingFactory
bindSymbol(Symbol, char) - Method in class org.biojava.bio.seq.io.CharacterTokenization
  Bind a Symbol to a character.
biojavaToFile(int, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqAlignReadWrite
  Converts a Biojava object to the given filetype.
biojavaToFile(String, String, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes a Biojava `SequenceIterator`, `SequenceDB`, `Sequence` or `Aligment` to an `OutputStream`
biojavaToFile(int, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Converts a Biojava object to the given filetype.
bitsOfInformation(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
  Calculates the total bits of information for a distribution.
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.
breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
  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
  Converts the symbol list passed in into an array of strings.
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, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
buildDataStore(File, SequenceStreamer, Packing, int, 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
buildLibInfoParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
  Generate a tag-value parser for the library info unigene files.
byAncestor(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
byAnnotation(Object, Object) - Static method in class org.biojava.bio.seq.FilterUtils
byAnnotationType(AnnotationType) - Static method in class org.biojava.bio.seq.FilterUtils
byAnnotationType(Object, Class) - Static method in class org.biojava.bio.seq.FilterUtils
byChild(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
byClass(Class) - Static method in class org.biojava.bio.seq.FilterUtils
byComponentName(String) - Static method in class org.biojava.bio.seq.FilterUtils
byDescendant(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
byFrame(FramedFeature.ReadingFrame) - Static method in class org.biojava.bio.seq.FilterUtils
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`.
byName - Static variable in interface org.biojava.bio.seq.db.IDMaker
  A simple implementation of IDMaker that hashes by sequence name.
byPairwiseScore(double, double) - Static method in class org.biojava.bio.seq.FilterUtils
byParent(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
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.
bySequenceName(String) - Static method in class org.biojava.bio.seq.FilterUtils
bySource(String) - Static method in class org.biojava.bio.seq.FilterUtils
byStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.FilterUtils
bySubHitCount - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit
  `bySubHitCount` contains a `SeqSimilaritySearchHit` comparator which compares by their number of sub-hits.
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.
byType(String) - Static method in class org.biojava.bio.seq.FilterUtils
byURN - Static variable in interface org.biojava.bio.seq.db.IDMaker
  A simple implementation of IDMaker that hashes by URN.

## C

CANDIES_NOT_SORTED - Static variable in interface org.biojava.utils.candy.CandyVocabulary
  A property name.
CHANGE_COMMON_NAME - Static variable in interface org.biojava.bio.taxa.Taxon
  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
  Change type to indicate that the scientific name of this Taxon is changing.
CHARACTER - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
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_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
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;
CNBr - Static variable in class org.biojava.bio.proteomics.Protease
CNBr - Static variable in class org.biojava.bio.proteomics.ProteaseManager
COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
CONFIG_FILE - Static variable in class org.biojava.directory.SystemRegistry
CONFIG_LOCATOR - Static variable in class org.biojava.directory.SystemRegistry
CONTENT - Static variable in interface org.biojava.bio.symbol.Alignment
  Signals that SymbolLists will be added to or removed from an alignment.
COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
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.
CREATE_DUMMYSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
CREATE_REALSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
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.
Cache - interface org.biojava.utils.cache.Cache.
  Interface for managing caches of objects.
CacheMap - interface org.biojava.utils.cache.CacheMap.
  Interface for managing caches of objects fetchable by key.
CacheReference - interface org.biojava.utils.cache.CacheReference.
  Interface for a reference to an object, analogous to `java.lang.ref.Referencce`, but more flexible.
CachingInputStream - class org.biojava.utils.io.CachingInputStream.
  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 org.biojava.stats.svm.CachingKernel.
  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 org.biojava.bio.seq.db.CachingSequenceDB.
  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.
CandyEntry - class org.biojava.utils.candy.CandyEntry.
  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.
CandyFinder - interface org.biojava.utils.candy.CandyFinder.
  This interface is a main entry point to a set of controlled vocabularies.
CandyVocabulary - interface org.biojava.utils.candy.CandyVocabulary.
  This interface defines functionality of a controlled vocabulary.
CardinalityConstraint - class org.biojava.bio.CardinalityConstraint.
  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 org.biojava.bio.dp.twohead.Cell.
  A single cell in the DP matrix.
Cell() - Constructor for class org.biojava.bio.dp.twohead.Cell
CellCalculator - interface org.biojava.bio.dp.twohead.CellCalculator.
  The interface for all functions that can calculate the 'scores' array for a given cell.
CellCalculatorFactory - interface org.biojava.bio.dp.twohead.CellCalculatorFactory.
CellCalculatorFactoryMaker - interface org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker.
  The interface for all functions that can calculate the 'scores' array for a given cell.
ChangeAdapter - class org.biojava.utils.ChangeAdapter.
  This is a ChangeListener that ignores everything.
ChangeAdapter() - Constructor for class org.biojava.utils.ChangeAdapter
ChangeEvent - class org.biojava.utils.ChangeEvent.
  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.
ChangeForwarder - class org.biojava.utils.ChangeForwarder.
  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
ChangeHub - interface org.biojava.utils.ChangeHub.
  Interface implemented by ChangeHubs, i.e.
ChangeListener - interface org.biojava.utils.ChangeListener.
  Interface for objects which listen to ChangeEvents.
ChangeListener.AlwaysVetoListener - class org.biojava.utils.ChangeListener.AlwaysVetoListener.
  An implementation that always vetoes everything.
ChangeListener.AlwaysVetoListener() - Constructor for class org.biojava.utils.ChangeListener.AlwaysVetoListener
  Private constructor.
ChangeListener.LoggingListener - class org.biojava.utils.ChangeListener.LoggingListener.
  A listener that writes information about the event stream to a PrintStream.
ChangeListener.LoggingListener(PrintStream) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener
  Create a LoggingListener that will log all events to 'out'.
ChangeListener.LoggingListener(PrintStream, String) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener
  Create a LoggingListener that will log all events to 'out' with a prefix.
ChangeSupport - class org.biojava.utils.ChangeSupport.
  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 org.biojava.bio.program.tagvalue.ChangeTable.
  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 org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger.
  An implementation of Changer that applies a list of Changer instances to the value in turn.
ChangeTable.ChainedChanger(ChangeTable.Changer[]) - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
ChangeTable.Changer - interface org.biojava.bio.program.tagvalue.ChangeTable.Changer.
  Callback used to produce a new value from an old one.
ChangeTable.Splitter - interface org.biojava.bio.program.tagvalue.ChangeTable.Splitter.
  Callback used to produce a list of values from a single old one.
ChangeType - class org.biojava.utils.ChangeType.
  Class for all constants which are used to indicate change types.
ChangeType(String, Field, 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, 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 with supertype UNKNOWN
ChangeType(String, String, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
ChangeType(String, String, String) - Constructor for class org.biojava.utils.ChangeType
ChangeVetoException - exception org.biojava.utils.ChangeVetoException.
  Exception which is thrown when a ChangeListener does not wish a change to take place.
ChangeVetoException() - Constructor for class org.biojava.utils.ChangeVetoException
ChangeVetoException(ChangeEvent) - Constructor for class org.biojava.utils.ChangeVetoException
  Construct an exception to veto a change without explanation.
ChangeVetoException(String) - Constructor for class org.biojava.utils.ChangeVetoException
  Create an exception with a detail message
ChangeVetoException(ChangeEvent, String) - Constructor for class org.biojava.utils.ChangeVetoException
  Construct an exception to veto a change for a specified reason.
ChangeVetoException(Exception, ChangeEvent) - Constructor for class org.biojava.utils.ChangeVetoException
  Propogate an exception without (additional) explanation.
ChangeVetoException(Exception, String) - Constructor for class org.biojava.utils.ChangeVetoException
  Propogate an exception, giving a detail message
ChangeVetoException(Exception, ChangeEvent, String) - Constructor for class org.biojava.utils.ChangeVetoException
  Propogate an exception, giving a detail message
Changeable - interface org.biojava.utils.Changeable.
  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 org.biojava.utils.cache.ChangeableCache.
  A cache that clears values as the keys fire ChangeEvents of a given type.
ChangeableCache(ChangeType) - Constructor for class org.biojava.utils.cache.ChangeableCache
CharElementHandlerBase - class org.biojava.utils.stax.CharElementHandlerBase.
  StAX handler for any element which just contains a string representation of a char.
CharElementHandlerBase() - Constructor for class org.biojava.utils.stax.CharElementHandlerBase
CharacterTokenization - class org.biojava.bio.seq.io.CharacterTokenization.
  Implementation of SymbolTokenization which binds symbols to single unicode characters.
CharacterTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.CharacterTokenization
Chromatogram - interface org.biojava.bio.chromatogram.Chromatogram.
  Encapsulates the basic information you would want from a chromatogram.
ChromatogramFactory - class org.biojava.bio.chromatogram.ChromatogramFactory.
  A factory that creates `Chromatogram` objects from files or streams.
ChromatogramFactory() - Constructor for class org.biojava.bio.chromatogram.ChromatogramFactory
ChromatogramGraphic - class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.
  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 org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option.
  A typesafe enumeration of the options available for configuring the behavior of a `ChromatogramGraphic` instance.
ChromatogramTools - class org.biojava.bio.chromatogram.ChromatogramTools.
  Utility class for dealing with `Chromatogram`s.
ChunkedSymbolListBuilder - class org.biojava.bio.seq.io.ChunkedSymbolListBuilder.
ChunkedSymbolListBuilder() - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListBuilder
ChunkedSymbolListFactory - class org.biojava.bio.seq.io.ChunkedSymbolListFactory.
  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
CircularLocation - class org.biojava.bio.symbol.CircularLocation.
  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.
CircularReferenceException - exception org.biojava.bio.taxa.CircularReferenceException.
CircularReferenceException() - Constructor for class org.biojava.bio.taxa.CircularReferenceException
CircularReferenceException(Throwable) - Constructor for class org.biojava.bio.taxa.CircularReferenceException
CircularReferenceException(String) - Constructor for class org.biojava.bio.taxa.CircularReferenceException
CircularReferenceException(Throwable, String) - Constructor for class org.biojava.bio.taxa.CircularReferenceException
CircularView - class org.biojava.bio.seq.CircularView.
  A circular view onto another Sequence object.
CircularView(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.CircularView
CircularView(Sequence) - Constructor for class org.biojava.bio.seq.CircularView
ClassifierExample - class org.biojava.stats.svm.tools.ClassifierExample.
  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 org.biojava.stats.svm.tools.ClassifierExample.PointClassifier.
  An extention of JComponent that contains the points & encapsulates the classifier.
ClassifierExample.PointClassifier() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Make a new PointClassifier.
Classify - class org.biojava.stats.svm.tools.Classify.
Classify() - Constructor for class org.biojava.stats.svm.tools.Classify
ClustalWAlignmentSAXParser - class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser.
  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
CollectionConstraint - interface org.biojava.bio.CollectionConstraint.
  Used by `AnnotationType` to represent the constraint on the collection of values in a property-slot.
CollectionConstraint.AllValuesIn - class org.biojava.bio.CollectionConstraint.AllValuesIn.
  CollectionConstraint which validates all members of a Collection.
CollectionConstraint.AllValuesIn(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.AllValuesIn
CollectionConstraint.And - class org.biojava.bio.CollectionConstraint.And.
  A collection constraint that accpepts collections iff they are accepted by both child constraints.
CollectionConstraint.And(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.And
  Create a new `And` from two child constraints.
CollectionConstraint.Contains - class org.biojava.bio.CollectionConstraint.Contains.
  CollectionConstraint which validates a portion of a Collection.
CollectionConstraint.Contains(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.Contains
CollectionConstraint.Or - class org.biojava.bio.CollectionConstraint.Or.
  A collection constraint that accepts items iff they are accepted by either child constraints.
CollectionConstraint.Or(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.Or
  Create a new `Or` from two child constraints.
ColourCommand - interface org.biojava.bio.program.blast2html.ColourCommand.
  Interface for specifying whether a particular pair of residues/bases should be coloured.
Commitable - interface org.biojava.utils.Commitable.
  Implementations of `Commitable` support atomic changes from one known state to another via commit/rollback semantics.
CompactedDataStore - class org.biojava.bio.program.ssaha.CompactedDataStore.
  An implementation of DataStore that will map onto a file using the NIO constructs.
CompactedDataStoreFactory - class org.biojava.bio.program.ssaha.CompactedDataStoreFactory.
  Builder for a data store that is backed by a java.nio.MappedByteBuffer.
CompactedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
ComponentFeature - interface org.biojava.bio.seq.ComponentFeature.
  Feature which represents a component in an assembly (contig).
ComponentFeature.Template - class org.biojava.bio.seq.ComponentFeature.Template.
  Template for constructing a new ComponentFeature.
ComponentFeature.Template() - Constructor for class org.biojava.bio.seq.ComponentFeature.Template
ComputeObject - interface org.biojava.utils.math.ComputeObject.
  interface for classes that return a single double precision value for a single double precision argument.
Constants - class org.biojava.utils.Constants.
  Some usefull constants for working with binary files.
Constants() - Constructor for class org.biojava.utils.Constants
Count - interface org.biojava.bio.dist.Count.
  An encapsulation of a count over the Symbols within an alphabet.
CountedBufferedReader - class org.biojava.utils.io.CountedBufferedReader.
CountedBufferedReader(Reader) - Constructor for class org.biojava.utils.io.CountedBufferedReader
CrossProductTokenization - class org.biojava.bio.seq.io.CrossProductTokenization.
  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
CrosshairRenderer - class org.biojava.bio.gui.sequence.CrosshairRenderer.
  `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.
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.RNATools
cState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
  Gets the c loop state
cache - Variable in class org.biojava.utils.io.CachingInputStream
  The byte cache itself.
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
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 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
calculateScore(Distribution, Symbol) - Method in interface org.biojava.bio.dp.ScoreType
  Calculates the score associated with a distribution and a symbol.
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
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
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, Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
change(Object) - Method in class org.biojava.bio.program.tagvalue.RegexChanger
changeSupport() - Method in class org.biojava.utils.ChangeForwarder
  Return the underlying `ChangeSupport` instance that can be used to fire `ChangeEvent`s and mannage listeners.
charAt(int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
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 interface org.biojava.bio.seq.io.StreamParser
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 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(char[], int, int) - Method in class org.biojava.utils.xml.XMLPeerBuilder
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
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() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Learn a model from the current points.
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 interface org.biojava.stats.svm.SVMClassifierModel
clear() - Method in interface org.biojava.stats.svm.SVMTarget
clear() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
clear() - Method in class org.biojava.stats.svm.SimpleSVMTarget
clear() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Remove all points from the canvas, and discard any model.
clear() - Method in class org.biojava.utils.FileAsList
clear() - Method in interface org.biojava.utils.cache.CacheReference
clearCounts(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.DistributionTrainer
  Clears all of the counts to zero.
clearCounts() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  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
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.
clearEnzymes() - Method in class org.biojava.bio.molbio.RestrictionMapper
  `clearEnzymes` removes all enzymes from those to be searched for in the `Sequence`.
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.
clearTraceValues() - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
  Sets all the traces to null.
clearTraces() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Sets the trace data structures to null.
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.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.TypedProperties
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 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 interface org.biojava.bio.seq.io.StreamParser
close() - Method in class org.biojava.utils.io.CountedBufferedReader
close() - Method in class org.biojava.utils.io.RandomAccessReader
  `close` closes the underlying `RandomAccessFile`.
closeTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
closeTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
closeTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
closeTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
  Closes an element
closeTag(String) - Method in interface org.biojava.utils.xml.XMLWriter
  Closes an un-qualified element.
codes - Variable in class org.biojava.bibliography.BiblioSubject
  Classification code (call number) is usually either Dewey decimal or Congress classification.
colors - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  The map containing the colors for drawing traces.
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.
columns - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
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 '`#`'.
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
commitStore() - Method in class org.biojava.bio.seq.db.TabIndexStore
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.Feature.ByLocationComparator
complement(Symbol) - Static method in class org.biojava.bio.seq.DNATools
  Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
  Retrieve a complement view of list.
complement(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
  Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools
  Retrieve a complement view of list.
complement(Symbol) - Static method in class org.biojava.bio.seq.RNATools
  Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
  Retrieve a complement view of list.
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.
completedActivity(Object) - Static method in class org.biojava.bio.program.das.DAS
completedActivity(Object) - Method in interface org.biojava.utils.ActivityListener
  Notification that an activity is complete.
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
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.
conditionedDistributions() - Method in interface org.biojava.bio.dist.OrderNDistribution
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(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.
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.
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
containedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
contains(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
contains(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
contains(int) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
contains(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet
  Returns whether or not this Alphabet contains the symbol.
contains(int) - Method in class org.biojava.bio.symbol.CircularLocation
contains(Location) - Method in class org.biojava.bio.symbol.CircularLocation
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
contains(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
contains(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
contains(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
contains(Location) - Method in interface org.biojava.bio.symbol.Location
  Checks if this location contains the other.
contains(int) - Method in interface org.biojava.bio.symbol.Location
  Checks if this location contains a point.
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(int) - Method in class org.biojava.bio.symbol.PointLocation
contains(Object) - Method in class org.biojava.utils.SmallSet
contains(String) - Method in interface org.biojava.utils.candy.CandyVocabulary
  It checks if a given entry exists in this vocabulary.
containsFeature(Feature) - Method in class org.biojava.bio.program.das.DASSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.DummySequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
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.LazyFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.MergeFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.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.biojava.bio.seq.SimpleGappedSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.SubSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.ViewSequence
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.SimpleSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
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.OverlayMap
containsKey(Object) - Method in class org.biojava.utils.SmallMap
containsKey(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
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
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
contextForLabel(SequenceRenderContext, Object) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
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
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.
coordinateDisplayOn(boolean) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `coordinateDisplayOn` toggles the display of sequence coordinates.
cost - Variable in class org.biojava.bibliography.BiblioWebResource
countFeatures() - Method in class org.biojava.bio.program.das.DASSequence
countFeatures() - Method in class org.biojava.bio.seq.DummySequence
countFeatures() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
countFeatures() - Method in interface org.biojava.bio.seq.FeatureHolder
  Count how many features are contained.
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.ProjectedFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.SimpleAssembly
countFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.SimpleGappedSequence
countFeatures() - Method in class org.biojava.bio.seq.SubSequence
countFeatures() - Method in class org.biojava.bio.seq.ViewSequence
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.SimpleSequence
countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
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.
create(File) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
  Creates a new `Chromatogram` object from the named file.
create(InputStream) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
  Creates a new `Chromatogram` object from the supplied stream.
create(File) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
  Create a new ABIF object from a file.
create(InputStream) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
  Create a new ABIF object from a stream of bytes.
create(File) - Static method in class org.biojava.bio.program.scf.SCF
create(InputStream, long) - Static method in class org.biojava.bio.program.scf.SCF
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.
createDNA(String) - Static method in class org.biojava.bio.seq.DNATools
  Return a new DNA SymbolList for dna.
createDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools
  Return a new DNA Sequence for dna.
createDP(MarkovModel) - Method in class org.biojava.bio.dp.DPFactory.DefaultFactory
createDP(MarkovModel) - Method in interface org.biojava.bio.dp.DPFactory
createDistribution(Alphabet) - Method in class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
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.OrderNDistributionFactory
  Creates an OrderNDistribution of the appropriate type
createDummySequence(String, Alphabet, int) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
createEmblParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
createFeature(Feature.Template) - Method in class org.biojava.bio.program.das.DASSequence
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 class org.biojava.bio.seq.DummySequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
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.LazyFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
createFeature(Feature, Feature.Template) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.SimpleGappedSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.SubSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.ViewSequence
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.SimpleSequence
createFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
  Deprecated. Please use new 1-arg createFeature instead.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
createFeature(Feature, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Delegate for createFeature
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
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
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.
createList(List) - Static method in class org.biojava.utils.ListTools
createList(Object[]) - Static method in class org.biojava.utils.ListTools
createMatches() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
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.
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.
createProtease(SymbolList, boolean, SymbolList, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
  Creates and registers a new Protease.
createProtease(SymbolList, 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(String, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
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.
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.
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.
createRegex(SymbolList) - Static method in class org.biojava.bio.symbol.MotifTools
  `createRegex` creates a regular expression which matches the `SymbolList`.
createSequence(SymbolList, String, String, Annotation) - Method in interface org.biojava.bio.seq.SequenceFactory
  Creates a sequence using these parameters.
createSequence(SymbolList, String, String, Annotation) - Static method in class org.biojava.bio.seq.SequenceTools
createSequence(SymbolList, String, String, Annotation) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
createSwissprotParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
createSymbol(String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Generate a new AtomicSymbol instance with a name and Annotation.
createSymbol(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Generate a new AtomicSymbol instance with a name and an Empty Annotation.
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(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(char, Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Deprecated. use the three-arg version of this method instead.
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.
createTaxon(String, String) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
createTaxon(String, String) - Method in interface org.biojava.bio.taxa.TaxonFactory
  Create a new orphan Taxon with a given scientific and common name.
createTaxon(String, String) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
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.
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
createType(String, FeatureFilter, Set) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
  Create a new type in this repository.
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.
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.
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
cutType - Variable in class org.biojava.bio.molbio.RestrictionEnzyme

## D

DAS - class org.biojava.bio.program.das.DAS.
  A collection of DAS datasources.
DAS() - Constructor for class org.biojava.bio.program.das.DAS
DASLink - class org.biojava.bio.program.das.DASLink.
  A memento class for storing a link.
DASLink(String, String) - Constructor for class org.biojava.bio.program.das.DASLink
DASSequence - class org.biojava.bio.program.das.DASSequence.
  Sequence reflecting a DAS reference sequence, possibly decorated with one of more annotation sets.
DASSequenceDB - class org.biojava.bio.program.das.DASSequenceDB.
  Collection of sequences retrieved from the DAS network.
DASSequenceDB(URL) - Constructor for class org.biojava.bio.program.das.DASSequenceDB
DASSequenceDBProvider - class org.biojava.bio.program.das.DASSequenceDBProvider.
  Hook DAS into the OBDA directory system.
DASSequenceDBProvider() - Constructor for class org.biojava.bio.program.das.DASSequenceDBProvider
DATASOURCE - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
DATASOURCE_SELECTION - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
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
DATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
DATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
DBHelper - class org.biojava.bio.seq.db.biosql.DBHelper.
DBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.DBHelper
DBHelper.DeleteStyle - class org.biojava.bio.seq.db.biosql.DBHelper.DeleteStyle.
DB_NUCLEOTIDE - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
DB_PROTEIN - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
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
DEFAULT - Static variable in class org.biojava.bio.seq.io.FastaFormat
DEFAULT - Static variable in class org.biojava.bio.seq.io.GAMEFormat
DEFAULT - Static variable in class org.biojava.bio.seq.io.GenbankFormat
DEFAULT - Static variable in class org.biojava.bio.seq.projection.ProjectionEngine
  The standard projection engine object.
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_TERM_CHAR - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree
DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
DELETE_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
DELETE_MYSQL4 - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
DELETE_POSTGRESQL - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
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
DISPLACEMENT - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Constant `DISPLACEMENT` indicating a change to the Y-axis displacement of the features.
DISTRIBUTION - Static variable in interface org.biojava.bio.dp.EmissionState
  This signals that the distribution associate with an EmissionState has been altered.
DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
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 org.biojava.bio.symbol.DNAAmbPack.
  Packing utility class for DNA.
DNAAmbPack() - Constructor for class org.biojava.bio.symbol.DNAAmbPack
DNANoAmbPack - class org.biojava.bio.symbol.DNANoAmbPack.
  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 org.biojava.bio.gui.DNAStyle.
  A simple implementation of SymbolStyle optimized for DNA.
DNAStyle() - Constructor for class org.biojava.bio.gui.DNAStyle
DNATools - class org.biojava.bio.seq.DNATools.
  Useful functionality for processing DNA sequences.
DNATools() - Constructor for class org.biojava.bio.seq.DNATools
DP - class org.biojava.bio.dp.DP.
  Objects that can perform dymamic programming operations upon sequences with HMMs.
DP(MarkovModel) - Constructor for class org.biojava.bio.dp.DP
DP.ReverseIterator - class org.biojava.bio.dp.DP.ReverseIterator.
DP.ReverseIterator(SymbolList) - Constructor for class org.biojava.bio.dp.DP.ReverseIterator
DPCompiler - class org.biojava.bio.dp.twohead.DPCompiler.
  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
DPFactory - interface org.biojava.bio.dp.DPFactory.
  The interface for objects that can generate a DP object for a MarkovModel.
DPFactory.DefaultFactory - class org.biojava.bio.dp.DPFactory.DefaultFactory.
DPFactory.DefaultFactory(CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.DPFactory.DefaultFactory
DPInterpreter - class org.biojava.bio.dp.twohead.DPInterpreter.
DPInterpreter(DP) - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter
DPInterpreter.Maker - class org.biojava.bio.dp.twohead.DPInterpreter.Maker.
DPInterpreter.Maker() - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter.Maker
DPMatrix - interface org.biojava.bio.dp.DPMatrix.
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.
DataSource - class org.biojava.bio.program.das.DataSource.
  Reflect a datasource (reference or annotation) in the DAS1 network.
DataStore - interface org.biojava.bio.program.ssaha.DataStore.
  A repository that can be searched with a sequence.
DataStoreFactory - interface org.biojava.bio.program.ssaha.DataStoreFactory.
  Builder for a data store.
DatabaseURLGenerator - interface org.biojava.bio.program.blast2html.DatabaseURLGenerator.
  Takes a database ID and some configuration properties ( such as base URL ) and returns either a URL or a full anchor tag.
DefaultURLGeneratorFactory - class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory.
  A simple default `URLGeneratorFactory` which returns a single `NcbiDatabaseURLGenerator` instance.
DefaultURLGeneratorFactory() - Constructor for class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
DelegationManager - interface org.biojava.bio.seq.io.agave.DelegationManager.
  Interface which exposes delegation services offered by a StAX event source.
DelegationManager - interface org.biojava.utils.stax.DelegationManager.
  Interface which exposes delegation services offered by a StAX event source.
DiagonalAddKernel - class org.biojava.stats.svm.DiagonalAddKernel.
  Adds a class specific constant to k(x, x).
DiagonalAddKernel() - Constructor for class org.biojava.stats.svm.DiagonalAddKernel
DiagonalCachingKernel - class org.biojava.stats.svm.DiagonalCachingKernel.
  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.
Digest - class org.biojava.bio.proteomics.Digest.
  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
DistDataSource - interface org.biojava.bio.seq.distributed.DistDataSource.
  Object which contributes data to a DistributedSequenceDB.
DistributedSequenceDB - class org.biojava.bio.seq.distributed.DistributedSequenceDB.
  Sequence database from the meta-DAS system.
DistributedSequenceDB() - Constructor for class org.biojava.bio.seq.distributed.DistributedSequenceDB
Distribution - interface org.biojava.bio.dist.Distribution.
  An encapsulation of a probability distribution over the Symbols within an alphabet.
Distribution.NullModelForwarder - class org.biojava.bio.dist.Distribution.NullModelForwarder.
  This listens to the null model distribution events and converts them into NULL_MODEL events.
Distribution.NullModelForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.dist.Distribution.NullModelForwarder
DistributionFactory - interface org.biojava.bio.dist.DistributionFactory.
  A thing that can make Distributions.
DistributionFactory.DefaultDistributionFactory - class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory.
  The default DistributionFactory implementation.
DistributionFactory.DefaultDistributionFactory() - Constructor for class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
DistributionLogo - class org.biojava.bio.gui.DistributionLogo.
  The GUI component for rendering a DistributionLogo.
DistributionLogo() - Constructor for class org.biojava.bio.gui.DistributionLogo
  Create a new DistributionLogo object.
DistributionTools - class org.biojava.bio.dist.DistributionTools.
  Title: DistributionTools.java Description: A class to hold static methods for calculations and manipulations using Distributions.
DistributionTrainer - interface org.biojava.bio.dist.DistributionTrainer.
  An object that can be used to train a distribution up.
DistributionTrainerContext - interface org.biojava.bio.dist.DistributionTrainerContext.
  A context within a group of DistributionTrainers can be trained together.
DivisionLkpReader - class org.biojava.bio.seq.db.emblcd.DivisionLkpReader.
  `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`.
DotState - interface org.biojava.bio.dp.DotState.
  A Dot state.
DoubleAlphabet - class org.biojava.bio.symbol.DoubleAlphabet.
  An efficient implementation of an Alphabet over the infinite set of double values.
DoubleAlphabet.DoubleRange - class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange.
  A range of double values.
DoubleAlphabet.DoubleRange(double, double) - Constructor for class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
DoubleAlphabet.DoubleSymbol - class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol.
  A single double value.
DoubleAlphabet.SubDoubleAlphabet - class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet.
  A class to represent a contiguous range of double symbols.
DoubleElementHandlerBase - class org.biojava.utils.stax.DoubleElementHandlerBase.
  StAX handler for any element which just contains a string representation of a double.
DoubleElementHandlerBase() - Constructor for class org.biojava.utils.stax.DoubleElementHandlerBase
DoubleTokenization - class org.biojava.bio.seq.io.DoubleTokenization.
DoubleTokenization() - Constructor for class org.biojava.bio.seq.io.DoubleTokenization
DummySequence - class org.biojava.bio.seq.DummySequence.
DummySequence(String, String) - Constructor for class org.biojava.bio.seq.DummySequence
DummySequenceDB - class org.biojava.bio.seq.db.DummySequenceDB.
  `DummySequenceDB` is an implementation which contains only a `DummySequence`.
DummySequenceDB(String) - Constructor for class org.biojava.bio.seq.db.DummySequenceDB
DummySequenceDBInstallation - class org.biojava.bio.seq.db.DummySequenceDBInstallation.
  `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 org.biojava.bio.symbol.DummySymbolList.
  Symbol list which just consists of non-informative symbols.
DummySymbolList(FiniteAlphabet, int) - Constructor for class org.biojava.bio.symbol.DummySymbolList
d() - Static method in class org.biojava.bio.seq.NucleotideTools
data - Variable in class org.biojava.bio.alignment.FlexibleAlignment
dataRecord - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
dataSourceURLs() - Method in class org.biojava.bio.program.das.DASSequence
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.
debug(String) - Method in class org.biojava.bio.alignment.AbstractULAlignment
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
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
delegationCache - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
depth - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
depth - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
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
  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.utils.candy.CandyEntry
  A value of this entry.
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.
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
diddleQueue() - Method in class org.biojava.utils.IndexedChangeHub
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.
distOverAlignment(Alignment) - Static method in class org.biojava.bio.dist.DistributionTools
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
distOverAlignment(Alignment, boolean) - Static method in class org.biojava.bio.dist.DistributionTools
  Creates an array of distributions, one for each column of the alignment.
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
doAnnotation(Sequence) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
  Apply the annotation to a sequence.
doLayer(SequenceRenderContext, FeatureFilter) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
doProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Internal method to process an individual Sequence.
docNumber - Variable in class org.biojava.bibliography.BiblioPatent
docOffice - Variable in class org.biojava.bibliography.BiblioPatent
docType - Variable in class org.biojava.bibliography.BiblioPatent
domain1 - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
doubleValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
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.
drawableCallboxesValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
dsCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
dumpBlocks() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Debugging method

## E

ECHIN_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the echinoderm mitochondrial genetic code.
EDIT - Static variable in interface org.biojava.bio.symbol.SymbolList
  Signals that the SymbolList is being edited.
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.SeqAlignReadWrite
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_GENBANK_FEATURE_TABLE_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
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
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_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_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.
END_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
END_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
ENTRY_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
ERROR_FEATURES_PROPERTY - Static variable in class org.biojava.bio.seq.io.SequenceBuilderBase
EUPL_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the euplotid nuclear genetic code.
EbiDatabaseURLGenerator - class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator.
  Simple URL generator for EMBL at the EBI.
EbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
EbiFormat - class org.biojava.bio.taxa.EbiFormat.
  Encapsulate the 'EBI' species format used in Embl, Genbank and Swissprot files.
EbiFormat() - Constructor for class org.biojava.bio.taxa.EbiFormat
Echo - class org.biojava.bio.program.tagvalue.Echo.
  A simple listener that just echoes events back to the console.
Echo() - Constructor for class org.biojava.bio.program.tagvalue.Echo
Edit - class org.biojava.bio.symbol.Edit.
  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, Alphabet, Symbol) - Constructor for class org.biojava.bio.symbol.Edit
  Convenience construtor for making single residue changes
EditableAlignment - interface org.biojava.bio.alignment.EditableAlignment.
  EditableAlignment is an interface that defines methods for shifting bases within an Alignment.
ElementRecognizer - interface org.biojava.bio.program.xff.ElementRecognizer.
  Simple interface for filtering SAX/StAX startElement events
ElementRecognizer - interface org.biojava.bio.seq.io.agave.ElementRecognizer.
  This class is copied to agave package Simple interface for filtering SAX/StAX startElement events
ElementRecognizer - interface org.biojava.bio.seq.io.game.ElementRecognizer.
  Simple interface for filtering SAX/StAX startElement events
ElementRecognizer.AllElementRecognizer - class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer.
ElementRecognizer.AllElementRecognizer() - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
ElementRecognizer.AllElementRecognizer - class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer.
ElementRecognizer.AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
ElementRecognizer.AllElementRecognizer - class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer.
ElementRecognizer.AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
ElementRecognizer.ByLocalName - class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName.
  Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
ElementRecognizer.ByLocalName - class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName.
  Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
ElementRecognizer.ByLocalName - class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName.
  Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
ElementRecognizer.ByNSName - class org.biojava.bio.program.xff.ElementRecognizer.ByNSName.
  Filter elements by name and namespace.
ElementRecognizer.ByNSName(String, String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
ElementRecognizer.ByNSName - class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName.
  Filter elements by name and namespace.
ElementRecognizer.ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
ElementRecognizer.ByNSName - class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName.
  Filter elements by name and namespace.
ElementRecognizer.ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
ElementRecognizer.HasAttribute - class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute.
  Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
ElementRecognizer.HasAttribute - class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute.
  Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute
ElementRecognizer.HasAttribute - class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute.
  Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute
EllipticalBeadRenderer - class org.biojava.bio.gui.sequence.EllipticalBeadRenderer.
  `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`.
Embl2AgaveAnnotFilter - class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter.
  Map EMBL data into AGAVE format
EmblCDROMIndexReader - class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader.
  `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 org.biojava.bio.seq.db.EmblCDROMIndexStore.
  `EmblCDROMIndexStore`s implement a read-only `IndexStore` backed by EMBL CD-ROM format binary indices.
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.
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.
EmblCDROMRandomAccess - class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess.
  `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 org.biojava.bio.seq.io.EmblFileFormer.
  `EmblFileFormer` performs the detailed formatting of EMBL entries for writing to a `PrintStream`.
EmblFileFormer() - Constructor for class org.biojava.bio.seq.io.EmblFileFormer
  Creates a new `EmblFileFormer` using `System.out` stream.
EmblFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.EmblFileFormer
  Creates a new `EmblFileFormer` using the specified stream.
EmblLikeFormat - class org.biojava.bio.seq.io.EmblLikeFormat.
  Format processor for handling EMBL records and similar files.
EmblLikeFormat() - Constructor for class org.biojava.bio.seq.io.EmblLikeFormat
EmblLikeLocationParser - class org.biojava.bio.seq.io.EmblLikeLocationParser.
  `EmblLikeLocationParser` parses EMBL/Genbank style locations.
EmblProcessor - class org.biojava.bio.seq.io.EmblProcessor.
  Simple filter which handles attribute lines from an EMBL file.
EmblProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.EmblProcessor
EmblProcessor.Factory - class org.biojava.bio.seq.io.EmblProcessor.Factory.
  Factory which wraps SequenceBuilders in an EmblProcessor
EmblProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.EmblProcessor.Factory
EmissionCache - class org.biojava.bio.dp.twohead.EmissionCache.
  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
EmissionState - interface org.biojava.bio.dp.EmissionState.
  A state in a markov process that has an emission spectrum.
EntryNamIdxReader - class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader.
  `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 org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess.
  `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
eCache - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
eCache - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
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.program.das.DASSequence
edit(Edit) - Method in class org.biojava.bio.seq.DummySequence
edit(Edit) - Method in class org.biojava.bio.seq.SimpleAssembly
edit(Edit) - Method in class org.biojava.bio.seq.SubSequence
edit(Edit) - Method in class org.biojava.bio.seq.ViewSequence
edit(Edit) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
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.symbol.AbstractSymbolList
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 class org.biojava.bio.symbol.SymbolList.EmptySymbolList
edit(Edit) - Method in interface org.biojava.bio.symbol.SymbolList
  Apply an edit to the SymbolList as specified by the edit object.
edition - Variable in class org.biojava.bibliography.BiblioBook
editor - Variable in class org.biojava.bibliography.BiblioBook
elementLength - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
email - Variable in class org.biojava.bibliography.BiblioPerson
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
emissions - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
emissions - Variable in class org.biojava.bio.dp.twohead.Cell
empty - Static variable in interface org.biojava.bio.symbol.Location
  The `Location` which contains no points.
emptyBP - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
emptyBP - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
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 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
endDocument() - Method in class org.biojava.utils.xml.XMLPeerBuilder
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, 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() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
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, 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.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.bio.seq.ragbag.RagbagMap
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) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
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
endElement(String) - Method in class org.biojava.utils.xml.XMLPeerBuilder
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.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.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.SeqRelHandler
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.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
endFeature() - Method in class org.biojava.bio.seq.io.FeatureTableParser
endFeature() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
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
  Null implementation.
endFeature() - Method in class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
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.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.
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.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.
endLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
endLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
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.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 interface org.biojava.bio.program.tagvalue.TagValueListener
  The current record has ended.
endRecord() - Method in class org.biojava.bio.program.tagvalue.TagValueWrapper
endSearch() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
endSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger
endSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener
  Indicates that a sequence has been searched against a DataStore.
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.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.
endSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer
endSequence() - Method in class org.biojava.bio.seq.io.EmblProcessor
endSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
endSequence() - Method in class org.biojava.bio.seq.io.GenbankProcessor
endSequence() - Method in class org.biojava.bio.seq.io.OrganismParser
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
  Notify the listener that processing of the sequence is complete.
endSequence() - Method in class org.biojava.bio.seq.io.SwissprotProcessor
endSequence() - Method in class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
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.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.
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.RegexFieldFinder
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.
endTag() - Method in class org.biojava.bio.program.tagvalue.TagValueWrapper
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 class org.biojava.bio.seq.ragbag.RagbagMap
endTree() - Method in interface org.biojava.utils.stax.StAXContentHandler
endTree() - Method in class org.biojava.utils.stax.StAXContentHandlerBase
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.
entrySet() - Method in class org.biojava.utils.BeanAsMap
entrySet() - Method in class org.biojava.utils.OverlayMap
entrySet() - Method in class org.biojava.utils.SmallMap
entrySet() - Method in class org.biojava.utils.cache.WeakValueHashMap
entryStatus - Variable in class org.biojava.bibliography.BibRef
  It defines information related to the citation itself rather than to the cited resource.
enzyme - Variable in class org.biojava.bio.molbio.RestrictionSite.Template
  `enzyme` `RestrictionEnzyme` field.
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.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.gui.sequence.SequencePanel
equals(Object) - Method in class org.biojava.bio.molbio.RestrictionEnzyme
equals(Object) - Method in class org.biojava.bio.program.das.DataSource
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.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.db.SimpleSequenceDBInstallation
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(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
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
equals(Object) - Method in interface org.biojava.bio.taxa.Taxon
  Two taxa are equal if they have equivalent children, common and scientific names.
equals(Object) - Method in class org.biojava.utils.ListTools.Doublet
equals(Object) - Method in class org.biojava.utils.ListTools.Triplet
equals(boolean, boolean) - 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(float, float) - Static method in class org.biojava.utils.ObjectUtil
equals(double, double) - Static method in class org.biojava.utils.ObjectUtil
equals(boolean[], boolean[]) - 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(float[], float[]) - Static method in class org.biojava.utils.ObjectUtil
equals(double[], double[]) - Static method in class org.biojava.utils.ObjectUtil
equals(Object[], Object[]) - Static method in class org.biojava.utils.ObjectUtil
equals(Object, Object) - Static method in class org.biojava.utils.ObjectUtil
equals(Object) - Method in class org.biojava.utils.TypedProperties
equals(Object) - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
estimatedSize - Variable in class org.biojava.bibliography.BiblioWebResource
  An estomated size in kilobytes.
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 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.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 class org.biojava.stats.svm.tools.SuffixTreeKernel
  Calculate the dot product between the SuffixTrees a and b.
expandCache(int) - Method in class org.biojava.utils.io.CachingInputStream
  Expands the cache to hold some number of `additionalBytes`.
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

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 class org.biojava.bio.seq.ragbag.RagbagFeatureTypeCatcher
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.SeqAlignReadWrite
FASTA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `FASTA` indicates that the sequence format is Fasta.
FASTAALIGN - Static variable in class org.biojava.bio.seq.io.SeqAlignReadWrite
FASTADNA - Static variable in class org.biojava.bio.seq.io.SeqAlignReadWrite
FASTAPROTEIN - Static variable in class org.biojava.bio.seq.io.SeqAlignReadWrite
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_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.
FEATURES - Static variable in interface org.biojava.bio.seq.FeatureHolder
  Signals that features have been added or removed directly within this FeatureHolder.
FEATURE_COLLAPSING - Static variable in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
FEATURE_FLAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.FeatureHandler
FEATURE_LINE_PREFIX - Static variable in class org.biojava.bio.seq.io.GenbankFormat
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
FEATURE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
FEATURE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
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
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.
FIXEDWIDTH - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
FORWARD - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
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
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.
FWORM_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the flatworm mitochondrial genetic code.
FastXMLWriter - class org.biojava.utils.xml.FastXMLWriter.
  Simple implementation of XMLWriter, optimized for speed.
FastXMLWriter(PrintWriter) - Constructor for class org.biojava.utils.xml.FastXMLWriter
FastaAlignmentFormat - class org.biojava.bio.seq.io.FastaAlignmentFormat.
  This class implements the AlignmentFormat interface to read FASTA alignments.
FastaAlignmentFormat() - Constructor for class org.biojava.bio.seq.io.FastaAlignmentFormat
FastaDescriptionLineParser - class org.biojava.bio.seq.io.FastaDescriptionLineParser.
  Simple filter which performs a default extraction of data from the description lines of FASTA files.
FastaDescriptionLineParser(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.FastaDescriptionLineParser
FastaDescriptionLineParser.Factory - class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory.
  Factory which wraps SequenceBuilders in a FastaDescriptionLineParser
FastaDescriptionLineParser.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory
FastaFormat - class org.biojava.bio.seq.io.FastaFormat.
  Format object representing FASTA files.
FastaFormat() - Constructor for class org.biojava.bio.seq.io.FastaFormat
FastaSearchSAXParser - class org.biojava.bio.program.sax.FastaSearchSAXParser.
  `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 org.biojava.bio.program.sax.FastaSequenceSAXParser.
  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"
Feature - interface org.biojava.bio.seq.Feature.
  A feature within a sequence, or nested within another feature.
Feature.ByLocationComparator - class org.biojava.bio.seq.Feature.ByLocationComparator.
  `ByLocationComparator` compares `Feature`s by the minimum base position of their `Location`.
Feature.ByLocationComparator() - Constructor for class org.biojava.bio.seq.Feature.ByLocationComparator
Feature.Template - class org.biojava.bio.seq.Feature.Template.
  Template class for a plain feature.
Feature.Template() - Constructor for class org.biojava.bio.seq.Feature.Template
FeatureBlockSequenceRenderer - class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer.
  `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`.
FeatureFilter - interface org.biojava.bio.seq.FeatureFilter.
  A filter for accepting or rejecting a feature.
FeatureFilter.And - class org.biojava.bio.seq.FeatureFilter.And.
  A filter that returns all features accepted by both child filter.
FeatureFilter.And(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.And
FeatureFilter.AnnotationContains - class org.biojava.bio.seq.FeatureFilter.AnnotationContains.
  Retrieve features that contain a given annotation, and that the set of values contains the value given.
FeatureFilter.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`.
FeatureFilter.ByAncestor - class org.biojava.bio.seq.FeatureFilter.ByAncestor.
  Filter by applying a nested `FeatureFilter` to all ancestor features.
FeatureFilter.ByAncestor(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAncestor
FeatureFilter.ByAnnotation - class org.biojava.bio.seq.FeatureFilter.ByAnnotation.
  Retrieve features that contain a given annotation with a given value.
FeatureFilter.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'.
FeatureFilter.ByAnnotationType - class org.biojava.bio.seq.FeatureFilter.ByAnnotationType.
  A filter that returns all features that have an annotation bundle that is of a given annotation type.
FeatureFilter.ByAnnotationType() - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
FeatureFilter.ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
FeatureFilter.ByChild - class org.biojava.bio.seq.FeatureFilter.ByChild.
  Filter by applying a nested `FeatureFilter` to the child features.
FeatureFilter.ByChild(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByChild
FeatureFilter.ByClass - class org.biojava.bio.seq.FeatureFilter.ByClass.
  Filter which accepts only those filters which are an instance of a specific Java class
FeatureFilter.ByClass(Class) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByClass
FeatureFilter.ByComponentName - class org.biojava.bio.seq.FeatureFilter.ByComponentName.
  Accepts features which are ComponentFeatures and have a `componentSequenceName` property of the specified value.
FeatureFilter.ByComponentName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByComponentName
FeatureFilter.ByDescendant - class org.biojava.bio.seq.FeatureFilter.ByDescendant.
  Filter by applying a nested `FeatureFilter` to all descendant features.
FeatureFilter.ByDescendant(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByDescendant
FeatureFilter.ByFeature - class org.biojava.bio.seq.FeatureFilter.ByFeature.
  Accept only features which are equal to the specified feature
FeatureFilter.ByFeature(Feature) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByFeature
FeatureFilter.ByPairwiseScore - class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore.
  `ByPairwiseScore` is used to filter `SimilarityPairFeature`s by their score.
FeatureFilter.ByPairwiseScore(double, double) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
  Creates a new `ByPairwiseScore`.
FeatureFilter.ByParent - class org.biojava.bio.seq.FeatureFilter.ByParent.
  Filter by applying a nested `FeatureFilter` to the parent feature.
FeatureFilter.ByParent(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByParent
FeatureFilter.BySequenceName - class org.biojava.bio.seq.FeatureFilter.BySequenceName.
  Accept features that reside on a sequence with a particular name.
FeatureFilter.BySequenceName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySequenceName
FeatureFilter.BySource - class org.biojava.bio.seq.FeatureFilter.BySource.
  Construct one of these to filter features by source.
FeatureFilter.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.
FeatureFilter.ByType - class org.biojava.bio.seq.FeatureFilter.ByType.
  Construct one of these to filter features by type.
FeatureFilter.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.
FeatureFilter.ContainedByLocation - class org.biojava.bio.seq.FeatureFilter.ContainedByLocation.
  A filter that returns all features contained within a location.
FeatureFilter.ContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
  Creates a filter that returns everything contained within loc.
FeatureFilter.FrameFilter - class org.biojava.bio.seq.FeatureFilter.FrameFilter.
  Accept features with a given reading frame.
FeatureFilter.FrameFilter(FramedFeature.ReadingFrame) - Constructor for class org.biojava.bio.seq.FeatureFilter.FrameFilter
  Build a new filter that matches all features of a reading frame.
FeatureFilter.HasAnnotation - class org.biojava.bio.seq.FeatureFilter.HasAnnotation.
  Retrieve features that contain a given annotation with any value.
FeatureFilter.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'.
FeatureFilter.Not - class org.biojava.bio.seq.FeatureFilter.Not.
  A filter that returns all features not accepted by a child filter.
FeatureFilter.Not(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Not
FeatureFilter.OnlyChildren - class org.biojava.bio.seq.FeatureFilter.OnlyChildren.
  Accepts features where all immediate children meet the supplied filter.
FeatureFilter.OnlyChildren(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.OnlyChildren
FeatureFilter.OnlyDescendants - class org.biojava.bio.seq.FeatureFilter.OnlyDescendants.
  Accepts features where all descendants meet the supplied filter.
FeatureFilter.OnlyDescendants(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
FeatureFilter.Or - class org.biojava.bio.seq.FeatureFilter.Or.
  A filter that returns all features accepted by at least one child filter.
FeatureFilter.Or(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Or
FeatureFilter.OverlapsLocation - class org.biojava.bio.seq.FeatureFilter.OverlapsLocation.
  A filter that returns all features overlapping a location.
FeatureFilter.OverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
  Creates a filter that returns everything overlapping loc.
FeatureFilter.ShadowContainedByLocation - class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation.
  A filter that accepts all features whose shadow is contained by a specified `Location`.
FeatureFilter.ShadowContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
  Creates a filter that returns everything contained within loc.
FeatureFilter.ShadowOverlapsLocation - class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation.
  A filter that accepts all features whose shadow overlaps a specified `Location`.
FeatureFilter.ShadowOverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
  Creates a filter that returns everything overlapping loc.
FeatureFilter.StrandFilter - class org.biojava.bio.seq.FeatureFilter.StrandFilter.
  Accept features with a given strandedness.
FeatureFilter.StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.seq.FeatureFilter.StrandFilter
  Build a new filter that matches all features of a given strand.
FeatureHandler - class org.biojava.bio.program.xff.FeatureHandler.
  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 org.biojava.bio.seq.FeatureHolder.
  The interface for objects that contain features.
FeatureHolder.EmptyFeatureHolder - class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder.
FeatureHolder.EmptyFeatureHolder() - Constructor for class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
FeatureImpl - class org.biojava.bio.seq.impl.FeatureImpl.
  Wrap up default sets of Feature implementations.
FeatureImpl() - Constructor for class org.biojava.bio.seq.impl.FeatureImpl
FeatureLabelRenderer - class org.biojava.bio.gui.sequence.FeatureLabelRenderer.
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 org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker.
FeatureLabelRenderer.AnnotationLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
FeatureLabelRenderer.AnnotationLabelMaker(Object) - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
FeatureLabelRenderer.LabelMaker - interface org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker.
FeatureLabelRenderer.SourceLabelMaker - class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker.
FeatureLabelRenderer.SourceLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker
FeatureLabelRenderer.TypeLabelMaker - class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker.
FeatureLabelRenderer.TypeLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker
FeatureRealizer - interface org.biojava.bio.seq.FeatureRealizer.
  Interface for translators which map from Feature.Template instances to real Feature objects.
FeatureRenderer - interface org.biojava.bio.gui.sequence.FeatureRenderer.
FeatureTableParser - class org.biojava.bio.seq.io.FeatureTableParser.
  Simple parser for feature tables.
FeatureTree - class org.biojava.bio.gui.FeatureTree.
  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
FeatureTypes - class org.biojava.bio.seq.FeatureTypes.
  Registry of known types of features.
FeatureTypes() - Constructor for class org.biojava.bio.seq.FeatureTypes
FeatureTypes.Repository - interface org.biojava.bio.seq.FeatureTypes.Repository.
  A named collection of Types.
FeatureTypes.RepositoryImpl - class org.biojava.bio.seq.FeatureTypes.RepositoryImpl.
  A simple implementation of a Repository.
FeatureTypes.RepositoryImpl(String) - Constructor for class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
  Create a named repository.
FeatureTypes.Type - interface org.biojava.bio.seq.FeatureTypes.Type.
  A type of feature.
FetchURL - class org.biojava.bio.seq.db.FetchURL.
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 org.biojava.utils.FileAsList.
  `FileAsList` creates a writable `List` implementation backed by a random access file.
FileAsList(File, int) - Constructor for class org.biojava.utils.FileAsList
  Creates a new `FileAsList` and corresponding backing file.
FileAsList(File, boolean) - Constructor for class org.biojava.utils.FileAsList
  Creates a new `FileAsList` instance from an existing backing file.
FilterUtils - class org.biojava.bio.seq.FilterUtils.
  A set of FeatureFilter algebraic operations.
FilterUtils() - Constructor for class org.biojava.bio.seq.FilterUtils
FilterUtils.DelegatingTransformer - class org.biojava.bio.seq.FilterUtils.DelegatingTransformer.
  An implementation of FilterTransformer that attempts to transform by one transformer, and if that fails, by another.
FilterUtils.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.
FilterUtils.FilterTransformer - interface org.biojava.bio.seq.FilterUtils.FilterTransformer.
  An object able to transform some FeatureFilter instances sytematically into others.
FilteringRenderer - class org.biojava.bio.gui.sequence.FilteringRenderer.
FilteringRenderer() - Constructor for class org.biojava.bio.gui.sequence.FilteringRenderer
FilteringRenderer(SequenceRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.FilteringRenderer
FiniteAlphabet - interface org.biojava.bio.symbol.FiniteAlphabet.
  An alphabet over a finite set of Symbols.
FixedSizeCache - class org.biojava.utils.cache.FixedSizeCache.
  Cache which stores up to `limit` Objects.
FixedSizeCache(int) - Constructor for class org.biojava.utils.cache.FixedSizeCache
FixedSizeMap - class org.biojava.utils.cache.FixedSizeMap.
  A cache that only remembers a given number of keys.
FixedSizeMap(int) - Constructor for class org.biojava.utils.cache.FixedSizeMap
FlatFileUnigeneFactory - class org.biojava.bio.program.unigene.FlatFileUnigeneFactory.
  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 org.biojava.bio.seq.db.flat.FlatSequenceDB.
  `FlatSequenceDB` is an OBDA flatfile sequence databank implementation.
FlatSequenceDB(String, String) - Constructor for class org.biojava.bio.seq.db.flat.FlatSequenceDB
FlatSequenceDBProvider - class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider.
  `FlatSequenceDBProvider` directory-services plugin for flatfile databases.
FlatSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
FlexibleAlignment - class org.biojava.bio.alignment.FlexibleAlignment.
  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) - 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).
FloatElementHandlerBase - class org.biojava.utils.stax.FloatElementHandlerBase.
  StAX handler for any element which just contains a string representation of a float.
FloatElementHandlerBase() - Constructor for class org.biojava.utils.stax.FloatElementHandlerBase
Formats - class org.biojava.bio.program.tagvalue.Formats.
  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
Frame - interface org.biojava.bio.seq.Frame.
  Title: Frame.
FramedFeature - interface org.biojava.bio.seq.FramedFeature.
  Title: FramedFeature.
FramedFeature.ReadingFrame - class org.biojava.bio.seq.FramedFeature.ReadingFrame.
  A singleton to hold the frame information
FramedFeature.Template - class org.biojava.bio.seq.FramedFeature.Template.
FramedFeature.Template() - Constructor for class org.biojava.bio.seq.FramedFeature.Template
FullHmmerProfileHMM - class org.biojava.bio.program.hmmer.FullHmmerProfileHMM.
  This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
FundamentalAtomicSymbol - class org.biojava.bio.symbol.FundamentalAtomicSymbol.
  An atomic symbol consisting only of itself.
FundamentalAtomicSymbol(String, Annotation) - Constructor for class org.biojava.bio.symbol.FundamentalAtomicSymbol
FuzzyLocation - class org.biojava.bio.symbol.FuzzyLocation.
  A 'fuzzy' location a-la Embl fuzzy locations.
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(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.RangeResolver - interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver.
  Determines how a `FuzzyLocation` should be treated when used as a normal `Location`.
FuzzyPointLocation - class org.biojava.bio.symbol.FuzzyPointLocation.
  `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 org.biojava.bio.symbol.FuzzyPointLocation.PointResolver.
  Determines how a `FuzzyPointLocation` should be treated when used as a normal `Location`.
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.
featureData(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
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
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
featureTemplate - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
featureTemplate - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
features() - Method in class org.biojava.bio.program.das.DASSequence
features() - Method in class org.biojava.bio.seq.DummySequence
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.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.ProjectedFeatureHolder
features() - Method in class org.biojava.bio.seq.SimpleAssembly
features() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
features() - Method in class org.biojava.bio.seq.SimpleGappedSequence
features() - Method in class org.biojava.bio.seq.SubSequence
features() - Method in class org.biojava.bio.seq.ViewSequence
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.SimpleSequence
features - Variable in class org.biojava.bio.seq.io.GenbankProcessor
features() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
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
fileToBiojava(int, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqAlignReadWrite
  Reads a file and returns the corresponding Biojava object.
fileToBiojava(String, String, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Reads a file with the specified format and alphabet
fileToBiojava(int, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Reads a file and returns the corresponding Biojava object.
fillBuffer(StringBuffer, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  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(RemoteFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
fillTemplate(SimilarityPairFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
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 `FeatureHolder`s.
filter(FeatureFilter) - Method in class org.biojava.bio.program.das.DASSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.program.das.DASSequence
filter(FeatureFilter) - Method in class org.biojava.bio.program.das.DASSequenceDB
filter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Filter this entry set into another set.
filter(FeatureFilter) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.DummySequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.DummySequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
filter(FeatureFilter) - 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) - 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.LazyFeatureHolder
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) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.SimpleAssembly
filter(FeatureFilter) - Method in class org.biojava.bio.seq.SimpleAssembly
filter(FeatureFilter) - Method in class org.biojava.bio.seq.SimpleGappedSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.SimpleGappedSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.SubSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.SubSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.ViewSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.ViewSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
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.db.biosql.BioSQLSequenceDB
filter(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleFeature
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleFeature
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
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 class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.program.xff.ElementRecognizer
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 class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute
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.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 class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.seq.io.game.ElementRecognizer
finalize() - Method in class org.biojava.bio.seq.io.NameTokenization
finalize() - Method in class org.biojava.bio.symbol.SimpleAlignment
finalize() - Method in class org.biojava.bio.symbol.SimpleSymbolList
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.
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.
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.
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(String, Object, Object) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(String, Object, Object) - Method in class org.biojava.bio.gui.TextLogoPainter
firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.TextLogoPainter
firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.TextLogoPainter
firePropertyChange(PropertyChangeEvent) - 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
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
firstToken(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
fivePrimeBlockIterator() - Method in class org.biojava.bio.symbol.CircularLocation
  Iterates over the location blocks in order starting with the most 5'
flatView(MarkovModel) - Static method in class org.biojava.bio.dp.DP
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.
flipStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
flushFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
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.
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.
force() - Method in class org.biojava.utils.io.LargeBuffer
format - Variable in class org.biojava.bibliography.BibRef
  It describes the physical or digital manifestation of the cited resource.
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
  `formatLocation` creates a String representation of a `Location`.
formatLocation(Feature) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
  Formats the location of a feature.
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  `formatLocation` creates a String representation of a `Location`.
formatLocation(Feature) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Creates a string representation of the location of a feature
formatLocation(StringBuffer, Location) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  `formatLocation` creates a String representation of a `Location`.
formatPoint(int, int, boolean) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Formats the points from fuzzy locations.
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`.
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
forwardChangeEvent(ChangeEvent) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
  Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolder
forwardFeatureChangeEvent(Feature, ChangeEvent) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
  Called internally to generate a forwarded version of a ChangeEvent from a ProjectedFeature
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
forwardRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
forwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP
forwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
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
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
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
fromJournal - Variable in class org.biojava.bibliography.BiblioJournalArticle

## G

GAMEAnnotationHandler - class org.biojava.bio.seq.io.game.GAMEAnnotationHandler.
  Handles the GAME <annotation> element
GAMEAnnotationHandler - class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler.
  Handles the GAME <annotation> element
GAMEAspectHandler - class org.biojava.bio.seq.io.game12.GAMEAspectHandler.
  Handles the GAME <aspect> element
GAMEAspectPropHandler - class org.biojava.bio.seq.io.game.GAMEAspectPropHandler.
  Handles the GAME <aspect> element
GAMEDbxrefHandler - class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler.
  Handles the GAME <dbxref> element
GAMEDbxrefPropHandler - class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.
  Deals with database crossreferences
GAMEDbxrefPropHandler.DbXrefElement - class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement.
GAMEDescriptionPropHandler - class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler.
  StAX handler for GAME <description> elements.
GAMEDescriptionPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
GAMEFeatureCallbackItf - interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf.
  An interface that can be tested for by nested handlers when trying to do a callback.
GAMEFeatureSetHandler - class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler.
  Handles the <feature_set> element
GAMEFeatureSetHandler - class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler.
  Handles the GAME <feature_set> element this element is used to represent transcripts.
GAMEFeatureSetPropHandler - class org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler.
  Handles the GAME <feature_set> element
GAMEFeatureSpanHandler - class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler.
  Handles the <feature_span> element
GAMEFeatureSpanHandler - class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler.
  Handles the GAME <feature_span> element
GAMEFeatureSpanHandler.SeqRelHandler - class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler.SeqRelHandler.
GAMEFormat - class org.biojava.bio.seq.io.GAMEFormat.
  A rudimentary read-only GAME 1.2 Format object.
GAMEFormat() - Constructor for class org.biojava.bio.seq.io.GAMEFormat
GAMEGeneHandler - class org.biojava.bio.seq.io.game12.GAMEGeneHandler.
  Handles the GAME <annotation> element
GAMEGenePropHandler - class org.biojava.bio.seq.io.game.GAMEGenePropHandler.
  Handles the GAME <gene> element
GAMEHandler - class org.biojava.bio.seq.io.game.GAMEHandler.
  Handles the root GAME element
GAMEHandler() - Constructor for class org.biojava.bio.seq.io.game.GAMEHandler
GAMEHandler - class org.biojava.bio.seq.io.game12.GAMEHandler.
  Handles the root GAME element
GAMEHandler(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.game12.GAMEHandler
  Constructor for the GAMEHandler object
GAMEMapPosPropHandler - class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler.
  Handles the GAME <map_position> element Currently, it just ignores it!
GAMENameCallbackItf - interface org.biojava.bio.seq.io.game.GAMENameCallbackItf.
  An interface that can be tested for by nested handlers when trying to do a callback.
GAMENamePropHandler - class org.biojava.bio.seq.io.game.GAMENamePropHandler.
  StAX handler for the GAME <name> element.
GAMENamePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMENamePropHandler
GAMEPropertyHandler - class org.biojava.bio.seq.io.game12.GAMEPropertyHandler.
  Handles the GAME <dbxref> element
GAMEResiduesPropHandler - class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler.
  StAX handler for GAME <residues> elements.
GAMEResiduesPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
GAMESeqHandler - class org.biojava.bio.seq.io.game12.GAMESeqHandler.
  Handles the GAME <seq> element
GAMESeqPropHandler - class org.biojava.bio.seq.io.game.GAMESeqPropHandler.
  Handles the GAME <seq> element
GAMESeqRelHandler - class org.biojava.bio.seq.io.game12.GAMESeqRelHandler.
  Handles the GAME <<seq_relationship>> element
GAMESeqRelPropHandler - class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler.
  Handles the GAME <aspect> element
GAMESpanHandler - class org.biojava.bio.seq.io.game12.GAMESpanHandler.
  Handles the GAME <> element.
GAMESpanPropHandler - class org.biojava.bio.seq.io.game.GAMESpanPropHandler.
  Handles the GAME <span> element Currently, it just ignores it!
GAMETranscriptCallbackItf - interface org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf.
  An interface that can be tested for by nested handlers when trying to do a callback.
GAMETypePropHandler - class org.biojava.bio.seq.io.game.GAMETypePropHandler.
  StAX handler for GAME <type> elements.
GAMETypePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMETypePropHandler
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_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_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_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_SEQREL_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler
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_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
GAPS - Static variable in interface org.biojava.bio.alignment.EditableAlignment
GCG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GCG` indicates that the sequence format is GCG.
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.SeqAlignReadWrite
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_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GENBANK_DNA` premade GENBANK | RNA.
GENERIC_PROVIDER - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a provider type.
GENPEPT - Static variable in class org.biojava.bio.seq.io.SeqAlignReadWrite
GENPEPT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GENPEPT` indicates that the sequence format is GENPEPT.
GFF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GFF` indicates that the sequence format is GFF.
GFFDataSource - class org.biojava.bio.seq.distributed.GFFDataSource.
  Use a GFFEntrySet as a DataSource for adding annotation to sequences.
GFFDataSource(GFFEntrySet) - Constructor for class org.biojava.bio.seq.distributed.GFFDataSource
GFFDocumentHandler - interface org.biojava.bio.program.gff.GFFDocumentHandler.
  The interface for things that listen to GFF event streams.
GFFEntrySet - class org.biojava.bio.program.gff.GFFEntrySet.
  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 org.biojava.bio.program.gff.GFFErrorHandler.
  Interface which captures any errors which occur when parsing a GFF stream.
GFFErrorHandler.AbortErrorHandler - class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler.
GFFErrorHandler.AbortErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
GFFErrorHandler.SkipRecordErrorHandler - class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler.
GFFErrorHandler.SkipRecordErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
GFFFilterer - class org.biojava.bio.program.gff.GFFFilterer.
  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.
GFFParser - class org.biojava.bio.program.gff.GFFParser.
  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 org.biojava.bio.program.gff.GFFRecord.
  A single GFF record.
GFFRecordFilter - interface org.biojava.bio.program.gff.GFFRecordFilter.
  A filter that will accept or reject a GFFEntry.
GFFRecordFilter.AcceptAll - class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll.
  Implementation of GFFRecordFilter that accepts everything.
GFFRecordFilter.AcceptAll() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
GFFRecordFilter.FeatureFilter - class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter.
  Implementation of GFFRecordFilter that accepts records based upon the feature field.
GFFRecordFilter.FeatureFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
GFFRecordFilter.FeatureFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
GFFRecordFilter.FrameFilter - class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter.
GFFRecordFilter.FrameFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
GFFRecordFilter.FrameFilter(int) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
GFFRecordFilter.NotFilter - class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter.
GFFRecordFilter.NotFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
GFFRecordFilter.NotFilter(GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
GFFRecordFilter.SequenceFilter - class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter.
  Implementation of GFFRecordFilter that accepts records based upon the sequence name.
GFFRecordFilter.SequenceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
GFFRecordFilter.SequenceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
GFFRecordFilter.SourceFilter - class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter.
  Implementation of GFFRecordFilter that accepts records based upon the source field.
GFFRecordFilter.SourceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
GFFRecordFilter.SourceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
GFFRecordFilter.StrandFilter - class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter.
GFFRecordFilter.StrandFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
GFFRecordFilter.StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
GFFTools - class org.biojava.bio.program.gff.GFFTools.
GFFTools() - Constructor for class org.biojava.bio.program.gff.GFFTools
GFFWriter - class org.biojava.bio.program.gff.GFFWriter.
  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
GLOBAL - Static variable in class org.biojava.bio.taxa.SimpleTaxonFactory
  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
  The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.
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
GapDistribution - class org.biojava.bio.dist.GapDistribution.
  This distribution emits gap symbols.
GapDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.GapDistribution
GappedSequence - interface org.biojava.bio.seq.GappedSequence.
  Extension of GappedSymbolList which also projects features into the gapped coordinate system.
GappedSymbolList - interface org.biojava.bio.symbol.GappedSymbolList.
  This extends SymbolList with API for manipulating, inserting and deleting gaps.
GenbankFileFormer - class org.biojava.bio.seq.io.GenbankFileFormer.
  `GenbankFileFormer` performs the detailed formatting of Genbank entries for writing to a `PrintStream`.
GenbankFileFormer() - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer
  Creates a new `GenbankFileFormer` using `System.out` stream.
GenbankFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer
  Creates a new `GenbankFileFormer` using the specified stream.
GenbankFormat - class org.biojava.bio.seq.io.GenbankFormat.
  Format reader for GenBank files.
GenbankFormat() - Constructor for class org.biojava.bio.seq.io.GenbankFormat
GenbankProcessor - class org.biojava.bio.seq.io.GenbankProcessor.
  Simple filter which handles attribute lines from a Genbank file
GenbankProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor
GenbankProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor
GenbankProcessor.Factory - class org.biojava.bio.seq.io.GenbankProcessor.Factory.
  Factory which wraps sequence builders in a GenbankProcessor
GenbankProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor.Factory
GenbankSequenceDB - class org.biojava.bio.seq.db.GenbankSequenceDB.
  This class contains functions accessing DNA sequences in Genbank format.
GenbankSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenbankSequenceDB
GeneticCodes - class org.biojava.bio.seq.GeneticCodes.
  Collects the references to translation methods in one place.
GeneticCodes() - Constructor for class org.biojava.bio.seq.GeneticCodes
GenpeptSequenceDB - class org.biojava.bio.seq.db.GenpeptSequenceDB.
GenpeptSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenpeptSequenceDB
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.RNATools
gappedToLocation(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Translates a Location from the gapped view into the underlying sequence.
generate(int) - Method in class org.biojava.bio.dp.DP
  Generates an alignment from a model.
generateBackwardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
generateCallboxes() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Precomputes the `Rectangle2D`s 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.
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
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.dist.Distribution.NullModelForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.dp.MarkovModel.DistributionForwarder
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.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.
generateForardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
generateOrderNSequence(String, OrderNDistribution, int) - Static method in class org.biojava.bio.dist.DistributionTools
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 `GeneralPath`s used to draw the traces.
generateViterbiClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
get(String) - Method in class org.biojava.bio.program.indexdb.BioStore
get(String, 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 interface org.biojava.bio.program.indexdb.IndexStore
  `get` returns a list of `Record`s by searching against the primary identifiers if the namespace argument is equal to the primary namespace or otherwise by searching the secondary namespaces.
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.Triplet
get(Object) - Method in class org.biojava.utils.OverlayMap
get(int) - Method in class org.biojava.utils.SingletonList
get(Object) - Method in class org.biojava.utils.SmallMap
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() - Method in interface org.biojava.utils.cache.CacheReference
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(long) - Method in class org.biojava.utils.io.LargeBuffer
get() - Method in class org.biojava.utils.io.LargeBuffer
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.utils.ListTools.Doublet
getA() - Method in class org.biojava.utils.ListTools.Triplet
getAE(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
getAccession(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAddHandler() - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Get the GFFDocumentHandler for adding to this set.
getAddPos() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Retrieve the current value of addPos.
getAddedFeatures() - Method in class org.biojava.bio.seq.ViewSequence
getAddress(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.GenbankSequenceDB
  Get the URL object for locating sequence object using eutils.
getAddress(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getAddress(String, 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
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
getAlignLength(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAlignLength(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAlignUnits(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAlignUnits(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
getAlignment() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
  Gets the Alignment - one of LEADING, TRAILING or CENTER.
getAlignment(SymbolList) - Static method in class org.biojava.bio.program.abi.ABITools
  View a symbol list over the QUALITY alphabet as an alignment.
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 `HomologyFeature`s as keys.
getAlignment() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
  `getAlignment` returns the alignment between the two features.
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.
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.
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
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.
getAllTypes() - Method in class org.biojava.bio.seq.ragbag.RagbagFeatureTypeCatcher
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(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
getAlpha(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getAlpha(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
getAlphaStar(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
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.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.das.DASSequence
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.DummySequence
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 class org.biojava.bio.seq.SubSequence
getAlphabet() - Method in class org.biojava.bio.seq.ViewSequence
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.SimpleSequence
getAlphabet() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getAlphabet(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  `getAlphabet` accepts a value which represents a sequence format and returns the relevant `FiniteAlphabet` object.
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 interface org.biojava.bio.symbol.AlphabetIndex
  Retrieve the alphabet that this indexes.
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.PackedDnaSymbolList
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.SimpleAlignment
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.SuffixTree
  Return the Alphabet containing all Symbols which might be found in this SuffixTree.
getAlphabet() - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
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
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.
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.SubDoubleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SimpleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SingletonAlphabet
getAltIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
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 interface org.biojava.bio.symbol.Alphabet
  Get a symbol that represents the set of symbols in syms.
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAmbiguityImpl(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet
  Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
getAnnotatedQuerySeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
getAnnotatedSubjectSeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
getAnnotaters() - Method in class org.biojava.bio.program.das.ReferenceServer
getAnnotation() - Method in interface org.biojava.bio.Annotatable
  Should return the associated annotation object.
getAnnotation() - Method in class org.biojava.bio.dp.SimpleEmissionState
getAnnotation(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `getAnnotation` returns an immutable, static annotation describing the enzyme.
getAnnotation() - Method in class org.biojava.bio.program.das.DASSequence
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.DummySequence
getAnnotation() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getAnnotation(Feature) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
getAnnotation() - Method in class org.biojava.bio.seq.SimpleAssembly
getAnnotation() - Method in class org.biojava.bio.seq.SimpleGappedSequence
getAnnotation() - Method in class org.biojava.bio.seq.SubSequence
getAnnotation() - Method in class org.biojava.bio.seq.ViewSequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleSequence
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.projection.ProjectedFeature
getAnnotation(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Get the annotation bundle of the projected feature.
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.SubDoubleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
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.IntegerAlphabet
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.taxa.AbstractTaxon
getAnnotationType() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
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
getArray() - Method in class org.biojava.bio.symbol.PackedDnaSymbolList
  returns the byte array backing the SymbolList.
getArrowScoop() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getArrowSize() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getAsp_N() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getAuthorityId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Return the authority id for this identifier.
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
getBackwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
getBackwardTransitions() - Method in class org.biojava.bio.dp.DP
getBaseCalls() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
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.
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).
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
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.
getBlockDepth() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
getBlockDepth() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
getBlockPainter() - Method in class org.biojava.bio.gui.DistributionLogo
getBlockPainter() - Method in interface org.biojava.bio.gui.LogoContext
getBlockWidth() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getBounds() - Method in interface org.biojava.bio.gui.LogoContext
getBuilderFactory(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  `getBuilderFactory` accepts a value which represents a sequence format and returns the relevant `SequenceBuilderFactory` object.
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
getCNBr() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getCallContaining(Point2D, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the 0-based index of the call containing a given point.
getCallContaining(Point2D) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Synonym for `ChromatogramGraphic.getCallContaining(Point2D, 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(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Synonym for `ChromatogramGraphic.getCallContaining(float, boolean)` with `pointOnScreen`=true.
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.
getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains
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 class org.biojava.utils.ChangeVetoException
  Return the ChangeEvent which is being vetoed.
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.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
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.program.das.DASSequence
getChangeSupport(ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
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.FeatureTypes.RepositoryImpl
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.LazyFeatureHolder
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.SimpleAssembly
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper
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.seq.impl.SimpleFeature
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleSequence
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
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.
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.
getChar(long) - Method in class org.biojava.utils.io.LargeBuffer
getChar() - Method in class org.biojava.utils.io.LargeBuffer
getCharacterOffset() - Method in class org.biojava.utils.ParserException
  Get the character offset in the line where an error was detected.
getChild() - Method in class org.biojava.bio.seq.FeatureFilter.Not
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.
getChild(SuffixTree.SuffixNode, int) - Method in class org.biojava.bio.symbol.SuffixTree
  Get the n'th child of a node.
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
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
getChildren() - Method in class org.biojava.bio.taxa.SimpleTaxon
getChildren() - Method in interface org.biojava.bio.taxa.Taxon
  The children of this Taxon.
getChildren() - Method in class org.biojava.bio.taxa.WeakTaxon
getChildrenRaw() - Method in class org.biojava.bio.taxa.WeakTaxon
getChromNum(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getChromatogram() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Accessor for the in-use chromatogram.
getChromosome(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
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 class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getChymotrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getClassifyId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassifySystem(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassifyType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCleaveageResidues() - Method in class org.biojava.bio.proteomics.Protease
  The list of residues that the protease will cleave at.
getCloneId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCloneLibrary(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
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.
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
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.
getComment() - Method in class org.biojava.bio.AnnotationType.Impl
getComment(Object) - Method in class org.biojava.bio.AnnotationType.Impl
getComment() - Method in interface org.biojava.bio.AnnotationType
  Get the comment for the whole AnnotationType.
getComment(Object) - Method in interface org.biojava.bio.AnnotationType
  Get the comment for a particular property.
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.stats.svm.tools.SVM_Light.LabelledVector
getComments() - Method in class org.biojava.bio.program.scf.SCF
  Returns the comments fields as a `Properties` mapping.
getCommonName() - Method in class org.biojava.bio.taxa.AbstractTaxon
getCommonName() - Method in interface org.biojava.bio.taxa.Taxon
  The common name of the Taxon.
getComparator() - Method in class org.biojava.utils.FileAsList
getComponentFeature(String) - Method in class org.biojava.bio.seq.ragbag.RagbagComponentDirectory.EmptyComponentDirectory
getComponentFeature(String) - Method in interface org.biojava.bio.seq.ragbag.RagbagComponentDirectory
getComponentFeature(String) - Method in class org.biojava.bio.seq.ragbag.RagbagHashedComponentDirectory
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
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.
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 interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Composite
getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Impl
getConfigLocator() - Method in interface org.biojava.directory.RegistryConfiguration
  `getConfigLocator` returns a locator for the configuration.
getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Composite
getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Impl
getConfiguration() - Method in interface org.biojava.directory.RegistryConfiguration
  `getConfiguration` returns a mapping of registry database names to collections of tag-value pairs.
getConstant() - Method in class org.biojava.stats.svm.PolynomialKernel
getConstant() - Method in class org.biojava.stats.svm.SigmoidKernel
getConstraint(Object) - Method in class org.biojava.bio.AnnotationType.Impl
getConstraint(Object) - Method in interface org.biojava.bio.AnnotationType
  Retrieve the constraint that will be applied to all properties with a given key.
getContext(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getContext() - Method in class org.biojava.stats.svm.TrainingEvent
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.
getCount(AtomicSymbol) - Method in interface org.biojava.bio.dist.Count
  Return the counts for a given Symbol.
getCount(DistributionTrainerContext, AtomicSymbol) - Method in interface org.biojava.bio.dist.DistributionTrainer
  Get the current count for this state.
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(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
getCount(AtomicSymbol) - Method in class org.biojava.bio.dist.IndexedCount
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
getCount(Distribution, Symbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
getCount() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns a number of entries contained in this vocabulary.
getCreateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCreateOnUnderlyingSequence() - Method in class org.biojava.bio.seq.SimpleGappedSequence
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
getCrossProductAlphabet(List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCurrentCycle() - Method in interface org.biojava.stats.svm.TrainingContext
getCurrentScore() - Method in class org.biojava.bio.dp.AbstractTrainer
getCurrentScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
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
getDB() - Method in class org.biojava.bio.program.das.ReferenceServer
getDB() - Method in class org.biojava.bio.seq.db.FetchURL
getDBHelperForURL(String) - Static method in class org.biojava.bio.seq.db.biosql.DBHelper
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
getDNASequence(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
  Get the called DNA sequence from a chromatogram.
getDP() - Method in class org.biojava.bio.dp.AbstractTrainer
getDP() - 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() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
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.
getDataSources() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
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
getDatabase(String) - Method in class org.biojava.directory.Registry
  `getDatabase` retrieves a database instance known by a name `String`.
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.
getDbCode() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getDbId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
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 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
getDbXrefId() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
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 <class>decoratorClass</class> 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 class org.biojava.bio.AnnotationType.Impl
getDefaultConstraint() - Method in interface org.biojava.bio.AnnotationType
  Get the CollectionConstraint that will be applied to all properties without an explicit binding.
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 interface org.biojava.bio.seq.io.SequenceFormat
  Deprecated. new implementations should only write a single format.
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.TagValueWrapper
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.
getDelegateParser() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
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
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper
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(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.BasicFeatureRenderer
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.LabelledSequenceRenderer
getDepth(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
  `getDepth` returns the total depth of a list of `SequenceRenderer`s.
getDepth(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LineInfo
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
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() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
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
getDepthScaler() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
  Retrieve the current DepthScaler.
getDescription() - Method in class org.biojava.bio.program.das.DataSource
getDescription(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getDescription() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns a description of this vocabulary.
getDetailsHandler() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
  Return a handler for the XFF `details` element.
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.
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.SequencePoster
  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.
getDistDataSource() - Method in class org.biojava.bio.program.das.DataSource
getDistDataSource() - Method in class org.biojava.bio.program.das.ReferenceServer
getDistribution(Symbol) - Method in interface org.biojava.bio.dist.OrderNDistribution
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
getDotStatesIndex() - Method in class org.biojava.bio.dp.DP
getDouble(long) - Method in class org.biojava.utils.io.LargeBuffer
getDouble() - 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.
getDstLength() - Method in class org.biojava.bio.seq.ragbag.RagbagMap
getDstLocation() - Method in class org.biojava.bio.seq.ragbag.RagbagMap.MapElement
getE() - Method in class org.biojava.bio.proteomics.StructureTools
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
getEcNumber(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
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
getElementId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
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 class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getElementIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
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 class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getElideSymbols() - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Return a flag indicating if symbol data will be skipped when parsing streams.
getElideSymbols() - Method in class org.biojava.bio.seq.io.GenbankFormat
getEmblBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Get a default SequenceBuilderFactory for handling EMBL files.
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
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 class org.biojava.bio.seq.SubSequence
getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
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.
getEntryByName(String) - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns a selected vocabulary entry.
getEnumeration(String) - Method in class org.biojava.bio.seq.ragbag.RagbagMap
getEnzyme(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `getEnzyme` returns an enzyme by name.
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
getEpsilon() - Method in class org.biojava.stats.svm.SMOTrainer
getErrorHandler() - Method in class org.biojava.bio.program.gff.GFFParser
  Find the error handler used by this parser.
getExonIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getFastaBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
  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
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
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 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
getFeatureRealizer() - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
  Returns the FeatureRealizer set by "setFeatureRealizer".
getFeatureRenderer() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
  `getFeatureRenderer` returns the currently active renderer.
getFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler
  Get the template for the feature being constructed.
getFeatureType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
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 `Feature`s 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
getFeatures() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  The features to render.
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 `Feature`s belonging to the currently rendered `Sequence`.
getFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
  Returns the list of features in this featureholder.
getFeatures() - Method in class org.biojava.bio.seq.SubSequence
getFeatures(FeatureFilter) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
  Get all features matching a FeatureFilter provided by this DistDataSource.
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(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
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 `HomologyFeature`s which are also used as the keys in the alignment.
getField() - Method in class org.biojava.utils.ChangeType
  Return a Field object where this change type is declared.
getFile() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getFile() - Method in interface org.biojava.bio.program.indexdb.Record
  `getFile` returns the random access file in which the record belongs.
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.bio.seq.db.emblcd.EmblCDROMRandomAccess
  `getFile` returns the `File` wrapped.
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`.
getFilename() - Method in class org.biojava.bio.seq.ragbag.RagbagMap.MapElement
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.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
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.
getFloat(long) - Method in class org.biojava.utils.io.LargeBuffer
getFloat() - 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
getForwardRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getForwardRegex` returns a regular expression which matches the forward strand of the recognition site.
getForwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
getForwardTransitions() - Method in class org.biojava.bio.dp.DP
getForwarders(ChangeType) - Method in class org.biojava.utils.Unchangeable
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
getFrom() - Method in class org.biojava.bio.dp.IllegalTransitionException
getG() - Method in class org.biojava.bio.proteomics.StructureTools
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(List) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Get the gap symbol appropriate to this list of alphabets.
getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getGenbankBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Get a default SequenceBuilderFactory for handling GenBank files.
getGeneticCode(String) - Static method in class org.biojava.bio.seq.RNATools
  Retrieve a TranslationTable by name.
getGeneticCodeNames() - Static method in class org.biojava.bio.seq.RNATools
  Retrieve a Set containing the name of each genetic code.
getGenpeptBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
  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
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 interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getH() - Method in class org.biojava.bio.proteomics.StructureTools
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(String, String) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
  Retrieve a `FilterHandler` for the specified tag name.
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(int) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  return iterator to callbackStack
getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
  get iterator for current stack starting at the position below mine.
getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  return iterator to callbackStack
getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
  get iterator for current stack starting at the position below mine.
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.
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
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.program.indexdb.Record.Impl
getID() - Method in interface org.biojava.bio.program.indexdb.Record
  `getID` returns the primary identifier of the record.
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
getIDMaker() - Method in class org.biojava.bio.seq.db.HashSequenceDB
  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
getId() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getIdAlias(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
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.
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.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.
getIndexStore() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
  Retrieve the IndexStore.
getInnerMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
getInnerMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
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
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper
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
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
getInt(long) - Method in class org.biojava.utils.io.LargeBuffer
getInt() - Method in class org.biojava.utils.io.LargeBuffer
getIntFromSymbolList(SymbolList, int) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
  Retrieves, unwraps, and returns an `int` from a SymbolList containing `IntegerAlphabet.IntegerSymbol`s.
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.
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
getIterator() - Method in class org.biojava.utils.ListTools.Doublet
getIterator() - Method in class org.biojava.utils.ListTools.Triplet
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.SimpleSVMClassifierModel
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 interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getKmpNextTable() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
  Returns the table of border lengths
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(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getLabel() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
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 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.dp.SimpleStatePath
getLabels() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
getLabels() - Method in interface org.biojava.bio.symbol.Alignment
  The list of SymbolLists in the alignment.
getLabels() - Method in class org.biojava.bio.symbol.RelabeledAlignment
getLabels() - Method in class org.biojava.bio.symbol.SimpleAlignment
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
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
  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
getLength() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getLength() - Method in interface org.biojava.bio.program.indexdb.Record
  `getLength` returns the length of the record in bytes.
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
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 class org.biojava.utils.ParserException
  Get the text of the line where the exception occured.
getLineNumber() - Method in class org.biojava.utils.ParserException
  Get the line number in the stream where this exception occured.
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
  Retrive the current line width.
getLines() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Retrieve the number of lines that the sequence will be rendered over.
getLinkURL() - Method in class org.biojava.bio.program.das.DASLink
getListener() - Method in class org.biojava.bio.program.tagvalue.ParserListener
  `getListener` returns the listener of the pair.
getListener(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getListeners(ChangeType) - Method in class org.biojava.utils.Unchangeable
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(Feature) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
getLocation() - Method in class org.biojava.bio.seq.RemoteFeature.Region
  Retrieve the Location of the Region.
getLocation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getLocation() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getLocation(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Get the location of the projected feature
getLocationHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getLocator() - Method in class org.biojava.utils.ParserException
  Get a locator for the stream which caused this exception.
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(long) - Method in class org.biojava.utils.io.LargeBuffer
getLong() - Method in class org.biojava.utils.io.LargeBuffer
getLys_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
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 interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMapPosition(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMapType() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getMapURL() - Method in class org.biojava.bio.program.das.DataSource
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
getMass(SymbolList, String, boolean) - Static method in class org.biojava.bio.proteomics.MassCalc
  `getMass` calculates the mass of this peptide.
getMass(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc
  Get the Mass of this peptide.
getMatch(int) - Method in class org.biojava.bio.dp.ProfileHMM
  Retrieve the match state at column indx.
getMatchAlign(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMatchDesc(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMatchRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchRegion(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.
getMax() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
getMax(AtomicSymbol) - 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(AtomicSymbol) - Method in interface org.biojava.bio.chromatogram.Chromatogram
  Gets the max intensity on the trace for the specified nucleotide.
getMax() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
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
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
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.
getMin() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
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
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
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.LabelledSequenceRenderer
getMinimumLeader(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
  `getMinimumLeader` returns the maximum value of getMinimumLeader() for a list of `SequenceRenderer`s.
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
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(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.LabelledSequenceRenderer
getMinimumTrailer(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
  `getMinimumTrailer` returns the maximum value of getMinimumTrailer() for a list of `SequenceRenderer`s.
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
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 class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
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.SimpleLabelRenderer
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
getMolType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
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.
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
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.
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 class org.biojava.bio.program.das.DASSequence
getName() - Method in class org.biojava.bio.program.das.DASSequenceDB
getName() - Method in class org.biojava.bio.program.das.DASSequenceDBProvider
getName() - Method in class org.biojava.bio.program.das.DataSource
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.DummySequence
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 interface org.biojava.bio.seq.Sequence
  The name of this sequence.
getName() - Method in class org.biojava.bio.seq.SimpleAssembly
getName() - Method in class org.biojava.bio.seq.SimpleGappedSequence
getName() - Method in class org.biojava.bio.seq.SubSequence
getName() - Method in class org.biojava.bio.seq.ViewSequence
getName() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
getName() - Method in class org.biojava.bio.seq.db.BioIndex
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.GenbankSequenceDB
getName() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getName() - Method in class org.biojava.bio.seq.db.HashSequenceDB
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.IndexedSequenceDB
  Get the name of this sequence database.
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.db.biofetch.BioFetchSequenceDB
getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
getName() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
getName() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
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.distributed.DistributedSequenceDB
getName() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getName() - Method in class org.biojava.bio.seq.ragbag.RagbagAssembly
getName() - Method in interface org.biojava.bio.symbol.Alphabet
  Get the name of the alphabet.
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.SubDoubleAlphabet
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getName() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
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.IntegerAlphabet
getName() - Method in class org.biojava.bio.symbol.SimpleAlphabet
getName() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
getName() - Method in class org.biojava.bio.symbol.SingletonAlphabet
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
getName() - Method in interface org.biojava.bio.taxa.TaxonFactory
  Name for this TaxonFactory.
getName() - Method in class org.biojava.bio.taxa.WeakTaxonFactory
getName() - Method in interface org.biojava.directory.SequenceDBProvider
  The name of this provider.
getName() - Method in class org.biojava.utils.ChangeType
  Return the name of this change.
getName() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns a name of this vocabulary.
getNameToSymbol() - Method in class org.biojava.bio.seq.io.NameTokenization
getNames() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getNamespaceId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Return the namespace id for this identifier within the authority.
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.
getNewTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper
  `getNewTag` returns the tag which substitutes the specified value.
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(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getNucleotide() - Static method in class org.biojava.bio.seq.NucleotideTools
  Return the Nucleotide alphabet.
getNucleotideIDs() - Method in class org.biojava.bio.seq.db.LocusLinkParser
getNucleotideIDs_array() - Method in class org.biojava.bio.seq.db.LocusLinkParser
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(Distribution, Distribution) - Static method in class org.biojava.bio.dist.PairDistribution
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
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
  Retrieve the weight of the background distribution
getNumCount() - Method in interface org.biojava.utils.candy.CandyFinder
  It returns the number of available vocabularies.
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.
getOS(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getObjectId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Return the object id of this identifier.
getOffset() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getOffset() - Method in interface org.biojava.bio.program.indexdb.Record
  `getOffset` returns the byte offset in the file at which the record begins.
getOldIDHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getOmimIDs() - Method in class org.biojava.bio.seq.db.LocusLinkParser
getOmimIDs_array() - Method in class org.biojava.bio.seq.db.LocusLinkParser
getOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the current value for the specified option.
getOrder() - Method in class org.biojava.stats.svm.PolynomialKernel
getOrganism(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getOrientation() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getOuterMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
getOuterMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
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
getOverlay() - Method in class org.biojava.bio.OverlayAnnotation
getOverlayMap() - Method in class org.biojava.utils.OverlayMap
  Return the object containing the overlay mappings.
getPI(SymbolList, boolean, boolean) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc
  Computes isoelectric point of specified peptide.
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
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.
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.ProjectedFeatureHolder
  Return the parent of all top-level features in this FeatureHolder.
getParent(Feature) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
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 class org.biojava.bio.seq.impl.SimpleFeature
getParent() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getParent(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Get the parent FeatureHolder into which a feature should be projected
getParent() - Method in class org.biojava.bio.taxa.SimpleTaxon
getParent() - Method in interface org.biojava.bio.taxa.Taxon
  The parent of this Taxon.
getParent() - Method in class org.biojava.bio.taxa.WeakTaxon
getParentDB() - Method in class org.biojava.bio.program.das.DASSequence
getParentMap() - Method in class org.biojava.utils.OverlayMap
  Return the object containing the fallback mappings.
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
getParser(File) - Method in interface org.biojava.bio.seq.ragbag.RagbagFileParserFactory
  Return a RagbagFileParser for given file
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
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.
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).
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
getPosShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Retrieve the shape used to represent positive points.
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
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
getPrintStream() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
getPrintStream() - Method in interface org.biojava.bio.seq.io.SeqFileFormer
  `getPrintStream` returns the `PrintStream` to which an instance will write the formatted data.
getPrintStream() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  `getPrintStream` returns the `PrintStream` to which an instance of SwissprotFileFormer will write the formatted data.
getProbabilityAlphabet() - Static method in class org.biojava.bio.program.scf.SCF
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
getPropType() - 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 class org.biojava.bio.AnnotationType.Impl
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.BeanAsAnnotation
getProperties() - Method in class org.biojava.bio.SimpleAnnotation
getProperties() - Method in class org.biojava.bio.SmallAnnotation
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(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(Object) - Method in class org.biojava.bio.MergeAnnotation
getProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
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.Agave2AgaveAnnotFilter
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, 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.
getPropertyClass() - Method in class org.biojava.bio.PropertyConstraint.ByClass
getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains
getPropertyConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandler
getProps() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
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.
getProteinIDs() - Method in class org.biojava.bio.seq.db.LocusLinkParser
getProteinIDs_array() - Method in class org.biojava.bio.seq.db.LocusLinkParser
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.
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
getQueryRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
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 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
getRNA() - Static method in class org.biojava.bio.seq.RNATools
  Return the RNA alphabet.
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.SequencePoster
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.
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.
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
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 `Record`s 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
getRef() - Method in class org.biojava.bio.seq.ragbag.RagbagMap.MapElement
getRef(String) - Method in class org.biojava.bio.seq.ragbag.RagbagMap
  gets reference string for a given filename
getReferenceServers() - Method in class org.biojava.bio.program.das.DAS
getRegions() - Method in interface org.biojava.bio.seq.RemoteFeature
  Retrieve the list of Regions that locate this feature both localy and remotely.
getRegions() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
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
getRelatedAnnot(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getRemoteFeature() - Method in interface org.biojava.bio.seq.RemoteFeature
  Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.
getRemoteFeature() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
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.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.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.SequencePoster
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getRenderingHints` returns the `RenderingHints` currently being used by the `Graphics2D` instances of delegate renderers.
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.
getResolver() - Method in interface org.biojava.bio.seq.RemoteFeature
getResolver() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
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 interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getReturnFormat() - Method in class org.biojava.bio.seq.db.FetchURL
getReverseRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getReverseRegex` returns a regular expression which matches the reverse strand of the recognition site.
getRevisionId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Return the revision id of this identifier.
getRole() - Method in class org.biojava.bio.program.das.DASLink
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
getRoot() - Method in interface org.biojava.bio.taxa.TaxonFactory
  Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.
getRoot() - Method in class org.biojava.bio.taxa.WeakTaxonFactory
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.SequencePoster
  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 class org.biojava.bio.program.das.DASSequence
getSchema() - Method in class org.biojava.bio.seq.DummySequence
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.LazyFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.MergeFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
getSchema(Feature) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.SimpleAssembly
getSchema() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.SimpleGappedSequence
getSchema() - Method in class org.biojava.bio.seq.SubSequence
getSchema() - Method in class org.biojava.bio.seq.ViewSequence
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.SimpleSequence
getSchema() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getSchema(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Delegate for getSchema
getScientificName() - Method in class org.biojava.bio.taxa.AbstractTaxon
getScientificName() - Method in interface org.biojava.bio.taxa.Taxon
  The scientific name of this taxon.
getScore() - Method in interface org.biojava.bio.dp.DPMatrix
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.onehead.SingleDPMatrix
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.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
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 recieve 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
getSearchableDBs() - Method in interface org.biojava.bio.search.SeqSimilaritySearcher
  Return a set of all databases that can be searched with this sequence similarity searcher.
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 `Feature`s 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.
getSecondarySymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSecondarySymbolTranslation` returns the current translation in `Symbol`s which will be applied when rendering.
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 `Symbol`s belonging to the currently rendered secondary `Sequence`.
getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
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
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.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.SequencePoster
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(String) - Method in class org.biojava.bio.program.das.DASSequenceDB
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(Feature) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
getSequence() - Method in class org.biojava.bio.seq.SubSequence
  Return the parent sequence of which this is a partial view
getSequence(String) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
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.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 class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
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() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSequence() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getSequence(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Get the Sequence which defines the coordinate system for the projected feature.
getSequenceDB(Map) - Method in class org.biojava.bio.program.das.DASSequenceDBProvider
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
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
  `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
getSequenceLength() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
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
getSequenceName() - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
getSequenceObject(String, String) - Method in class org.biojava.bio.seq.ragbag.RagbagFilteredCachedSeqFactory
getSequenceObject(String, String) - Method in class org.biojava.bio.seq.ragbag.RagbagFixedCacheSeqFactory
getSequenceObject(String, String) - Method in interface org.biojava.bio.seq.ragbag.RagbagSequenceFactory
  return a RagbagSequence object of desired type
getSequenceObject(String, String) - Method in class org.biojava.bio.seq.ragbag.RagbagSoftRefSeqFactory
getSequenceObject(String, String) - Method in class org.biojava.bio.seq.ragbag.RagbagUncachedSeqFactory
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
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)
getShort(long) - Method in class org.biojava.utils.io.LargeBuffer
getShort() - 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
getSignificantBits() - Method in interface org.biojava.bio.chromatogram.Chromatogram
  Returns the number of bits of the traces which are significant.
getSize() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
getSize() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
getSize() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
  Gets the current size of the border in pixels.
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.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.bio.seq.projection.ProjectedFeature
getSource() - Method in class org.biojava.utils.ChangeForwarder
  Retrieve the 'source' object for `ChangeEvent`s fired by this forwarder.
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.
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
  Return the underlying (ungapped) SymbolList.
getSpacer() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  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).
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.
getSrcLocation() - Method in class org.biojava.bio.seq.ragbag.RagbagMap.MapElement
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.
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 class org.biojava.bio.seq.SubSequence
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.io.agave.AGAVEMatchRegion
getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
getStates() - Method in class org.biojava.bio.dp.DP
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.
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 class org.biojava.bio.seq.FeatureFilter.StrandFilter
  Retrieve the strand this matches.
getStrand() - Method in interface org.biojava.bio.seq.FramedFeature
getStrand(StrandedFeature) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
getStrand() - Method in interface org.biojava.bio.seq.StrandedFeature
  Retrieve the strand that this feature lies upon.
getStrand() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
getStrand() - Method in class org.biojava.bio.seq.projection.ProjectedStrandedFeature
getStrand(StrandedFeature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Get the strand of the projected feature.
getStrand() - Method in class org.biojava.bio.seq.ragbag.RagbagMap.MapElement
getStrandedFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
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 `FeatureHolder`s filtered using the current filter.
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
getSubSeqStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
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 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
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
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
  Get a default SequenceBuilderFactory for handling Swissprot files.
getSymbol(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet
getSymbol(List) - Method in interface org.biojava.bio.symbol.Alphabet
  Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet
  Retrieve the Symbol for a double.
getSymbol(double, double) - Method in class org.biojava.bio.symbol.DoubleAlphabet
  Retrieve the symbol for a range of doubles.
getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet
getSymbol() - Method in class org.biojava.bio.symbol.IllegalSymbolException
  Retrieve the symbol that caused this exception, or null.
getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet
  Retrieve the Symbol for an int.
getSymbol(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet
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
getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSymbolTranslation` returns the current translation in `Symbol`s which will be applied when rendering.
getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getSymbolTranslation` returns the current translation in `Symbol`s which will be applied when rendering.
getSymbols() - Method in class org.biojava.bio.dp.SimpleEmissionState
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 `Symbol`s 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
  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.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 `Symbol`s belonging to the currently rendered `Sequence`.
getSymbols() - Method in class org.biojava.bio.program.das.DASSequence
getSymbols() - Method in interface org.biojava.bio.seq.Feature
  Return a list of symbols that are contained in this feature.
getSymbols() - Method in interface org.biojava.bio.seq.StrandedFeature
  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 class org.biojava.bio.seq.projection.ProjectedStrandedFeature
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
getSyms() - Method in class org.biojava.bio.symbol.PackedSymbolList
  Return the long array within which the symbols are bit-packed.
getT() - Method in class org.biojava.bio.proteomics.StructureTools
getTAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools
  Gets the protein alphabet including the translation termination symbols
getTable() - Method in class org.biojava.bio.dist.TranslatedDistribution
  Retrieve the translation table encapsulating the map from this emission spectrum to the underlying one.
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
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 interface org.biojava.stats.svm.SVMTarget
getTarget(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
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.
getTaxonId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getTermMass() - Method in class org.biojava.bio.proteomics.MassCalc
  `getTermMass` returns the terminal mass being used by the instance methods.
getTestClass() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
getThreadFetches() - Static method in class org.biojava.bio.program.das.DAS
getThreshold() - Method in interface org.biojava.stats.svm.SVMClassifierModel
getThreshold() - Method in class org.biojava.stats.svm.SVMRegressionModel
getThreshold() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
getTitle() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
  The cluster title.
getTo() - Method in class 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.
getTokenTable() - Method in class org.biojava.bio.seq.io.CharacterTokenization
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
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.SubDoubleAlphabet
getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet
getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
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.SingletonAlphabet
getTopLevelObject() - Method in class org.biojava.utils.xml.XMLPeerBuilder
  Once the XMLPeerBuilder has been used, return an Object which represents the whole document.
getTotalDepth() - Method in class org.biojava.bio.gui.sequence.LineInfo
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() - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
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.
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
  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.
getTranslation() - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
  Return the translation component of the transformation applied by this FeatureHolder
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.
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 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(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
getType(String) - Static method in class org.biojava.bio.seq.FeatureTypes
  Get a Type by URI.
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.bio.seq.projection.ProjectedFeature
getType() - Method in class org.biojava.utils.ChangeEvent
  Find the type of this event.
getTypeHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getTypes(URL) - Static method in class org.biojava.bio.program.das.DAS
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
getURI() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
  Get the URI for this type.
getURL() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
  `getURL` returns the hotspot URL.
getURL() - Method in class org.biojava.bio.program.das.DASSequenceDB
  Return the URL of the reference server for this database.
getURL() - Method in class org.biojava.bio.program.das.DataSource
getURN() - Method in class org.biojava.bio.program.das.DASSequence
getURN() - Method in class org.biojava.bio.seq.DummySequence
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.biojava.bio.seq.SimpleGappedSequence
getURN() - Method in class org.biojava.bio.seq.SubSequence
getURN() - Method in class org.biojava.bio.seq.ViewSequence
getURN() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getURN() - Method in class org.biojava.bio.seq.ragbag.RagbagAssembly
getUniGeneIDs() - Method in class org.biojava.bio.seq.db.LocusLinkParser
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
getUpdateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
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.
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.PropertyConstraint.ExactValue
getValue() - Method in class org.biojava.bio.program.tagvalue.TagValue
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.StrandedFeature.Strand
  Returns the integer label for strandedness.
getValue() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
getValue() - Method in interface org.biojava.stats.svm.ItemValue
getValue() - Method in class org.biojava.stats.svm.SimpleItemValue
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.
getVariableMasses(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc
  Get all masses including the variable mass.
getVector(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getVector() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
getVectorNTISupport() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Is VectorNTI compatable output being produced?
getVersion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getVersion() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getVersion() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns a vesrion of this vocabulary.
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
getVisibleSecondarySymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getVisibleSecondarySymbolCount` returns the maximum number of secondary `Symbol`s 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 `Symbol`s 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 `Symbol`s which can be rendered in the visible area (excluding all borders) of the `TranslatedSequencePanel` at the current scale.
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.
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 emited 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
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
getWeights() - Method in class org.biojava.bio.dist.SimpleDistribution
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.stats.svm.RadialBaseKernel
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.seq.ProjectedFeatureHolder
getWrapped() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getWrappedException() - Method in class org.biojava.utils.NestedError
getWrappedKernel() - Method in class org.biojava.stats.svm.SigmoidKernel
getXFFEnvironment() - Method in class org.biojava.bio.program.xff.FeatureHandler
  Return the XFF processing environment passed in when this handler was created.
getXMLPeer(String, List, AttributeList) - Method in class org.biojava.utils.xml.XMLDispatcher
getXMLPeer(String, List, AttributeList) - Method in interface org.biojava.utils.xml.XMLPeerFactory
  Return a Java object to reflect an XML element.
getXrefDb() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
getXrefProps() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
getXrefs(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
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 class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
get_() - Method in class org.biojava.bio.proteomics.StructureTools
getbaseURL() - Method in class org.biojava.bio.seq.db.FetchURL
gffFromSequence(Sequence) - Static method in class org.biojava.bio.program.gff.GFFTools
  Creates a GFFEntrySet containing one entry for each feature on a sequence.
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(Point) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
  `graphicsToSecondarySequence` converts a graphical position to a secondary sequence index.
graphicsToSecondarySequence(double) - 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.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 class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
graphicsToSequence(Point) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
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(Point) - 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(Point) - Method in class org.biojava.bio.gui.sequence.SequencePanel
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster
graphicsToSequence(Point) - Method in class org.biojava.bio.gui.sequence.SequencePoster
graphicsToSequence(double) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  Converts a graphical position into a sequence coordinate.
graphicsToSequence(Point) - 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(Point) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
graphicsToSequence(Point) - 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(Point) - 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
growIfNecessary() - Method in class org.biojava.utils.ChangeSupport
  Grows the internal resources if by adding one more listener they would be full.
guessFileType(String) - Static method in class org.biojava.bio.seq.io.SeqAlignReadWrite
  Attempts to guess the filetype of a file given the name
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

## H

HEADER_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HeaderStAXHandler
HEIGHTSCALING - Static variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
  Constant `HEIGHTSCALING` indicating a change to the feature height scaling policy.
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.
HIT_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HitStAXHandler
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 `HomologyFeature`s.
HSPSUMMARY_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler
HSPStAXHandler - class org.biojava.bio.program.ssbind.HSPStAXHandler.
  `HSPStAXHandler` handles the HSP element of BioJava BlastLike XML.
HSPSummaryStAXHandler - class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler.
  `HSPSummaryStAXHandler` handles the HSPSummary element of BioJava BlastLike XML.
HSP_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HSPStAXHandler
HTMLRenderer - class org.biojava.bio.program.blast2html.HTMLRenderer.
  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.
HashSequenceDB - class org.biojava.bio.seq.db.HashSequenceDB.
  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(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(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, 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.
Havg - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Hydrogen average mass
HeaderStAXHandler - class org.biojava.bio.program.ssbind.HeaderStAXHandler.
  `HeaderStAXHandler` handles the Header element of BioJava BlastLike XML.
HeadlessRenderContext - class org.biojava.bio.gui.sequence.HeadlessRenderContext.
  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
HitMerger - class org.biojava.bio.program.ssaha.HitMerger.
  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 org.biojava.bio.program.ssbind.HitStAXHandler.
  `AlignmentStAXHandler` handles the Hit element of BioJava BlastLike XML.
HmmerProfileHMM - class org.biojava.bio.program.hmmer.HmmerProfileHMM.
  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 org.biojava.bio.program.hmmer.HmmerProfileParser.
  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
Hmono - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Hydrogen monoisotopic mass
Homology - interface org.biojava.bio.seq.homol.Homology.
  Signifies that two or more features are homologous.
HomologyDB - interface org.biojava.bio.seq.homol.HomologyDB.
HomologyFeature - interface org.biojava.bio.seq.homol.HomologyFeature.
HomologyFeature.Template - class org.biojava.bio.seq.homol.HomologyFeature.Template.
HomologyFeature.Template() - Constructor for class org.biojava.bio.seq.homol.HomologyFeature.Template
h() - Static method in class org.biojava.bio.seq.NucleotideTools
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.HitStAXHandler
handleEndElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
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.HitStAXHandler
handleStartElement(String, String, String, Attributes) - 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.
hasAnnotation(Object) - Static method in class org.biojava.bio.seq.FilterUtils
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
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.
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
hasListeners(String) - Method in class org.biojava.bio.gui.StackedLogoPainter
hasListeners(String) - Method in class org.biojava.bio.gui.TextLogoPainter
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.program.das.ReferenceServer
hasListeners() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
hasListeners() - Method in class org.biojava.utils.AbstractChangeable
hasListeners() - Method in class org.biojava.utils.ChangeSupport
hasMoreElements() - Method in class org.biojava.bio.seq.ragbag.RagbagMap.MapEnum
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.dp.DP.ReverseIterator
hasNext() - Method in class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
hasNext() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Method
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 class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
hasNext() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
hasNext() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
hasNext() - Method in interface org.biojava.bio.seq.SequenceIterator
  Returns whether there are more sequences to iterate over.
hasNext() - Method in class org.biojava.bio.seq.io.StreamReader
hasNext() - Method in class org.biojava.bio.symbol.Alignment.SymbolListIterator
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
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.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.gui.sequence.SequencePanel
hashCode() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
hashCode() - Method in class org.biojava.bio.program.das.DataSource
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.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.db.SimpleSequenceDBInstallation
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
hashCode() - Method in interface org.biojava.bio.taxa.Taxon
  The hash-code of a Taxon is equal to the hash-code of it's scientific name.
hashCode() - Method in class org.biojava.utils.ListTools.Doublet
hashCode() - Method in class org.biojava.utils.ListTools.Triplet
hashCode(int, boolean) - 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, float) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, double) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, boolean[]) - 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, float[]) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, double[]) - 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
hashCode() - Method in class org.biojava.utils.TypedProperties
hashCode() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
heads() - Method in interface org.biojava.bio.dp.MarkovModel
  The number of heads on this model.
heads() - Method in class org.biojava.bio.dp.SimpleMarkovModel
heads() - Method in class org.biojava.bio.dp.WMAsMM
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.HitMerger
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.
hmm() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
  Gets the inner HmmerProfileHMM state
hmm - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
homology - Variable in class org.biojava.bio.seq.homol.HomologyFeature.Template
hotSpots() - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide
hotSpots() - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide
hotSpots() - Method in interface org.biojava.bio.gui.sequence.ImageMap
  `hotSpots` iterates over the hotspots in the map

## I

IDMaker - interface org.biojava.bio.seq.db.IDMaker.
  Interface for objects that define how to make an ID for a sequence.
IDMaker.ByName - class org.biojava.bio.seq.db.IDMaker.ByName.
IDMaker.ByName() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByName
IDMaker.ByURN - class org.biojava.bio.seq.db.IDMaker.ByURN.
IDMaker.ByURN() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByURN
ID_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
IG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `IG` indicates that the sequence format is IG.
INDENT - Static variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  use a two space indent
INDEX - Static variable in interface org.biojava.bio.symbol.AlphabetIndex
  Indicates that the index is changing, probably due to the underlying alphabet changing.
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").
INSTANCE - Static variable in class org.biojava.bio.gui.sequence.LayeredRenderer
  Static `LayeredRenderer` `INSTANCE` used by `MultiLineRenderer`s.
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
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.
INVERT_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the invertebrate mitochondrial genetic code.
Identifiable - interface org.biojava.utils.lsid.Identifiable.
  Marks an implementor as having a LifeScienceIdentifier.
IgnoreCountsTrainer - class org.biojava.bio.dist.IgnoreCountsTrainer.
  A distribution trainer that just ignores all counts.
IgnoreCountsTrainer() - Constructor for class org.biojava.bio.dist.IgnoreCountsTrainer
IgnoreRecordException - exception org.biojava.bio.program.gff.IgnoreRecordException.
  Ignore this record in the stream.
IgnoreRecordException() - Constructor for class org.biojava.bio.program.gff.IgnoreRecordException
IllegalAlignmentEditException - exception org.biojava.bio.alignment.IllegalAlignmentEditException.
  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 class org.biojava.bio.alignment.IllegalAlignmentEditException
  Just make the exception.
IllegalAlignmentEditException(String) - Constructor for class org.biojava.bio.alignment.IllegalAlignmentEditException
  Make the exception with a message.
IllegalAlignmentEditException(Throwable) - Constructor for class org.biojava.bio.alignment.IllegalAlignmentEditException
IllegalAlignmentEditException(Throwable, String) - Constructor for class org.biojava.bio.alignment.IllegalAlignmentEditException
IllegalAlphabetException - exception org.biojava.bio.symbol.IllegalAlphabetException.
  The exception to indicate that an invalid alphabet has been used.
IllegalAlphabetException() - Constructor for class org.biojava.bio.symbol.IllegalAlphabetException
  Just make the exception.
IllegalAlphabetException(String) - Constructor for class org.biojava.bio.symbol.IllegalAlphabetException
  Make the exception with a message.
IllegalAlphabetException(Throwable) - Constructor for class org.biojava.bio.symbol.IllegalAlphabetException
IllegalAlphabetException(Throwable, String) - Constructor for class org.biojava.bio.symbol.IllegalAlphabetException
IllegalIDException - exception org.biojava.bio.seq.db.IllegalIDException.
IllegalIDException() - Constructor for class org.biojava.bio.seq.db.IllegalIDException
IllegalIDException(Throwable) - Constructor for class org.biojava.bio.seq.db.IllegalIDException
IllegalIDException(String) - Constructor for class org.biojava.bio.seq.db.IllegalIDException
IllegalIDException(Throwable, String) - Constructor for class org.biojava.bio.seq.db.IllegalIDException
IllegalSymbolException - exception org.biojava.bio.symbol.IllegalSymbolException.
  The exception to indicate that a symbol is not valid within a context.
IllegalSymbolException(String) - Constructor for class org.biojava.bio.symbol.IllegalSymbolException
  Make the exception with a message.
IllegalSymbolException(Symbol, String) - Constructor for class org.biojava.bio.symbol.IllegalSymbolException
  Make the exception with a message and a symbol.
IllegalSymbolException(Throwable, String) - Constructor for class org.biojava.bio.symbol.IllegalSymbolException
IllegalSymbolException(Throwable, Symbol, String) - Constructor for class org.biojava.bio.symbol.IllegalSymbolException
IllegalTransitionException - exception org.biojava.bio.dp.IllegalTransitionException.
  This exception indicates that there is no transition between two states.
IllegalTransitionException(State, State, String) - Constructor for class org.biojava.bio.dp.IllegalTransitionException
IllegalTransitionException(State, State) - Constructor for class org.biojava.bio.dp.IllegalTransitionException
IllegalTransitionException() - Constructor for class org.biojava.bio.dp.IllegalTransitionException
ImageMap - interface org.biojava.bio.gui.sequence.ImageMap.
  `ImageMap` represents a collection of image map hotspots.
ImageMap.ClientSide - class org.biojava.bio.gui.sequence.ImageMap.ClientSide.
  `ClientSide` represents a client-side style image map.
ImageMap.ClientSide(String) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ClientSide
  Creates a new `ClientSide` image map.
ImageMap.HotSpot - class org.biojava.bio.gui.sequence.ImageMap.HotSpot.
  `HotSpot`s represent an image map hotspot.
ImageMap.HotSpot(String, URL, Integer[]) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.HotSpot
  Creates a new `HotSpot` with a null user object.
ImageMap.HotSpot(String, URL, Integer[], Object) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.HotSpot
  Creates a new `HotSpot`.
ImageMap.ServerSide - class org.biojava.bio.gui.sequence.ImageMap.ServerSide.
  `ServerSide` represents a server-side style image map.
ImageMap.ServerSide() - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ServerSide
  Creates a new `ServerSide` image map.
ImageMapRenderer - interface org.biojava.bio.gui.sequence.ImageMapRenderer.
  `ImageMapRenderer`s create strings representing `Feature`s suitable for use in HTML image maps.
Index - interface org.biojava.bio.seq.db.Index.
  This defines an index entry for an individual sequence within a set of indexed files.
Index2Model - class org.biojava.bio.program.tagvalue.Index2Model.
Index2Model() - Constructor for class org.biojava.bio.program.tagvalue.Index2Model
IndexStore - interface org.biojava.bio.program.indexdb.IndexStore.
  `IndexStore` is an interface for indexing flatfiles according to the OBDA specification.
IndexStore - interface org.biojava.bio.seq.db.IndexStore.
  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.
IndexTools - class org.biojava.bio.program.indexdb.IndexTools.
  `IndexTools` contains static utility methods for creating flatfile indices according to the OBDA standard.
IndexedChangeHub - class org.biojava.utils.IndexedChangeHub.
  implements Changeable support with a ChangeHub that stores ChangeListener by key.
IndexedChangeHub() - Constructor for class org.biojava.utils.IndexedChangeHub
IndexedChangeHub.ListenerMemento - class org.biojava.utils.IndexedChangeHub.ListenerMemento.
IndexedChangeHub.ListenerMemento(ChangeType, Reference) - Constructor for class org.biojava.utils.IndexedChangeHub.ListenerMemento
IndexedCount - class org.biojava.bio.dist.IndexedCount.
  An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.
IndexedCount(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.IndexedCount
IndexedCount(AlphabetIndex) - Constructor for class org.biojava.bio.dist.IndexedCount
IndexedSequenceDB - class org.biojava.bio.seq.db.IndexedSequenceDB.
  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.
Indexer - class org.biojava.bio.program.tagvalue.Indexer.
  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 org.biojava.bio.program.tagvalue.Indexer2.
  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.
Initializable - interface org.biojava.utils.xml.Initializable.
IntElementHandlerBase - class org.biojava.utils.stax.IntElementHandlerBase.
  StAX handler for any element which just contains a string representation of an integer.
IntElementHandlerBase() - Constructor for class org.biojava.utils.stax.IntElementHandlerBase
IntegerAlphabet - class org.biojava.bio.symbol.IntegerAlphabet.
  An efficient implementation of an Alphabet over the infinite set of integer values.
IntegerAlphabet.IntegerSymbol - class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol.
  A single int value.
IntegerAlphabet.IntegerSymbol(int) - Constructor for class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
IntegerAlphabet.SubIntegerAlphabet - class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet.
  A class to represent a finite contiguous subset of the infinite IntegerAlphabet
IntegerTokenization - class org.biojava.bio.seq.io.IntegerTokenization.
IntegerTokenization() - Constructor for class org.biojava.bio.seq.io.IntegerTokenization
IsoelectricPointCalc - class org.biojava.bio.proteomics.IsoelectricPointCalc.
  class that computes isoelectric point for proteins
IsoelectricPointCalc() - Constructor for class org.biojava.bio.proteomics.IsoelectricPointCalc
IsoelectricPointCalc.ChargeCalculator - class org.biojava.bio.proteomics.IsoelectricPointCalc.ChargeCalculator.
ItemValue - interface org.biojava.stats.svm.ItemValue.
  A simple Object-double tuple.
iNumberOfColours - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
  The number of unique colours.
identifier - Variable in class org.biojava.bibliography.BibRef
  It is an unambiguous reference to this citation "within the world".
identifyFormat(String, String) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  `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.
ids() - Method in class org.biojava.bio.program.das.DASSequenceDB
ids() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
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.db.biosql.BioSQLSequenceDB
ids(boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
  Get the complete set of sequence IDs provided by this DistDataSource.
ids() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
ids(boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
ids(boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
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
ignorableWhitespace(char[], int, int) - Method in class org.biojava.utils.xml.XMLPeerBuilder
importTaxon(Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
importTaxon(Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
  Import a Taxon and all its children into the implementation provided by this factory.
importTaxon(Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
in - Variable in class org.biojava.utils.io.CachingInputStream
  The underlying input stream whose data we're caching
inFeature() - Method in class org.biojava.bio.seq.io.FeatureTableParser
incCounts(int, int) - Method in class org.biojava.bio.symbol.SuffixTree
increaseCount(AtomicSymbol, double) - Method in interface org.biojava.bio.dist.Count
  Set the probability or odds that Symbol s is emited 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
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.
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.
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.
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.
init() - Method in interface org.biojava.utils.xml.Initializable
initialiseProfileHMM(int) - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
initialize(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator
  Initialize the cell at [0][0] to the recursion initial parameters.
initialize() - Method in class org.biojava.bio.seq.db.TabIndexStore
initializeVariables(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver) - Method in class org.biojava.bio.symbol.FuzzyLocation
  Refactored initialization code from the constructors.
input - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
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.
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
intValue() - Method in 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.
internalClassify(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
intersection(AnnotationType, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
  Calculate an AnnotationType that matches all Annotation instances matched by both types.
intersection(PropertyConstraint, PropertyConstraint) - Static method in class org.biojava.bio.AnnotationTools
  Calculate the intersection of two PropertyConstraint instances.
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(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, Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Return the intersection of two locations.
invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
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, 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 class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
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, 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 class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
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, 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 class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
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, 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 class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
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.GFFWriter
isActive() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `isActive` returns true if both the `Sequence`s 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.SequencePoster
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.
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.
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.
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.
isEndoProtease() - Method in class org.biojava.bio.proteomics.Protease
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
isMyChangeEvent(ChangeEvent, IndexedChangeHub.ListenerMemento) - Method in class org.biojava.utils.IndexedChangeHub
isNewTag() - Method in class org.biojava.bio.program.tagvalue.TagValue
isOppositeStrand() - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
  Return true if projected features should be flipped to the opposite strand
isPalindromic() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `isPalindromic` returns true if the recognition site is palindromic.
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.
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.
isRemote() - Method in class org.biojava.bio.seq.RemoteFeature.Region
  Return whether this Region is remote or local.
isScaleByInformation() - Method in class org.biojava.bio.gui.DistributionLogo
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.
isTerminal() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
  Determine is this node is terminal (has no children).
isTrainingComplete(TrainingAlgorithm) - Method in interface org.biojava.bio.dp.StoppingCriteria
  Decide if the training has completed.
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
isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
isUnchanging(ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.SubSequence
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
isUnchanging(ChangeType) - Method in class org.biojava.utils.AbstractChangeable
isUnchanging(ChangeType) - Method in class org.biojava.utils.ChangeSupport
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.Unchangeable
isbn - Variable in class org.biojava.bibliography.BiblioBook
issn - Variable in class org.biojava.bibliography.BiblioJournal
  A standard number for journals.
issue - Variable in class org.biojava.bibliography.BiblioJournalArticle
issueSupplement - Variable in class org.biojava.bibliography.BiblioJournalArticle
itemAlphas() - Method in interface org.biojava.stats.svm.SVMClassifierModel
itemAlphas() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
itemTargets() - Method in interface org.biojava.stats.svm.SVMTarget
itemTargets() - 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
items() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
items() - Method in class org.biojava.stats.svm.SimpleSVMTarget
iterator() - Method in class org.biojava.bio.dp.SimpleStatePath
iterator() - Method in class org.biojava.bio.program.das.DASSequence
iterator() - Method in class org.biojava.bio.seq.DummySequence
iterator() - Method in class org.biojava.bio.seq.SimpleAssembly
iterator() - Method in class org.biojava.bio.seq.SubSequence
iterator() - Method in class org.biojava.bio.seq.ViewSequence
iterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
iterator() - Method in class org.biojava.bio.seq.impl.SimpleSequence
iterator() - Method in class org.biojava.bio.symbol.AbstractSymbolList
iterator() - Method in interface org.biojava.bio.symbol.FiniteAlphabet
  Retrieve an Iterator over the Symbols 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.SymbolList.EmptySymbolList
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.SmallSet

## J

JDBCConnectionPool - class org.biojava.utils.JDBCConnectionPool.
  Really simple connection pool for JDBC databases
JDBCConnectionPool(String, String, String) - Constructor for class org.biojava.utils.JDBCConnectionPool
JDBCConnectionPool(String) - Constructor for class org.biojava.utils.JDBCConnectionPool
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
JOURNAL_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
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
jointDistOverAlignment(Alignment, boolean, double, int[]) - Static method in class org.biojava.bio.dist.DistributionTools
  Creates a joint distribution
jumpTo(UkkonenSuffixTree.SuffixNode, String, 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

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.
KEYWORDS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
KEYWORDS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
KLDistance(Distribution, Distribution, double) - Static method in class org.biojava.bio.dist.DistributionTools
  A method to calculate the Kullback-Liebler Distance (relative entropy)
KeyedWeakReference - class org.biojava.utils.cache.KeyedWeakReference.
  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
KnuthMorrisPrattSearch - class org.biojava.bio.search.KnuthMorrisPrattSearch.
  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.
k() - Static method in class org.biojava.bio.seq.NucleotideTools
kernel - Static variable in class org.biojava.stats.svm.SparseVector
keySet() - Method in class org.biojava.utils.OverlayMap
keySet() - Method in class org.biojava.utils.SmallMap
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
  Return a `Set` containing all key objects visible in this annotation.
keys() - Method in class org.biojava.bio.OverlayAnnotation
  Return a `Set` containing all key objects visible in this annotation.
keywords - Variable in class org.biojava.bibliography.BiblioSubject
  The keywords are usually (but not limited to) one word long.

## L

LABEL - Static variable in class org.biojava.bio.gui.sequence.AlignmentRenderer
LABEL_MAKER - Static variable in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
LANGUAGES - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
LAYOUT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext
LIBRARY_ANNOTATION - Static variable in class org.biojava.bio.program.unigene.UnigeneTools
  Annotation schema for all Unigene libraries.
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.
LOCUS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
LOG_TO_OUT - Static variable in interface org.biojava.utils.ChangeListener
  Convenience implementation that echoes all events to out.
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_C - Static variable in class org.biojava.bio.proteomics.Protease
LYS_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager
LabelRenderer - interface org.biojava.bio.gui.sequence.LabelRenderer.
  The interface for things that can render labels for a line of information about a sequence.
LabelRenderer.RenderNothing - class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing.
LabelRenderer.RenderNothing() - Constructor for class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
LabelledSequenceRenderer - class org.biojava.bio.gui.sequence.LabelledSequenceRenderer.
  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.
LargeBuffer - class org.biojava.utils.io.LargeBuffer.
  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
LayeredRenderer - class org.biojava.bio.gui.sequence.LayeredRenderer.
  `LayeredRenderer` handles the lane offsets for `MultiLineRender`s.
LayeredRenderer() - Constructor for class org.biojava.bio.gui.sequence.LayeredRenderer
LazyFeatureHolder - class org.biojava.bio.seq.LazyFeatureHolder.
  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
LazyFilterFeatureHolder - class org.biojava.bio.seq.impl.LazyFilterFeatureHolder.
  FeatureHolder which lazily applies a specified filter to another FeatureHolder.
LazyFilterFeatureHolder(FeatureHolder, FeatureFilter) - Constructor for class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
LifeScienceIdentifier - class org.biojava.utils.lsid.LifeScienceIdentifier.
  Life Science Identifier (LSID).
LifeScienceIdentifierParseException - exception org.biojava.utils.lsid.LifeScienceIdentifierParseException.
  Exception thrown in the event of an error in parsing a LSID-formatted string.
LifeScienceIdentifierParseException() - Constructor for class org.biojava.utils.lsid.LifeScienceIdentifierParseException
  Construct a new parse exception with no message.
LifeScienceIdentifierParseException(String) - Constructor for class org.biojava.utils.lsid.LifeScienceIdentifierParseException
  Construct a new parse exception with the specified error message.
LightPairDPCursor - class org.biojava.bio.dp.twohead.LightPairDPCursor.
  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
LineInfo - class org.biojava.bio.gui.sequence.LineInfo.
  Encapsulates the rendering info for a single line of the display.
LineInfo() - Constructor for class org.biojava.bio.gui.sequence.LineInfo
LineSplitParser - class org.biojava.bio.program.tagvalue.LineSplitParser.
  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
LinearKernel - class org.biojava.stats.svm.LinearKernel.
  Deprecated. Just use SparseVector.kernel instead...
LinearKernel() - Constructor for class org.biojava.stats.svm.LinearKernel
  Deprecated.
ListSumKernel - class org.biojava.stats.svm.ListSumKernel.
  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 org.biojava.utils.ListTools.
ListTools() - Constructor for class org.biojava.utils.ListTools
ListTools.Doublet - class org.biojava.utils.ListTools.Doublet.
ListTools.Doublet() - Constructor for class org.biojava.utils.ListTools.Doublet
ListTools.Doublet(Object, Object) - Constructor for class org.biojava.utils.ListTools.Doublet
ListTools.Triplet - class org.biojava.utils.ListTools.Triplet.
ListTools.Triplet() - Constructor for class org.biojava.utils.ListTools.Triplet
ListTools.Triplet(Object, Object, Object) - Constructor for class org.biojava.utils.ListTools.Triplet
Location - interface org.biojava.bio.symbol.Location.
  A set of integers, often used to represent positions on biological sequences.
LocationHandlerBase - class org.biojava.bio.program.xff.LocationHandlerBase.
  Handler to the XFF location type.
LocationHandlerBase() - Constructor for class org.biojava.bio.program.xff.LocationHandlerBase
LocationTools - class org.biojava.bio.symbol.LocationTools.
  Tools class containing a number of operators for working with `Location` objects.
LocusLinkParser - class org.biojava.bio.seq.db.LocusLinkParser.
LocusLinkParser(String) - Constructor for class org.biojava.bio.seq.db.LocusLinkParser
LogoContext - interface org.biojava.bio.gui.LogoContext.
LogoPainter - interface org.biojava.bio.gui.LogoPainter.
  The interface for something that will draw the sequence logo for a state.
LongElementHandlerBase - class org.biojava.utils.stax.LongElementHandlerBase.
  StAX handler for any element which just contains a string representation of a long.
LongElementHandlerBase() - Constructor for class org.biojava.utils.stax.LongElementHandlerBase
label - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement
labelOrder - Variable in class org.biojava.bio.alignment.FlexibleAlignment
labelsAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
labelsAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment
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.SubULAlignment
labelsInRange(Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment
labelsInRange(Location) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment
  Returns list of all the labels that intersect that range
language - Variable in class org.biojava.bibliography.BibRef
  It defines a language of the intellectual contents of the cited resource.
language - Variable in class org.biojava.bibliography.BiblioDescription
  It defines a language used for `BiblioDescription.theAbstract` and `BiblioDescription.tableOfContents`.
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
layer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
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
leftMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment
  leftMost and rightMost return labels.
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.dp.SimpleStatePath
length() - Method in class org.biojava.bio.program.das.DASSequence
length() - Method in class org.biojava.bio.seq.DummySequence
length() - Method in class org.biojava.bio.seq.SimpleAssembly
length() - Method in class org.biojava.bio.seq.SubSequence
length() - Method in class org.biojava.bio.seq.ViewSequence
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.SimpleSequence
length() - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
length() - Method in class org.biojava.bio.symbol.DummySymbolList
length - Variable in class org.biojava.bio.symbol.Edit
length() - Method in class org.biojava.bio.symbol.PackedDnaSymbolList
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.SimpleAlignment
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 class org.biojava.bio.symbol.SymbolList.EmptySymbolList
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`.
lesser(int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
line - Variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  `line` is the line to be drawn for each feature.
lineIterator() - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Loop over all lines in the set.
listIntersection(List, List) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
listener - Variable in class org.biojava.utils.IndexedChangeHub.ListenerMemento
load(File) - Method in class org.biojava.bio.program.abi.ABIFChromatogram
load(InputStream) - Method in class org.biojava.bio.program.abi.ABIFChromatogram
load(File) - Method in class org.biojava.bio.program.scf.SCF
load(InputStream, long) - Method in class org.biojava.bio.program.scf.SCF
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.
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.
loadAlphabets(InputSource) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Load additional Alphabets, defined in XML format, into the AlphabetManager's registry.
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
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
location - Variable in class org.biojava.bio.seq.Feature.Template
locationToGapped(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Translate a Location onto the gapped view, splitting blocks if necessary
lockModel() - Method in class org.biojava.bio.dp.DP
log2(double) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
log2(double) - Static method in class org.biojava.bio.program.hmmer.ProfileEmissionState
logProb(Symbol) - Method in class org.biojava.bio.program.hmmer.ProfileEmissionState
lookup(String) - Static method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Looks up an `Option` instance based on its string description.

## M

META_DATA_TYPE - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
  AnnotationType that all meta-data files should fit.
MOLD_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the mold mitochondrial genetic code.
MONO_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
MSF - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `MSF` indicates that the alignment format is MSF.
MSFAlignmentFormat - class org.biojava.bio.seq.io.MSFAlignmentFormat.
MSFAlignmentFormat() - Constructor for class org.biojava.bio.seq.io.MSFAlignmentFormat
MSFDNA - Static variable in class org.biojava.bio.seq.io.SeqAlignReadWrite
MSFPROTEIN - Static variable in class org.biojava.bio.seq.io.SeqAlignReadWrite
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;
MagicalState - class org.biojava.bio.dp.MagicalState.
  Start/end state for HMMs.
MappedDataStoreFactory - class org.biojava.bio.program.ssaha.MappedDataStoreFactory.
  Builder for a data store that is backed by a java.nio.MappedByteBuffer.
MappedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.MappedDataStoreFactory
MarkovModel - interface org.biojava.bio.dp.MarkovModel.
  A markov model.
MarkovModel.DistributionForwarder - class org.biojava.bio.dp.MarkovModel.DistributionForwarder.
  Add this as a listener to each distribution in a model.
MarkovModel.DistributionForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.dp.MarkovModel.DistributionForwarder
MassCalc - class org.biojava.bio.proteomics.MassCalc.
  `MassCalc` calculates the mass of peptides which for our purposes are `SymbolList`s which contain `Symbol`sfrom the protein `Alphabet`.
MassCalc(String, boolean) - Constructor for class org.biojava.bio.proteomics.MassCalc
  Creates a new `MassCalc`.
MatrixPairDPCursor - class org.biojava.bio.dp.twohead.MatrixPairDPCursor.
MatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.MatrixPairDPCursor
Meme - class org.biojava.bio.program.Meme.
  The results of a meme run.
Meme(InputStream, SymbolTokenization) - Constructor for class org.biojava.bio.program.Meme
MergeAnnotation - class org.biojava.bio.MergeAnnotation.
  Merged view onto a list of underlying Annotation objects.
MergeAnnotation() - Constructor for class org.biojava.bio.MergeAnnotation
MergeAnnotation.PropertyForwarder - class org.biojava.bio.MergeAnnotation.PropertyForwarder.
MergeAnnotation.PropertyForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.MergeAnnotation.PropertyForwarder
MergeFeatureHolder - class org.biojava.bio.seq.MergeFeatureHolder.
  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 org.biojava.bio.symbol.MergeLocation.
  Produced by LocationTools as a result of union operations.
ModelInState - interface org.biojava.bio.dp.ModelInState.
  A state that contains an entire sub-model.
ModelTrainer - interface org.biojava.bio.dp.ModelTrainer.
  Encapsulates the training of an entire model.
MotifTools - class org.biojava.bio.symbol.MotifTools.
  `MotifTools` contains utility methods for sequence motifs.
MotifTools() - Constructor for class org.biojava.bio.symbol.MotifTools
MultiLineRenderer - class org.biojava.bio.gui.sequence.MultiLineRenderer.
  `MultiLineRenderer` is a `SequenceRenderer` which collects a number of other `SequenceRenderer`s each of which render their own view of a `Sequence`.
MultiLineRenderer() - Constructor for class org.biojava.bio.gui.sequence.MultiLineRenderer
MySQLDBHelper - class org.biojava.bio.seq.db.biosql.MySQLDBHelper.
MySQLDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.MySQLDBHelper
m() - Static method in class org.biojava.bio.seq.NucleotideTools
mAnnotFilter - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  The AnnotationMap to use for getting AGAVE XML attributes from a Sequence Annotation.
mFilter - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  writes PCDATA replacing XML characters with escape entities
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
mOut - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  Write to XML document
mWriteDocType - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  write DOCTYPE if true
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
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.bio.seq.io.SeqAlignReadWrite
  Just for testing purposes.
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.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.
makeAnnotation(Map) - Static method in class org.biojava.bio.program.ssbind.AnnotationFactory
  `makeAnnotation` creates the annotation.
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.
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
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.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
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
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 class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.EmblProcessor.Factory
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.GenbankProcessor.Factory
makeSequenceBuilder(String) - Method in class org.biojava.bio.seq.io.GenbankProcessor.Factory
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.OrganismParser.Factory
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory
makeSequenceBuilder() - Method in interface org.biojava.bio.seq.io.SequenceBuilderFactory
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.SwissprotProcessor.Factory
makeSequenceBuilder(String) - Method in class org.biojava.bio.seq.io.SwissprotProcessor.Factory
makeSubjectViewSequence(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
makeSymbolList() - Method in class org.biojava.bio.seq.io.ChunkedSymbolListBuilder
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
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.biojava.bio.seq.projection.ProjectedStrandedFeature
map(Set) - Method in class org.biojava.bio.symbol.RelabeledAlignment
map(Object) - Method in class org.biojava.bio.symbol.RelabeledAlignment
mapTag(String, XMLPeerFactory) - Method in class org.biojava.utils.xml.XMLDispatcher
  Add an XMLPeerFactory which constructs objects corresponding to a specific XML tag.
mark(int) - Method in class org.biojava.utils.io.CountedBufferedReader
markSupported() - Method in class org.biojava.utils.io.CountedBufferedReader
matchingTypes() - Method in class org.biojava.utils.ChangeType
  Return an iterator which contains this type, and all supertypes.
max - Variable in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
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
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
midInitials - Variable in class org.biojava.bibliography.BiblioPerson
min - Variable in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
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
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
mutuallyExclusiveWith - Variable in class org.biojava.bibliography.BiblioCriterion
  A list of other criteria names that this criterion is mutually exclusive with.
myLocalName - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler

## N

NAMESPACE - Static variable in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
NBRF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `NBRF` indicates that the sequence format is NBRF.
NCBISequenceDB - class org.biojava.bio.seq.db.NCBISequenceDB.
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, SequenceFormat) - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB
  Parameterized constructor
NCBISequenceDB(String, String, String, SequenceFormat) - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB
  Parameterized constructor
NEGATIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature
  Flag to indicate that a feature is on the negative strand.
NIODataStoreFactory - class org.biojava.bio.program.ssaha.NIODataStoreFactory.
  Builder for a datastore that has no practical file size limit.
NIODataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.NIODataStoreFactory
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.
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_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.
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
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
NameTokenization - class org.biojava.bio.seq.io.NameTokenization.
  Simple implementation of SymbolTokenization which uses the `name' field of the symbols.
NameTokenization(FiniteAlphabet, boolean) - Constructor for class org.biojava.bio.seq.io.NameTokenization
NameTokenization(FiniteAlphabet) - Constructor for class org.biojava.bio.seq.io.NameTokenization
  Construct a new NameTokenization, defaulting to case-insensitive.
Navg - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Nitrogen average mass
NcbiDatabaseURLGenerator - class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator.
  Simple URL generator for Entrez at the NCBI.
NcbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator
NestedError - error org.biojava.utils.NestedError.
  A general purpose Error that can wrap another Throwable object.
NestedError(String) - Constructor for class org.biojava.utils.NestedError
NestedError(Throwable) - Constructor for class org.biojava.utils.NestedError
NestedError(Throwable, String) - Constructor for class org.biojava.utils.NestedError
NestedError() - Constructor for class org.biojava.utils.NestedError
NestedException - exception org.biojava.utils.NestedException.
  A general perpose Exception that can wrap another exception.
NestedException(String) - Constructor for class org.biojava.utils.NestedException
NestedException(Throwable) - Constructor for class org.biojava.utils.NestedException
NestedException(Throwable, String) - Constructor for class org.biojava.utils.NestedException
NestedException() - Constructor for class org.biojava.utils.NestedException
NestedKernel - class org.biojava.stats.svm.NestedKernel.
  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.
NestedRuntimeException - exception org.biojava.utils.NestedRuntimeException.
  A general perpose RuntimeException that can wrap another exception.
NestedRuntimeException(String) - Constructor for class org.biojava.utils.NestedRuntimeException
NestedRuntimeException(Throwable) - Constructor for class org.biojava.utils.NestedRuntimeException
NestedRuntimeException(Throwable, String) - Constructor for class org.biojava.utils.NestedRuntimeException
NestedRuntimeException() - Constructor for class org.biojava.utils.NestedRuntimeException
Nmono - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Nitrogen monoisotopic mass
NormalizingKernel - class org.biojava.stats.svm.NormalizingKernel.
  Performs a normalization on the results of a nested kernel.
NormalizingKernel() - Constructor for class org.biojava.stats.svm.NormalizingKernel
NormalizingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NormalizingKernel
NucleotideTools - class org.biojava.bio.seq.NucleotideTools.
  Useful functionality for processing nucleotide sequences.
NucleotideTools() - Constructor for class org.biojava.bio.seq.NucleotideTools
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.RNATools
nState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
  Gets the n loop state
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
name - Variable in class org.biojava.bibliography.BiblioService
name - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
name - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
naturalOrder - Static variable in interface org.biojava.bio.symbol.Location
  Comparator which orders Locations naturally.
newInstance(Constructor, Object[]) - Method in interface org.biojava.bio.seq.projection.ProjectionEngine.Instantiator
newInstance(Constructor, Object[]) - Method in class org.biojava.bio.seq.projection.ProjectionEngine.InstantiatorImpl
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`.
next() - Method in class org.biojava.bio.dp.DP.ReverseIterator
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
next() - Method in class org.biojava.bio.symbol.Alignment.SymbolListIterator
nextElement() - Method in class org.biojava.bio.seq.ragbag.RagbagMap.MapEnum
nextRequest() - Method in class org.biojava.utils.SimpleThreadPool
  `nextRequest` gets the next `Runnable` from the queue.
nextSequence() - Method in interface org.biojava.bio.seq.SequenceIterator
  Returns the next sequence in the iterator.
nextSequence() - Method in class org.biojava.bio.seq.io.StreamReader
  Pull the next sequence out of the stream.
nextWord(SymbolList, int, int, int, Packing) - Static method in class org.biojava.bio.symbol.PackingFactory
nl() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
none - Static variable in interface org.biojava.bio.seq.FeatureFilter
  No features are selected by this filter.
none() - Static method in class org.biojava.bio.seq.FilterUtils
normalLengthVector(SparseVector, double) - Static method in class org.biojava.stats.svm.SparseVector
not(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblProcessor
  Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat
  Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankProcessor
  Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
  Passes the event on to all the listeners registered for ParseErrorEvents.
nucleotideToken(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
  Get a single-character token for a Nucleotide symbol
nullModelForwarder - Variable in class org.biojava.bio.dist.AbstractDistribution
numStates - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
numStates - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
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

## O

OBDARegistryParser - class org.biojava.directory.OBDARegistryParser.
  This class encapsulates all the parsing of the OBDA registry configuration file.
OBDARegistryParser() - Constructor for class org.biojava.directory.OBDARegistryParser
OBDA_SEARCH_ENV - Static variable in class org.biojava.directory.SystemRegistry
ODDS - Static variable in interface org.biojava.bio.dp.ScoreType
OFFSETS - Static variable in interface org.biojava.bio.chromatogram.Chromatogram
  The sequence label for the trace offsets of the called bases
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.
ORGANISM_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
ORGANISM_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
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
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.
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.
Oavg - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Oxygen average mass
ObjectUtil - class org.biojava.utils.ObjectUtil.
  utility methods for implementing the equals() and hashCode() methods of Objects.
ObjectUtil() - Constructor for class org.biojava.utils.ObjectUtil
Omono - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Oxygen monoisotopic mass
OptimizableFilter - interface org.biojava.bio.seq.OptimizableFilter.
  The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.
OrderNDistribution - interface org.biojava.bio.dist.OrderNDistribution.
  Provides an N'th order distribution.
OrderNDistributionFactory - class org.biojava.bio.dist.OrderNDistributionFactory.
  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.
OrganismParser - class org.biojava.bio.seq.io.OrganismParser.
  A parser that is able to generate Taxon entries for sequence builder event streams.
OrganismParser(SequenceBuilder, TaxonFactory, TaxonParser, String, String, String) - Constructor for class org.biojava.bio.seq.io.OrganismParser
OrganismParser.Factory - class org.biojava.bio.seq.io.OrganismParser.Factory.
  Factory which wraps SequenceBuilders in an OrganismParser.
OrganismParser.Factory(SequenceBuilderFactory, TaxonFactory, TaxonParser, String, String, String) - Constructor for class org.biojava.bio.seq.io.OrganismParser.Factory
OverlayAnnotation - class org.biojava.bio.OverlayAnnotation.
  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 org.biojava.bio.OverlayAnnotation.PropertyForwarder.
OverlayAnnotation.PropertyForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.OverlayAnnotation.PropertyForwarder
OverlayMap - class org.biojava.utils.OverlayMap.
  Overlap one map onto another.
OverlayMap(Map, Map) - Constructor for class org.biojava.utils.OverlayMap
  Build a new map with default key-value pairs.
OverlayMap(Map) - Constructor for class org.biojava.utils.OverlayMap
  Build a new map with default key-value pairs.
OverlayMarker - interface org.biojava.bio.gui.sequence.OverlayMarker.
  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 org.biojava.bio.gui.sequence.OverlayRendererWrapper.
  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
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.
open(File) - Static method in class org.biojava.bio.seq.db.TabIndexStore
openTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
openTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
openTag(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.
openTag(String) - Method in interface org.biojava.utils.xml.XMLWriter
  Open a new unqualified XML tag.
optimize(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
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.Option`s and values for this instance.
or(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
or(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils
orderNSymbolList(SymbolList, int) - Static method in class org.biojava.bio.symbol.SymbolListViews
  An n-th order view of another SymbolList.
orderedLables(Comparator) - Method in class org.biojava.bio.alignment.AbstractULAlignment
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
  Implementation of the `Alignment` interface.
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.sequence - package org.biojava.bio.gui.sequence
  Graphical displays of biological sequences and associated annotations.
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.das - package org.biojava.bio.program.das
  Development client for the Distributed Annotation System.
org.biojava.bio.program.gff - package org.biojava.bio.program.gff
  GFF manipulation.
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.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.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.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 into alternate coordinate systems.
org.biojava.bio.seq.ragbag - package org.biojava.bio.seq.ragbag
  The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code.
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.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.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.stax - package org.biojava.utils.stax
  The Stack API for XML (StAX).
org.biojava.utils.xml - package org.biojava.utils.xml
  Utility classes for handling and generating XML documents.
origSeq - Variable in class org.biojava.bio.seq.impl.RevCompSequence
outline - Variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  `outline` is the line colour.
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.
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, 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
overlapsOrigin() - Method in class org.biojava.bio.symbol.CircularLocation
  Does the Location overlap the origin (position 1) of the sequence?

## P

PADDING - Static variable in class org.biojava.bio.gui.sequence.PaddingRenderer
  Event type for when the size of the padding changes.
PARAMETER - Static variable in interface org.biojava.bio.dp.MarkovModel
  Signals that one or more parameters have altered.
PARSERS - Static variable in interface org.biojava.bio.symbol.Alphabet
  This signals that the available parsers have changed.
PDB - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `PDB` indicates that the sequence format is PDB.
PEPTIDE_FEATURE_TYPE - Static variable in class org.biojava.bio.proteomics.Digest
PHRED - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `PHRED` indicates that the sequence format is PHRED.
PK - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
PK_COOH - Static variable in class org.biojava.bio.proteomics.IsoelectricPointCalc
PK_NH2 - Static variable in class org.biojava.bio.proteomics.IsoelectricPointCalc
POLY - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
  `POLY` indicates a polygonal image map hotspot.
POSITIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature
  Flag to indicate that a feature is on the positive strand.
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.
PROBABILITY - Static variable in interface org.biojava.bio.dp.ScoreType
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.
PROPDETAIL_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.PropDetailHandler
PROPERTY - Static variable in interface org.biojava.bio.Annotation
  This type symbolizes that one or more properties have changed.
PROPERTY_ANNOTATIONSERVER - Static variable in class org.biojava.bio.program.das.DASSequence
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
  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
PROPERTY_FEATUREID - Static variable in class org.biojava.bio.program.das.DASSequence
PROPERTY_FEATURELABEL - Static variable in class org.biojava.bio.program.das.DASSequence
PROPERTY_GENBANK_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.GenbankProcessor
PROPERTY_GFF_SCORE - Static variable in class org.biojava.bio.program.gff.GFFEntrySet
PROPERTY_LINKS - Static variable in class org.biojava.bio.program.das.DASSequence
PROPERTY_NCBI_TAXON - Static variable in class org.biojava.bio.taxa.EbiFormat
PROPERTY_ORGANISM - Static variable in class org.biojava.bio.seq.io.OrganismParser
PROPERTY_SEQUENCEVERSION - Static variable in class org.biojava.bio.program.das.DASSequence
PROPERTY_SWISSPROT_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor
PROPERTY_SWISSPROT_COMMENT - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor
PROPERTY_SWISSPROT_FEATUREATTRIBUTE - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor
PROPERTY_XFF_ID - Static variable in class org.biojava.bio.program.xff.XFFFeatureSetHandler
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_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.
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.
PROTEIN - Static variable in class org.biojava.bio.seq.io.FastaAlignmentFormat
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.
PackedDnaSymbolList - class org.biojava.bio.symbol.PackedDnaSymbolList.
  a class that implements storage of symbols in packed form (2 symbols per byte).
PackedDnaSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.PackedDnaSymbolList
  constructor taking another symbol list.
PackedDnaSymbolList(int, byte[]) - Constructor for class org.biojava.bio.symbol.PackedDnaSymbolList
  constructor taking a byte array previously created by another PackedDnaSymbolList object.
PackedSymbolList - class org.biojava.bio.symbol.PackedSymbolList.
  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, SymbolList) - Constructor for class org.biojava.bio.symbol.PackedSymbolList
  Create a new PackedSymbolList as a packed copy of another symbol list.
PackedSymbolList(Packing, Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.PackedSymbolList
  Create a new PackedSymbolList from an array of Symbols.
PackedSymbolListFactory - class org.biojava.bio.symbol.PackedSymbolListFactory.
  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 org.biojava.bio.symbol.Packing.
  An encapsulation of the way symbols map to bit-patterns.
PackingFactory - class org.biojava.bio.symbol.PackingFactory.
  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
PaddingRenderer - class org.biojava.bio.gui.sequence.PaddingRenderer.
  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`.
PairDPCursor - interface org.biojava.bio.dp.twohead.PairDPCursor.
  A cursor over a DP matrix.
PairDPMatrix - class org.biojava.bio.dp.twohead.PairDPMatrix.
  Storage structure for intermediate values from a pairwise dynamic programming run.
PairDPMatrix(DP, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.twohead.PairDPMatrix
PairDistribution - class org.biojava.bio.dist.PairDistribution.
  Class for pairing up two independant distributions.
PairDistribution(Distribution, Distribution) - Constructor for class org.biojava.bio.dist.PairDistribution
PairwiseDP - class org.biojava.bio.dp.twohead.PairwiseDP.
  Algorithms for dynamic programming (alignments) between pairs of SymbolLists.
PairwiseDP(MarkovModel, CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.twohead.PairwiseDP
PairwiseDiagonalRenderer - class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer.
  `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`.
PairwiseFilteringRenderer - class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer.
  `PairwiseFilteringRenderer` wraps a `PairwiseSequenceRenderer` and filters the `PairwiseRenderContext`s 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 org.biojava.bio.gui.sequence.PairwiseOverlayRenderer.
  `PairwiseOverlayRenderer` allows a list of other `PairwiseSequenceRenderer`s to superimpose their output.
PairwiseOverlayRenderer() - Constructor for class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
  Creates a new, empty `PairwiseOverlayRenderer`.
PairwiseRenderContext - interface org.biojava.bio.gui.sequence.PairwiseRenderContext.
  `PairwiseRenderContext` encapsulates information required for the rendering of a pair of sequences.
PairwiseSequencePanel - class org.biojava.bio.gui.sequence.PairwiseSequencePanel.
  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 org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.
  `PairwiseSequenceRenderer`s render information about the relationship between two sequences.
PairwiseSequenceRenderer.PairwiseRendererForwarder - class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder.
  `PairwiseRendererForwarder` forward events to other renderers.
PairwiseSequenceRenderer.PairwiseRendererForwarder(PairwiseSequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder
  Creates a new `PairwiseRendererForwarder`.
ParseErrorEvent - class org.biojava.utils.ParseErrorEvent.
  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 org.biojava.utils.ParseErrorListener.
  Listener for a ParseErrorEvent.
ParseErrorSource - interface org.biojava.utils.ParseErrorSource.
  Source for a ParseErrorEvent.
ParseException - exception org.biojava.bio.seq.io.ParseException.
  ParseException should be thrown to indicate that there was a problem with parsing sequence information.
ParseException() - Constructor for class org.biojava.bio.seq.io.ParseException
ParseException(String) - Constructor for class org.biojava.bio.seq.io.ParseException
ParseException(Throwable) - Constructor for class org.biojava.bio.seq.io.ParseException
ParseException(Throwable, String) - Constructor for class org.biojava.bio.seq.io.ParseException
Parser - class org.biojava.bio.program.tagvalue.Parser.
  Encapsulate the parsing of lines from a buffered reader into tag-value events.
Parser() - Constructor for class org.biojava.bio.program.tagvalue.Parser
ParserException - exception org.biojava.utils.ParserException.
  Exception thrown when an error occurs in document parsing.
ParserException(String) - Constructor for class org.biojava.utils.ParserException
ParserException(String, String) - Constructor for class org.biojava.utils.ParserException
ParserException(String, String, int) - Constructor for class org.biojava.utils.ParserException
ParserException(String, String, int, String) - Constructor for class org.biojava.utils.ParserException
ParserException(String, String, int, String, int) - Constructor for class org.biojava.utils.ParserException
ParserException(Throwable) - Constructor for class org.biojava.utils.ParserException
ParserException(Throwable, String) - Constructor for class org.biojava.utils.ParserException
ParserException(Throwable, String, String) - Constructor for class org.biojava.utils.ParserException
ParserException(Throwable, String, String, int) - Constructor for class org.biojava.utils.ParserException
ParserException(Throwable, String, String, int, String) - Constructor for class org.biojava.utils.ParserException
ParserException(Throwable, String, String, int, String, int) - Constructor for class org.biojava.utils.ParserException
ParserListener - class org.biojava.bio.program.tagvalue.ParserListener.
  `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.
PdbSAXParser - class org.biojava.bio.program.sax.PdbSAXParser.
  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 org.biojava.bio.program.PdbToXMLConverter.
  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.
PhredFormat - class org.biojava.bio.program.phred.PhredFormat.
  Format object representing Phred Quality files.
PhredFormat() - Constructor for class org.biojava.bio.program.phred.PhredFormat
PhredSequence - class org.biojava.bio.program.phred.PhredSequence.
  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.
PhredTools - class org.biojava.bio.program.phred.PhredTools.
  PhredTools contains static methods for working with phred quality data.
PhredTools() - Constructor for class org.biojava.bio.program.phred.PhredTools
PlainBlock - class org.biojava.bio.gui.PlainBlock.
  A painter that just draws a block (or bar).
PlainBlock() - Constructor for class org.biojava.bio.gui.PlainBlock
PlainStyle - class org.biojava.bio.gui.PlainStyle.
  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
PointLocation - class org.biojava.bio.symbol.PointLocation.
  A location representing a single point.
PointLocation(int) - Constructor for class org.biojava.bio.symbol.PointLocation
PolynomialKernel - class org.biojava.stats.svm.PolynomialKernel.
  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
PostgreSQLDBHelper - class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper.
PostgreSQLDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
PrettyXMLWriter - class org.biojava.utils.xml.PrettyXMLWriter.
  Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter.
PrettyXMLWriter(PrintWriter) - Constructor for class org.biojava.utils.xml.PrettyXMLWriter
ProfileEmissionState - class org.biojava.bio.program.hmmer.ProfileEmissionState.
  A state in a HMMer model.
ProfileEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.program.hmmer.ProfileEmissionState
ProfileHMM - class org.biojava.bio.dp.ProfileHMM.
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.
ProjectedFeature - class org.biojava.bio.seq.projection.ProjectedFeature.
  Internal class used by ProjectionEngine to wrap Feature objects.
ProjectedFeature(Feature, ProjectionContext) - Constructor for class org.biojava.bio.seq.projection.ProjectedFeature
ProjectedFeatureHolder - class org.biojava.bio.seq.ProjectedFeatureHolder.
  Helper class for projecting Feature objects into an alternative coordinate system.
ProjectedFeatureHolder(FeatureHolder, FeatureFilter, FeatureHolder, int, boolean) - Constructor for class org.biojava.bio.seq.ProjectedFeatureHolder
  Deprecated. Now just wraps up a LazyFilterFeatureHolder
ProjectedFeatureHolder(FeatureHolder, FeatureHolder, int, boolean) - Constructor for class org.biojava.bio.seq.ProjectedFeatureHolder
  Construct a new FeatureHolder which projects a set of features into a new coordinate system.
ProjectedStrandedFeature - class org.biojava.bio.seq.projection.ProjectedStrandedFeature.
  Internal class used by ProjectedFeatureHolder to wrap StrandedFeatures.
ProjectedStrandedFeature(StrandedFeature, ProjectionContext) - Constructor for class org.biojava.bio.seq.projection.ProjectedStrandedFeature
Projection - interface org.biojava.bio.seq.projection.Projection.
  Interface implemented by all projected feature objects.
ProjectionContext - interface org.biojava.bio.seq.projection.ProjectionContext.
  Context for projected features.
ProjectionEngine - class org.biojava.bio.seq.projection.ProjectionEngine.
  Factory for proxy objects which project BioJava features into alternate coordinate systems.
ProjectionEngine.Instantiator - interface org.biojava.bio.seq.projection.ProjectionEngine.Instantiator.
  Internal helper class.
ProjectionEngine.InstantiatorImpl - class org.biojava.bio.seq.projection.ProjectionEngine.InstantiatorImpl.
  Internal helper class.
ProjectionEngine.InstantiatorImpl() - Constructor for class org.biojava.bio.seq.projection.ProjectionEngine.InstantiatorImpl
ProjectionUtils - class org.biojava.bio.seq.projection.ProjectionUtils.
ProjectionUtils() - Constructor for class org.biojava.bio.seq.projection.ProjectionUtils
PropDetailHandler - class org.biojava.bio.program.xff.PropDetailHandler.
  StAX handler for xff:prop detail elements.
PropDetailHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.PropDetailHandler
PropertyConstraint - interface org.biojava.bio.PropertyConstraint.
  `PropertyConstraint`s describes a constraint applied to the members of an annotation bundle.
PropertyConstraint.And - class org.biojava.bio.PropertyConstraint.And.
  A property constraint that accpepts items iff they are accepted by both child constraints.
PropertyConstraint.And(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.And
  Create a new `And` from two child constraints.
PropertyConstraint.ByAnnotationType - class org.biojava.bio.PropertyConstraint.ByAnnotationType.
  `ByAnnotationType` accepts a property value if it belongs to type defined by AnnotationType.
PropertyConstraint.ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.PropertyConstraint.ByAnnotationType
  Create a new constraint by type.
PropertyConstraint.ByClass - class org.biojava.bio.PropertyConstraint.ByClass.
  `ByClass` accepts a property value if it is an instance of a specific Java class.
PropertyConstraint.ByClass(Class) - Constructor for class org.biojava.bio.PropertyConstraint.ByClass
  Create a new ByClass instance.
PropertyConstraint.Enumeration - class org.biojava.bio.PropertyConstraint.Enumeration.
  `Enumeration` accepts a property if it is present in the specified set of values.
PropertyConstraint.Enumeration(Set) - Constructor for class org.biojava.bio.PropertyConstraint.Enumeration
  Creates a new `Enumeration` using the members of the specified set as a constraint.
PropertyConstraint.Enumeration(Object[]) - Constructor for class org.biojava.bio.PropertyConstraint.Enumeration
  Creates a new `Enumeration` using the elements of the specified array as a constraint.
PropertyConstraint.ExactValue - class org.biojava.bio.PropertyConstraint.ExactValue.
  Matches properties if they have exactly this one value.
PropertyConstraint.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).
PropertyConstraint.Or - class org.biojava.bio.PropertyConstraint.Or.
  A property constraint that accepts items iff they are accepted by either child constraints.
PropertyConstraint.Or(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.Or
  Create a new `Or` from two child constraints.
PropertyWriter - class org.biojava.bio.program.xff.PropertyWriter.
PropertyWriter() - Constructor for class org.biojava.bio.program.xff.PropertyWriter
Protease - class org.biojava.bio.proteomics.Protease.
  The protease class stores parameters needed by Digest to digest a protein sequence.
Protease(SymbolList, boolean, SymbolList, String) - Constructor for class org.biojava.bio.proteomics.Protease
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(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(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())
ProteaseManager - class org.biojava.bio.proteomics.ProteaseManager.
  Registry and utility methods for Proteases.
ProteaseManager() - Constructor for class org.biojava.bio.proteomics.ProteaseManager
ProteinRefSeqFileFormer - class org.biojava.bio.seq.io.ProteinRefSeqFileFormer.
  This class performs the detailed formatting of refseq protein entries.
ProteinRefSeqFileFormer() - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
ProteinRefSeqFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
ProteinRefSeqProcessor - class org.biojava.bio.seq.io.ProteinRefSeqProcessor.
  Class description
ProteinRefSeqProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqProcessor
ProteinRefSeqProcessor.Factory - class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory.
  Factory which wraps sequence builders in a ProteinRefSeqProcessor
ProteinRefSeqProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory
ProteinTools - class org.biojava.bio.seq.ProteinTools.
  The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.
ProteinTools() - Constructor for class org.biojava.bio.seq.ProteinTools
ProviderNotFoundException - exception org.biojava.directory.ProviderNotFoundException.
  `ProviderNotFoundException` is thrown when a sequence database provider can not be located.
ProviderNotFoundException() - Constructor for class org.biojava.directory.ProviderNotFoundException
  Creates a `ProviderNotFoundException` with no detail message.
ProviderNotFoundException(String) - Constructor for class org.biojava.directory.ProviderNotFoundException
  Creates a `ProviderNotFoundException` with the specified detail message.
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)
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.
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, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
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, int, int, SequenceRenderContext.Border) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
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) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
paint(Graphics2D, List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
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, 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
  `paint`s some or all of the information about the sequence pair.
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, int, int, SequenceRenderContext.Border) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
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
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.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.SequencePoster
  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
parent - Variable in class org.biojava.bio.taxa.SimpleTaxon
parent - Variable in class org.biojava.bio.taxa.WeakTaxon
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(File) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileParser
  Returns a profile HMM representing the core HMMER hmm
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.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(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser
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.
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() - Method in class org.biojava.bio.seq.ragbag.RagbagMap
  Parse the specified mapping file for this object now.
parse(TaxonFactory, String) - Method in class org.biojava.bio.taxa.EbiFormat
parse(TaxonFactory, String) - Method in interface org.biojava.bio.taxa.TaxonParser
  Convert a stringified Taxon into a Taxon instance.
parseAttribute(String) - Method in class org.biojava.bio.program.gff.GFFParser
  Parse attValList into a Map of attributes and value lists.
parseExample(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
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.
parseLocation(String, Feature.Template) - Method in class org.biojava.bio.seq.io.EmblLikeLocationParser
  `parseLocation` creates a `Location` from the String and returns a stranded location.
parseModel(File) - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
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.
parseStrand(String) - Static method in class org.biojava.bio.seq.StrandParser
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
parseString(String) - Method in class org.biojava.bio.seq.io.WordTokenization
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 interface org.biojava.bio.seq.io.SymbolTokenization
  Returns the symbol for a single token.
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
pcs - Variable in class org.biojava.bio.gui.sequence.SequencePanel.Border
pcs - Variable in class org.biojava.bio.gui.sequence.SequencePoster.Border
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.
phredToDistArray(PhredSequence) - Static method in class org.biojava.bio.program.phred.PhredTools
  Converts a Phred sequence to an array of distributions.
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.
polyKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
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) - Method in class org.biojava.bio.seq.Feature.Template
  This attempts to populate the fields of this template using the publically accessible information in a feature.
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
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.
postalAddress - Variable in class org.biojava.bibliography.BiblioPerson
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.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
  Description of the Method
press() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor
  press out a new correctly sized cell array
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
printOutSequenceHeaderLine(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  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.
printStackTrace() - Method in class org.biojava.utils.NestedError
printStackTrace(PrintStream) - Method in class org.biojava.utils.NestedError
printStackTrace(PrintWriter) - Method in class org.biojava.utils.NestedError
printStackTrace() - Method in class org.biojava.utils.NestedException
printStackTrace(PrintStream) - Method in class org.biojava.utils.NestedException
printStackTrace(PrintWriter) - Method in class org.biojava.utils.NestedException
printStackTrace() - Method in class org.biojava.utils.NestedRuntimeException
printStackTrace(PrintStream) - Method in class org.biojava.utils.NestedRuntimeException
printStackTrace(PrintWriter) - Method in class org.biojava.utils.NestedRuntimeException
printTree() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
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.
priority - Variable in class org.biojava.utils.SimpleThreadPool
processDB(SequenceDB, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Process all Sequences within a SequenceDB, informing handler of any suitable features.
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
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.BasicFeatureRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `processMouseEvent` processes any `MouseEvent`s directed to the renderer.
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
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(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(List, MouseEvent, List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
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.OverlayRendererWrapper
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
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(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
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(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(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.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
  Dispatch symbol data from SQ-block line of an EMBL-like file.
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
processingInstruction(String, String) - Method in class org.biojava.utils.xml.XMLPeerBuilder
projectChildFeatures(Feature, FeatureHolder) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
projectChildFeatures(Feature, FeatureHolder) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Get the child features of the projected feature.
projectFeature(Feature) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
  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.
properties - Variable in class org.biojava.bibliography.BibRef
  Additional attributes of this citation.
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.
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.SimpleAnnotation
propertiesAllocated() - Method in class org.biojava.bio.SmallAnnotation
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.
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(int, double) - Method in class org.biojava.stats.svm.SparseVector
  Set the value at a particular dimension.
put(Object, Object) - Method in class org.biojava.utils.BeanAsMap
put(Object, Object) - Method in class org.biojava.utils.OverlayMap
put(Object, Object) - Method in class org.biojava.utils.SmallMap
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(long, byte) - Method in class org.biojava.utils.io.LargeBuffer
put(byte) - Method in class org.biojava.utils.io.LargeBuffer
putChar(long, char) - Method in class org.biojava.utils.io.LargeBuffer
putChar(char) - Method in class org.biojava.utils.io.LargeBuffer
putComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
putComponent(Location, SymbolList) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
putConnection(Connection) - Method in class org.biojava.utils.JDBCConnectionPool
putDouble(long, double) - Method in class org.biojava.utils.io.LargeBuffer
putDouble(double) - Method in class org.biojava.utils.io.LargeBuffer
putFloat(long, float) - Method in class org.biojava.utils.io.LargeBuffer
putFloat(float) - Method in class org.biojava.utils.io.LargeBuffer
putInt(long, int) - Method in class org.biojava.utils.io.LargeBuffer
putInt(int) - Method in class org.biojava.utils.io.LargeBuffer
putLong(long, long) - Method in class org.biojava.utils.io.LargeBuffer
putLong(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
putTokenization(String, SymbolTokenization) - Method in class org.biojava.bio.symbol.AbstractAlphabet
  Assigns a symbol parser to a String object.

## Q

QUALIFIER - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
QUALITY - Static variable in class org.biojava.bio.program.abi.ABITools
  The quality alphabet.
QUERY_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion
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.
Qualitative - interface org.biojava.bio.program.phred.Qualitative.
  Qualitative is an interface for classes wanting to hold quality data in symbolic form such as Phred scores.
QualitativeAlignment - interface org.biojava.bio.alignment.QualitativeAlignment.
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.
query(String, Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery
  It queries the current collection using a query language.
querySeqHolder - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
queryViewCache - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory

## R

RAF - class org.biojava.utils.io.RAF.
RAF(File, String) - Constructor for class org.biojava.utils.io.RAF
RAF(String, String) - Constructor for class org.biojava.utils.io.RAF
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.
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.
RECT - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
  `RECT` indicates a rectangular image map hotspot.
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.
REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
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.
REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
REMOVE_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
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
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.
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
RENDER_NOTHING - Static variable in interface org.biojava.bio.gui.sequence.LabelRenderer
REPAINT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext
REPOSITORY_SUBSETS - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
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.
RESOURCE_TYPES - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
RESULT_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `RNA` indicates that a sequence contains RNA (ribonucleic acid) symbols.
RNATools - class org.biojava.bio.seq.RNATools.
  Useful functionality for processing DNA and RNA sequences.
RNATools() - Constructor for class org.biojava.bio.seq.RNATools
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.
RadialBaseKernel - class org.biojava.stats.svm.RadialBaseKernel.
  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
RagbagAssembly - class org.biojava.bio.seq.ragbag.RagbagAssembly.
  object that instantiates a sequence when given a Ragbag directory.
RagbagAssembly(String, String, File, RagbagSequenceFactory, RagbagComponentDirectory) - Constructor for class org.biojava.bio.seq.ragbag.RagbagAssembly
RagbagComponentDirectory - interface org.biojava.bio.seq.ragbag.RagbagComponentDirectory.
  provides a mapping of a reference to a specific ComponentFeature It exists primarily to support the getComponent method of DASDataSource.
RagbagComponentDirectory.EmptyComponentDirectory - class org.biojava.bio.seq.ragbag.RagbagComponentDirectory.EmptyComponentDirectory.
  Dummy class that does nothing.
RagbagComponentDirectory.EmptyComponentDirectory() - Constructor for class org.biojava.bio.seq.ragbag.RagbagComponentDirectory.EmptyComponentDirectory
RagbagFeatureTypeCatcher - class org.biojava.bio.seq.ragbag.RagbagFeatureTypeCatcher.
  A class that assists in wrapping a feature filter that records all types encountered around a SequenceBuilder class.
RagbagFeatureTypeCatcher() - Constructor for class org.biojava.bio.seq.ragbag.RagbagFeatureTypeCatcher
RagbagFileParserFactory - interface org.biojava.bio.seq.ragbag.RagbagFileParserFactory.
  Factory for Ragbag file parsers.
RagbagFilterFactory - interface org.biojava.bio.seq.ragbag.RagbagFilterFactory.
RagbagFilteredCachedSeqFactory - class org.biojava.bio.seq.ragbag.RagbagFilteredCachedSeqFactory.
  class that is passed to a RagbagAssembly to use a SoftReferenceCache-backed RagbagCachedSequences.
RagbagFilteredCachedSeqFactory() - Constructor for class org.biojava.bio.seq.ragbag.RagbagFilteredCachedSeqFactory
RagbagFixedCacheSeqFactory - class org.biojava.bio.seq.ragbag.RagbagFixedCacheSeqFactory.
  class that is passed to a RagbagAssembly to use a FixedSizeCache cache-backed RagbagCachedSequences.
RagbagFixedCacheSeqFactory(int) - Constructor for class org.biojava.bio.seq.ragbag.RagbagFixedCacheSeqFactory
RagbagHashedComponentDirectory - class org.biojava.bio.seq.ragbag.RagbagHashedComponentDirectory.
  provides a mapping of a reference to a specific ComponentFeature It exists primarily to support the getComponent method of DASDataSource.
RagbagHashedComponentDirectory() - Constructor for class org.biojava.bio.seq.ragbag.RagbagHashedComponentDirectory
RagbagIdleSequenceBuilder - class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder.
  A breakfast cereal of a SequenceBuilder, jes' sits there soakin' up all those events and doin' absolutely nuffin'.
RagbagIdleSequenceBuilder() - Constructor for class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
RagbagMap - class org.biojava.bio.seq.ragbag.RagbagMap.
  This class is an object that encapsulates all information present in a Map file in a Ragbag directory.
RagbagMap(File) - Constructor for class org.biojava.bio.seq.ragbag.RagbagMap
  create a RagbagMap from the specified File
RagbagMap.MapElement - class org.biojava.bio.seq.ragbag.RagbagMap.MapElement.
  class that represents a single mapping in mapFile
RagbagMap.MapEnum - class org.biojava.bio.seq.ragbag.RagbagMap.MapEnum.
  Enumeration object for RagbagMap.
RagbagSequenceFactory - interface org.biojava.bio.seq.ragbag.RagbagSequenceFactory.
  class that is passed to a RagbagAssembly to use a specified RagbagSequence object type.
RagbagSoftRefSeqFactory - class org.biojava.bio.seq.ragbag.RagbagSoftRefSeqFactory.
  class that is passed to a RagbagAssembly to use a SoftReferenceCache-backed RagbagCachedSequences.
RagbagSoftRefSeqFactory() - Constructor for class org.biojava.bio.seq.ragbag.RagbagSoftRefSeqFactory
RagbagUncachedSeqFactory - class org.biojava.bio.seq.ragbag.RagbagUncachedSeqFactory.
  class that is passed to a RagbagAssembly to use the vanilla uncached RagbagSequence object.
RagbagUncachedSeqFactory() - Constructor for class org.biojava.bio.seq.ragbag.RagbagUncachedSeqFactory
RandomAccessReader - class org.biojava.utils.io.RandomAccessReader.
  `RandomAccessReader` extends `Reader` to provide a means to create buffered `Reader`s from `RandomAccessFile`s.
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.
RangeLocation - class org.biojava.bio.symbol.RangeLocation.
  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`.
RealizingFeatureHolder - interface org.biojava.bio.seq.RealizingFeatureHolder.
  Interface for `FeatureHolder` objects which know how to instantiate new child Features.
Record - interface org.biojava.bio.program.indexdb.Record.
  `Record` represents a record within an indexed flat file databank as defined by the OBDA standard.
Record.Impl - class org.biojava.bio.program.indexdb.Record.Impl.
  `Impl` is the default implementation of Record.
Record.Impl(String, RAF, long, int) - Constructor for class org.biojava.bio.program.indexdb.Record.Impl
  Creates a new `Impl` record.
RectangularBeadRenderer - class org.biojava.bio.gui.sequence.RectangularBeadRenderer.
  `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 org.biojava.bio.gui.sequence.RectangularImapRenderer.
  `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`.
ReferenceServer - class org.biojava.bio.program.das.ReferenceServer.
  Reflects a reference server on the DAS network.
RegexChanger - class org.biojava.bio.program.tagvalue.RegexChanger.
  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.
RegexFieldFinder - class org.biojava.bio.program.tagvalue.RegexFieldFinder.
RegexFieldFinder(TagValueListener, Pattern, String[], boolean) - Constructor for class org.biojava.bio.program.tagvalue.RegexFieldFinder
RegexParser - class org.biojava.bio.program.tagvalue.RegexParser.
  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 org.biojava.bio.program.tagvalue.RegexSplitter.
  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.
Registry - class org.biojava.directory.Registry.
  `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 org.biojava.directory.RegistryConfiguration.
  The BioDirectory Registry is a simple system for specifying where to find services which provide sequence databases.
RegistryConfiguration.Composite - class org.biojava.directory.RegistryConfiguration.Composite.
  A RegistryConfiguration that allows you to treat other configurations as providing important or default configuration information.
RegistryConfiguration.Composite() - Constructor for class org.biojava.directory.RegistryConfiguration.Composite
RegistryConfiguration.Impl - class org.biojava.directory.RegistryConfiguration.Impl.
  A simple implementation of RegistryConfiguration backed by a Map.
RegistryConfiguration.Impl(String, Map) - Constructor for class org.biojava.directory.RegistryConfiguration.Impl
RegistryException - exception org.biojava.directory.RegistryException.
  A `RegistryException` thrown when the registry cannot find an implementation of a requested `SequenceDB`.
RegistryException() - Constructor for class org.biojava.directory.RegistryException
  Creates a new `RegistryException` with no detail message.
RegistryException(String) - Constructor for class org.biojava.directory.RegistryException
  Creates a new `RegistryException` with the specified detail message.
RegistryException(Throwable) - Constructor for class org.biojava.directory.RegistryException
  Creates a new `RegistryException` with no detail message, wrapping another `Throwable`.
RegistryException(Throwable, String) - Constructor for class org.biojava.directory.RegistryException
  Creates a new `RegistryException` with the specified detail message, wrapping another `Throwable`.
RelabeledAlignment - class org.biojava.bio.symbol.RelabeledAlignment.
  An alignment that relabels another alignment.
RelabeledAlignment(Alignment) - Constructor for class org.biojava.bio.symbol.RelabeledAlignment
RemoteFeature - interface org.biojava.bio.seq.RemoteFeature.
  A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.
RemoteFeature.Region - class org.biojava.bio.seq.RemoteFeature.Region.
  A tuple of Location and sequence ID.
RemoteFeature.Region(Location, String, boolean) - Constructor for class org.biojava.bio.seq.RemoteFeature.Region
  Create a new Region.
RemoteFeature.Resolver - interface org.biojava.bio.seq.RemoteFeature.Resolver.
  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 org.biojava.bio.seq.RemoteFeature.Template.
RemoteFeature.Template() - Constructor for class org.biojava.bio.seq.RemoteFeature.Template
RemoteFeature.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.
ResourceEntityResolver - class org.biojava.utils.xml.ResourceEntityResolver.
  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 org.biojava.bio.molbio.RestrictionEnzyme.
  `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 org.biojava.bio.molbio.RestrictionEnzymeManager.
  `RestrictionEnzymeManager` manages collections of static `RestrictionEnzyme` instances.
RestrictionMapper - class org.biojava.bio.molbio.RestrictionMapper.
  `RestrictionMapper` is a class for annotating `Sequence`s with `Feature`s which represent restriction sites.
RestrictionMapper(ThreadPool) - Constructor for class org.biojava.bio.molbio.RestrictionMapper
  Creates a new `RestrictionMapper` which will use the specified `ThreadPool`.
RestrictionSite - interface org.biojava.bio.molbio.RestrictionSite.
  `RestrictionSite` represents the recognition site of a restriction enzyme.
RestrictionSite.Template - class org.biojava.bio.molbio.RestrictionSite.Template.
  `Template` for construction of `RestrictionSite`s.
RestrictionSite.Template() - Constructor for class org.biojava.bio.molbio.RestrictionSite.Template
RevCompSequence - class org.biojava.bio.seq.impl.RevCompSequence.
  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
ReversibleTranslationTable - interface org.biojava.bio.symbol.ReversibleTranslationTable.
  A translation table that can also translate from the target to source alphabet.
RoundRectangularBeadRenderer - class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer.
  `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`.
RulerRenderer - class org.biojava.bio.gui.sequence.RulerRenderer.
  `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.
r() - Static method in class org.biojava.bio.seq.NucleotideTools
raIndexFile - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
randomizeDistribution(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
  Randomizes the weights of a `Distribution`
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
read(BufferedReader, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.Parser
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() - Method in class org.biojava.utils.io.CachingInputStream
read(byte[], int, int) - Method in class org.biojava.utils.io.CachingInputStream
read() - Method in class org.biojava.utils.io.CountedBufferedReader
read(char[]) - Method in class org.biojava.utils.io.CountedBufferedReader
read(char[], int, int) - 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(char[], int, int) - Method in class org.biojava.utils.io.RandomAccessReader
  `read` reads from the underlying `RandomAccessFile` into an array.
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
  Iterate over the sequences in an EMBL-format stream.
readEmblNucleotide(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Iterate over the sequences in an EMBL-format stream.
readEmblRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Iterate over the sequences in an EMBL-format stream, but for RNA.
readFasta(InputStream, Alphabet) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  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
  Iterate over the sequences in an FASTA-format stream of DNA sequences.
readFastaProtein(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Iterate over the sequences in an FASTA-format stream of Protein sequences.
readFastaRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Iterate over the sequences in an FASTA-format stream of RNA sequences.
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
readGFF(String) - Static method in class org.biojava.bio.program.gff.GFFTools
  Reads a `GFFEntrySet` from a file with no filtering
readGFF(String, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
  Reads a GFFEntrySet from a file with the specified filter
readGFF(BufferedReader) - Static method in class org.biojava.bio.program.gff.GFFTools
readGFF(BufferedReader, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
readGenbank(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Iterate over the sequences in an GenBank-format stream.
readGenpept(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Iterate over the sequences in an Genpept-format stream.
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
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.
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
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
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.FastaFormat
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
  Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in interface org.biojava.bio.seq.io.SequenceFormat
  Read a sequence and pass data on to a SeqIOListener.
readSwissprot(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  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.
readXFF(File, String, FiniteAlphabet) - Static method in class org.biojava.bio.program.xff.XFFTools
readingFrame - Static variable in class org.biojava.bio.seq.FramedFeature.Template
ready() - Method in class org.biojava.utils.io.CountedBufferedReader
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.program.das.DASSequence
realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.FeatureRealizer
  Install a feature on the specified sequence.
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 class org.biojava.bio.seq.SimpleFeatureRealizer
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.ViewSequence
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
realizeSubFeatures(Feature) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  recursively attach children features to parent
reapGarbageListeners() - Method in class org.biojava.utils.ChangeSupport
  Remove all references to listeners which have been cleared by the garbage collector.
recBytes - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
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.
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.
rect - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
rect - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
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.
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 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
registerFactory(UnigeneFactory) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
  Register a UnigeneFactory.
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
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(ModelTrainer) - Method in class org.biojava.bio.dist.PairDistribution
  Register this paired distribution with a model trainer.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.PairDistribution
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution
  Register a simple 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
  Dummy implementation which registers an IgnoreCountsTrainer.
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
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
remove() - Method in class org.biojava.bio.dp.DP.ReverseIterator
remove() - Method in class org.biojava.bio.symbol.Alignment.SymbolListIterator
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
removeActivityListener(ActivityListener) - Static method in class org.biojava.bio.program.das.DAS
removeAnnotationSource(URL) - Method in class org.biojava.bio.program.das.DASSequence
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `removeChangeListener` removes a listener.
removeChangeListener(ChangeListener, ChangeType) - 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, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `removeChangeListener` removes a listener.
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `removeChangeListener` removes a listener.
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.program.das.ReferenceServer
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
removeChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.SubSequence
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.SubSequence
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
removeChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Delegate for removeChangeListener
removeChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
removeChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport
  Remove a listener that was interested in all 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) - Method in interface org.biojava.utils.Changeable
  Remove a listener that was interested in all types of changes.
removeChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable
  Remove a listener that was interested in a specific types of changes.
removeChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
removeChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
  Remove a Taxon as a child to this one.
removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
removeComponent(Location) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
removeDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
removeDelegateRenderer(OptimizableFilter) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `removeDelegateRenderer` removes any association of the given `OptimizableFilter` with a `BeadFeatureRenderer`.
removeEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper
  `removeEnzyme` removes an enzyme from those to be searched for in the `Sequence`.
removeFeature(Feature) - Method in class org.biojava.bio.program.das.DASSequence
removeFeature(Feature) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
removeFeature(Feature) - Method in class org.biojava.bio.seq.DummySequence
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.LazyFeatureHolder
removeFeature(Feature) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
removeFeature(Feature, Feature) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
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.biojava.bio.seq.SimpleGappedSequence
removeFeature(Feature) - Method in class org.biojava.bio.seq.SubSequence
removeFeature(Feature) - Method in class org.biojava.bio.seq.ViewSequence
  Remove a feature from this sequence.
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.SimpleSequence
  Remove a feature attached to this sequence.
removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
removeFeature(Feature, Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Delegate for removeFeature
removeFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder
  Remove a FeatureHolder from the set of FeatureHolders which are merged.
removeForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
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(GappedSymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
  because there is a bug in GappedSymbolList
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
removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
removeItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
removeItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
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
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
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  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
  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
  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
  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
  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
  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(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.
removeProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
removeProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
removePropertyChangeListener(String, 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.TextLogoPainter
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
  `removeRenderer` removes a renderer.
removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
  `removeRenderer` removes a renderer.
removeRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
removeRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes
  Remove a repository from FeaturTypes.
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.program.das.DASSequenceDB
removeSequence(String) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
removeSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB
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.db.biofetch.BioFetchSequenceDB
removeSequence(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
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.distributed.DistributedSequenceDB
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `removeSequenceViewerListener` removes a listener for mouse click `SequenceViewerEvent`s.
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
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 `SequenceViewerEvent`s.
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `addSequenceViewerMotionListener` removes a listener for mouse motion `SequenceViewerEvent`s.
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
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 `SequenceViewerEvent`s.
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(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
removeTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
  Remove a tag so that it will not be retained.
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.
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.
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.BasicFeatureRenderer
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.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 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.
renderers - Variable in class org.biojava.bio.gui.sequence.MultiLineRenderer
renumber(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Renumber the view indexes from block, adding delta to each offset.
replacement - Variable in class org.biojava.bio.symbol.Edit
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.
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
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 `Runnable`s currently queued.
reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
reset() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
reset() - Method in class org.biojava.utils.io.CountedBufferedReader
resetRange() - Method in class org.biojava.bio.alignment.FlexibleAlignment
  check that begining is at 1 otherwise shift everything over
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.SequencePoster
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 interface org.biojava.bio.seq.RemoteFeature.Resolver
  Resolve rFeat.
resolve(RemoteFeature) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
resolve(FuzzyPointLocation) - Method in interface org.biojava.bio.symbol.FuzzyPointLocation.PointResolver
  Return the actual point that the specified location should claim to occupy.
resolveAlphabet(String) - Static method in class org.biojava.bio.program.ssbind.AlphabetResolver
  `resolveAlphabet` returns an appropriate `Alphabet` for an arbitrary identifier.
resolveEntity(String, String) - Method in class org.biojava.utils.xml.ResourceEntityResolver
resolveMax(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver
  Delegate for the getMax() method.
resolveMin(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver
  Delegate for the getMin() method.
resolver - Variable in class org.biojava.bio.seq.RemoteFeature.Template
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
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(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.
reverseComplement(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools
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(Object) - 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
reverseRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
rightMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment
rights - Variable in class org.biojava.bibliography.BibRef
  It specifies information about rights over the cited resource.
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

## S

SAX2StAXAdaptor - class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor.
  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 - class org.biojava.utils.stax.SAX2StAXAdaptor.
  Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services.
SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.utils.stax.SAX2StAXAdaptor
  Construct a new SAX Content handler which wraps a StAX handler.
SCF - class org.biojava.bio.program.scf.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
SCOOP - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
SCORES - Static variable in interface org.biojava.bio.dp.StatePath
  Alignment label for the likelyhood at each step.
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
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.
SEQUENCES - Static variable in interface org.biojava.bio.seq.db.SequenceDBLite
  Signals that sequences are being added to or remove from the database.
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.
SERVERS - Static variable in class org.biojava.bio.program.das.DAS
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 - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
  The sibling of this feature has altered.
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 `SimilarityPairFeature`s.
SIMPLE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
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 `Feature`s.
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 `Feature`s.
SIZE - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
SIZE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
SIZE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
SIZE_THRESHOLD - Static variable in class org.biojava.bio.program.das.DASSequence
SKIP_RECORD - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
SMORegressionTrainer - class org.biojava.stats.svm.SMORegressionTrainer.
  Train a regression support vector machine using the Sequential Minimal Optimization algorithm.
SMORegressionTrainer() - Constructor for class org.biojava.stats.svm.SMORegressionTrainer
SMOTrainer - class org.biojava.stats.svm.SMOTrainer.
  Train a support vector machine using the Sequential Minimal Optimization algorithm.
SMOTrainer() - Constructor for class org.biojava.stats.svm.SMOTrainer
SORT_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion
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
SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
SQLUnigeneFactory - class org.biojava.bio.program.unigene.SQLUnigeneFactory.
  An implementatoin of UnigeneFactory that manages it's data in an SQL database.
SQLUnigeneFactory() - Constructor for class org.biojava.bio.program.unigene.SQLUnigeneFactory
START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
STATES - Static variable in interface org.biojava.bio.dp.StatePath
  Alignment label for the state path.
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.
STRANDEDFEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.StrandedFeatureHandler
STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
STRING_TO_INT - Static variable in class org.biojava.bio.program.tagvalue.ChangeTable
STROKE - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Constant `STROKE` indicating a change to the outline stroke of the features.
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.
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.
SUPPORT - Static variable in class org.biojava.bio.program.abi.ABITools
  Alignment label for the support row.
SVMClassifierModel - interface org.biojava.stats.svm.SVMClassifierModel.
  An SVM classifier model.
SVMKernel - interface org.biojava.stats.svm.SVMKernel.
  Kernel for support vector machines and related methods.
SVMRegressionModel - class org.biojava.stats.svm.SVMRegressionModel.
SVMRegressionModel() - Constructor for class org.biojava.stats.svm.SVMRegressionModel
SVMRegressionModel(int) - Constructor for class org.biojava.stats.svm.SVMRegressionModel
SVMTarget - interface org.biojava.stats.svm.SVMTarget.
  An SVM classifier model.
SVM_Light - class org.biojava.stats.svm.tools.SVM_Light.
SVM_Light() - Constructor for class org.biojava.stats.svm.tools.SVM_Light
SVM_Light.LabelledVector - class org.biojava.stats.svm.tools.SVM_Light.LabelledVector.
SVM_Light.LabelledVector(SparseVector, double) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
SVM_Light.LabelledVector(SparseVector, double, String) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
SWISSPROT - Static variable in class org.biojava.bio.seq.io.SeqAlignReadWrite
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
SYMBOLS - Static variable in interface org.biojava.bio.symbol.Alphabet
  This ChangeType indicates that some symbols have been added or removed from the alphabet.
ScoreType - interface org.biojava.bio.dp.ScoreType.
  This class computes the score that is used to be used in a DP optimisation.
ScoreType.NullModel - class org.biojava.bio.dp.ScoreType.NullModel.
  In this class, calculateScore returns the probability of a Symbol being emitted by the null model.
ScoreType.NullModel() - Constructor for class org.biojava.bio.dp.ScoreType.NullModel
ScoreType.Odds - class org.biojava.bio.dp.ScoreType.Odds.
  In this class, calculateScore returns the odds ratio of a symbol being emitted.
ScoreType.Odds() - Constructor for class org.biojava.bio.dp.ScoreType.Odds
ScoreType.Probability - class org.biojava.bio.dp.ScoreType.Probability.
  In this class, calculateScore returns the probability of a Symbol being emitted.
ScoreType.Probability() - Constructor for class org.biojava.bio.dp.ScoreType.Probability
SearchBuilder - interface org.biojava.bio.search.SearchBuilder.
  The `SearchBuilder` interface is to be used by objects which accumulate state via a `SearchContentHandler` and then construct a `SeqSimilaritySearchResult` object.
SearchContentAdapter - class org.biojava.bio.search.SearchContentAdapter.
  An adapter for SearchContentHandler.
SearchContentAdapter() - Constructor for class org.biojava.bio.search.SearchContentAdapter
SearchContentFilter - class org.biojava.bio.search.SearchContentFilter.
  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 org.biojava.bio.search.SearchContentHandler.
  `SearchContentHandler` is a notification interface for objects which listen to search stream parsers.
SearchListener - interface org.biojava.bio.program.ssaha.SearchListener.
  The interface used to inform interested parties that some sequence has been searched and something found.
Seekable - interface org.biojava.utils.io.Seekable.
  This interface provides a collective name for IO classes that implement a seek function (e.g., `RandomAccessFile`).
SeqAlignReadWrite - class org.biojava.bio.seq.io.SeqAlignReadWrite.
  Title: File2Biojava Description: This project will take in a file of any common bioinformatics file formats and convert it to the appropriate Biojava object.
SeqAlignReadWrite() - Constructor for class org.biojava.bio.seq.io.SeqAlignReadWrite
SeqFileFormer - interface org.biojava.bio.seq.io.SeqFileFormer.
  Objects implementing the `SeqFileFormer` interface are responsible for the detailed formatting of sequence data prior to writing to a `PrintStream`.
SeqIOAdapter - class org.biojava.bio.seq.io.SeqIOAdapter.
  Adapter class for SeqIOListener that has empty methods.
SeqIOAdapter() - Constructor for class org.biojava.bio.seq.io.SeqIOAdapter
SeqIOConstants - class org.biojava.bio.seq.io.SeqIOConstants.
  `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
SeqIOFilter - class org.biojava.bio.seq.io.SeqIOFilter.
  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 org.biojava.bio.seq.io.SeqIOListener.
  Notification interface for objects which listen to a sequence stream parser.
SeqIOTools - class org.biojava.bio.seq.io.SeqIOTools.
  A set of convenience methods for handling common file formats.
SeqSimilarityAdapter - class org.biojava.bio.program.ssbind.SeqSimilarityAdapter.
  A `SeqSimilarityAdapter` converts SAX events into method calls on a `SearchContentHandler` implementation.
SeqSimilarityAdapter() - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
SeqSimilaritySearchHit - interface org.biojava.bio.search.SeqSimilaritySearchHit.
  Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
SeqSimilaritySearchHit.ByScoreComparator - class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator.
  `ByScoreComparator` compares `SeqSimilaritySearchHit`s by their score.
SeqSimilaritySearchHit.ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
SeqSimilaritySearchHit.BySubHitCountComparator - class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator.
  `BySubHitCountComparator` compares `SeqSimilaritySearchHit`s by their number of sub-hits.
SeqSimilaritySearchHit.BySubHitCountComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
SeqSimilaritySearchResult - interface org.biojava.bio.search.SeqSimilaritySearchResult.
  Objects of this type represent one particular result of a sequence similarity search.
SeqSimilaritySearchSubHit - interface org.biojava.bio.search.SeqSimilaritySearchSubHit.
  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 org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator.
  `ByScoreComparator` compares `SeqSimilaritySearchSubHit`s by their score.
SeqSimilaritySearchSubHit.ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
SeqSimilaritySearchSubHit.BySubjectStartComparator - class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator.
  `BySubjectStartComparator` compares `SeqSimilaritySearchSubHit`s by their start position on the subject sequence.
SeqSimilaritySearchSubHit.BySubjectStartComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
SeqSimilaritySearcher - interface org.biojava.bio.search.SeqSimilaritySearcher.
  Objects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP.
SeqSimilarityStAXAdapter - class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter.
  `SeqSimilarityStAXAdapter` is a handler for XML conforming to the BioJava BlastLike DTD.
SeqSimilarityStAXAdapter() - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
SeqSimilarityStAXHandler - class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler.
  `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 `StAXHandlerBinding`s and delegates to any suitable `StAXContentHandler` bound by one of them.
Sequence - interface org.biojava.bio.seq.Sequence.
  A biological sequence.
SequenceAlignmentSAXParser - class org.biojava.bio.program.sax.SequenceAlignmentSAXParser.
  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"
SequenceAnnotator - interface org.biojava.bio.seq.SequenceAnnotator.
  An object which adds some additional information to a Sequence.
SequenceBuilder - interface org.biojava.bio.seq.io.SequenceBuilder.
  Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object.
SequenceBuilderBase - class org.biojava.bio.seq.io.SequenceBuilderBase.
  Basic SequenceBuilder implementation which accumulates all notified information.
SequenceBuilderBase() - Constructor for class org.biojava.bio.seq.io.SequenceBuilderBase
SequenceBuilderFactory - interface org.biojava.bio.seq.io.SequenceBuilderFactory.
  Simple factory for constructing new SequenceBuilder objects.
SequenceBuilderFilter - class org.biojava.bio.seq.io.SequenceBuilderFilter.
  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 org.biojava.bio.seq.io.game.SequenceContentHandlerBase.
  StAX handler for elements containing sequence
SequenceContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
SequenceDB - interface org.biojava.bio.seq.db.SequenceDB.
  A database of sequences with accessible keys and iterators over all sequences.
SequenceDBDataSource - class org.biojava.bio.seq.distributed.SequenceDBDataSource.
  Turn an entire SequenceDB instance into a DistDataSource.
SequenceDBDataSource(SequenceDB) - Constructor for class org.biojava.bio.seq.distributed.SequenceDBDataSource
SequenceDBInstallation - interface org.biojava.bio.seq.db.SequenceDBInstallation.
  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 org.biojava.bio.seq.db.SequenceDBLite.
  A database of sequences.
SequenceDBProvider - interface org.biojava.directory.SequenceDBProvider.
  Interfaces for named resources that can provide sequences via a database given some configuration information as defined by the OBDA standard.
SequenceDBSearchHit - class org.biojava.bio.search.SequenceDBSearchHit.
  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 org.biojava.bio.search.SequenceDBSearchResult.
  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 org.biojava.bio.search.SequenceDBSearchSubHit.
  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 org.biojava.bio.seq.io.SequenceDBSequenceBuilder.
  This SequenceBuilder has a variety of modes of operation.
SequenceDBSequenceBuilder(SequenceDB, int) - Constructor for class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
  constructor
SequenceDBWrapper - class org.biojava.bio.seq.db.SequenceDBWrapper.
  An abstract implementation of SequenceDB that wraps up another database.
SequenceDBWrapper(SequenceDB) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper
SequenceDBWrapper.SequencesForwarder - class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder.
SequenceDBWrapper.SequencesForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
SequenceFactory - interface org.biojava.bio.seq.SequenceFactory.
  The interface for objects that will manufacture sequences.
SequenceFormat - interface org.biojava.bio.seq.io.SequenceFormat.
  Defines what a sequence format does.
SequenceHandler - interface org.biojava.bio.seq.io.agave.SequenceHandler.
  mark interface
SequenceIterator - interface org.biojava.bio.seq.SequenceIterator.
  An iterator over a bag of sequences.
SequencePanel - class org.biojava.bio.gui.sequence.SequencePanel.
  A panel that displays a Sequence.
SequencePanel() - Constructor for class org.biojava.bio.gui.sequence.SequencePanel
  Create a new SequencePanel.
SequencePanel.Border - class org.biojava.bio.gui.sequence.SequencePanel.Border.
SequencePoster - class org.biojava.bio.gui.sequence.SequencePoster.
  A panel that displays a Sequence.
SequencePoster() - Constructor for class org.biojava.bio.gui.sequence.SequencePoster
  Create a new SeqeuncePanel.
SequencePoster.Border - class org.biojava.bio.gui.sequence.SequencePoster.Border.
SequenceRenderContext - interface org.biojava.bio.gui.sequence.SequenceRenderContext.
  A context within which sequence information may be rendered.
SequenceRenderContext.Border - class org.biojava.bio.gui.sequence.SequenceRenderContext.Border.
  The metric object for the 'border' area - the area between the extent of the rendered area and the beginning or end of the sequence.
SequenceRenderContext.Border() - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
SequenceRenderer - interface org.biojava.bio.gui.sequence.SequenceRenderer.
  The interface for things that can render a line of information about a sequence.
SequenceRenderer.RendererForwarder - class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder.
SequenceRenderer.RendererForwarder(SequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder
SequenceRendererWrapper - class org.biojava.bio.gui.sequence.SequenceRendererWrapper.
SequenceRendererWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper
SequenceRendererWrapper(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper
SequenceStreamer - interface org.biojava.bio.program.ssaha.SequenceStreamer.
SequenceStreamer.FileStreamer - class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer.
SequenceStreamer.FileStreamer(SequenceFormat, SymbolTokenization, List) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
SequenceStreamer.FileStreamer(SequenceFormat, SymbolTokenization, File) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
SequenceStreamer.SequenceDBStreamer - class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer.
SequenceStreamer.SequenceDBStreamer(SequenceDB) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
SequenceTools - class org.biojava.bio.seq.SequenceTools.
  Methods for manipulating sequences.
SequenceTools() - Constructor for class org.biojava.bio.seq.SequenceTools
SequenceViewerEvent - class org.biojava.bio.gui.sequence.SequenceViewerEvent.
  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 org.biojava.bio.gui.sequence.SequenceViewerListener.
SequenceViewerMotionListener - interface org.biojava.bio.gui.sequence.SequenceViewerMotionListener.
SequenceViewerMotionSupport - class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport.
SequenceViewerMotionSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
SequenceViewerSupport - class org.biojava.bio.gui.sequence.SequenceViewerSupport.
SequenceViewerSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerSupport
SequencesAsGFF - class org.biojava.bio.program.gff.SequencesAsGFF.
  Turns a sequence database into a GFF event stream.
SequencesAsGFF() - Constructor for class org.biojava.bio.program.gff.SequencesAsGFF
Services - class org.biojava.utils.Services.
  Utility methods for handling META-INF/services files
Services() - Constructor for class org.biojava.utils.Services
SigmoidKernel - class org.biojava.stats.svm.SigmoidKernel.
  This kernel implements a three layer neural net.
SigmoidKernel() - Constructor for class org.biojava.stats.svm.SigmoidKernel
SimilarityPairBuilder - class org.biojava.bio.program.ssbind.SimilarityPairBuilder.
  `SimilarityPairBuilder` annotates query and subject `Sequence` with `SimilarityPairFeature`s created from SAX events supplied via a `SeqSimilarityAdapter`.
SimilarityPairBuilder() - Constructor for class org.biojava.bio.program.ssbind.SimilarityPairBuilder
SimilarityPairFeature - interface org.biojava.bio.seq.homol.SimilarityPairFeature.
  `SimilarityPairFeature` describes a pairwise similarity between two nucleotide sequences (as it extends `StrandedFeature`).
SimilarityPairFeature.EmptyPairwiseAlignment - class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment.
  `EmptyPairwiseAlignment` empty pairwise alignment which has labels to empty symbol lists.
SimilarityPairFeature.Template - class org.biojava.bio.seq.homol.SimilarityPairFeature.Template.
  `Template` for construction of `SimilarityPairFeature`s.
SimilarityPairFeature.Template() - Constructor for class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
SimpleAlignment - class org.biojava.bio.symbol.SimpleAlignment.
  A simple implementation of an Alignment.
SimpleAlignment(Map) - Constructor for class org.biojava.bio.symbol.SimpleAlignment
  Generate an alignment from a list of SymbolLists.
SimpleAlignmentElement - class org.biojava.bio.alignment.SimpleAlignmentElement.
  SimpleSimpleAlignment is a simple implementation of AlignmentElement.
SimpleAlignmentElement(Object, SymbolList, Location) - Constructor for class org.biojava.bio.alignment.SimpleAlignmentElement
SimpleAlignmentStyler - class org.biojava.bio.program.blast2html.SimpleAlignmentStyler.
  Simple implementation for specifying markup styles.
SimpleAlignmentStyler(int) - Constructor for class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
  Creates a new `SimpleAlignmentStyler` instance.
SimpleAlphabet - class org.biojava.bio.symbol.SimpleAlphabet.
  A simple no-frills implementation of the FiniteAlphabet interface.
SimpleAlphabet() - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
SimpleAlphabet(Set) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
SimpleAlphabet(String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
SimpleAlphabet(Set, String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
SimpleAnnotFilter - class org.biojava.bio.seq.io.agave.SimpleAnnotFilter.
  Basic implementation of AGAVEAnnotFilter
SimpleAnnotation - class org.biojava.bio.SimpleAnnotation.
  A no-frills implementation of Annotation that is just a wrapper around a Map.
SimpleAnnotation() - Constructor for class org.biojava.bio.SimpleAnnotation
  Create a new, empty SimpleAnnotation instance.
SimpleAnnotation(Annotation) - Constructor for class org.biojava.bio.SimpleAnnotation
  Create a new SimpleAnnotation by copying the properties from another one.
SimpleAnnotation(Map) - Constructor for class org.biojava.bio.SimpleAnnotation
  Create a new SimpleAnnotation using the values in a Map.
SimpleAssembly - class org.biojava.bio.seq.SimpleAssembly.
  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 org.biojava.bio.seq.io.SimpleAssemblyBuilder.
  Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.
SimpleAssemblyBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleAssemblyBuilder
SimpleAtomicSymbol - class org.biojava.bio.symbol.SimpleAtomicSymbol.
  A basic implementation of AtomicSymbol.
SimpleAtomicSymbol(Annotation, List) - Constructor for class org.biojava.bio.symbol.SimpleAtomicSymbol
SimpleChromatogram - class org.biojava.bio.chromatogram.SimpleChromatogram.
  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
SimpleDistribution - class org.biojava.bio.dist.SimpleDistribution.
  A simple implementation of a distribution, which works with any finite alphabet.
SimpleDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.SimpleDistribution
SimpleDistribution.Trainer - class org.biojava.bio.dist.SimpleDistribution.Trainer.
SimpleDistribution.Trainer() - Constructor for class org.biojava.bio.dist.SimpleDistribution.Trainer
SimpleDistributionTrainer - class org.biojava.bio.dist.SimpleDistributionTrainer.
  A simple implemenation of a distribution trainer.
SimpleDistributionTrainer(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainer
SimpleDistributionTrainerContext - class org.biojava.bio.dist.SimpleDistributionTrainerContext.
  A no-frills implementation of DistributionTrainerContext.
SimpleDistributionTrainerContext() - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainerContext
SimpleDotState - class org.biojava.bio.dp.SimpleDotState.
  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, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState
  Construct a new state with the specified name and annotation
SimpleDotState(String) - Constructor for class org.biojava.bio.dp.SimpleDotState
SimpleEmissionState - class org.biojava.bio.dp.SimpleEmissionState.
SimpleEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.dp.SimpleEmissionState
SimpleFeature - class org.biojava.bio.seq.impl.SimpleFeature.
  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 org.biojava.bio.seq.SimpleFeatureHolder.
  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 org.biojava.bio.seq.SimpleFeatureRealizer.
  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 org.biojava.bio.seq.impl.SimpleFramedFeature.
  Title: SimpleFramedFeature.
SimpleFramedFeature(Sequence, FeatureHolder, FramedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFramedFeature
SimpleGFFRecord - class org.biojava.bio.program.gff.SimpleGFFRecord.
  A no-frills implementation of a GFFRecord.
SimpleGFFRecord(GFFRecord) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
  Create a new SimpleGFFRecord from GFFRecord object
SimpleGFFRecord(String, String, String, int, int, double, StrandedFeature.Strand, int, String, Map) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
SimpleGFFRecord() - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
  Create a new SimpleGFFRecord with values set to null or zero
SimpleGappedSequence - class org.biojava.bio.seq.SimpleGappedSequence.
  Simple implementation of GappedSequence.
SimpleGappedSequence(Sequence) - Constructor for class org.biojava.bio.seq.SimpleGappedSequence
SimpleGappedSymbolList - class org.biojava.bio.symbol.SimpleGappedSymbolList.
  This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
SimpleGappedSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList
  Create a new SimpleGappedSymbolList that will view source.
SimpleGappedSymbolList.Block - class org.biojava.bio.symbol.SimpleGappedSymbolList.Block.
  An aligned block.
SimpleGappedSymbolList.Block(int, int, int, int) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
SimpleHomology - class org.biojava.bio.seq.homol.SimpleHomology.
  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 org.biojava.bio.seq.impl.SimpleHomologyFeature.
SimpleHomologyFeature(Sequence, FeatureHolder, HomologyFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleHomologyFeature
SimpleIndex - class org.biojava.bio.seq.db.SimpleIndex.
  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
SimpleItemValue - class org.biojava.stats.svm.SimpleItemValue.
  A no-frills implementation of ItemValue.
SimpleItemValue(Object, double) - Constructor for class org.biojava.stats.svm.SimpleItemValue
SimpleLabelRenderer - class org.biojava.bio.gui.sequence.SimpleLabelRenderer.
SimpleLabelRenderer() - Constructor for class org.biojava.bio.gui.sequence.SimpleLabelRenderer
SimpleMarkovModel - class org.biojava.bio.dp.SimpleMarkovModel.
SimpleMarkovModel(int, Alphabet, String) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
SimpleMarkovModel(int, Alphabet) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
  Deprecated.
SimpleModelInState - class org.biojava.bio.dp.SimpleModelInState.
SimpleModelInState(MarkovModel, String) - Constructor for class org.biojava.bio.dp.SimpleModelInState
SimpleModelTrainer - class org.biojava.bio.dp.SimpleModelTrainer.
SimpleModelTrainer() - Constructor for class org.biojava.bio.dp.SimpleModelTrainer
SimpleRemoteFeature - class org.biojava.bio.seq.impl.SimpleRemoteFeature.
  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 org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver.
SimpleRemoteFeature.DBResolver(SequenceDB) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
SimpleRestrictionSite - class org.biojava.bio.seq.impl.SimpleRestrictionSite.
  `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 org.biojava.bio.symbol.SimpleReversibleTranslationTable.
  A no-frills implementation of ReversibleTranslationTable that uses two Maps to map between symbols in a finite source alphabet into a finite target alphabet.
SimpleReversibleTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleReversibleTranslationTable
  Construct a new translation table.
SimpleSVMClassifierModel - class org.biojava.stats.svm.SimpleSVMClassifierModel.
  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 org.biojava.stats.svm.SimpleSVMTarget.
  No-frills implementation of SVMTarget.
SimpleSVMTarget() - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
SimpleSVMTarget(Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
SimpleSeqSimilaritySearchHit - class org.biojava.bio.search.SimpleSeqSimilaritySearchHit.
  `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 org.biojava.bio.search.SimpleSeqSimilaritySearchResult.
  `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 org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit.
  `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 org.biojava.bio.seq.impl.SimpleSequence.
  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 org.biojava.bio.seq.io.SimpleSequenceBuilder.
  Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.
SimpleSequenceBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleSequenceBuilder
SimpleSequenceDBInstallation - class org.biojava.bio.seq.db.SimpleSequenceDBInstallation.
  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 org.biojava.bio.seq.impl.SimpleSequenceFactory.
  A no-frills implementation of SequenceFactory that produces SimpleSequence objects.
SimpleSequenceFactory() - Constructor for class org.biojava.bio.seq.impl.SimpleSequenceFactory
SimpleSimilarityPairFeature - class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature.
  `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`.
SimpleStatePath - class org.biojava.bio.dp.SimpleStatePath.
  A no-frills implementation of StatePath.
SimpleStatePath(double, SymbolList, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.SimpleStatePath
SimpleStrandedFeature - class org.biojava.bio.seq.impl.SimpleStrandedFeature.
  A no-frills implementation of StrandedFeature.
SimpleStrandedFeature(Sequence, FeatureHolder, StrandedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleStrandedFeature
SimpleSymbolList - class org.biojava.bio.symbol.SimpleSymbolList.
  Basic implementation of SymbolList.
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(SymbolTokenization, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
  Construct a SymbolList from a string.
SimpleSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
  Construct a copy of an existing SymbolList.
SimpleSymbolList(Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
  Construct a SimpleSymbolList given the Symbol array that backs it.
SimpleSymbolListFactory - class org.biojava.bio.symbol.SimpleSymbolListFactory.
  This class makes SimpleSymbolLists.
SimpleSymbolListFactory() - Constructor for class org.biojava.bio.symbol.SimpleSymbolListFactory
SimpleSymbolPropertyTable - class org.biojava.bio.symbol.SimpleSymbolPropertyTable.
  Class that implements the SymbolPropertyTable interface
SimpleSymbolPropertyTable(Alphabet, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolPropertyTable
SimpleSymbolStyle - class org.biojava.bio.gui.SimpleSymbolStyle.
  A no-frills implementation of SymbolStyle.
SimpleSymbolStyle(FiniteAlphabet) - Constructor for class org.biojava.bio.gui.SimpleSymbolStyle
SimpleTaxon - class org.biojava.bio.taxa.SimpleTaxon.
  A no-frills implementatation of Taxon.
SimpleTaxon() - Constructor for class org.biojava.bio.taxa.SimpleTaxon
SimpleTaxon(String, String) - Constructor for class org.biojava.bio.taxa.SimpleTaxon
  Create a new instance with no parent, no children and given scientific and common names.
SimpleTaxonFactory - class org.biojava.bio.taxa.SimpleTaxonFactory.
  A no-frills implementation of TaxaFactory that builds an in-memory Taxa tree.
SimpleTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.SimpleTaxonFactory
SimpleThreadPool - class org.biojava.utils.SimpleThreadPool.
  `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.
SimpleTranslationTable - class org.biojava.bio.symbol.SimpleTranslationTable.
  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 org.biojava.bio.dp.SimpleWeightMatrix.
SimpleWeightMatrix(Alphabet, int, DistributionFactory) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
SimpleWeightMatrix(Distribution[]) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
SimpleXMLEmitter - class org.biojava.bio.program.xml.SimpleXMLEmitter.
  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 org.biojava.bio.dp.onehead.SingleDP.
  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 org.biojava.bio.dp.onehead.SingleDPMatrix.
  The dynamic programming matrix for a single sequence.
SingleDPMatrix(DP, SymbolList) - Constructor for class org.biojava.bio.dp.onehead.SingleDPMatrix
SingletonAlphabet - class org.biojava.bio.symbol.SingletonAlphabet.
  An alphabet that contains a single atomic symbol.
SingletonAlphabet(AtomicSymbol) - Constructor for class org.biojava.bio.symbol.SingletonAlphabet
SingletonList - class org.biojava.utils.SingletonList.
SingletonList(Object) - Constructor for class org.biojava.utils.SingletonList
SixFrameRenderer - class org.biojava.bio.gui.sequence.SixFrameRenderer.
  Class that handles drawing in six frames for other classes.
SixFrameRenderer() - Constructor for class org.biojava.bio.gui.sequence.SixFrameRenderer
SixFrameZiggyRenderer - class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer.
  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
SmallAnnotation - class org.biojava.bio.SmallAnnotation.
  Annotation that is optimized for memory usage.
SmallAnnotation() - Constructor for class org.biojava.bio.SmallAnnotation
SmallAnnotation(Annotation) - Constructor for class org.biojava.bio.SmallAnnotation
SmallAnnotation(Map) - Constructor for class org.biojava.bio.SmallAnnotation
SmallMap - class org.biojava.utils.SmallMap.
  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 org.biojava.utils.SmallSet.
  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(Set) - Constructor for class org.biojava.utils.SmallSet
SmartSequenceBuilder - class org.biojava.bio.seq.io.SmartSequenceBuilder.
  Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.
SmartSequenceBuilder() - Constructor for class org.biojava.bio.seq.io.SmartSequenceBuilder
SoftReferenceCache - class org.biojava.utils.cache.SoftReferenceCache.
  Cache which is cleared according to memory pressure.
SoftReferenceCache() - Constructor for class org.biojava.utils.cache.SoftReferenceCache
SparseVector - class org.biojava.stats.svm.SparseVector.
  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 org.biojava.stats.svm.SparseVector.NormalizingKernel.
  A version of the standard dot-product kernel that scales each column independently.
SparseVector.NormalizingKernel(SparseVector) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel
  Generate a normalizing kernel with the normalizing vector s.
SparseVector.NormalizingKernel(List) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel
  Generate a normalizing kernel defined by the SparseVectors in vectors.
StAXContentHandler - interface org.biojava.bio.seq.io.agave.StAXContentHandler.
  Interface for StAX content handlers.
StAXContentHandler - interface org.biojava.utils.stax.StAXContentHandler.
  Interface for StAX content handlers.
StAXContentHandlerBase - class org.biojava.bio.seq.io.agave.StAXContentHandlerBase.
  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 - class org.biojava.utils.stax.StAXContentHandlerBase.
  Simple implementation of the `StAXContentHandler` interface, with empty implementations for all the methods.
StAXContentHandlerBase() - Constructor for class org.biojava.utils.stax.StAXContentHandlerBase
StAXFeatureHandler - class org.biojava.bio.seq.io.agave.StAXFeatureHandler.
  StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXFeatureHandler - class org.biojava.bio.seq.io.game.StAXFeatureHandler.
  StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXFeatureHandler() - Constructor for class org.biojava.bio.seq.io.game.StAXFeatureHandler
StAXFeatureHandler - class org.biojava.bio.seq.io.game12.StAXFeatureHandler.
  StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXHandlerBinding - class org.biojava.bio.program.ssbind.StAXHandlerBinding.
  `StAXHandlerBinding`s associates an `ElementRecognizer` with a factory which creates `StAXContentHandler`s for elements which it the `ElementRecognizer` accepts.
StAXHandlerFactory - interface org.biojava.bio.program.ssbind.StAXHandlerFactory.
  `StAXHandlerFactory` is an interface for factories producing `StAXContentHandler`s which are used by the `SeqSimilarityStAXAdapter`.
StAXHandlerFactory - interface org.biojava.bio.seq.io.agave.StAXHandlerFactory.
  Factory for StAX content handlers.
StAXHandlerFactory - interface org.biojava.bio.seq.io.game.StAXHandlerFactory.
  Factory for StAX content handlers.
StAXHandlerFactory - interface org.biojava.bio.seq.io.game12.StAXHandlerFactory.
  Factory for StAX content handlers.
StAXPropertyHandler - class org.biojava.bio.seq.io.agave.StAXPropertyHandler.
  StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXPropertyHandler - class org.biojava.bio.seq.io.game.StAXPropertyHandler.
  StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StackedFeatureRenderer - class org.biojava.bio.gui.sequence.StackedFeatureRenderer.
  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 org.biojava.bio.gui.StackedLogoPainter.
  A logo painter that paints in stacked areas.
StackedLogoPainter() - Constructor for class org.biojava.bio.gui.StackedLogoPainter
State - interface org.biojava.bio.dp.State.
  A state in a markov process.
StatePath - interface org.biojava.bio.dp.StatePath.
  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.
StaticMemberPlaceHolder - class org.biojava.utils.StaticMemberPlaceHolder.
StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
StaticMemberPlaceHolder() - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
StopRenderer - class org.biojava.bio.gui.sequence.StopRenderer.
  Compute sites of stop codons.
StopRenderer(SixFrameRenderer, int, StrandedFeature.Strand) - Constructor for class org.biojava.bio.gui.sequence.StopRenderer
StoppingCriteria - interface org.biojava.bio.dp.StoppingCriteria.
  A callback that is invoked during the training of an HMM.
StrandParser - class org.biojava.bio.seq.StrandParser.
  Process strings and return strand objects.
StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser
StrandedFeature - interface org.biojava.bio.seq.StrandedFeature.
  Adds the concept of 'strand' to features.
StrandedFeature.Strand - class org.biojava.bio.seq.StrandedFeature.Strand.
  Class to represent the 'strandedness' of a feature.
StrandedFeature.Template - class org.biojava.bio.seq.StrandedFeature.Template.
  Template class for parameterizing the creation of a new `StrandedFeature`.
StrandedFeature.Template() - Constructor for class org.biojava.bio.seq.StrandedFeature.Template
StrandedFeatureHandler - class org.biojava.bio.program.xff.StrandedFeatureHandler.
  StAX handler for XFF strandedFeature type.
StrandedFeatureHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.StrandedFeatureHandler
StreamParser - interface org.biojava.bio.seq.io.StreamParser.
  Parse a stream of characters into BioJava symbols.
StreamReader - class org.biojava.bio.seq.io.StreamReader.
  Parses a stream into sequences.
StreamReader(InputStream, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
StreamReader(BufferedReader, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
StreamWriter - class org.biojava.bio.seq.io.StreamWriter.
  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.
StringElementHandlerBase - class org.biojava.utils.stax.StringElementHandlerBase.
  StAX handler for any element which just contains a string.
StringElementHandlerBase() - Constructor for class org.biojava.utils.stax.StringElementHandlerBase
StructureTools - class org.biojava.bio.proteomics.StructureTools.
  Simple access to protein seccondary structure assignments.
StructureTools() - Constructor for class org.biojava.bio.proteomics.StructureTools
SubPairwiseRenderContext - class org.biojava.bio.gui.sequence.SubPairwiseRenderContext.
  `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`.
SubSequence - class org.biojava.bio.seq.SubSequence.
  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.SubSequence
  Construct a new SubSequence of the specified sequence.
SubSequence(Sequence, int, int, String) - Constructor for class org.biojava.bio.seq.SubSequence
  Construct a new SubSequence of the specified sequence.
SubSequence(Sequence, int, int, FeatureFilter, boolean) - Constructor for class org.biojava.bio.seq.SubSequence
  Construct a new SubSequence of the specified sequence.
SubSequence(Sequence, int, int, FeatureFilter, boolean, String) - Constructor for class org.biojava.bio.seq.SubSequence
  Construct a new SubSequence of the specified sequence with a new name.
SubSequenceDB - class org.biojava.bio.seq.db.SubSequenceDB.
SubSequenceDB(SequenceDB, Set) - Constructor for class org.biojava.bio.seq.db.SubSequenceDB
SubSequenceRenderContext - class org.biojava.bio.gui.sequence.SubSequenceRenderContext.
SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext
SuffixTree - class org.biojava.bio.symbol.SuffixTree.
  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 org.biojava.bio.symbol.SuffixTree.SuffixNode.
  A node in the suffix tree.
SuffixTree.SuffixNode() - Constructor for class org.biojava.bio.symbol.SuffixTree.SuffixNode
SuffixTreeKernel - class org.biojava.stats.svm.tools.SuffixTreeKernel.
  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 org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler.
  Encapsulates the scale factor to apply at a given depth.
SuffixTreeKernel.MultipleScalar - class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar.
  Scale using a multiple of two DepthScalers.
SuffixTreeKernel.MultipleScalar(SuffixTreeKernel.DepthScaler, SuffixTreeKernel.DepthScaler) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
SuffixTreeKernel.NullModelScaler - class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler.
  Scales by 4^depth - equivalent to dividing by a probablistic flatt prior null model
SuffixTreeKernel.NullModelScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
SuffixTreeKernel.SelectionScalar - class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar.
  Scale using a BitSet to allow/disallow depths.
SuffixTreeKernel.SelectionScalar(BitSet) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
  Make a new SelectionScalar that masks in different depths.
SuffixTreeKernel.UniformScaler - class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler.
  Scale all depths by 1.0
SuffixTreeKernel.UniformScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
SwissprotFileFormer - class org.biojava.bio.seq.io.SwissprotFileFormer.
  Formats a sequence into Swissprot/TrEMBL format.
SwissprotFileFormer() - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer
  Creates a new `SwissprotFileFormer` using `System.out` stream.
SwissprotFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer
  Creates a new `SwissprotFileFormer` using the specified stream.
SwissprotProcessor - class org.biojava.bio.seq.io.SwissprotProcessor.
  Simple filter which handles attribute lines from an Swissprot entry.
SwissprotProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor
  Constructor that sets the source of the feature to theSource.
SwissprotProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor
SwissprotProcessor.Factory - class org.biojava.bio.seq.io.SwissprotProcessor.Factory.
  Factory which wraps SequenceBuilders in a SwissprotProcessor
SwissprotProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor.Factory
SwissprotSequenceDB - class org.biojava.bio.seq.db.SwissprotSequenceDB.
  This class contains functions accessing sequences in swiss-prot.
SwissprotSequenceDB() - Constructor for class org.biojava.bio.seq.db.SwissprotSequenceDB
Symbol - interface org.biojava.bio.symbol.Symbol.
  A single symbol.
SymbolList - interface org.biojava.bio.symbol.SymbolList.
  A sequence of symbols that belong to an alphabet.
SymbolList.EmptySymbolList - class org.biojava.bio.symbol.SymbolList.EmptySymbolList.
  The empty immutable implementation.
SymbolList.EmptySymbolList() - Constructor for class org.biojava.bio.symbol.SymbolList.EmptySymbolList
SymbolListCharSequence - class org.biojava.bio.seq.io.SymbolListCharSequence.
  `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 org.biojava.bio.symbol.SymbolListFactory.
  This interface exists to hide implementational details of SymbolLists when making chunked symbol lists.
SymbolListViews - class org.biojava.bio.symbol.SymbolListViews.
  Tools class for constructing views of `SymbolList` objects.
SymbolPropertyTable - interface org.biojava.bio.symbol.SymbolPropertyTable.
  class for maintaining properties associated with a symbol
SymbolReader - interface org.biojava.bio.seq.io.SymbolReader.
  Encapsulate a stream of Symbols being parsed from some input stream.
SymbolSequenceRenderer - class org.biojava.bio.gui.sequence.SymbolSequenceRenderer.
  `SymbolSequenceRenderer` renders symbols of a `SymbolList`.
SymbolSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
SymbolStyle - interface org.biojava.bio.gui.SymbolStyle.
  The interface for things that say how to paint a symbol.
SymbolTokenization - interface org.biojava.bio.seq.io.SymbolTokenization.
  Encapsulate a mapping between BioJava Symbol objects and some string representation.
SymbolTokenization.TokenType - class org.biojava.bio.seq.io.SymbolTokenization.TokenType.
SystemRegistry - class org.biojava.directory.SystemRegistry.
  A registry that loads up the standard biodirectory files.
SystemRegistry() - Constructor for class org.biojava.directory.SystemRegistry
s() - Static method in class org.biojava.bio.seq.NucleotideTools
sMatrix - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
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
sb - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
scaleHeight - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
score - Variable in class org.biojava.bio.dp.BackPointer
score - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
  `score` of the search which produced the alignment.
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.
scores - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
scores - Variable in class org.biojava.bio.dp.twohead.Cell
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(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(Object) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
search(Object) - Method in interface org.biojava.bio.taxa.TaxonFactory
  Retrieve a Taxon that matches some ID.
search(Object) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
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.
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
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.
seq - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement
seq - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
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.
seqString() - Method in class org.biojava.bio.dp.SimpleStatePath
seqString() - Method in class org.biojava.bio.program.das.DASSequence
seqString() - Method in class org.biojava.bio.seq.DummySequence
seqString() - Method in class org.biojava.bio.seq.SimpleAssembly
seqString() - Method in class org.biojava.bio.seq.SubSequence
seqString() - Method in class org.biojava.bio.seq.ViewSequence
seqString() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
seqString() - Method in class org.biojava.bio.seq.impl.SimpleSequence
seqString() - Method in class org.biojava.bio.symbol.AbstractSymbolList
seqString() - Method in class org.biojava.bio.symbol.RelabeledAlignment
seqString() - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
seqString() - Method in interface org.biojava.bio.symbol.SymbolList
  Stringify this symbol list.
seqs - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
sequenceExtentOfPixels(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
sequenceIterator() - Method in class org.biojava.bio.program.das.DASSequenceDB
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.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.biojava.bio.seq.db.biosql.BioSQLSequenceDB
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
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.
serialVersionUID - Static variable in class org.biojava.bio.dp.SimpleMarkovModel
serialize(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat
serialize(Taxon) - Method in interface org.biojava.bio.taxa.TaxonParser
  Convert a Taxon into a stringified representation.
series - Variable in class org.biojava.bibliography.BiblioBook
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
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
setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
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.
setAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
setAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
setAlpha(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
setAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
setAlphaStar(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
setAnnotation(Annotation) - Method in class org.biojava.bio.dp.SimpleEmissionState
setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
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.
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
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.
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
setChangeTable(ChangeTable) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
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.
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
setChromatogram(Chromatogram) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Sets the chromatogram to draw.
setChromosome(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
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`).
setComment(String) - Method in class org.biojava.bio.AnnotationType.Impl
setComment(Object, 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(Object, String) - Method in interface org.biojava.bio.AnnotationType
  Set the comment for a particular property.
setComment(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the comment to comment.
setCommonName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon
setCommonName(String) - Method in interface org.biojava.bio.taxa.Taxon
  Set the new common name of this Taxon.
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
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.SimpleGappedSequence
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.BlastLikeHomologyBuilder
setDatabaseID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
setDatabaseID(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
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.
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
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.
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.
setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagValueWrapper
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.
setDepth(double) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
setDepth(SequenceRenderer, double) - Method in class org.biojava.bio.gui.sequence.LineInfo
setDepth(double) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
setDepthScaler(SuffixTreeKernel.DepthScaler) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
  Change the current DepthScaler to depthScaler.
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.
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.SequencePoster
  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.
setDistribution(Symbol, Distribution) - Method in interface org.biojava.bio.dist.OrderNDistribution
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.
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
setDocumentLocator(Locator) - Method in class org.biojava.utils.xml.XMLPeerBuilder
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.
setElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Specifies whether the symbols (SQ) part of the entry should be ignored.
setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Use this method to toggle reading of sequence data.
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.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.
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.
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.
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.
setFeatureRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
  `setFeatureRenderer` sets the renderer to be used.
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
setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle
setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
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.
setFilter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
setFloatValue(float) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
  Override this method to do something useful with the float we collect.
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.
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.
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(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
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.
setIntValue(int) - Method in class org.biojava.utils.stax.IntElementHandlerBase
  Override this method to do something useful with the int we collect.
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.
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
setLabel(Object) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
setLabel(String) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
setLabelMaker(FeatureLabelRenderer.LabelMaker) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
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
setLength(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
setLimit(int) - Method in class org.biojava.utils.cache.FixedSizeCache
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
  Set the line width.
setLines(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Set the absolute number of lines that the sequence will be rendered on.
setListener(Object, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
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.biojava.bio.seq.projection.ProjectedFeature
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.
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
setMaxMissedCleavages(int) - Method in class org.biojava.bio.proteomics.Digest
  Sets the maximum number of partial digest products to be annotated.
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.
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.
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.
setMultiplier(double) - Method in class org.biojava.stats.svm.PolynomialKernel
setMultiplier(double) - Method in class org.biojava.stats.svm.SigmoidKernel
setName(String) - Method in class org.biojava.bio.dp.SimpleEmissionState
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
setName(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
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
  The name is printed out as part of the identifier line.
setName(String) - Method in class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
setName(String) - Method in class org.biojava.bio.symbol.SimpleAlphabet
  Assign a name to the alphabet
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`.
setNormalizingVector(SparseVector) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
  Set the normalizing vector.
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
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
  Assign a weight to the background distribution
setNumber(float) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
  Set the number associated with this node.
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
setOrientation(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
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
setPadding(double) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
  Set the padding.
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.
setPos(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
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
setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
setPrintStream(PrintStream) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
  `setPrintStream` informs an instance which `PrintStream` to use.
setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  `setPrintStream` informs an instance which `PrintStream` to use.
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(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.
setProperty(Object, Object) - Method in class org.biojava.bio.MergeAnnotation
setProperty(Object, Object) - Method in class org.biojava.bio.OverlayAnnotation
setProperty(String, String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
setProperty(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
setProtease(Protease) - Method in class org.biojava.bio.proteomics.Digest
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.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.
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.
setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanel
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
setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
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(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.SequencePanel
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster
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.SequencePoster
  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.
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.SequencePoster
  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
setScientificName(String) - Method in interface org.biojava.bio.taxa.Taxon
  Change the scientific name of this species.
setScore(double) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the score to score.
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.
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 `Symbol`s which will be applied when rendering.
setSeqID(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
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(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.SequencePanel
  Set the SymboList to be rendered.
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Set the SymboList to be rendered.
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `setSequence` sets the `Sequence` to be rendered.
setSequence(Sequence) - Method in class org.biojava.bio.proteomics.Digest
setSequenceDB(SequenceDB) - Method in class org.biojava.bio.gui.FeatureTree
  Use this method to provide the sequences for the tree to work with.
setSequenceFormat(LifeScienceIdentifier) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `setSequenceFormat` sets the sequence format name which will be indicated in the index.
setSequenceFormat(SequenceFormat) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
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.
setSize(double) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
  Sets the size of the border in number of pixels.
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.biojava.bio.seq.projection.ProjectedFeature
setSpacer(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  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.
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.seq.io.agave.AGAVEMatchRegion
setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
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.
setStreamParser(StreamParser) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
  assign a StreamParser object to instance.
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.
setSubSeqStart(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
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.
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 `Symbol`s which will be applied when rendering.
setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `setSymbolTranslation` sets the translation in `Symbol`s which will be applied when rendering.
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 interface org.biojava.stats.svm.SVMTarget
setTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
setThreadFetches(boolean) - Static method in class org.biojava.bio.program.das.DAS
setThreshold() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
setThreshold(double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
setThreshold(double) - Method in class org.biojava.stats.svm.SVMRegressionModel
setThreshold(double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
setTrace(AtomicSymbol, int[], int) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Provides the trace samples for a particular nucleotide.
setTrace(ABITrace) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
setTraceValues(AtomicSymbol, int[], int) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
  Sets the trace array for one of the DNA nucleotides.
setTrailingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
  Alter the translation mapping.
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().
setType(String) - Method in interface org.biojava.bio.seq.Feature
  Change the type of this feature.
setType(AnnotationType) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
setType(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature
setType(String) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
setURI(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer
setURI(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
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
  Null implementation.
setURI(String) - Method in class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
setURN(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence
  Provide the URN for this sequence
setUnits(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
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
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
  VectorNTI requires GenBank format to be a little more specific than required by the GenBank definition.
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).
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 emited 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
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
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(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Sets the width of the whole graphic (in pixels).
setWidth(double) - Method in class org.biojava.stats.svm.RadialBaseKernel
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.
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
sibling - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
  `sibling` `SimilarityPairFeature` field.
sign(double) - Static method in class org.biojava.stats.svm.tools.Classify
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
site - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
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.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.stats.svm.SVMRegressionModel
size() - Method in class org.biojava.stats.svm.SparseVector
  The number of used dimensions.
size() - Method in class org.biojava.utils.BeanAsMap
size() - Method in class org.biojava.utils.FileAsList
size() - Method in class org.biojava.utils.ListTools.Doublet
size() - Method in class org.biojava.utils.ListTools.Triplet
size() - Method in class org.biojava.utils.SingletonList
size() - Method in class org.biojava.utils.SmallMap
size() - Method in class org.biojava.utils.SmallSet
skip(long) - Method in class org.biojava.utils.io.CachingInputStream
skip(long) - Method in class org.biojava.utils.io.CountedBufferedReader
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
solve(double, double, double, ComputeObject) - Static method in class org.biojava.utils.math.BinarySearch
  method that will attempt solving the equation.
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.
source - Variable in class org.biojava.bio.seq.Feature.Template
sourceEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
sourceStart - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
sourceToView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Coordinate conversion from source to view.
sourceToView(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Coordinate conversion from source to view.
sourceToView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
spatialLocation - Variable in class org.biojava.bibliography.BiblioScope
  It defines a spatial location of the cited resource.
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
ssContext - Variable in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
stackLevel - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
stackLevel - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
start(String[]) - Method in interface org.biojava.utils.xml.AppEntry
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() - 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() - Method in class org.biojava.utils.xml.XMLPeerBuilder
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, 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) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
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) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
startElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
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, 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.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.bio.seq.ragbag.RagbagMap
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) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
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, AttributeList) - Method in class org.biojava.utils.xml.XMLPeerBuilder
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, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
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, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEHandler
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
  Description of the Method
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.
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.EmblFileFormer
startFeature(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
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
  Null implementation.
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
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.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.
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.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.
startLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
startLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
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.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 interface org.biojava.bio.program.tagvalue.TagValueListener
  A new record is about to start.
startRecord() - Method in class org.biojava.bio.program.tagvalue.TagValueWrapper
startSearch() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
startSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger
startSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener
  Indicates that a sequence is about to be searched against a DataStore.
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.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.
startSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer
startSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
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
  Start the processing of a sequence.
startSequence() - Method in class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
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.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.
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.RegexFieldFinder
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.TagValueWrapper
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.
startedActivity(Object) - Static method in class org.biojava.bio.program.das.DAS
startedActivity(Object) - Method in interface org.biojava.utils.ActivityListener
  Notification that an activity has started.
state - Variable in class org.biojava.bio.dp.BackPointer
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) - Static method in class org.biojava.bio.dp.DP
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
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
stopThreads() - Method in class org.biojava.utils.SimpleThreadPool
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
strand - Variable in class org.biojava.bio.seq.StrandedFeature.Template
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
streamRecords(GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Write all records in this set out to a handler.
stringToSymbolList(String) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
  Converts a string that came from symbolListToString back to a SymbolList.
stringifyAttributes(Map) - Static method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Create a String representation of attMap.
subAlignment(Set, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
subAlignment(Set, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment
  Retrieves a subalignment specified by the location.
subAlignment(Set, int, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment
  Retreives a subAlignment
subAlignment(Set, Location) - Method in class org.biojava.bio.dp.SimpleStatePath
subAlignment(Set, Location) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
subAlignment(Set, Location) - Method in interface org.biojava.bio.symbol.Alignment
  Make a view onto this alignment.
subAlignment(Set, Location) - Method in class org.biojava.bio.symbol.RelabeledAlignment
subAlignment(Set, Location) - Method in class org.biojava.bio.symbol.SimpleAlignment
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.
subFeatures - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
subList(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
subList(int, int) - Method in class org.biojava.bio.program.das.DASSequence
subList(int, int) - Method in class org.biojava.bio.seq.CircularView
  Over rides ViewSequence.
subList(int, int) - Method in class org.biojava.bio.seq.DummySequence
subList(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly
subList(int, int) - Method in class org.biojava.bio.seq.SubSequence
subList(int, int) - Method in class org.biojava.bio.seq.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.SimpleSequence
subList(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
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 class org.biojava.bio.symbol.SymbolList.EmptySymbolList
subList(int, int) - Method in interface org.biojava.bio.symbol.SymbolList
  Return a new SymbolList for the symbols start to end inclusive.
subSequence(Sequence, int, int) - Static method in class org.biojava.bio.seq.SequenceTools
subSequence(Sequence, int, int, String) - Static method in class org.biojava.bio.seq.SequenceTools
subSequence(int, int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
subStr(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
subStr(int, int) - Method in class org.biojava.bio.program.das.DASSequence
subStr(int, int) - Method in class org.biojava.bio.seq.CircularView
  Over rides ViewSequence.
subStr(int, int) - Method in class org.biojava.bio.seq.DummySequence
subStr(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly
subStr(int, int) - Method in class org.biojava.bio.seq.SubSequence
subStr(int, int) - Method in class org.biojava.bio.seq.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.SimpleSequence
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 class org.biojava.bio.symbol.SymbolList.EmptySymbolList
subStr(int, int) - Method in interface org.biojava.bio.symbol.SymbolList
  Return a region of this symbol list as a String.
subStringExists(String) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
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.
subject - Variable in class org.biojava.bibliography.BibRef
  It defines the topic of the content of the cited resource.
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
subpathsValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
subtract(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Subtract one location from another.
surname - Variable in class org.biojava.bibliography.BiblioPerson
symList() - Method in interface org.biojava.bio.dp.DPMatrix
symList() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
symList() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
symbolAt(Object, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
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(Object, 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(int) - Method in class org.biojava.bio.dp.SimpleStatePath
symbolAt(Object, int) - Method in class org.biojava.bio.dp.SimpleStatePath
symbolAt(int) - Method in class org.biojava.bio.program.das.DASSequence
symbolAt(int) - Method in class org.biojava.bio.seq.CircularView
  Over rides ViewSequence.
symbolAt(int) - Method in class org.biojava.bio.seq.DummySequence
symbolAt(int) - Method in class org.biojava.bio.seq.SimpleAssembly
symbolAt(int) - Method in class org.biojava.bio.seq.SubSequence
symbolAt(int) - Method in class org.biojava.bio.seq.ViewSequence
symbolAt(Object, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
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.SimpleSequence
symbolAt(Object, int) - Method in interface org.biojava.bio.symbol.Alignment
  Retrieve a symbol by label and column.
symbolAt(int) - Method in class org.biojava.bio.symbol.DummySymbolList
symbolAt(int) - Method in class org.biojava.bio.symbol.PackedDnaSymbolList
symbolAt(int) - Method in class org.biojava.bio.symbol.PackedSymbolList
symbolAt(Object, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
symbolAt(int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleAlignment
symbolAt(Object, int) - Method in class org.biojava.bio.symbol.SimpleAlignment
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 class org.biojava.bio.symbol.SymbolList.EmptySymbolList
symbolAt(int) - Method in interface org.biojava.bio.symbol.SymbolList
  Return the symbol at index, counting from 1.
symbolForIndex(int) - Method in interface org.biojava.bio.symbol.AlphabetIndex
  Retrieve the symbol for an index.
symbolForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Retrieve the symbol represented a String object
symbolIndices - Variable in class org.biojava.bio.dist.AbstractDistribution
symbolListForLabel(Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
symbolListForLabel(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
symbolListForLabel(Object) - Method in class org.biojava.bio.dp.SimpleStatePath
symbolListForLabel(Object) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
symbolListForLabel(Object) - Method in interface org.biojava.bio.symbol.Alignment
  Retrieve a single row of the alignment by label.
symbolListForLabel(Object) - Method in class org.biojava.bio.symbol.RelabeledAlignment
symbolListForLabel(Object) - Method in class org.biojava.bio.symbol.SimpleAlignment
symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment
symbolListIterator() - Method in class org.biojava.bio.dp.SimpleStatePath
symbolListIterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
symbolListIterator() - Method in interface org.biojava.bio.symbol.Alignment
  Creates an Iterator over the SymbolLists in the alignment.
symbolListIterator() - Method in class org.biojava.bio.symbol.RelabeledAlignment
symbolListIterator() - Method in class org.biojava.bio.symbol.SimpleAlignment
symbolListToString(SymbolList) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
  Makes a string out of a SymbolList, this string should only be used for internal or testing purposes, as it will necessarily consist of visible characters.
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.

## T

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.RulerRenderer
  `TICKS_UP` indicates that the ticks will point upwards from a baseline.
TITLE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
TITLE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
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.
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.
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.
TRYPSIN - Static variable in class org.biojava.bio.proteomics.Protease
TRYPSIN - Static variable in class org.biojava.bio.proteomics.ProteaseManager
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_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_JOURNAL_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
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_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
TYPE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
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_WEB_RESOURCE - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
TabIndexStore - class org.biojava.bio.seq.db.TabIndexStore.
  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
TagDelegator - class org.biojava.bio.program.tagvalue.TagDelegator.
  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 org.biojava.bio.program.tagvalue.TagDropper.
  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.
TagMapper - class org.biojava.bio.program.tagvalue.TagMapper.
  `TagMapper` maps arbitrary object keys to new keys.
TagMapper() - Constructor for class org.biojava.bio.program.tagvalue.TagMapper
  Creates a new, empty `TagMapper`.
TagRenamer - class org.biojava.bio.program.tagvalue.TagRenamer.
  Rename tags using a TagMapper.
TagRenamer(TagValueListener, TagMapper) - Constructor for class org.biojava.bio.program.tagvalue.TagRenamer
  Build a new TagRenamer with a delegate and mapper.
TagValue - class org.biojava.bio.program.tagvalue.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 org.biojava.bio.program.tagvalue.TagValueContext.
  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 org.biojava.bio.program.tagvalue.TagValueListener.
  An object that wishes to be informed of events during the parsing of a file.
TagValueParser - interface org.biojava.bio.program.tagvalue.TagValueParser.
  Tokenize single records (lines of text, objects) into a tag and a value.
TagValueWrapper - class org.biojava.bio.program.tagvalue.TagValueWrapper.
  Helper class to wrap one TagValueListener inside another one.
TagValueWrapper(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.TagValueWrapper
  Build a TagValueWrapper that will forward everything to a delegate.
TagValueWrapper() - Constructor for class org.biojava.bio.program.tagvalue.TagValueWrapper
Taxon - interface org.biojava.bio.taxa.Taxon.
  A taxon within a classification.
TaxonFactory - interface org.biojava.bio.taxa.TaxonFactory.
  Factory for handling a particular implementation of a Taxon.
TaxonParser - interface org.biojava.bio.taxa.TaxonParser.
  Encapsulate the mapping between Taxon and stringified representations of taxa.
TextBlock - class org.biojava.bio.gui.TextBlock.
  A BlockPainter that renders letters in proportion to the size of the signal.
TextBlock() - Constructor for class org.biojava.bio.gui.TextBlock
TextLogoPainter - class org.biojava.bio.gui.TextLogoPainter.
  A logo painter that paints in stacked letters.
TextLogoPainter() - Constructor for class org.biojava.bio.gui.TextLogoPainter
ThreadPool - interface org.biojava.utils.ThreadPool.
  `ThreadPool` specifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava.
TickFeatureRenderer - class org.biojava.bio.gui.sequence.TickFeatureRenderer.
TickFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.TickFeatureRenderer
Train - class org.biojava.stats.svm.tools.Train.
Train() - Constructor for class org.biojava.stats.svm.tools.Train
TrainRegression - class org.biojava.stats.svm.tools.TrainRegression.
TrainRegression() - Constructor for class org.biojava.stats.svm.tools.TrainRegression
Trainable - interface org.biojava.bio.dp.Trainable.
  Flags an object as being able to register itself with a model trainer.
TrainerTransition - class org.biojava.bio.dp.TrainerTransition.
  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
TrainingAlgorithm - interface org.biojava.bio.dp.TrainingAlgorithm.
TrainingContext - interface org.biojava.stats.svm.TrainingContext.
TrainingEvent - class org.biojava.stats.svm.TrainingEvent.
TrainingEvent(TrainingContext) - Constructor for class org.biojava.stats.svm.TrainingEvent
TrainingListener - interface org.biojava.stats.svm.TrainingListener.
Transition - class org.biojava.bio.dp.Transition.
  This is a small and ugly class for storing a transition.
Transition(State, State) - Constructor for class org.biojava.bio.dp.Transition
TransitionTrainer - interface org.biojava.bio.dp.TransitionTrainer.
  An object that can be used to train the transitions within a MarkovModel.
TranslatedDistribution - class org.biojava.bio.dist.TranslatedDistribution.
  Creates a distribution that is a translated view of an underlying distribution.
TranslatedDistribution(ReversibleTranslationTable, Distribution, DistributionFactory) - Constructor for class org.biojava.bio.dist.TranslatedDistribution
  Users should make these thigs via getDistribuiton.
TranslatedSequencePanel - class org.biojava.bio.gui.sequence.TranslatedSequencePanel.
  `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).
TranslationTable - interface org.biojava.bio.symbol.TranslationTable.
  Encapsulates the mapping from a source to a destination alphabet.
TypedProperties - class org.biojava.utils.TypedProperties.
  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.
t() - Static method in class org.biojava.bio.seq.DNATools
t() - Static method in class org.biojava.bio.seq.NucleotideTools
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.
tagName - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
tagNumber - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
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
temporalPeriod - Variable in class org.biojava.bibliography.BiblioScope
  It defines temporal period of the cited resource.
theAbstract - Variable in class org.biojava.bibliography.BiblioDescription
  It is an abstract of the cited resource.
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.
title - Variable in class org.biojava.bibliography.BibRef
  A title given to the cited resource (a name by which the resource is formally known).
to - Variable in class org.biojava.bio.dp.TrainerTransition
to - Variable in class org.biojava.bio.dp.Transition
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.program.das.DASSequence
toList() - Method in class org.biojava.bio.seq.DummySequence
toList() - Method in class org.biojava.bio.seq.SimpleAssembly
toList() - Method in class org.biojava.bio.seq.SubSequence
toList() - Method in class org.biojava.bio.seq.ViewSequence
toList() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
toList() - Method in class org.biojava.bio.seq.impl.SimpleSequence
toList() - Method in class org.biojava.bio.symbol.AbstractSymbolList
toList() - Method in class org.biojava.bio.symbol.RelabeledAlignment
toList() - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
toList() - Method in interface org.biojava.bio.symbol.SymbolList
  Returns a List of symbols.
toString() - Method in class org.biojava.bio.AbstractAnnotation
toString() - Method in class org.biojava.bio.AnnotationType.Abstract
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.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.chromatogram.graphic.ChromatogramGraphic.Option
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.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.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.FramedFeature.ReadingFrame
toString() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
toString() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
toString() - Method in class org.biojava.bio.seq.db.biosql.DBHelper.DeleteStyle
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.SimpleSimilarityPairFeature
toString() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
toString() - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
toString() - 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() - 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
  * @param indent the leading space * @param indent_unit the unit of indenting for xml format *
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.agave.AgaveWriter.Indent
  Return the current indent
toString() - Method in class org.biojava.bio.seq.projection.ProjectedStrandedFeature
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.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
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.ChangeEvent
toString() - Method in class org.biojava.utils.ChangeType
  Return a string representation of this change.
toString() - Method in class org.biojava.utils.ParseErrorEvent
toString() - Method in class org.biojava.utils.ParserException
  Represent this exception as a string.
toString() - Method in class org.biojava.utils.TypedProperties
toString() - Method in class org.biojava.utils.candy.CandyEntry
  It prints the entry contents.
toString() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
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
toggleSelectionStatus() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
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 interface org.biojava.bio.seq.io.SymbolTokenization
  Return a token representing a single symbol.
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
topLevel() - Static method in class org.biojava.bio.seq.FilterUtils
top_level - Static variable in interface org.biojava.bio.seq.FeatureFilter
  A filter which accepts only top-level Features.
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.
train(DistributionTrainerContext, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
  Trains the Distribution, given a null model.
train() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  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
train() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
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(double, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
  Trains the transition, given an expected probability, and a weight for that probability.
trainImpl(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
trainModel(SVMRegressionModel, double[]) - Method in class org.biojava.stats.svm.SMORegressionTrainer
trainModel(SVMTarget, SVMKernel, TrainingListener) - Method in class org.biojava.stats.svm.SMOTrainer
trainer - Variable in class org.biojava.bio.dp.TrainerTransition
trainer - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
trainingComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener
trainingCycleComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener
transScore(State, State, Symbol, Symbol) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
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
  Transcribe DNA into 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.
transformFilter(FeatureFilter) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
  Called to transform a FeatureFilter applying to our parent FeatureHolder into the coordinate system of our parent.
transformLocation(Location) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
  Called to transform a location from underlying to projection coordinates.
transformLocation(Location, int, boolean) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
transformStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
  Called to transform a strand property between projection and underlying coordinates.
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
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(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(Symbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
translate(SymbolList, TranslationTable) - Static method in class org.biojava.bio.symbol.SymbolListViews
  Provides a 'translated' view of an underlying SymbolList.
translate(Symbol) - Method in interface org.biojava.bio.symbol.TranslationTable
  Translate a single symbol from source alphabet to the target alphabet.
type - Variable in class org.biojava.bibliography.BibRef
  It defines the nature or genre of the cited resource.
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.bio.seq.Feature.Template
type - Variable in class org.biojava.utils.IndexedChangeHub.ListenerMemento

## U

UNIGENE_ANNOTATION - Static variable in class org.biojava.bio.program.unigene.UnigeneTools
  Annotation schema for all UnigeneCluster instances.
UNIVERSAL - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the universal genetic code.
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.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 class org.biojava.utils.ChangeType
  Constant ChangeType field which indicates that a change has occured which can't otherwise be represented.
UNLOGGED - Static variable in interface org.biojava.bio.seq.ragbag.RagbagComponentDirectory
URI_PREFIX - Static variable in class org.biojava.bio.seq.FeatureTypes
  The standard prefix for all type URIs
URLFactory - interface org.biojava.utils.net.URLFactory.
  `URLFactory` defines a means of obtaining a URL associated with an object.
URLGeneratorFactory - interface org.biojava.bio.program.blast2html.URLGeneratorFactory.
  Interface for a factory method to return a list of 0, 1 or more `DatabaseURLGenerator` instances.
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.
UkkonenSuffixTree - class org.biojava.bio.symbol.UkkonenSuffixTree.
  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
Unchangeable - class org.biojava.utils.Unchangeable.
  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
UnequalLengthAlignment - interface org.biojava.bio.alignment.UnequalLengthAlignment.
  UnequalLengthAlignment has the following behavior.
UniformDistribution - class org.biojava.bio.dist.UniformDistribution.
  An implementation of an uniform distribution
UniformDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.UniformDistribution
UnigeneCluster - interface org.biojava.bio.program.unigene.UnigeneCluster.
  A single unigene cluster.
UnigeneDB - interface org.biojava.bio.program.unigene.UnigeneDB.
  A database of Unigene clusters.
UnigeneFactory - interface org.biojava.bio.program.unigene.UnigeneFactory.
  Objects that can be used to produce a `UnigeneDB` instance given a URL.
UnigeneTools - class org.biojava.bio.program.unigene.UnigeneTools.
  Usefull tools for working with Unigene.
UnigeneTools() - Constructor for class org.biojava.bio.program.unigene.UnigeneTools
UnknownDBHelper - class org.biojava.bio.seq.db.biosql.UnknownDBHelper.
UnknownDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.UnknownDBHelper
UnsupportedChromatogramFormatException - exception org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException.
  Exception indicating that some provided data does not represent a supported chromatogram format.
UnsupportedChromatogramFormatException() - Constructor for class org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException
UnsupportedChromatogramFormatException(String) - Constructor for class org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException
UntrainableDistribution - class org.biojava.bio.dist.UntrainableDistribution.
  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
UtilHelper - class org.biojava.bio.seq.io.agave.UtilHelper.
  Just make the property follow the common case
UtilHelper() - Constructor for class org.biojava.bio.seq.io.agave.UtilHelper
u() - Static method in class org.biojava.bio.seq.NucleotideTools
u() - Static method in class org.biojava.bio.seq.RNATools
unIndent() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
  Remove a level of indentation
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(PropertyConstraint, PropertyConstraint) - Static method in class org.biojava.bio.AnnotationTools
  Create a PropertyConstraint that matches all Objects that are accepted by two others.
union(CollectionConstraint, CollectionConstraint) - Static method in class org.biojava.bio.AnnotationTools
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, Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Return the union of two locations.
union(Collection) - Static method in class org.biojava.bio.symbol.LocationTools
  The n-way union of a Collection of locations.
unlockModel() - Method in class org.biojava.bio.dp.DP
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.
untransformFilter(FeatureFilter) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
  Called to transform a FeatureFilter applying to our projections into a corresponding filter on the parent FeatureHolder.
untransformLocation(Location) - Method in class org.biojava.bio.seq.ProjectedFeatureHolder
  Called to transform a location from projection to underlying coordinates.
untranslate(Symbol) - Method in interface org.biojava.bio.symbol.ReversibleTranslationTable
  Translate a single symbol from target alphabet to the source alphabet.
untranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
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
uri - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
url - Variable in class org.biojava.bibliography.BiblioWebResource
usCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
useSuppliedSymListFactory() - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
  Call this to convert from default SymbolList implementation to user-supplied implementation.

## V

VALUES - Static variable in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
VERSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
VERSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
VERT_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the vertebrate mitochondrial genetic code.
ValueChanger - class org.biojava.bio.program.tagvalue.ValueChanger.
  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.
ViewSequence - class org.biojava.bio.seq.ViewSequence.
  A view onto another Sequence object.
ViewSequence(Sequence, String) - Constructor for class org.biojava.bio.seq.ViewSequence
  Construct a view onto an existing sequence and give it a new name.
ViewSequence(Sequence) - Constructor for class org.biojava.bio.seq.ViewSequence
  Construct a view onto an existing sequence which takes on that sequence's name.
ViewSequence(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.ViewSequence
  Construct a view onto a sequence, using a specific FeatureRealizer
ViewSequenceFactory - class org.biojava.bio.program.ssbind.ViewSequenceFactory.
  `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
ViewingSequenceDB - class org.biojava.bio.seq.db.ViewingSequenceDB.
  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.
v() - Static method in class org.biojava.bio.seq.NucleotideTools
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.
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
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.
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.RegexFieldFinder
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.TagValueWrapper
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
valueOf(String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Create a new LifeScienceIdentifier parsed from the properly formatted string `lsid`.
valueOf(String, String, String, String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Create a new LifeScienceIdentifier from the specified parameters.
valueOf(String, String, String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Create a new LifeScienceIdentifier from the specified parameters.
vectorToString(SparseVector) - Static method in class org.biojava.stats.svm.tools.SVM_Light
view(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools
view(Sequence, String) - Static method in class org.biojava.bio.seq.SequenceTools
viewEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
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(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Coordinate conversion from view to source.
viewToSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
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.twohead.PairwiseDP
volume - Variable in class org.biojava.bibliography.BiblioBook
volume - Variable in class org.biojava.bibliography.BiblioJournalArticle

## W

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.
WMAsMM - class org.biojava.bio.dp.WMAsMM.
  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
WeakCacheMap - class org.biojava.utils.cache.WeakCacheMap.
  A cache which retains weak references to objects
WeakCacheMap() - Constructor for class org.biojava.utils.cache.WeakCacheMap
WeakTaxon - class org.biojava.bio.taxa.WeakTaxon.
  An implementation of Taxon that keeps only weak references to children, but full references to parents.
WeakTaxon() - Constructor for class org.biojava.bio.taxa.WeakTaxon
WeakTaxon(String, String) - Constructor for class org.biojava.bio.taxa.WeakTaxon
WeakTaxonFactory - class org.biojava.bio.taxa.WeakTaxonFactory.
  An implementation of TaxonFactory that builds a weak in-memory Taxon tree.
WeakTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.WeakTaxonFactory
WeakValueHashMap - class org.biojava.utils.cache.WeakValueHashMap.
  Map implementation which keeps weak references to values.
WeakValueHashMap() - Constructor for class org.biojava.utils.cache.WeakValueHashMap
WebSequenceDB - class org.biojava.bio.seq.db.WebSequenceDB.
  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
WeightMatrix - interface org.biojava.bio.dp.WeightMatrix.
  A log odds weight matrix.
WeightMatrixAnnotator - class org.biojava.bio.dp.WeightMatrixAnnotator.
  Annotates a sequence with hits to a weight-matrix.
WeightMatrixAnnotator(WeightMatrix, double) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator
WordTokenization - class org.biojava.bio.seq.io.WordTokenization.
  Base class for tokenizations which accept whitespace-separated `words'.
WordTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.WordTokenization
w() - Static method in class org.biojava.bio.seq.NucleotideTools
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.
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.
wasEmpty() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer
  Returns true if no HitSummary and no Hit elements were encountered
weightForwarder - Variable in class org.biojava.bio.dist.AbstractOrderNDistribution
windowedSymbolList(SymbolList, int) - Static method in class org.biojava.bio.symbol.SymbolListViews
  A view of windows onto another SymbolList.
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.
wrap(SequenceBuilder) - Method in class org.biojava.bio.seq.ragbag.RagbagFeatureTypeCatcher
wrap(SequenceBuilder) - Method in interface org.biojava.bio.seq.ragbag.RagbagFilterFactory
  returns a SequenceBuilder object wrapped with an a filter.
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(Sequence) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  Writing Sequence.
writeAnnotationType(AnnotationType, XMLWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  Write an `AnnotationType` to the specified XMLWriter.
writeAnnotations(FeatureHolder) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeAssembly(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeBioSequence(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeClassification(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
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
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, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes a stream of Sequences to an OutputStream in EMBL format.
writeEmbl(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes a single Sequence to an OutputStream in EMBL 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
  Write a sequenceDB to an output stream in fasta format.
writeFasta(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes sequences from a SequenceIterator to an OutputStream in Fasta Format.
writeFasta(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes a single Sequence to an OutputStream in Fasta format.
writeFeatureSet(FeatureHolder, XMLWriter) - Method in class org.biojava.bio.program.xff.XFFWriter
writeFilter(FeatureFilter, XMLWriter, XMLFilterWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterWriter.FilterWriter
writeFilter(FeatureFilter, XMLWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
  Write a FeatureFilter to the supplied XMLWriter
writeFooter() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  Write </sciobj>
writeGFF(String, 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
writeGenbank(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes a stream of Sequences to an OutputStream in Genbank format.
writeGenbank(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes a single Sequence to an OutputStream in Genbank format.
writeGene(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeGenpept(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes a stream of Sequences to an OutputStream in Genpept format.
writeGenpept(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes a single Sequence to an OutputStream in Genpept format.
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
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
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`
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, String, PrintStream) - Method in class org.biojava.bio.program.phred.PhredFormat
  Deprecated. use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated. use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GAMEFormat
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.GAMEFormat
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated. use writeSequence(Sequence seq, PrintStream os)
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, String, PrintStream) - Method in interface org.biojava.bio.seq.io.SequenceFormat
  Deprecated. use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  Write sequence into AGAVE XML format.
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
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.
writeSwissprot(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes a stream of Sequences to an OutputStream in SwissProt format.
writeSwissprot(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Writes a single Sequence to an OutputStream in SwissProt format.
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.
writeTranscript(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
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

XFFFeatureSetHandler - class org.biojava.bio.program.xff.XFFFeatureSetHandler.
  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 org.biojava.bio.program.xff.XFFHelper.
XFFPartHandlerFactory - interface org.biojava.bio.program.xff.XFFPartHandlerFactory.
  Factory for StAX content handlers.
XFFTools - class org.biojava.bio.program.xff.XFFTools.
  Common functionality for manipulating XFF.
XFFTools() - Constructor for class org.biojava.bio.program.xff.XFFTools
XFFWriter - class org.biojava.bio.program.xff.XFFWriter.
  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
XMLAnnotationTypeHandler - class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.
  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 org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandler.
  Handler for an individual `CollectionConstraint` in an AnnotationType.
XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory - interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory.
  Handler Factory for a `CollectionConstraint` in an AnnotationType.
XMLAnnotationTypeHandler.PropertyConstraintHandler - interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandler.
  Handler for an individual `PropertyConstraint` in an AnnotationType.
XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory - interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory.
  Handler Factory for a `PropertyConstraint` in an AnnotationType.
XMLAnnotationTypeWriter - class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.
  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 org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLCollectionConstraintWriter.
  Writer for types of CollectionConstraint.
XMLAnnotationTypeWriter.XMLPropertyConstraintWriter - interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLPropertyConstraintWriter.
  Writer for types of PropertyConstraint.
XMLBeans - class org.biojava.utils.xml.XMLBeans.
  Construct java beans from XML elements
XMLBeans() - Constructor for class org.biojava.utils.xml.XMLBeans
XMLDispatcher - class org.biojava.utils.xml.XMLDispatcher.
  Simple implementation of XMLPeerFactory which delegates object- construction on the basis of tag name.
XMLDispatcher() - Constructor for class org.biojava.utils.xml.XMLDispatcher
  Construct a new XMLDispatcher which does not know about any tag names.
XMLDistributionReader - class org.biojava.bio.dist.XMLDistributionReader.
  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 org.biojava.bio.dist.XMLDistributionWriter.
  Writes an OrderNDistribution or simple Distribution to an XML file.
XMLDistributionWriter() - Constructor for class org.biojava.bio.dist.XMLDistributionWriter
XMLFilterHandler - class org.biojava.bio.seq.io.filterxml.XMLFilterHandler.
  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 org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandler.
  StAXContentHandler for a particular type of FeatureFilter.
XMLFilterHandler.FilterHandlerFactory - interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandlerFactory.
  Factory of StAXContentHandlers for a particular type of FeatureFilter.
XMLFilterWriter - class org.biojava.bio.seq.io.filterxml.XMLFilterWriter.
  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 org.biojava.bio.seq.io.filterxml.XMLFilterWriter.FilterWriter.
  Interface for an object which can write a FeatureFilter as XML.
XMLPeerBuilder - class org.biojava.utils.xml.XMLPeerBuilder.
  SAX DocumentHandler which uses an XMLPeerFactory to construct Java objects reflecting an XML document.
XMLPeerBuilder(XMLPeerFactory) - Constructor for class org.biojava.utils.xml.XMLPeerBuilder
  Construct a new XMLPeerBuilder, using the specified XMLPeerFactory
XMLPeerFactory - interface org.biojava.utils.xml.XMLPeerFactory.
  Interface to an factory which produces Java objects which reflect element in an XML document.
XMLWritable - interface org.biojava.utils.xml.XMLWritable.
  Object which knows how to represent itself as an XML element.
XMLWriter - interface org.biojava.utils.xml.XMLWriter.
  Simple interface for building XML documents.
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
XREF_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
XmlMarkovModel - class org.biojava.bio.dp.XmlMarkovModel.
XmlMarkovModel() - Constructor for class org.biojava.bio.dp.XmlMarkovModel
xHair - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `xHair` is the vertical line positioned along the X-axis.

## Y

YEAST_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the yeast mitochondrial genetic code.
y() - Static method in class org.biojava.bio.seq.NucleotideTools
yHair - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `yHair` is the horizontal line positioned along the Y-axis.

## Z

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.
ZiggyFeatureRenderer - class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer.
  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 org.biojava.bio.gui.sequence.ZiggyImapRenderer.
  `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`.
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

## _

_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.
_addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
_addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
_removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
_removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
_setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanel
_setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster

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 _