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 FeatureRenderers which use a 'string of beads' metaphor for displaying features.
AbstractBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Creates a new AbstractBeadRenderer with no delegates.
AbstractBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
Creates a new AbstractBeadRenderer object.
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.
AlphabetResolvers are helpers which determine which type of sequence Alphabet to expect from a search result.
AlphabetResolver() - Constructor for class org.biojava.bio.program.ssbind.AlphabetResolver
 
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 Annotations from Maps.
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 Annotations and AnnotationTypes.
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 SequenceViewerEvents.
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 SequenceViewerEvents.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addSequenceViewerMotionListener adds a listener for mouse motion SequenceViewerEvents.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.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 SequenceViewerEvents.
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 Features 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.
BeadFeatureRenderers 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.
BioStores represent directory and file structures which index flat files according to the OBDA specification.
BioStore(File, boolean) - Constructor for class org.biojava.bio.program.indexdb.BioStore
Creates a new BioStore flatfile index at the specified location with the specified caching behaviour.
BioStoreFactory - class 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 SeqSimilaritySearchResults from SAX events via a SeqSimilarityAdapter.
BlastLikeSearchBuilder(List) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
Creates a new BlastLikeSearchBuilder which will instantiate results into the List target.
BlastLikeSearchBuilder(List, SequenceDB, SequenceDBInstallation) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
Creates a new BlastLikeSearchBuilder which will instantiate results into the List target.
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 Chromatograms.
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 ChangeEvents 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.
EmblCDROMIndexStores 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 Features 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 SimilarityPairFeatures 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 FeatureHolders.
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 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 <> 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 Rectangle2Ds that are the in-memory representation of the callboxes.
generateChangeSupport() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
 
generateChangeSupport() - Method in class org.biojava.utils.AbstractChangeable
Called the first time a ChangeSupport object is needed.
generateCrossProductAlphaFromName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generates a new CrossProductAlphabet from the give name.
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 GeneralPaths 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 Records by searching against the primary identifiers if the namespace argument is equal to the primary namespace or otherwise by searching the secondary namespaces.
get(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 HomologyFeatures 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 decoratorClass and return it if found.
getDefaultChanger() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
Get the changer that will be applied to values of tags with no specific handler registered.
getDefaultConstraint() - Method in 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 SequenceRenderers.
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 Features belonging to the currently rendered Sequence.
getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePoster
 
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 Features 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 HomologyFeatures 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.IntegerSymbols.
getIntOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Helper method for converting a Number-valued option into an int primitive.
getInvTransform() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
Returns a new AffineTransform describing the transformation from output space to chromatogram space.
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 SequenceRenderers.
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 SequenceRenderers.
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 Records in the index.
getRecurse() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
 
getRecurse() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
getRecurse returns the recursion flag of the filter.
getRecurse() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Return whether features will be filtered recursively or not.
getRecursive() - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
 
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 Features belonging to the currently rendered secondary Sequence.
getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getSecondaryRange() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
getSecondaryRange returns the range of the secondary sequence currently rendered.
getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondaryRange returns a RangeLocation representing the region of the secondary sequence currently being rendered.
getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
 
getSecondarySequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondarySequence returns the entire secondary Sequence currently being rendered.
getSecondarySymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondarySymbolTranslation returns the current translation in Symbols 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 Symbols 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 ChangeEvents 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 FeatureHolders 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 Symbols which will be applied when rendering.
getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getSymbolTranslation returns the current translation in Symbols which will be applied when rendering.
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 Symbols belonging to the currently rendered Sequence.
getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePanel
Retrieve the currently rendered SymbolList
getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePoster
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 Symbols 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 Symbols which can be rendered in the visible area (excluding all borders) of the PairwiseSequencePanel at the current scale.
getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the PairwiseSequencePanel at the current scale.
getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the TranslatedSequencePanel at the current scale.
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 HomologyFeatures.
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 MultiLineRenderers.
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.
HotSpots 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.
ImageMapRenderers create strings representing Features 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 Sequences to be rendered and the PairwiseHomologyRenderer are not null.
isActive() - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
isActive() - Method in class org.biojava.bio.gui.sequence.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 MultiLineRenders.
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 SymbolLists which contain Symbolsfrom 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 SequenceRenderers 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.Options 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 PairwiseRenderContexts passed to it.
PairwiseFilteringRenderer(PairwiseSequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
Creates a new PairwiseFilteringRenderer which uses a filter which accepts all features.
PairwiseFilteringRenderer(PairwiseSequenceRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
Creates a new PairwiseFilteringRenderer.
PairwiseOverlayRenderer - class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer.
PairwiseOverlayRenderer allows a list of other PairwiseSequenceRenderers to superimpose their output.
PairwiseOverlayRenderer() - Constructor for class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
Creates a new, empty PairwiseOverlayRenderer.
PairwiseRenderContext - interface 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.
PairwiseSequenceRenderers 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.
PropertyConstraints 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
paints 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 MouseEvents 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 Readers from RandomAccessFiles.
RandomAccessReader(RandomAccessFile) - Constructor for class org.biojava.utils.io.RandomAccessReader
Creates a new RandomAccessReader wrapping the RandomAccessFile and using a default-sized buffer (8192 bytes).
RandomAccessReader(RandomAccessFile, int) - Constructor for class org.biojava.utils.io.RandomAccessReader
Creates a new RandomAccessReader wrapping the RandomAccessFile and using a buffer of the specified size.
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 Sequences with Features 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 RestrictionSites.
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 SequenceViewerEvents.
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 SequenceViewerEvents.
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
addSequenceViewerMotionListener removes a listener for mouse motion SequenceViewerEvents.
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
 
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.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 SequenceViewerEvents.
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 Runnables 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 SimilarityPairFeatures.
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 Features.
SITE_FEATURE_TYPE - Static variable in class org.biojava.bio.molbio.RestrictionMapper
SITE_FEATURE_TYPE the type String used by RestrictionMapper when creating restriction site Features.
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 SeqSimilaritySearchHits 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 SeqSimilaritySearchHits 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 SeqSimilaritySearchSubHits 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 SeqSimilaritySearchSubHits 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 StAXHandlerBindings 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 SimilarityPairFeatures 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 SimilarityPairFeatures.
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.
StAXHandlerBindings associates an ElementRecognizer with a factory which creates StAXContentHandlers for elements which it the ElementRecognizer accepts.
StAXHandlerFactory - interface org.biojava.bio.program.ssbind.StAXHandlerFactory.
StAXHandlerFactory is an interface for factories producing StAXContentHandlers 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 Symbols 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 Symbols which will be applied when rendering.
setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
setSymbolTranslation sets the translation in Symbols which will be applied when rendering.
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
 

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