Uses of Class
org.biojava.bio.seq.StrandedFeature.Strand

Packages that use StrandedFeature.Strand

Package	Description
org.biojava.bio.gui.sequence	Graphical displays of biological sequences and associated annotations.
org.biojava.bio.program.gff	GFF manipulation.
org.biojava.bio.program.gff3	Support for reading and writing GFF3.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.agave	Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.io.game	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.projection	Code for projecting Feature objects and systematically altering their properties.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.

Uses of StrandedFeature.Strand in org.biojava.bio.gui.sequence

Methods in org.biojava.bio.gui.sequence with parameters of type StrandedFeature.Strand

Modifier and Type	Method and Description
void	SixFrameRenderer.drawLine(Graphics2D g, SequenceRenderContext src, int base, StrandedFeature.Strand strand) draws required bar in correct translation frame.
void	SixFrameRenderer.startZiggy(StrandedFeature.Strand strand) Used to initialise the spliced transcript renderer for a CDS feature where the ends of the feature define the frame of the feature.
void	SixFrameRenderer.startZiggy(StrandedFeature.Strand strand, int phase) This method is called to initialise the renderer for a spliced transcript.

Constructors in org.biojava.bio.gui.sequence with parameters of type StrandedFeature.Strand

Constructor and Description
StopRenderer(SixFrameRenderer pane, int moduloFrame, StrandedFeature.Strand strand)

Uses of StrandedFeature.Strand in org.biojava.bio.program.gff

Methods in org.biojava.bio.program.gff that return StrandedFeature.Strand

Modifier and Type	Method and Description
StrandedFeature.Strand	SimpleGFFRecord.getStrand()
StrandedFeature.Strand	GFFRecordFilter.StrandFilter.getStrand()
StrandedFeature.Strand	GFFRecord.getStrand() The strand of the feature.
StrandedFeature.Strand	GFFErrorHandler.invalidStrand(String token) The `strand' field of the GFF entry was not a valid value.
StrandedFeature.Strand	GFFErrorHandler.AbortErrorHandler.invalidStrand(String token)
StrandedFeature.Strand	GFFErrorHandler.SkipRecordErrorHandler.invalidStrand(String token)

Methods in org.biojava.bio.program.gff with parameters of type StrandedFeature.Strand

Modifier and Type	Method and Description
void	SimpleGFFRecord.setStrand(StrandedFeature.Strand strand) Set the strand to strand.
void	GFFRecordFilter.StrandFilter.setStrand(StrandedFeature.Strand strand)

Constructors in org.biojava.bio.program.gff with parameters of type StrandedFeature.Strand

Constructor and Description
GFFRecordFilter.StrandFilter(StrandedFeature.Strand strand)
SimpleGFFRecord(String seqName, String source, String feature, int start, int end, double score, StrandedFeature.Strand strand, int frame, String comment, Map groupAttributes)

Uses of StrandedFeature.Strand in org.biojava.bio.program.gff3

Methods in org.biojava.bio.program.gff3 that return StrandedFeature.Strand

Modifier and Type	Method and Description
StrandedFeature.Strand	GFF3Record.getStrand()
StrandedFeature.Strand	GFF3Record.Impl.getStrand()

Methods in org.biojava.bio.program.gff3 with parameters of type StrandedFeature.Strand

Modifier and Type	Method and Description
void	GFF3Record.Impl.setStrand(StrandedFeature.Strand strand)

Uses of StrandedFeature.Strand in org.biojava.bio.search

Methods in org.biojava.bio.search that return StrandedFeature.Strand

Modifier and Type	Method and Description
StrandedFeature.Strand	SimpleSeqSimilaritySearchSubHit.getQueryStrand()
StrandedFeature.Strand	SimpleSeqSimilaritySearchHit.getQueryStrand()
StrandedFeature.Strand	SequenceDBSearchSubHit.getQueryStrand() Deprecated.
StrandedFeature.Strand	SequenceDBSearchHit.getQueryStrand() Deprecated.
StrandedFeature.Strand	SeqSimilaritySearchSubHit.getQueryStrand() Return the strand of the sub-hit with respect to the query sequence.
StrandedFeature.Strand	SeqSimilaritySearchHit.getQueryStrand() Return the strand of the hit with respect to the query sequence.
StrandedFeature.Strand	SimpleSeqSimilaritySearchSubHit.getSubjectStrand()
StrandedFeature.Strand	SimpleSeqSimilaritySearchHit.getSubjectStrand()
StrandedFeature.Strand	SequenceDBSearchSubHit.getSubjectStrand() Deprecated.
StrandedFeature.Strand	SequenceDBSearchHit.getSubjectStrand() Deprecated.
StrandedFeature.Strand	SeqSimilaritySearchSubHit.getSubjectStrand() Return the strand of the sub-hit with respect to the subject sequence.
StrandedFeature.Strand	SeqSimilaritySearchHit.getSubjectStrand() Return the strand of the sub-hit with respect to the subject sequence.

Constructors in org.biojava.bio.search with parameters of type StrandedFeature.Strand

Constructor and Description
SequenceDBSearchHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, String subjectID, Annotation annotation, List subHits) Deprecated. Creates a new SequenceDBSearchHit object.
SequenceDBSearchSubHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, Alignment alignment, Annotation annotation) Deprecated. Creates a new SequenceDBSearchSubHit object.
SimpleSeqSimilaritySearchHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, String subjectID, Annotation annotation, List subHits) Creates a new SimpleSeqSimilaritySearchHit object.
SimpleSeqSimilaritySearchSubHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, Alignment alignment, Annotation annotation) Creates a new SimpleSeqSimilaritySearchSubHit object.

Uses of StrandedFeature.Strand in org.biojava.bio.seq

Fields in org.biojava.bio.seq declared as StrandedFeature.Strand

Modifier and Type	Field and Description
static StrandedFeature.Strand	StrandedFeature.NEGATIVE Flag to indicate that a feature is on the negative strand.
static StrandedFeature.Strand	StrandedFeature.POSITIVE Flag to indicate that a feature is on the positive strand.
StrandedFeature.Strand	StrandedFeature.Template.strand
static StrandedFeature.Strand	StrandedFeature.UNKNOWN Flag to indicate that a feature has an unknown strand.

Methods in org.biojava.bio.seq that return StrandedFeature.Strand

Modifier and Type	Method and Description
StrandedFeature.Strand	StrandedFeature.Strand.flip() Return a strand that represents flipping this onto the opposite strand.
StrandedFeature.Strand	StrandedFeature.getStrand() Retrieve the strand that this feature lies upon.
StrandedFeature.Strand	FramedFeature.getStrand()
StrandedFeature.Strand	FeatureFilter.StrandFilter.getStrand() Retrieve the strand this matches.
static StrandedFeature.Strand	StrandParser.parseStrand(String strand)

Methods in org.biojava.bio.seq with parameters of type StrandedFeature.Strand

Modifier and Type	Method and Description
static FeatureFilter	FilterUtils.byStrand(StrandedFeature.Strand strand) Match StrandedFeatures on the specified strand.
static SymbolList	DNATools.flip(SymbolList list, StrandedFeature.Strand strand) Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
void	StrandedFeature.setStrand(StrandedFeature.Strand strand) Set the strand that this feature lies upon.
static Sequence	SequenceTools.subSequence(Sequence seq, int start, int end, String name, StrandedFeature.Strand strand) Extract a sub-sequence from a sequence.

Constructors in org.biojava.bio.seq with parameters of type StrandedFeature.Strand

Constructor and Description
FeatureFilter.StrandFilter(StrandedFeature.Strand strand) Build a new filter that matches all features of a given strand.

Uses of StrandedFeature.Strand in org.biojava.bio.seq.impl

Methods in org.biojava.bio.seq.impl that return StrandedFeature.Strand

Modifier and Type	Method and Description
StrandedFeature.Strand	SimpleStrandedFeature.getStrand()

Methods in org.biojava.bio.seq.impl with parameters of type StrandedFeature.Strand

Modifier and Type	Method and Description
void	SimpleStrandedFeature.setStrand(StrandedFeature.Strand strand)

Uses of StrandedFeature.Strand in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io with parameters of type StrandedFeature.Strand

Modifier and Type	Method and Description
StringBuffer	SwissprotFileFormer.formatLocation(StringBuffer theBuffer, Location theLocation, StrandedFeature.Strand theStrand) Deprecated. formatLocation creates a String representation of a Location.
StringBuffer	SeqFileFormer.formatLocation(StringBuffer sb, Location loc, StrandedFeature.Strand strand) Deprecated. formatLocation creates a String representation of a Location.

Uses of StrandedFeature.Strand in org.biojava.bio.seq.io.agave

Methods in org.biojava.bio.seq.io.agave with parameters of type StrandedFeature.Strand

Modifier and Type	Method and Description
void	AGAVESeqFeatureHandler.reportStrand(StrandedFeature.Strand strand)
void	AGAVEGeneHandler.reportStrand(StrandedFeature.Strand strand)
void	AGAVEFragmentOrientationHandler.reportStrand(StrandedFeature.Strand strand)
void	AGAVEFragmentOrderHandler.reportStrand(StrandedFeature.Strand strand)
void	AGAVEFeatureCallbackItf.reportStrand(StrandedFeature.Strand strand)
void	AGAVECompResultHandler.reportStrand(StrandedFeature.Strand strand)
void	AGAVEBioSequenceHandler.reportStrand(StrandedFeature.Strand strand)
void	AGAVEBioSeqHandler.reportStrand(StrandedFeature.Strand strand)
void	AGAVEBioSeqCallbackItf.reportStrand(StrandedFeature.Strand strand)

Uses of StrandedFeature.Strand in org.biojava.bio.seq.io.game

Methods in org.biojava.bio.seq.io.game with parameters of type StrandedFeature.Strand

Modifier and Type	Method and Description
void	GAMETranscriptCallbackItf.reportExon(RangeLocation range, StrandedFeature.Strand strand) Allows nesting class that manages a transcript template to gain information about its extent from nested elements that represent exons.
void	GAMEFeatureSetHandler.reportExon(RangeLocation range, StrandedFeature.Strand strand)
void	GAMEFeatureCallbackItf.reportStrand(StrandedFeature.Strand strand)
void	GAMEAnnotationHandler.reportStrand(StrandedFeature.Strand strand)

Uses of StrandedFeature.Strand in org.biojava.bio.seq.projection

Methods in org.biojava.bio.seq.projection that return StrandedFeature.Strand

Modifier and Type	Method and Description
static StrandedFeature.Strand	ProjectionUtils.flipStrand(StrandedFeature.Strand s)
StrandedFeature.Strand	TranslateFlipContext.projectStrand(StrandedFeature.Strand strand)
StrandedFeature.Strand	TranslateFlipContext.revertStrand(StrandedFeature.Strand strand)

Methods in org.biojava.bio.seq.projection with parameters of type StrandedFeature.Strand

Modifier and Type	Method and Description
static StrandedFeature.Strand	ProjectionUtils.flipStrand(StrandedFeature.Strand s)
StrandedFeature.Strand	TranslateFlipContext.projectStrand(StrandedFeature.Strand strand)
StrandedFeature.Strand	TranslateFlipContext.revertStrand(StrandedFeature.Strand strand)

Uses of StrandedFeature.Strand in org.biojavax.bio.seq

Methods in org.biojavax.bio.seq that return StrandedFeature.Strand

Modifier and Type	Method and Description
StrandedFeature.Strand	SimpleRichFeature.getStrand() Retrieve the strand that this feature lies upon.

Methods in org.biojavax.bio.seq with parameters of type StrandedFeature.Strand

Modifier and Type	Method and Description
void	SimpleRichFeature.setStrand(StrandedFeature.Strand strand) Set the strand that this feature lies upon.