Uses of Class
org.biojava.bio.seq.StrandedFeature.Strand
Packages that use StrandedFeature.Strand
Package
Description
Graphical displays of biological sequences and associated annotations.
GFF manipulation.
Support for reading and writing GFF3.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Code for projecting Feature objects and systematically altering their
properties.
Rich implementations of Sequences, Locations and Features.
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Uses of StrandedFeature.Strand in org.biojava.bio.gui.sequence
Methods in org.biojava.bio.gui.sequence with parameters of type StrandedFeature.StrandModifier and TypeMethodDescriptionvoid
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.StrandModifierConstructorDescriptionStopRenderer
(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.StrandModifier and TypeMethodDescriptionGFFRecord.getStrand()
The strand of the feature.GFFRecordFilter.StrandFilter.getStrand()
SimpleGFFRecord.getStrand()
GFFErrorHandler.AbortErrorHandler.invalidStrand
(String token) GFFErrorHandler.invalidStrand
(String token) The `strand' field of the GFF entry was not a valid value.GFFErrorHandler.SkipRecordErrorHandler.invalidStrand
(String token) Methods in org.biojava.bio.program.gff with parameters of type StrandedFeature.StrandModifier and TypeMethodDescriptionvoid
GFFRecordFilter.StrandFilter.setStrand
(StrandedFeature.Strand strand) void
SimpleGFFRecord.setStrand
(StrandedFeature.Strand strand) Set the strand to strand.Constructors in org.biojava.bio.program.gff with parameters of type StrandedFeature.StrandModifierConstructorDescriptionSimpleGFFRecord
(String seqName, String source, String feature, int start, int end, double score, StrandedFeature.Strand strand, int frame, String comment, Map groupAttributes) StrandFilter
(StrandedFeature.Strand strand) -
Uses of StrandedFeature.Strand in org.biojava.bio.program.gff3
Methods in org.biojava.bio.program.gff3 that return StrandedFeature.StrandMethods in org.biojava.bio.program.gff3 with parameters of type StrandedFeature.Strand -
Uses of StrandedFeature.Strand in org.biojava.bio.search
Methods in org.biojava.bio.search that return StrandedFeature.StrandModifier and TypeMethodDescriptionSeqSimilaritySearchHit.getQueryStrand()
Return the strand of the hit with respect to the query sequence.SeqSimilaritySearchSubHit.getQueryStrand()
Return the strand of the sub-hit with respect to the query sequence.SequenceDBSearchHit.getQueryStrand()
Deprecated.SequenceDBSearchSubHit.getQueryStrand()
Deprecated.SimpleSeqSimilaritySearchHit.getQueryStrand()
SimpleSeqSimilaritySearchSubHit.getQueryStrand()
SeqSimilaritySearchHit.getSubjectStrand()
Return the strand of the sub-hit with respect to the subject sequence.SeqSimilaritySearchSubHit.getSubjectStrand()
Return the strand of the sub-hit with respect to the subject sequence.SequenceDBSearchHit.getSubjectStrand()
Deprecated.SequenceDBSearchSubHit.getSubjectStrand()
Deprecated.SimpleSeqSimilaritySearchHit.getSubjectStrand()
SimpleSeqSimilaritySearchSubHit.getSubjectStrand()
Constructors in org.biojava.bio.search with parameters of type StrandedFeature.StrandModifierConstructorDescriptionSequenceDBSearchHit
(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 newSequenceDBSearchHit
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 newSequenceDBSearchSubHit
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 newSimpleSeqSimilaritySearchHit
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 newSimpleSeqSimilaritySearchSubHit
object. -
Uses of StrandedFeature.Strand in org.biojava.bio.seq
Fields in org.biojava.bio.seq declared as StrandedFeature.StrandModifier and TypeFieldDescriptionstatic final StrandedFeature.Strand
StrandedFeature.NEGATIVE
Flag to indicate that a feature is on the negative strand.static final StrandedFeature.Strand
StrandedFeature.POSITIVE
Flag to indicate that a feature is on the positive strand.StrandedFeature.Template.strand
static final StrandedFeature.Strand
StrandedFeature.UNKNOWN
Flag to indicate that a feature has an unknown strand.Methods in org.biojava.bio.seq that return StrandedFeature.StrandModifier and TypeMethodDescriptionStrandedFeature.Strand.flip()
Return a strand that represents flipping this onto the opposite strand.FeatureFilter.StrandFilter.getStrand()
Retrieve the strand this matches.FramedFeature.getStrand()
StrandedFeature.getStrand()
Retrieve the strand that this feature lies upon.static final StrandedFeature.Strand
StrandParser.parseStrand
(String strand) Methods in org.biojava.bio.seq with parameters of type StrandedFeature.StrandModifier and TypeMethodDescriptionstatic final 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.StrandModifierConstructorDescriptionStrandFilter
(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.StrandMethods in org.biojava.bio.seq.impl with parameters of type StrandedFeature.StrandModifier and TypeMethodDescriptionvoid
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.StrandModifier and TypeMethodDescriptionSeqFileFormer.formatLocation
(StringBuffer sb, Location loc, StrandedFeature.Strand strand) Deprecated.formatLocation
creates a String representation of aLocation
.SwissprotFileFormer.formatLocation
(StringBuffer theBuffer, Location theLocation, StrandedFeature.Strand theStrand) Deprecated.formatLocation
creates a String representation of aLocation
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Uses of StrandedFeature.Strand in org.biojava.bio.seq.io.agave
Methods in org.biojava.bio.seq.io.agave with parameters of type StrandedFeature.StrandModifier and TypeMethodDescriptionvoid
AGAVEBioSeqCallbackItf.reportStrand
(StrandedFeature.Strand strand) void
AGAVEBioSeqHandler.reportStrand
(StrandedFeature.Strand strand) void
AGAVEBioSequenceHandler.reportStrand
(StrandedFeature.Strand strand) void
AGAVECompResultHandler.reportStrand
(StrandedFeature.Strand strand) void
AGAVEFeatureCallbackItf.reportStrand
(StrandedFeature.Strand strand) void
AGAVEFragmentOrderHandler.reportStrand
(StrandedFeature.Strand strand) void
AGAVEFragmentOrientationHandler.reportStrand
(StrandedFeature.Strand strand) void
AGAVEGeneHandler.reportStrand
(StrandedFeature.Strand strand) void
AGAVESeqFeatureHandler.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.StrandModifier and TypeMethodDescriptionvoid
GAMEFeatureSetHandler.reportExon
(RangeLocation range, StrandedFeature.Strand strand) 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
GAMEAnnotationHandler.reportStrand
(StrandedFeature.Strand strand) void
GAMEFeatureCallbackItf.reportStrand
(StrandedFeature.Strand strand) -
Uses of StrandedFeature.Strand in org.biojava.bio.seq.projection
Methods in org.biojava.bio.seq.projection that return StrandedFeature.StrandModifier and TypeMethodDescriptionstatic StrandedFeature.Strand
ProjectionUtils.flipStrand
(StrandedFeature.Strand s) final StrandedFeature.Strand
TranslateFlipContext.projectStrand
(StrandedFeature.Strand strand) final StrandedFeature.Strand
TranslateFlipContext.revertStrand
(StrandedFeature.Strand strand) Methods in org.biojava.bio.seq.projection with parameters of type StrandedFeature.StrandModifier and TypeMethodDescriptionstatic StrandedFeature.Strand
ProjectionUtils.flipStrand
(StrandedFeature.Strand s) final StrandedFeature.Strand
TranslateFlipContext.projectStrand
(StrandedFeature.Strand strand) final 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.StrandModifier and TypeMethodDescriptionSimpleRichFeature.getStrand()
Retrieve the strand that this feature lies upon.Methods in org.biojavax.bio.seq with parameters of type StrandedFeature.StrandModifier and TypeMethodDescriptionvoid
SimpleRichFeature.setStrand
(StrandedFeature.Strand strand) Set the strand that this feature lies upon.