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

Packages that use StrandedFeature.Strand
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
 void SixFrameRenderer.drawLine(java.awt.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
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
 StrandedFeature.Strand SimpleGFFRecord.getStrand()
           
 StrandedFeature.Strand GFFRecord.getStrand()
          The strand of the feature.
 StrandedFeature.Strand GFFRecordFilter.StrandFilter.getStrand()
           
 StrandedFeature.Strand GFFErrorHandler.invalidStrand(java.lang.String token)
          The `strand' field of the GFF entry was not a valid value.
 StrandedFeature.Strand GFFErrorHandler.AbortErrorHandler.invalidStrand(java.lang.String token)
           
 StrandedFeature.Strand GFFErrorHandler.SkipRecordErrorHandler.invalidStrand(java.lang.String token)
           
 

Methods in org.biojava.bio.program.gff with parameters of type StrandedFeature.Strand
 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
GFFRecordFilter.StrandFilter(StrandedFeature.Strand strand)
           
SimpleGFFRecord(java.lang.String seqName, java.lang.String source, java.lang.String feature, int start, int end, double score, StrandedFeature.Strand strand, int frame, java.lang.String comment, java.util.Map groupAttributes)
           
 

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

Methods in org.biojava.bio.program.gff3 that return StrandedFeature.Strand
 StrandedFeature.Strand GFF3Record.getStrand()
           
 StrandedFeature.Strand GFF3Record.Impl.getStrand()
           
 

Methods in org.biojava.bio.program.gff3 with parameters of type StrandedFeature.Strand
 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
 StrandedFeature.Strand SequenceDBSearchSubHit.getQueryStrand()
          Deprecated.  
 StrandedFeature.Strand SimpleSeqSimilaritySearchHit.getQueryStrand()
           
 StrandedFeature.Strand SeqSimilaritySearchHit.getQueryStrand()
          Return the strand of the hit with respect to the query sequence.
 StrandedFeature.Strand SequenceDBSearchHit.getQueryStrand()
          Deprecated.  
 StrandedFeature.Strand SimpleSeqSimilaritySearchSubHit.getQueryStrand()
           
 StrandedFeature.Strand SeqSimilaritySearchSubHit.getQueryStrand()
          Return the strand of the sub-hit with respect to the query sequence.
 StrandedFeature.Strand SequenceDBSearchSubHit.getSubjectStrand()
          Deprecated.  
 StrandedFeature.Strand SimpleSeqSimilaritySearchHit.getSubjectStrand()
           
 StrandedFeature.Strand SeqSimilaritySearchHit.getSubjectStrand()
          Return the strand of the sub-hit with respect to the subject sequence.
 StrandedFeature.Strand SequenceDBSearchHit.getSubjectStrand()
          Deprecated.  
 StrandedFeature.Strand SimpleSeqSimilaritySearchSubHit.getSubjectStrand()
           
 StrandedFeature.Strand SeqSimilaritySearchSubHit.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
SequenceDBSearchHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, java.lang.String subjectID, Annotation annotation, java.util.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, java.lang.String subjectID, Annotation annotation, java.util.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
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
 StrandedFeature.Strand StrandedFeature.Strand.flip()
          Return a strand that represents flipping this onto the opposite strand.
 StrandedFeature.Strand FeatureFilter.StrandFilter.getStrand()
          Retrieve the strand this matches.
 StrandedFeature.Strand FramedFeature.getStrand()
           
 StrandedFeature.Strand StrandedFeature.getStrand()
          Retrieve the strand that this feature lies upon.
static StrandedFeature.Strand StrandParser.parseStrand(java.lang.String strand)
           
 

Methods in org.biojava.bio.seq with parameters of type StrandedFeature.Strand
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, java.lang.String name, StrandedFeature.Strand strand)
          Extract a sub-sequence from a sequence.
 

Constructors in org.biojava.bio.seq with parameters of type StrandedFeature.Strand
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
 StrandedFeature.Strand SimpleStrandedFeature.getStrand()
           
 

Methods in org.biojava.bio.seq.impl with parameters of type StrandedFeature.Strand
 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
 java.lang.StringBuffer SeqFileFormer.formatLocation(java.lang.StringBuffer sb, Location loc, StrandedFeature.Strand strand)
          Deprecated. formatLocation creates a String representation of a Location.
 java.lang.StringBuffer SwissprotFileFormer.formatLocation(java.lang.StringBuffer theBuffer, Location theLocation, StrandedFeature.Strand theStrand)
          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
 void AGAVEFragmentOrderHandler.reportStrand(StrandedFeature.Strand strand)
           
 void AGAVEFeatureCallbackItf.reportStrand(StrandedFeature.Strand strand)
           
 void AGAVESeqFeatureHandler.reportStrand(StrandedFeature.Strand strand)
           
 void AGAVEBioSeqHandler.reportStrand(StrandedFeature.Strand strand)
           
 void AGAVEBioSequenceHandler.reportStrand(StrandedFeature.Strand strand)
           
 void AGAVEGeneHandler.reportStrand(StrandedFeature.Strand strand)
           
 void AGAVECompResultHandler.reportStrand(StrandedFeature.Strand strand)
           
 void AGAVEFragmentOrientationHandler.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
 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
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
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
 StrandedFeature.Strand SimpleRichFeature.getStrand()
          Retrieve the strand that this feature lies upon.
 

Methods in org.biojavax.bio.seq with parameters of type StrandedFeature.Strand
 void SimpleRichFeature.setStrand(StrandedFeature.Strand strand)
          Set the strand that this feature lies upon.