Uses of Class org.biojava.bio.seq.StrandedFeature.Strand (BioJava-1.5-beta API)

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## 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(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` | `GFFRecordFilter.StrandFilter.getStrand()`
`StrandedFeature.Strand` | `GFFRecord.getStrand()` The strand of the feature.
`StrandedFeature.Strand` | `SimpleGFFRecord.getStrand()`
`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
`void` | `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.Strand
`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
`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` | `SequenceDBSearchHit.getQueryStrand()` Deprecated.
`StrandedFeature.Strand` | `SimpleSeqSimilaritySearchSubHit.getQueryStrand()`
`StrandedFeature.Strand` | `SeqSimilaritySearchHit.getQueryStrand()` Return the strand of the hit with respect to the query sequence.
`StrandedFeature.Strand` | `SeqSimilaritySearchSubHit.getQueryStrand()` Return the strand of the sub-hit with respect to the query sequence.
`StrandedFeature.Strand` | `SequenceDBSearchSubHit.getQueryStrand()` Deprecated.
`StrandedFeature.Strand` | `SimpleSeqSimilaritySearchHit.getQueryStrand()`
`StrandedFeature.Strand` | `SequenceDBSearchHit.getSubjectStrand()` Deprecated.
`StrandedFeature.Strand` | `SimpleSeqSimilaritySearchSubHit.getSubjectStrand()`
`StrandedFeature.Strand` | `SeqSimilaritySearchHit.getSubjectStrand()` Return the strand of the sub-hit with respect to the subject sequence.
`StrandedFeature.Strand` | `SeqSimilaritySearchSubHit.getSubjectStrand()` Return the strand of the sub-hit with respect to the subject sequence.
`StrandedFeature.Strand` | `SequenceDBSearchSubHit.getSubjectStrand()` Deprecated.
`StrandedFeature.Strand` | `SimpleSeqSimilaritySearchHit.getSubjectStrand()`

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, 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
`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` | `StrandedFeature.getStrand()` Retrieve the strand that this feature lies upon.
`StrandedFeature.Strand` | `FramedFeature.getStrand()`
`static StrandedFeature.Strand` | `StrandParser.parseStrand(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, 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
`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
`void` | `AGAVEGeneHandler.reportStrand(StrandedFeature.Strand strand)`
`void` | `AGAVEFragmentOrientationHandler.reportStrand(StrandedFeature.Strand strand)`
`void` | `AGAVEFeatureCallbackItf.reportStrand(StrandedFeature.Strand strand)`
`void` | `AGAVECompResultHandler.reportStrand(StrandedFeature.Strand strand)`
`void` | `AGAVEFragmentOrderHandler.reportStrand(StrandedFeature.Strand strand)`
`void` | `AGAVEBioSequenceHandler.reportStrand(StrandedFeature.Strand strand)`
`void` | `AGAVESeqFeatureHandler.reportStrand(StrandedFeature.Strand strand)`
`void` | `AGAVEBioSeqCallbackItf.reportStrand(StrandedFeature.Strand strand)`
`void` | `AGAVEBioSeqHandler.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. NOT IMPLEMENTED.

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