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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.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 into alternate coordinate systems. |
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. |
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.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. |
void |
SixFrameRenderer.drawLine(java.awt.Graphics2D g,
SequenceRenderContext src,
int base,
StrandedFeature.Strand strand)
draws required bar in correct translation frame. |
Constructors in org.biojava.bio.gui.sequence with parameters of type StrandedFeature.Strand | |
StopRenderer(SixFrameRenderer pane,
int moduloFrame,
StrandedFeature.Strand strand)
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Uses of StrandedFeature.Strand in org.biojava.bio.program.gff |
Methods in org.biojava.bio.program.gff that return StrandedFeature.Strand | |
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)
|
StrandedFeature.Strand |
GFFRecordFilter.StrandFilter.getStrand()
|
StrandedFeature.Strand |
GFFRecord.getStrand()
The strand of the feature. |
StrandedFeature.Strand |
SimpleGFFRecord.getStrand()
|
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)
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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.search |
Methods in org.biojava.bio.search that return StrandedFeature.Strand | |
StrandedFeature.Strand |
SeqSimilaritySearchHit.getQueryStrand()
Return the strand of the hit with respect to the query sequence. |
StrandedFeature.Strand |
SeqSimilaritySearchHit.getSubjectStrand()
Return the strand of the sub-hit with respect to the subject sequence. |
StrandedFeature.Strand |
SequenceDBSearchHit.getQueryStrand()
Deprecated. |
StrandedFeature.Strand |
SequenceDBSearchHit.getSubjectStrand()
Deprecated. |
StrandedFeature.Strand |
SimpleSeqSimilaritySearchSubHit.getQueryStrand()
|
StrandedFeature.Strand |
SimpleSeqSimilaritySearchSubHit.getSubjectStrand()
|
StrandedFeature.Strand |
SimpleSeqSimilaritySearchHit.getQueryStrand()
|
StrandedFeature.Strand |
SimpleSeqSimilaritySearchHit.getSubjectStrand()
|
StrandedFeature.Strand |
SequenceDBSearchSubHit.getQueryStrand()
Deprecated. |
StrandedFeature.Strand |
SequenceDBSearchSubHit.getSubjectStrand()
Deprecated. |
StrandedFeature.Strand |
SeqSimilaritySearchSubHit.getQueryStrand()
Return the strand of the sub-hit with respect to the query sequence. |
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. |
|
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. |
|
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. |
|
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. |
Uses of StrandedFeature.Strand in org.biojava.bio.seq |
Fields in org.biojava.bio.seq declared as StrandedFeature.Strand | |
static StrandedFeature.Strand |
StrandedFeature.POSITIVE
Flag to indicate that a feature is on the positive strand. |
static StrandedFeature.Strand |
StrandedFeature.NEGATIVE
Flag to indicate that a feature is on the negative strand. |
static StrandedFeature.Strand |
StrandedFeature.UNKNOWN
Flag to indicate that a feature has an unknown strand. |
StrandedFeature.Strand |
StrandedFeature.Template.strand
|
Methods in org.biojava.bio.seq that return StrandedFeature.Strand | |
StrandedFeature.Strand |
FramedFeature.getStrand()
|
StrandedFeature.Strand |
FeatureFilter.StrandFilter.getStrand()
Retrieve the strand this matches. |
StrandedFeature.Strand |
StrandedFeature.getStrand()
Retrieve the strand that this feature lies upon. |
StrandedFeature.Strand |
StrandedFeature.Strand.flip()
Return a strand that represents flipping this onto the opposite strand. |
static StrandedFeature.Strand |
StrandParser.parseStrand(java.lang.String strand)
|
protected StrandedFeature.Strand |
ProjectedFeatureHolder.transformStrand(StrandedFeature.Strand strand)
Called to transform a strand property between projection and underlying coordinates. |
StrandedFeature.Strand |
ProjectedFeatureHolder.getStrand(StrandedFeature sf)
|
Methods in org.biojava.bio.seq with parameters of type StrandedFeature.Strand | |
static FeatureFilter |
FilterUtils.byStrand(StrandedFeature.Strand strand)
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protected StrandedFeature.Strand |
ProjectedFeatureHolder.transformStrand(StrandedFeature.Strand strand)
Called to transform a strand property between projection and underlying coordinates. |
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()
|
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 |
SwissprotFileFormer.formatLocation(java.lang.StringBuffer theBuffer,
Location theLocation,
StrandedFeature.Strand theStrand)
formatLocation creates a String representation of
a Location . |
java.lang.StringBuffer |
SeqFileFormer.formatLocation(java.lang.StringBuffer sb,
Location loc,
StrandedFeature.Strand strand)
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 |
AGAVEBioSeqCallbackItf.reportStrand(StrandedFeature.Strand strand)
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void |
AGAVEFragmentOrientationHandler.reportStrand(StrandedFeature.Strand strand)
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void |
AGAVEGeneHandler.reportStrand(StrandedFeature.Strand strand)
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void |
AGAVEBioSequenceHandler.reportStrand(StrandedFeature.Strand strand)
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void |
AGAVEBioSeqHandler.reportStrand(StrandedFeature.Strand strand)
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void |
AGAVESeqFeatureHandler.reportStrand(StrandedFeature.Strand strand)
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void |
AGAVECompResultHandler.reportStrand(StrandedFeature.Strand strand)
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void |
AGAVEFeatureCallbackItf.reportStrand(StrandedFeature.Strand strand)
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void |
AGAVEFragmentOrderHandler.reportStrand(StrandedFeature.Strand strand)
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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 |
GAMEAnnotationHandler.reportStrand(StrandedFeature.Strand strand)
|
void |
GAMEFeatureCallbackItf.reportStrand(StrandedFeature.Strand strand)
|
void |
GAMEFeatureSetHandler.reportExon(RangeLocation range,
StrandedFeature.Strand strand)
|
Uses of StrandedFeature.Strand in org.biojava.bio.seq.projection |
Methods in org.biojava.bio.seq.projection that return StrandedFeature.Strand | |
StrandedFeature.Strand |
ProjectedStrandedFeature.getStrand()
|
static StrandedFeature.Strand |
ProjectionUtils.flipStrand(StrandedFeature.Strand s)
|
StrandedFeature.Strand |
ProjectionContext.getStrand(StrandedFeature f)
Get the strand of the projected feature. |
Methods in org.biojava.bio.seq.projection with parameters of type StrandedFeature.Strand | |
static StrandedFeature.Strand |
ProjectionUtils.flipStrand(StrandedFeature.Strand s)
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Uses of StrandedFeature.Strand in org.biojava.bio.seq.ragbag |
Methods in org.biojava.bio.seq.ragbag that return StrandedFeature.Strand | |
StrandedFeature.Strand |
RagbagMap.MapElement.getStrand()
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