Package picard.annotation
Class Gene.Transcript
- java.lang.Object
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- picard.annotation.Gene.Transcript
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
Gene.Transcript.Exon
1-based, inclusive representation of an exon.
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Field Summary
Fields Modifier and Type Field Description int
codingEnd
int
codingStart
Gene.Transcript.Exon[]
exons
String
name
int
transcriptionEnd
int
transcriptionStart
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Constructor Summary
Constructors Constructor Description Transcript(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addCoverageCounts(int genomeStart, int genomeEnd, int[] coverage)
Gene.Transcript.Exon
addExon(int start, int end)
void
assignLocusFunctionForRange(int start, LocusFunction[] locusFunctions)
Write into locusFunctions the function of each position from start to start + locusFunctions.length relative to this transcript.int
end()
boolean
equals(Object o)
Gene
getGene()
int
getTranscriptCoordinate(int genomeCoordinate)
Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.int
hashCode()
boolean
isSoloTranscript()
int
length()
int
start()
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Field Detail
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name
public final String name
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transcriptionStart
public final int transcriptionStart
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transcriptionEnd
public final int transcriptionEnd
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codingStart
public final int codingStart
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codingEnd
public final int codingEnd
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exons
public final Gene.Transcript.Exon[] exons
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Constructor Detail
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Transcript
public Transcript(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons)
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Method Detail
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addExon
public Gene.Transcript.Exon addExon(int start, int end)
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start
public int start()
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end
public int end()
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length
public int length()
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isSoloTranscript
public boolean isSoloTranscript()
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getGene
public Gene getGene()
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assignLocusFunctionForRange
public void assignLocusFunctionForRange(int start, LocusFunction[] locusFunctions)
Write into locusFunctions the function of each position from start to start + locusFunctions.length relative to this transcript. Does not overwrite an existing value in locusFunctions that is stronger than the function for that locus in this transcript.- Parameters:
start
- 1-based genomic coordinate of the first position in locusFunctions.locusFunctions
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addCoverageCounts
public void addCoverageCounts(int genomeStart, int genomeEnd, int[] coverage)
- Parameters:
genomeStart
-genomeEnd
-coverage
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getTranscriptCoordinate
public int getTranscriptCoordinate(int genomeCoordinate)
Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.
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