Package picard.annotation
Class Gene.Transcript
java.lang.Object
picard.annotation.Gene.Transcript
- Enclosing class:
- Gene
A single transcript of a gene. Sequence name is stored in the enclosing object (class Gene).
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionclass
1-based, inclusive representation of an exon. -
Field Summary
FieldsModifier and TypeFieldDescriptionfinal int
final int
final Gene.Transcript.Exon[]
final String
final int
final int
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Constructor Summary
ConstructorsConstructorDescriptionTranscript
(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons) -
Method Summary
Modifier and TypeMethodDescriptionvoid
addCoverageCounts
(int genomeStart, int genomeEnd, int[] coverage) 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
getGene()
int
getTranscriptCoordinate
(int genomeCoordinate) Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.int
hashCode()
boolean
int
length()
int
start()
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Field Details
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name
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transcriptionStart
public final int transcriptionStart -
transcriptionEnd
public final int transcriptionEnd -
codingStart
public final int codingStart -
codingEnd
public final int codingEnd -
exons
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Constructor Details
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Transcript
public Transcript(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons)
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Method Details
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addExon
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start
public int start() -
end
public int end() -
length
public int length() -
isSoloTranscript
public boolean isSoloTranscript() -
getGene
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assignLocusFunctionForRange
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. -
equals
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hashCode
public int hashCode()
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