picard.annotation

Class Gene.Transcript

java.lang.Object

picard.annotation.Gene.Transcript

Enclosing class:

Gene

public class Gene.Transcript
extends java.lang.Object

A single transcript of a gene. Sequence name is stored in the enclosing object (class Gene).

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Gene.Transcript.Exon 1-based, inclusive representation of an exon.

Field Summary

Fields

Modifier and Type	Field and Description
int	codingEnd
int	codingStart
Gene.Transcript.Exon[]	exons
java.lang.String	name
int	transcriptionEnd
int	transcriptionStart

Constructor Summary

Constructors

Constructor and Description
Transcript(java.lang.String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons)

Method Summary

Modifier and Type	Method and 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(java.lang.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()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Detail

name

public final java.lang.String name

transcriptionStart

public final int transcriptionStart

transcriptionEnd

public final int transcriptionEnd

codingStart

public final int codingStart

codingEnd

public final int codingEnd

exons

public final Gene.Transcript.Exon[] exons

Constructor Detail

Transcript

public Transcript(java.lang.String name,
                  int transcriptionStart,
                  int transcriptionEnd,
                  int codingStart,
                  int codingEnd,
                  int numExons)

Method Detail

addExon

public Gene.Transcript.Exon addExon(int start,
                                    int end)

start

public int start()

end

public int end()

length

public int length()

isSoloTranscript

public boolean isSoloTranscript()

getGene

public Gene getGene()

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 -

addCoverageCounts

public void addCoverageCounts(int genomeStart,
                              int genomeEnd,
                              int[] coverage)

Parameters:

genomeStart -

genomeEnd -

coverage -

getTranscriptCoordinate

public int getTranscriptCoordinate(int genomeCoordinate)

Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object