java.lang.Object
- picard.annotation.Gene.Transcript

Enclosing class:

Gene
```
public class Gene.Transcript
extends 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 Description

class Gene.Transcript.Exon
1-based, inclusive representation of an exon.

Field Summary

Fields
Modifier and Type Field Description

int codingEnd

int codingStart

Gene.Transcript.Exon[] exons

String name

int transcriptionEnd

int transcriptionStart

Constructor Summary

Constructors
Constructor	Description
`Transcript(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons)`

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()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Detail

name
```
public final 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(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(Object o)
```
  Overrides:
  
  equals in class Object
- hashCode
```
public int hashCode()
```
  Overrides:
  
  hashCode in class Object

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

Class Gene.Transcript

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

name

transcriptionStart

transcriptionEnd

codingStart

codingEnd

exons

Constructor Detail

Transcript

Method Detail

addExon

start

end

length

isSoloTranscript

getGene

assignLocusFunctionForRange

addCoverageCounts

getTranscriptCoordinate

equals

hashCode