htsjdk.tribble.bed

Class FullBEDFeature.Exon

java.lang.Object

htsjdk.tribble.bed.FullBEDFeature.Exon

Enclosing class:

FullBEDFeature

public class FullBEDFeature.Exon
extends java.lang.Object

A sub region of a feature. For example, a Gene exon

Constructor Summary

Constructors

Constructor and Description
Exon(int start, int end) Constructs ...

Method Summary

Modifier and Type	Method and Description
int	getCdEnd() Method description
int	getCdStart() Method description
int	getCodingLength() Method description
int	getNumber()
java.lang.String	getValueString(double position)
void	setCodingEnd(int codingEnd) Method description
void	setCodingStart(int codingStart) Method description
void	setMrnaBase(int base)
void	setNumber(int number)
void	setPhase(int phase) Method description
void	setReadingFrame(int offset) Method description
void	setUTR(boolean utr) Flag indicating that the entire exon is the UTR.

Methods inherited from class java.lang.Object

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

Constructor Detail

Exon

public Exon(int start,
            int end)

Constructs ...

Parameters:

start -

end -

Method Detail

setMrnaBase

public void setMrnaBase(int base)

setUTR

public void setUTR(boolean utr)

Flag indicating that the entire exon is the UTR.

Parameters:

utr -

setCodingStart

public void setCodingStart(int codingStart)

Method description

Parameters:

codingStart -

setCodingEnd

public void setCodingEnd(int codingEnd)

Method description

Parameters:

codingEnd -

setReadingFrame

public void setReadingFrame(int offset)

Method description

Parameters:

offset -

setPhase

public void setPhase(int phase)

Method description

Parameters:

phase -

getCdStart

public int getCdStart()

Method description

Returns:

getCdEnd

public int getCdEnd()

Method description

Returns:

getCodingLength

public int getCodingLength()

Method description

Returns:

getValueString

public java.lang.String getValueString(double position)

getNumber

public int getNumber()

setNumber

public void setNumber(int number)