htsjdk.tribble

Class MutableFeature

java.lang.Object

htsjdk.tribble.MutableFeature

All Implemented Interfaces:

Locatable, Feature

public class MutableFeature
extends java.lang.Object
implements Feature

A mutable concrete Feature.

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	contig
int	end
int	start

Constructor Summary

Constructors

Constructor and Description
MutableFeature(Feature feature)
MutableFeature(java.lang.String contig, int start, int end)

Method Summary

Modifier and Type	Method and Description
java.lang.String	getContig() Gets the contig name for the contig this is mapped to.
int	getEnd()
int	getStart()
void	setAll(Feature feature)

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.tribble.Feature

getChr

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Field Detail

contig

public java.lang.String contig

start

public int start

end

public int end

Constructor Detail

MutableFeature

public MutableFeature(Feature feature)

MutableFeature

public MutableFeature(java.lang.String contig,
                      int start,
                      int end)

Method Detail

setAll

public void setAll(Feature feature)

getContig

public java.lang.String getContig()

Description copied from interface: Locatable

Gets the contig name for the contig this is mapped to. May return null if there is no unique mapping.

Specified by:

getContig in interface Locatable

Returns:

name of the contig this is mapped to, potentially null

getStart

public int getStart()

Specified by:

getStart in interface Locatable

Returns:

1-based start position, undefined if getContig() == null

getEnd

public int getEnd()

Specified by:

getEnd in interface Locatable

Returns:

1-based closed-ended position, undefined if getContig() == null