htsjdk.tribble.gff

Class SequenceRegion

java.lang.Object

htsjdk.tribble.gff.SequenceRegion

All Implemented Interfaces:

Locatable

public class SequenceRegion
extends java.lang.Object
implements Locatable

Represents a sequence region feature in a gff3 file. May be linear or circular.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object other)
java.lang.String	getContig() Gets the contig name for the contig this is mapped to.
int	getEnd()
int	getStart()
int	hashCode()
boolean	isCircular()

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Method Detail

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

isCircular

public boolean isCircular()

equals

public boolean equals(java.lang.Object other)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object