htsjdk.tribble

Class SimpleFeature

java.lang.Object

htsjdk.tribble.SimpleFeature

All Implemented Interfaces:

Locatable, Feature

public class SimpleFeature
extends java.lang.Object
implements Feature

A simple concrete Feature.

Constructor Summary

Constructors

Constructor and Description
SimpleFeature(java.lang.String contig, int start, int end)

Method Summary

Methods

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

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleFeature

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

Method Detail

getChr

@Deprecated
public java.lang.String getChr()

Deprecated.

Description copied from interface: Feature

Return the features reference sequence name, e.g chromosome or contig

Specified by:

getChr in interface 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