htsjdk.tribble.bed

Class FullBEDFeature

java.lang.Object

htsjdk.tribble.bed.SimpleBEDFeature

htsjdk.tribble.bed.FullBEDFeature

All Implemented Interfaces:

Locatable, BEDFeature, Feature

public class FullBEDFeature
extends SimpleBEDFeature
implements BEDFeature

Object for full BED file.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	FullBEDFeature.Exon A sub region of a feature.
class	FullBEDFeature.Exon2

Field Summary

Fields inherited from class htsjdk.tribble.bed.SimpleBEDFeature

chr, end, start, strand

Constructor Summary

Constructors

Constructor and Description
FullBEDFeature(java.lang.String chr, int start, int end)

Method Summary

Methods

Modifier and Type	Method and Description
void	addExon(FullBEDFeature.Exon exon)
void	addExon(int exonStart, int exonEnd, int cdStart, int cdEnd, int exonNumber)
java.util.List<FullBEDFeature.Exon>	getExons()
void	setExons(java.util.List<FullBEDFeature.Exon> exons)

Methods inherited from class htsjdk.tribble.bed.SimpleBEDFeature

getChr, getColor, getContig, getDescription, getEnd, getLink, getName, getScore, getStart, getStrand, getType, setChr, setColor, setDescription, setEnd, setLink, setName, setScore, setStart, setStrand, setType

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.tribble.bed.BEDFeature

getColor, getDescription, getLink, getName, getScore, getStrand, getType

Methods inherited from interface htsjdk.tribble.Feature

getChr

Methods inherited from interface htsjdk.samtools.util.Locatable

getContig, getEnd, getStart

Constructor Detail

FullBEDFeature

public FullBEDFeature(java.lang.String chr,
              int start,
              int end)

Method Detail

getExons

public java.util.List<FullBEDFeature.Exon> getExons()

Specified by:

getExons in interface BEDFeature

Overrides:

getExons in class SimpleBEDFeature

setExons

public void setExons(java.util.List<FullBEDFeature.Exon> exons)

addExon

public void addExon(FullBEDFeature.Exon exon)

addExon

public void addExon(int exonStart,
           int exonEnd,
           int cdStart,
           int cdEnd,
           int exonNumber)