Package htsjdk.tribble.bed

Class FullBEDFeature

java.lang.Object

htsjdk.tribble.bed.SimpleBEDFeature

htsjdk.tribble.bed.FullBEDFeature

All Implemented Interfaces:

Locatable, BEDFeature, Feature, NamedFeature

public class FullBEDFeature
extends SimpleBEDFeature
implements BEDFeature

Object for full BED file.

Nested Class Summary

Nested Classes

Modifier and Type	Class	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	Description
FullBEDFeature(String chr, int start, int end)

Method Summary

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

Methods inherited from class htsjdk.tribble.bed.SimpleBEDFeature

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, getScore, getStrand, getType

Methods inherited from interface htsjdk.tribble.Feature

getChr

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getContig, getEnd, getLengthOnReference, getStart, overlaps, withinDistanceOf

Methods inherited from interface htsjdk.tribble.NamedFeature

getName

Constructor Details

FullBEDFeature

public FullBEDFeature(String chr,
 int start,
 int end)

Method Details

getExons

public List<FullBEDFeature.Exon> getExons()

Specified by:

getExons in interface BEDFeature

Overrides:

getExons in class SimpleBEDFeature

setExons

public void setExons(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)