Package htsjdk.tribble.bed

Class SimpleBEDFeature

java.lang.Object

htsjdk.tribble.bed.SimpleBEDFeature

All Implemented Interfaces:

Locatable, BEDFeature, Feature, NamedFeature

Direct Known Subclasses:

FullBEDFeature

public class SimpleBEDFeature
extends Object
implements BEDFeature

Feature from a BED file without exon blocks.

Field Summary

Fields

Modifier and Type	Field	Description
protected String	chr
protected int	end
protected int	start
protected Strand	strand

Constructor Summary

Constructors

Constructor	Description
SimpleBEDFeature(int start, int end, String chr)

Method Summary

Modifier and Type	Method	Description
Color	getColor()
String	getContig()	Gets the contig name for the contig this is mapped to.
String	getDescription()
int	getEnd()
List<FullBEDFeature.Exon>	getExons()
String	getLink()
String	getName()
float	getScore()
int	getStart()
Strand	getStrand()
String	getType()
void	setChr(String chr)
void	setColor(Color color)
void	setDescription(String description)
void	setEnd(int end)
void	setLink(String link)
void	setName(String name)
void	setScore(float score)
void	setStart(int start)
void	setStrand(Strand strand)
void	setType(String type)

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 Details

chr

protected String chr

start

protected int start

end

protected int end

strand

protected Strand strand

Constructor Details

SimpleBEDFeature

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

Method Details

getContig

public 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

getStrand

public Strand getStrand()

Specified by:

getStrand in interface BEDFeature

setStrand

public void setStrand(Strand strand)

setChr

public void setChr(String chr)

setStart

public void setStart(int start)

setEnd

public void setEnd(int end)

getType

public String getType()

Specified by:

getType in interface BEDFeature

setType

public void setType(String type)

getColor

public Color getColor()

Specified by:

getColor in interface BEDFeature

setColor

public void setColor(Color color)

getDescription

public String getDescription()

Specified by:

getDescription in interface BEDFeature

setDescription

public void setDescription(String description)

getName

public String getName()

Specified by:

getName in interface NamedFeature

setName

public void setName(String name)

getScore

public float getScore()

Specified by:

getScore in interface BEDFeature

setScore

public void setScore(float score)

getLink

public String getLink()

Specified by:

getLink in interface BEDFeature

setLink

public void setLink(String link)

getExons

public List<FullBEDFeature.Exon> getExons()

Specified by:

getExons in interface BEDFeature