Package htsjdk.tribble.bed
Class SimpleBEDFeature
- java.lang.Object
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- htsjdk.tribble.bed.SimpleBEDFeature
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- All Implemented Interfaces:
Locatable
,BEDFeature
,Feature
- Direct Known Subclasses:
FullBEDFeature
public class SimpleBEDFeature extends Object implements BEDFeature
Feature from a BED file without exon blocks.
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Constructor Summary
Constructors Constructor Description SimpleBEDFeature(int start, int end, String chr)
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Method Summary
All Methods Instance Methods Concrete Methods 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)
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface htsjdk.samtools.util.Locatable
contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf
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Constructor Detail
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SimpleBEDFeature
public SimpleBEDFeature(int start, int end, String chr)
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Method Detail
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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.
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getStart
public int getStart()
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getEnd
public int getEnd()
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getStrand
public Strand getStrand()
- Specified by:
getStrand
in interfaceBEDFeature
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setStrand
public void setStrand(Strand strand)
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setChr
public void setChr(String chr)
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setStart
public void setStart(int start)
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setEnd
public void setEnd(int end)
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getType
public String getType()
- Specified by:
getType
in interfaceBEDFeature
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setType
public void setType(String type)
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getColor
public Color getColor()
- Specified by:
getColor
in interfaceBEDFeature
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setColor
public void setColor(Color color)
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getDescription
public String getDescription()
- Specified by:
getDescription
in interfaceBEDFeature
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setDescription
public void setDescription(String description)
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getName
public String getName()
- Specified by:
getName
in interfaceBEDFeature
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setName
public void setName(String name)
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getScore
public float getScore()
- Specified by:
getScore
in interfaceBEDFeature
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setScore
public void setScore(float score)
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getLink
public String getLink()
- Specified by:
getLink
in interfaceBEDFeature
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setLink
public void setLink(String link)
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getExons
public List<FullBEDFeature.Exon> getExons()
- Specified by:
getExons
in interfaceBEDFeature
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