SimpleBEDFeature (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.tribble.bed.SimpleBEDFeature

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.

Field Summary

Fields
Modifier and Type Field Description

protected String chr

protected int end

protected int start

protected Strand strand

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)

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

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)`

Methods inherited from interface htsjdk.tribble.Feature
getChr

Methods inherited from interface htsjdk.samtools.util.Locatable
contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - chr
```
protected String chr
```
  - start
```
protected int start
```
  - end
```
protected int end
```
  - strand
```
protected Strand strand
```
- Constructor Detail
  - SimpleBEDFeature
```
public SimpleBEDFeature(int start,
                        int end,
                        String chr)
```
- Method Detail
  - 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 BEDFeature
  - 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

Class SimpleBEDFeature

Field Summary

Constructor Summary

Method Summary

Methods inherited from interface htsjdk.tribble.Feature

Methods inherited from interface htsjdk.samtools.util.Locatable

Methods inherited from class java.lang.Object

Field Detail

chr

start

end

strand

Constructor Detail

SimpleBEDFeature

Method Detail

getContig

getStart

getEnd

getStrand

setStrand

setChr

setStart

setEnd

getType

setType

getColor

setColor

getDescription

setDescription

getName

setName

getScore

setScore

getLink

setLink

getExons