htsjdk.tribble.bed.FullBEDFeature

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, getName, 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

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)

Class FullBEDFeature

Nested Class Summary