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)

Class FullBEDFeature

Nested Class Summary

Field Summary

Fields inherited from class htsjdk.tribble.bed.SimpleBEDFeature

Constructor Summary

Method Summary

Methods inherited from class htsjdk.tribble.bed.SimpleBEDFeature

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.tribble.bed.BEDFeature

Methods inherited from interface htsjdk.tribble.Feature

Methods inherited from interface htsjdk.samtools.util.Locatable

Methods inherited from interface htsjdk.tribble.NamedFeature

Constructor Details

FullBEDFeature

Method Details

getExons

setExons

addExon

addExon