org.utgenome.gwt.utgb.client.bio
Class Gene

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.Interval
      org.utgenome.gwt.utgb.client.bio.Read
          org.utgenome.gwt.utgb.client.bio.Gene

All Implemented Interfaces:

Serializable, Comparable<Interval>, GenomeRange

Direct Known Subclasses:

BEDGene

public class Gene
extends Read
implements Serializable

Gene with Exon and CDS regions

Author:

leo

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.utgenome.gwt.utgb.client.bio.Read

Read.ReadType

Constructor Summary

Gene()

Gene(Gene other)

Gene(int start, int end)

Gene(String name, int start, int end)

Method Summary

void	accept(GenomeRangeVisitor visitor)
void	addCDS(CDS cds)
void	addExon(Exon exon)
void	adjustToOneOrigin()
List<CDS>	getCDS()
List<Exon>	getExon()
Exon	getExon(int index)

Methods inherited from class org.utgenome.gwt.utgb.client.bio.Read

downstreamRegion, getColor, getName, getStrand, isAntiSense, isSense, setColor, setName, setStrand, upstreamRegion

Methods inherited from class org.utgenome.gwt.utgb.client.bio.Interval

atomicSetStartAndEnd, compareTo, contains, contains, correctInterval, follows, getEnd, getStart, hasOverlap, intersect, intersectsWith, length, precedes, setEnd, setStart, toJSONArray, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Gene

public Gene()

Gene

public Gene(Gene other)

Gene

public Gene(int start,
            int end)

Gene

public Gene(String name,
            int start,
            int end)

Method Detail

addExon

public void addExon(Exon exon)

getExon

public List<Exon> getExon()

getExon

public Exon getExon(int index)

addCDS

public void addCDS(CDS cds)

getCDS

public List<CDS> getCDS()

adjustToOneOrigin

public void adjustToOneOrigin()

Overrides:

adjustToOneOrigin in class Interval

accept

public void accept(GenomeRangeVisitor visitor)

Specified by:

accept in interface GenomeRange

Overrides:

accept in class Read