com.hfg.bio.seq

Class Gene

java.lang.Object

com.hfg.bio.seq.Gene

All Implemented Interfaces:

Comparable

public class Gene
extends Object
implements Comparable

A gene representation.

Constructor Summary

Constructors

Constructor and Description
Gene()

Method Summary

Modifier and Type	Method and Description
Gene	addExon(Exon inValue)
Gene	addExons(Collection<? extends Exon> inValues)
Gene	addURL(Link inValue) Add a URL to the gene.
int	compareTo(Object inObj2)
Color	getColor()
String	getDescription()
Integer	getEndLocation()
List<Exon>	getExons()
String	getId()
int	getLeft() The leftmost basepair of the gene (the start location if the gene is on the forward strand or the end location if the gene is on the reverse strand).
GenomicLocation	getLocation()
int	getRight() The rightmost basepair of the gene (the end location if the gene is on the forward strand or the start location if the gene is on the reverse strand).
SeqMappingCoverage	getSeqMappingCoverage()
NCBITaxon	getSpecies()
Integer	getStartLocation() Basepair location of the start of the gene.
Strand	getStrand()
List<Link>	getURLs()
Gene	setColor(Color inValue)
Gene	setDescription(String inValue)
Gene	setEndLocation(int inValue)
Gene	setId(String inValue)
Gene	setLocation(GenomicLocation inValue)
void	setSeqMappingCoverage(SeqMappingCoverage inValue)
Gene	setSpecies(NCBITaxon inValue)
Gene	setStartLocation(int inValue)
Gene	setStrand(Strand inValue)

Methods inherited from class java.lang.Object

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

Constructor Detail

Gene

public Gene()

Method Detail

setLocation

public Gene setLocation(GenomicLocation inValue)

getLocation

public GenomicLocation getLocation()

addExons

public Gene addExons(Collection<? extends Exon> inValues)

addExon

public Gene addExon(Exon inValue)

getExons

public List<Exon> getExons()

setId

public Gene setId(String inValue)

getId

public String getId()

setDescription

public Gene setDescription(String inValue)

getDescription

public String getDescription()

setSeqMappingCoverage

public void setSeqMappingCoverage(SeqMappingCoverage inValue)

getSeqMappingCoverage

public SeqMappingCoverage getSeqMappingCoverage()

setSpecies

public Gene setSpecies(NCBITaxon inValue)

getSpecies

public NCBITaxon getSpecies()

addURL

public Gene addURL(Link inValue)

Add a URL to the gene. If more than one URL is defined, a popup menu will be shown.

Parameters:

inValue - the link to associate with the gene

getURLs

public List<Link> getURLs()

getStartLocation

public Integer getStartLocation()

Basepair location of the start of the gene.

Returns:

the 1-based location

setStartLocation

public Gene setStartLocation(int inValue)

getEndLocation

public Integer getEndLocation()

setEndLocation

public Gene setEndLocation(int inValue)

getLeft

public int getLeft()

The leftmost basepair of the gene (the start location if the gene is on the forward strand or the end location if the gene is on the reverse strand).

Returns:

the 1-based left location

getRight

public int getRight()

The rightmost basepair of the gene (the end location if the gene is on the forward strand or the start location if the gene is on the reverse strand).

Returns:

the 1-based right location

setStrand

public Gene setStrand(Strand inValue)

getStrand

public Strand getStrand()

setColor

public Gene setColor(Color inValue)

getColor

public Color getColor()

compareTo

public int compareTo(Object inObj2)

Specified by:

compareTo in interface Comparable