com.hfg.bio.seq

Class GenomicLocation

java.lang.Object

com.hfg.bio.seq.format.feature.genbank.GenBankFeatureLocation

com.hfg.bio.seq.GenomicLocation

All Implemented Interfaces:

SeqFeatureLocation, Comparable

public class GenomicLocation
extends GenBankFeatureLocation

Genomic location.

Constructor Summary

Constructors

Constructor and Description
GenomicLocation()
GenomicLocation(String inLocationString)
GenomicLocation(XMLTag inXMLTag)

Method Summary

Modifier and Type	Method and Description
GenomicLocation	clone()
int	compareTo(GenomicLocation inObj2)
String	getAssembly()
String	getBuild()
String	getChromosome()
String	getContig()
Strand	getStrand()
NCBITaxon	getTaxon()
GenomicLocation	setAssembly(String inValue)
GenomicLocation	setBuild(String inValue)
GenomicLocation	setChromosome(String inValue)
GenomicLocation	setContig(String inValue)
GenomicLocation	setSeqLength(Integer inValue)
GenomicLocation	setStrand(Strand inValue)
GenomicLocation	setTaxon(NCBITaxon inValue)
XMLTag	toXMLTag()

Methods inherited from class com.hfg.bio.seq.format.feature.genbank.GenBankFeatureLocation

append, compareTo, equals, eval, eval, extend3Prime, extend5Prime, get3Prime, get5Prime, getIntrons, getSeqLength, hashCode, length, set3Prime, set5Prime, toIntRange, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

GenomicLocation

public GenomicLocation()

GenomicLocation

public GenomicLocation(String inLocationString)

GenomicLocation

public GenomicLocation(XMLTag inXMLTag)

Method Detail

clone

public GenomicLocation clone()

Overrides:

clone in class GenBankFeatureLocation

toXMLTag

public XMLTag toXMLTag()

setAssembly

public GenomicLocation setAssembly(String inValue)

getAssembly

public String getAssembly()

setBuild

public GenomicLocation setBuild(String inValue)

getBuild

public String getBuild()

setChromosome

public GenomicLocation setChromosome(String inValue)

getChromosome

public String getChromosome()

setContig

public GenomicLocation setContig(String inValue)

getContig

public String getContig()

setSeqLength

public GenomicLocation setSeqLength(Integer inValue)

Overrides:

setSeqLength in class GenBankFeatureLocation

setTaxon

public GenomicLocation setTaxon(NCBITaxon inValue)

getTaxon

public NCBITaxon getTaxon()

setStrand

public GenomicLocation setStrand(Strand inValue)

getStrand

public Strand getStrand()

compareTo

public int compareTo(GenomicLocation inObj2)