apollo.dataadapter
Class GFFSyntenyAdapter

java.lang.Object
  apollo.dataadapter.GFFSyntenyAdapter

All Implemented Interfaces:

SyntenyAdapterI

public class GFFSyntenyAdapter
extends java.lang.Object
implements SyntenyAdapterI

Constructor Summary

GFFSyntenyAdapter(java.lang.String filePref, java.lang.String fileSuff, KaryotypeAdapterI ka, java.lang.String org1, java.lang.String org2)

Method Summary

void	addSyntenyRegionForChromosome(java.lang.String chromosome, SyntenyRegion region)
KaryotypeAdapterI	getKaryotypeAdapter()
java.lang.String	getName()
java.util.Vector	getSyntenyRegions(java.lang.String chr)
java.util.Vector	getSyntenyRegionsByChromosome(Chromosome chr)
java.lang.String	getType()
void	setName(java.lang.String name)
void	setType(java.lang.String type)

Methods inherited from class java.lang.Object

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

Constructor Detail

GFFSyntenyAdapter

public GFFSyntenyAdapter(java.lang.String filePref,
                         java.lang.String fileSuff,
                         KaryotypeAdapterI ka,
                         java.lang.String org1,
                         java.lang.String org2)

Method Detail

getType

public java.lang.String getType()

Specified by:

getType in interface SyntenyAdapterI

getName

public java.lang.String getName()

Specified by:

getName in interface SyntenyAdapterI

getKaryotypeAdapter

public KaryotypeAdapterI getKaryotypeAdapter()

Specified by:

getKaryotypeAdapter in interface SyntenyAdapterI

getSyntenyRegions

public java.util.Vector getSyntenyRegions(java.lang.String chr)

getSyntenyRegionsByChromosome

public java.util.Vector getSyntenyRegionsByChromosome(Chromosome chr)

Specified by:

getSyntenyRegionsByChromosome in interface SyntenyAdapterI

addSyntenyRegionForChromosome

public void addSyntenyRegionForChromosome(java.lang.String chromosome,
                                          SyntenyRegion region)

Specified by:

addSyntenyRegionForChromosome in interface SyntenyAdapterI

setName

public void setName(java.lang.String name)

Specified by:

setName in interface SyntenyAdapterI

setType

public void setType(java.lang.String type)

Specified by:

setType in interface SyntenyAdapterI