org.metaqtl
Class MapCluster

java.lang.Object
  org.metaqtl.MapCluster

public class MapCluster
extends java.lang.Object

Constructor Summary

MapCluster()
Creates a new instance of MapCluster.

Method Summary

void	addAllMap(IBioGenome[] maps)
void	addChromosome(IBioLGroup group, IBioCross crossDesign, int mappingFunction, int mappingUnit, boolean rescale, boolean skeleton) Add a chromosome to the map cluster framework.
void	addMap(IBioGenome map, boolean skeleton) Add a map to the cluster.
java.lang.String	getChromosomeName(java.lang.String name) This method returns the name of the chromosome from the given name.
ChromCluster[]	getClusters() Returns the chromosome clusters.
MetaDico	getMarkerDico()
void	setDubiousMarker(IBioLocus[] dubious) This method sets the list of dubious marker.
void	setMarkerDico(MetaDico mrkDico)

Methods inherited from class java.lang.Object

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

Constructor Detail

MapCluster

public MapCluster()

Creates a new instance of MapCluster.

Method Detail

addMap

public void addMap(IBioGenome map,
                   boolean skeleton)

Add a map to the cluster. This automatically classifies the chromosomes of the given map into clusters of chromosome using their names.

Parameters:

map - the map to add.

skeleton - true if the chromosomes of this map must flagged as the skeleton chromosomes.

See Also:

ChromCluster, ChromCluster.addChromosome(IBioLGroup, IBioCross, int, int, boolean, boolean)

addChromosome

public void addChromosome(IBioLGroup group,
                          IBioCross crossDesign,
                          int mappingFunction,
                          int mappingUnit,
                          boolean rescale,
                          boolean skeleton)

Add a chromosome to the map cluster framework.

Parameters:

group - the chromosome.

crossDesign - the cross design

mappingFunction - the mapping function.

mappingUnit - the mapping unit.

rescale - true if the chromosome must be rescaled

skeleton - true if the chromosome is the skeleton chromosome.

getChromosomeName

public java.lang.String getChromosomeName(java.lang.String name)

This method returns the name of the chromosome from the given name. If no synonym dictionnary is defined then the method returns the same name.

Parameters:

name -

Returns:

getClusters

public ChromCluster[] getClusters()

Returns the chromosome clusters. This method must be invoked after that all the maps have been added using the method addMap(IBioGenome, boolean). Otherwise if any valid call has been done to this method then the returned array will be null. IBioGenome[] mymaps = ...; MapCluster mapCluster = new MapCluster(); for(i=0;i

Returns:

an array of ChromCluster.

See Also:

ChromCluster

setDubiousMarker

public void setDubiousMarker(IBioLocus[] dubious)

This method sets the list of dubious marker. Any call to the method addMap(IBioGenome, boolean) will then taken into account this list.

Parameters:

dubious - the array of dubious loci.

See Also:

ChromCluster.setDubiousMarker(IBioLocus[])

getMarkerDico

public MetaDico getMarkerDico()

Returns:

Returns the mrkDico.

setMarkerDico

public void setMarkerDico(MetaDico mrkDico)

Parameters:

mrkDico - The mrkDico to set.

addAllMap

public void addAllMap(IBioGenome[] maps)

Parameters:

maps -