org.metaqtl
Class ChromCluster

java.lang.Object
  org.metaqtl.ChromCluster

public class ChromCluster
extends java.lang.Object

A cluster of chromosomes which share the same name inside a MapCluster framwork.

Version:

$Version$

Author:

Jean-Baptiste Veyrieras

See Also:

MapCluster

Nested Class Summary

class	ChromCluster.ClusterEdge
class	ChromCluster.ClusterGraph

Field Summary

java.util.ArrayList	clusters The list of the cluster members.
java.util.Hashtable	locusNames Ths locus name index table
java.lang.String	name The name of the chromosome cluster.
int	ni The total number of marker intervals.
int	nmc Total number of common marker between clusters

Constructor Summary

ChromCluster()
Creates a new instance if ChromCluster.

Method Summary

void	addChromosome(IBioLGroup group, IBioCross crossDesign, int mappingFunction, int mappingUnit, boolean rescale, boolean skeleton) Add a chromosome to the cluster
void	fixCluster() This methods frozes the index of the distinct markers over all the members of the cluster.
Chromosome[]	getClusterMembers() This method returns the members of the cluster as an array of Chromosomes.
double[]	getCMrkTotalNumbers()
ChromCluster.ClusterGraph	getGraph()
MetaDico	getMarkerDico()
int	getMarkerIndexByName(java.lang.String mrkName) For a given marker name this method returns the marker index of the marker table if found.
int	getMarkerIntervalNumber() This method returns the total number of marker intervals, i.e the sum over chromosomes of the number of marker intervals.
java.lang.String	getMarkerName(java.lang.String name) This method returns the name of the locus from the given name.
java.lang.String	getMarkerNameByIndex(int i) This method returns the name of the marker according to this indice.
int	getMarkerNumber() This method returns the number of distinct markers implied in this cluster, i.e the size of the marker table.
int	getMarkerOccurence(int i) Returns the number of times the marker with the indice i has been seen over the chromosomes of the cluster.
java.lang.String	getName() Returns the name of the cluster.
boolean	isConnected(int nMrk) Tests if the cluster of chromosome is connected using a graph approach.
boolean	isDubiousLocus(IBioLocus locus) If a list of dubious markers has been set before then this routine checks if the given locus is not included into this list.
void	setDubiousMarker(IBioLocus[] dubious) This method sets the list of dubious marker.
void	setMarkerDico(MetaDico mrkDico)
void	setMrkThresh(int mrkThresh)

Methods inherited from class java.lang.Object

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

Field Detail

nmc

public int nmc

Total number of common marker between clusters

ni

public int ni

The total number of marker intervals.

name

public java.lang.String name

The name of the chromosome cluster.

locusNames

public java.util.Hashtable locusNames

Ths locus name index table

clusters

public java.util.ArrayList clusters

The list of the cluster members.

Constructor Detail

ChromCluster

public ChromCluster()

Creates a new instance if ChromCluster.

Method Detail

addChromosome

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

Add a chromosome to the cluster

Parameters:

group - the chromosome to add.

crossDesign - the cross design properties.

mappingFunction - the mapping function for this chromosome.

mappingUnit - the mapping unit for this chromosome

rescale - true if the chromosome must be rescaled @see Chromosome#R2r()

skeleton - true if the chromosome if a skeleton chromosome.

isDubiousLocus

public boolean isDubiousLocus(IBioLocus locus)

If a list of dubious markers has been set before then this routine checks if the given locus is not included into this list.

Parameters:

locus - the locus to check.

Returns:

true if the locus is in the dubious marker list, false otherwise.

See Also:

setDubiousMarker(IBioLocus[])

getClusterMembers

public Chromosome[] getClusterMembers()

This method returns the members of the cluster as an array of Chromosomes. If any chromosome has been added to the cluster the method returns null.

Returns:

an array of Chromosomes.

getMarkerNumber

public int getMarkerNumber()

This method returns the number of distinct markers implied in this cluster, i.e the size of the marker table.

Returns:

the number of distinct markers.

getMarkerIntervalNumber

public int getMarkerIntervalNumber()

This method returns the total number of marker intervals, i.e the sum over chromosomes of the number of marker intervals.

Returns:

the total number of marker intervals.

fixCluster

public void fixCluster()

This methods frozes the index of the distinct markers over all the members of the cluster.

See Also:

getMarkerNameByIndex(int), getMarkerIndexByName(String)

getMarkerIndexByName

public int getMarkerIndexByName(java.lang.String mrkName)

For a given marker name this method returns the marker index of the marker table if found. Otherwise it returns -1.

Parameters:

mrkName - the name of the marker.

Returns:

the indice of the marker if found, -1 otherwise.

See Also:

fixCluster()

getMarkerNameByIndex

public java.lang.String getMarkerNameByIndex(int i)

This method returns the name of the marker according to this indice. The given indice is assumed to be inside the correct range.

Parameters:

i - the indice of the marker.

Returns:

the name of the marker.

See Also:

fixCluster()

getMarkerOccurence

public int getMarkerOccurence(int i)

Returns the number of times the marker with the indice i has been seen over the chromosomes of the cluster.

Parameters:

i -

Returns:

See Also:

fixCluster()

getMarkerName

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

This method returns the name of the locus from the given name. If no locus name dictionnary for the clusters is defined then the method returns an exact copy of the given name.

Parameters:

name - the raw name of the locus.

Returns:

the standard name of the locus.

setDubiousMarker

public void setDubiousMarker(IBioLocus[] dubious)

This method sets the list of dubious marker. It must be used before adding chromosomes to the chromosome cluster. Then the the markers which names matches those of the list will be ignored.

Parameters:

dubious -

getName

public java.lang.String getName()

Returns the name of the cluster.

Returns:

the name of the cluster.

getMarkerDico

public MetaDico getMarkerDico()

Returns:

Returns the mrkDico.

setMarkerDico

public void setMarkerDico(MetaDico mrkDico)

Parameters:

mrkDico - The mrkDico to set.

getCMrkTotalNumbers

public double[] getCMrkTotalNumbers()

isConnected

public boolean isConnected(int nMrk)

Tests if the cluster of chromosome is connected using a graph approach. Each chromosome is related to another by a set of common markers. The use can supply a minimal number of common marker to declare that a chromosome is connected to the other ones. The cluster is said to be connected if there is a path connecting every pair of chromosomes.

Returns:

setMrkThresh

public void setMrkThresh(int mrkThresh)

Parameters:

mrkThresh -

getGraph

public ChromCluster.ClusterGraph getGraph()

Returns: