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java.lang.Objectorg.metaqtl.ChromCluster
public class ChromCluster
A cluster of chromosomes which share the same name inside a
MapCluster
framwork.
MapCluster
Nested Class Summary | |
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class |
ChromCluster.ClusterEdge
|
class |
ChromCluster.ClusterGraph
|
Field Summary | |
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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 | |
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ChromCluster()
Creates a new instance if ChromCluster. |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public int nmc
public int ni
public java.lang.String name
public java.util.Hashtable locusNames
public java.util.ArrayList clusters
Constructor Detail |
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public ChromCluster()
Method Detail |
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public void addChromosome(IBioLGroup group, IBioCross crossDesign, int mappingFunction, int mappingUnit, boolean rescale, boolean skeleton)
group
- the chromosome to add.crossDesign
- the cross design properties.mappingFunction
- the mapping function for this chromosome.mappingUnit
- the mapping unit for this chromosomerescale
- true if the chromosome must be rescaled @see Chromosome#R2r()skeleton
- true if the chromosome if a skeleton chromosome.public boolean isDubiousLocus(IBioLocus locus)
locus
- the locus to check.
setDubiousMarker(IBioLocus[])
public Chromosome[] getClusterMembers()
Chromosomes
. If any chromosome has been
added to the cluster the method returns null.
Chromosomes
.public int getMarkerNumber()
public int getMarkerIntervalNumber()
public void fixCluster()
getMarkerNameByIndex(int)
,
getMarkerIndexByName(String)
public int getMarkerIndexByName(java.lang.String mrkName)
mrkName
- the name of the marker.
fixCluster()
public java.lang.String getMarkerNameByIndex(int i)
i
- the indice of the marker.
fixCluster()
public int getMarkerOccurence(int i)
i
-
fixCluster()
public java.lang.String getMarkerName(java.lang.String name)
name
- the raw name of the locus.
public void setDubiousMarker(IBioLocus[] dubious)
dubious
- public java.lang.String getName()
public MetaDico getMarkerDico()
public void setMarkerDico(MetaDico mrkDico)
mrkDico
- The mrkDico to set.public double[] getCMrkTotalNumbers()
public boolean isConnected(int nMrk)
public void setMrkThresh(int mrkThresh)
mrkThresh
- public ChromCluster.ClusterGraph getGraph()
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