org.metaqtl.algo
Class MetaMapAlgorithm

java.lang.Object
  extended by org.metaqtl.algo.MetaAlgorithm
      extended by org.metaqtl.algo.MetaMapAlgorithm
All Implemented Interfaces:
IMetaAlgorithm

public class MetaMapAlgorithm
extends MetaAlgorithm

This class is dedicated to the construction of a consensus genetic map from a set of genetic maps based on a Weigthed Least Square approach.


Field Summary
 
Fields inherited from class org.metaqtl.algo.MetaAlgorithm
logger, loggerUp, workAmount, workProgress
 
Constructor Summary
MetaMapAlgorithm(IBioGenome[] maps, IBioGenome skeleton, IBioLocus[] dubious, MetaDico mrkDico)
           
 
Method Summary
protected  MetaChrom buildMetaChrom(ChromCluster cluster)
          For a cluster of chromosomes cluster this method builds the consensus chromosome using a Weighted Least Square strategy and returns the result as a MetaChrom object.
 MetaMap getResult()
           
 void run()
          This method builds a consensus genetic map from the given array of maps.
 void setMarkerDico(MetaDico mrkDico)
           
 void setMrkThreshold(int mrkThresh)
           
 
Methods inherited from class org.metaqtl.algo.MetaAlgorithm
disableLogger, getLogger, getWorkAmount, getWorkProgress, isLoggerEnable, setLogger, setLogger
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MetaMapAlgorithm

public MetaMapAlgorithm(IBioGenome[] maps,
                        IBioGenome skeleton,
                        IBioLocus[] dubious,
                        MetaDico mrkDico)
Parameters:
maps -
skeleton -
dubious -
mrkDico -
Method Detail

getResult

public MetaMap getResult()
Returns:

run

public void run()
This method builds a consensus genetic map from the given array of maps. The consensus map is returned as a MetaMap. If skeleton is not null then the positions of the markers on this map are assumed to be known and are used as anchor points in the construction of the consensus map. If dubious is no null or not empty then the loci of this array won't be included in the consensus map.

Parameters:
maps - the array of genetic maps.
skeleton - a genetic map used as skeleton.
dubious - an array of dubious loci to not include in the construction.

buildMetaChrom

protected MetaChrom buildMetaChrom(ChromCluster cluster)
For a cluster of chromosomes cluster this method builds the consensus chromosome using a Weighted Least Square strategy and returns the result as a MetaChrom object.

Parameters:
cluster - the cluster of chromosomes.
Returns:
the consensus chromosome.

setMarkerDico

public void setMarkerDico(MetaDico mrkDico)
Parameters:
mrkDico -

setMrkThreshold

public void setMrkThreshold(int mrkThresh)
Parameters:
mrkThresh -