org.metaqtl.algo
Class QtlProjAlgorithm

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

public class QtlProjAlgorithm
extends MetaAlgorithm

This class defines some methods to project QTL positions from a genetic map to another.


Field Summary
 int sd_mode
          The mode of compuation of the standard deviation of the QTL positions.
 
Fields inherited from class org.metaqtl.algo.MetaAlgorithm
logger, loggerUp, workAmount, workProgress
 
Constructor Summary
QtlProjAlgorithm(IBioGenome[] maps, IBioGenome skeleton, IBioLocus[] dubious)
          Creates a new instance of QtlProjAlgorithm for the given configuration of projection.
 
Method Summary
 void checkProjection(ChromCluster[] chromClusters)
           
 void doProjection(ChromCluster[] chromClusters)
           
 Chromosome[] getResult()
           
 void run()
          This routine performs the projection of the QTL from the maps onto the skeleton and returns the chromosomes on which the projection has been done.
 void setPvalue(double p)
           
 void setRatio(double r)
           
 
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
 

Field Detail

sd_mode

public int sd_mode
The mode of compuation of the standard deviation of the QTL positions.

Constructor Detail

QtlProjAlgorithm

public QtlProjAlgorithm(IBioGenome[] maps,
                        IBioGenome skeleton,
                        IBioLocus[] dubious)
Creates a new instance of QtlProjAlgorithm for the given configuration of projection.

Parameters:
maps - the maps from which the Qtl would to be projected.
skeleton - the map on which the Qtl would be projected.
dubious - an optional list of dubious marker which would not be taken into account in the projection.
Method Detail

getResult

public Chromosome[] getResult()
Returns:

run

public void run()
This routine performs the projection of the QTL from the maps onto the skeleton and returns the chromosomes on which the projection has been done.


checkProjection

public void checkProjection(ChromCluster[] chromClusters)
Parameters:
chromClusters -

doProjection

public void doProjection(ChromCluster[] chromClusters)
Parameters:
chromClusters -

setRatio

public void setRatio(double r)
Parameters:
d -

setPvalue

public void setPvalue(double p)