org.metaqtl.algo
Class ClustAlgorithm

java.lang.Object
  org.metaqtl.algo.MetaAlgorithm
      org.metaqtl.algo.ClustAlgorithm

All Implemented Interfaces:

IMetaAlgorithm

Direct Known Subclasses:

QtlClustAlgorithm, QtlTreeAlgorithm

public abstract class ClustAlgorithm
extends MetaAlgorithm

Field Summary

protected java.lang.String	chrName The name of the chromosome to study.
protected Chromosome[]	chromosomes The chromosome on which the clustering is performed.
protected int	missing_sd_mode This global variable defines the mode of imputation for the QTL for which the standard deviation of the position is not available.
protected IBioOntology	ontology The optional trait ontology to use to group Qtl.
protected MetaQtlAnalysis	result The result of the clustering.
protected int	sd_mode This global variable defines 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

ClustAlgorithm(IBioGenome map, IBioOntology ontology)

ClustAlgorithm(IBioGenome map, java.lang.String name, IBioOntology ontology)

Method Summary

MetaQtlAnalysis	getResult() When the algorithm is finished use this method to get the result.
void	setCIMiss(int missing_sd_mode)
void	setCIMode(int sd_mode)

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

Methods inherited from interface org.metaqtl.IMetaAlgorithm

run

Field Detail

result

protected MetaQtlAnalysis result

The result of the clustering.

chromosomes

protected Chromosome[] chromosomes

The chromosome on which the clustering is performed.

ontology

protected IBioOntology ontology

The optional trait ontology to use to group Qtl.

chrName

protected java.lang.String chrName

The name of the chromosome to study.

sd_mode

protected int sd_mode

This global variable defines the mode of compuation of the standard deviation of the QTL positions.

missing_sd_mode

protected int missing_sd_mode

This global variable defines the mode of imputation for the QTL for which the standard deviation of the position is not available.

Constructor Detail

ClustAlgorithm

public ClustAlgorithm(IBioGenome map,
                      IBioOntology ontology)

Parameters:

map -

ontology -

ClustAlgorithm

public ClustAlgorithm(IBioGenome map,
                      java.lang.String name,
                      IBioOntology ontology)

Method Detail

setCIMode

public void setCIMode(int sd_mode)

Parameters:

sd_mode -

setCIMiss

public void setCIMiss(int missing_sd_mode)

Parameters:

missing_sd_mode -

getResult

public MetaQtlAnalysis getResult()

When the algorithm is finished use this method to get the result. It returns a MetaQtlAnalysis instance which store in each chromosome the different clustering models which have been tested.

Returns:

a instance of MetaQtlAnalysis.

See Also:

MetaQtlAnalysis