org.metaqtl.algo
Class ClustAlgorithm

java.lang.Object
  extended by org.metaqtl.algo.MetaAlgorithm
      extended by 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