org.metaqtl.algo
Class QtlTreeAlgorithm

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

All Implemented Interfaces:

IMetaAlgorithm

public class QtlTreeAlgorithm
extends ClustAlgorithm

This class defines methods to perform agglomerative hierarchical QTL clustering.

Field Summary

int	tree_method This global variable defines the method used by the aglomerative hierarchical clustering.

Fields inherited from class org.metaqtl.algo.ClustAlgorithm

chrName, chromosomes, missing_sd_mode, ontology, result, sd_mode

Fields inherited from class org.metaqtl.algo.MetaAlgorithm

logger, loggerUp, workAmount, workProgress

Constructor Summary

QtlTreeAlgorithm(IBioGenome map, IBioOntology ontology)

Method Summary

MetaQtlResult[]	buildQtlTree(MetaQtlData data) For the given data points this method build the tree which represents the hierarchical clustering.
void	run() This method performs an agglomerative hierarchical QTL clustering on each chromosome and returns the result as a MetaQtlAnalysis object.
void	setTreeMethod(int tree_method)

Methods inherited from class org.metaqtl.algo.ClustAlgorithm

getResult, setCIMiss, setCIMode

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

tree_method

public int tree_method

This global variable defines the method used by the aglomerative hierarchical clustering.

Constructor Detail

QtlTreeAlgorithm

public QtlTreeAlgorithm(IBioGenome map,
                        IBioOntology ontology)

Method Detail

run

public void run()

This method performs an agglomerative hierarchical QTL clustering on each chromosome and returns the result as a MetaQtlAnalysis object. To control the behaviour of the algorithm use the global variables of the class.

Parameters:

map -

buildQtlTree

public MetaQtlResult[] buildQtlTree(MetaQtlData data)

For the given data points this method build the tree which represents the hierarchical clustering.

Parameters:

data - the QTK data points.

Returns:

the results of the hierarchical clustering.

See Also:

HClustAlgorithm

setTreeMethod

public void setTreeMethod(int tree_method)

Parameters:

centroid_method -