org.metaqtl.algo
Class QtlTreeAlgorithm

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