de.unibi.techfak.jpredictor.clustering
Class RelationalCalculation

java.lang.Object
  de.unibi.techfak.jpredictor.clustering.Clustering
      de.unibi.techfak.jpredictor.clustering.RelationalCalculation

public class RelationalCalculation
extends Clustering

This class is designed to simply calculate all possible distance values between every two motifs and then print these values in a huge table.

Field Summary

Fields inherited from class de.unibi.techfak.jpredictor.clustering.Clustering

clusters, comm, consensus, mma, n, nucleotideVector, sma

Constructor Summary

RelationalCalculation(ICommunicator comm, SingleMotifAlignment sma, MultiMotifAlignment mma)
Inits the forward clustering.

Method Summary

(package private) void	clusterStep() Does nothing since it is never called.
(package private) void	initClustering() Does nothing.
(package private) void	outputResults() Prints out every relational value between each two motifs as a huge table.
(package private) boolean	stopTest(double threshold, int clusternumber) Returns true to stop immediately.

Methods inherited from class de.unibi.techfak.jpredictor.clustering.Clustering

alignMotifs, setMotifList, start

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RelationalCalculation

public RelationalCalculation(ICommunicator comm,
                             SingleMotifAlignment sma,
                             MultiMotifAlignment mma)
                      throws java.lang.NullPointerException

Inits the forward clustering. Simply calls the constructor from the Clustering class.

Throws:

java.lang.NullPointerException

Method Detail

stopTest

boolean stopTest(double threshold,
                 int clusternumber)

Returns true to stop immediately.

Specified by:

stopTest in class Clustering

Parameters:

threshold - The threshold to end the clustering. Might be Double.NaN to indicate, that the clustering should continue fully.

clusternumber - The number of clusters wished. Give zero or -1 to have a full clustering.

Returns:

true

See Also:

Clustering.stopTest(double, int)

initClustering

void initClustering()

Does nothing.

Specified by:

initClustering in class Clustering

See Also:

Clustering.start(double, int)

clusterStep

void clusterStep()
           throws java.lang.IllegalStateException

Does nothing since it is never called.

Specified by:

clusterStep in class Clustering

Throws:

java.lang.IllegalStateException - If a clustering could not be performed due to some reason.

outputResults

void outputResults()

Prints out every relational value between each two motifs as a huge table.

Overrides:

outputResults in class Clustering