de.unibi.techfak.jpredictor.evolution
Class MotifEvolutionES

java.lang.Object
  de.unibi.techfak.jpredictor.evolution.MotifEvolution
      de.unibi.techfak.jpredictor.evolution.MotifEvolutionES

Direct Known Subclasses:

MotifEvolutionRewardedSelection

public class MotifEvolutionES
extends MotifEvolution

Class for evolute double motifs on the sequences of two (background and model) training sets.

Field Summary

Fields inherited from class de.unibi.techfak.jpredictor.evolution.MotifEvolution

buffIn, comm, generatingCharacters, generatingDistribution, gML, motifCounter, mutationProbabilities, numberOfNnucs, op, recombinationProbability, temperature

Constructor Summary

MotifEvolutionES(ICommunicator comm)
Creates the object but does not start the evolution.

Method Summary

(package private) void	evolveMotifLists() The lists of motifs are evolved into the next generation.
(package private) int	initMotifLists() Generates the initial populations.
(package private) void	selectMotifLists() Goes through all motif lists and selects the motifs to be kept.

Methods inherited from class de.unibi.techfak.jpredictor.evolution.MotifEvolution

evolveMotif, evolveMultiMotif, evolveSequenceMotif, fillNewWeights, outputResults, recombineParentSet, restrainMotifList, setMutationProbabilities, setRecombinationProbability, start, weightMotifLists, weightMotifs

Methods inherited from class java.lang.Object

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

Constructor Detail

MotifEvolutionES

public MotifEvolutionES(ICommunicator comm)
                 throws java.lang.NullPointerException,
                        java.lang.IllegalArgumentException

Creates the object but does not start the evolution.

Parameters:

comm - The communicater in which at least the training sets must be defined.

Throws:

java.lang.NullPointerException

java.lang.IllegalArgumentException

Method Detail

initMotifLists

int initMotifLists()

Description copied from class: MotifEvolution

Generates the initial populations. This method is the first in start(int) to be called.

Specified by:

initMotifLists in class MotifEvolution

Returns:

zero in case of no error, one, if an error occured while weighting the motifs

See Also:

MotifEvolution.start(int)

evolveMotifLists

void evolveMotifLists()

Description copied from class: MotifEvolution

The lists of motifs are evolved into the next generation. Evolution in this sense means any combination of cloning, recombination or mutation. Within the evolutionary loop this method is the first to be called.

Specified by:

evolveMotifLists in class MotifEvolution

See Also:

MotifEvolution.start(int)

selectMotifLists

void selectMotifLists()

Description copied from class: MotifEvolution

Goes through all motif lists and selects the motifs to be kept. Within the evolutionary loop this method is the third (last) to be called. A good start for the selection would be to call restrainMotifList(MotifList, int).

Specified by:

selectMotifLists in class MotifEvolution

See Also:

MotifEvolution.start(int), MotifEvolution.restrainMotifList(MotifList, int)