de.unibi.techfak.jpredictor.evolution
Class MotifEvolutionFull

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

public class MotifEvolutionFull
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

MotifEvolutionFull(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.
(package private) boolean	weightMotifLists() Weights the motifs in all motif lists.

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

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

Methods inherited from class java.lang.Object

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

Constructor Detail

MotifEvolutionFull

public MotifEvolutionFull(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)

weightMotifLists

boolean weightMotifLists()

Description copied from class: MotifEvolution

Weights the motifs in all motif lists. Within the evolutionary loop this method is the second to be called. This method simple sets one motif list after the other in the communicator and then calls weightMotifs( null, null ). If you want another way of weighting, or if some motif lists might be left out of weighting overwrite this method

Overrides:

weightMotifLists in class MotifEvolution

See Also:

MotifEvolution.start(int), MotifEvolution.weightMotifs(Vector[], Vector[])

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)