com.softtechdesign.ga
Class GASequenceList

java.lang.Object
  |
  +--com.softtechdesign.ga.GA
        |
        +--com.softtechdesign.ga.GAString
              |
              +--com.softtechdesign.ga.GASequenceList

All Implemented Interfaces:

java.lang.Runnable

public abstract class GASequenceList

extends GAString

 The GASequenceList class models chromosomes as strings and extends GAString 
 while adding one main capability:
 the ability to prevent duplicate genes from appearing in a chromosome.

 For example, if you extend this class to optimize some sort of list (set), you don't
 want chromosomes to evolve that violate the rule that there be no duplicates in
 the list.
 
 If you just extended GAString, you could wind up with duplicate genes. For example,
 with GAString, if your gene space is "ABCDEF", you may wind up with chromosomes like
 "ADDCBE".

 The GASequenceList methods prevent duplicate gene entries in your chromosomes. So a gene
 space like "ABCDEF" can result in chromosomes like "FABCDE" and "EFABCD" but NEVER
 "ADDCBE".


Author: 
Jeff Smith jeff@SoftTechDesign.com










Field Summary




protected  double[]
sequence



          sequence of genes


 
Fields inherited from class com.softtechdesign.ga.GAString
chromDecPts, possGeneValues
 
Fields inherited from class com.softtechdesign.ga.GA
bestFitnessChromIndex, chromNextGen, chromosomeDim, chromosomes, computeStatistics, crossoverProb, crossoverType, genAvgDeviation, genAvgFitness, maxGenerations, maxPrelimGenerations, mutationProb, numPrelimRuns, populationDim, prelimChrom, randomSelectionChance, worstFitnessChromIndex
 



Constructor Summary
GASequenceList(int pChromosomeDim,
               int pPopulationDim,
               double pCrossoverProb,
               int pRandomSelectionChance,
               int pMaxGenerations,
               int pNumPrelimRuns,
               int pMaxPrelimGenerations,
               double pMutationProb,
               int pChromDecPts,
               java.lang.String pPossGeneValues,
               int pCrossoverType,
               boolean computeStatistics)



          Initialize the GASequenceList
 



Method Summary




protected  void
doOnePtCrossover(Chromosome Chrom1,
                 Chromosome Chrom2)



          Perform one point crossover on the two given chromosomes



protected  void
doTwoPtCrossover(Chromosome Chrom1,
                 Chromosome Chrom2)



          Perform two point crossover on the two given chromosomes



protected  void
doUniformCrossover(Chromosome Chrom1,
                   Chromosome Chrom2)



          Perform uniform crossover on the given two chromosomes



protected  java.lang.String
getChromWithoutDuplicates(java.lang.String sChromosome)



          Take the given chromosome which may have duplicated genes and eliminate any duplicated genes
 by replacing duplicates with genes which were left out of the chromosome (that is they exist
 in the gene space but not in the given chromosome).



protected  void
initPopulation()



          Create random chromosomes from the given gene space.


 
Methods inherited from class com.softtechdesign.ga.GAString
chromStrToFloat, doRandomMutation, getChromosome, getChromValAsDouble, getRandomGeneFromPossGenes
 
Methods inherited from class com.softtechdesign.ga.GA
addChromosomesToLog, binaryStrToInt, computeFitnessRankings, copyNextGenToThisGen, doGeneticMating, evolve, getAvgDeviation, getAvgDeviationAmongChroms, getAvgFitness, getAvgFitness, getChromosomeDim, getComputeStatistics, getCrossoverProb, getCrossoverType, getFitness, getFitnessRank, getFittestChromosome, getFittestChromosomesFitness, getMaxGenerations, getMaxPrelimGenerations, getMutationProb, getNumPrelimRuns, getPopulationDim, getRandom, getRandom, getRandomSelectionChance, run, selectTwoParents
 
Methods inherited from class java.lang.Object
, clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, toString, wait, wait, wait
 





Field Detail



sequence
protected double[] sequence

sequence of genes




Constructor Detail



GASequenceList
public GASequenceList(int pChromosomeDim,
                      int pPopulationDim,
                      double pCrossoverProb,
                      int pRandomSelectionChance,
                      int pMaxGenerations,
                      int pNumPrelimRuns,
                      int pMaxPrelimGenerations,
                      double pMutationProb,
                      int pChromDecPts,
                      java.lang.String pPossGeneValues,
                      int pCrossoverType,
                      boolean computeStatistics)
               throws GAException

Initialize the GASequenceList

Parameters:
pChromosomeDim -  
pPopulationDim -  
pCrossoverProb -  
pRandomSelectionChance -  
pMaxGenerations -  
pNumPrelimRuns -  
pMaxPrelimGenerations -  
pMutationProb -  
pChromDecPts -  
pPossGeneValues -  
pCrossoverType -  
computeStatistics -  
Throws:
GAException -  






Method Detail



getChromWithoutDuplicates
protected java.lang.String getChromWithoutDuplicates(java.lang.String sChromosome)

Take the given chromosome which may have duplicated genes and eliminate any duplicated genes
 by replacing duplicates with genes which were left out of the chromosome (that is they exist
 in the gene space but not in the given chromosome).
 For example if gene space = 'ABCDEFGH' and sChrom1 = 'ABCDDEFG', then the
 gene 'D' is duplicated and 'H' has been left out. Swap the 2nd 'D' with 'H' and
 the chromosome is fixed.

Parameters:
sChromosome -  
Returns:
Chromosome string without any duplicate genes.





initPopulation
protected void initPopulation()

Create random chromosomes from the given gene space.

Overrides:
initPopulation in class GAString





doOnePtCrossover
protected void doOnePtCrossover(Chromosome Chrom1,
                                Chromosome Chrom2)

Perform one point crossover on the two given chromosomes

Overrides:
doOnePtCrossover in class GAString


Parameters:
Chrom1 -  
Chrom2 -  





doTwoPtCrossover
protected void doTwoPtCrossover(Chromosome Chrom1,
                                Chromosome Chrom2)

Perform two point crossover on the two given chromosomes

Overrides:
doTwoPtCrossover in class GAString


Parameters:
Chrom1 -  
Chrom2 -  





doUniformCrossover
protected void doUniformCrossover(Chromosome Chrom1,
                                  Chromosome Chrom2)

Perform uniform crossover on the given two chromosomes

Overrides:
doUniformCrossover in class GAString


Parameters:
Chrom1 -  
Chrom2 -