Uses of Class
org.jgap.ChromosomeMaterial

Packages that use ChromosomeMaterial
com.anji.neat com.anji.neat contains classes implementing NEAT framework, including genes, mutation operators, and fitness function used for XOR. 
org.jgap   
 

Uses of ChromosomeMaterial in com.anji.neat
 

Methods in com.anji.neat that return ChromosomeMaterial
protected  ChromosomeMaterial NeatCrossoverReproductionOperator.reproduce(Configuration config, Chromosome dominantChrom, Chromosome recessiveChrom)
          Crossover according to NEAT crossover methodology.
static ChromosomeMaterial NeatChromosomeUtility.newSampleChromosomeMaterial(short newNumInputs, short newNumHidden, short newNumOutputs, NeatConfiguration config, boolean fullyConnected)
          factory method to construct chromosome material for neural net with specified input and output dimension, JGAP/NEAT configuration, and amount of connectivity
 

Methods in com.anji.neat with parameters of type ChromosomeMaterial
protected  void WeightMutationOperator.mutate(Configuration jgapConfig, ChromosomeMaterial target, java.util.Set genesToAdd, java.util.Set genesToRemove)
          Removes from genesToAdd and adds to genesToRemove all connection genes that are modified.
protected  void SingleTopologicalMutationOperator.mutate(Configuration jgapConfig, ChromosomeMaterial target, java.util.Set allelesToAdd, java.util.Set allelesToRemove)
           
protected  void RemoveConnectionMutationOperator.mutate(Configuration jgapConfig, ChromosomeMaterial target, java.util.Set allelesToAdd, java.util.Set allelesToRemove)
          Removes, in ascending order of weight magnitude, those connections whose weight magnitude is less than the maximum weight to be removed.
protected  void PruneMutationOperator.mutate(Configuration config, ChromosomeMaterial target, java.util.Set genesToAdd, java.util.Set genesToRemove)
          Traverse network flowing forward and backward to identify unvisited connections and neurons.
protected  void AddNeuronMutationOperator.mutate(Configuration jgapConfig, ChromosomeMaterial target, java.util.Set allelesToAdd, java.util.Set allelesToRemove)
          Adds connections according to NEAT add node mutation.
protected  void AddConnectionMutationOperator.mutate(Configuration jgapConfig, ChromosomeMaterial target, java.util.Set allelesToAdd, java.util.Set allelesToRemove)
          Adds connections according to NEAT add connection mutation.
 

Uses of ChromosomeMaterial in org.jgap
 

Methods in org.jgap that return ChromosomeMaterial
protected abstract  ChromosomeMaterial CrossoverReproductionOperator.reproduce(Configuration config, Chromosome dominantChrom, Chromosome recessiveChrom)
           
 ChromosomeMaterial Configuration.getSampleChromosomeMaterial()
          Retrieves sample ChromosomeMaterial that contains the desired Gene setup for each respective gene position (locus).
 ChromosomeMaterial ChromosomeMaterial.clone(java.lang.Long parentId)
          Returns a copy of this ChromosomeMaterial.
static ChromosomeMaterial ChromosomeMaterial.randomInitialChromosomeMaterial(Configuration a_activeConfiguration)
          Convenience method that returns a new Chromosome instance with its genes values (alleles) randomized.
 ChromosomeMaterial Chromosome.cloneMaterial()
           
 

Methods in org.jgap with parameters of type ChromosomeMaterial
protected abstract  void MutationOperator.mutate(Configuration config, ChromosomeMaterial target, java.util.Set allelesToAdd, java.util.Set allelesToRemove)
          Leaves material unmodified, but updates allelesToAdd and allelesToRemove with modifications.
protected static void MutationOperator.updateMaterial(ChromosomeMaterial material, java.util.Set allelesToAdd, java.util.Set allelesToRemove)
          updates material with specified sets of alleles; alleles present in both lists will be added (or replaced if the gene existed on original material)
protected  void Genotype.addChromosomeFromMaterial(ChromosomeMaterial cMat)
           
 void Configuration.setSampleChromosomeMaterial(ChromosomeMaterial a_sampleChromosomeMaterial)
          Sets sample ChromosomeMaterial that is to be used as a guide for the construction of other Chromosomes.
 double ChromosomeMaterial.distance(ChromosomeMaterial target, SpeciationParms speciationParms)
          Calculates compatibility distance between this and target according to NEAT speciation methodology.
 

Constructors in org.jgap with parameters of type ChromosomeMaterial
Chromosome(ChromosomeMaterial a_material, java.lang.Long an_id)
          this should only be called when a chromosome is being created from persistence; otherwise, the ID should be generated by a_activeConfiguration.