Examples of Genome

au.org.intersect.samifier.domain.Genome
com.heatonresearch.aifh.evolutionary.genome.Genome
A genome is the basic blueprint for creating an phenome (organism) in Encog. Some genomes also function as phenomes.
de.mh4j.solver.genetic.Genome
TODO write class description
org.broad.igv.feature.genome.Genome
Simple model of a genome. Keeps an ordered list of Chromosomes, an alias table, and genome position offsets for each chromosome to support a whole-genome view.
org.digibots.genetique.Genome
The Genome of a digibot @author Amos Wenger (aka BlueSky)
org.encog.ml.ea.genome.Genome
A genome is the basic blueprint for creating an phenome (organism) in Encog. Some genomes also function as phenomes.
org.encog.ml.genetic.genome.Genome
A genome is the basic blueprint for creating an organism in Encog. A genome is made up of one or more chromosomes, which are in turn made up of genes.
versusSNP.genome.Genome

Examples of org.digibots.genetique.Genome

        
        try {
            
            app.getUI().getStats().notifyCopulation();
            
            Genome childGen = new Genome();
            
            childGen.alleleB1 = rnd.nextBoolean() ? partner.genome.alleleB1
                    : this.genome.alleleB1;
            childGen.alleleB2 = rnd.nextBoolean() ? partner.genome.alleleB2
                    : this.genome.alleleB2;

View Full Code Here

Examples of org.encog.ml.ea.genome.Genome

    adjustCompatibilityThreshold();


    // assign genomes to species (if any exist)
    for (final Genome g : genomes) {
      Species currentSpecies = null;
      final Genome genome = g;


      if (!Double.isNaN(genome.getAdjustedScore())
          && !Double.isInfinite(genome.getAdjustedScore())) {
        maxScore = Math.max(genome.getAdjustedScore(), maxScore);
      }


      for (final Species s : speciesCollection) {
        final double compatibility = getCompatibilityScore(genome,
            s.getLeader());


        if (compatibility <= this.compatibilityThreshold) {
          currentSpecies = s;
          addSpeciesMember(s, genome);
          genome.setSpecies(s);
          break;
        }
      }


      // if this genome did not fall into any existing species, create a

View Full Code Here

Examples of org.encog.ml.genetic.genome.Genome

      calculateScore(genome);
    }


    getPopulation().sort();


    final Genome genome = getPopulation().getBest();
    final double currentBest = genome.getScore();


    if (getComparator().isBetterThan(currentBest, this.bestEverScore)) {
      this.bestEverScore = currentBest;
      this.bestEverNetwork = ((NEATNetwork) genome.getOrganism());
    }


    this.bestEverScore = getComparator().bestScore(getError(),
        this.bestEverScore);
  }

View Full Code Here

Examples of org.encog.ml.genetic.genome.Genome

    }


    // set the species leader links
    for (Species species : leaderMap.keySet()) {
      int leaderID = leaderMap.get(species);
      Genome leader = genomeMap.get(leaderID);
      species.setLeader(leader);
      ((BasicSpecies)species).setPopulation(result);
    }


    return result;

View Full Code Here

Examples of org.encog.ml.genetic.genome.Genome

  public class NeuralGeneticAlgorithmHelper extends BasicGeneticAlgorithm {
    /**
     * @return The error from the last iteration.
     */
    public final double getError() {
      final Genome genome = getPopulation().getBest();
      return genome.getScore();
    }

View Full Code Here

Examples of org.encog.ml.genetic.genome.Genome

     * Get the current best neural network.
     * 
     * @return The current best neural network.
     */
    public final MLMethod getMethod() {
      final Genome genome = getPopulation().getBest();
      return (BasicNetwork) genome.getOrganism();
    }

View Full Code Here

Examples of org.encog.ml.genetic.genome.Genome

   * 
   * @return The parent.
   */
  @Override
  public final Genome chooseParent() {
    Genome baby;


    // If there is a single member, then choose that one.
    if (this.members.size() == 1) {
      baby = this.members.get(0);
    } else {

View Full Code Here

Examples of org.encog.ml.genetic.genome.Genome

    final TaskGroup group = EngineConcurrency.getInstance()
        .createTaskGroup();


    // mate and form the next generation
    for (int i = 0; i < countToMate; i++) {
      final Genome mother = getPopulation().getGenomes().get(i);
      final int fatherInt = (int) (Math.random() * matingPopulationSize);
      final Genome father = getPopulation().getGenomes().get(fatherInt);
      final Genome child1 = getPopulation().getGenomes().get(
          offspringIndex);
      final Genome child2 = getPopulation().getGenomes().get(
          offspringIndex + 1);


      final MateWorker worker = new MateWorker(mother, father, child1,
          child2);

View Full Code Here

Examples of org.encog.ml.genetic.genome.Genome

      String prefix = dialog.getPrefix().getValue();
      int count = dialog.getGenomesToExtract().getValue();
      
      for(int i=0;i<count;i++)
      {
        Genome genome = this.population.getGenomes().get(i);
        genome.decode();
        NEATNetwork network = (NEATNetwork)genome.getOrganism();
        String name = FileUtil.forceExtension( prefix + i, "eg" );
        File path = new File(EncogWorkBench.getInstance().getProjectDirectory(),name);
        EncogWorkBench.getInstance().save(path, network);
        
      }

View Full Code Here

Examples of org.encog.ml.genetic.genome.Genome

    
    String type = "Unknown";
    
    if( population.getGenomes().size()>0 )
    {
      Genome genome = population.getGenomes().get(0);
      if( genome instanceof NEATGenome )
      {
        type = "Neat";
      }
      else if( genome instanceof NeuralGenome )

View Full Code Here

0 1 2 3 4 5

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.