Examples of Genotype

abra.utils.trio.LocusGenotype.Genotype
htsjdk.variant.variantcontext.Genotype
org.broad.igv.variant.Genotype
Represents a genotype, that is a variant call on a single sample @author Jim Robinson @date Aug 1, 2011
org.jgap.Genotype
Genotypes are fixed-length populations of chromosomes. As an instance of a Genotype is evolved, all of its Chromosomes are also evolved. A Genotype may be constructed normally via constructor, or the static randomInitialGenotype() method can be used to generate a Genotype with a randomized Chromosome population.
Please note that among all created Genotype instances there may only be one configuration, used by all Genotype instances. @author Neil Rotstan @author Klaus Meffert @since 1.0

Examples of org.broad.igv.variant.Genotype

            genotypeMap.put(sample, vcfGenotype);
        }


        zygosityCount = new ZygosityCount();
        for (String sample : getSampleNames()) {
            Genotype genotype = getGenotype(sample);
            zygosityCount.incrementCount(genotype);
        }


        String afString = null;
        String[] alleleFreqKeys = {"AF", "GMAF"};

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Examples of org.broad.igv.variant.Genotype

        double methTotal = 0;
        int samplesWithData = 0;
        final int size = getSampleNames().size();
        if (size > 0) {
            for (String sample : getSampleNames()) {
                Genotype genotype = getGenotype(sample);
                double mr = genotype.getAttributeAsDouble("MR");
                double goodBaseCount = genotype.getAttributeAsDouble("MR");
                if (!Double.isNaN(mr) && !Double.isNaN(goodBaseCount) && goodBaseCount > VariantTrack.METHYLATION_MIN_BASE_COUNT) {
                    methTotal += mr;
                    samplesWithData++;
                }
            }

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Examples of org.jgap.Genotype

    final EcEvolver myFunc = new EcEvolver(source, destination, requiredActions);
    evolvers[threadIndex] = myFunc;


    final Configuration conf = constructConfiguration(threadIndex, myFunc);


    final Genotype population = Genotype.randomInitialGenotype(conf);


    //Please justify this code.
    //-Lomilar
//    if (!firstrun)
//    {
//      int totalevoSinceDiscoveryOnBest = 0;
//      int numBestThreads = 0;
//      synchronized (bestScores)
//      {
//        for (int i = 0; i < bestScores.length; i++)
//        {
//          if (bestScores[i] >= bestScore)
//          {
//            numBestThreads++;
//            totalevoSinceDiscoveryOnBest += evolutionsSinceDiscovery[i];
//          }
//        }
//      }
//
//      if (!(totalevoSinceDiscoveryOnBest > Math.max(stagnationLimit, STAGNATION_LIMIT_MIN) * numBestThreads)
//          && numBestThreads < Math.max(Math.ceil(NUM_THREADS / 3), 1))
//      {
//        loadOldBuildOrders(population, conf, myFunc);
//      }
//    }
//    else 
      if (firstrun && threadIndex == 0)
    {
      loadOldBuildOrders(population, conf, myFunc);
    }
    else if (firstrun && threadIndex == NUM_THREADS - 1)
    {
      firstrun = false;
    }


    final Thread thread = new Thread(population);
    conf.getEventManager().addEventListener(GeneticEvent.GENOTYPE_EVOLVED_EVENT, new GeneticEventListener()
    {
      @Override
      public void geneticEventFired(GeneticEvent a_firedEvent)
      {
        Collections.shuffle(conf.getGeneticOperators());
        BASE_MUTATION_RATE += .001;
        if (BASE_MUTATION_RATE >= (double) CHROMOSOME_LENGTH / 2.0 )
          BASE_MUTATION_RATE = 1;
        IChromosome fittestChromosome = population.getFittestChromosome();
        if (killThreads)
        {
          threads.remove(thread);
          thread.interrupt();
        }

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