List of bases() Examples

Examples of bases()

com.fray.evo.EcState.bases()
org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer.bases()
Get the bases of this kmer. May create a copy of the bases, depending on how this kmer was constructed. Note that this function is efficient in that if it needs to copy the bases this only occurs once. @return a non-null byte[] containing length() bases of this kmer, regardless of how this kmer was created

Examples of com.fray.evo.EcState.bases()


  public double augmentScore(EcState current, EcState destination, double score, boolean waypoint)
  {
    EcState c = current;
    
    score = augmentCappedScore(score, c.getDrones(), destination.getDrones(), c.bases()*30, 50, 4, waypoint);
    score = augmentScore(score, c.getZerglings(), destination.getZerglings(), 25, .25, waypoint);
    score = augmentScore(score, c.getBanelings(), destination.getBanelings(), 75, .75, waypoint);
    score = augmentScore(score, c.getRoaches(), destination.getRoaches(), 100, 1.0, waypoint);
    score = augmentScore(score, c.getMutalisks(), destination.getMutalisks(), 200, 2.0, waypoint);
    score = augmentCappedScore(score, c.getQueens(), destination.getQueens(), c.bases()*2, 150, 2.5, waypoint);

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Examples of com.fray.evo.EcState.bases()

    score = augmentCappedScore(score, c.getDrones(), destination.getDrones(), c.bases()*30, 50, 4, waypoint);
    score = augmentScore(score, c.getZerglings(), destination.getZerglings(), 25, .25, waypoint);
    score = augmentScore(score, c.getBanelings(), destination.getBanelings(), 75, .75, waypoint);
    score = augmentScore(score, c.getRoaches(), destination.getRoaches(), 100, 1.0, waypoint);
    score = augmentScore(score, c.getMutalisks(), destination.getMutalisks(), 200, 2.0, waypoint);
    score = augmentCappedScore(score, c.getQueens(), destination.getQueens(), c.bases()*2, 150, 2.5, waypoint);
    score = augmentScore(score, c.getHydralisks(), destination.getHydralisks(), 150, 1.5, waypoint);
    score = augmentScore(score, c.getInfestors(), destination.getInfestors(), 250, 2.5, waypoint);
    score = augmentScore(score, c.getCorruptors(), destination.getCorruptors(), 250, 2.5, waypoint);
    score = augmentScore(score, c.getUltralisks(), destination.getUltralisks(), 500, 5.0, waypoint);
    score = augmentScore(score, c.getBroodlords(), destination.getBroodlords(), 400, 4.0, waypoint);

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Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer.bases()

            if (--pendingChildrenCounts[indexByVertex.get(p)] == 0)
                ready.add(p);


        final Kmer mergedKmer = new Kmer(sequence);
        if (uniqueKmers.containsKey(mergedKmer)) {
            uniqueKmersToUpdate.add(new Kmer(mergedKmer.bases().clone()));
            uniqueKmers.remove(mergedKmer);
        }
        boolean foundMergedVertex = false;
        for (final MultiDeBruijnVertex v : vertices)
            if (v == vertexToKeep)

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