Examples of GlobalSequenceAlignment

Examples of bgu.bio.algorithms.alignment.GlobalSequenceAlignment

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  @Test
  public void testSameSimilarity() {
    GlobalStemSimilarity sim = new GlobalStemSimilarity(new ScoringMatrix(
        "matrix/tests/STEMS-test2.matrix",
        StemStructureAlphabet.getInstance()),
        new GlobalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new IdentityScoringMatrix(RnaAlphabet.getInstance())));

    StemStructure str1 = new StemStructure(
        ">ID: add , START: 1 , STRAND: UNKNOWN , ENERGY: -14.1 (base)",
        new CharBuffer("UCUACCGGGCAAAGUCCGACUAUGGG"), new CharBuffer(
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Examples of bgu.bio.algorithms.alignment.GlobalSequenceAlignment

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  @Test
  public void testSameSimilarity() {
    GlobalStemSimilarity simGlobal = new GlobalStemSimilarity(
        new ScoringMatrix("matrix/tests/STEMS-test2.matrix",
            StemStructureAlphabet.getInstance()),
        new GlobalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new IdentityScoringMatrix(RnaAlphabet.getInstance())));

    AffineGapStemSimilarity simAffine = new AffineGapStemSimilarity(
        new AffineGapScoringMatrix(
            "matrix/tests/STEMS-test2-affine.matrix",
            StemStructureAlphabet.getInstance()),
        new GlobalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new IdentityScoringMatrix(RnaAlphabet.getInstance())));

    StemStructure str1 = new StemStructure(
        ">ID: add , START: 1 , STRAND: UNKNOWN , ENERGY: -14.1 (base)",
        new CharBuffer("UCUACCGGGCAAAGUCCGACUAUGGG"), new CharBuffer(
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Examples of bgu.bio.algorithms.alignment.GlobalSequenceAlignment

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  private class ComparissonRunner implements Runnable {

    @Override
    public void run() {
      GlobalSequenceAlignment seq = new GlobalSequenceAlignment(1000,
          1000, RnaAlphabet.getInstance(), new IdentityScoringMatrix(
              RnaAlphabet.getInstance(), 1, 0));
      int i = startIndex.getAndIncrement();
      while (i < list.size()) {
        final String seq1 = list.get(i).getPrimary();
        for (int j = i + 1; j < list.size(); j++) {
          final String seq2 = list.get(j).getPrimary();
          seq.setSequences(seq1, seq2);
          seq.buildMatrix();
          final double s = 2 * seq.getAlignmentScore()
              / (seq1.length() + seq2.length());
          scores[i][j] = s;
        }
        System.out.println(Thread.currentThread().getName() + " " + i
            + " Finished " + (list.size() - i + 1));
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