Examples of decodePair()

Examples of bgu.bio.util.alphabet.StemStructureAlphabet.decodePair()

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    sim.buildMatrix();
    double score = sim.getAlignmentScore();
    String[] alignment = sim.getAlignment();
    for (int i = 0; i < alignment[0].length(); i++) {
      System.out.print(" "
          + Arrays.toString(stemAlphabet.decodePair(alignment[0]
              .charAt(i))));
    }
    System.out.println();
    for (int i = 0; i < alignment[1].length(); i++) {
      System.out.print(" "
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Examples of bgu.bio.util.alphabet.StemStructureAlphabet.decodePair()

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              .charAt(i))));
    }
    System.out.println();
    for (int i = 0; i < alignment[1].length(); i++) {
      System.out.print(" "
          + Arrays.toString(stemAlphabet.decodePair(alignment[1]
              .charAt(i))));
    }
    System.out.println();

    sim.setStem1(str1);
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Examples of bgu.bio.util.alphabet.StemStructureAlphabet.decodePair()

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    sim.run();
    double score = sim.getAlignmentScore();
    String[] alignment = sim.getAlignment();
    for (int i = 0; i < alignment[0].length(); i++) {
      System.out.print(" "
          + Arrays.toString(stemAlphabet.decodePair(alignment[0]
              .charAt(i))));
    }
    System.out.println();
    for (int i = 0; i < alignment[1].length(); i++) {
      System.out.print(" "
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Examples of bgu.bio.util.alphabet.StemStructureAlphabet.decodePair()

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              .charAt(i))));
    }
    System.out.println();
    for (int i = 0; i < alignment[1].length(); i++) {
      System.out.print(" "
          + Arrays.toString(stemAlphabet.decodePair(alignment[1]
              .charAt(i))));
    }
    System.out.println();

    sim.setStem1(str1);
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