Examples of mapAndHash()

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

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    sim.setStem2(str1);
    sim.run();
    double scoreSelf = sim.getAlignmentScore();
    double diff = scoreSelf - score;
    double expected = structureScoringMatrix.score(
        stemAlphabet.mapAndHash("G|C"), stemAlphabet.mapAndHash("G|C"))
        - structureScoringMatrix.score(stemAlphabet.mapAndHash("G|C"),
            stemAlphabet.mapAndHash("G|U"));
    Assert.assertEquals(expected, diff, 0.01);
  }
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Examples of bgu.bio.util.alphabet.StemStructureAlphabet.mapAndHash()

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    sim.setStem2(str1);
    sim.run();
    double scoreSelf = sim.getAlignmentScore();
    double diff = scoreSelf - score;
    double expected = structureScoringMatrix.score(
        stemAlphabet.mapAndHash("G|C"), stemAlphabet.mapAndHash("G|C"))
        - structureScoringMatrix.score(stemAlphabet.mapAndHash("G|C"),
            stemAlphabet.mapAndHash("G|U"));
    Assert.assertEquals(expected, diff, 0.01);
  }
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Examples of bgu.bio.util.alphabet.StemStructureAlphabet.mapAndHash()

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    sim.run();
    double scoreSelf = sim.getAlignmentScore();
    double diff = scoreSelf - score;
    double expected = structureScoringMatrix.score(
        stemAlphabet.mapAndHash("G|C"), stemAlphabet.mapAndHash("G|C"))
        - structureScoringMatrix.score(stemAlphabet.mapAndHash("G|C"),
            stemAlphabet.mapAndHash("G|U"));
    Assert.assertEquals(expected, diff, 0.01);
  }

  @Test
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Examples of bgu.bio.util.alphabet.StemStructureAlphabet.mapAndHash()

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    double scoreSelf = sim.getAlignmentScore();
    double diff = scoreSelf - score;
    double expected = structureScoringMatrix.score(
        stemAlphabet.mapAndHash("G|C"), stemAlphabet.mapAndHash("G|C"))
        - structureScoringMatrix.score(stemAlphabet.mapAndHash("G|C"),
            stemAlphabet.mapAndHash("G|U"));
    Assert.assertEquals(expected, diff, 0.01);
  }

  @Test
  public void testSameSimilarity3() {
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Examples of bgu.bio.util.alphabet.StemStructureAlphabet.mapAndHash()

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    sim.setStem2(str1);
    sim.run();
    double scoreSelf = sim.getAlignmentScore();
    double diff = scoreSelf - score;
    double expected = structureScoringMatrix.score(
        stemAlphabet.mapAndHash("U|G"), stemAlphabet.mapAndHash("U|G"))
        + structureScoringMatrix.score(stemAlphabet.mapAndHash("G|C"),
            stemAlphabet.mapAndHash("G|C"))
        - (structureScoringMatrix.score(stemAlphabet.mapAndHash("U|G"),
            stemAlphabet.emptyLetterHashed()) + structureScoringMatrix
            .score(stemAlphabet.mapAndHash("G|C"),
View Full Code Here

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

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    sim.setStem2(str1);
    sim.run();
    double scoreSelf = sim.getAlignmentScore();
    double diff = scoreSelf - score;
    double expected = structureScoringMatrix.score(
        stemAlphabet.mapAndHash("U|G"), stemAlphabet.mapAndHash("U|G"))
        + structureScoringMatrix.score(stemAlphabet.mapAndHash("G|C"),
            stemAlphabet.mapAndHash("G|C"))
        - (structureScoringMatrix.score(stemAlphabet.mapAndHash("U|G"),
            stemAlphabet.emptyLetterHashed()) + structureScoringMatrix
            .score(stemAlphabet.mapAndHash("G|C"),
View Full Code Here

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

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    sim.run();
    double scoreSelf = sim.getAlignmentScore();
    double diff = scoreSelf - score;
    double expected = structureScoringMatrix.score(
        stemAlphabet.mapAndHash("U|G"), stemAlphabet.mapAndHash("U|G"))
        + structureScoringMatrix.score(stemAlphabet.mapAndHash("G|C"),
            stemAlphabet.mapAndHash("G|C"))
        - (structureScoringMatrix.score(stemAlphabet.mapAndHash("U|G"),
            stemAlphabet.emptyLetterHashed()) + structureScoringMatrix
            .score(stemAlphabet.mapAndHash("G|C"),
                stemAlphabet.emptyLetterHashed()));
View Full Code Here

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

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    double scoreSelf = sim.getAlignmentScore();
    double diff = scoreSelf - score;
    double expected = structureScoringMatrix.score(
        stemAlphabet.mapAndHash("U|G"), stemAlphabet.mapAndHash("U|G"))
        + structureScoringMatrix.score(stemAlphabet.mapAndHash("G|C"),
            stemAlphabet.mapAndHash("G|C"))
        - (structureScoringMatrix.score(stemAlphabet.mapAndHash("U|G"),
            stemAlphabet.emptyLetterHashed()) + structureScoringMatrix
            .score(stemAlphabet.mapAndHash("G|C"),
                stemAlphabet.emptyLetterHashed()));
    Assert.assertEquals(expected, diff, 0.01);
View Full Code Here

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

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    double diff = scoreSelf - score;
    double expected = structureScoringMatrix.score(
        stemAlphabet.mapAndHash("U|G"), stemAlphabet.mapAndHash("U|G"))
        + structureScoringMatrix.score(stemAlphabet.mapAndHash("G|C"),
            stemAlphabet.mapAndHash("G|C"))
        - (structureScoringMatrix.score(stemAlphabet.mapAndHash("U|G"),
            stemAlphabet.emptyLetterHashed()) + structureScoringMatrix
            .score(stemAlphabet.mapAndHash("G|C"),
                stemAlphabet.emptyLetterHashed()));
    Assert.assertEquals(expected, diff, 0.01);
  }
View Full Code Here

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

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        stemAlphabet.mapAndHash("U|G"), stemAlphabet.mapAndHash("U|G"))
        + structureScoringMatrix.score(stemAlphabet.mapAndHash("G|C"),
            stemAlphabet.mapAndHash("G|C"))
        - (structureScoringMatrix.score(stemAlphabet.mapAndHash("U|G"),
            stemAlphabet.emptyLetterHashed()) + structureScoringMatrix
            .score(stemAlphabet.mapAndHash("G|C"),
                stemAlphabet.emptyLetterHashed()));
    Assert.assertEquals(expected, diff, 0.01);
  }

  @Test
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