Package bgu.bio.util

Examples of bgu.bio.util.IdentityScoringMatrix

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  }

  public static void main(String[] args) {
    GlobalSequenceAlignment alignment = new GlobalSequenceAlignment(
        "AGCGCGUU", "GUCAGACG", RnaAlphabet.getInstance(),
        new IdentityScoringMatrix(RnaAlphabet.getInstance()));
    alignment.buildMatrix();

    // alignment.printAlignments();
    alignment.printDPMatrix();
    System.out.println("score is: " + alignment.getAlignmentScore());
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    int jobSize = Integer.parseInt(args[3]); //amount of cells for each thread to fill
   
   
    Check2 alignment = new Check2(str1, str2, RnaAlphabet.getInstance(),
        new IdentityScoringMatrix(RnaAlphabet.getInstance()), n, jobSize);
   
   
    System.out.println("shorter string length: " + alignment.getLength(1));
    System.out.println("longer string length: " + alignment.getLength(2));
    System.out.println("amount of diagonals = " + (alignment.getLength(1)+alignment.getLength(2)));
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  @Test
  public void testSmallScore() {
    DiagonalSequenceAlignmentNoMatrix dsanm = new DiagonalSequenceAlignmentNoMatrix(
        "AGCGCGUU", "GUCAGACG", RnaAlphabet.getInstance(),
        new IdentityScoringMatrix(RnaAlphabet.getInstance()), 24, 2);
    dsanm.buildMatrix();
    assertEquals(5.0, dsanm.getMaxScore(), 0);
  }
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  @Test
  public void testSmallMatrices() {
    DiagonalSequenceAlignmentNoMatrix dsanm = new DiagonalSequenceAlignmentNoMatrix(
        "AGCGCGUU", "GUCAGACG", RnaAlphabet.getInstance(),
        new IdentityScoringMatrix(RnaAlphabet.getInstance()), 24, 2);
    dsanm.buildMatrix();
    GlobalSequenceAlignment gsa = new GlobalSequenceAlignment("AGCGCGUU",
        "GUCAGACG", RnaAlphabet.getInstance(),
        new IdentityScoringMatrix(RnaAlphabet.getInstance()));
    gsa.buildMatrix();
    assertEquals(gsa.getAlignmentScore(), dsanm.getMaxScore(), 0);
  }
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  @Test
  public void testLargeScore() {
    GlobalSequenceAlignment dsanm = new GlobalSequenceAlignment(
        "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGGGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTCTGACGGGACTCACCGCCGCCCAGCCGGGATTCCCGCTGGCGCAACTGAAAACTTTCGTCGACCAGGAATTTG",
        "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT",
        RnaAlphabet.getInstance(), new IdentityScoringMatrix(
            RnaAlphabet.getInstance()));
    dsanm.buildMatrix();
    assertEquals(623.0, dsanm.getAlignmentScore(), 0);
  }
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  @Test
  public void testLargeScoreDiagonalNoMatrix() {
    DiagonalSequenceAlignmentNoMatrix dsanm = new DiagonalSequenceAlignmentNoMatrix(
        "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGGGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTCTGACGGGACTCACCGCCGCCCAGCCGGGATTCCCGCTGGCGCAACTGAAAACTTTCGTCGACCAGGAATTTG",
        "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT",
        RnaAlphabet.getInstance(), new IdentityScoringMatrix(
            RnaAlphabet.getInstance()), 24, 100);
    dsanm.buildMatrix();
    assertEquals(623.0, dsanm.getMaxScore(), 0);
  }
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        sequence.getAlignmentScore(), 0.001);
  }

  private SequenceAlignment initLocal() {
    return new LocalSequenceAlignmentNoMatrix(10, 10,
        RnaAlphabet.getInstance(), new IdentityScoringMatrix(
            RnaAlphabet.getInstance(), 1, -1));
  }
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            RnaAlphabet.getInstance(), 1, -1));
  }

  private SequenceAlignment initGlobal() {
    return new GlobalSequenceAlignmentNoMatrix(10, 10,
        RnaAlphabet.getInstance(), new IdentityScoringMatrix(
            RnaAlphabet.getInstance(), 1, -1));
  }
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            RnaAlphabet.getInstance(), 1, -1));
  }

  private SequenceAlignment initSuffixFree() {
    return new SuffixFreeLocalAlignment(10, 10, RnaAlphabet.getInstance(),
        new IdentityScoringMatrix(RnaAlphabet.getInstance(), 1, -1));
  }
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  }

  @Test
  public void randomTest() {
    AlphabetUtils alphabet = RnaAlphabet.getInstance();
    ScoringMatrix matrix = new IdentityScoringMatrix(alphabet);

    GlobalSequenceAlignment alignMat = new GlobalSequenceAlignment(0, 0,
        alphabet, matrix);
    GlobalSequenceAlignmentNoMatrix alignNoMat = new GlobalSequenceAlignmentNoMatrix(
        0, 0, alphabet, matrix);
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Related Classes of bgu.bio.util.IdentityScoringMatrix

  • bgu.bio.algorithms.alignment.Check
  • bgu.bio.algorithms.alignment.Check2
  • bgu.bio.algorithms.alignment.Check3
  • bgu.bio.algorithms.alignment.DiagonalSequenceAlignment
  • bgu.bio.algorithms.alignment.DiagonalSequenceAlignmentNoMatrix
  • bgu.bio.algorithms.alignment.DiagonalSequenceAlignmentTest
  • bgu.bio.algorithms.alignment.GlobalSequenceAlignment
  • bgu.bio.algorithms.alignment.stems.TestAffineGapStemSimilarity
  • bgu.bio.algorithms.alignment.stems.TestGlobalStemSimilarity
  • bgu.bio.algorithms.alignment.TestCacheMemorySequenceAlignment
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