Package bgu.bio.util

Examples of bgu.bio.util.CharBuffer

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      while (header != null) {
        line1 = reader.readLine();
        line2 = reader.readLine();

        list.add(new StemStructure(header.substring(1), new CharBuffer(line1),
            new CharBuffer(line2)));

        header = reader.readLine();

      }
      reader.close();
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        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(
            "((((.(((((...)))))....))))"));

    StemStructure str2 = new StemStructure(
        ">ID: add , START: 1 , STRAND: UNKNOWN , ENERGY: -14.1 (base)",
        new CharBuffer(
            "UCACACCCGUUCCCAUACCGAACACGGAAACCGAUGGUAGUCGGGGGUUUCCCCCUGUGA"),
        new CharBuffer(
            "(((((...(..(((...((((.(((((...))).))....)))))))...)....)))))"));
    sim.setStem1(str1);
    sim.setStem2(str2);
    sim.run();
    double score = sim.getAlignmentScore();
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            10, 10, RnaAlphabet.getInstance(),
            new AffineGapScoringMatrix(
                "matrix/NUC-Affine-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())));

    StemStructure str1 = new StemStructure(">1", new CharBuffer(
        "AGAGGUAAAAUGCAUCU"), new CharBuffer("((..(((...)))..))"));

    StemStructure str2 = new StemStructure(">1", new CharBuffer(
        "AGAGGUAAAAUGCAUUU"), new CharBuffer("((..(((...)))..))"));

    sim.setStem1(str1);
    sim.setStem2(str2);
    sim.run();
    sim.buildMatrix();
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            10, 10, RnaAlphabet.getInstance(),
            new AffineGapScoringMatrix(
                "matrix/NUC-Affine-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())));

    StemStructure str1 = new StemStructure(">1", new CharBuffer(
        "AGAGGUAAAAUGCAUCU"), new CharBuffer("((..(((...)))..))"));

    StemStructure str2 = new StemStructure(">1", new CharBuffer(
        "AGAGAAAAUAUCU"), new CharBuffer("((..(...)..))"));

    sim.setStem1(str1);
    sim.setStem2(str2);
    sim.run();
    double score = sim.getAlignmentScore();
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                RnaAlphabet.getInstance())),
        new LocalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new ScoringMatrix("matrix/NUC-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())));

    StemStructure str1 = new StemStructure(">1", new CharBuffer(
        "AAAGAGGUAAAAUGCAUCUAA"), new CharBuffer(
        "..((..(((...)))..)).."));

    StemStructure str2 = new StemStructure(">1", new CharBuffer(
        "AAAGAGAAAAUAUCUAA"), new CharBuffer("..((..(...)..)).."));

    StemStructure str3 = new StemStructure(">1", new CharBuffer(
        "UUUUAAACAGAGAAAAUAUCUCAAAGGGG"), new CharBuffer(
        "........((..(...)..))........"));

    sim.setStem1(str1);
    sim.setStem2(str2);
    sim.run();
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                RnaAlphabet.getInstance())),
        new LocalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new ScoringMatrix("matrix/NUC-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())));

    StemStructure str1 = new StemStructure(">1", new CharBuffer(
        "AGAGGUAAAAUGCAUCU"), new CharBuffer("((..(((...)))..))"));

    StemStructure str2 = new StemStructure(">1", new CharBuffer(
        "AGAGAAAAUAUCU"), new CharBuffer("((..(...)..))"));

    StemStructure str3 = new StemStructure(">1", new CharBuffer(
        "UUUUAAACAGAGAAAAUAUCUCAAAGGGG"), new CharBuffer(
        "........((..(...)..))........"));

    sim.setStem1(str1);
    sim.setStem2(str2);
    sim.run();
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            new ScoringMatrix("matrix/NUC-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())));

    StemStructure str1 = new StemStructure(
        ">1",
        new CharBuffer(
            "AUUUCAUGAAGAGUGGCUGAGGGACGGGCCCUGUGACGCCACGACAACCGGCUCGAGCAAUUCGGGACAUCGGUGUCAACUCUCUCC"),
        new CharBuffer(
            "..............((..(((((........................................................))))).))"));

    StemStructure str2 = new StemStructure(
        ">1",
        new CharBuffer(
            "UGAGACUUAUUACUGCACCAUAAUUAAGCCAUCCAAUGAGGAAGACUCGAUUUUGGUGGAAAGGUUUAUCUGGCACAAUGGUAGUGUUUUG"),
        new CharBuffer(
            "((((((..((((((.................................................................))))))))))))"));

    StemStructure str1no = new StemStructure(
        ">1",
        new CharBuffer(
            "GGCUGAGGGACGGGCCCUGUGACGCCACGACAACCGGCUCGAGCAAUUCGGGACAUCGGUGUCAACUCUCUCC"),
        new CharBuffer(
            "((..(((((........................................................))))).))"));

    sim.setStem1(str1);
    sim.setStem2(str2);
    sim.run();
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        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(
            "((((.(((((...)))))....))))"));

    StemStructure str2 = new StemStructure(
        ">ID: add , START: 1 , STRAND: UNKNOWN , ENERGY: -14.1 (base)",
        new CharBuffer("GGGGGGUCUACCGGGCAAAGUCCGACUAUGGGCCCCCC"),
        new CharBuffer("((((((((((.(((((...)))))....))))))))))"));

    StemStructure str15 = new StemStructure(
        ">ID: add , START: 1 , STRAND: UNKNOWN , ENERGY: -14.1 (base)",
        new CharBuffer("UCUACCGGGCAAAGUCCGACUAUGGG"), new CharBuffer(
            "((((.(((((...)))))....))))"));

    simGlobal.setStem1(str1);
    simGlobal.setStem2(str15);
    simGlobal.run();
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Related Classes of bgu.bio.util.CharBuffer

  • bgu.bio.algorithms.alignment.stems.TestAffineGapStemSimilarity
  • bgu.bio.algorithms.alignment.stems.TestGlobalStemSimilarity
  • bgu.bio.ds.rna.StemStructure
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