Package bgu.bio.ds.rna

Examples of bgu.bio.ds.rna.StemStructure$StemStructureShuffleData

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        "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(
            "((((.(((((...)))))....))))"));

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

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

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

    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);
View Full Code Here
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Related Classes of bgu.bio.ds.rna.StemStructure$StemStructureShuffleData

  • bgu.bio.adt.tuples.IntPair
  • bgu.bio.algorithms.alignment.stems.TestAffineGapStemSimilarity
  • bgu.bio.algorithms.alignment.stems.TestGlobalStemSimilarity
  • bgu.bio.util.CharBuffer
  • gnu.trove.list.array.TCharArrayList
  • gnu.trove.list.array.TIntArrayList
  • java.io.File
  • java.io.FileReader
  • java.io.BufferedReader
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