Examples of AffineGapScoringMatrix

Examples of bgu.bio.util.AffineGapScoringMatrix

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        "matrix/Structure-sim-RIBOSUM85-60.matrix", stemAlphabet);

    GlobalStemSimilarity sim = new GlobalStemSimilarity(
        structureScoringMatrix, new AffineGapGlobalSequenceAlignment(
            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("((..(((...)))..))"));
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Examples of bgu.bio.util.AffineGapScoringMatrix

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        "matrix/Structure-sim-RIBOSUM85-60.matrix", stemAlphabet);

    GlobalStemSimilarity sim = new GlobalStemSimilarity(
        structureScoringMatrix, new AffineGapGlobalSequenceAlignment(
            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("((..(((...)))..))"));
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Examples of bgu.bio.util.AffineGapScoringMatrix

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        "matrix/Structure-sim-RIBOSUM85-60.matrix", stemAlphabet);

    GlobalStemSimilarity sim = new GlobalStemSimilarity(
        structureScoringMatrix, new AffineGapGlobalSequenceAlignment(
            10, 10, RnaAlphabet.getInstance(),
            new AffineGapScoringMatrix(
                "matrix/NUC-Affine-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())),
        new LocalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new ScoringMatrix("matrix/NUC-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())));
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Examples of bgu.bio.util.AffineGapScoringMatrix

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        "matrix/Structure-sim-RIBOSUM85-60.matrix", stemAlphabet);

    GlobalStemSimilarity sim = new GlobalStemSimilarity(
        structureScoringMatrix, new AffineGapGlobalSequenceAlignment(
            10, 10, RnaAlphabet.getInstance(),
            new AffineGapScoringMatrix(
                "matrix/NUC-Affine-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())),
        new LocalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new ScoringMatrix("matrix/NUC-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())));
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Examples of bgu.bio.util.AffineGapScoringMatrix

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        "matrix/Structure-sim-RIBOSUM85-60.matrix", stemAlphabet);

    GlobalStemSimilarity sim = new GlobalStemSimilarity(
        structureScoringMatrix, new AffineGapGlobalSequenceAlignment(
            10, 10, RnaAlphabet.getInstance(),
            new AffineGapScoringMatrix(
                "matrix/NUC-Affine-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())),
        new LocalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new ScoringMatrix("matrix/NUC-sim-RIBOSUM85-60.matrix",
                RnaAlphabet.getInstance())));
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Examples of bgu.bio.util.AffineGapScoringMatrix

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            StemStructureAlphabet.getInstance()),
        new GlobalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new IdentityScoringMatrix(RnaAlphabet.getInstance())));

    AffineGapStemSimilarity simAffine = new AffineGapStemSimilarity(
        new AffineGapScoringMatrix(
            "matrix/tests/STEMS-test2-affine.matrix",
            StemStructureAlphabet.getInstance()),
        new GlobalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new IdentityScoringMatrix(RnaAlphabet.getInstance())));
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