Package bgu.bio.algorithms.alignment

Examples of bgu.bio.algorithms.alignment.AffineGapGlobalSequenceAlignment

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        .getInstance();
    ScoringMatrix structureScoringMatrix = new ScoringMatrix(
        "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())));
View Full Code Here
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        .getInstance();
    ScoringMatrix structureScoringMatrix = new ScoringMatrix(
        "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())));
View Full Code Here
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        .getInstance();
    ScoringMatrix structureScoringMatrix = new ScoringMatrix(
        "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(),
View Full Code Here
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        .getInstance();
    ScoringMatrix structureScoringMatrix = new ScoringMatrix(
        "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(),
View Full Code Here
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        .getInstance();
    ScoringMatrix structureScoringMatrix = new ScoringMatrix(
        "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(),
View Full Code Here
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Related Classes of bgu.bio.algorithms.alignment.AffineGapGlobalSequenceAlignment

  • bgu.bio.algorithms.alignment.stems.TestGlobalStemSimilarity
  • gnu.trove.list.array.TCharArrayList
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