Package bgu.bio.algorithms.alignment

Examples of bgu.bio.algorithms.alignment.SequenceAlignment

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  private static void testRNAShuffleExample() throws IOException {
    RnaSpecificTypeRelatedTreePruning prune2 = new RnaSpecificTypeRelatedTreePruning(
        false, true);
    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();

    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));
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  public static void testRNAExample() {

    RnaSpecificTypeRelatedTreePruning prune = new RnaSpecificTypeRelatedTreePruning(
        false, true);
    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();
    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));
View Full Code Here
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  public void testRNAShuffleExample() {
    RnaSpecificTypeRelatedTreePruning prune = new RnaSpecificTypeRelatedTreePruning(
        false, true);
    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();

    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));
View Full Code Here
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    RnaSpecificTypeRelatedTreePruning pruneUnrooted = new RnaSpecificTypeRelatedTreePruning(
        false, false);

    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();

    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));
View Full Code Here
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    RnaSpecificTypeRelatedTreePruning prune = new RnaSpecificTypeRelatedTreePruning(
        true, false);
   
    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();

    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));
View Full Code Here
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  public static void testRNAExample() {

    RnaSpecificTypeRelatedTreePruning prune = new RnaSpecificTypeRelatedTreePruning(
        false, true);
    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();
    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));
View Full Code Here
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Related Classes of bgu.bio.algorithms.alignment.SequenceAlignment

  • bgu.bio.algorithms.graphs.Test
  • bgu.bio.algorithms.graphs.TestHSA
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