Package bgu.bio.util

Examples of bgu.bio.util.AffineGapScoringMatrix

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public class TestSequenceAlignmentAndWithOutMatrix {

  @Test
  public void testAffineSmall1() {
    AffineGapGlobalSequenceAlignment affine = new AffineGapGlobalSequenceAlignment(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix/NUC-Affine-sim-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));
    affine.setSequences("GA", "");
    affine.buildMatrix();
    Assert.assertEquals(-3.0, affine.getAlignmentScore(), 0.001);
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public class TestAffineGapWithAndWithoutMatrix {

  @Test
  public void randomTest() {
    AlphabetUtils alphabet = RnaAlphabet.getInstance();
    AffineGapScoringMatrix matrix = new IdentityAffineScoringMatrix(
        alphabet, 1, -10f, -1f, 0f);

    AffineGapGlobalSequenceAlignment alignMat = new AffineGapGlobalSequenceAlignment(
        0, 0, alphabet, matrix);
    AffineGapGlobalSequenceAlignmentNoMatrix alignNoMat = new AffineGapGlobalSequenceAlignmentNoMatrix(
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  public void test1() {
    String str1 = "CNCNANGUNC";
    String str2 = "UNUUG";

    AlphabetUtils alphabet = RnaAlphabet.getInstance();
    AffineGapScoringMatrix matrix = new IdentityAffineScoringMatrix(
        alphabet, 1, -10f, -0.5f, 0f);

    AffineGapGlobalSequenceAlignment alignMat = new AffineGapGlobalSequenceAlignment(
        0, 0, alphabet, matrix);
    AffineGapGlobalSequenceAlignmentNoMatrix alignNoMat = new AffineGapGlobalSequenceAlignmentNoMatrix(
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  public void test2() {
    String str1 = "CNCNANGUNC";
    String str2 = "CNCNANGUNCAAAAAA";

    AlphabetUtils alphabet = RnaAlphabet.getInstance();
    AffineGapScoringMatrix matrix = new IdentityAffineScoringMatrix(
        alphabet, 1, -10f, -0.5f, 0f);

    AffineGapGlobalSequenceAlignment alignMat = new AffineGapGlobalSequenceAlignment(
        0, 0, alphabet, matrix);
    AffineGapGlobalSequenceAlignmentNoMatrix alignNoMat = new AffineGapGlobalSequenceAlignmentNoMatrix(
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    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()));

    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
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    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()));

    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
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    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()));

    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
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        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()));

    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
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        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()));

    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
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    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()));

    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
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Related Classes of bgu.bio.util.AffineGapScoringMatrix

  • bgu.bio.algorithms.alignment.stems.TestAffineGapStemSimilarity
  • bgu.bio.algorithms.alignment.stems.TestGlobalStemSimilarity
  • bgu.bio.algorithms.alignment.TestAffineGapWithAndWithoutMatrix
  • bgu.bio.algorithms.alignment.TestSequenceAlignmentAndWithOutMatrix
  • bgu.bio.algorithms.graphs.Test
  • bgu.bio.algorithms.graphs.TestHSA
  • java.util.MissingResourceException
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