Package bgu.bio.util

Examples of bgu.bio.util.IdentityAffineScoringMatrix

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  public static void main(String[] args) {
    String s1 = "GAAUAAGCAUCGGCCCACAUCGGUGGUG";
    String s2 = "GAAUAAGCAUCGGCUAAAUAAUUGGCCCCCACAUCGAGUGAUCGAGUGGUGCAAAC";
    SemiAffineGapSemiLocalSequenceAlignment alignment = new SemiAffineGapSemiLocalSequenceAlignment(
        s1, s2, RnaAlphabet.getInstance(),
        new IdentityAffineScoringMatrix(RnaAlphabet.getInstance(), 1,
            -10, -1, -5));
    alignment.buildMatrix();
    System.out.println(alignment.getMaxScore());
    String[] ans = alignment.getAlignment();
    // alignment.printDPMatrix();
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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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Related Classes of bgu.bio.util.IdentityAffineScoringMatrix

  • bgu.bio.algorithms.alignment.SemiAffineGapSemiLocalSequenceAlignment
  • bgu.bio.algorithms.alignment.TestAffineGapWithAndWithoutMatrix
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