Examples of IdentityScoringMatrix

bgu.bio.util.IdentityScoringMatrix

Examples of bgu.bio.util.IdentityScoringMatrix

    backUp = smu.getIndices();
    
//    bestAlignments = new StringRange[BEST];
    
    alphabet = RnaAlphabet.getInstance();
    matrix = new IdentityScoringMatrix(RnaAlphabet.getInstance());
    this.workers = workers;
    this.cells = cells;
    score = 0;
    this.alignment = this.mainProcedure(); //start the main procedure
  }

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Examples of bgu.bio.util.IdentityScoringMatrix

public class TestCacheMemorySequenceAlignment {


  @Test
  public void testRunRandom() {
    SequenceAlignment aligner = new GlobalSequenceAlignmentNoMatrix(1, 1,
        RnaAlphabet.getInstance(), new IdentityScoringMatrix(
            RnaAlphabet.getInstance()));
    int size = 6;
    CacheMemorySequenceAlignment cache = new CacheMemorySequenceAlignment(
        size, aligner);

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Examples of bgu.bio.util.IdentityScoringMatrix

  }


  @Test
  public void testRun1() {
    SequenceAlignment aligner = new GlobalSequenceAlignmentNoMatrix(1, 1,
        RnaAlphabet.getInstance(), new IdentityScoringMatrix(
            RnaAlphabet.getInstance()));
    int size = 6;
    CacheMemorySequenceAlignment cache = new CacheMemorySequenceAlignment(
        size, aligner);

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Examples of bgu.bio.util.IdentityScoringMatrix

     */
    System.out.println(new Date());


    DiagonalSequenceAlignment alignment = new DiagonalSequenceAlignment(
        str2, 15412, 15917, str1, 15411, 16187,
        RnaAlphabet.getInstance(), new IdentityScoringMatrix(
            RnaAlphabet.getInstance()), n, jobSize);


    System.out.println("Score is: " + alignment.getAlignmentScore());
    System.out.println("alignment is:\n" + alignment.getAlignmentString());
    // System.out.println(alignment.getAlignmentScore());

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Examples of bgu.bio.util.IdentityScoringMatrix

    
    int jobSize = Integer.parseInt(args[3]); //amount of cells for each thread to fill
    
    
    Check3 alignment = new Check3(str1, str2, RnaAlphabet.getInstance(), 
        new IdentityScoringMatrix(RnaAlphabet.getInstance()), n, jobSize);
    
    
    System.out.println("shorter string length: " + alignment.getLength(1));
    System.out.println("longer string length: " + alignment.getLength(2));
    System.out.println("amount of diagonals = " + (alignment.getLength(1)+alignment.getLength(2)));

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Examples of bgu.bio.util.IdentityScoringMatrix

  public void testSameSimilarity() {
    GlobalStemSimilarity sim = new GlobalStemSimilarity(new ScoringMatrix(
        "matrix/tests/STEMS-test2.matrix",
        StemStructureAlphabet.getInstance()),
        new GlobalSequenceAlignment(10, 10, RnaAlphabet.getInstance(),
            new IdentityScoringMatrix(RnaAlphabet.getInstance())));


    StemStructure str1 = new StemStructure(
        ">ID: add , START: 1 , STRAND: UNKNOWN , ENERGY: -14.1 (base)",
        new CharBuffer("UCUACCGGGCAAAGUCCGACUAUGGG"), new CharBuffer(
            "((((.(((((...)))))....))))"));

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Examples of bgu.bio.util.IdentityScoringMatrix

  public void testSameSimilarity() {
    GlobalStemSimilarity simGlobal = new GlobalStemSimilarity(
        new ScoringMatrix("matrix/tests/STEMS-test2.matrix",
            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())));


    StemStructure str1 = new StemStructure(
        ">ID: add , START: 1 , STRAND: UNKNOWN , ENERGY: -14.1 (base)",
        new CharBuffer("UCUACCGGGCAAAGUCCGACUAUGGG"), new CharBuffer(
            "((((.(((((...)))))....))))"));

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Examples of bgu.bio.util.IdentityScoringMatrix

    
    int jobSize = Integer.parseInt(args[3]); //amount of cells for each thread to fill
    
    
    Check alignment = new Check(str1, str2, RnaAlphabet.getInstance(), 
        new IdentityScoringMatrix(RnaAlphabet.getInstance()), n, jobSize);
    
    
    System.out.println("shorter string length: " + alignment.getLength(1));
    System.out.println("longer string length: " + alignment.getLength(2));
    System.out.println("amount of diagonals = " + (alignment.getLength(1)+alignment.getLength(2)));

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Examples of bgu.bio.util.IdentityScoringMatrix

  private class ComparissonRunner implements Runnable {


    @Override
    public void run() {
      GlobalSequenceAlignment seq = new GlobalSequenceAlignment(1000,
          1000, RnaAlphabet.getInstance(), new IdentityScoringMatrix(
              RnaAlphabet.getInstance(), 1, 0));
      int i = startIndex.getAndIncrement();
      while (i < list.size()) {
        final String seq1 = list.get(i).getPrimary();
        for (int j = i + 1; j < list.size(); j++) {

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Examples of bgu.bio.util.IdentityScoringMatrix

    
    int jobSize = Integer.parseInt(args[3]); //amount of cells for each thread to fill
    
    
    DiagonalSequenceAlignmentNoMatrix alignment = new DiagonalSequenceAlignmentNoMatrix(str1, str2, RnaAlphabet.getInstance(), 
        new IdentityScoringMatrix(RnaAlphabet.getInstance()), n, jobSize);
    alignment.buildMatrix();
    //System.out.println(alignment.getAlignmentScore());
    //alignment.printAlignments();
  //  alignment.printDPMatrix();
  //  alignment.printDPMatrixInLatexMatrix();

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