Package bgu.bio.ds.rna

Examples of bgu.bio.ds.rna.InnerStructure

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    }
    if ((this.structureAlphabet.isSpecial(c1) && this.structureAlphabet
        .isSpecial(c2))) {
      // inner loop to right or left

      InnerStructure in1 = stem1.getInnerStructure(i - 1);
      InnerStructure in2 = stem2.getInnerStructure(j - 1);

      double score = 0;

      this.sequenceSimilarity.setSequences(in1.getSequenceLeft(),
          in2.getSequenceLeft());

      this.sequenceSimilarity.buildMatrix();

      score = this.sequenceSimilarity.getAlignmentScore();

      this.sequenceSimilarity.setSequences(in1.getSequenceRight(),
          in2.getSequenceRight());

      this.sequenceSimilarity.buildMatrix();
      score += this.sequenceSimilarity.getAlignmentScore();

      return score;
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    // empty letter and special character i.e. the deletion of a special
    // character
    if ((i == 0 && this.structureAlphabet.isSpecial(c2))
        || (j == 0 && this.structureAlphabet.isSpecial(c1))) {
      InnerStructure in1 = this.structureAlphabet.isSpecial(c1) ? stem1
          .getInnerStructure(i - 1) : null;
      InnerStructure in2 = this.structureAlphabet.isSpecial(c2) ? stem2
          .getInnerStructure(j - 1) : null;
      double innerScore = 0;
      if (in1 != null) {
        // calculate the deletion of the left side and the right side
        InnerStructure in = in1;
        this.sequenceSimilarity.setSequences(in.getSequenceLeft(),
            emptyListHelper);

        this.sequenceSimilarity.buildMatrix();
        innerScore += this.sequenceSimilarity.getAlignmentScore();

        this.sequenceSimilarity.setSequences(in.getSequenceRight(),
            emptyListHelper);

        this.sequenceSimilarity.buildMatrix();
        innerScore += this.sequenceSimilarity.getAlignmentScore();
      }
      if (in2 != null) {
        InnerStructure in = in2;
        this.sequenceSimilarity.setSequences(in.getSequenceLeft(),
            emptyListHelper);

        this.sequenceSimilarity.buildMatrix();
        innerScore += this.sequenceSimilarity.getAlignmentScore();

        this.sequenceSimilarity.setSequences(in.getSequenceRight(),
            emptyListHelper);

        this.sequenceSimilarity.buildMatrix();
        innerScore += this.sequenceSimilarity.getAlignmentScore();
      }

      return scoringMatrix.score(c1, c2) + innerScore;
    }

    if (!this.structureAlphabet.isSpecial(c1)
        && !this.structureAlphabet.isSpecial(c2)) {
      // not a special case
      return super.similarity(i, j);
    }
    if ((c1 == StemStructureAlphabet.INNER_LOOP && this.structureAlphabet
        .isSpecial(c2))
        || (c2 == StemStructureAlphabet.INNER_LOOP && this.structureAlphabet
            .isSpecial(c1))) {
      // inner loop to right or left

      InnerStructure in1 = stem1.getInnerStructure(i - 1);
      InnerStructure in2 = stem2.getInnerStructure(j - 1);

      double score = 0;

      this.sequenceSimilarity.setSequences(in1.getSequenceLeft(),
          in2.getSequenceLeft());

      this.sequenceSimilarity.buildMatrix();

      score = this.sequenceSimilarity.getAlignmentScore();

      this.sequenceSimilarity.setSequences(in1.getSequenceRight(),
          in2.getSequenceRight());

      this.sequenceSimilarity.buildMatrix();
      score += this.sequenceSimilarity.getAlignmentScore();

      return score;

    } else if (c1 == StemStructureAlphabet.BULDGE_RIGHT
        && c2 == StemStructureAlphabet.BULDGE_RIGHT) {
      // right to right
      InnerStructure in1 = stem1.getInnerStructure(i - 1);
      InnerStructure in2 = stem2.getInnerStructure(j - 1);

      this.sequenceSimilarity.setSequences(in1.getSequenceRight(),
          in2.getSequenceRight());
      this.sequenceSimilarity.buildMatrix();
      return this.sequenceSimilarity.getAlignmentScore();

    } else if ((c1 == StemStructureAlphabet.BULDGE_LEFT && c2 == StemStructureAlphabet.BULDGE_LEFT)) {
      // left to left
      InnerStructure in1 = stem1.getInnerStructure(i - 1);
      InnerStructure in2 = stem2.getInnerStructure(j - 1);

      this.sequenceSimilarity.setSequences(in1.getSequenceLeft(),
          in2.getSequenceLeft());

      this.sequenceSimilarity.buildMatrix();
      return this.sequenceSimilarity.getAlignmentScore();
    }
    return Double.NEGATIVE_INFINITY;
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Related Classes of bgu.bio.ds.rna.InnerStructure

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