Examples of NASecStructure

   * the specified sequence.
   * Throws exception if allowPolys is true.*/
  public NASecStructure calculateStructure(NucleotideSequence seq, boolean doTemp) {
    Alignment la = doStrongestIntramolecularLocalAlignment(seq.seqString(), seq.getType());
    if (la == null) return null;
    NASecStructure s = new DefaultNASecStructure(la,seq.length());
    return s;
  }

Examples of org.moltools.lib.struct.NASecStructure

  }


  @Override
  public NASecStructure calculateStructure(NucleotideSequence seq, boolean doStability) {
    Alignment la = doStrongestIntramolecularLocalAlignment(seq.seqString(), seq.getType());
    NASecStructure s = null;
    double maxScore = 0;
    for (int i = 0;i<25;i++) {
      if (la == null) return s;
      NASecStructure temp = new DefaultNASecStructure(la, seq.length());
      double score = 0;
      if (temp.getFirstString() != null && temp.getSecondString() != null) {
        score = ssc.getStabilityScore(seq, temp);
      }
      if (i == 0) {
        s = temp;
      }

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