Package org.moltools.lib.alignment

Examples of org.moltools.lib.alignment.SimpleAlignment

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      return null;
    }

    //Adjust the alignment values if seq2 upstream of seq1
    if (la.getFirstStart() > la.getSecondStart()) {
      la = new SimpleAlignment(la.getSecondStart(),la.getSecondEnd(),la.getSecondString(),la.getFirstStart(),la.getFirstEnd(),la.getFirstString());
    }

    boolean overlap = isOverlap(la,seq.length());
    while (overlap) {
      la = getNextIntramolecularAlignment(length);
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        return null;
      }

      //Adjust the alignment values if seq2 upstream of seq1
      if (la.getFirstStart() > la.getSecondStart()) {
        la = new SimpleAlignment(la.getSecondStart(),la.getSecondEnd(),la.getSecondString(),la.getFirstStart(),la.getFirstEnd(),la.getFirstString());
      }

      //Now check for overlap
      overlap = isOverlap(la, length);
    }
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    Alignment la = lac.getNextAlignment();
    int length = seq.length();
    if (la == null) {
      return null;
    }
    la = new SimpleAlignment(la.getFirstStart(),la.getFirstEnd(),la.getFirstString(),length-la.getSecondEnd()+1,length-la.getSecondStart()+1,la.getSecondString());
    //Adjust the alignment values if seq2 upstream of seq1
    if (la.getFirstStart() > la.getSecondStart()) {
      la = new SimpleAlignment(la.getSecondStart(),la.getSecondEnd(),la.getSecondString(),la.getFirstStart(),la.getFirstEnd(),la.getFirstString());
    }

    boolean overlap = isOverlap(la,seq.length());
    while (overlap) {
      la = getNextIntramolecularAlignment(length);
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        return null;
      }
      //la = new SimpleLocalAlignment(la.getFirstStart(),la.getFirstEnd(),la.getFirstString(),length-la.getSecondEnd()+1,length-la.getSecondStart()+1,la.getSecondString());
      //Adjust the alignment values if seq2 upstream of seq1
      if (la.getFirstStart() > la.getSecondStart()) {
        la = new SimpleAlignment(la.getSecondStart(),la.getSecondEnd(),la.getSecondString(),la.getFirstStart(),la.getFirstEnd(),la.getFirstString());
      }

      //Now check for overlap
      overlap = isOverlap(la, length);
    }
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Related Classes of org.moltools.lib.alignment.SimpleAlignment

  • org.moltools.apps.probemaker.calculators.HighestStabilityStructureCalculator
  • org.moltools.apps.probemaker.calculators.SWStructureCalculator
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