Package org.moltools.design.data

Examples of org.moltools.design.data.PropertyAcceptorNucleotideSequence.seqString()

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              String.valueOf(threePrime == null ? 0 : ProbeMakerPropertyUtils.getAllMessages(threePrime).size()),
              String.valueOf(ProbeMakerPropertyUtils.getOwnMessages(pr.getTSSPair()).size()),
              String.valueOf(ProbeMakerPropertyUtils.getOwnMessages(pr).size()),
              fivePrime == null ? "" : fivePrime.seqString(), //$NON-NLS-1$
                  String.valueOf(fivePrime == null ? 0 : ProbeMakerPropertyUtils.getHybridizationTemp(fivePrime)),
                  threePrime == null ? "" : threePrime.seqString(), //$NON-NLS-1$
                      String.valueOf(threePrime == null ? 0 : ProbeMakerPropertyUtils.getHybridizationTemp(threePrime))
      });
      for (int t = 0; t < pr.getTags().size(); t++) {
        outStr += VALUE_SEPARATOR;
        NucleotideSequence tag = pr.getTagAt(t);
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    PropertyAcceptorNucleotideSequence tss5 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_FIVE_PRIME);
    PropertyAcceptorNucleotideSequence tss3 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_THREE_PRIME);
   
    String seq5 = tss5.seqString();
    String seq3 = tss3.seqString();
   
    assertTrue("5' arm sequence failed, expected '" + expect5 + "', got: '" + seq5 + "'", seq5.equals(expect5)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    assertTrue("3' arm sequence failed, expected '" + expect3 + "', got: '" + seq3 + "'", seq3.equals(expect3));        //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
  }
 
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    PropertyAcceptorNucleotideSequence tss5 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_FIVE_PRIME);
    PropertyAcceptorNucleotideSequence tss3 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_THREE_PRIME);
   
    String seq5 = tss5.seqString();
    String seq3 = tss3.seqString();
   
    assertTrue("5' arm sequence failed, expected '" + expect5 + "', got: '" + seq5 + "'", seq5.equals(expect5)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    assertTrue("3' arm sequence failed, expected '" + expect3 + "', got: '" + seq3 + "'", seq3.equals(expect3));        //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
  }
 
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          Element seqE = new Element(TSS,ns);
          seqE.setAttribute("key",key,ns); //$NON-NLS-1$
          seqE.setAttribute(ID,tss.getID(),ns);
          tssIDs.add(tss.getID());
          seqE.addContent(new Element(TYPE,ns).addContent(String.valueOf(tss.getType())));
          seqE.addContent(new Element(SEQUENCE,ns).addContent(tss.seqString()));
          seqE.addContent(new Element(TM,ns).addContent(String.valueOf(ProbeMakerPropertyUtils.getHybridizationTemp(tss))));
          seqE.addContent(getMessageListElement(ProbeMakerPropertyUtils.getAllMessages(tss)));                   
          tssPairE.addContent(seqE);
        }         
      }
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      if (fixedEnd != TemplateHandler.BOTH) {

        //Now cut off one base at a time until we reach either minimum length, or
        //preferred temperature.
        boolean done = false; //are we done yet?
        String oldseq = pa.seqString(); //store old seq here
        float oldTm = 0.0f;
        float Tm = 0.0f; //melting temp

        while (!done) {
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              }
            }
            break;
          }
          //Here we cut of the sequence at the appropriate end and do all again
          oldseq = pa.seqString(); //but first store the old sequence
          //remove nucleotides form the non-fixed end of the arm
          switch (fixedEnd) {
            case TemplateHandler.THREEPRIME:
              try {
                cns.edit(new SimpleSequenceEdit(1, 1, "")); //$NON-NLS-1$
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