Package org.moltools.apps.probemaker.seq

Examples of org.moltools.apps.probemaker.seq.ProbeMakerTarget.seqString()

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    p.println(TITLE_DESCRIPTOR + TARGETS);
    for (Iterator<ProbeMakerTarget> i = proj.getTargets().iterator(); i.hasNext(); ) {
      ProbeMakerTarget t = i.next();
      setStatus(t.getID(),1);
      String descStr = t.getID();
      String seqStr = t instanceof SequenceView ? ((SequenceView) t).getViewSequence() : t.seqString();
      String typeStr = String.valueOf(t.getType());
      String varStr = ""; //$NON-NLS-1$
      if (t instanceof VariantTarget) {
        VariantTarget vt = (VariantTarget) t;
        if (vt.getVariant() != null) {
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    for (int i = 0; i < libraries.length; i++) {
      TagLibrary l = libraries[i];
      p.println(TITLE_DESCRIPTOR + LIBRARY);
      for (Iterator<NucleotideSequence> ti = l.iterator(); ti.hasNext(); ) {
        NucleotideSequence t = ti.next();
        p.println(tio.getOutString(new String[] {t.getID(),t.seqString(),String.valueOf(t.getType())}));
      }
      p.println(TITLE_DESCRIPTOR + LISTEND);
    }

    increaseProgress();
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              FIVE_PRIME_HYBRIDIZATION_INTERFERENCE,
              Message.ALERT));
        }
        else if (fiveTemplate != null) {
          int targetLength = t.length();
          String tseq = t.seqString();
          int probeLength = p.length();       
          int[] positions = TemplateHandler.subTemplatePositions(fiveTemplate,pa5.length(),t.getFivePrimeFixedEnd());
          int begin = positions[0];
          int end = positions[1];
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              THREE_PRIME_HYBRIDIZATION_INTERFERENCE,
              Message.ALERT));
        }
        else if (threeTemplate != null) {
          int targetLength = t.length();
          String tseq = t.seqString();      
          int[] positions = TemplateHandler.subTemplatePositions(threeTemplate,pa3.length(),t.getThreePrimeFixedEnd());

          int begin = positions[0];
          int end = positions[1];
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