Examples of seqString()

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

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        }


        hw.printEnclosed(p.getName(), HTMLWriter.H4);
        hw.println(Messages.getString("HTMLOutputFormat.ID") + p.getID()); //$NON-NLS-1$
        String seqstr = p.seqString();
        //String seq = "";
        int index = 0;
        int width = 60;
        while (index <= seqstr.length() - width) {
          hw.printEnclosed(seqstr.substring(index, index += width), HTMLWriter.TT);
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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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Examples of org.moltools.apps.probemaker.seq.ProbeMakerTarget.seqString()

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

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

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

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

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

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

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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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