Examples of addTagAt()

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

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      for (int i = 16; i < substrings.length; i+=2, t++) {
        String l_str = substrings[i];
        String t_str = substrings[i+1];
        if (l_str.startsWith("Spacer")) { //$NON-NLS-1$
          NucleotideSequence tag = new SimpleNucleotideSequence("Spacer " + t_str, t_str, p.getType()); //$NON-NLS-1$
          p.addTagAt(tag,t);
        }
        else {
          int lib_no = Integer.parseInt(l_str);
          int tag_no = Integer.parseInt(t_str);
          NucleotideSequence tag = libraries[lib_no].getSequenceAt(tag_no);
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Examples of org.moltools.apps.probemaker.seq.Probe.addTagAt()

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        }
        else {
          int lib_no = Integer.parseInt(l_str);
          int tag_no = Integer.parseInt(t_str);
          NucleotideSequence tag = libraries[lib_no].getSequenceAt(tag_no);
          p.addTagAt(tag, t);
          proj.getTagAllocationTable().use(tag,p,t);
        }
      }

      //UITexts for 5' TSS
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Examples of org.moltools.apps.probemaker.seq.Probe.addTagAt()

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              l.get(i), NucleotideSequence.DNA,  "Tag " + i)); //$NON-NLS-1$
        }
        PropertyAcceptorNucleotideSequence tss3 = ProbeMakerSequenceFactory.createTSS(new SimpleChangeableNucleotideSequence("3' TSS", l.get(l.size() - 1), NucleotideSequence.DNA,"3' TSS"),null); //$NON-NLS-1$
        Probe p = new DefaultProbe(ProbeMakerSequenceFactory.createTSSPair(tss5, tss3, null),0,0,NucleotideSequence.DNA);
        for (int i = 0;i<tags.size();i++) {
          p.addTagAt(tags.get(i),i); 
        }
       
        p.setName(name);
        p.setID(id);
        p.setTagsAllocated(true);
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Examples of org.moltools.apps.probemaker.seq.Probe.addTagAt()

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      //Go through and add tags
      int pos = 0;
      for (Iterator ti = tags.keySet().iterator();ti.hasNext();pos++) {
        NucleotideSequence t = (NucleotideSequence) ti.next();
        p.addTagAt(t,pos);       
        project.getTagAllocationTable().use(t,p,pos);       
      }
      tags.clear();

      addMessagesFromElement(p,probeE.getChild("messageList",ns));       //$NON-NLS-1$
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Examples of org.moltools.apps.probemaker.seq.Probe.addTagAt()

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              l.get(i), NucleotideSequence.DNA,  "Tag " + i)); //$NON-NLS-1$
        }
        PropertyAcceptorNucleotideSequence tss3 = ProbeMakerSequenceFactory.createTSS(new SimpleChangeableNucleotideSequence("3' TSS", l.get(l.size() - 1), NucleotideSequence.DNA,"3' TSS"),null); //$NON-NLS-1$
        Probe p = new DefaultProbe(ProbeMakerSequenceFactory.createTSSPair(tss5, tss3, null),0,0,NucleotideSequence.DNA);
        for (int i = 0;i<tags.size();i++) {
          p.addTagAt(tags.get(i),i); 
        }
       
        p.setName(name);
        p.setID(id);
        p.setTagsAllocated(true);
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Examples of org.moltools.apps.probemaker.seq.impl.DefaultProbe.addTagAt()

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      for (int i = 16; i < substrings.length; i+=2, t++) {
        String l_str = substrings[i];
        String t_str = substrings[i+1];
        if (l_str.startsWith("Spacer")) { //$NON-NLS-1$
          NucleotideSequence tag = new SimpleNucleotideSequence("Spacer " + t_str, t_str, p.getType()); //$NON-NLS-1$
          p.addTagAt(tag,t);
        }
        else {
          int lib_no = Integer.parseInt(l_str);
          int tag_no = Integer.parseInt(t_str);
          NucleotideSequence tag = libraries[lib_no].getSequenceAt(tag_no);
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Examples of org.moltools.apps.probemaker.seq.impl.DefaultProbe.addTagAt()

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        }
        else {
          int lib_no = Integer.parseInt(l_str);
          int tag_no = Integer.parseInt(t_str);
          NucleotideSequence tag = libraries[lib_no].getSequenceAt(tag_no);
          p.addTagAt(tag, t);
          proj.getTagAllocationTable().use(tag,p,t);
        }
      }

      //UITexts for 5' TSS
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Examples of org.moltools.apps.probemaker.seq.impl.DefaultProbe.addTagAt()

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      //Go through and add tags
      int pos = 0;
      for (Iterator ti = tags.keySet().iterator();ti.hasNext();pos++) {
        NucleotideSequence t = (NucleotideSequence) ti.next();
        p.addTagAt(t,pos);       
        project.getTagAllocationTable().use(t,p,pos);       
      }
      tags.clear();

      addMessagesFromElement(p,probeE.getChild("messageList",ns));       //$NON-NLS-1$
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