Package org.moltools.lib.seq

Examples of org.moltools.lib.seq.NucleotideSequence.seqString()

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    /**Other probe's tag*/
    //Check number of tag libraries in other probe
    if (otherProbe.getTags().size() > tagpos) {
      //Get the tag from the other probe
      tag = otherProbe.getTagAt(tagpos);
      tagseq = tag.seqString();
      //Check that tag sequence is longer than 0
      if (tagseq.length() > 0) {
        /**Tag*/
        if (checkSequence) {
          //search for the tag sequence in this probe
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        /**Complement*/
        if (checkComplement) {
          if (otherProbe.getTags().size() > tagpos) {
            //Get the tag from the other probe
            tag = otherProbe.getTagAt(tagpos);
            tagseq = tag.seqString();
            //Search for the tag sequence in this probe
            occurrences = tsc1.getOccurrences(NucleotideSequenceHandler.
                getRevComp(tag,
                    thisProbe.getType()), thisSeq, tag.getType(),
                    otherProbe.getType(), true);
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      NucleotideSequence t = (NucleotideSequence) getSequenceAt(parm1);
      switch (parm2) {
        case 0:
          return t.getID();
        case 1:
          return t.seqString();
        case 2:
          List<String> c = new ArrayList<String>(tagAllocationTable.getUserIDs(t));
          if (c == null) {
            return Collections.EMPTY_LIST;
          }
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    try {
      NucleotideSequence tss5 = p.getTSSPair().getSequence(TSSPair.KEY_FIVE_PRIME);
      NucleotideSequence tss3 = p.getTSSPair().getSequence(TSSPair.KEY_THREE_PRIME);
     
//    The sequence of the probe arms (full arms)
      String tssSeq = tss3.seqString() + tss5.seqString();
      NucleotideSequence fullTSS = new SimpleNucleotideSequence("TSS",tssSeq,p.getType()); //$NON-NLS-1$

     
      //Get the sequence to search for in other probes  
      String threeseq = p.subsequence(p.length() - min3Length + 1, p.length());
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    if (tp == null || fp == null) throw new UnsupportedOperationException("Can't perform ligation calculations with missing TSSs"); //$NON-NLS-1$
   
    int[] results = isLigationTemplate(
        new SimpleChangeableNucleotideSequence(
            "TSS|"+p.getName(), //$NON-NLS-1$
            tp.seqString() + fp.seqString(),
            p.getType()
        ), p, false, false);
    if (results != null) {
      for (int i = 0; i < results.length; i++) {
        ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message(
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          tp = null;
        }
       
        if (tp == null || fp == null) throw new UnsupportedOperationException("Can't perform ligation calculations with missing TSSs"); //$NON-NLS-1$
       
        if (isLigationTemplate(new SimpleNucleotideSequence(tp.
            seqString() + fp.seqString(),
            "Arms of " + p.getName(), //$NON-NLS-1$
            p.getType()), other, false, false) != null) {
          ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message("May act as template for " + //$NON-NLS-1$
              other.getName(),
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