List of seqString() Examples

Examples of seqString()

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

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

  /**Assemble the parts (subsequences) of the Probe*/
  protected String composeSequence() {
    StringBuffer sequencestring = new StringBuffer();
    for (int i = 1; i <= getSequenceCount(); i++) {
      NucleotideSequence si = getSequence(i);
      sequencestring.append(si == null ? "" : si.seqString()); //$NON-NLS-1$
    }
    return sequencestring.toString();
  }


  /**Set the TSSPair of this probe*/

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

    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.lib.seq.NucleotideSequence.seqString()

        NucleotideSequence tag = pr.getTagAt(t);
        //This isn't perfect but will work (if noone calls their tags 'Spacer')
        if (tag.getID().startsWith("Spacer")) { //$NON-NLS-1$
          outStr += "Spacer"; //$NON-NLS-1$
          outStr += VALUE_SEPARATOR;
          outStr += tag.seqString();
        }
        else {
          int lib_no = -1;
          int tag_no = -1;
          for (int l = 0; l < libraries.length; l++) {

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

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

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

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


    for (Iterator<NucleotideSequence> i = library.iterator(); i.hasNext(); ) {
      NucleotideSequence t = i.next();
      HTMLWriter.appendEnclosed(html,t.getID(),HTMLWriter.B);
      html.append("<br>\n"); //$NON-NLS-1$ 
      html.append("<tt>" + SequenceHTMLRenderer.getHardWrappedString(t.seqString(),60) + "</tt><br>\n"); //$NON-NLS-1$ //$NON-NLS-2$
    }
    return html.toString();
  }


  public String getHTMLContainerTitle(Object obj) {

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

  /**Assemble the parts (subsequences) of the Probe*/
  protected String composeSequence() {
    StringBuffer sequencestring = new StringBuffer();
    for (int i = 1; i <= getSequenceCount(); i++) {
      NucleotideSequence si = getSequence(i);
      sequencestring.append(si == null ? "" : si.seqString()); //$NON-NLS-1$
    }
    return sequencestring.toString();
  }


  /**Set the TSSPair of this probe*/

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

      //If the tag is of 0 length don't do anything
      if (tag.length() > 0) {
        //Search for the tag sequence in the probe
        if (!allowsSeq) {
          
          occurrences = tsc.getOccurrences(tag.seqString(), p.seqString(),
              tag.getType(), p.getType(), true);
          //Go through each of the occurrences
          for (int occ = 0; occ < occurrences.length; occ++) {            
            int pos = occurrences[occ].intValue() + 1;
            if (pos != blockStart) {

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