List of seqString() Examples

Examples of seqString()

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

    boolean foundTIO = false;
    boolean foundOIT = false;
    
    /**This probe's tag*/
    NucleotideSequence tag = thisProbe.getTagAt(tagpos);
    String tagseq = tag.seqString();
    //Check that tag sequence is longer than 0
    if (tagseq.length() > 0) {
      //Go through each tag position of this probe ...
      /**Tag*/
      if (checkSequence) {

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

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

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

      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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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.Sequence.seqString()


        for (Iterator<? extends NucleotideSequence> i = transferdb.iterator();i.hasNext();) {
          Sequence s = i.next();
          Map<String,String> m = new HashMap<String, String>();
          m.put(SequenceBuilder.PROPERTY_NAME,s.getID());
          m.put(SequenceBuilder.PROPERTY_SEQUENCE_DATA,s.seqString());
          m.put(SequenceBuilder.PROPERTY_ID,s.getID());
          maps.add(m);
        }
        database.addSequences(dbBuilder.buildDB(maps,seqBuilder));
      }

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

      //ID starts with "Spacer" - spacer tag
      else if (seqID.startsWith("Spacer")) { //$NON-NLS-1$
        seqE = new Element(SPACER,ns);
        seqE.setAttribute(ID,seqID,ns);
        seqE.addContent(new Element(TYPE,ns).addContent(String.valueOf(((NucleotideSequence) seq).getType())));
        seqE.addContent(new Element(SEQUENCE,ns).addContent(seq.seqString()));            
      }
      //Otherwise - normal tag
      else if (seq instanceof NucleotideSequence){
        KeyValue kv = getLibraryTag(libraries,seqID);
        if (kv == null) {

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


  public static String sequenceOf(List<SequenceElement> elements) {
    String sequenceString = ""; //$NON-NLS-1$
    for (Iterator<SequenceElement> i = elements.iterator(); i.hasNext(); ) {
      SequenceStringElement e = (SequenceStringElement) i.next();
      sequenceString += e.seqString();
    }
    return sequenceString;
  }


  /**Parses a sequence string and returns an ArrayList of nucleotides and polymorphisms

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