Package org.moltools.lib.seq

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

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  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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    int index = 0;
    List<SequenceElement> el = getElements();
    for (int i = 0;i<el.size();i++) {
      SequenceStringElement se = (SequenceStringElement) el.get(i);
      if (se instanceof InDel) {
        viewString.append(inDelBeginSymbol + se.seqString() + inDelEndSymbol);
        index += se.length();
      }
      else {
        viewString.append(se.seqString());
        index += se.length();
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      if (se instanceof InDel) {
        viewString.append(inDelBeginSymbol + se.seqString() + inDelEndSymbol);
        index += se.length();
      }
      else {
        viewString.append(se.seqString());
        index += se.length();
      }

      if (index == pos) {
        viewString.append(positionSymbol);
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    int index = 0;
    List<SequenceElement> el = getElements();
    for (int i = 0;i<el.size();i++) {
      SequenceStringElement se = (SequenceStringElement) el.get(i);
      if (se instanceof InDel)
        viewString += inDelBeginSymbol + se.seqString() + inDelEndSymbol;
      else
        viewString += se.seqString();

      index += se.length();
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    for (int i = 0;i<el.size();i++) {
      SequenceStringElement se = (SequenceStringElement) el.get(i);
      if (se instanceof InDel)
        viewString += inDelBeginSymbol + se.seqString() + inDelEndSymbol;
      else
        viewString += se.seqString();

      index += se.length();

      if (index == pos) {
        viewString += positionSymbol;
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