Package org.moltools.lib.seq

Examples of org.moltools.lib.seq.SequenceElement

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  /**Returns an array of all Polymorphisms present in this sequence at the top level*/
  public Polymorphism[] getPolys() {
    Polymorphism[] polys = new Polymorphism[countPolys()];
    int polypos = 0;
    for (Iterator<SequenceElement> i = sequence.iterator(); i.hasNext(); ) {
      SequenceElement e = i.next();
      if (e instanceof Polymorphism) {
        polys[polypos++] = (Polymorphism) e;
      }
    }
    return polys;
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  }

  protected static List<SequenceElement> expandElements(SequenceElementContainer sc) {
    List<SequenceElement> expandedElements = new ArrayList<SequenceElement>();
    for (Iterator<SequenceElement> i = sc.getElements().iterator(); i.hasNext(); ) {
      SequenceElement e = i.next();
      if (e instanceof SequenceElementContainer) {
        expandedElements.addAll(expandElements((SequenceElementContainer) e));
      }
      else {
        expandedElements.add(e);
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  protected int getPolyPosition(int poly) {
    int pos = 1;
    int polyno = 0;
    for (Iterator<SequenceElement> i = sequence.iterator(); i.hasNext(); ) {
      SequenceElement e = i.next();
      if (e instanceof Polymorphism) {
        polyno++;
      }
      if (polyno == poly) {
        return pos;
      }
      pos += e.length();
    }
    throw new UnsupportedOperationException("No such polymorphism found"); //$NON-NLS-1$
  }
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  protected int getPolyPosition(int poly) {
    int pos = 1;
    int polyno = 0;
    for (Iterator<SequenceElement> i = sequence.iterator(); i.hasNext(); ) {
      SequenceElement e = i.next();
      if (e instanceof Polymorphism) {
        polyno++;
      }
      if (polyno == poly) {
        return pos;
      }
      pos += e.length();
    }
    throw new UnsupportedOperationException("No such polymorphism found"); //$NON-NLS-1$
  }
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  @Override
  protected int getPolyPosition(int poly) {
    int pos = 1;
    int polyno = -1;
    for (Iterator<SequenceElement> i = sequence.iterator(); i.hasNext(); ) {
      SequenceElement e = i.next();
      if (e instanceof Polymorphism) {
        polyno++;
      }
      if (polyno == poly) {
        return pos;
      }
      pos += e.length();
    }
    throw new UnsupportedOperationException("No such polymorphism found"); //$NON-NLS-1$
  }
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Related Classes of org.moltools.lib.seq.SequenceElement

  • org.moltools.apps.probemaker.ext.target.AlleleSpecificPadlockTarget
  • org.moltools.apps.probemaker.ext.target.MinisequencingTarget
  • org.moltools.apps.probemaker.ext.target.OLATarget
  • org.moltools.apps.probemaker.seq.impl.AbstractComplexTarget
  • org.moltools.apps.probemaker.seq.impl.VariationSequenceElementContainer
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