Package org.moltools.design.data

Examples of org.moltools.design.data.TargettedSequence

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      temp = (TargettedSubSequence) target.getTemplateCluster().getSequence(ProbeMakerTarget.KEY_THREE_PRIME);
    }
    catch (ClusterException e) {
      temp = null;
    }
    TargettedSequence sub = null;

    if (temp != null) {
      if (fixedEnd != TemplateHandler.BOTH)
        sub = TemplateHandler.subTemplate(temp, maxlength,fixedEnd);
      else
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    }
    catch (ClusterException e) {
      temp = null;
    }

    TargettedSequence sub  = null;

    if (temp != null) {
      if (fixedEnd != TemplateHandler.BOTH)
        sub = TemplateHandler.subTemplate(temp, maxlength,fixedEnd);
      else
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  /**Returns the downstream part of the template. This is different depending on the type of Poly
   * currently selected, if any. If a SNP is the current Poly, the target nucleotide is included.*/
  @Override
  protected void setTemplateForThreePrimeArm() {
    //There are three different modes to consider, target is position (no poly), SNP or InDel
    TargettedSequence template;
    String tempID = "TEMPLATE|3|"+getID(); //$NON-NLS-1$
    if (targetPoly == 0) { //No poly
      template = new SimpleSubSequenceTemplate(this, "Template for 3' arm", getType(), //$NON-NLS-1$
                             getTargetPosition(), length(), getID());
    }
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           "sequences as target-specific sequences." + //$NON-NLS-1$
           "No Tm calculations are performed"; //$NON-NLS-1$
  }
 
  public PropertyAcceptorNucleotideSequence get3PrimeTSS(ProbeMakerTarget target, byte type) {
    TargettedSequence temp;
    try {
      temp = (TargettedSequence) target.getTemplateCluster().getSequence(ProbeMakerTarget.KEY_THREE_PRIME);
    }
    catch (ClusterException e) {
      temp = null;
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      return ProbeMakerSequenceFactory.createTSS(temp,target.getID());
    return ProbeMakerSequenceFactory.createTSS(new SimpleNucleotideSequence("TSS3|"+target.getID(),"",type),target.getID()); //$NON-NLS-1$ //$NON-NLS-2$
  }

  public PropertyAcceptorNucleotideSequence get5PrimeTSS(ProbeMakerTarget target, byte type) {
    TargettedSequence temp;
    try {
      temp = (TargettedSequence) target.getTemplateCluster().getSequence(ProbeMakerTarget.KEY_FIVE_PRIME);
    }
    catch (ClusterException e) {
      temp = null;
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  /**Returns the downstream part of the template. This is different depending on the type of Poly
   * currently selected, if any. If a SNP is the current Poly, the target nucleotide is included.*/
  @Override
  protected void setTemplateForFivePrimeArm() {
    //There are three different modes to consider, target is position (no poly), SNP or InDel
    TargettedSequence template;
    String tempID = "TEMPLATE|5|" + getID(); //$NON-NLS-1$
    if (targetPoly == 0) { //No poly
      template = new SimpleSubSequenceTemplate(this, tempID, getType(),
                             getTargetPosition(), length(), getID());
    }
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Related Classes of org.moltools.design.data.TargettedSequence

  • org.moltools.apps.probemaker.ext.target.AlleleSpecificPadlockTarget
  • org.moltools.apps.probemaker.ext.target.OLATarget
  • org.moltools.apps.probemaker.ext.tc.DefaultTSSConstructor
  • org.moltools.apps.probemaker.ext.tc.TemplateTSSConstructor
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