Examples of VariantTarget

org.moltools.apps.probemaker.seq.VariantTarget
The VariantTarget interface should be implemented by targets that have several variants, such as SNP alleles, target strand, or probe position.
The set and get variant methods allow programmatic selection of target variant, while the expand method allows Targets that have been loaded to be expanded, meaning that a set of Targets is created for this target, and all put into the same group. This is useful e.g. when designing allele-specific probes. @author joste021

Examples of org.moltools.apps.probemaker.seq.VariantTarget

      String descStr = t.getID();
      String seqStr = t instanceof SequenceView ? ((SequenceView) t).getViewSequence() : t.seqString();
      String typeStr = String.valueOf(t.getType());
      String varStr = ""; //$NON-NLS-1$
      if (t instanceof VariantTarget) {
        VariantTarget vt = (VariantTarget) t;
        if (vt.getVariant() != null) {
          String str = vt.getVariant().toString();
          for (int v = 0; v < vt.getVariants().length; v++) {
            if (vt.getVariants()[v].toString().equals(str)) {
              varStr = String.valueOf(v);
              //Break the loop
              break;
            }
          }

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Examples of org.moltools.apps.probemaker.seq.VariantTarget

      else
        varno = Integer.parseInt(substrings[3]);


      //Set variant
      if (varno > -1) {
        VariantTarget vt = (VariantTarget) t;
        vt.setVariant(vt.getVariants()[varno]);
      }


      //Set the target group
      int grpno = Integer.parseInt(substrings[4]);
      if (grpno > -1) {

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Examples of org.moltools.apps.probemaker.seq.VariantTarget

  
  @Override
  protected void setUp() throws DuplicateIDException {
    pm = new ProbeMakerPlugIn();
    ProbeMakerTarget t1 = new AlleleSpecificPadlockTarget("T1","ACTACGAGCGACGAGC|ACACGCTACATCGAGC","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    VariantTarget t2 = new MinisequencingTarget("T2","ACTACGAGCGACGAGCSACACGCTACATCGAGC","Target 2"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    t2.setVariant(t2.getVariants()[0]);
    ProbeMakerTarget t3 = new UnchangedTarget("T3","ACGTCAGCGAGCGACGACTACTACGAC","Target 3"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    project = new Project("IOTest"); //$NON-NLS-1$
    pm.setProject(project);
    project.getTargets().addSequence(t1);
    project.getTargets().addSequence(t2);

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Examples of org.moltools.apps.probemaker.seq.VariantTarget

  
  @Override
  protected void setUp() throws DuplicateIDException {
    pm = new ProbeMakerPlugIn();
    ProbeMakerTarget t1 = new AlleleSpecificPadlockTarget("T1","ACTACGAGCGACGAGC|ACACGCTACATCGAGC","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    VariantTarget t2 = new MinisequencingTarget("T2","ACTACGAGCGACGAGCSACACGCTACATCGAGC","Target 2"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    t2.setVariant(t2.getVariants()[0]);
    ProbeMakerTarget t3 = new UnchangedTarget("T3","ACGTCAGCGAGCGACGACTACTACGAC","Target 3"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    project = new Project("IOTest"); //$NON-NLS-1$
    pm.setProject(project);
    project.getTargets().addSequence(t1);
    project.getTargets().addSequence(t2);

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Examples of org.moltools.apps.probemaker.seq.VariantTarget

    Group<?> group = DesignUtils.getGroupWithType(t,TargetGroup.GROUP_TYPE);    
    String groupStr = group  == null ? null : String.valueOf(group.getID());
    targetE.addContent(new Element(TARGET_GROUP,ns).addContent(groupStr));
    String varStr = ""; //$NON-NLS-1$
    if (t instanceof VariantTarget) {
      VariantTarget vt = (VariantTarget) t;
      if (vt.getVariant() != null) {
        String str = vt.getVariant().toString();
        for (int v = 0; v < vt.getVariants().length; v++) {
          if (vt.getVariants()[v].toString().equals(str)) {
            varStr = String.valueOf(v);
            //Break the loop
            break;
          }
        }

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Examples of org.moltools.apps.probemaker.seq.VariantTarget

          varno = -1;
        else
          varno = Integer.parseInt(variantStr);
        //Set variant
        if (varno > -1) {
          VariantTarget vt = (VariantTarget) t; 
          vt.setVariant(vt.getVariants()[varno]);
        }
      }


      //Set the target group
      if (groupStr.length() > 0) {

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Examples of org.moltools.apps.probemaker.seq.VariantTarget

    Iterator<? extends ProbeMakerTarget> ti = targets.iterator();
    while (ti.hasNext()) {
      ProbeMakerTarget target = ti.next();
      //Check if target is expandable
      if (target instanceof VariantTarget) {
        VariantTarget vt = (VariantTarget) target;
        //If target is not in a group, expand it and add the new targets to temp
        TargetGroup tg = (TargetGroup) DesignUtils.getGroupWithType(vt,TargetGroup.GROUP_TYPE); 
        if (tg == null) {
          tg = new TargetGroup(vt.getID());
          List<? extends ProbeMakerTarget> nts = vt.expand();
          if (nts.size() <= 1) {
            try {
              temp.addSequence(vt);
            } 
            catch (DuplicateIDException e) {

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Examples of org.moltools.apps.probemaker.seq.VariantTarget

    ListSequenceDB<S> targets = (ListSequenceDB<S>) ListSequenceDB.getDefaultBuilder().buildDB(sequenceDataMaps,sequenceBuilder);
    for (Iterator<S> i = targets.iterator();i.hasNext();) {
      try {
        Target t = (Target) i.next();
        if (t instanceof VariantTarget) {
          VariantTarget vt = (VariantTarget) t;
          Variant[] variants = vt.getVariants();
          if (variants != null)
            if (variants.length > 0) 
              vt.setVariant(variants[0]);
        }
      }
      catch (ClassCastException cx) {
        throw new UnsupportedOperationException("Only Target sequences may be modified with this modifier"); //$NON-NLS-1$
      }

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