Examples of org.moltools.apps.probemaker.design.ProbeGroup

Package org.moltools.apps.probemaker.design

Examples of org.moltools.apps.probemaker.design.ProbeGroup

org.moltools.apps.probemaker.design.ProbeGroup
A ProbeGroup is used to to group those probes that have targets belonging to the same target group. This is used when allocating tags in the USE_PER_GROUP and USE_UNIQUE_IN_GROUP (per allele) mode. @author Johan Stenberg

    return ACCEPT; 
  }


  public byte accept(Candidate c) {
    Probe p = (Probe) c;
    ProbeGroup group = (ProbeGroup) DesignUtils.getGroupWithType(c,ProbeGroup.GROUP_TYPE);
    Collection<Probe> probes = group.getMembers();
    for (Iterator<Probe> i = probes.iterator();i.hasNext();) {
      Probe pr = i.next();
      if (pr.tagsAllocated() && ProbeMakerPropertyUtils.getRank(p) == ProbeMakerConstants.GOOD_QUALITY) {
        return REJECT;
      }

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        //Nothing
      }
      else {
        //We also have to set the selected probe's group to be the correct one.
        //Find the group
        ProbeGroup pg = (ProbeGroup) DesignUtils.getGroupWithType(p, ProbeGroup.GROUP_TYPE);        
        //Remove the current probe from the group
        if (pg != null) {
          pg.removeMember(p);                      
        }        
        //Copy the selected probe
        p.copy(selected);


        //Add the copied probe to the group
        if (pg != null) {
          pg.addMember(p);
        }
        //Print the selected probe to the log        
        String s = "Selected: "; //$NON-NLS-1$
        for (int i = 1; i <= p.getSequenceCount(); i++) {
          if (i > 1) {

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      if (selected == null) {
        //Nothing
      }
      else {
        //We also have to set the selected probe's group to be the correct one.
        ProbeGroup pg = (ProbeGroup) DesignUtils.getGroupWithType(p, ProbeGroup.GROUP_TYPE);
        if (pg != null) {
          pg.removeMember(p);
        }
        
        //Copy the selected probe
        p.copy(selected);


        if (pg != null) {
          pg.addMember(p);
        }
        //Print the selected probe to the log        
        String s = "Selected: "; //$NON-NLS-1$
        for (int i = 1; i <= p.getSequenceCount(); i++) {
          if (i > 1) {

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org.moltools.apps.probemaker.ext.ta.GreedyTagAllocator

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org.moltools.apps.probemaker.project.ProjectXMLIOTask

org.moltools.apps.probemaker.seq.ProbeMakerSequenceFactory

org.moltools.apps.probemaker.test.DataStructureTest

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