Package org.moltools.apps.probemaker.seq

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

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        default:
          return probes.getSequenceAt(0);
      }
    }
    //3 or more probes... do it recursivily
    Probe p;
    switch (compare( probes.getSequenceAt(0), p = getBest(probes, 1))) {
      case -1:
        return p;
      case 1:
        return probes.getSequenceAt(0);
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        default:
          return probes.getSequenceAt(i);
      }
    }
    //3 or more probes... do it recursivily
    Probe p;
    switch (compare( probes.getSequenceAt(i), p = getBest(probes, i + 1))) {
      case -1:
        return p;
      case 1:
        return probes.getSequenceAt(i);
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  }

  @Override
  public boolean acceptTag(NucleotideSequence t, DefiniteSequenceDB<? extends Probe> probes) {
    for (Iterator<? extends Probe> i = probes.iterator();i.hasNext();) {
      Probe p  =i.next();
      if (ltc.isLigationTemplate(t, p, false, false) != null) {
        return false; 
      }
    }
    return true;
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    //This is only necessary to check if there are templating messages on this probe
   
    if (! (CollectionUtils.select(ProbeMakerPropertyUtils.getAllMessages(p),new IncludeTypesFilter(new MessageType[] {  
        PadlockLigationCalculator.TEMPLATE_FOR_OTHER_PROBE})).isEmpty())) {
      for (Iterator<? extends Probe> i = probes.iterator(); i.hasNext(); ) {
        Probe other = i.next();
        //If other is not yet allocated, this will be found when checking other's arms
        if (other != p && other.tagsAllocated()) {
          if (ltc.isLigationTemplate(p, other, true, false) != null) {
            ProbeMakerPropertyUtils.addMessage(other,new Message("May be templated by " + //$NON-NLS-1$
                                         p.getName(),
                                         PadlockLigationCalculator.
                                         OTHER_PROBE_IS_TEMPLATE,
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  public byte acceptPrimary(Probe p) {
    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;
      }
    }
   
    int len = ((ProbeMakerTarget) p.getTarget()).length();
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      }

     
      if (! (allowsSeq && allowsComp)) {
        for (Iterator<? extends Probe> probeit = probes.iterator(); probeit.hasNext(); ) {
          Probe other = probeit.next();
          //Don't do anything if other is same as probe being analysed
          if (other != p && other.tagsAllocated()) {
            byte result = compareTag(p, other, tagpos, allowsSeq, allowsComp, taglibraries, tsc);
            if (result == THIS_IN_OTHER || result == BOTH) {
              pd.setCurrentTagBad(tagpos);
            }
          }
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  public void doConfirmUpdate(Probe p, TagAllocator pd, DefiniteSequenceDB<? extends Probe> probes) {
    //Check tags externally for each earlier probe towards this probe
    //as probes have not been tested 'both ways'
    for (Iterator<? extends Probe> i = probes.iterator(); i.hasNext(); ) {
      Probe other = i.next();
      if (other != p && other.tagsAllocated()) {
        for (int tagpos = 0; tagpos < other.getTags().size(); tagpos++) {
          boolean allowsSeq = true;
          for (int pos = 0;pos<seqPositions.length;pos++) {
            if (seqPositions[pos] == tagpos+1)
              allowsSeq = false;
          }
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    //This is only necessary to check if there are templating messages on this probe

    if (! (CollectionUtils.select(ProbeMakerPropertyUtils.getAllMessages(p),new IncludeTypesFilter(new MessageType[] {  
        PadlockLigationCalculator.TEMPLATE_FOR_OTHER_PROBE})).isEmpty())) {
      for (Iterator<? extends Probe> i = probes.iterator(); i.hasNext(); ) {
        Probe other = i.next();
        //If other is not yet allocated, this will be found when checking other's arms
        if (other != p && other.tagsAllocated()) {
          if (ltc.isLigationTemplate(p, other, true, false) != null) {
            ProbeMakerPropertyUtils.addMessage(other,new Message("May be templated by " + //$NON-NLS-1$
                p.getName(),
                PadlockLigationCalculator.
                OTHER_PROBE_IS_TEMPLATE,
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  }

  @Override
  public boolean acceptTag(NucleotideSequence t, DefiniteSequenceDB<? extends Probe> probes) {
    for (Iterator<? extends Probe> i = probes.iterator();i.hasNext();) {
      Probe p = i.next();
      if (ltc.isLigationTemplate(t, p, false, false) != null) {
        return false;
      }
    }
    return true;
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  }

  public void doAnalysis(Probe p, TagAllocator pd, DefiniteSequenceDB<? extends Probe> probes) {
    if (tests[0].perform()) {
      for (Iterator<? extends Probe> probeit = probes.iterator(); probeit.hasNext(); ) {
        Probe other = probeit.next();
        //log.debug(System.out.println("Comparing " + other.getID() + " with " + p.getID()));
        //Don't do anything if other is same as probe being analysed
        if (!other.equals(p) && other.tagsAllocated()) {
          byte dimer = compare(p,other);
          if (dimer == HI_RISK)
            ProbeMakerPropertyUtils.addMessage(p,new Message("High risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                PROBE_DIMER_FORMATION, Message.ERROR));
          else if (dimer == RISK)
            ProbeMakerPropertyUtils.addMessage(p,new Message("Risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                 PROBE_DIMER_FORMATION, Message.WARNING));

        }
      }     
    }
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Related Classes of org.moltools.apps.probemaker.seq.Probe

  • org.moltools.apps.probemaker.calculators.PadlockLigationCalculator
  • org.moltools.apps.probemaker.design.DefaultProbeDesigner
  • org.moltools.apps.probemaker.ext.acc.LengthBinAcceptor
  • org.moltools.apps.probemaker.ext.mod.DefaultTagOccurrenceModule
  • org.moltools.apps.probemaker.ext.mod.FalsePrimingModule
  • org.moltools.apps.probemaker.ext.mod.GapFillPadlockLigationModule
  • org.moltools.apps.probemaker.ext.mod.PadlockLigationModule
  • org.moltools.apps.probemaker.ext.mod.SelectorLigationModule
  • org.moltools.apps.probemaker.ext.mod.StringHeteroDimerModule
  • org.moltools.apps.probemaker.ext.mod.TmProbeDimerModule
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