List of tagsAllocated() Examples

Examples of tagsAllocated()

org.moltools.apps.probemaker.seq.Probe.tagsAllocated()
Returns a boolean describing if tags have been allocated to this probe

Examples of org.moltools.apps.probemaker.seq.Probe.tagsAllocated()

    for (Iterator<? extends Probe> pi = probes.iterator(); pi.hasNext(); ) {
      Probe other = pi.next();
      //Check for templating and add messages accordingly
      if (other != p) {
        //Does other probe template this probe
        if (other.tagsAllocated()) {
          //Tags allocated, test as circle
          if (isLigationTemplate(other, p, true, false) != null) {
            ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message("May be templated by " + //$NON-NLS-1$
                other.getName(),
                OTHER_PROBE_IS_TEMPLATE,

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Examples of org.moltools.apps.probemaker.seq.Probe.tagsAllocated()

    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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Examples of org.moltools.apps.probemaker.seq.Probe.tagsAllocated()

    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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Examples of org.moltools.apps.probemaker.seq.Probe.tagsAllocated()

      
      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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Examples of org.moltools.apps.probemaker.seq.Probe.tagsAllocated()

  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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Examples of org.moltools.apps.probemaker.seq.Probe.tagsAllocated()

    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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Examples of org.moltools.apps.probemaker.seq.Probe.tagsAllocated()

    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)

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Examples of org.moltools.apps.probemaker.seq.Probe.tagsAllocated()

    //This is only necessary to check if there are dimer messages on this probe
    if (tests[0].perform())
    if (!CollectionUtils.select(ProbeMakerPropertyUtils.getAllMessages(p),new IncludeTypesFilter(new MessageType[] {PROBE_DIMER_FORMATION})).isEmpty()) {
      for (Iterator<? extends Probe> i = otherProbes.iterator(); i.hasNext(); ) {
        Probe other = i.next();
        if (!other.equals(p) && other.tagsAllocated()) {
          byte dimer = compare(p,other);
          if (dimer == HI_RISK)
            ProbeMakerPropertyUtils.addMessage(other,new Message("High risk of hetero-dimer formation with " + p.getName(), //$NON-NLS-1$
                PROBE_DIMER_FORMATION, Message.ERROR));
          else if (dimer == RISK)

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Examples of org.moltools.apps.probemaker.seq.Probe.tagsAllocated()


    if (!CollectionUtils.select(ProbeMakerPropertyUtils.getAllMessages(p),new IncludeTypesFilter(new MessageType[] {PROBE_HETERODIMER_FORMATION})).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()) {
          boolean dimer = dimer(p,other);
          if (dimer)
            ProbeMakerPropertyUtils.addMessage(other,new Message("High risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                PROBE_HETERODIMER_FORMATION, Message.ERROR));
          /*else if (dimer == RISK)

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Examples of org.moltools.apps.probemaker.seq.Probe.tagsAllocated()

  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();
        //Don't do anything if other is same as probe being analysed
        if (other != p && other.tagsAllocated()) {
          boolean dimer = dimer(p,other);
          if (dimer)
            ProbeMakerPropertyUtils.addMessage(p,new Message("High risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                PROBE_HETERODIMER_FORMATION, Message.ERROR));
          /*else if (dimer == RISK)

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