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()

    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()

  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.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()

    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 is not yet allocated, this will be found when checking other's arms
        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 " + 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()

    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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