Examples of IncludeTypesFilter

org.moltools.apps.probemaker.messages.IncludeTypesFilter

Title: IncludeTypesFilter

Description: A message filter that accepts only messages of the types specified in the constructr.

Copyright: Copyright (c) 2002
@author Johan Stenberg @version 1.0

Examples of org.moltools.apps.probemaker.messages.IncludeTypesFilter

  public void doConfirmUpdate(Probe p, TagAllocator pd, DefiniteSequenceDB<? extends Probe> probes) {
    if (tests[1].perform())
    //If another probe is templated by this probe, add message to it.
    //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()) {

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Examples of org.moltools.apps.probemaker.messages.IncludeTypesFilter


  public void doConfirmUpdate(Probe p, TagAllocator pd, DefiniteSequenceDB<? extends Probe> probes) {
    //If another probe is templated by this probe, add message to it.
    //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()) {

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Examples of org.moltools.apps.probemaker.messages.IncludeTypesFilter

  public void doConfirmUpdate(Probe p, TagAllocator pd, DefiniteSequenceDB<? extends Probe> otherProbes) {


    //If another probe forms dimer with this probe, add message to it.
    //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)

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Examples of org.moltools.apps.probemaker.messages.IncludeTypesFilter

    setData(KEY_STRINGENCY,new Integer(6));
  }


  public void doConfirmUpdate(Probe p, TagAllocator pd, DefiniteSequenceDB<? extends Probe> probes) {


    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);

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Examples of org.moltools.apps.probemaker.messages.IncludeTypesFilter


  public void doConfirmUpdate(Probe p, TagAllocator pd, DefiniteSequenceDB<? extends Probe> probes) {
    //If another probe is templated by this probe, add message to it.
    //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()) {

View Full Code Here

Examples of org.moltools.apps.probemaker.messages.IncludeTypesFilter


  public void doConfirmUpdate(Probe p, TagAllocator pd, DefiniteSequenceDB<? extends Probe> otherProbes) {
    //If another probe is templated by this probe, add message to it.
    //This is only necessary to check if there are templating 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 is not yet allocated, this will be found when checking other's arms
        if (!other.equals(p) && other.tagsAllocated()) {
          byte dimer = compare(p,other);

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