Examples of ProbeAnalysisModule

org.moltools.apps.probemaker.modules.ProbeAnalysisModule

The AnalysisModule interface is an extension of the PlugIn interface to be implemented by classes that define design constraints. This interface is extended by the IntraAnalysisModule and InterAnalysisModule interfaces that provide the methods used to carry out the particular tests. Each module defines a number of Test objects that represent the tests carried out by the module, and a number of AnalysisParameter objects that are used to set parameter values for the tests through the GUI.

Copyright: Copyright (c) 2003, 2005
@author Johan Stenberg @version 1.0

Examples of org.moltools.apps.probemaker.modules.ProbeAnalysisModule

  /**Call the doConfirmUpdate method of all Modules registered. 
   * This will complete any reciprocal messages for other affected
   * probes.*/
  public void confirmUpdate(Probe p, TagAllocator pd, DefiniteSequenceDB<Probe> probeset) {
    for (Iterator<CandidateAnalysisModule> i = armModules.iterator(); i.hasNext(); ) {
      ProbeAnalysisModule m = (ProbeAnalysisModule) i.next();
      m.doConfirmUpdate(p, pd, probeset);
    }


    for (Iterator<CandidateAnalysisModule> i = candidateModulesStage1.iterator(); i.hasNext(); ) {
      ProbeAnalysisModule m = (ProbeAnalysisModule) i.next();
      m.doConfirmUpdate(p, pd, probeset);
    }


    for (Iterator<CandidateAnalysisModule> i = candidateModulesStage2.iterator(); i.hasNext(); ) {
      ProbeAnalysisModule m = (ProbeAnalysisModule) i.next();
      m.doConfirmUpdate(p, pd, probeset);
    }
  }

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Examples of org.moltools.apps.probemaker.modules.ProbeAnalysisModule

        //Iterate through each tag...
        for (int tagno = 0; tagno < libraries[i].size(); tagno++) {
          NucleotideSequence t = libraries[i].getSequenceAt(tagno);
          //setStatus(t.getName());
          for (Iterator<CandidateAnalysisModule> m = modules.iterator(); m.hasNext(); ) {
            ProbeAnalysisModule mod = (ProbeAnalysisModule) m.next();
            if (!mod.acceptTag(t, probeset)) {
              //log.printLine(t.getName() + " not accepted by " + PlugInDescriptor.getBriefDescription(mod)); //$NON-NLS-1$
              badTags[i].add(new Integer(tagno));
            }
          }
        }

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Examples of org.moltools.apps.probemaker.modules.ProbeAnalysisModule


  /**Analyze the specified probe with the list of modules*/
  public static void analyzeProbe(Probe p, List<CandidateAnalysisModule> modules, TagAllocator pd, DefiniteSequenceDB<Probe> probeset) {


    for (Iterator<CandidateAnalysisModule> i = modules.iterator();i.hasNext();) {
      ProbeAnalysisModule am = (ProbeAnalysisModule) i.next();
      //am.reset(pd,probeset);
      am.doAnalysis(p, pd, probeset);
    } 
    calculateAndSetQuality(p);
  }

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Examples of org.moltools.apps.probemaker.modules.ProbeAnalysisModule

  /**Call the doConfirmUpdate method of all Modules registered. 
   * This will complete any reciprocal messages for other affected
   * probes.*/
  public void confirmUpdate(Probe p, TagAllocator pd, DefiniteSequenceDB<Probe> probeset) {
    for (Iterator<CandidateAnalysisModule> i = armModules.iterator(); i.hasNext(); ) {
      ProbeAnalysisModule m = (ProbeAnalysisModule) i.next();
      m.doConfirmUpdate(p, pd, probeset);
    }


    for (Iterator<CandidateAnalysisModule> i = candidateModulesStage1.iterator(); i.hasNext(); ) {
      ProbeAnalysisModule m = (ProbeAnalysisModule) i.next();
      m.doConfirmUpdate(p, pd, probeset);
    }


    for (Iterator<CandidateAnalysisModule> i = candidateModulesStage2.iterator(); i.hasNext(); ) {
      ProbeAnalysisModule m = (ProbeAnalysisModule) i.next();
      m.doConfirmUpdate(p, pd, probeset);
    }
  }

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Examples of org.moltools.apps.probemaker.modules.ProbeAnalysisModule

        //Iterate through each tag...
        for (int tagno = 0; tagno < libraries[i].size(); tagno++) {
          NucleotideSequence t = libraries[i].getSequenceAt(tagno);
          //setStatus(t.getName());
          for (Iterator<CandidateAnalysisModule> m = modules.iterator(); m.hasNext(); ) {
            ProbeAnalysisModule mod = (ProbeAnalysisModule) m.next();
            if (!mod.acceptTag(t, probeset)) {
              //log.printLine(t.getName() + " not accepted by " + PlugInDescriptor.getBriefDescription(mod)); //$NON-NLS-1$
              badTags[i].add(new Integer(tagno));
            }
          }
        }

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Examples of org.moltools.apps.probemaker.modules.ProbeAnalysisModule


  /**Analyze the specified probe with the list of modules*/
  public static void analyzeProbe(Probe p, List<CandidateAnalysisModule> modules, TagAllocator pd, DefiniteSequenceDB<Probe> probeset) {


    for (Iterator<CandidateAnalysisModule> i = modules.iterator();i.hasNext();) {
      ProbeAnalysisModule am = (ProbeAnalysisModule) i.next();
      //am.reset(pd,probeset);
      am.doAnalysis(p, pd, probeset);
    } 
    calculateAndSetQuality(p);
  }

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