Package org.moltools.apps.probemaker.design

Examples of org.moltools.apps.probemaker.design.Analyzer

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        fnfx.printStackTrace();
        log = defaultLog;
      }
    }
           
    Analyzer analyzer = new Analyzer(project.getSettings(),acc,sel);   
   
    //setStatus(UITexts.getString("ProbeDesignTask.MESSAGE_READY"),0); //$NON-NLS-1$

    //Print some project and time info to the log
    log.begin(project.getName(), logFile == null ? "" : logFile.getName(), //$NON-NLS-1$
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  public ProbeAnalysisTask(Project proj, ErrorHandler ecb) throws InstantiationException, IllegalAccessException {
    super(CoreMessages.getString("ProbeAnalysisTask.TITLE_ANALYZING_PROBES"),0,proj.getProbes().size(),1,ecb); //$NON-NLS-1$
    project = proj;
    probes = project.getProbes();
   
    analyzer = new Analyzer(project.getSettings(),null,null);
   
    try {
      defaultMpc = new NNMeltingPointCalculator();
    }
    catch (IOException ex) {
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  public ProbeAnalysisTask(Project proj, ErrorHandler ecb) throws InstantiationException, IllegalAccessException {
    super(CoreMessages.getString("ProbeAnalysisTask.TITLE_ANALYZING_PROBES"),0,proj.getProbes().size(),1,ecb); //$NON-NLS-1$
    project = proj;
    probes = project.getProbes();
   
    analyzer = new Analyzer(project.getSettings(),null,null);
   
    try {
      defaultMpc = new NNMeltingPointCalculator();
    }
    catch (IOException ex) {
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    boolean done = false;
    try {

      project.getTagAllocationTable().setSpacerSettings(project.getSettings().getDesignParameters());

      Analyzer analyzer = new Analyzer(project.getSettings(),acc,sel);         
      designer.setup(project, analyzer, con, namer,log,ecb);

      log.printSectionHeader("Validating targets"); //$NON-NLS-1$
      setStatus(CoreMessages.getString("ProbeDesignTask.MESSAGE_VALIDATING")); //$NON-NLS-1$
      //Check the validity of validatable targets
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    //Setup the spacer tag settings
    project.getTagAllocationTable().setSpacerSettings(project.getSettings().getDesignParameters());

    //Create the analyzer
    Analyzer analyzer = new Analyzer(project.getSettings(),acc,sel);

    //Setup the designer for this design job
    designer.setup(project, analyzer, td, namer, log, ecb);

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  public ProbeAnalysisTask(Project proj, ErrorHandler ecb) throws InstantiationException, IllegalAccessException {
    super(CoreMessages.getString("ProbeAnalysisTask.TITLE_ANALYZING_PROBES"),0,proj.getProbes().size(),1,ecb); //$NON-NLS-1$
    project = proj;
    probes = project.getProbes();
   
    analyzer = new Analyzer(project.getSettings(),null,null);
   
    try {
      defaultMpc = new NNMeltingPointCalculator();
    }
    catch (IOException ex) {
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Related Classes of org.moltools.apps.probemaker.design.Analyzer

  • org.moltools.apps.probemaker.messages.Message
  • org.moltools.apps.probemaker.messages.MessageType
  • org.moltools.apps.probemaker.messages.SeverityFilter
  • org.moltools.apps.probemaker.modules.ProbeAnalysisModule
  • org.moltools.apps.probemaker.ProbeAnalysisTask
  • org.moltools.apps.probemaker.ProbeDesignTask
  • org.moltools.apps.probemaker.ProbeMakerPlugIn
  • org.moltools.apps.probemaker.seq.ProbeMakerTarget
  • org.moltools.design.data.PropertyAcceptorNucleotideSequence
  • org.moltools.lib.seq.NucleotideSequence
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