Examples of MZmineProcessingModule

net.sf.mzmine.modules.MZmineProcessingModule
Interface representing a data processing method which can be executed in a batch

Examples of net.sf.mzmine.modules.MZmineProcessingModule


        // Processing module? Exclude the batch mode module.
        if (!module.getClass().equals(BatchModeModule.class)
            && module instanceof MZmineProcessingModule) {


          final MZmineProcessingModule step = (MZmineProcessingModule) module;


          // Correct category?
          if (step.getModuleCategory() == category) {


            // Add category item?
            if (!categoryItemAdded) {
              methodsCombo.addItem("--- " + category + " ---");
              categoryItemAdded = true;

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Examples of net.sf.mzmine.modules.MZmineProcessingModule

      final Object selectedItem = methodsCombo.getSelectedItem();
      if (selectedItem instanceof MZmineModuleWrapper) {


        // Show method's set-up dialog.
        final MZmineModuleWrapper wrappedModule = (MZmineModuleWrapper) selectedItem;
        final MZmineProcessingModule selectedMethod = (MZmineProcessingModule) wrappedModule
            .getModule();
        final ParameterSet methodParams = MZmineCore.getConfiguration()
            .getModuleParameters(selectedMethod.getClass());


        if (methodParams.getParameters().length > 0) {
          ExitCode exitCode = methodParams.showSetupDialog();
          if (exitCode != ExitCode.OK)
            return;

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Examples of net.sf.mzmine.modules.MZmineProcessingModule


    // Run next step of the batch
    MZmineProcessingStep currentStep = queue.get(stepNumber);


    logger.fine("running step: " + currentStep);
    MZmineProcessingModule method = (MZmineProcessingModule) currentStep
        .getModule();
    ParameterSet batchStepParameters = currentStep.getParameterSet();


    // Update dataFiles and peakLists in the batchStepParameters
    for (Parameter p : batchStepParameters.getParameters()) {
      if (p instanceof RawDataFilesParameter)
        ((RawDataFilesParameter) p).setValue(dataFiles);
      if (p instanceof PeakListsParameter)
        ((PeakListsParameter) p).setValue(peakLists);
      if (p instanceof RawDataFilesMultiChoiceParameter)
        ((RawDataFilesMultiChoiceParameter) p).setChoices(dataFiles);
    }


    // Check if the parameter settings are valid
    ArrayList<String> messages = new ArrayList<String>();
    boolean paramsCheck = batchStepParameters
        .checkAllParameterValues(messages);
    if (!paramsCheck) {
      setStatus(TaskStatus.ERROR);
      errorMessage = "Invalid parameter settings for module " + method
          + ": " + Arrays.toString(messages.toArray());
    }


    ArrayList<Task> currentStepTasks = new ArrayList<Task>();
    ExitCode exitCode = method.runModule(batchStepParameters,
        currentStepTasks);


    if (exitCode != ExitCode.OK) {
      setStatus(TaskStatus.ERROR);
      errorMessage = "Could not start batch step " + method.getName();
      return;
    }


    // If current step didn't produce any tasks, continue with next step
    if (currentStepTasks.isEmpty()) {

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Examples of net.sf.mzmine.modules.MZmineProcessingModule

   */
  public void actionPerformed(ActionEvent e) {


    Object src = e.getSource();


    MZmineProcessingModule module = moduleMenuItems.get(src);
    if (module != null) {
      RawDataFile selectedFiles[] = MZmineCore.getDesktop()
          .getSelectedDataFiles();
      PeakList selectedPeakLists[] = MZmineCore.getDesktop()
          .getSelectedPeakLists();


      ParameterSet moduleParameters = MZmineCore.getConfiguration()
          .getModuleParameters(module.getClass());


      boolean allParametersOK = true;
      LinkedList<String> errorMessages = new LinkedList<String>();
      for (Parameter p : moduleParameters.getParameters()) {
        if (p instanceof RawDataFilesParameter) {
          RawDataFilesParameter rdp = (RawDataFilesParameter) p;
          rdp.setValue(selectedFiles);
          boolean checkOK = rdp.checkValue(errorMessages);
          if (!checkOK) {
            allParametersOK = false;
          }
        }
        if (p instanceof PeakListsParameter) {
          PeakListsParameter plp = (PeakListsParameter) p;
          plp.setValue(selectedPeakLists);
          boolean checkOK = plp.checkValue(errorMessages);
          if (!checkOK) {
            allParametersOK = false;
          }
        }
      }


      if (!allParametersOK) {
        StringBuilder message = new StringBuilder();
        for (String m : errorMessages) {
          message.append(m);
          message.append("\n");
        }
        MZmineCore.getDesktop().displayMessage(message.toString());
        return;
      }


      logger.finest("Setting parameters for module " + module.getName());
      ExitCode exitCode = moduleParameters.showSetupDialog();
      if (exitCode == ExitCode.OK) {
        ParameterSet parametersCopy = moduleParameters.cloneParameter();
        logger.finest("Starting module " + module.getName()
            + " with parameters " + parametersCopy);
        ArrayList<Task> tasks = new ArrayList<Task>();
        module.runModule(parametersCopy, tasks);
        MZmineCore.getTaskController().addTasks(
            tasks.toArray(new Task[0]));
      }
      return;
    }

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