Examples of net.sf.mzmine.modules.MZmineProcessingModule.runModule()

net.sf.mzmine.modules.MZmineProcessingModule.runModule()

Run this module with given parameters. The module may create new Tasks and add them to the 'tasks' collection. The module is not supposed to submit the tasks to the TaskController by itself. @param parameters ParameterSet to invoke this module with. The ParameterSet has already been cloned for exclusive use by this module, therefore the module does not need to clone it again. Upon invocation of the runModule() method it is guaranteed that the ParameterSet is of the proper class as returned by getParameterSetClass(). Also, it is guaranteed that the ParameterSet is checked by checkParameters(), therefore the module does not need to perform these checks again. @param tasks A collection where the module should add its newly created Tasks, if it creates any. @return Exit code of the operation. ExitCode.OK means the module wasstarted properly, however it does not guarantee that the Tasks will finish without error. ExitCode.ERROR means there was a problem starting the module.

      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();

      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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