Package net.sf.mzmine.util

Examples of net.sf.mzmine.util.ExitCode

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      parameters.getParameter(TwoDParameters.retentionTimeRange)
          .setValue(rtRange);
    if (mzRange != null)
      parameters.getParameter(TwoDParameters.mzRange).setValue(mzRange);

    ExitCode exitCode = parameters.showSetupDialog();

    if (exitCode != ExitCode.OK)
      return;

    int msLevel = parameters.getParameter(TwoDParameters.msLevel)
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        numOfThreads, proxySettings, windowState});
  }

  public ExitCode showSetupDialog() {

    ExitCode retVal = super.showSetupDialog();

    if (retVal == ExitCode.OK) {

      // Update proxy settings
      updateSystemProxySettings();
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            .getModule();
        final ParameterSet methodParams = MZmineCore.getConfiguration()
            .getModuleParameters(selectedMethod.getClass());

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

        // Make a new step
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  }

  @Override
  public ExitCode showSetupDialog() {

    ExitCode exitCode = super.showSetupDialog();

    // If the parameters are not complete, let's just stop here
    if (exitCode != ExitCode.OK)
      return exitCode;
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      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();
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        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>();
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      MZmineCore.getCurrentProject().removeFile(dataFile);

    File batchFile = new File(
        "src/test/resources/deconvolutedanalysis/famealignment.xml");
    Assert.assertTrue(batchFile.exists());
    ExitCode exitCode = BatchModeModule.runBatch(batchFile);
    assert (exitCode == ExitCode.OK);

    // Check that new files have been created
    assert (MZmineCore.getCurrentProject().getDataFiles().length > 0);
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    MZmineCore.initializeHeadless();

    File batchFile = new File("src/test/resources/readFiles.xml");
    Assert.assertTrue(batchFile.exists());
    ExitCode code = BatchModeModule.runBatch(batchFile);

    assertTrue(code == ExitCode.OK);

  }
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    MZmineCore.initializeHeadless();

    File batchFile = new File("src/test/resources/readDirectory.xml");
    Assert.assertTrue(batchFile.exists());
    ExitCode code = BatchModeModule.runBatch(batchFile);

    assertTrue(code == ExitCode.OK);

  }
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    MZmineCore.initializeHeadless();

    File batchFile = new File(
        "src/test/resources/readDirectoryWithRowFilterAndAlignment.xml");
    Assert.assertTrue(batchFile.exists());
    ExitCode code = BatchModeModule.runBatch(batchFile);

    System.out.println("result code: " + code);
    assertTrue(code == ExitCode.OK);

  }
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Related Classes of net.sf.mzmine.util.ExitCode

  • MacSpecificSetup
  • net.sf.mzmine.desktop.impl.MainMenu
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeMouseHandler
  • net.sf.mzmine.desktop.preferences.MZminePreferences
  • net.sf.mzmine.main.MZmineCore
  • net.sf.mzmine.modules.batchmode.BatchModeModuleTest
  • net.sf.mzmine.modules.batchmode.BatchSetupComponent
  • net.sf.mzmine.modules.batchmode.BatchTask
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameAlignmentTest
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.MassDetectionTest
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