Package net.sf.mzmine.util

Examples of net.sf.mzmine.util.ExitCode

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      MZmineCore.getCurrentProject().removeFile(dataFile);

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

    // Confirm that a new file was made
    int filesCount = MZmineCore.getCurrentProject().getDataFiles().length;
    assert (filesCount > 0);
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        .getModuleParameters(MzRangeCalculatorModule.class);

    if (myParameters == null)
      return null;

    ExitCode exitCode = myParameters.showSetupDialog();
    if (exitCode != ExitCode.OK)
      return null;

    String formula = myParameters.getParameter(
        MzRangeCalculatorParameters.formula).getValue();
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      MZmineCore.getCurrentProject().removePeakList(peakList);

    File batchFile = new File(
        "src/test/resources/deconvolutedanalysis/massdetection_set1.xml");
    Assert.assertTrue(batchFile.exists());
    ExitCode exitCode = BatchModeModule.runBatch(batchFile);
    assert (exitCode == ExitCode.OK);

    assert (MZmineCore.getCurrentProject().getPeakLists().length > 0);

    PeakList peakList = MZmineCore.getCurrentProject().getPeakLists()[0];
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    MZmineCore.initializeHeadless();

    File batchFile = new File(
        "src/test/resources/deconvolutedanalysis/massdetection_set2.xml");
    Assert.assertTrue(batchFile.exists());
    ExitCode exitCode = BatchModeModule.runBatch(batchFile);
    assert (exitCode == ExitCode.OK);

    assert (MZmineCore.getCurrentProject().getPeakLists().length > 0);

    PeakList peakList = MZmineCore.getCurrentProject().getPeakLists()[0];
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    MZmineCore.initializeHeadless();

    File batchFile = new File(
        "src/test/resources/deconvolutedanalysis/massdetection_set3.xml");
    Assert.assertTrue(batchFile.exists());
    ExitCode exitCode = BatchModeModule.runBatch(batchFile);
    assert (exitCode == ExitCode.OK);

    assert (MZmineCore.getCurrentProject().getPeakLists().length > 0);

    PeakList peakList = MZmineCore.getCurrentProject().getPeakLists()[0];
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  public static IsotopePattern showIsotopePredictionDialog() {

    ParameterSet parameters = MZmineCore.getConfiguration()
        .getModuleParameters(IsotopePatternCalculator.class);
    ExitCode exitCode = parameters.showSetupDialog();
    if (exitCode != ExitCode.OK)
      return null;

    String formula = parameters.getParameter(
        IsotopePatternCalculatorParameters.formula).getValue();
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          .setValue(rtRange);
      parameters.getParameter(ManualPickerParameters.mzRange).setValue(
          mzRange);
    }

    ExitCode exitCode = parameters.showSetupDialog();

    if (exitCode != ExitCode.OK)
      return;

    ManualPickerTask task = new ManualPickerTask(peakListRow, dataFiles,
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    String command = event.getActionCommand();

    if (command.equals("PROPERTIES")) {

      ExitCode exitCode = parameters.showSetupDialog();
      if (exitCode == ExitCode.OK) {
        int rowHeight = parameters.getParameter(
            PeakListTableParameters.rowHeight).getValue();
        table.setRowHeight(rowHeight);
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  public static void exportIsotopePattern(PeakListRow row) {

    ParameterSet parameters = MZmineCore.getConfiguration()
        .getModuleParameters(IsotopePatternExportModule.class);

    ExitCode exitCode = parameters.showSetupDialog();
    if (exitCode != ExitCode.OK)
      return;

    File outputFile = parameters.getParameter(
        IsotopePatternExportParameters.outputFile).getValue();
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  public static void exportMSMS(PeakListRow row) {

    ParameterSet parameters = MZmineCore.getConfiguration()
        .getModuleParameters(MSMSExportModule.class);

    ExitCode exitCode = parameters.showSetupDialog();
    if (exitCode != ExitCode.OK)
      return;

    File outputFile = parameters.getParameter(
        MSMSExportParameters.outputFile).getValue();
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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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