io.github.msdk.datamodel.RawDataFile Java Examples

public void removeFile(final RawDataFile rawDataFile) {
  super.removeFile(rawDataFile);
  for (TreeItem<?> df1 : rawDataRootItem.getChildren()) {
    if (df1.getValue() == rawDataFile) {
      rawDataRootItem.getChildren().remove(df1);
      break;
    }
  }
}
 

public static @Nonnull List<RawDataFile> getSelectedRawDataFiles() {

    final ArrayList<RawDataFile> list = new ArrayList<>();
    final TreeView<Object> rawDataTree = mainWindowController.getRawDataTree();
    for (TreeItem<Object> item : rawDataTree.getSelectionModel().getSelectedItems()) {
      if (!(item.getValue() instanceof RawDataFile))
        continue;
      RawDataFile file = (RawDataFile) item.getValue();
      list.add(file);
    }

    return list;

  }
 

public void removeRawData(ActionEvent event) {
  // Get selected tree items
  ObservableList<TreeItem<Object>> rows = null;
  if (rawDataTree.getSelectionModel() != null) {
    rows = rawDataTree.getSelectionModel().getSelectedItems();
  }

  // Loop through all selected tree items
  if (rows != null) {
    for (int i = rows.size() - 1; i >= 0; i--) {
      TreeItem<Object> row = rows.get(i);

      if (!(row.getValue() instanceof RawDataFile))
        continue;

      // Remove feature table from current project
      RawDataFile rawDataFile = (RawDataFile) row.getValue();
      MZmineCore.getCurrentProject().removeFile(rawDataFile);

      // Remove raw data file from tree table view
      TreeItem<?> parent = row.getParent();
      if (parent == null)
        continue;
      parent.getChildren().remove(row);
    }
    rawDataTree.getSelectionModel().clearSelection();
  }
}
 

/**
 * Generates a single-line textual description of a given MS/MS scan, taking the precursor m/z
 * from a given isolation (a single scan can have multiple isolations)
 */
public static String createSingleLineMsScanDescription(MsScan scan, IsolationInfo isolation) {

  RawDataFile rdf = scan.getRawDataFile();

  StringBuilder sb = new StringBuilder();

  if (rdf != null) {
    sb.append(rdf.getName());
    sb.append(" ");
  }

  sb.append("#");
  sb.append(scan.getScanNumber());
  ChromatographyInfo scanRt = scan.getChromatographyInfo();
  if (scanRt != null) {
    NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
    sb.append(" @");
    sb.append(rtFormat.format(scanRt.getRetentionTime() / 60f));
    sb.append(" min");
  }
  if (isolation != null) {
    Double precursorMz = isolation.getPrecursorMz();
    if (precursorMz != null) {
      NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
      sb.append(", precursor ");
      sb.append(mzFormat.format(precursorMz));
      sb.append(" m/z");
    }
  }
  return sb.toString();
}
 

@Override
public void runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters,
    @Nonnull Collection<Task<?>> tasks) {

  final RawDataFilesSelection rawDataFiles =
      parameters.getParameter(LocalMaxCentroidingParameters.dataFiles).getValue();
  final String suffix = parameters.getParameter(LocalMaxCentroidingParameters.suffix).getValue();

  if (rawDataFiles == null || rawDataFiles.getMatchingRawDataFiles().isEmpty()) {
    logger.warn("Centroiding module started with no raw data files selected");
    return;
  }

  for (RawDataFile rawDataFile : rawDataFiles.getMatchingRawDataFiles()) {

    // Create the data structures
    DataPointStore dataStore = DataPointStoreFactory.getTmpFileDataStore();

    final String newName = rawDataFile.getName() + " " + suffix;
    LocalMaximaCentroidingAlgorithm algorithm = new LocalMaximaCentroidingAlgorithm(dataStore);

    MSDKCentroidingMethod method = new MSDKCentroidingMethod(rawDataFile, algorithm, dataStore);

    MSDKTask newTask =
        new MSDKTask("Local maxima centroiding method", rawDataFile.getName(), method);

    // Add the feature table to the project
    newTask.setOnSucceeded(e -> {
      RawDataFile newRawFile = method.getResult();
      newRawFile.setName(newName);
      project.addFile(newRawFile);
    });

    // Add the task to the queue
    tasks.add(newTask);

  }

}
 

@Override
public void run() {

  logger.info("Running post-shutdown code");

  // Cancel all running tasks - this is important because tasks can spawn
  // additional processes (such as ThermoRawDump.exe on Windows) and these
  // will block the shutdown of the JVM. If we cancel the tasks, the
  // processes will be killed immediately.
  /*
   * for (WrappedTask wt : MZmineCore.getTaskController().getTaskQueue() .getQueueSnapshot()) {
   * Task t = wt.getActualTask(); if ((t.getStatus() == TaskStatus.WAITING) || (t.getStatus() ==
   * TaskStatus.PROCESSING)) { t.cancel(); } }
   */

  // Save configuration
  try {
    MZmineConfiguration configuration = MZmineCore.getConfiguration();
    if (configuration != null) {
      configuration.saveConfiguration(MZmineConfiguration.CONFIG_FILE);
    }
  } catch (Exception e) {
    e.printStackTrace();
  }

  // Remove all temporary files
  MZmineProject currentProject = MZmineCore.getCurrentProject();
  if (currentProject != null) {
    for (RawDataFile dataFile : currentProject.getRawDataFiles()) {
      dataFile.dispose();
    }
    for (FeatureTable featureTable : currentProject.getFeatureTables()) {
      featureTable.dispose();
    }
  }

}
 

@Override
public void runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters,
    @Nonnull Collection<Task<?>> tasks) {

  final RawDataFilesSelection rawDataFiles =
      parameters.getParameter(ExactMassCentroidingParameters.dataFiles).getValue();
  final String suffix = parameters.getParameter(ExactMassCentroidingParameters.suffix).getValue();

  if (rawDataFiles == null || rawDataFiles.getMatchingRawDataFiles().isEmpty()) {
    logger.warn("Centroiding module started with no raw data files selected");
    return;
  }

  for (RawDataFile rawDataFile : rawDataFiles.getMatchingRawDataFiles()) {

    // Create the data structures
    DataPointStore dataStore = DataPointStoreFactory.getTmpFileDataStore();

    final String newName = rawDataFile.getName() + " " + suffix;
    ExactMassCentroidingAlgorithm algorithm = new ExactMassCentroidingAlgorithm(dataStore);

    MSDKCentroidingMethod method = new MSDKCentroidingMethod(rawDataFile, algorithm, dataStore);

    MSDKTask newTask =
        new MSDKTask("Exact mass centroiding method", rawDataFile.getName(), method);

    // Add the feature table to the project
    newTask.setOnSucceeded(e -> {
      RawDataFile newRawFile = method.getResult();
      newRawFile.setName(newName);
      project.addFile(newRawFile);
    });

    // Add the task to the queue
    tasks.add(newTask);

  }

}
 

@Override
public void runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters,
    @Nonnull Collection<Task<?>> tasks) {

  final RawDataFilesSelection rawDataFiles =
      parameters.getParameter(BinningCentroidingParameters.dataFiles).getValue();
  final Double binSize = parameters.getParameter(BinningCentroidingParameters.binSize).getValue();
  final String suffix = parameters.getParameter(BinningCentroidingParameters.suffix).getValue();

  if (rawDataFiles == null || rawDataFiles.getMatchingRawDataFiles().isEmpty()) {
    logger.warn("Centroiding module started with no raw data files selected");
    return;
  }

  for (RawDataFile rawDataFile : rawDataFiles.getMatchingRawDataFiles()) {

    // Create the data structures
    DataPointStore dataStore = DataPointStoreFactory.getTmpFileDataStore();

    final String newName = rawDataFile.getName() + " " + suffix;
    BinningCentroidingAlgorithm algorithm = new BinningCentroidingAlgorithm(dataStore, binSize);

    MSDKCentroidingMethod method = new MSDKCentroidingMethod(rawDataFile, algorithm, dataStore);

    MSDKTask newTask = new MSDKTask("Binning centroiding method", rawDataFile.getName(), method);

    // Add the feature table to the project
    newTask.setOnSucceeded(e -> {
      RawDataFile newRawFile = method.getResult();
      newRawFile.setName(newName);
      project.addFile(newRawFile);
    });

    // Add the task to the queue
    tasks.add(newTask);

  }

}
 

@Override
public void runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters,
    @Nonnull Collection<Task<?>> tasks) {

  final RawDataFilesSelection rawDataFiles =
      parameters.getParameter(WaveletCentroidingParameters.dataFiles).getValue();
  final Integer scaleLevel =
      parameters.getParameter(WaveletCentroidingParameters.scaleLevel).getValue();
  final Double waveletWindow =
      parameters.getParameter(WaveletCentroidingParameters.waveletWindow).getValue();
  final String suffix = parameters.getParameter(WaveletCentroidingParameters.suffix).getValue();

  if (rawDataFiles == null || rawDataFiles.getMatchingRawDataFiles().isEmpty()) {
    logger.warn("Centroiding module started with no raw data files selected");
    return;
  }

  for (RawDataFile rawDataFile : rawDataFiles.getMatchingRawDataFiles()) {

    // Create the data structures
    DataPointStore dataStore = DataPointStoreFactory.getTmpFileDataStore();

    final String newName = rawDataFile.getName() + " " + suffix;
    WaveletCentroidingAlgorithm algorithm =
        new WaveletCentroidingAlgorithm(dataStore, scaleLevel, waveletWindow);

    MSDKCentroidingMethod method = new MSDKCentroidingMethod(rawDataFile, algorithm, dataStore);

    MSDKTask newTask = new MSDKTask("Wavelet centroiding method", rawDataFile.getName(), method);

    // Add the feature table to the project
    newTask.setOnSucceeded(e -> {
      RawDataFile newRawFile = method.getResult();
      newRawFile.setName(newName);
      project.addFile(newRawFile);
    });

    // Add the task to the queue
    tasks.add(newTask);

  }

}
 

@Override
public RawDataFile getRawDataFile() {
  return null;
}
 

/**
 * Generates a multi-line textual description of a given MsScan
 */
public static String createFullMsScanDescription(MsScan scan) {

  RawDataFile rdf = scan.getRawDataFile();
  Integer scanNum = scan.getScanNumber();
  MsFunction msFunc = scan.getMsFunction();
  Integer msLevel = msFunc.getMsLevel();
  ChromatographyInfo chromInfo = scan.getChromatographyInfo();

  StringBuilder sb = new StringBuilder();

  if (rdf != null)
    sb.append("Raw data file: " + rdf.getName() + "\n");

  sb.append("Scan number: " + scanNum + "\n");

  if (chromInfo != null) {
    NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
    Float rt = chromInfo.getRetentionTime();
    sb.append("Retention time: ");
    sb.append(rtFormat.format(rt / 60f));
    sb.append(" min\n");
    Float secondRT = chromInfo.getSecondaryRetentionTime();
    if (secondRT != null) {
      sb.append("Secondary retention time: ");
      sb.append(rtFormat.format(secondRT / 60f));
      sb.append(" min\n");
    }
  }

  sb.append("MS function: ");
  sb.append(msFunc.getName());
  sb.append("\n");
  if (msLevel != null) {
    sb.append("MS level: ");
    sb.append(msLevel);
    sb.append("\n");
  }
  sb.append("Scan definition: ");
  sb.append(scan.getScanDefinition());
  sb.append("\n");
  sb.append("Polarity: ");
  sb.append(scan.getPolarity());
  sb.append("\n");

  return sb.toString();
}
 

@Override
public RawDataFile getRawDataFile() {
  return null;
}
 

@Override
public void runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters,
    @Nonnull Collection<Task<?>> tasks) {

  final RawDataFilesSelection rawDataFiles =
      parameters.getParameter(RecursiveCentroidingParameters.dataFiles).getValue();
  final Range<Double> mzPeakWidth = RecursiveCentroidingParameters.mzPeakWidth.getValue();
  final String suffix = parameters.getParameter(RecursiveCentroidingParameters.suffix).getValue();

  if (rawDataFiles == null || rawDataFiles.getMatchingRawDataFiles().isEmpty()) {
    logger.warn("Centroiding module started with no raw data files selected");
    return;
  }

  for (RawDataFile rawDataFile : rawDataFiles.getMatchingRawDataFiles()) {

    // Create the data structures
    DataPointStore dataStore = DataPointStoreFactory.getTmpFileDataStore();

    final String newName = rawDataFile.getName() + " " + suffix;
    RecursiveCentroidingAlgorithm algorithm =
        new RecursiveCentroidingAlgorithm(dataStore, mzPeakWidth);

    MSDKCentroidingMethod method = new MSDKCentroidingMethod(rawDataFile, algorithm, dataStore);

    MSDKTask newTask =
        new MSDKTask("Recursive centroiding method", rawDataFile.getName(), method);

    // Add the feature table to the project
    newTask.setOnSucceeded(e -> {
      RawDataFile newRawFile = method.getResult();
      newRawFile.setName(newName);
      project.addFile(newRawFile);
    });

    // Add the task to the queue
    tasks.add(newTask);

  }

}
 

public @Nonnull List<RawDataFile> getRawDataFiles() {
  synchronized (rawDataFiles) {
    return ImmutableList.copyOf(rawDataFiles);
  }
}
 

public void removeFile(final RawDataFile rawDataFile) {
  synchronized (rawDataFiles) {
    rawDataFiles.remove(rawDataFile);
  }
}
 

public void addFile(final RawDataFile rawDataFile) {
  synchronized (rawDataFiles) {
    rawDataFiles.add(rawDataFile);
  }
}
 

public void addFile(final RawDataFile rawDataFile) {
  super.addFile(rawDataFile);
  TreeItem<Object> df1 = new TreeItem<>(rawDataFile);
  df1.setGraphic(new ImageView(fileIcon));
  rawDataRootItem.getChildren().add(df1);
}