Examples of RawDataFileImpl

net.sf.mzmine.project.impl.RawDataFileImpl
RawDataFile implementation. It provides storage of data points for scans and mass lists using the storeDataPoints() and readDataPoints() methods. The data points are stored in a temporary file (dataPointsFile) and the structure of the file is stored in two TreeMaps. The dataPointsOffsets maps storage ID to the offset in the dataPointsFile. The dataPointsLength maps the storage ID to the number of data points stored under this ID. When stored data points are deleted using removeStoredDataPoints(), the dataPointsFile is not modified, the storage ID is just deleted from the two TreeMaps. When the project is saved, the contents of the dataPointsFile are consolidated - only data points referenced by the TreeMaps are saved (see the RawDataFileSaveHandler class).

Examples of net.sf.mzmine.project.impl.RawDataFileImpl

    return initializedModules.values();
  }


  public static RawDataFileWriter createNewFile(String name)
      throws IOException {
    return new RawDataFileImpl(name);
  }

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Examples of net.sf.mzmine.project.impl.RawDataFileImpl

    // Set total number of scans to process
    totalScans = 2 * dataFile.getNumOfScans();


    try {
      // Create a new file
      final RawDataFileImpl rawDataFileWriter = (RawDataFileImpl) MZmineCore
          .createNewFile(dataFile.getName() + ' ' + suffix);


      // Process each spectrum
      for (int scanNumber : dataFile.getScanNumbers(1)) {
        // Canceled?
        if (isCanceled())
          return;


        Scan spectrum = dataFile.getScan(scanNumber);


        // Add scan to new data file
        int storageID = rawDataFileWriter.storeDataPoints(spectrum
            .getDataPoints());
        CorrectedSpectrum newSpectrum = new CorrectedSpectrum(spectrum,
            rawDataFileWriter, spectrum.getNumberOfDataPoints(),
            storageID);


        rawDataFileWriter.addScan(newSpectrum);


        // Store spectrum locally for processing and analysis
        spectra.add(newSpectrum);


        processedScans++;
      }


      // Finalize writing
      correctedDataFile = rawDataFileWriter.finishWriting();


      // Process spectrum depending on ionization type
      switch (ionizationType) {
        case PCI :
        case PCI_METHANE :

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Examples of net.sf.mzmine.project.impl.RawDataFileImpl

    // Set total number of scans to process
    totalScans = dataFile.getNumOfScans();


    try {
      // Create a new file
      final RawDataFileImpl rawDataFileWriter = (RawDataFileImpl) MZmineCore
          .createNewFile(dataFile.getName() + ' ' + suffix);


      // Process each deconvoluted spectrum
      for (int scanNumber : dataFile.getScanNumbers(1)) {
        // Canceled?
        if (isCanceled())
          return;


        // Duplicate current spectrum
        Scan spectrum = dataFile.getScan(scanNumber);


        // Exclude the entire spectrum if its base peak intensity is
        // less than the given threshold
        if (spectrum.getBasePeak().getIntensity() < basePeakThreshold)
          continue;


        // Exclude the entire spectrum if its unique mass intensity is
        // less than the given threshold
        if (spectrum instanceof CorrectedSpectrum) {
          CorrectedSpectrum s = ((CorrectedSpectrum) spectrum);


          if (s.getUniqueMass() != null
              && s.getUniqueMass().getIntensity() < uniqueMassThreshold)
            continue;
        }


        // Get the data points from the spectrum and sort by m/z
        List<DataPoint> dataPoints = Lists.newArrayList(spectrum
            .getDataPoints());
        Collections.sort(dataPoints, new Comparator<DataPoint>() {
          @Override
          public int compare(DataPoint a, DataPoint b) {
            return a.getMZ() < b.getMZ() ? -1 : a.getMZ() > b
                .getMZ() ? 1 : 0;
          }
        });


        // Create a list for the filtered points
        List<DataPoint> filteredDataPoints = new ArrayList<DataPoint>();


        // Filter the data points given pre-defined conditions
        for (int i = dataPoints.size() - 1; i >= 0; i--) {
          // Step #1: Remove C13 Isotope ions
          if (i > 0
              && dataPoints.get(i).getMZ()
                  - dataPoints.get(i - 1).getMZ() < 1 + EPSILON
              && dataPoints.get(i - 1).getIntensity() >= (1 + c13IsotopeCut)
                  * dataPoints.get(i).getIntensity())
            continue;


          // Step #2: Remove all ions < 100 counts
          else if (dataPoints.get(i).getIntensity() < intensityThreshold)
            continue;


          // Step #3: Remove all ions < 1% of base peak
          else if (dataPoints.get(i).getIntensity() < intensityPercentageThreshold
              * spectrum.getBasePeak().getIntensity())
            continue;


          // If the data point passes all filters, keep it.
          else
            filteredDataPoints.add(0, dataPoints.get(i));
        }


        // Add scan to new data file
        int storageID = rawDataFileWriter
            .storeDataPoints(filteredDataPoints
                .toArray(new DataPoint[filteredDataPoints
                    .size()]));
        CorrectedSpectrum newSpectrum = new CorrectedSpectrum(spectrum,
            rawDataFileWriter, filteredDataPoints.size(), storageID);
        rawDataFileWriter.addScan(newSpectrum);


        processedScans++;
      }


      // If this task was canceled, stop processing
      if (!isCanceled()) {
        // Finalize writing
        filteredDataFile = rawDataFileWriter.finishWriting();


        // Add the newly created file to the project
        final MZmineProject project = MZmineCore.getCurrentProject();
        project.addFile(filteredDataFile);

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