Examples of RawDataFileWriter

net.sf.mzmine.data.RawDataFileWriter
This interface represents a raw data file which is being modified. Scans can be added to the file by calling the addScan() method. Final RawDataFile instance is obtained by calling finishWriting() method.

Examples of net.sf.mzmine.data.RawDataFileWriter

        File temp = File.createTempFile(sampleID, extension);
        temp.deleteOnExit();
        FileOutputStream fos = new FileOutputStream(temp);
        fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);


        RawDataFileWriter newMZmineFile;
        try {
          newMZmineFile = MZmineCore.createNewFile(sampleID);
        } catch (IOException e) {
          MZmineCore.getDesktop().displayErrorMessage(
              "Could not create a new temporary file " + e);

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Examples of net.sf.mzmine.data.RawDataFileWriter

    try {


      // Create new raw data file


      String newName = dataFile.getName() + " " + suffix;
      RawDataFileWriter rawDataFileWriter = MZmineCore
          .createNewFile(newName);


      for (int i = 0; i < totalScans; i++) {


        if (isCanceled()) {
          return;
        }


        Scan scan = dataFile.getScan(scanNumbers[i]);
        if ((scan.getMSLevel() != 1)
            && (scan.getParentScanNumber() <= 0)) {
          return;
        }
        Scan newScan = rawDataFilter.getModule().filterScan(scan,
            rawDataFilter.getParameterSet());
        if (newScan != null) {
          rawDataFileWriter.addScan(newScan);
        }


        processedScans++;
      }


      // Finalize writing
      try {
        filteredRawDataFile = rawDataFileWriter.finishWriting();
        MZmineCore.getCurrentProject().addFile(filteredRawDataFile);


        // Remove the original file if requested
        if (removeOriginal) {
          MZmineCore.getCurrentProject().removeFile(dataFile);

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Examples of net.sf.mzmine.data.RawDataFileWriter

    // Update the status of this task
    setStatus(TaskStatus.PROCESSING);


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


      // Determine number of bins.
      final int numBins = useBins ? (int) Math.ceil(origDataFile
          .getDataMZRange().getSize() / binWidth) : 1;


      // Get MS levels.
      final int[] levels = origDataFile.getMSLevels();


      // Measure progress and find MS-level.
      boolean foundLevel = msLevel == 0;
      progressMax = 0;
      for (final int level : levels) {
        final boolean isMSLevel = msLevel == level;
        final int numScans = origDataFile.getScanNumbers(level).length;
        foundLevel |= isMSLevel;
        progressMax += isMSLevel || msLevel == 0 ? 2 * numScans
            + numBins : numScans;
      }


      // Is the specified MS-level present?
      if (!foundLevel) {
        throw new IllegalArgumentException(
            "The data file doesn't contain data for MS-level "
                + msLevel + '.');
      }


      // Which chromatogram type.
      final boolean useTIC = chromatogramType == ChromatogramType.TIC;


      // Process each MS level.
      for (final int level : levels) {


        if (!isCanceled()) {
          if (level == msLevel || msLevel == 0) {


            // Correct baseline for this MS-level.
            if (useTIC) {
              correctTICBaselines(rawDataFileWriter, level,
                  numBins);
            } else {
              correctBasePeakBaselines(rawDataFileWriter, level,
                  numBins);
            }
          } else {


            // Copy scans for this MS-level.
            copyScansToWriter(rawDataFileWriter, level);
          }
        }
      }


      // If this task was canceled, stop processing
      if (!isCanceled()) {


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


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

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Examples of net.sf.mzmine.data.RawDataFileWriter


    setStatus(TaskStatus.PROCESSING);


    try {
      for (RawDataFile dataFile : dataFiles) {
        RawDataFileWriter rawDataFileWriter = MZmineCore
            .createNewFile(dataFile.getName() + " " + suffix);
        filteredRawDataFile = rawDataFilter.getModule().filterDatafile(
            dataFile, rawDataFileWriter,
            rawDataFilter.getParameterSet());
        if (filteredRawDataFile != null) {

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Examples of net.sf.mzmine.data.RawDataFileWriter

        null);
    ticPlot.addTICDataset(ticDataset);


    try {
      // Create a new filtered raw data file
      RawDataFileWriter rawDataFileWriter = MZmineCore
          .createNewFile(dataFile.getName() + " filtered");
      RawDataFile newDataFile = rawDataFilter.filterDatafile(dataFile,
          rawDataFileWriter, filterParameters);


      // If successful, add the new data file

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Examples of net.sf.mzmine.data.RawDataFileWriter

          "Cannot read file " + fileName);
      logger.warning("Cannot read file " + fileName);
      return true;
    }


    RawDataFileWriter newMZmineFile;
    try {
      newMZmineFile = MZmineCore.createNewFile(fileName.getName());
    } catch (IOException e) {
      MZmineCore.getDesktop().displayErrorMessage(
          "Could not create a new temporary file " + e);

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