Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.RawDataFile

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    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
      if (newDataFile != null) {
        int newScanNumbers[] = newDataFile.getScanNumbers(1, rtRange);
        TICDataSet newDataset = new TICDataSet(newDataFile,
            newScanNumbers, mzRange, null);
        ticPlot.addTICDataset(newDataset);
      }
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  public String generateToolTip(CategoryDataset dataset, int row, int column) {
    Format intensityFormat = MZmineCore.getConfiguration()
        .getIntensityFormat();
    ChromatographicPeak peaks[] = ((IntensityPlotDataset) dataset)
        .getPeaks(row, column);
    RawDataFile files[] = ((IntensityPlotDataset) dataset).getFiles(column);

    StringBuffer sb = new StringBuffer();
    for (int i = 0; i < files.length; i++) {
      sb.append(files[i].getName());
      sb.append(": ");
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    // Get total number of rows
    totalRows = peakList.getNumberOfRows();

    // Get peak list columns
    RawDataFile columns[] = peakList.getRawDataFiles();

    // Create new peak list
    processedPeakList = new SimplePeakList(peakList + " " + suffix, columns);

    // Fill gaps in given column
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    ChromatographicPeak previewPeak = previewRow.getPeaks()[0];

    ticPlot.removeAllTICDataSets();

    // Load the intensities into array
    RawDataFile dataFile = previewPeak.getDataFile();
    int scanNumbers[] = previewPeak.getScanNumbers();
    double retentionTimes[] = new double[scanNumbers.length];
    for (int i = 0; i < scanNumbers.length; i++)
      retentionTimes[i] = dataFile.getScan(scanNumbers[i])
          .getRetentionTime();
    double intensities[] = new double[scanNumbers.length];
    for (int i = 0; i < scanNumbers.length; i++) {
      DataPoint dp = previewPeak.getDataPoint(scanNumbers[i]);
      if (dp != null)
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    Class shapeModelClass = shapeModelerType.getModelClass();
    Constructor<?> shapeModelConstruct;
    shapeModelConstruct = shapeModelClass.getConstructors()[0];

    // Get data file information
    RawDataFile dataFile = originalPeakList.getRawDataFile(0);

    // Create new peak list
    newPeakList = new SimplePeakList(originalPeakList + " " + suffix,
        dataFile);

    totalRows = originalPeakList.getNumberOfRows();
    int[] scanNumbers;
    double[] retentionTimes, intensities;
    SimplePeakListRow newRow;

    for (PeakListRow row : originalPeakList.getRows()) {

      if (isCanceled())
        return;

      newRow = new SimplePeakListRow(newPeakID);

      try {
        for (ChromatographicPeak peak : row.getPeaks()) {

          // Load the intensities into array
          dataFile = peak.getDataFile();
          scanNumbers = peak.getScanNumbers();
          retentionTimes = new double[scanNumbers.length];
          for (int i = 0; i < scanNumbers.length; i++)
            retentionTimes[i] = dataFile.getScan(scanNumbers[i])
                .getRetentionTime();

          intensities = new double[scanNumbers.length];
          for (int i = 0; i < scanNumbers.length; i++) {
            DataPoint dp = peak.getDataPoint(scanNumbers[i]);
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      MZmineCore.getDesktop().displayErrorMessage(
          "Please select a single peak list");
      return ExitCode.CANCEL;
    }

    RawDataFile plDataFiles[] = selectedPeakLists[0].getRawDataFiles();
    PeakListRow plRows[] = selectedPeakLists[0].getRows();
    Arrays.sort(plRows, new PeakListRowSorter(SortingProperty.MZ,
        SortingDirection.Ascending));

    getParameter(dataFiles).setChoices(plDataFiles);
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      if (predictedPattern == null)
        return;

      ChromatographicPeak peak = peakListRow.getBestPeak();

      RawDataFile dataFile = peak.getDataFile();
      int scanNumber = peak.getRepresentativeScanNumber();
      SpectraVisualizerModule.showNewSpectrumWindow(dataFile, scanNumber,
          null, peak.getIsotopePattern(), predictedPattern);

    }
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  private void fillParameterElement(UserParameter parameter,
      TransformerHandler hd) throws SAXException, IOException {

    AttributesImpl atts = new AttributesImpl();

    RawDataFile dataFiles[] = project.getDataFiles();

    if (parameter instanceof ComboParameter) {
      Object choices[] = ((ComboParameter<Object>) parameter)
          .getChoices();
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    }

    // <RAW_FILE>
    if (qName.equals(PeakListElementName_2_5.RAWFILE.getElementName())) {
      rawDataFileID = getTextOfElement();
      RawDataFile dataFile = dataFilesIDMap.get(rawDataFileID);
      if (dataFile == null) {
        throw new SAXException(
            "Cannot open peak list, because raw data file "
                + rawDataFileID + " is missing.");
      }
      currentPeakListDataFiles.add(dataFile);
    }

    // <SCAN_ID>
    if (qName.equals(PeakListElementName_2_5.SCAN_ID.getElementName())) {

      byte[] bytes = Base64.decodeToBytes(getTextOfElement());
      // make a data input stream
      DataInputStream dataInputStream = new DataInputStream(
          new ByteArrayInputStream(bytes));
      scanNumbers = new int[numOfMZpeaks];
      for (int i = 0; i < numOfMZpeaks; i++) {
        try {
          scanNumbers[i] = dataInputStream.readInt();
        } catch (IOException ex) {
          throw new SAXException(ex);
        }
      }
    }

    // <REPRESENTATIVE_SCAN>
    if (qName.equals(PeakListElementName_2_5.REPRESENTATIVE_SCAN
        .getElementName())) {
      representativeScan = Integer.valueOf(getTextOfElement());
    }

    // <FRAGMENT_SCAN>

    if (qName
        .equals(PeakListElementName_2_5.FRAGMENT_SCAN.getElementName())) {
      fragmentScan = Integer.valueOf(getTextOfElement());
    }

    // <MASS>
    if (qName.equals(PeakListElementName_2_5.MZ.getElementName())) {

      byte[] bytes = Base64.decodeToBytes(getTextOfElement());
      // make a data input stream
      DataInputStream dataInputStream = new DataInputStream(
          new ByteArrayInputStream(bytes));
      masses = new double[numOfMZpeaks];
      for (int i = 0; i < numOfMZpeaks; i++) {
        try {
          masses[i] = (double) dataInputStream.readFloat();
        } catch (IOException ex) {
          throw new SAXException(ex);
        }
      }
    }

    // <HEIGHT>
    if (qName.equals(PeakListElementName_2_5.HEIGHT.getElementName())) {

      byte[] bytes = Base64.decodeToBytes(getTextOfElement());
      // make a data input stream
      DataInputStream dataInputStream = new DataInputStream(
          new ByteArrayInputStream(bytes));
      intensities = new double[numOfMZpeaks];
      for (int i = 0; i < numOfMZpeaks; i++) {
        try {
          intensities[i] = (double) dataInputStream.readFloat();
        } catch (IOException ex) {
          throw new SAXException(ex);
        }
      }
    }

    // <PEAK>
    if (qName.equals(PeakListElementName_2_5.PEAK.getElementName())) {

      DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
      Range peakRTRange = null, peakMZRange = null, peakIntensityRange = null;
      RawDataFile dataFile = dataFilesIDMap.get(peakColumnID);

      if (dataFile == null)
        throw new SAXException("Error in project: data file "
            + peakColumnID + " not found");

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

        Scan sc = dataFile.getScan(scanNumbers[i]);
        double retentionTime = sc.getRetentionTime();

        double mz = masses[i];
        double intensity = intensities[i];
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    for (SimpleMassList ml : allMassLists) {
      Scan s = ml.getScan();
      s.addMassList(ml);
    }

    RawDataFile rawDataFile = newRawDataFile.finishWriting();
    return rawDataFile;

  }
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Related Classes of net.sf.mzmine.data.RawDataFile

  • net.sf.mzmine.data.impl.SimplePeakList
  • net.sf.mzmine.desktop.impl.MainMenu
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeModel
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeMouseHandler
  • net.sf.mzmine.main.ShutDownHook
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.table.ResultsListTableColumnModel
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.table.MassListTable
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.table.MassListTableColumnModel
  • net.sf.mzmine.modules.deconvolutedanalysis.spectrafilter.SpectraFilterTest
  • net.sf.mzmine.modules.peaklistmethods.alignment.ransac.RansacAlignerSetupDialog
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