Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.RawDataFile

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    }

    // <RAW_FILE>
    if (qName.equals(PeakListElementName_2_0.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_0.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_0.REPRESENTATIVE_SCAN
        .getElementName())) {
      representativeScan = Integer.valueOf(getTextOfElement());
    }

    // <FRAGMENT_SCAN>

    if (qName
        .equals(PeakListElementName_2_0.FRAGMENT_SCAN.getElementName())) {
      fragmentScan = Integer.valueOf(getTextOfElement());
    }

    // <MASS>
    if (qName.equals(PeakListElementName_2_0.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_0.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_0.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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      currentOptions.add(optionValue);
    }

    // <VALUE>
    if (qName.equals(UserParameterElementName_2_3.VALUE.getElementName())) {
      RawDataFile currentDataFile = dataFilesIDMap.get(currentDataFileID);
      String valueString = getTextOfElement();
      Object value;
      if (currentParameter instanceof DoubleParameter) {
        value = new Double(valueString);
      } else
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      currentOptions.add(optionValue);
    }

    // <VALUE>
    if (qName.equals(UserParameterElementName_2_5.VALUE.getElementName())) {
      RawDataFile currentDataFile = dataFilesIDMap.get(currentDataFileID);
      String valueString = getTextOfElement();
      Object value;
      if (currentParameter instanceof DoubleParameter) {
        value = new Double(valueString);
      } else
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  private void saveRawDataFiles(ZipOutputStream zipStream)
      throws IOException, TransformerConfigurationException, SAXException {

    rawDataFileSaveHandler = new RawDataFileSaveHandler(zipStream);

    RawDataFile rawDataFiles[] = savedProject.getDataFiles();

    for (int i = 0; i < rawDataFiles.length; i++) {

      if (isCanceled())
        return;
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    SAXParser saxParser = factory.newSAXParser();
    saxParser.parse(xmlInputStream, this);

    // Adds the raw data file to MZmine
    newRawDataFile.openDataPointsFile(tempFile);
    RawDataFile rawDataFile = newRawDataFile.finishWriting();
    return rawDataFile;

  }
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    SAXParser saxParser = factory.newSAXParser();
    saxParser.parse(xmlInputStream, this);

    // Adds the raw data file to MZmine
    newRawDataFile.openDataPointsFile(tempFile);
    RawDataFile rawDataFile = newRawDataFile.finishWriting();
    return rawDataFile;

  }
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          // Check if there is any MS/MS scan
          if (msmsScanNum <= 0) {
            statement.setNull(i + 1, Types.BLOB);
            break;
          }
          RawDataFile dataFile = row.getBestPeak().getDataFile();
          Scan msmsScan = dataFile.getScan(msmsScanNum);
          MassList msmsMassList = msmsScan.getMassList(dataValue);
          // Check if there is a masslist for the scan
          if (msmsMassList == null) {
            statement.setNull(i + 1, Types.BLOB);
            break;
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    SAXParser saxParser = factory.newSAXParser();
    saxParser.parse(xmlInputStream, this);

    // Adds the raw data file to MZmine
    newRawDataFile.openDataPointsFile(tempFile);
    RawDataFile rawDataFile = newRawDataFile.finishWriting();
    return rawDataFile;

  }
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    setStatus(TaskStatus.PROCESSING);
    logger.info("Running isotopic peak grouper on " + peakList);

    // We assume source peakList contains one datafile
    RawDataFile dataFile = peakList.getRawDataFile(0);

    // Create a new deisotoped peakList
    deisotopedPeakList = new SimplePeakList(peakList + " " + suffix,
        peakList.getRawDataFiles());
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        averageGroup.add(newColumn);

    }

    for (int i = 0; i < peakList.getNumberOfRawDataFiles(); i++) {
      RawDataFile dataFile = peakList.getRawDataFile(i);
      ColumnGroup fileGroup = new ColumnGroup(dataFile.getName());
      header.addColumnGroup(fileGroup);

      for (int j = 0; j < DataFileColumnType.values().length; j++) {

        DataFileColumnType dataFileColumn = DataFileColumnType.values()[j];
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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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