Package net.sf.mzmine.project.impl

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

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        TreeMap<Integer, Integer> dataPointsLengths = newRawDataFile
            .getDataPointsLengths();
        if (!dataPointsOffsets.isEmpty())
          newStorageID = dataPointsOffsets.lastKey().intValue() + 1;

        StorableScan storableScan = new StorableScan(newRawDataFile,
            newStorageID, dataPointsNumber, scanNumber, msLevel,
            retentionTime, parentScan, precursorMZ,
            precursorCharge, fragmentScan, centroided);
        newRawDataFile.addScan(storableScan);
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        TreeMap<Integer, Integer> dataPointsLengths = newRawDataFile
            .getDataPointsLengths();
        if (!dataPointsOffsets.isEmpty())
          newStorageID = dataPointsOffsets.lastKey().intValue() + 1;

        StorableScan storableScan = new StorableScan(newRawDataFile,
            newStorageID, dataPointsNumber, scanNumber, msLevel,
            retentionTime, parentScan, precursorMZ,
            precursorCharge, fragmentScan, centroided);
        newRawDataFile.addScan(storableScan);
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          .parseInt(getTextOfElement());
    }

    if (qName.equals(RawDataElementName_2_5.SCAN.getElementName())) {

      StorableScan storableScan = new StorableScan(newRawDataFile,
          currentStorageID, dataPointsNumber, scanNumber, msLevel,
          retentionTime, parentScan, precursorMZ, precursorCharge,
          fragmentScan, centroided);

      try {
        newRawDataFile.addScan(storableScan);
      } catch (IOException e) {
        throw new SAXException(e);
      }

      for (StorableMassList newML : massLists) {
        newML.setScan(storableScan);
        storableScan.addMassList(newML);
      }
      massLists.clear();

    }
  }
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    for (int scanNumber : rawDataFile.getScanNumbers()) {

      if (canceled)
        return;

      StorableScan scan = (StorableScan) rawDataFile.getScan(scanNumber);
      int storageID = scan.getStorageID();
      atts.addAttribute("", "",
          RawDataElementName.STORAGE_ID.getElementName(), "CDATA",
          String.valueOf(storageID));
      hd.startElement("", "", RawDataElementName.SCAN.getElementName(),
          atts);
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    }

    if (qName.equals(RawDataElementName_2_5_FiehnlabFork.SCAN
        .getElementName())) {

      StorableScan scan = null;

      if (isCorrectedSpectrum) {
        scan = new CorrectedSpectrum(newRawDataFile, currentStorageID,
            scanNumber, originalRetentionTime,
            (int) retentionIndex, (int) uniqueMass,
            dataPointsNumber, centroided);
      } else {
        scan = new StorableScan(newRawDataFile, currentStorageID,
            dataPointsNumber, scanNumber, msLevel, retentionTime,
            parentScan, precursorMZ, precursorCharge, fragmentScan,
            centroided);
      }

      try {
        newRawDataFile.addScan(scan);
      } catch (IOException e) {
        throw new SAXException(e);
      }

      for (StorableMassList newML : massLists) {
        newML.setScan(scan);
        scan.addMassList(newML);
      }
      massLists.clear();
    }

    if (qName.equals(RawDataElementName_2_5_FiehnlabFork.CORRECTED_SPECTRUM
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Related Classes of net.sf.mzmine.project.impl.StorableScan

  • net.sf.mzmine.data.DataPoint
  • net.sf.mzmine.data.MassList
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeModel
  • net.sf.mzmine.modules.projectmethods.projectload.version_2_0.RawDataFileOpenHandler_2_0
  • net.sf.mzmine.modules.projectmethods.projectload.version_2_3.RawDataFileOpenHandler_2_3
  • net.sf.mzmine.modules.projectmethods.projectload.version_2_5.RawDataFileOpenHandler_2_5
  • net.sf.mzmine.modules.projectmethods.projectload.version_2_5_fiehnlab.RawDataFileOpenHandler_2_5_FiehnlabFork
  • net.sf.mzmine.modules.projectmethods.projectsave.RawDataFileSaveHandler
  • net.sf.mzmine.util.Range
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