Examples of net.sf.mzmine.data.impl.SimpleMassList

net.sf.mzmine.data.impl.SimpleMassList
This class represent detected masses (ions) in one mass spectrum


      MassDetector detector = massDetector.getModule();
      DataPoint mzPeaks[] = detector.getMassValues(scan,
          massDetector.getParameterSet());


      SimpleMassList newMassList = new SimpleMassList(name, scan, mzPeaks);


      // Add new mass list to the scan
      scan.addMassList(newMassList);


      processedScans++;

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    }


    if (qName.equals(RawDataElementName_2_3.MASS_LIST.getElementName())) {
      String name = attrs.getValue(RawDataElementName_2_3.NAME
          .getElementName());
      SimpleMassList newML = new SimpleMassList(name, null, null);
      currentMassLists.add(newML);
    }
  }

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    if (qName.equals(RawDataElementName_2_3.MASS_LIST.getElementName())) {
      char encodedDataPoints[] = getTextOfElement().toCharArray();
      DataPoint dataPoints[] = ScanUtils
          .decodeDataPointsBase64(encodedDataPoints);
      SimpleMassList newML = currentMassLists
          .get(currentMassLists.size() - 1);
      newML.setDataPoints(dataPoints);
    }


    if (qName.equals(RawDataElementName_2_3.SCAN.getElementName())) {


      try {
        int newStorageID = 1;
        TreeMap<Integer, Long> dataPointsOffsets = newRawDataFile
            .getDataPointsOffsets();
        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);


        dataPointsOffsets.put(newStorageID, storageFileOffset);
        dataPointsLengths.put(newStorageID, dataPointsNumber);


        for (SimpleMassList newML : currentMassLists) {
          newML.setScan(storableScan);
        }
        allMassLists.addAll(currentMassLists);
        currentMassLists.clear();


      } catch (IOException e) {

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      DataPoint mzPeaks[] = massList.getDataPoints();


      DataPoint newMzPeaks[] = ShoulderPeaksFilter.filterMassValues(
          mzPeaks, parameters);


      SimpleMassList newMassList = new SimpleMassList(massListName + " "
          + suffix, scan, newMzPeaks);


      scan.addMassList(newMassList);


      // Remove old mass list

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Related Classes of net.sf.mzmine.data.impl.SimpleMassList

net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterTask

net.sf.mzmine.modules.projectmethods.projectload.version_2_3.RawDataFileOpenHandler_2_3

net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionTask

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