Package net.sf.mzmine.data.impl

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

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        allDataFiles.add(dataFile);
      }
    }

    // Create a new aligned peak list
    alignedPeakList = new SimplePeakList(peakListName,
        allDataFiles.toArray(new RawDataFile[0]));

    // Iterate source peak lists
    for (PeakList peakList : peakLists) {
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    // We assume source peakList contains one datafile
    RawDataFile dataFile = peakList.getRawDataFile(0);

    // Create a new deisotoped peakList
    extendedPeakList = new SimplePeakList(peakList + " " + suffix,
        peakList.getRawDataFiles());

    // Sort peaks by descending height
    ChromatographicPeak[] sortedPeaks = peakList.getPeaks(dataFile);
    Arrays.sort(sortedPeaks, new PeakSorter(SortingProperty.Height,
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    totalRows = originalPeakLists[0].getNumberOfRows();

    // Create new peak lists
    normalizedPeakLists = new SimplePeakList[originalPeakLists.length];
    for (int i = 0; i < originalPeakLists.length; i++) {
      normalizedPeakLists[i] = new SimplePeakList(originalPeakLists[i]
          + " " + suffix, originalPeakLists[i].getRawDataFiles());

      // Remember how many rows we need to normalize
      totalRows += originalPeakLists[i].getNumberOfRows();
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    // This hashtable maps rows from original alignment result to rows of
    // the normalized alignment
    Hashtable<PeakListRow, SimplePeakListRow> rowMap = new Hashtable<PeakListRow, SimplePeakListRow>();

    // Create new peak list
    normalizedPeakList = new SimplePeakList(
        originalPeakList + " " + suffix,
        originalPeakList.getRawDataFiles());

    // Loop through all raw data files, and find the peak with biggest
    // height
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        allDataFiles.add(dataFile);
      }
    }

    // Create a new aligned peak list
    alignedPeakList = new SimplePeakList(peakListName,
        allDataFiles.toArray(new RawDataFile[0]));

    // Iterate source peak lists
    for (PeakList peakList : peakLists) {
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Related Classes of net.sf.mzmine.data.impl.SimplePeakList

  • net.sf.mzmine.data.ChromatographicPeak
  • net.sf.mzmine.data.PeakListRow
  • net.sf.mzmine.data.RawDataFile
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeModel
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameAlignmentVisualizationTask
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.SpectraMatcherModule
  • net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderTask
  • net.sf.mzmine.modules.peaklistmethods.alignment.join.JoinAlignerTask
  • net.sf.mzmine.modules.peaklistmethods.alignment.path.functions.ScoreAligner
  • net.sf.mzmine.modules.peaklistmethods.alignment.ransac.RansacAlignerTask
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