Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.MassList

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      return;

    // Get mass list
    String massListName = parameters.getParameter(
        ShoulderPeaksFilterParameters.massList).getValue();
    MassList massList = previewScan.getMassList(massListName);
    if (massList == null)
      return;

    // Perform filtering
    DataPoint mzValues[] = massList.getDataPoints();
    DataPoint remainingMzValues[] = ShoulderPeaksFilter.filterMassValues(
        mzValues, parameters);

    Vector<DataPoint> removedPeaks = new Vector<DataPoint>();
    removedPeaks.addAll(Arrays.asList(mzValues));
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    // Check if we have at least one scan with a mass list of given name
    boolean haveMassList = false;
    for (int i = 0; i < totalScans; i++) {
      Scan scan = dataFile.getScan(scanNumbers[i]);
      MassList massList = scan.getMassList(massListName);
      if (massList != null) {
        haveMassList = true;
        break;
      }
    }
    if (!haveMassList) {
      setStatus(TaskStatus.ERROR);
      this.errorMessage = dataFile.getName()
          + " has no mass list called '" + massListName + "'";
      return;
    }

    // Process all scans
    for (int i = 0; i < totalScans; i++) {

      if (isCanceled())
        return;

      Scan scan = dataFile.getScan(scanNumbers[i]);

      MassList massList = scan.getMassList(massListName);

      // Skip those scans which do not have a mass list of given name
      if (massList == null) {
        processedScans++;
        continue;
      }

      DataPoint mzPeaks[] = massList.getDataPoints();

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

      SimpleMassList newMassList = new SimpleMassList(massListName + " "
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    }

    // MS/MS scan must exist, because msmsScanNumber was > 0
    Scan msmsScan = bestPeak.getDataFile().getScan(msmsScanNumber);

    MassList massList = msmsScan.getMassList(massListName);
    if (massList == null) {
      MZmineCore.getDesktop().displayErrorMessage(
          "There is no mass list called " + massListName
              + " for MS/MS scan #" + msmsScanNumber + " ("
              + bestPeak.getDataFile() + ")");
      return;
    }

    DataPoint peaks[] = massList.getDataPoints();

    try {
      FileWriter fileWriter = new FileWriter(outputFile);
      BufferedWriter writer = new BufferedWriter(fileWriter);
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Related Classes of net.sf.mzmine.data.MassList

  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeModel
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeMouseHandler
  • net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderTask
  • net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterSetupDialog
  • net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterTask
  • net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.SingleRowPredictionTask
  • net.sf.mzmine.modules.peaklistmethods.io.sqlexport.SQLExportTask
  • net.sf.mzmine.modules.peaklistmethods.msms.msmsscore.MSMSScoreCalculator
  • net.sf.mzmine.modules.projectmethods.projectsave.RawDataFileSaveHandler
  • net.sf.mzmine.modules.visualization.peaklist.export.MSMSExportModule
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