Package net.sf.mzmine.data.impl

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

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        continue;
      }

      assert maxPoint != null;

      SimpleChromatographicPeak c = new SimpleChromatographicPeak(
          dataFile, scan.getPrecursorMZ(),
          bestScan.getRetentionTime(), maxPoint.getIntensity(),
          maxPoint.getIntensity(),
          new int[]{bestScan.getScanNumber()},
          new DataPoint[]{maxPoint}, PeakStatus.DETECTED,
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      // Find the best fragmentation scan, if available
      int fragmentScan = ScanUtils.findBestFragmentScan(rawDataFile,
          finalRTRange, finalMZRange);

      SimpleChromatographicPeak newPeak = new SimpleChromatographicPeak(
          rawDataFile, mz, rt, height, area, scanNumbers,
          finalDataPoint, PeakStatus.ESTIMATED, representativeScan,
          fragmentScan, finalRTRange, finalMZRange,
          finalIntensityRange);
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              if (!isCanceled() && maxScanNumber >= 0) {

                // Create a new peak.
                newRow.addPeak(
                    dataFile,
                    new SimpleChromatographicPeak(
                        dataFile,
                        maxDataPoint.getMZ(),
                        peak.getRT(),
                        maxIntensity,
                        area,
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        }
      }

      PeakStatus status = PeakStatus.valueOf(peakStatus);

      SimpleChromatographicPeak peak = new SimpleChromatographicPeak(
          dataFile, mass, rt, height, area, scanNumbers, mzPeaks,
          status, representativeScan, fragmentScan, peakRTRange,
          peakMZRange, peakIntensityRange);

      peak.setCharge(currentPeakCharge);

      if (currentIsotopes.size() > 0) {
        SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
            currentIsotopes.toArray(new DataPoint[0]),
            currentIsotopePatternStatus,
            currentIsotopePatternDescription);
        peak.setIsotopePattern(newPattern);
        currentIsotopes.clear();
      }

      buildingRow.addPeak(dataFile, peak);
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        }
      }

      PeakStatus status = PeakStatus.valueOf(peakStatus);

      SimpleChromatographicPeak peak = new SimpleChromatographicPeak(
          dataFile, mass, rt, height, area, scanNumbers, mzPeaks,
          status, representativeScan, fragmentScan, peakRTRange,
          peakMZRange, peakIntensityRange);

      peak.setCharge(currentPeakCharge);

      if (currentIsotopes.size() > 0) {
        SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
            currentIsotopes.toArray(new DataPoint[0]),
            currentIsotopePatternStatus,
            currentIsotopePatternDescription);
        peak.setIsotopePattern(newPattern);
        currentIsotopes.clear();
      }

      buildingRow.addPeak(dataFile, peak);
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        PeakUtils.copyPeakListRowProperties(row, newRow);

        // Copy the peaks.
        for (final ChromatographicPeak peak : row.getPeaks()) {

          final ChromatographicPeak newPeak = new SimpleChromatographicPeak(
              peak);
          PeakUtils.copyPeakProperties(peak, newPeak);
          newRow.addPeak(peak.getDataFile(), newPeak);
        }
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      } else {
        Arrays.sort(originalPeaks, new PeakSorter(SortingProperty.MZ,
            SortingDirection.Ascending));
      }

      ChromatographicPeak newPeak = new SimpleChromatographicPeak(
          originalPeaks[0]);
      newPeak.setIsotopePattern(newPattern);
      newPeak.setCharge(bestFitCharge);

      // Keep old ID
      int oldID = oldRow.getID();
      SimplePeakListRow newRow = new SimplePeakListRow(oldID);
      PeakUtils.copyPeakListRowProperties(oldRow, newRow);
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        }
      }

      PeakStatus status = PeakStatus.valueOf(peakStatus);

      SimpleChromatographicPeak peak = new SimpleChromatographicPeak(
          dataFile, mass, rt, height, area, scanNumbers, mzPeaks,
          status, representativeScan, fragmentScan, peakRTRange,
          peakMZRange, peakIntensityRange);

      peak.setCharge(currentPeakCharge);

      if (currentIsotopes.size() > 0) {
        SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
            currentIsotopes.toArray(new DataPoint[0]),
            currentIsotopePatternStatus,
            currentIsotopePatternDescription);
        peak.setIsotopePattern(newPattern);
        currentIsotopes.clear();
      }

      buildingRow.addPeak(dataFile, peak);
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        // Normalize peak
        ChromatographicPeak originalPeak = row.getPeak(file);
        if (originalPeak != null) {

          SimpleChromatographicPeak normalizedPeak = new SimpleChromatographicPeak(
              originalPeak);

          PeakUtils.copyPeakProperties(originalPeak, normalizedPeak);

          double normalizedHeight = originalPeak.getHeight()
              / normalizationFactor;
          double normalizedArea = originalPeak.getArea()
              / normalizationFactor;
          normalizedPeak.setHeight(normalizedHeight);
          normalizedPeak.setArea(normalizedArea);

          normalizedRow.addPeak(file, normalizedPeak);
        }

      }
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    PeakUtils.copyPeakListRowProperties(row, newRow);

    // Copy the peaks.
    for (final ChromatographicPeak peak : row.getPeaks()) {

      final ChromatographicPeak newPeak = new SimpleChromatographicPeak(
          peak);
      PeakUtils.copyPeakProperties(peak, newPeak);
      newRow.addPeak(peak.getDataFile(), newPeak);
    }
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Related Classes of net.sf.mzmine.data.impl.SimpleChromatographicPeak

  • net.sf.mzmine.modules.peaklistmethods.filtering.duplicatefilter.DuplicateFilterTask
  • net.sf.mzmine.modules.peaklistmethods.filtering.rowsfilter.RowsFilterTask
  • net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.Gap
  • net.sf.mzmine.modules.peaklistmethods.isotopes.deisotoper.IsotopeGrouperTask
  • net.sf.mzmine.modules.peaklistmethods.normalization.linear.LinearNormalizerTask
  • net.sf.mzmine.modules.peaklistmethods.normalization.rtnormalizer.RTNormalizerTask
  • net.sf.mzmine.modules.peaklistmethods.normalization.standardcompound.StandardCompoundNormalizerTask
  • net.sf.mzmine.modules.peaklistmethods.peakpicking.smoothing.SmoothingTask
  • net.sf.mzmine.modules.projectmethods.projectload.version_2_0.PeakListOpenHandler_2_0
  • net.sf.mzmine.modules.projectmethods.projectload.version_2_3.PeakListOpenHandler_2_3
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