public FragmentIdentity(final PeakListRow mainPeakListRow) { super( "Fragment of " + MZmineCore.getConfiguration().getMZFormat().format(mainPeakListRow.getAverageMZ()) + " m/z"); setPropertyValue(PROPERTY_METHOD, "Fragment search"); }
private double getValue(PeakListRow row) { switch (property) { case Area: ChromatographicPeak[] areaPeaks = row.getPeaks(); double[] peakAreas = new double[areaPeaks.length]; for (int i = 0; i < peakAreas.length; i++) peakAreas[i] = areaPeaks[i].getArea(); double medianArea = MathUtils.calcQuantile(peakAreas, 0.5); return medianArea; case Intensity: ChromatographicPeak[] intensityPeaks = row.getPeaks(); double[] peakIntensities = new double[intensityPeaks.length]; for (int i = 0; i < intensityPeaks.length; i++) peakIntensities[i] = intensityPeaks[i].getArea(); double medianIntensity = MathUtils.calcQuantile(peakIntensities, 0.5); return medianIntensity; case Height: ChromatographicPeak[] heightPeaks = row.getPeaks(); double[] peakHeights = new double[heightPeaks.length]; for (int i = 0; i < peakHeights.length; i++) peakHeights[i] = heightPeaks[i].getHeight(); double medianHeight = MathUtils.calcQuantile(peakHeights, 0.5); return medianHeight; case MZ: return row.getAverageMZ(); case RT: return row.getAverageRT(); case ID: return row.getID(); } // We should never get here, so throw exception throw (new IllegalStateException()); }