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());
}