@Override
public MsScan performFilter(MsScan scan) {
if (!Avalues.containsKey(numOfDataPoints) || !Hvalues.containsKey(numOfDataPoints)) {
return scan;
}
int[] aVals = Avalues.get(numOfDataPoints);
int h = Hvalues.get(numOfDataPoints);
int marginSize = (numOfDataPoints + 1) / 2 - 1;
float sumOfInts;
// Create data point list object and fill it with the scan data points
MsSpectrumDataPointList dataPoints = MSDKObjectBuilder.getMsSpectrumDataPointList();
scan.getDataPoints(dataPoints);
float intensityValues[] = dataPoints.getIntensityBuffer();
double mzValues[] = dataPoints.getMzBuffer();
int newDataPointsLength = dataPoints.getSize() - (marginSize * 2);
// only process MS level 1 scans
if (scan.getMsFunction().getMsLevel() != 1) {
return scan;
}
// only process scans with datapoints
if (newDataPointsLength < 1) {
return scan;
}
MsSpectrumDataPointList newDataPoints = MSDKObjectBuilder.getMsSpectrumDataPointList();
for (int spectrumInd = marginSize;
spectrumInd < (dataPoints.getSize() - marginSize);
spectrumInd++) {
// zero intensity data points must be left unchanged
if (intensityValues[spectrumInd] == 0) {
intensityValues[spectrumInd - marginSize] = intensityValues[spectrumInd];
continue;
}
sumOfInts = aVals[0] * intensityValues[spectrumInd];
for (int windowInd = 1; windowInd <= marginSize; windowInd++) {
sumOfInts +=
aVals[windowInd]
* (intensityValues[spectrumInd + windowInd]
+ intensityValues[spectrumInd - windowInd]);
}
sumOfInts = sumOfInts / h;
if (sumOfInts < 0) {
sumOfInts = 0;
}
newDataPoints.add(mzValues[spectrumInd], sumOfInts);
}
// Return a new scan with the new data points
MsScan result = MSDKObjectBuilder.getMsScan(store, scan.getScanNumber(), scan.getMsFunction());
result.setDataPoints(newDataPoints);
result.setChromatographyInfo(scan.getChromatographyInfo());
result.setRawDataFile(scan.getRawDataFile());
return result;
}
