/**
* {@inheritDoc}
*
* <p>endElement()
*/
@SuppressWarnings("null")
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {
if (canceled) throw new SAXException("Parsing Cancelled");
// <spectrumInstrument>
if (qName.equalsIgnoreCase("spectrumInstrument")) {
spectrumInstrumentFlag = false;
}
// <precursor>
if (qName.equalsIgnoreCase("precursor")) {
precursorFlag = false;
}
// <spectrum>
if (qName.equalsIgnoreCase("spectrum")) {
spectrumInstrumentFlag = false;
// Auto-detect whether this scan is centroided
MsSpectrumType spectrumType =
SpectrumTypeDetectionAlgorithm.detectSpectrumType(mzBuffer, intensityBuffer, peaksCount);
// Create a new scan
MsFunction msFunction = MSDKObjectBuilder.getMsFunction(msLevel);
MsScan newScan = MSDKObjectBuilder.getMsScan(dataStore, scanNumber, msFunction);
newScan.setDataPoints(mzBuffer, intensityBuffer, peaksCount);
newScan.setSpectrumType(spectrumType);
newScan.setPolarity(polarity);
if (retentionTime != null) {
ChromatographyInfo chromInfo =
MSDKObjectBuilder.getChromatographyInfo1D(SeparationType.UNKNOWN, retentionTime);
newScan.setChromatographyInfo(chromInfo);
}
if (precursorMz != null) {
IsolationInfo isolation =
MSDKObjectBuilder.getIsolationInfo(
Range.singleton(precursorMz), null, precursorMz, precursorCharge, null);
newScan.getIsolations().add(isolation);
}
// Add the scan to the file
newRawFile.addScan(newScan);
parsedScans++;
}
// <mzArrayBinary>
if (qName.equalsIgnoreCase("mzArrayBinary")) {
mzArrayBinaryFlag = false;
// Allocate space for the whole array
if (mzBuffer.length < peaksCount) mzBuffer = new double[peaksCount * 2];
byte[] peakBytes = Base64.decodeBase64(charBuffer.toString().getBytes());
ByteBuffer currentMzBytes = ByteBuffer.wrap(peakBytes);
if (endian.equals("big")) {
currentMzBytes = currentMzBytes.order(ByteOrder.BIG_ENDIAN);
} else {
currentMzBytes = currentMzBytes.order(ByteOrder.LITTLE_ENDIAN);
}
for (int i = 0; i < peaksCount; i++) {
if (precision == null || precision.equals("32"))
mzBuffer[i] = (double) currentMzBytes.getFloat();
else mzBuffer[i] = currentMzBytes.getDouble();
}
}
// <intenArrayBinary>
if (qName.equalsIgnoreCase("intenArrayBinary")) {
intenArrayBinaryFlag = false;
// Allocate space for the whole array
if (intensityBuffer.length < peaksCount) intensityBuffer = new float[peaksCount * 2];
byte[] peakBytes = Base64.decodeBase64(charBuffer.toString().getBytes());
ByteBuffer currentIntensityBytes = ByteBuffer.wrap(peakBytes);
if (endian.equals("big")) {
currentIntensityBytes = currentIntensityBytes.order(ByteOrder.BIG_ENDIAN);
} else {
currentIntensityBytes = currentIntensityBytes.order(ByteOrder.LITTLE_ENDIAN);
}
for (int i = 0; i < peaksCount; i++) {
if (precision == null || precision.equals("32"))
intensityBuffer[i] = currentIntensityBytes.getFloat();
else intensityBuffer[i] = (float) currentIntensityBytes.getDouble();
}
}
}
@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;
}