public SimpleIsotopePattern(
DataPoint dataPoints[], IsotopePatternStatus status, String description) {
assert dataPoints.length > 0;
highestIsotope = ScanUtils.findTopDataPoint(dataPoints);
this.dataPoints = dataPoints;
this.status = status;
this.description = description;
this.mzRange = ScanUtils.findMzRange(dataPoints);
}
/** @see java.lang.Runnable#run() */
public void run() {
setStatus(TaskStatus.PROCESSING);
logger.info("Started parsing file " + file);
MzMLUnmarshaller unmarshaller = new MzMLUnmarshaller(file);
totalScans = unmarshaller.getObjectCountForXpath("/run/spectrumList/spectrum");
MzMLObjectIterator<Spectrum> spectrumIterator =
unmarshaller.unmarshalCollectionFromXpath("/run/spectrumList/spectrum", Spectrum.class);
try {
while (spectrumIterator.hasNext()) {
Spectrum spectrum = spectrumIterator.next();
String scanId = spectrum.getId();
int scanNumber = convertScanIdToScanNumber(scanId);
int msLevel = extractMSLevel(spectrum);
double retentionTime = extractRetentionTime(spectrum);
// Get parent scan number
int parentScan = extractParentScanNumber(spectrum);
double precursorMz = extractPrecursorMz(spectrum);
int precursorCharge = extractPrecursorCharge(spectrum);
DataPoint dataPoints[] = extractDataPoints(spectrum);
// Auto-detect whether this scan is centroided
boolean centroided = ScanUtils.isCentroided(dataPoints);
// Remove zero data points
DataPoint optimizedDataPoints[] = ScanUtils.removeZeroDataPoints(dataPoints, centroided);
SimpleScan scan =
new SimpleScan(
null,
scanNumber,
msLevel,
retentionTime,
parentScan,
precursorMz,
precursorCharge,
null,
optimizedDataPoints,
centroided);
for (SimpleScan s : parentStack) {
if (s.getScanNumber() == parentScan) {
s.addFragmentScan(scanNumber);
}
}
/*
* Verify the size of parentStack. The actual size of the window
* to cover possible candidates is defined by limitSize.
*/
if (parentStack.size() > PARENT_STACK_SIZE) {
SimpleScan firstScan = parentStack.removeLast();
newMZmineFile.addScan(firstScan);
}
parentStack.addFirst(scan);
parsedScans++;
}
while (!parentStack.isEmpty()) {
SimpleScan scan = parentStack.removeLast();
newMZmineFile.addScan(scan);
}
finalRawDataFile = newMZmineFile.finishWriting();
} catch (Throwable e) {
setStatus(TaskStatus.ERROR);
errorMessage = "Error parsing mzML: " + ExceptionUtils.exceptionToString(e);
e.printStackTrace();
return;
}
if (parsedScans == 0) {
setStatus(TaskStatus.ERROR);
errorMessage = "No scans found";
return;
}
logger.info("Finished parsing " + file + ", parsed " + parsedScans + " scans");
setStatus(TaskStatus.FINISHED);
}