public static void main(String[] args) throws IOException {
Modification methylH = Modification.parseModification("CH2");
Modification methylD = Modification.parseModification("CH[2]3H-1");
PeakProcessorChain<PeakAnnotation> ppc = new PeakProcessorChain<>();
SpectraPairExtractor mse = new SpectraPairExtractor(methylH, methylD);
FilenameFilter filter = new SuffixFileFilter(".mgf", IOCase.INSENSITIVE);
File specFile = new File(args[0]);
if (specFile.isDirectory()) {
File[] files = specFile.listFiles(filter);
for (File aFile : files) {
System.out.println("Processing File:" + aFile.getName());
mse.process(aFile.getAbsolutePath(), ppc, 6);
}
} else {
System.out.println("Processing File:" + specFile.getName());
mse.process(specFile.getAbsolutePath(), ppc, 10);
}
}
public void process(String mgfFile, PeakProcessorChain<PeakAnnotation> aChain, double scoreLimit)
throws IOException {
MgfReader reader = new MgfReader(new File(mgfFile));
String core = FilePathUtil.removeExtension(mgfFile);
PrintWriter log = new PrintWriter(core + "_log.csv");
log.println("Scan1,Mz1,Charge1,Scan2,Mz2,Charge2,DeltaCount,NewMz,PeakCount,FilterPeakCount");
MgfWriter writer = new MgfWriter(new File(core + "_pair.mgf"));
List<MsnSpectrum> specList = loadMgf(reader, aChain);
PeakListExtractor extractor = new PeakListExtractor(iMs2Tol);
HashMap<Integer, SpectrumSpectrumMatch> map = new HashMap<>();
double labelDelta = iHeavyMod.getMolecularMass() - iLightMod.getMolecularMass();
double maxDelta = labelDelta * iMaxModCount;
for (int lId = 0; lId < specList.size(); lId++) {
MsnSpectrum lSpec = specList.get(lId);
Peak lPeak = lSpec.getPrecursor();
for (int hId = lId + 1; hId < specList.size(); hId++) {
MsnSpectrum hSpec = specList.get(hId);
Peak hPeak = hSpec.getPrecursor();
double delta = hPeak.getMass() - lPeak.getMass();
if (iMs1Tol.check(maxDelta, delta).equals(Location.LARGER)) break;
if (iMs1Tol.check(labelDelta, delta).equals(Location.SMALLER)) continue;
if (iChargeTol.isPresent()) {
int deltaE = iChargeTol.get();
int lightE = lPeak.getCharge();
int heavyE = hPeak.getCharge();
if (Math.abs(lightE - heavyE) > deltaE) break;
}
if (iIntensityTol.isPresent()) {
double deltaIn = iIntensityTol.get();
double lightI = lPeak.getIntensity();
double heavyI = hPeak.getIntensity();
if (Math.abs(Math.log(lightI / heavyI)) > Math.log(deltaIn)) break;
}
if (iTimeTol.isPresent()) {
double lightT = lSpec.getRetentionTimes().getFirst().getTime();
double heavyT = hSpec.getRetentionTimes().getFirst().getTime();
int deltaTime = iTimeTol.get();
if (Math.abs(lightT - heavyT) > deltaTime) break;
}
for (int mCount = iMaxModCount; mCount > 0; mCount--) {
if (!iMs1Tol.withinTolerance(mCount * labelDelta, delta)) continue;
double lBaseIn = lSpec.getBasePeakIntensity();
double hBaseIn = hSpec.getBasePeakIntensity();
MsnSpectrum lFilterSpec = lSpec.copy(new ThresholdFilter<>(lBaseIn * 0.01));
MsnSpectrum hFilterSpec = hSpec.copy(new ThresholdFilter<>(hBaseIn * 0.01));
HashMap<Integer, Integer> filterMatch =
extractor.getMatchPeaks(lFilterSpec, hFilterSpec, labelDelta, mCount);
if (filterMatch.size() < scoreLimit) break;
HashMap<Integer, Integer> pairPeaksIndex =
extractor.getMatchPeaks(lSpec, hSpec, labelDelta, mCount);
MsnSpectrum peaks = new MsnSpectrum();
for (Entry<Integer, Integer> entry : pairPeaksIndex.entrySet()) {
double lightMz = lSpec.getMz(entry.getKey());
double heavyMz = hSpec.getMz(entry.getValue());
double intensity = lSpec.getIntensity(entry.getKey());
int count = (int) (FastMath.round((heavyMz - lightMz) / labelDelta));
if (count != 0) {
lightMz = lightMz - count * iLightMod.getMolecularMass();
}
peaks.add(lightMz, intensity);
}
double newMz = lPeak.getMz() - mCount * iLightMod.getMolecularMass() / lPeak.getCharge();
Peak rPeak = Peak.noIntensity(newMz, lPeak.getCharge());
peaks.setPrecursor(rPeak);
log.print(lSpec.getScanNumbers().getFirst().getValue() + ",");
log.print(lPeak.getMz() + ",");
log.print(lPeak.getCharge() + ",");
log.print(hSpec.getScanNumbers().getFirst().getValue() + ",");
log.print(hPeak.getMz() + ",");
log.print(hPeak.getCharge() + ",");
log.print(mCount + ",");
log.print(newMz + ",");
log.print(pairPeaksIndex.size() + ",");
log.print(filterMatch.size() + "\n");
SpectrumSpectrumMatch aMatch =
new SpectrumSpectrumMatch(lSpec.getComment(), hSpec.getComment());
aMatch.setFirstPrecursorPeak(lPeak);
aMatch.setSecondPrecursorPeak(hPeak);
aMatch.setFirstRetentionTime(lSpec.getRetentionTimes().getFirst());
aMatch.setSecondRetentionTime(hSpec.getRetentionTimes().getFirst());
aMatch.setFirstScanNumber(lSpec.getScanNumbers().getFirst());
aMatch.setSecondScanNumber(hSpec.getScanNumbers().getFirst());
aMatch.setCommonPeaks(peaks);
aMatch.setLabelDelta(mCount);
aMatch.setMatchCount(peaks.size());
if (map.containsKey(lId)) {
SpectrumSpectrumMatch spectrumSpectrumMatch = map.get(lId);
if (spectrumSpectrumMatch.getMatchCount() < peaks.size()) {
map.put(lId, aMatch);
}
} else {
map.put(lId, aMatch);
}
break;
}
}
}
for (SpectrumSpectrumMatch match : map.values()) {
MsnSpectrum spec = match.getCommonPeaks();
spec.setComment(String.valueOf(match.getLabelDelta().get()));
spec.addScanNumber(match.getFirstScanNumber());
spec.addScanNumber(match.getSecondScanNumber());
spec.addRetentionTime(match.getFirstRetentionTime());
spec.addRetentionTime(match.getSecondRetentionTime());
writer.write(spec);
}
writer.close();
log.close();
}