//Called by DataProcessor, entry point to Alex's program
public bool evaluate(Spectra spec)
{
currentTime = spec.getStartTime();
updateExclusionList(spec);
if (spec.getMSLevel() == 1)
{
log.Debug("Evaluating ms1 scan");
processMS1(spec);
}
else if (spec.getMSLevel() == 2)
{
log.Debug("evaluating ms2 scan");
if (spec.getIndex() % GlobalVar.ScansPerOutput == 0)
{
#if SIMULATION
double progressPercent = spec.getIndex() / GlobalVar.ExperimentTotalScans * 100;
log.Info("Progress: {0:F2}% Processing ID: {1}\t ScanNum: {2} \t Excluded: {3}", progressPercent, spec.getIndex(), spec.getScanNum(),
excludedSpectra.Count);
#else
log.Info("Progress: {0}\t{1} excluded------------------------", spec.getIndex(), excludedSpectra.Count);
log.Info("ExclusionListSize: {0}\tRTOffset: {1}", exclusionList.getExclusionList().Count, RetentionTime.getRetentionTimeOffset());
#endif
}
return(processMS2(spec));
}
else
{
log.Debug("unrecognized msScan");
}
return(true);
}
protected bool processMS2(Spectra spec)
{
performanceEvaluator.countMS2();
log.Debug(spec);
IDs id = performDatabaseSearch(spec);
Boolean isExcluded = false;
if (id != null)
{
Peptide pep = getPeptideFromIdentification(id);
isExcluded = exclusionList.containsPeptide(pep);
}
if (isExcluded)
{
#if SIMULATION
//log.Debug("Mass " + spectraMass + " is on the exclusion list. Scan " + spec.getScanNum() + " excluded.");
evaluateExclusion(id);
WriterClass.LogScanTime("Excluded", (int)spec.getIndex());
#endif
performanceEvaluator.countExcludedSpectra();
excludedSpectra.Add(spec.getScanNum());
return(false);
}
else
{
performanceEvaluator.countAnalyzedSpectra();
//log.Debug("Mass " + spectraMass + " was not on the exclusion list. Scan " + spec.getScanNum() + " analyzed.");
evaluateIdentification(id);
includedSpectra.Add(spec.getScanNum());
// calibrate peptide if the observed retention time doesn't match the predicted
//WriterClass.LogScanTime("Processed", (int)spec.getIndex());
return(true);
}
}
public static void parseMZML()
{
String mzmlPath = "/Users/lavalleelab/Desktop/JoshLab/Temp/60minMZML.csv";
MZMLFile mzml = Loader.parseMZMLCSV(mzmlPath);
for (int i = 0; i < 7000; i++)
{
if (i % 500 == 0)
{
Spectra spec = mzml.getSpectraArray()[i];
Console.WriteLine("ID {0} scanNum{1} RT{2} Mass{3} MSLevel{4}", spec.getIndex(), spec.getScanNum(), spec.getStartTime(),
spec.getCalculatedPrecursorMass(), spec.getMSLevel());
}
}
}
protected bool processMS2(Spectra spec)
{
performanceEvaluator.countMS2();
log.Debug(spec);
IDs id = performDatabaseSearch(spec);
// check if mass is on exclusion list
Boolean isExcluded = false;
if (id != null)
{
Peptide pep = getPeptideFromIdentification(id);
isExcluded = exclusionList.containsPeptide(pep); //checks if the mass should've been excluded,
//in a real experiment, this should never equal to true
//since the mass should not have been scanned in the first place
//if MS exclusion table was updated correctly through API
if (!peptideRT.Keys.Contains(pep.getSequence()))
{
peptideRT.Add(pep.getSequence(), spec.getStartTime());
}
}
if (isExcluded)
{
#if SIMULATION
//log.Debug("Mass " + spectraMass + " is on the exclusion list. Scan " + spec.getScanNum() + " excluded.");
evaluateExclusion(id);
WriterClass.LogScanTime("Excluded", (int)spec.getIndex());
#endif
performanceEvaluator.countExcludedSpectra();
excludedSpectra.Add(spec.getScanNum());
return(false);
}
else
{
performanceEvaluator.countAnalyzedSpectra();
//log.Debug("Mass " + spectraMass + " was not on the exclusion list. Scan " + spec.getScanNum() + " analyzed.");
evaluateIdentification(id);
includedSpectra.Add(spec.getScanNum());
// calibrate peptide if the observed retention time doesn't match the predicted
//WriterClass.LogScanTime("Processed", (int)spec.getIndex());
return(true);
}
}
protected virtual bool processMS2(Spectra spec)
{
performanceEvaluator.countMS2();
log.Debug(spec);
// check if mass is on exclusion list
double spectraMass = spec.getCalculatedPrecursorMass();
Boolean isExcluded = exclusionList.isExcluded(spectraMass); //checks if the mass should've been excluded,
//in a real experiment, this should never equal to true
//since the mass should not have been scanned in the first place
//if MS exclusion table was updated correctly through API
if (isExcluded)
{
#if (SIMULATION)
IDs id = performDatabaseSearch(spec);
log.Debug("Mass " + spectraMass + " is on the exclusion list. Scan " + spec.getScanNum() + " excluded.");
evaluateExclusion(id);
WriterClass.LogScanTime("Excluded", (int)spec.getIndex());
#endif
performanceEvaluator.countExcludedSpectra();
excludedSpectra.Add(spec.getScanNum());
return(false);
}
else
{
IDs id = performDatabaseSearch(spec);
performanceEvaluator.countAnalyzedSpectra();
log.Debug("Mass " + spectraMass + " was not on the exclusion list. Scan " + spec.getScanNum() + " analyzed.");
evaluateIdentification(id);
includedSpectra.Add(spec.getScanNum());
// calibrate peptide if the observed retention time doesn't match the predicted
//WriterClass.LogScanTime("Processed", (int)spec.getIndex());
return(true);
}
}
