public List <ChromPeakQualityData> GetChromPeakQualityData(Run run, IqTarget target, List <Peak> chromPeakList)
{
var peakQualityList = new List <ChromPeakQualityData>();
if (MSGenerator == null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
MSGenerator.IsTICRequested = false;
}
//iterate over peaks within tolerance and score each peak according to MSFeature quality
#if DEBUG
var tempMinScanWithinTol = (int)run.NetAlignmentInfo.GetScanForNet(target.ElutionTimeTheor - Parameters.ChromNETTolerance);
var tempMaxScanWithinTol = (int)run.NetAlignmentInfo.GetScanForNet(target.ElutionTimeTheor + Parameters.ChromNETTolerance);
var tempCenterTol = (int)run.NetAlignmentInfo.GetScanForNet(target.ElutionTimeTheor);
Console.WriteLine("SmartPeakSelector --> NETTolerance= " + Parameters.ChromNETTolerance + "; chromMinCenterMax= " +
tempMinScanWithinTol + "\t" + tempCenterTol + "" +
"\t" + tempMaxScanWithinTol);
Console.WriteLine("MT= " + target.ID + ";z= " + target.ChargeState + "; mz= " + target.MZTheor.ToString("0.000") +
"; ------------------------- PeaksWithinTol = " + chromPeakList.Count);
#endif
//target.NumChromPeaksWithinTolerance = peaksWithinTol.Count;
foreach (ChromPeak chromPeak in chromPeakList)
{
// TODO: Currently hard-coded to sum only 1 scan
var lcscanset = _chromPeakUtilities.GetLCScanSetForChromPeak(chromPeak, run, 1);
//generate a mass spectrum
var massSpectrumXYData = MSGenerator.GenerateMS(run, lcscanset);
//find isotopic profile
var mspeakList = new List <Peak>();
var observedIso = TargetedMSFeatureFinder.IterativelyFindMSFeature(massSpectrumXYData, target.TheorIsotopicProfile, out mspeakList);
double fitScore = 1;
double iscore = 1;
//get fit score
fitScore = FitScoreCalc.CalculateFitScore(target.TheorIsotopicProfile, observedIso, massSpectrumXYData);
//get i_score
iscore = InterferenceScorer.GetInterferenceScore(target.TheorIsotopicProfile, mspeakList);
var leftOfMonoPeakLooker = new LeftOfMonoPeakLooker();
var peakToTheLeft = leftOfMonoPeakLooker.LookforPeakToTheLeftOfMonoPeak(target.TheorIsotopicProfile.getMonoPeak(), target.ChargeState,
mspeakList);
var hasPeakTotheLeft = peakToTheLeft != null;
//collect the results together
var pq = new ChromPeakQualityData(chromPeak);
if (observedIso == null)
{
pq.IsotopicProfileFound = false;
}
else
{
pq.IsotopicProfileFound = true;
pq.Abundance = observedIso.IntensityMostAbundant;
pq.FitScore = fitScore;
pq.InterferenceScore = iscore;
pq.IsotopicProfile = observedIso;
pq.IsIsotopicProfileFlagged = hasPeakTotheLeft;
pq.ScanLc = lcscanset.PrimaryScanNumber;
}
peakQualityList.Add(pq);
#if DEBUG
pq.Display();
#endif
}
return(peakQualityList);
}
public override void Execute(ResultCollection resultList)
{
Check.Require(resultList.Run.CurrentMassTag != null, this.Name + " failed. MassTag was not defined.");
var currentResult = resultList.GetTargetedResult(resultList.Run.CurrentMassTag);
if (msgen == null)
{
msgen = MSGeneratorFactory.CreateMSGenerator(resultList.Run.MSFileType);
msgen.IsTICRequested = false;
}
var currentTarget = resultList.Run.CurrentMassTag;
// Set the MS Generator to use a window around the target so that we do not grab a lot of unecessary data from the UIMF file
msgen.MinMZ = currentTarget.MZ - 10;
msgen.MaxMZ = currentTarget.MZ + 10;
float normalizedElutionTime;
if (currentResult.Run.CurrentMassTag.ElutionTimeUnit == DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum)
{
normalizedElutionTime = resultList.Run.CurrentMassTag.ScanLCTarget / (float)currentResult.Run.GetNumMSScans();
}
else
{
normalizedElutionTime = resultList.Run.CurrentMassTag.NormalizedElutionTime;
}
//collect Chrom peaks that fall within the NET tolerance
var peaksWithinTol = new List <ChromPeak>(); //
foreach (ChromPeak peak in resultList.Run.PeakList)
{
if (Math.Abs(peak.NETValue - normalizedElutionTime) <= Parameters.NETTolerance) //peak.NETValue was determined by the ChromPeakDetector or a future ChromAligner Task
{
peaksWithinTol.Add(peak);
}
}
var peakQualityList = new List <ChromPeakQualityData>();
//iterate over peaks within tolerance and score each peak according to MSFeature quality
#if DEBUG
var tempMinScanWithinTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime - Parameters.NETTolerance);
var tempMaxScanWithinTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime + Parameters.NETTolerance);
var tempCenterTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime);
Console.WriteLine("SmartPeakSelector --> NETTolerance= " + Parameters.NETTolerance + "; chromMinCenterMax= " + tempMinScanWithinTol + "\t" + tempCenterTol + "" +
"\t" + tempMaxScanWithinTol);
Console.WriteLine("MT= " + currentResult.Target.ID + ";z= " + currentResult.Target.ChargeState + "; mz= " + currentResult.Target.MZ.ToString("0.000") + "; ------------------------- PeaksWithinTol = " + peaksWithinTol.Count);
#endif
currentResult.NumChromPeaksWithinTolerance = peaksWithinTol.Count;
currentResult.NumQualityChromPeaks = -1;
ChromPeak bestChromPeak;
if (currentResult.NumChromPeaksWithinTolerance > _parameters.NumChromPeaksAllowed)
{
bestChromPeak = null;
}
else
{
foreach (var chromPeak in peaksWithinTol)
{
var pq = new ChromPeakQualityData(chromPeak);
peakQualityList.Add(pq);
// TODO: Currently hard-coded to sum only 1 scan
resultList.Run.CurrentScanSet = ChromPeakUtilities.GetLCScanSetForChromPeakUIMF(chromPeak, resultList.Run, 1);
//This resets the flags and the scores on a given result
currentResult.ResetResult();
//generate a mass spectrum
msgen.Execute(resultList);
//find isotopic profile
TargetedMSFeatureFinder.Execute(resultList);
//get fit score
fitScoreCalc.Execute(resultList);
//get i_score
resultValidator.Execute(resultList);
//collect the results together
AddScoresToPeakQualityData(pq, currentResult);
#if DEBUG
pq.Display();
#endif
}
//run a algorithm that decides, based on fit score mostly.
bestChromPeak = determineBestChromPeak(peakQualityList, currentResult);
}
currentResult.ChromPeakQualityList = peakQualityList;
resultList.Run.CurrentScanSet = ChromPeakUtilities.GetLCScanSetForChromPeakUIMF(bestChromPeak, resultList.Run, Parameters.NumScansToSum);
UpdateResultWithChromPeakAndLCScanInfo(currentResult, bestChromPeak);
}
public override void Execute(ResultCollection resultList)
{
Check.Require(resultList.Run.CurrentMassTag != null, this.Name + " failed. MassTag was not defined.");
var currentResult = resultList.GetTargetedResult(resultList.Run.CurrentMassTag);
if (msgen == null)
{
msgen = MSGeneratorFactory.CreateMSGenerator(resultList.Run.MSFileType);
msgen.IsTICRequested = false;
}
var mt = resultList.Run.CurrentMassTag;
float normalizedElutionTime;
if (currentResult.Run.CurrentMassTag.ElutionTimeUnit == DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum)
{
normalizedElutionTime = resultList.Run.CurrentMassTag.ScanLCTarget / (float)currentResult.Run.GetNumMSScans();
}
else
{
normalizedElutionTime = resultList.Run.CurrentMassTag.NormalizedElutionTime;
}
//collect Chrom peaks that fall within the NET tolerance
var peaksWithinTol = new List <ChromPeak>(); //
foreach (ChromPeak peak in resultList.Run.PeakList)
{
if (Math.Abs(peak.NETValue - normalizedElutionTime) <= Parameters.NETTolerance) //peak.NETValue was determined by the ChromPeakDetector or a future ChromAligner Task
{
peaksWithinTol.Add(peak);
}
}
var peakQualityList = new List <ChromPeakQualityData>();
//iterate over peaks within tolerance and score each peak according to MSFeature quality
var tempMinScanWithinTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime - Parameters.NETTolerance);
var tempMaxScanWithinTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime + Parameters.NETTolerance);
var tempCenterTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime);
IqLogger.Log.Debug("SmartPeakSelector --> NETTolerance= " + Parameters.NETTolerance + "; chromMinCenterMax= " + tempMinScanWithinTol + "\t" + tempCenterTol + "" +
"\t" + tempMaxScanWithinTol);
IqLogger.Log.Debug("MT= " + currentResult.Target.ID + ";z= " + currentResult.Target.ChargeState + "; mz= " + currentResult.Target.MZ.ToString("0.000") + "; ------------------------- PeaksWithinTol = " + peaksWithinTol.Count);
currentResult.NumChromPeaksWithinTolerance = peaksWithinTol.Count;
currentResult.NumQualityChromPeaks = -1;
ChromPeak bestChromPeak;
if (currentResult.NumChromPeaksWithinTolerance > _parameters.NumChromPeaksAllowed)
{
bestChromPeak = null;
}
else
{
foreach (var chromPeak in peaksWithinTol)
{
var pq = new ChromPeakQualityData(chromPeak);
peakQualityList.Add(pq);
var lcscanSet = ChromPeakUtilities.GetLCScanSetForChromPeak(chromPeak, resultList.Run, _parameters.NumMSSummedInSmartSelector);
resultList.Run.CurrentScanSet = lcscanSet;
//This resets the flags and the scores on a given result
currentResult.ResetResult();
//generate a mass spectrum
msgen.Execute(resultList);
//find isotopic profile
TargetedMSFeatureFinder.Execute(resultList);
try
{
//get fit score
fitScoreCalc.Execute(resultList);
//get i_score
resultValidator.Execute(resultList);
}
catch (Exception)
{
currentResult.FailedResult = true;
}
//collect the results together
AddScoresToPeakQualityData(pq, currentResult);
#if DEBUG
IqLogger.Log.Debug(pq.Display() + Environment.NewLine);
#endif
}
//run a algorithm that decides, based on fit score mostly.
bestChromPeak = determineBestChromPeak(peakQualityList, currentResult);
}
currentResult.ChromPeakQualityList = peakQualityList;
if (Parameters.SummingMode == SummingModeEnum.SUMMINGMODE_STATIC)
{
resultList.Run.CurrentScanSet = ChromPeakUtilities.GetLCScanSetForChromPeak(bestChromPeak, resultList.Run, Parameters.NumScansToSum);
}
else
{
resultList.Run.CurrentScanSet = ChromPeakUtilities.GetLCScanSetForChromPeakBasedOnPeakWidth(bestChromPeak, resultList.Run,
Parameters.AreaOfPeakToSumInDynamicSumming, Parameters.MaxScansSummedInDynamicSumming);
}
UpdateResultWithChromPeakAndLCScanInfo(currentResult, bestChromPeak);
}