public void getPeakChromAndStoreInPeakChromObject_Test1()
{
double chromToleranceInPPM = 20;
var targetMZ = 831.48;
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var chromGen = new ChromatogramGenerator();
PeakChrom chrom = new BasicPeakChrom();
chrom.ChromSourceData = chromGen.GeneratePeakChromatogram(run.ResultCollection.MSPeakResultList, run.MinLCScan, run.MaxLCScan, targetMZ, chromToleranceInPPM);
Assert.AreEqual(59, chrom.ChromSourceData.Count);
}
public override void Execute()
{
var uimfRun = (UIMFRun)this.Run;
//for each frame
foreach (var frame in uimfRun.ScanSetCollection.ScanSetList)
{
uimfRun.CurrentScanSet = frame;
// detect all peaks in frame
var masterPeakList = getAllPeaksInFrame(uimfRun, NumMSScansToSumWhenBuildingMasterPeakList);
// sort peaks
masterPeakList.Sort(delegate(MSPeakResult peak1, MSPeakResult peak2)
{
return(peak2.MSPeak.Height.CompareTo(peak1.MSPeak.Height));
});
// for each peak
var peakCounter = 0;
var peaksThatGenerateAChromatogram = 0;
foreach (var peak in masterPeakList)
{
peakCounter++;
//if (peakCounter > 500) break;
if (peak.MSPeak.Height < 1000)
{
break;
}
var peakFate = "Undefined";
var peakResultAlreadyIncludedInChromatogram = (peak.ChromID != -1);
if (peakResultAlreadyIncludedInChromatogram)
{
peakFate = "Chrom_Already";
displayPeakInfoAndFate(peak, peakFate);
continue;
}
else
{
peakFate = "CHROM";
//bool peakResultAlreadyFoundInAnMSFeature = findPeakWithinMSFeatureResults(run.ResultCollection.ResultList, peakResult, scanTolerance);
//if (peakResultAlreadyFoundInAnMSFeature)
//{
// peakFate = "MSFeature_Already";
//}
//else
//{
// peakFate = "CHROM";
//}
}
peaksThatGenerateAChromatogram++;
PeakChrom chrom = new BasicPeakChrom();
// create drift profile from raw data
var driftTimeProfileMZTolerance = this.DriftTimeProfileExtractionPPMTolerance * peak.MSPeak.XValue / 1e6;
//TODO: Fix this: update to use UIMF library and not DeconTools
//uimfRun.GetDriftTimeProfile (frame.PrimaryFrame, this.Run.MinScan, this.Run.MaxScan, peak.MSPeak.XValue, driftTimeProfileMZTolerance);
var driftTimeProfileIsEmpty = (uimfRun.XYData.Xvalues == null);
if (driftTimeProfileIsEmpty)
{
addPeakToProcessedPeakList(peak);
peakFate = peakFate + " DriftProfileEmpty";
displayPeakInfoAndFate(peak, peakFate);
continue;
}
chrom.XYData = uimfRun.XYData;
// smooth drift profile
chrom.XYData = ChromSmoother.Smooth(uimfRun.XYData);
// detect peaks in chromatogram
chrom.PeakList = this.ChromPeakDetector.FindPeaks(chrom.XYData, 0, 0);
if (chrom.PeakDataIsNullOrEmpty)
{
addPeakToProcessedPeakList(peak);
peakFate = peakFate + " NoChromPeaksDetected";
displayPeakInfoAndFate(peak, peakFate);
continue;
}
// find which drift profile peak, if any, the source peak is a member of
var chromPeak = chrom.GetChromPeakForGivenSource(peak);
if (chromPeak == null)
{
addPeakToProcessedPeakList(peak);
peakFate = peakFate + " TargetChromPeakNotFound";
displayPeakInfoAndFate(peak, peakFate);
continue;
}
// find other peaks in the master peaklist that are members of the found drift profile peak
// tag these peaks with the source peak's ID
var peakWidthSigma = chromPeak.Width / 2.35; // width@half-height = 2.35σ (Gaussian peak theory)
var minScanForChrom = (int)Math.Floor(chromPeak.XValue - peakWidthSigma * 4);
var maxScanForChrom = (int)Math.Floor(chromPeak.XValue + peakWidthSigma * 4);
var peakToleranceInMZ = driftTimeProfileMZTolerance;
var minMZForChromFilter = peak.MSPeak.XValue - peakToleranceInMZ;
var maxMZForChromFilter = peak.MSPeak.XValue + peakToleranceInMZ;
chrom.ChromSourceData = (from n in masterPeakList
where n.Scan_num >= minScanForChrom && n.Scan_num <= maxScanForChrom &&
n.MSPeak.XValue >= minMZForChromFilter && n.MSPeak.XValue < maxMZForChromFilter
select n).ToList();
foreach (var item in chrom.ChromSourceData)
{
item.ChromID = peak.PeakID;
}
displayPeakInfoAndFate(peak, peakFate);
}
Console.WriteLine("peaksProcessed = " + peakCounter);
Console.WriteLine("peaks generating a chrom = " + peaksThatGenerateAChromatogram);
}
// generate MS by integrating over drift profile peak
// find MS peaks within range
// find MS Features.
// find MS Feature for which the source peak is a member of.
// if found, add it.
// And, for each MS peaks of the found MS Feature, mark all peaks of the masterpeak list that correspond to the found drift time peak and m/z
}
public void ExecuteWorkflow2(DeconTools.Backend.Core.Run run)
{
double scanTolerance = 100;
Check.Require(run != null, String.Format("{0} failed. Run not defined.", this.Name));
Check.Require(run.ResultCollection != null && run.ResultCollection.MSPeakResultList != null && run.ResultCollection.MSPeakResultList.Count > 0,
String.Format("{0} failed. Workflow requires MSPeakResults, but these were not defined.", this.Name));
var sortedMSPeakResultList = run.ResultCollection.MSPeakResultList.OrderByDescending(p => p.MSPeak.Height).ToList();
var msGeneratorNeedsInitializing = (this.MSgen == null);
if (msGeneratorNeedsInitializing)
{
this.MSgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
}
var sw = new System.Diagnostics.Stopwatch();
var deconTimes = new List <long>();
var sb = new StringBuilder();
var totalPeaks = sortedMSPeakResultList.Count;
var counter = -1;
var whatPeakWentWhere = new Dictionary <int, string>();
var lastPeakResult = sortedMSPeakResultList.Last();
var chromPeaksCounter = 0;
foreach (var peakResult in sortedMSPeakResultList)
{
counter++;
//if (counter > 10000)
//{
// break;
//}
if (counter % 1000 == 0)
{
var logEntry = DateTime.Now + "\tWorking on peak " + counter + " of " + totalPeaks + "\tMSFeaturesCount =\t" + m_msFeatureCounter + "\tChomPeaks =\t" + chromPeaksCounter;
Logger.Instance.AddEntry(logEntry, m_logFileName);
Console.WriteLine(logEntry);
chromPeaksCounter = 0;
}
//if (peakResult.PeakID == 396293)
//{
// Console.WriteLine(DateTime.Now + "\tWorking on peak " + peakResult.PeakID);
//}
var peakFate = "Undefined";
var peakResultAlreadyIncludedInChromatogram = (peakResult.ChromID != -1);
if (peakResultAlreadyIncludedInChromatogram)
{
peakFate = "Chrom_Already";
}
else
{
var peakResultAlreadyFoundInAnMSFeature = findPeakWithinMSFeatureResults(run.ResultCollection.ResultList, peakResult, scanTolerance);
if (peakResultAlreadyFoundInAnMSFeature)
{
peakFate = "MSFeature_Already";
}
else
{
peakFate = "CHROM";
}
}
whatPeakWentWhere.Add(peakResult.PeakID, peakFate);
try
{
if (peakFate == "CHROM")
{
//generate chromatogram & tag MSPeakResults
var minScanForChrom = peakResult.Scan_num - (int)scanTolerance;
if (minScanForChrom < run.MinLCScan)
{
minScanForChrom = run.MinLCScan;
}
var maxScanForChrom = peakResult.Scan_num + (int)scanTolerance;
if (maxScanForChrom > run.MaxLCScan)
{
maxScanForChrom = run.MaxLCScan;
}
PeakChrom chrom = new BasicPeakChrom();
chrom.ChromSourceData = this.ChromGenerator.GeneratePeakChromatogram(run.ResultCollection.MSPeakResultList, minScanForChrom, maxScanForChrom,
peakResult.MSPeak.XValue, this.ChromGenToleranceInPPM);
if (chrom.IsNullOrEmpty)
{
continue;
}
chrom.XYData = chrom.GetXYDataFromChromPeakData(minScanForChrom, maxScanForChrom);
//remove points from chromatogram due to MS/MS level data
if (run.ContainsMSMSData)
{
chrom.XYData = filterOutMSMSRelatedPoints(run, chrom.XYData);
}
//smooth the chromatogram
chrom.XYData = this.ChromSmoother.Smooth(chrom.XYData);
//detect peaks in chromatogram
chrom.PeakList = this.ChromPeakDetector.FindPeaks(chrom.XYData, 0, 0);
//Console.WriteLine("source peak -> scan= " + peakResult.Scan_num + "; m/z= " + peakResult.MSPeak.XValue);
//chrom.XYData.Display();
if (!chrom.PeakDataIsNullOrEmpty)
{
var chromPeak = chrom.GetChromPeakForGivenSource(peakResult);
if (chromPeak == null)
{
continue;
}
var peakWidthSigma = chromPeak.Width / 2.35; // width@half-height = 2.35σ (Gaussian peak theory)
//now mark all peakResults that are members of this chromPeak
chrom.GetMSPeakMembersForGivenChromPeakAndAssignChromID(chromPeak, peakWidthSigma * 4, peakResult.PeakID);
run.CurrentScanSet = createScanSetFromChromatogramPeak(run, chromPeak);
var tempChromPeakMSFeatures = new List <IsosResult>();
MSgen.Execute(run.ResultCollection);
//trim the XYData to help the peak detector and Deconvolutor work faster
if (run.XYData == null)
{
continue;
}
run.XYData = run.XYData.TrimData(peakResult.MSPeak.XValue - 2, peakResult.MSPeak.XValue + 2);
if (run.XYData == null || run.XYData.Xvalues == null || run.XYData.Xvalues.Length == 0)
{
continue;
}
this.MSPeakDetector.Execute(run.ResultCollection);
//HACK: calling 'deconvolute' will write results to 'isosResultBin' but not to 'ResultList'; I will manually add what I want to the official 'ResultList'
run.ResultCollection.IsosResultBin.Clear();
this.Deconvolutor.Deconvolute(run.ResultCollection);
this.Validator.Execute(run.ResultCollection);
//now, look in the isosResultBin and see what IsosResult (if any) the source peak is a member of
var msfeature = getMSFeatureForCurrentSourcePeak(peakResult, run);
//Console.WriteLine("source peak -> peakID= " + peakResult.PeakID + ";scan= " + peakResult.Scan_num + "; m/z= " + peakResult.MSPeak.XValue);
if (msfeature == null) // didn't find a feature. Source peak might be a 'lone wolf'
{
//Console.WriteLine("No MSFeature found!");
}
else
{
//Console.WriteLine("!!!!!!! MSFeature found!");
double toleranceInMZ = peakResult.MSPeak.Width / 2;
var msFeatureAlreadyExists = checkIfMSFeatureAlreadyExists(msfeature, run.ResultCollection.ResultList, toleranceInMZ, peakWidthSigma);
if (msFeatureAlreadyExists)
{
//Console.WriteLine("---- but MSFeature was already present");
}
else
{
//generate chromatograms and tag other peak members of the isotopic profile...
foreach (var isoPeak in msfeature.IsotopicProfile.Peaklist)
{
PeakChrom isoPeakChrom = new BasicPeakChrom();
isoPeakChrom.ChromSourceData = this.ChromGenerator.GeneratePeakChromatogram(run.ResultCollection.MSPeakResultList, minScanForChrom, maxScanForChrom,
isoPeak.XValue, this.ChromGenToleranceInPPM);
if (!isoPeakChrom.IsNullOrEmpty)
{
isoPeakChrom.GetMSPeakMembersForGivenChromPeakAndAssignChromID(chromPeak, peakWidthSigma * 4, peakResult.PeakID);
}
}
run.ResultCollection.ResultList.Add(msfeature);
m_msFeatureCounter++;
}
}
//Console.WriteLine();
}
}
}
catch (Exception ex)
{
Logger.Instance.AddEntry("ERROR: peakID = " + peakResult.PeakID + "\t" + ex.Message + ";\t" + ex.StackTrace, m_logFileName);
}
var triggerToExport = 10;
if (run.ResultCollection.ResultList.Count > triggerToExport)
{
isosExporter.ExportResults(run.ResultCollection.ResultList);
run.ResultCollection.ResultList.Clear();
exportPeakData(run, m_peakOutputFileName, whatPeakWentWhere);
whatPeakWentWhere.Clear();
}
}
//needs clean up.... sometimes there might be a case where the above loop is broken and we need the last few results written out.
isosExporter.ExportResults(run.ResultCollection.ResultList);
run.ResultCollection.ResultList.Clear();
exportPeakData(run, m_peakOutputFileName, whatPeakWentWhere);
whatPeakWentWhere.Clear();
//foreach (var item in deconTimes)
//{
// Console.WriteLine(item);
//}
//Console.WriteLine("Average = " + deconTimes.Average());
//Console.WriteLine("Top 50 = " + deconTimes.Take(50).Average());
//Console.WriteLine("Next 50 = " + deconTimes.Skip(50).Take(50).Average());
//Console.WriteLine(sb.ToString());
}
