/// <summary>
/// ChargeStateChildTopDownIqWorkflow
/// Generates theoretical isotopic profile, XIC, and creates ChromPeakIqTargets based on peaks found
/// </summary>
/// <param name="result"></param>
protected override void ExecuteWorkflow(IqResult result)
{
//Generate theoretical isotopic profile
result.Target.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(result.Target.EmpiricalFormula, result.Target.ChargeState);
if (!Parser.CheckSequenceIntegrity(result.Target.Code))
{
ShiftIsotopicProfile(result.Target.TheorIsotopicProfile, result.Target.MonoMassTheor, result.Target.ChargeState);
}
//Generate XIC and smooth
result.IqResultDetail.Chromatogram = ChromGen.GenerateChromatogram(Run, result.Target.TheorIsotopicProfile, result.Target.ElutionTimeTheor);
result.IqResultDetail.Chromatogram = ChromSmoother.Smooth(result.IqResultDetail.Chromatogram);
//Look for peaks in XIC
result.ChromPeakList = ChromPeakDetector.FindPeaks(result.IqResultDetail.Chromatogram);
ChromPeakDetector.CalculateElutionTimes(Run, result.ChromPeakList);
ChromPeakDetector.FilterPeaksOnNET(WorkflowParameters.ChromNETTolerance, result.Target.ElutionTimeTheor, result.ChromPeakList);
var tempMinScanWithinTol = (int)Run.NetAlignmentInfo.GetScanForNet(result.Target.ElutionTimeTheor - WorkflowParameters.ChromNETTolerance);
var tempMaxScanWithinTol = (int)Run.NetAlignmentInfo.GetScanForNet(result.Target.ElutionTimeTheor + WorkflowParameters.ChromNETTolerance);
var tempCenterTol = (int)Run.NetAlignmentInfo.GetScanForNet(result.Target.ElutionTimeTheor);
result.NumChromPeaksWithinTolerance = result.ChromPeakList.Count;
//General peak information output written to console.
Console.WriteLine("SmartPeakSelector --> NETTolerance= " + WorkflowParameters.ChromNETTolerance + "; chromMinCenterMax= " +
tempMinScanWithinTol + "\t" + tempCenterTol + "" +
"\t" + tempMaxScanWithinTol);
Console.WriteLine("MT= " + result.Target.ID + ";z= " + result.Target.ChargeState + "; mz= " + result.Target.MZTheor.ToString("0.000") +
"; ------------------------- PeaksWithinTol = " + result.ChromPeakList.Count);
//Creates a ChromPeakIqTarget for each peak found
foreach (ChromPeak peak in result.ChromPeakList)
{
var target = new ChromPeakIqTarget(new ChromPeakAnalyzerIqWorkflow(Run, WorkflowParameters));
TargetUtilities.CopyTargetProperties(result.Target, target, false);
target.ChromPeak = peak;
result.Target.AddTarget(target);
}
//Executes each grandchild ChromPeakAnalyzerIqWorkflow
var children = result.Target.ChildTargets();
foreach (var child in children)
{
child.DoWorkflow();
}
if (Utilities.SipperDataDump.OutputResults)
{
//Data Dump for use with Sipper
children = result.Target.ChildTargets();
foreach (var child in children)
{
Utilities.SipperDataDump.DataDump(child, Run);
}
}
}
protected override void ExecuteWorkflow(IqResult result)
{
if (ChromPeakAnalyzerIqWorkflow == null)
{
InitializeChromPeakAnalyzerWorkflow();
}
result.Target.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(result.Target.EmpiricalFormula, result.Target.ChargeState);
result.IqResultDetail.Chromatogram = ChromGen.GenerateChromatogram(Run, result.Target.TheorIsotopicProfile, result.Target.ElutionTimeTheor);
result.IqResultDetail.Chromatogram = ChromSmoother.Smooth(result.IqResultDetail.Chromatogram);
result.ChromPeakList = ChromPeakDetector.FindPeaks(result.IqResultDetail.Chromatogram);
ChromPeakDetector.CalculateElutionTimes(Run, result.ChromPeakList);
ChromPeakDetector.FilterPeaksOnNET(WorkflowParameters.ChromNETTolerance, result.Target.ElutionTimeTheor, result.ChromPeakList);
result.NumChromPeaksWithinTolerance = result.ChromPeakList.Count;
//Creates a ChromPeakIqTarget for each peak found
foreach (ChromPeak peak in result.ChromPeakList)
{
var target = new ChromPeakIqTarget(ChromPeakAnalyzerIqWorkflow);
TargetUtilities.CopyTargetProperties(result.Target, target, false);
target.ChromPeak = peak;
result.Target.AddTarget(target);
}
//Executes each grandchild ChromPeakAnalyzerIqWorkflow
var children = result.Target.ChildTargets();
var targetRemovalList = new List <IqTarget>();
foreach (var child in children)
{
child.DoWorkflow();
/*
* //Selects grandchildren with extremely poor metric scores for removal
* IqResult childResult = child.GetResult();
* if ((childResult.FitScore >= .8) || (childResult.CorrelationData.RSquaredValsMedian <= .15))
* {
* targetRemovalList.Add(child);
* }
*/
}
/*
* //Removes the poorly scoring grandchild ChromPeakIqTargets
* foreach (IqTarget iqTarget in targetRemovalList)
* {
* result.RemoveResult(iqTarget.GetResult());
* result.Target.RemoveTarget(iqTarget);
* }
*/
}
public UnevenChromSmoother(double rt_filter_len)
{
rt_filter_half_size = rt_filter_len / 2.0;
rt_per_filter_pt = rt_filter_len / sample_window_width;
weights = new float[sample_window_width];
//re-use the related class
ChromSmoother weight_factory = new ChromSmoother(sample_window_width);
weights = weight_factory.Weights;
}
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
}