private void GetDataFromFavoriteChild(IqResult result)
{
var fav = result.FavoriteChild;
if (fav == null)
{
result.LCScanSetSelected = null;
result.LcScanObs = -1;
result.MZObs = 0;
result.MZObsCalibrated = 0;
result.Abundance = 0;
result.ElutionTimeObs = -1;
result.IsotopicProfileFound = false;
result.InterferenceScore = 1;
result.FitScore = 1;
result.MassErrorBefore = 0;
result.MassErrorAfter = 0;
result.MonoMassObs = 0;
result.MonoMassObsCalibrated = 0;
}
else
{
result.LCScanSetSelected = fav.LCScanSetSelected;
result.LcScanObs = fav.LcScanObs;
result.CorrelationData = fav.CorrelationData;
result.FitScore = fav.FitScore;
result.ChromPeakSelected = fav.ChromPeakSelected;
result.MZObs = fav.MZObs;
result.MZObsCalibrated = fav.MZObsCalibrated;
result.MonoMassObs = fav.MonoMassObs;
result.MonoMassObsCalibrated = fav.MonoMassObsCalibrated;
result.ElutionTimeObs = fav.ElutionTimeObs;
result.Abundance = fav.ChromPeakSelected == null ? 0f : fav.ChromPeakSelected.Height;
}
}
/// <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 void RemoveResult(IqResult result)
{
foreach (var childResult in result._childResults)
{
childResult.ParentResult = result.ParentResult;
result.ParentResult._childResults.Add(childResult);
}
result.ParentResult._childResults.Remove(result);
}
protected override void ExecuteWorkflow(IqResult result)
{
//Executes the ChargeState level children workflows
var children = result.Target.ChildTargets();
foreach (var child in children)
{
child.DoWorkflow();
}
}
private void ExportChromGraph(IqResult result)
{
if (result.IqResultDetail.Chromatogram == null)
{
return;
}
var minScan = result.LcScanObs - 1000;
var maxScan = result.LcScanObs + 1000;
_graphGenerator.GraphHeight = 600;
_graphGenerator.GraphWidth = 800;
result.IqResultDetail.Chromatogram = result.IqResultDetail.Chromatogram.TrimData(minScan, maxScan);
_graphGenerator.GenerateGraph(result.IqResultDetail.Chromatogram.Xvalues, result.IqResultDetail.Chromatogram.Yvalues);
var line = _graphGenerator.GraphPane.CurveList[0] as LineItem;
line.Line.IsVisible = true;
line.Symbol.Size = 3;
line.Line.Width = 2;
line.Symbol.Type = SymbolType.None;
line.Color = Color.Black;
_graphGenerator.GraphPane.XAxis.Title.Text = "scan";
_graphGenerator.GraphPane.YAxis.Title.Text = "intensity";
_graphGenerator.GraphPane.XAxis.Scale.MinAuto = false;
_graphGenerator.GraphPane.XAxis.Scale.MaxAuto = false;
_graphGenerator.GraphPane.YAxis.Scale.MinAuto = false;
_graphGenerator.GraphPane.YAxis.Scale.MaxAuto = false;
_graphGenerator.GraphPane.YAxis.Scale.Min = 0;
_graphGenerator.GraphPane.YAxis.Scale.Max = result.IqResultDetail.Chromatogram.getMaxY();
_graphGenerator.GraphPane.YAxis.Scale.Format = "0";
_graphGenerator.GraphPane.XAxis.Scale.Min = minScan;
_graphGenerator.GraphPane.XAxis.Scale.Max = maxScan;
_graphGenerator.GraphPane.XAxis.Scale.FontSpec.Size = 12;
var outputGraphFilename = Path.Combine(OutputFolderForGraphs,
result.Target.ID + "_" +
result.Target.ChargeState + "_" +
result.Target.MZTheor.ToString("0.000") + "_chrom.png");
var graphInfoText = "ID= " + result.Target.ID + "; z= " + result.Target.ChargeState + "; m/z= " +
result.Target.MZTheor.ToString("0.000") + "; ScanLC= " + result.LcScanObs;
_graphGenerator.AddAnnotationRelativeAxis(graphInfoText, 0.3, 0.02);
_graphGenerator.AddVerticalLineToGraph(result.LcScanObs, 1);
_graphGenerator.AddAnnotationAbsoluteXRelativeY("*", result.Target.MZTheor, 0.03);
_graphGenerator.SaveGraph(outputGraphFilename);
}
/// <summary>
/// Performs charge correlation on parent level target
/// </summary>
/// <param name="result"></param>
private void PerformChargeCorrelation(IqResult result)
{
var iqChargeCorrelator = ChromatogramCorrelator as IqChargeCorrelator;
var topDownIqResult = result as TopDownIqResult;
if (iqChargeCorrelator != null && topDownIqResult != null)
{
topDownIqResult.ChargeCorrelationData = iqChargeCorrelator.CorrelateData(GetAllChromPeakIqTargets(result), Run);
}
else
{
throw new Exception("IqChargeCorrelator and/or TopDownIqResult is not compatible");
}
}
private void getRsquaredVal(IqResult result, out double?rsquaredVal, out double?slope)
{
if (result.CorrelationData != null && result.CorrelationData.CorrelationDataItems.Count > 0)
{
rsquaredVal = result.CorrelationData.RSquaredValsMedian;
slope = result.CorrelationData.CorrelationDataItems.First().CorrelationSlope;
}
else
{
rsquaredVal = -1;
slope = -1;
}
}
private void ExportGraphs(IqResult result)
{
if (string.IsNullOrEmpty(OutputFolderForGraphs))
{
OutputFolderForGraphs = Path.Combine(Run.DataSetPath, "OutputGraphs");
}
if (!Directory.Exists(OutputFolderForGraphs))
{
Directory.CreateDirectory(OutputFolderForGraphs);
}
ExportMassSpectrumGraph(result);
ExportChromGraph(result);
}
/// <summary>
/// Returns a list of all ChromPeakIqTarget objects under a parent target
/// </summary>
/// <param name="result"></param>
/// <returns></returns>
private List <ChromPeakIqTarget> GetAllChromPeakIqTargets(IqResult result)
{
var chromPeakTargets = new List <ChromPeakIqTarget>();
var children = result.Target.ChildTargets();
foreach (var child in children)
{
var grandchildTargets = child.ChildTargets();
foreach (ChromPeakIqTarget target in grandchildTargets)
{
chromPeakTargets.Add(target);
}
}
return(chromPeakTargets);
}
/// <summary>
/// Parent level workflow for Top-Down IQ analysis
/// </summary>
/// <param name="result"></param>
protected override void ExecuteWorkflow(IqResult result)
{
//Executes the ChargeState level children workflows
var children = result.Target.ChildTargets();
foreach (var child in children)
{
child.DoWorkflow();
}
PerformChargeCorrelation(result);
var referenceTarget = TargetSelector((TopDownIqResult)result);
ExpandChargeRange((TopDownIqTarget)result.Target, referenceTarget);
}
protected override void ExportResults(IqResult iqResult)
{
var resultsForExport = _iqResultUtilities.FlattenOutResultTree(iqResult);
var orderedResults = resultsForExport.OrderBy(p => p.Target.ChargeState).ToList();
var exportedResults = orderedResults.Where(orderedResult => orderedResult.IsExported).ToList();
if (IqResultExporter == null)
{
IqResultExporter = iqResult.Target.Workflow.CreateExporter();
}
SetupResultsFolder();
IqResultExporter.WriteOutResults(Path.Combine(_resultsFolder, Run.DatasetName), exportedResults);
}
private IqResult SelectBestChargeStateChildResult(IqResult result)
{
var filteredChargeStateResults = result.ChildResults().Where(p => p.FavoriteChild != null).ToList();
if (filteredChargeStateResults.Count == 0)
{
return(null);
}
if (filteredChargeStateResults.Count == 1)
{
return(filteredChargeStateResults.First());
}
//now to deal with the tough issue of multiple charge states having a possible results.
var filter2 = filteredChargeStateResults.Where(p => p.CorrelationData.CorrelationDataItems.First().CorrelationRSquaredVal > 0.7).ToList();
if (filter2.Count == 0)
{
filter2 = filteredChargeStateResults.Where(p => p.CorrelationData.CorrelationDataItems.First().CorrelationRSquaredVal > 0.5).ToList();
}
if (filter2.Count == 0)
{
filter2 = filteredChargeStateResults.Where(p => p.CorrelationData.CorrelationDataItems.First().CorrelationRSquaredVal > 0.3).ToList();
}
if (filter2.Count == 0)
{
//correlation values are no good. Now will sort by fit score.
filter2 = filteredChargeStateResults.OrderBy(p => p.FitScore).Take(1).ToList(); //sort by fit score let the first one be selected
}
if (filter2.Count == 1)
{
return(filter2.First());
}
else if (filter2.Count > 1)
{
//if we reached here, there are multiple charge state results with good correlation scores. Take the one of highest intensity.
return(filter2.OrderByDescending(p => p.Abundance).First());
}
return(null);
}
public List <IqResult> FlattenOutResultTree(IqResult iqResult)
{
var flattenedResults = new List <IqResult>();
if (iqResult.HasChildren())
{
var childresults = iqResult.ChildResults();
foreach (var childResult in childresults)
{
var moreResults = FlattenOutResultTree(childResult);
flattenedResults.AddRange(moreResults);
}
}
flattenedResults.Add(iqResult);
return(flattenedResults);
}
private void ExportMassSpectrumGraph(IqResult result)
{
_graphGenerator.GraphHeight = 600;
_graphGenerator.GraphWidth = 800;
_graphGenerator.GenerateGraph(result.IqResultDetail.MassSpectrum.Xvalues, result.IqResultDetail.MassSpectrum.Yvalues);
var line = _graphGenerator.GraphPane.CurveList[0] as LineItem;
line.Line.IsVisible = true;
line.Symbol.Size = 3;
line.Line.Width = 2;
line.Symbol.Type = SymbolType.None;
line.Color = Color.Black;
_graphGenerator.GraphPane.XAxis.Title.Text = "m/z";
_graphGenerator.GraphPane.YAxis.Title.Text = "intensity";
_graphGenerator.GraphPane.XAxis.Scale.MinAuto = true;
_graphGenerator.GraphPane.YAxis.Scale.MinAuto = false;
_graphGenerator.GraphPane.YAxis.Scale.MaxAuto = false;
_graphGenerator.GraphPane.YAxis.Scale.Min = 0;
_graphGenerator.GraphPane.YAxis.Scale.Max = result.IqResultDetail.MassSpectrum.getMaxY();
_graphGenerator.GraphPane.YAxis.Scale.Format = "0";
_graphGenerator.GraphPane.XAxis.Scale.FontSpec.Size = 12;
var outputGraphFilename = Path.Combine(OutputFolderForGraphs,
result.Target.ID + "_" +
result.Target.ChargeState + "_" +
result.Target.MZTheor.ToString("0.000") + "_MS.png");
var graphInfoText = "ID= " + result.Target.ID + "; z= " + result.Target.ChargeState + "; m/z= " +
result.Target.MZTheor.ToString("0.000") + "; ScanLC= " + result.LcScanObs;
_graphGenerator.AddAnnotationRelativeAxis(graphInfoText, 0.3, 0.02);
_graphGenerator.AddAnnotationAbsoluteXRelativeY("*", result.Target.MZTheor, 0.03);
_graphGenerator.SaveGraph(outputGraphFilename);
}
//Writes IqResult Data to Console
private void Display(IqResult result)
{
var target = result.Target as ChromPeakIqTarget;
if (target == null)
{
throw new NullReferenceException("The ChromPeakAnalyzerIqWorkflow only works with the ChromPeakIqTarget. "
+ "Due to an inherent shortcoming of the design pattern we used, we were unable to make this a compile time error instead of a runtime error. "
+ "Please change the IqTarget to ChromPeakIqTarget for proper use of the ChromPeakAnalyzerIqWorkflow.");
}
if (!_headerLogged)
{
_headerLogged = true;
IqLogger.Log.Debug(("\t\t" + "ChromPeak.XValue" + "\t" + "NETError" + "\t" + "MassError" + "\t" + "FitScore" + "\t" + "IsIsotopicProfileFlagged"));
}
IqLogger.Log.Debug(("\t\t" + target.ChromPeak.XValue.ToString("0.00") + "\t" + result.NETError.ToString("0.0000") + "\t" + result.MassErrorBefore.ToString("0.0000") + "\t" +
result.FitScore.ToString("0.0000") + "\t" + result.IsIsotopicProfileFlagged));
}
protected virtual float GetAbundance(IqResult result)
{
if (result.ObservedIsotopicProfile == null)
{
return(0);
}
var indexMostAbundantPeakTheor = result.Target.TheorIsotopicProfile.GetIndexOfMostIntensePeak();
if (result.ObservedIsotopicProfile.Peaklist.Count > indexMostAbundantPeakTheor)
{
result.ObservedIsotopicProfile.IntensityMostAbundantTheor = result.ObservedIsotopicProfile.Peaklist[indexMostAbundantPeakTheor].Height;
}
else
{
result.ObservedIsotopicProfile.IntensityMostAbundantTheor = result.ObservedIsotopicProfile.IntensityMostAbundant;
}
return(result.ObservedIsotopicProfile.IntensityMostAbundantTheor);
}
protected virtual void ExecutePostWorkflowHook(IqResult result)
{
if (result != null && Success)
{
WorkflowStatusMessage = "IqTarget " + result.Target.ID + "; m/z= " + result.Target.Code;
//if (Result.FailedResult == false)
//{
// if (Result.IsotopicProfile != null)
// {
// WorkflowStatusMessage = WorkflowStatusMessage + "; Target FOUND!";
// }
//}
//else
//{
// WorkflowStatusMessage = WorkflowStatusMessage + "; Target NOT found. Reason: " + Result.FailureType;
//}
}
}
public virtual void Execute(IqResult result)
{
Check.Require(this.Run != null, "Error in IqWorkflow.Execute: Run has not been defined.");
if (!IsWorkflowInitialized)
{
InitializeWorkflow();
}
try
{
ExecuteWorkflow(result);
ExecutePostWorkflowHook(result);
}
catch (Exception ex)
{
var errorMessage = "Critical error!!!! " + ex.Message + "; processing IqTargetID = " + result.Target.ID + "; charge = " + result.Target.ChargeState +
"; sequence= " + result.Target.Code + "; ScanLC= " + result.Target.ScanLC;
Console.WriteLine(errorMessage);
throw new ApplicationException(errorMessage, ex);
}
}
protected virtual void ExecuteWorkflow(IqResult result)
{
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.IqResultDetail.ChromPeakQualityData = ChromPeakAnalyzer.GetChromPeakQualityData(Run, result.Target, result.ChromPeakList);
var filterOutFlagged = result.Target.TheorIsotopicProfile.GetIndexOfMostIntensePeak() == 0;
result.ChromPeakSelected = ChromPeakSelector.SelectBestPeak(result.IqResultDetail.ChromPeakQualityData, filterOutFlagged);
result.LCScanSetSelected = ChromPeakUtilities.GetLCScanSetForChromPeak(result.ChromPeakSelected, Run,
WorkflowParameters.NumMSScansToSum);
result.LcScanObs = result.LCScanSetSelected == null ? -1 : result.LCScanSetSelected.PrimaryScanNumber;
result.IqResultDetail.MassSpectrum = MSGenerator.GenerateMS(Run, result.LCScanSetSelected);
TrimData(result.IqResultDetail.MassSpectrum, result.Target.MZTheor, MsLeftTrimAmount, MsRightTrimAmount);
List <Peak> mspeakList;
result.ObservedIsotopicProfile = MsfeatureFinder.IterativelyFindMSFeature(result.IqResultDetail.MassSpectrum, result.Target.TheorIsotopicProfile, out mspeakList);
result.FitScore = FitScoreCalc.CalculateFitScore(result.Target.TheorIsotopicProfile, result.ObservedIsotopicProfile,
result.IqResultDetail.MassSpectrum);
result.InterferenceScore = InterferenceScorer.GetInterferenceScore(result.ObservedIsotopicProfile, mspeakList);
//if (_workflowParameters.ChromatogramCorrelationIsPerformed)
//{
// ExecuteTask(_chromatogramCorrelator);
//}
result.MonoMassObs = result.ObservedIsotopicProfile == null ? 0 : result.ObservedIsotopicProfile.MonoIsotopicMass;
result.MZObs = result.ObservedIsotopicProfile == null ? 0 : result.ObservedIsotopicProfile.MonoPeakMZ;
result.MZObsCalibrated = result.ObservedIsotopicProfile == null ? 0 : Run.GetAlignedMZ(result.ObservedIsotopicProfile.MonoPeakMZ, result.LcScanObs);
result.MonoMassObsCalibrated = result.ObservedIsotopicProfile == null
? 0
: (result.MZObsCalibrated - DeconTools.Backend.Globals.PROTON_MASS) * result.Target.ChargeState;
var elutionTime = result.ChromPeakSelected == null ? 0d : ((ChromPeak)result.ChromPeakSelected).NETValue;
result.ElutionTimeObs = elutionTime;
result.Abundance = GetAbundance(result);
}
protected void ReportProcessingProgress(string reportString, int progressCounter, IqResult result)
{
if (_backgroundWorker == null)
{
if (progressCounter % 100 == 0)
{
Console.WriteLine(DateTime.Now + "\t" + reportString);
}
}
else
{
//TODO: fix this
int progressPercent = 0;
_backgroundWorker.ReportProgress(progressPercent, result);
}
if (progressCounter % 100 == 0)
{
writeToLogFile(DateTime.Now + "\t" + reportString);
}
}
protected override void ExecuteWorkflow(IqResult result)
{
var children = result.Target.ChildTargets().ToList();
foreach (var child in children)
{
child.DoWorkflow();
var childResult = child.GetResult();
var chromPeakLevelResults = childResult.ChildResults();
var filteredChromPeakResults = chromPeakLevelResults.Where(r => r.IsotopicProfileFound).ToList();
childResult.FavoriteChild = SelectBestChromPeakIqResult(childResult, filteredChromPeakResults);
GetDataFromFavoriteChild(childResult);
}
result.FavoriteChild = SelectBestChargeStateChildResult(result);
GetDataFromFavoriteChild(result);
var favResult = result.FavoriteChild;
double?rsquaredVal, slope;
getRsquaredVal(result, out rsquaredVal, out slope);
var favChargeState = result.FavoriteChild == null ? 0 : result.FavoriteChild.Target.ChargeState;
var favMz = result.FavoriteChild == null ? 0 : result.FavoriteChild.Target.MZTheor;
if (!_headerLogged)
{
_headerLogged = true;
IqLogger.Log.Info("\t" + "TargetID" + "\t\t\t" + "M/Z" + "\t" + "Charge" + "\t" + "LCScan" + "\t" + "RSquared" + "\t" + "Slope");
}
IqLogger.Log.Info("\t" + result.Target.ID + "\t\t\t" + favMz.ToString("0.000") + "\t" + favChargeState + "\t" + result.LcScanObs + "\t" + rsquaredVal + "\t" + slope);
//now get the mass spectrum given the info from the favorite child charge state result
if (favResult != null)
{
var scanset = new ScanSetFactory().CreateScanSet(Run, favResult.LCScanSetSelected.PrimaryScanNumber,
WorkflowParameters.NumMSScansToSum);
var selectedChromPeak = favResult.ChromPeakSelected;
var sigma = selectedChromPeak.Width / 2.35;
var chromScanWindowWidth = 4 * sigma;
//Determines where to start and stop chromatogram correlation
var startScan = scanset.PrimaryScanNumber - (int)Math.Round(chromScanWindowWidth / 2, 0);
var stopScan = scanset.PrimaryScanNumber + (int)Math.Round(chromScanWindowWidth / 2, 0);
var massSpectrum = MSGenerator.GenerateMS(Run, scanset);
foreach (var iqTarget in children)
{
var childStateIqResult = (O16O18IqResult)iqTarget.GetResult();
childStateIqResult.IqResultDetail.MassSpectrum = massSpectrum.TrimData(iqTarget.MZTheor - 3, iqTarget.MZTheor + 8);
var mspeakList = _mspeakDetector.FindPeaks(childStateIqResult.IqResultDetail.MassSpectrum.Xvalues,
childStateIqResult.IqResultDetail.MassSpectrum.Yvalues);
childStateIqResult.CorrelationData = ChromatogramCorrelator.CorrelateData(Run, childStateIqResult, startScan, stopScan);
childStateIqResult.CorrelationO16O18SingleLabel = childStateIqResult.GetCorrelationO16O18SingleLabel();
childStateIqResult.CorrelationO16O18DoubleLabel = childStateIqResult.GetCorrelationO16O18DoubleLabel();
childStateIqResult.CorrelationBetweenSingleAndDoubleLabel = childStateIqResult.GetCorrelationBetweenSingleAndDoubleLabel();
childStateIqResult.RatioO16O18DoubleLabel = childStateIqResult.GetRatioO16O18DoubleLabel();
childStateIqResult.RatioO16O18SingleLabel = childStateIqResult.GetRatioO16O18SingleLabel();
childStateIqResult.RatioSingleToDoubleLabel = childStateIqResult.GetRatioSingleToDoubleLabel();
childStateIqResult.ObservedIsotopicProfile = MsfeatureFinder.IterativelyFindMSFeature(childStateIqResult.IqResultDetail.MassSpectrum,
iqTarget.TheorIsotopicProfile);
if (childStateIqResult.ObservedIsotopicProfile != null)
{
var observedIsoList = childStateIqResult.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Take(4).ToList(); //first 4 peaks excludes the O18 double label peak (fifth peak)
var theorPeakList = iqTarget.TheorIsotopicProfile.Peaklist.Select(p => (Peak)p).Take(4).ToList();
childStateIqResult.FitScore = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
var o18Iso = childStateIqResult.ConvertO16ProfileToO18(iqTarget.TheorIsotopicProfile, 4);
theorPeakList = o18Iso.Peaklist.Select(p => (Peak)p).ToList();
observedIsoList = childStateIqResult.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Skip(4).ToList(); //skips the first 4 peaks and thus includes the O18 double label isotopic profile
childStateIqResult.FitScoreO18Profile = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
childStateIqResult.InterferenceScore = InterferenceScorer.GetInterferenceScore(childStateIqResult.ObservedIsotopicProfile, mspeakList);
childStateIqResult.MZObs = childStateIqResult.ObservedIsotopicProfile.MonoPeakMZ;
childStateIqResult.MonoMassObs = childStateIqResult.ObservedIsotopicProfile.MonoIsotopicMass;
childStateIqResult.MZObsCalibrated = Run.GetAlignedMZ(childStateIqResult.MZObs);
childStateIqResult.MonoMassObsCalibrated = (childStateIqResult.MZObsCalibrated - DeconTools.Backend.Globals.PROTON_MASS) * childStateIqResult.Target.ChargeState;
childStateIqResult.ElutionTimeObs = ((ChromPeak)favResult.ChromPeakSelected).NETValue;
}
else
{
childStateIqResult.FitScore = -1;
childStateIqResult.InterferenceScore = -1;
}
getRsquaredVal(childStateIqResult, out rsquaredVal, out slope);
IqLogger.Log.Info("\t\t\t" + childStateIqResult.Target.ID + "\t" + childStateIqResult.Target.MZTheor.ToString("0.000") + "\t" + childStateIqResult.Target.ChargeState
+ "\t" + childStateIqResult.LcScanObs + "\t" + childStateIqResult.FitScore.ToString("0.000") + "\t" + rsquaredVal + "\t" + slope);
childStateIqResult.LCScanSetSelected = favResult.LCScanSetSelected;
childStateIqResult.LcScanObs = favResult.LcScanObs;
if (GraphsAreOutputted)
{
if (_graphGenerator == null)
{
_graphGenerator = new BasicGraphControl();
}
ExportGraphs(childStateIqResult);
}
}
}
}
private IqResult SelectBestChromPeakIqResult(IqResult childResult, List <IqResult> filteredChromPeakResults)
{
var numCandidateResults = filteredChromPeakResults.Count;
IqResult bestChromPeakResult = null;
if (numCandidateResults == 0)
{
bestChromPeakResult = null;
}
else if (numCandidateResults == 1)
{
bestChromPeakResult = filteredChromPeakResults.First();
}
else
{
var furtherFilteredResults = new List <IqResult>();
double lowestFit = 1;
foreach (O16O18IqResult r in filteredChromPeakResults)
{
var currentLowFitVal = Math.Min(r.FitScore, r.FitScoreO18Profile);
if (currentLowFitVal < lowestFit)
{
lowestFit = currentLowFitVal;
if (lowestFit < 0.2)
{
furtherFilteredResults.Add(r);
}
}
}
if (furtherFilteredResults.Count == 0) // all potential candidates were filtered out above. So need a plan B.
{
bestChromPeakResult = filteredChromPeakResults.OrderBy(p => p.FitScore).Take(3).OrderByDescending(p => p.Abundance).FirstOrDefault();
}
else if (furtherFilteredResults.Count == 1)
{
bestChromPeakResult = furtherFilteredResults.First();
}
else //still more than one candidate. Will try to use another filter
{
var currentBestChromPeakResult = furtherFilteredResults.OrderByDescending(p => p.Abundance).FirstOrDefault();
var level3FilteredResults = new List <IqResult>();
foreach (O16O18IqResult furtherFilteredResult in furtherFilteredResults)
{
var currentCorrVal = Math.Max(furtherFilteredResult.GetCorrelationO16O18DoubleLabel(), furtherFilteredResult.GetCorrelationBetweenSingleAndDoubleLabel());
if (currentCorrVal > 0.7)
{
level3FilteredResults.Add(furtherFilteredResult);
}
}
if (level3FilteredResults.Count == 0)
{
bestChromPeakResult = currentBestChromPeakResult;
}
else if (level3FilteredResults.Count == 1)
{
bestChromPeakResult = level3FilteredResults.First();
}
else
{
//fit score is good. Correlation good. But still have multiple possibilities
bestChromPeakResult = level3FilteredResults.OrderByDescending(p => p.Abundance).First();
}
}
}
if (bestChromPeakResult != null)
{
childResult.CorrelationData = bestChromPeakResult.CorrelationData;
childResult.LcScanObs = bestChromPeakResult.LcScanObs;
childResult.ChromPeakSelected = bestChromPeakResult.ChromPeakSelected; //check this
childResult.LCScanSetSelected = bestChromPeakResult.LCScanSetSelected;
var elutionTime = childResult.ChromPeakSelected == null
? 0d
: ((ChromPeak)bestChromPeakResult.ChromPeakSelected).NETValue;
childResult.ElutionTimeObs = elutionTime;
childResult.Abundance = (float)(childResult.ChromPeakSelected == null
? 0d
: ((ChromPeak)bestChromPeakResult.ChromPeakSelected).Height);
}
return(bestChromPeakResult);
}
/// <summary>
/// Calculates Metrics based on ChromPeakIqTarget
/// NET Error, Mass Error, Isotopic Fit, & Isotope Correlation
/// </summary>
protected override void ExecuteWorkflow(IqResult result)
{
result.IsExported = false;
if (MSGenerator == null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
MSGenerator.IsTICRequested = false;
}
var target = result.Target as ChromPeakIqTarget;
if (target == null)
{
throw new NullReferenceException("The ChromPeakAnalyzerIqWorkflow only works with the ChromPeakIqTarget.");
}
var lcscanset = _chromPeakUtilities.GetLCScanSetForChromPeak(target.ChromPeak, Run, WorkflowParameters.SmartChromPeakSelectorNumMSSummed);
//Generate a mass spectrum
var massSpectrumXYData = MSGenerator.GenerateMS(Run, lcscanset);
massSpectrumXYData = massSpectrumXYData.TrimData(result.Target.MZTheor - 5, result.Target.MZTheor + 15);
//Find isotopic profile
List <Peak> mspeakList;
result.ObservedIsotopicProfile = TargetedMSFeatureFinder.IterativelyFindMSFeature(massSpectrumXYData, target.TheorIsotopicProfile, out mspeakList);
//Default Worst Scores
double iscore = 1;
//Get NET Error
var netError = target.ChromPeak.NETValue - target.ElutionTimeTheor;
var leftOfMonoPeakLooker = new LeftOfMonoPeakLooker();
var peakToTheLeft = leftOfMonoPeakLooker.LookforPeakToTheLeftOfMonoPeak(target.TheorIsotopicProfile.getMonoPeak(), target.ChargeState, mspeakList);
var hasPeakTotheLeft = peakToTheLeft != null;
if (result.ObservedIsotopicProfile == null)
{
result.IsotopicProfileFound = false;
result.FitScore = 1;
}
else
{
//Get fit score O16 profile
var observedIsoList = result.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Take(4).ToList(); //first 4 peaks excludes the O18 double label peak (fifth peak)
var theorPeakList = target.TheorIsotopicProfile.Peaklist.Select(p => (Peak)p).Take(4).ToList();
result.FitScore = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
// fit score O18 profile
var o18Iso = ((O16O18IqResult)result).ConvertO16ProfileToO18(target.TheorIsotopicProfile, 4);
theorPeakList = o18Iso.Peaklist.Select(p => (Peak)p).ToList();
observedIsoList = result.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Skip(4).ToList(); //skips the first 4 peaks and thus includes the O18 double label isotopic profile
((O16O18IqResult)result).FitScoreO18Profile = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
//get i_score
iscore = InterferenceScorer.GetInterferenceScore(result.ObservedIsotopicProfile, mspeakList);
//get ppm error
var massErrorInDaltons = TheorMostIntensePeakMassError(target.TheorIsotopicProfile, result.ObservedIsotopicProfile, target.ChargeState);
var ppmError = (massErrorInDaltons / target.MonoMassTheor) * 1e6;
//Get Isotope Correlation
var scan = lcscanset.PrimaryScanNumber;
var sigma = target.ChromPeak.Width / 2.35;
var chromScanWindowWidth = 4 * sigma;
//Determines where to start and stop chromatogram correlation
var startScan = scan - (int)Math.Round(chromScanWindowWidth / 2, 0);
var stopScan = scan + (int)Math.Round(chromScanWindowWidth / 2, 0);
result.CorrelationData = ChromatogramCorrelator.CorrelateData(Run, result, startScan, stopScan);
result.LcScanObs = lcscanset.PrimaryScanNumber;
result.ChromPeakSelected = target.ChromPeak;
result.LCScanSetSelected = new ScanSet(lcscanset.PrimaryScanNumber);
result.IsotopicProfileFound = true;
result.InterferenceScore = iscore;
result.IsIsotopicProfileFlagged = hasPeakTotheLeft;
result.NETError = netError;
result.MassErrorBefore = ppmError;
result.IqResultDetail.MassSpectrum = massSpectrumXYData;
result.Abundance = GetAbundance(result);
}
}
public void DoWorkflow()
{
_result = CreateResult(this);
DoWorkflow(_result);
}
protected void DoWorkflow(IqResult iqResult)
{
Workflow.Execute(iqResult);
}
public void AddResult(IqResult result)
{
result.ParentResult = this;
_childResults.Add(result);
}
/// <summary>
/// Calculates Metrics based on ChromPeakIqTarget
/// NET Error, Mass Error, Isotopic Fit, & Isotope Correlation
/// </summary>
protected override void ExecuteWorkflow(IqResult result)
{
result.IsExported = false;
if (MSGenerator == null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
MSGenerator.IsTICRequested = false;
}
var target = result.Target as ChromPeakIqTarget;
if (target == null)
{
throw new NullReferenceException("The ChromPeakAnalyzerIqWorkflow only works with the ChromPeakIqTarget.");
}
MSGenerator.MinMZ = target.MZTheor - 2;
MSGenerator.MaxMZ = target.MZTheor + 5;
//Sums Scan
var lcscanset = _chromPeakUtilities.GetLCScanSetForChromPeak(target.ChromPeak, Run, WorkflowParameters.NumMSScansToSum);
//Generate a mass spectrum
var massSpectrumXYData = MSGenerator.GenerateMS(Run, lcscanset);
//massSpectrumXYData = massSpectrumXYData.TrimData(result.Target.MZTheor - 5, result.Target.MZTheor + 15);
//Find isotopic profile
List <Peak> mspeakList;
result.ObservedIsotopicProfile = TargetedMSFeatureFinder.IterativelyFindMSFeature(massSpectrumXYData, target.TheorIsotopicProfile, out mspeakList);
//Get NET Error
var netError = target.ChromPeak.NETValue - target.ElutionTimeTheor;
var leftOfMonoPeakLooker = new LeftOfMonoPeakLooker();
var peakToTheLeft = leftOfMonoPeakLooker.LookforPeakToTheLeftOfMonoPeak(target.TheorIsotopicProfile.getMonoPeak(), target.ChargeState, mspeakList);
var hasPeakTotheLeft = peakToTheLeft != null;
if (result.ObservedIsotopicProfile == null)
{
result.IsotopicProfileFound = false;
result.FitScore = 1;
}
else
{
//Get fit score
var observedIsoList = result.ObservedIsotopicProfile.Peaklist.Cast <Peak>().ToList();
var minIntensityForScore = 0.05;
var fitScore = PeakFitter.GetFit(target.TheorIsotopicProfile.Peaklist.Select(p => (Peak)p).ToList(), observedIsoList, minIntensityForScore, WorkflowParameters.MSToleranceInPPM);
//get i_score
var iscore = InterferenceScorer.GetInterferenceScore(result.ObservedIsotopicProfile, mspeakList);
//get ppm error
var massErrorInDaltons = TheorMostIntensePeakMassError(target.TheorIsotopicProfile, result.ObservedIsotopicProfile, target.ChargeState);
var ppmError = (massErrorInDaltons / target.MonoMassTheor) * 1e6;
//Get Isotope Correlation
var scan = lcscanset.PrimaryScanNumber;
double chromScanWindowWidth = target.ChromPeak.Width * 2;
//Determines where to start and stop chromatogram correlation
var startScan = scan - (int)Math.Round(chromScanWindowWidth / 2, 0);
var stopScan = scan + (int)Math.Round(chromScanWindowWidth / 2, 0);
result.CorrelationData = ChromatogramCorrelator.CorrelateData(Run, result, startScan, stopScan);
result.LcScanObs = lcscanset.PrimaryScanNumber;
result.ChromPeakSelected = target.ChromPeak;
result.LCScanSetSelected = new ScanSet(lcscanset.PrimaryScanNumber);
result.IsotopicProfileFound = true;
result.FitScore = fitScore;
result.InterferenceScore = iscore;
result.IsIsotopicProfileFlagged = hasPeakTotheLeft;
result.NETError = netError;
result.MassErrorBefore = ppmError;
result.IqResultDetail.MassSpectrum = massSpectrumXYData;
result.Abundance = GetAbundance(result);
}
Display(result);
}
//Captured what the original IqWorkflow does
protected override void ExecuteWorkflow(IqResult result)
{
var peakSelector = ChromPeakSelector as IqSmartChromPeakSelector;
//Executes the ChargeState level children workflows
var children = result.Target.ChildTargets();
foreach (var child in children)
{
child.DoWorkflow();
var childResult = child.GetResult();
var peakTargetList = new List <ChromPeakIqTarget>();
var peakTargets = child.ChildTargets();
foreach (ChromPeakIqTarget target in peakTargets)
{
peakTargetList.Add(target);
}
var filterOutFlagged = childResult.Target.TheorIsotopicProfile.GetIndexOfMostIntensePeak() == 0;
var chromPeakTarget = peakSelector.SelectBestPeak(peakTargetList, filterOutFlagged);
if (chromPeakTarget != null)
{
var chromPeakResult = chromPeakTarget.GetResult();
childResult.ChromPeakSelected = chromPeakTarget.ChromPeak;
childResult.LcScanObs = chromPeakResult.LcScanObs;
childResult.LCScanSetSelected = chromPeakResult.LCScanSetSelected;
childResult.IqResultDetail.MassSpectrum = chromPeakResult.IqResultDetail.MassSpectrum;
TrimData(childResult.IqResultDetail.MassSpectrum, childResult.Target.MZTheor, MsLeftTrimAmount, MsRightTrimAmount);
childResult.ObservedIsotopicProfile = chromPeakResult.ObservedIsotopicProfile;
childResult.FitScore = chromPeakResult.FitScore;
childResult.NETError = chromPeakResult.NETError;
childResult.InterferenceScore = chromPeakResult.InterferenceScore;
childResult.CorrelationData = chromPeakResult.CorrelationData;
childResult.MonoMassObs = chromPeakResult.ObservedIsotopicProfile == null
? 0
: chromPeakResult.ObservedIsotopicProfile.MonoIsotopicMass;
childResult.MZObs = chromPeakResult.ObservedIsotopicProfile == null
? 0
: chromPeakResult.ObservedIsotopicProfile.MonoPeakMZ;
childResult.MZObsCalibrated = chromPeakResult.ObservedIsotopicProfile == null
? 0
: Run.GetAlignedMZ(childResult.MZObs, chromPeakResult.LcScanObs);
childResult.MonoMassObsCalibrated = (childResult.MZObsCalibrated - DeconTools.Backend.Globals.PROTON_MASS) * childResult.Target.ChargeState;
childResult.MassErrorBefore = chromPeakResult.ObservedIsotopicProfile == null
? 0
: chromPeakResult.MassErrorBefore;
childResult.MassErrorAfter = (childResult.MZObsCalibrated - childResult.Target.MZTheor) / childResult.Target.MZTheor * 1e6;
var elutionTime = childResult.ChromPeakSelected == null ? 0d : ((ChromPeak)childResult.ChromPeakSelected).NETValue;
childResult.ElutionTimeObs = elutionTime;
childResult.Abundance = GetAbundance(childResult);
}
}
}
