/// <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);
* }
*/
}
/// <summary>
/// Updates parent charge state result based on the selected chrom peak target
/// </summary>
/// <param name="chromPeakTarget"></param>
private void UpdateSelection(ChromPeakIqTarget chromPeakTarget)
{
var childResult = chromPeakTarget.ParentTarget.GetResult();
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.MZObsCalibrated / 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);
}
/// <summary>
/// Expands charge range to cover all instances of a given sequence
/// </summary>
/// <param name="parentTarget"></param>
/// <param name="referenceTarget"></param>
private void ExpandChargeRange(TopDownIqTarget parentTarget, ChromPeakIqTarget referenceTarget)
{
var childWorkflow = new ChargeStateChildTopDownIqWorkflow(Run, WorkflowParameters);
var childTargets = parentTarget.ChildTargets().ToArray();
var fitTolerance = 0.5;
var correlationTolerance = 0.95;
var minCharge = (IqChargeStateTarget)childTargets.First();
var maxCharge = (IqChargeStateTarget)childTargets.Last();
if (minCharge.GetResult().IqResultDetail.Chromatogram != null)
{
var charge = minCharge.ChargeState;
var extendDown = true;
while (extendDown)
{
var extend = new IqChargeStateTarget(childWorkflow);
charge = charge - 1;
extend.ChargeState = charge;
parentTarget.AddTarget(extend);
extend.RefineTarget();
extend.DoWorkflow();
extendDown = ChargeExpansionPeakSelection(parentTarget, referenceTarget, extend, correlationTolerance, fitTolerance);
}
}
if (maxCharge.GetResult().IqResultDetail.Chromatogram != null)
{
var charge = maxCharge.ChargeState;
var extendUp = true;
while (extendUp)
{
var extend = new IqChargeStateTarget(childWorkflow);
charge = charge + 1;
extend.ChargeState = charge;
parentTarget.AddTarget(extend);
extend.RefineTarget();
extend.DoWorkflow();
extendUp = ChargeExpansionPeakSelection(parentTarget, referenceTarget, extend, correlationTolerance, fitTolerance);
}
}
parentTarget.SortChildTargetsByCharge();
}
/// <summary>
/// Selects a peak that correlates with the reference target and returns a bool to continue extending the charge range
/// </summary>
/// <param name="parentTarget"></param>
/// <param name="referenceTarget"></param>
/// <param name="chargeTarget"></param>
/// <param name="correlationCutoff"></param>
/// <param name="fitCutoff"></param>
/// <returns></returns>
private bool ChargeExpansionPeakSelection(TopDownIqTarget parentTarget, ChromPeakIqTarget referenceTarget, IqChargeStateTarget chargeTarget, double correlationCutoff, double fitCutoff)
{
var iqChargeCorrelator = ChromatogramCorrelator as IqChargeCorrelator;
var peakTargets = chargeTarget.ChildTargets();
var sortedPeakTargets = peakTargets.OrderBy(x => x.GetResult().FitScore);
foreach (ChromPeakIqTarget target in sortedPeakTargets)
{
if (referenceTarget.ChromPeak != null)
{
var minScan = referenceTarget.ChromPeak.XValue - (0.5 * referenceTarget.ChromPeak.Width);
var maxScan = referenceTarget.ChromPeak.XValue + (0.5 * +referenceTarget.ChromPeak.Width);
if ((target.ChromPeak.XValue > minScan) && (target.ChromPeak.XValue < maxScan))
{
var correlation = iqChargeCorrelator.PairWiseChargeCorrelation(referenceTarget, target, Run, 3);
if (correlation > correlationCutoff && target.GetResult().FitScore < fitCutoff)
{
UpdateSelection(target);
var parentResult = parentTarget.GetResult() as TopDownIqResult;
foreach (var item in parentResult.ChargeCorrelationData.CorrelationData)
{
if (referenceTarget == item.ReferenceTarget)
{
var corrItem = new ChromCorrelationDataItem(0, 0, correlation);
var corr = new ChromCorrelationData();
corr.AddCorrelationData(corrItem);
item.PeakCorrelationData.Add(target, corr);
}
}
return(true);
}
}
}
}
return(false);
}