public override IsotopicProfile IterativelyFindMSFeature(XYData xydata, IsotopicProfile theorIso)
{
var o16TheorFeature = theorIso;
var o16Profile = _iterativeTffStandard.IterativelyFindMSFeature(xydata, o16TheorFeature);
var o18TheorProfileSingleLabel = convertO16ProfileToO18(o16TheorFeature, 2);
var o18SingleLabelProfile = _iterativeTffStandard.IterativelyFindMSFeature(xydata, o18TheorProfileSingleLabel);
var o18TheorProfileDoubleLabel = convertO16ProfileToO18(o16TheorFeature, 4);
var o18DoubleLabelProfile = _iterativeTffStandard.IterativelyFindMSFeature(xydata, o18TheorProfileDoubleLabel);
IsotopicProfile foundO16O18Profile;
if (o16Profile == null)
{
if (o18DoubleLabelProfile == null)
{
return(null);
}
foundO16O18Profile = o18DoubleLabelProfile.CloneIsotopicProfile();
foundO16O18Profile.MonoIsotopicMass = o18DoubleLabelProfile.MonoIsotopicMass - 4 * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS;
foundO16O18Profile.MonoPeakMZ = foundO16O18Profile.MonoIsotopicMass / foundO16O18Profile.ChargeState +
Globals.PROTON_MASS;
}
else
{
foundO16O18Profile = o16Profile.CloneIsotopicProfile();
}
//rebuild isotopic peak list
AddIsotopePeaks(foundO16O18Profile, o16Profile, 2);
AddIsotopePeaks(foundO16O18Profile, o18SingleLabelProfile, 4); // add the O18(1) and the O18(2) if present
AddIsotopePeaks(foundO16O18Profile, o18DoubleLabelProfile, 100); // add as many peaks as possible
lookForMissingPeaksAndInsertZeroIntensityPeaksWhenMissing(foundO16O18Profile, o16TheorFeature);
return(foundO16O18Profile);
}
public override void Execute(ResultCollection resultList)
{
Check.Require(resultList?.Run != null, string.Format("{0} failed. Run is empty.", Name));
if (resultList?.Run == null)
{
return;
}
Check.Require(resultList.Run.CurrentMassTag != null, string.Format("{0} failed. CurrentMassTag hasn't been defined.", Name));
if (resultList.Run.CurrentMassTag == null)
{
return;
}
var result = resultList.CurrentTargetedResult;
if (resultList.Run.XYData?.Xvalues == null || resultList.Run.XYData.Xvalues.Length < 4)
{
result.IsotopicProfile = null;
return;
}
//TODO: decide whether not to trim or not. Trimming XYData may help with speed.
double mzWindowForPeakDetection = 20;
resultList.Run.XYData = resultList.Run.XYData.TrimData(resultList.Run.CurrentMassTag.MZ - mzWindowForPeakDetection / 2, resultList.Run.CurrentMassTag.MZ + mzWindowForPeakDetection / 2);
resultList.IsosResultBin.Clear();
var o16TheorFeature = resultList.Run.CurrentMassTag.IsotopicProfile;
var o16profile = _iterativeTFFStandard.IterativelyFindMSFeature(resultList.Run.XYData, o16TheorFeature, out var peakList);
var peakListToUseLater = new List <Peak>(peakList);
var o18TheorProfileSingleLabel = convertO16ProfileToO18(o16TheorFeature, 2);
var o18SingleLabelProfile = _iterativeTFFStandard.IterativelyFindMSFeature(resultList.Run.XYData, o18TheorProfileSingleLabel, out peakList);
if (peakList != null && peakList.Count > peakListToUseLater.Count)
{
peakListToUseLater = new List <Peak>(peakList);
}
var o18TheorProfileDoubleLabel = convertO16ProfileToO18(o16TheorFeature, 4);
var o18DoubleLabelProfile = _iterativeTFFStandard.IterativelyFindMSFeature(resultList.Run.XYData, o18TheorProfileDoubleLabel, out peakList);
if (peakList != null && peakList.Count > peakListToUseLater.Count)
{
peakListToUseLater = new List <Peak>(peakList);
}
//store best peakList for use in later tasks
resultList.Run.PeakList = peakListToUseLater;
IsotopicProfile foundO16O18Profile;
if (o16profile == null)
{
if (o18DoubleLabelProfile == null)
{
result.IsotopicProfile = null;
result.FailedResult = true;
result.FailureType = Globals.TargetedResultFailureType.MsfeatureNotFound;
return;
}
foundO16O18Profile = o18DoubleLabelProfile.CloneIsotopicProfile();
//lookForMissingPeaksAndInsertZeroIntensityPeaksWhenMissing(foundO16O18Profile, o16TheorFeature);
foundO16O18Profile.MonoIsotopicMass = o18DoubleLabelProfile.MonoIsotopicMass -
4 * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS;
foundO16O18Profile.MonoPeakMZ = foundO16O18Profile.MonoIsotopicMass / foundO16O18Profile.ChargeState +
Globals.PROTON_MASS;
}
else
{
foundO16O18Profile = o16profile.CloneIsotopicProfile();
}
//rebuild isotopic peak list
addIsotopePeaks(foundO16O18Profile, o16profile, 2);
addIsotopePeaks(foundO16O18Profile, o18SingleLabelProfile, 4); // add the O18(1) and the O18(2) if present
addIsotopePeaks(foundO16O18Profile, o18DoubleLabelProfile, 100); // add as many peaks as possible
lookForMissingPeaksAndInsertZeroIntensityPeaksWhenMissing(foundO16O18Profile, o16TheorFeature);
result.IsotopicProfile = foundO16O18Profile;
resultList.IsosResultBin.Add(result);
}