public LipidGroupSearchResult(LipidTarget lipidTarget, List <Lipid> lipidList, SpectrumSearchResult spectrumSearchResult, ScoreModel scoreModel)
{
LipidTarget = lipidTarget;
LipidList = lipidList;
SpectrumSearchResult = spectrumSearchResult;
ShouldExport = false;
Score = scoreModel.ScoreLipid(this);
if (spectrumSearchResult.HcdSpectrum != null)
{
DisplayScanNum = spectrumSearchResult.HcdSpectrum.ScanNum;
DisplayMz = spectrumSearchResult.HcdSpectrum.IsolationWindow.IsolationWindowTargetMz;
}
else if (spectrumSearchResult.CidSpectrum != null)
{
DisplayScanNum = spectrumSearchResult.CidSpectrum.ScanNum;
DisplayMz = spectrumSearchResult.CidSpectrum.IsolationWindow.IsolationWindowTargetMz;
}
if (spectrumSearchResult.PrecursorSpectrum == null)
{
return;
}
var pearsonCorrelationCalculator = new PearsonCorrelationFitUtil();
PearsonCorrScore = pearsonCorrelationCalculator.GetFitScore(spectrumSearchResult, lipidTarget.Composition);
PearsonCorrScoreMinus1 = pearsonCorrelationCalculator.GetFitMinus1Score(spectrumSearchResult, lipidTarget.Composition);
var cosineCalculator = new CosineFitUtil();
CosineScore = cosineCalculator.GetFitScore(spectrumSearchResult, lipidTarget.Composition);
CosineScoreMinus1 = cosineCalculator.GetFitMinus1Score(spectrumSearchResult, lipidTarget.Composition);
}
public LipidGroupSearchResult(LipidTarget lipidTarget, List <Lipid> lipidList, SpectrumSearchResult spectrumSearchResult)
{
LipidTarget = lipidTarget;
LipidList = lipidList;
SpectrumSearchResult = spectrumSearchResult;
DisplayScanNum = spectrumSearchResult.HcdSpectrum.ScanNum;
DisplayMz = spectrumSearchResult.HcdSpectrum.IsolationWindow.IsolationWindowTargetMz;
ShouldExport = false;
Score = 0;
}
public LipidGroupSearchResult(SpectrumSearchResult spectrumSearchResult, FragmentationMode fragmentationMode, Adduct adduct)
{
var msmsSpec = spectrumSearchResult.CidSpectrum ?? spectrumSearchResult.HcdSpectrum;
LipidTarget = new LipidTarget(msmsSpec.IsolationWindow.ToString(), LipidClass.Unknown, fragmentationMode, null, null, adduct);
LipidList = null;
SpectrumSearchResult = spectrumSearchResult;
DisplayScanNum = msmsSpec.ScanNum;
DisplayMz = msmsSpec.IsolationWindow.IsolationWindowTargetMz;
ShouldExport = false;
Score = 0;
}
protected bool Equals(LipidTarget other)
{
if (LipidClass != LipidClass.Unknown && other.LipidClass != LipidClass.Unknown)
{
return(LipidClass == other.LipidClass && FragmentationMode == other.FragmentationMode &&
Equals(Composition, other.Composition) &&
AcylChainList.OrderBy(x => x.NumCarbons)
.ThenBy(x => x.NumDoubleBonds)
.ThenBy(x => x.AcylChainType)
.SequenceEqual(
other.AcylChainList.OrderBy(x => x.NumCarbons)
.ThenBy(x => x.NumDoubleBonds)
.ThenBy(x => x.AcylChainType)));
}
return(LipidClass == other.LipidClass && FragmentationMode == other.FragmentationMode &&
CommonName.Equals(other.CommonName));
}
public SpectrumSearchResult(ProductSpectrum hcdSpectrum, ProductSpectrum cidSpectrum, Spectrum precursorSpectrum, List <MsMsSearchResult> hcdSearchResultList, List <MsMsSearchResult> cidSearchResultList, Xic xic, LcMsRun lcMsRun, ScoreModel scoreModel = null, LipidTarget lipidTarget = null)
{
HcdSpectrum = hcdSpectrum;
CidSpectrum = cidSpectrum;
PrecursorSpectrum = precursorSpectrum;
HcdSearchResultList = hcdSearchResultList;
CidSearchResultList = cidSearchResultList;
Xic = xic;
LcMsRun = lcMsRun;
PeakArea = null;
RunLength = lcMsRun.GetElutionTime(lcMsRun.MaxLcScan);
ApexScanNum = Xic.GetNearestApexScanNum(PrecursorSpectrum.ScanNum, performSmoothing: true);
ApexIntensity = Xic.Where(x => x.ScanNum == ApexScanNum).Sum(x => x.Intensity);
RetentionTime = LcMsRun.GetElutionTime(ApexScanNum);
if (scoreModel != null && lipidTarget != null)
{
ModelScore = scoreModel.ScoreLipid(lipidTarget, this);
}
}
public SpectrumSearchResult(ProductSpectrum hcdSpectrum, ProductSpectrum cidSpectrum, List <MsMsSearchResult> hcdSearchResultList, List <MsMsSearchResult> cidSearchResultList, LcMsRun lcMsRun, ScoreModel scoreModel = null, LipidTarget lipidTarget = null)
{
HcdSpectrum = hcdSpectrum;
CidSpectrum = cidSpectrum;
PrecursorSpectrum = null;
HcdSearchResultList = hcdSearchResultList;
CidSearchResultList = cidSearchResultList;
Xic = null;
LcMsRun = lcMsRun;
PeakArea = null;
RunLength = lcMsRun.GetElutionTime(lcMsRun.MaxLcScan);
ApexScanNum = 0;
ApexIntensity = 0;
RetentionTime = LcMsRun.GetElutionTime(hcdSpectrum?.ScanNum ?? cidSpectrum.ScanNum);
if (scoreModel != null && lipidTarget != null)
{
ModelScore = scoreModel.ScoreLipid(lipidTarget, this);
}
}
