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); } }