public SpecificFragment(LipidClass lipidClass, LipidType lipidType, string fragmentDescription, FragmentationMode fragmentationMode, FragmentationType fragmentationType) { LipidClass = lipidClass; LipidType = lipidType; FragmentDescription = fragmentDescription; FragmentationMode = fragmentationMode; FragmentationType = fragmentationType; }
public LipidTarget( string commonName, LipidClass lipidClass, FragmentationMode fragmentationMode, Composition composition, IEnumerable <AcylChain> acylChainList, Adduct adduct = Adduct.Hydrogen, int charge = 1) { CommonName = commonName; LipidClass = lipidClass; FragmentationMode = fragmentationMode; Composition = composition; AcylChainList = acylChainList.ToList(); Adduct = adduct; Charge = charge; LipidType = FigureOutLipidType(); }
public void TestSingleTarget() { // Testing PC(16:0/18:1) +H const string commonName = "PC(16:0/18:1)"; const string empiricalFormula = "C42H83NO8P"; const LipidClass lipidClass = LipidClass.PC; const FragmentationMode fragmentationMode = FragmentationMode.Positive; var acylChainList = new List <AcylChain> { new AcylChain("16:0"), new AcylChain("18:1") }; var lipidTarget = LipidUtil.CreateLipidTarget(commonName, empiricalFormula, lipidClass, fragmentationMode, acylChainList); var rawFileLocation = @"../../../testFiles/XGA121_lipid_Skin_1.raw"; var informedWorkflow = new InformedWorkflow(rawFileLocation); var resultList = informedWorkflow.RunInformedWorkflow(lipidTarget, 30, 500); foreach (var result in resultList.OrderByDescending(x => x.GetNumMatchingMsMsPeaks())) { Console.WriteLine(result.Xic.GetApexScanNum() + " - " + result.HcdSpectrum.ScanNum + " - " + result.CidSpectrum.ScanNum + " - " + result.GetNumMatchingMsMsPeaks()); } }
public void TestSingleConfidentTarget() { // Testing PE(18:3/20:5) +H const string commonName = "PE(18:3/20:5)"; const string empiricalFormula = "C43H71NO8P"; const LipidClass lipidClass = LipidClass.PE; const FragmentationMode fragmentationMode = FragmentationMode.Positive; var acylChainList = new List <AcylChain> { new AcylChain("18:3"), new AcylChain("20:5") }; var lipidTarget = LipidUtil.CreateLipidTarget(commonName, empiricalFormula, lipidClass, fragmentationMode, acylChainList); var rawFileLocation = @"../../../testFiles/Daphnia_gut_TLE_POS_Gimli_21Jan14_13-07-01.raw"; var informedWorkflow = new InformedWorkflow(rawFileLocation); var resultList = informedWorkflow.RunInformedWorkflow(lipidTarget, 30, 500); foreach (var result in resultList.OrderByDescending(x => x.GetNumMatchingMsMsPeaks())) { Console.WriteLine(result.Xic.GetApexScanNum() + " - " + result.HcdSpectrum.ScanNum + " - " + result.CidSpectrum.ScanNum + " - " + result.GetNumMatchingMsMsPeaks()); } }
public int CompareTo(ScoreModelUnit other) { if (!LipidClass.Equals(other.LipidClass)) { return(LipidClass.CompareTo(other.LipidClass)); } if (!LipidType.Equals(other.LipidType)) { return(LipidType.CompareTo(other.LipidType)); } if (!FragmentDescription.Equals(other.FragmentDescription)) { return(String.Compare(FragmentDescription, other.FragmentDescription, StringComparison.Ordinal)); } if (!FragmentationMode.Equals(other.FragmentationMode)) { return(FragmentationMode.CompareTo(other.FragmentationMode)); } if (!FragmentationType.Equals(other.FragmentationType)) { return(FragmentationType.CompareTo(other.FragmentationType)); } return(IntensityMax.CompareTo(other.IntensityMax)); }
public int CompareTo(SpecificFragment other) { if (!LipidClass.Equals(other.LipidClass)) { return(LipidClass.CompareTo(other.LipidClass)); } if (!LipidType.Equals(other.LipidType)) { return(LipidType.CompareTo(other.LipidType)); } if (!FragmentDescription.Equals(other.FragmentDescription)) { return(String.Compare(FragmentDescription, other.FragmentDescription, StringComparison.Ordinal)); } if (!FragmentationMode.Equals(other.FragmentationMode)) { return(FragmentationMode.CompareTo(other.FragmentationMode)); } return(FragmentationType.CompareTo(other.FragmentationType)); }