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));
}
