/// <summary>
/// Initializes a new instance of the <see cref="MolecularTarget"/> class.
/// </summary>
/// <param name="targetMz">
/// The Target MZ.
/// </param>
/// <param name="ionization">
/// The ionization.
/// </param>
/// <param name="correspondingChemical">
/// The CorrespondingChemical Identifier.
/// </param>
public MolecularTarget(double targetMz, IonizationMethod ionization, string correspondingChemical)
{
this.MassWithAdduct = targetMz;
this.TargetType = TargetType.Molecule;
this.Adduct = new IonizationAdduct(ionization);
this.correspondingChemical = correspondingChemical;
}
/// <summary>
/// Initializes a new instance of the <see cref="DriftTimeTarget"/> class for molercules
/// </summary>
/// <param name="libraryEntryName">
/// The library Entry Name.
/// </param>
/// <param name="normalizedDriftTimeInMs">
/// The drift time.
/// </param>
/// <param name="empiricalFormula">
/// The empirical formula.
/// </param>
/// <param name="ionizationMethod">
/// The ionization method.
/// </param>
/// <param name="adductMultiplier">
/// The adduct Multiplier.
/// </param>
public DriftTimeTarget(string libraryEntryName, double normalizedDriftTimeInMs, string empiricalFormula, IonizationMethod ionizationMethod, int adductMultiplier = 1)
: base(empiricalFormula, ionizationMethod, libraryEntryName, adductMultiplier)
{
this.NormalizedDriftTimeInMs = normalizedDriftTimeInMs;
this.TargetType = TargetType.MoleculeWithKnownDriftTime;
}
/// <summary>
/// Initializes a new instance of the <see cref="MolecularTarget"/> class.
/// </summary>
/// <param name="empiricalFormula">
/// The empirical formula.
/// </param>
/// <param name="ionization">
/// The ionization.
/// </param>
/// <param name="correspondingChemical">
/// </param>
/// <param name="adductMultiplier">
/// The adductMultiplier.
/// </param>
public MolecularTarget(string empiricalFormula, IonizationMethod ionization, string correspondingChemical, int adductMultiplier = 1)
{
this.correspondingChemical = correspondingChemical;
IonizationAdduct adduct = new IonizationAdduct(ionization, adductMultiplier);
this.Setup(empiricalFormula, adduct);
}
public int TestTargetDetectionWithIsomersClean(string formula, IonizationMethod method, string descriptor, string fileLocation)
{
MolecularTarget sample1 = new MolecularTarget(formula, method, descriptor);
CrossSectionSearchParameters parameters1 = new CrossSectionSearchParameters(CrossSectionSearchParameters.DefaultDriftTimeToleranceInMs, CrossSectionSearchParameters.DefaultMzWindowHalfWidthInPpm,
CrossSectionSearchParameters.DefaultNumPointForSmoothing, CrossSectionSearchParameters.DefaultFeatureFilterLevel, CrossSectionSearchParameters.DefaultAbsoluteIntensityThreshold, CrossSectionSearchParameters.DefaultPeakShapeThreshold, CrossSectionSearchParameters.DefaultIsotopicThreshold, CrossSectionSearchParameters.DefaultMaxOutliers, CrossSectionSearchParameters.DefaultPeakDetectorSelection, FitlineEnum.OrdinaryLeastSquares, CrossSectionSearchParameters.DefaultMinR2, CrossSectionSearchParameters.DefaultRelativeIntensityPercentageThreshold, "png", CrossSectionSearchParameters.DefaultInsufficientFramesFraction, testDriftTubeLength, true);
CrossSectionWorkfow workfow1 = new CrossSectionWorkfow(fileLocation, "output", parameters1);
CrossSectionWorkflowResult results1 = workfow1.RunCrossSectionWorkFlow(sample1, true);
int count = results1.IdentifiedIsomers.Count();
workfow1.Dispose();
return count;
}