/// <summary>
/// Calculate neighboring charge state ion labels for precursor.
/// </summary>
/// <param name="labelModifications">The heavy/light labels.</param>
/// <returns>A list of neighboring charge state labeled ions.</returns>
private ReactiveList <LabeledIonViewModel> GenerateChargePrecursorLabels(ReactiveList <SearchModification> labelModifications = null)
{
var ions = new ReactiveList <LabeledIonViewModel> {
ChangeTrackingEnabled = true
};
var numChargeStates = IonUtils.GetNumNeighboringChargeStates(this.SelectedPrSm.Charge);
if (this.SelectedPrSm.Sequence.Count == 0)
{
return(ions);
}
var sequence = this.SelectedPrSm.Sequence;
if (labelModifications != null)
{
sequence = IonUtils.GetHeavySequence(sequence, labelModifications.ToArray());
}
var composition = sequence.Aggregate(Composition.Zero, (current, aa) => current + aa.Composition);
var minCharge = Math.Max(1, this.SelectedPrSm.Charge - numChargeStates);
var maxCharge = this.SelectedPrSm.Charge + numChargeStates;
for (int i = minCharge; i <= maxCharge; i++)
{
var index = i - minCharge;
if (index == 0)
{
index = this.SelectedPrSm.Charge - minCharge;
}
if (i == this.SelectedPrSm.Charge)
{
index = 0; // guarantee that actual charge is index 0
}
#pragma warning disable 0618
var precursorIonType = new IonType("Precursor", Composition.H2O, i, false);
#pragma warning restore 0618
ions.Add(new LabeledIonViewModel(composition, precursorIonType, false, this.lcms, null, true, index));
}
return(ions);
}
/// <summary>
/// Calculate neighboring charge state ion labels for precursor.
/// </summary>
/// <param name="labelModifications">The heavy/light labels.</param>
/// <returns>A list of neighboring charge state labeled ions.</returns>
public List <LabeledIonViewModel> GetChargePrecursorLabels(IEnumerable <SearchModification> labelModifications = null)
{
var ions = new List <LabeledIonViewModel>();
var numChargeStates = IonUtils.GetNumNeighboringChargeStates(Charge);
if (Sequence.Count == 0 || LcMsRun == null)
{
return(ions);
}
var sequence = Sequence;
if (labelModifications != null)
{
sequence = IonUtils.GetHeavySequence(sequence, labelModifications.ToArray());
}
var composition = sequence.Aggregate(Composition.Zero, (current, aa) => current + aa.Composition);
var minCharge = Math.Max(1, Charge - numChargeStates);
var maxCharge = Charge + numChargeStates;
for (var i = minCharge; i <= maxCharge; i++)
{
var index = i - minCharge;
if (index == 0)
{
index = Charge - minCharge;
}
if (i == Charge)
{
index = 0; // guarantee that actual charge is index 0
}
#pragma warning disable 0618
var precursorIonType = new IonType("Precursor", Composition.H2O, i, false);
#pragma warning restore 0618
ions.Add(new LabeledIonViewModel(composition, precursorIonType, false, LcMsRun, null, true, index));
}
return(ions);
}
