/// <summary>
/// Initializes a new instance of the <see cref="PrecursorSequenceIonViewModel"/> class.
/// </summary>
public PrecursorSequenceIonViewModel()
{
FragmentationSequence = new FragmentationSequence(
new Sequence(new List <AminoAcid>()),
1,
null,
ActivationMethod.HCD);
HeavyModifications = new SearchModification[0];
PrecursorViewMode = PrecursorViewMode.Isotopes;
LabeledIonViewModels = new LabeledIonViewModel[0];
this.WhenAnyValue(x => x.ChargeViewMode).Subscribe(chargeViewMode => IsotopeViewMode = !chargeViewMode);
this.WhenAnyValue(x => x.IsotopeViewMode).Subscribe(isotopeViewMode => ChargeViewMode = !isotopeViewMode);
this.WhenAnyValue(x => x.IsotopeViewMode).Subscribe(isotopeViewMode =>
PrecursorViewMode = isotopeViewMode ? PrecursorViewMode.Isotopes : PrecursorViewMode.Charges);
this.WhenAnyValue(x => x.PrecursorViewMode).Subscribe(
viewMode =>
{
IsotopeViewMode = viewMode == PrecursorViewMode.Isotopes;
ChargeViewMode = viewMode == PrecursorViewMode.Charges;
});
this.WhenAnyValue(x => x.PrecursorViewMode, x => x.RelativeIntensityThreshold, x => x.HeavyModifications, x => x.FragmentationSequence)
.SelectMany(async _ => await GetLabeledIonViewModels())
.Subscribe(livms => LabeledIonViewModels = livms);
}
/// <summary>
/// Get a deconvoluted ion given a regular ion.
/// </summary>
/// <param name="labeledIon">The ion.</param>
/// <param name="ionTypeFactory">A Deconvoluted IonTypeFactory</param>
/// <returns>A deconvoluted ion.</returns>
public static LabeledIonViewModel GetDeconvolutedLabeledIon(LabeledIonViewModel labeledIon, IonTypeFactory ionTypeFactory)
{
var deconIonTypeName = labeledIon.IonType.Name.Insert(1, "'");
var ionType = ionTypeFactory.GetIonType(deconIonTypeName);
var deconLabeledIon = new LabeledIonViewModel(
labeledIon.Composition,
ionType,
labeledIon.IsFragmentIon,
null,
labeledIon.PrecursorIon,
labeledIon.IsChargeState,
labeledIon.Index);
return(deconLabeledIon);
}
/// <summary>
/// Get a color of fragment ion.
/// </summary>
/// <param name="label">LabeledIonViewModel for fragment ion.</param>
/// <returns>Color of fragment ion.</returns>
public OxyColor GetColor(LabeledIonViewModel label)
{
OxyColor color;
if (label.IsFragmentIon)
{
var index = Math.Min(label.IonType.Charge - 1, this.fragmentColors[label.IonType.BaseIonType.Symbol].Count - 1);
color = this.fragmentColors[label.IonType.BaseIonType.Symbol][index];
}
else
{
if (this.precursorColors.ContainsKey(label.Index))
{
color = this.precursorColors[label.Index];
}
else
{
color = label.Index > 0 ? OxyColors.DarkRed : OxyColors.AliceBlue;
}
}
return(color);
}
