/// <summary>
/// Calculate fragment ion labels.
/// </summary>
/// <param name="labelModifications">The heavy/light labels.</param>
/// <returns>A list of fragment labeled ions.</returns>
private ReactiveList <LabeledIonViewModel> GenerateFragmentLabels(ReactiveList <SearchModification> labelModifications = null)
{
var fragmentLabelList = new ReactiveList <LabeledIonViewModel> {
ChangeTrackingEnabled = true
};
if (this.SelectedPrSm.Sequence.Count < 1)
{
return(fragmentLabelList);
}
var sequence = this.SelectedPrSm.Sequence;
if (labelModifications != null)
{
sequence = IonUtils.GetHeavySequence(sequence, labelModifications.ToArray());
}
var precursorIon = IonUtils.GetPrecursorIon(sequence, this.SelectedPrSm.Charge);
lock (this.cacheLock)
{
var prefixCompositions = this.prefixCompositionCache.Get(sequence);
var suffixCompositions = this.suffixCompositionCache.Get(sequence);
foreach (var ionType in this.IonTypes)
{
var ionFragments = new List <LabeledIonViewModel>();
for (int i = 0; i < prefixCompositions.Length; i++)
{
var composition = ionType.IsPrefixIon
? prefixCompositions[i]
: suffixCompositions[i];
LabeledIonViewModel label =
this.fragmentCache.Get(new Tuple <Composition, IonType>(composition, ionType));
label.Index = ionType.IsPrefixIon ? i + 1 : (sequence.Count - (i + 1));
if (label.PrecursorIon == null)
{
label.PrecursorIon = precursorIon;
}
ionFragments.Add(label);
}
if (!ionType.IsPrefixIon)
{
ionFragments.Reverse();
}
fragmentLabelList.AddRange(ionFragments);
}
}
return(fragmentLabelList);
}
/// <summary>
/// Initializes a new instance of the <see cref="FragmentationSequenceViewModel"/> class.
/// </summary>
public FragmentationSequenceViewModel()
{
FragmentationSequence = new FragmentationSequence(
new Sequence(new List <AminoAcid>()),
1,
null,
ActivationMethod.HCD);
var baseIonTypes = BaseIonType.AllBaseIonTypes.Select(
bit =>
new BaseIonTypeViewModel
{
BaseIonType = bit,
IsSelected = bit == BaseIonType.B || bit == BaseIonType.Y
});
BaseIonTypes = new ReactiveList <BaseIonTypeViewModel>(baseIonTypes)
{
ChangeTrackingEnabled = true
};
NeutralLosses = new ReactiveList <NeutralLossViewModel>
{
new NeutralLossViewModel {
NeutralLoss = NeutralLoss.NoLoss, IsSelected = true
},
new NeutralLossViewModel {
NeutralLoss = NeutralLoss.H2O
},
new NeutralLossViewModel {
NeutralLoss = NeutralLoss.NH3
}
};
NeutralLosses.ChangeTrackingEnabled = true;
HeavyModifications = new SearchModification[0];
LabeledIonViewModels = new LabeledIonViewModel[0];
SelectedIonTypes = new IonType[0];
AddPrecursorIons = true;
// HideAllIonsCommand deselects all ion types and neutral losses.
HideAllIonsCommand = ReactiveCommand.Create(() =>
{
AddPrecursorIons = false;
foreach (var baseIonType in BaseIonTypes)
{
baseIonType.IsSelected = false;
}
foreach (var neutralLoss in NeutralLosses)
{
neutralLoss.IsSelected = neutralLoss.NeutralLoss == NeutralLoss.NoLoss && neutralLoss.IsSelected;
}
});
// When Base Ion Types are selected/deselected, update ion types.
BaseIonTypes.ItemChanged.Where(x => x.PropertyName == "IsSelected")
.Select(_ => GetIonTypes())
.Subscribe(ionTypes => SelectedIonTypes = ionTypes);
// When Neutral Losses are selected/deselected, update ion types
NeutralLosses.ItemChanged.Where(x => x.PropertyName == "IsSelected")
.Select(_ => GetIonTypes())
.Subscribe(ionTypes => SelectedIonTypes = ionTypes);
// When FragmentationSequence is set, select IonTypes for ActivationMethod.
this.WhenAnyValue(x => x.FragmentationSequence)
.Where(fragSeq => fragSeq != null)
.Subscribe(fragSeq => SetActivationMethod(fragSeq.ActivationMethod));
// When fragmentation sequence changes, update labeled ions
this.WhenAnyValue(x => x.FragmentationSequence, x => x.SelectedIonTypes, x => x.HeavyModifications, x => x.AddPrecursorIons)
.SelectMany(async _ => await GetLabeledIonViewModels())
.Subscribe(livms => LabeledIonViewModels = livms);
SelectAllIonsCommand = ReactiveCommand.Create(() =>
{
foreach (var ion in BaseIonTypes)
{
ion.IsSelected = true;
}
AddPrecursorIons = true;
});
IcParameters.Instance.WhenAnyValue(x => x.CidHcdIonTypes, x => x.EtdIonTypes)
.Throttle(TimeSpan.FromMilliseconds(50), RxApp.TaskpoolScheduler)
.Where(_ => FragmentationSequence != null)
.Subscribe(_ => SetActivationMethod(FragmentationSequence.ActivationMethod));
}
/// <summary>
/// Compare the label of this LabeledIon to another LabeledIon for equality.
/// </summary>
/// <param name="other">The LabeledIon to compare to.</param>
/// <returns>A value indicating whether this LabeledIon is equal to the other LabeledIon.</returns>
public bool Equals(LabeledIonViewModel other)
{
return(this.Label.Equals(other.Label));
}
/// <summary>
/// Compare the label of this LabeledIon to another LabeledIon.
/// </summary>
/// <param name="other">The LabeledIon to compare to.</param>
/// <returns>
/// A value indicating whether this LabeledIon is
/// equal to, greater than, or less than the other LabeledIon.
/// </returns>
public int CompareTo(LabeledIonViewModel other)
{
return(string.Compare(this.Label, other.Label, StringComparison.Ordinal));
}