/// <summary>
/// Calculate isotope ion labels for precursor.
/// </summary>
/// <param name="relativeIntensityThreshold">Relative intensity threshold (fraction of most abundant isotope)</param>
/// <param name="labelModifications">The heavy/light labels.</param>
/// <returns>A list of precursor labeled ions.</returns>
public List <LabeledIonViewModel> GetIsotopePrecursorLabels(double relativeIntensityThreshold = 0.1, IEnumerable <SearchModification> labelModifications = null)
{
var ions = new List <LabeledIonViewModel>();
if (Sequence.Count == 0 || LcMsRun == null)
{
return(ions);
}
var sequence = Sequence;
if (labelModifications != null)
{
sequence = IonUtils.GetHeavySequence(sequence, labelModifications.ToArray());
}
#pragma warning disable 0618
var precursorIonType = new IonType("Precursor", Composition.H2O, Charge, false);
#pragma warning restore 0618
var composition = sequence.Aggregate(Composition.Zero, (current, aa) => current + aa.Composition);
var relativeIntensities = composition.GetIsotopomerEnvelope();
var indices = new List <int> {
-1
};
for (var i = 0; i < relativeIntensities.Envelope.Length; i++)
{
if (relativeIntensities.Envelope[i] >= relativeIntensityThreshold || i == 0)
{
indices.Add(i);
}
}
ions.AddRange(indices.Select(index => new LabeledIonViewModel(composition, precursorIonType, false, LcMsRun, null, false, index)));
return(ions);
}
/// <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>
/// Calculate fragment ion labels.
/// </summary>
/// <param name="ionTypes">List of IonTypes.</param>
/// <param name="labelModifications">The heavy/light labels.</param>
/// <returns>A list of fragment labeled ions.</returns>
public List <LabeledIonViewModel> GetFragmentLabels(IList <IonType> ionTypes, SearchModification[] labelModifications = null)
{
var fragmentLabelList = new List <LabeledIonViewModel> {
Capacity = this.Sequence.Count * ionTypes.Count * this.Charge
};
if (this.Sequence.Count < 1 || this.LcMsRun == null)
{
return(fragmentLabelList);
}
var sequence = labelModifications == null ? this.Sequence : IonUtils.GetHeavySequence(this.Sequence, labelModifications);
var precursorIon = IonUtils.GetPrecursorIon(sequence, this.Charge);
lock (this.cacheLock)
{
foreach (var ionType in ionTypes)
{
var ionFragments = new List <LabeledIonViewModel>();
for (int i = 1; i < this.Sequence.Count; i++)
{
var startIndex = ionType.IsPrefixIon ? 0 : i;
var length = ionType.IsPrefixIon ? i : sequence.Count - i;
var fragment = new Sequence(this.Sequence.GetRange(startIndex, length));
var ions = ionType.GetPossibleIons(fragment);
foreach (var ion in ions)
{
var labeledIonViewModel = this.fragmentCache.Get(new Tuple <Composition, IonType>(ion.Composition, ionType));
labeledIonViewModel.Index = length;
labeledIonViewModel.PrecursorIon = precursorIon;
ionFragments.Add(labeledIonViewModel);
}
if (!ionType.IsPrefixIon)
{
ionFragments.Reverse();
}
}
fragmentLabelList.AddRange(ionFragments);
}
}
return(fragmentLabelList);
}
/// <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);
}
/// <summary>
/// Calculate isotope ion labels for precursor.
/// </summary>
/// <param name="labelModifications">The heavy/light labels.</param>
/// <returns>A list of precursor labeled ions.</returns>
private ReactiveList <LabeledIonViewModel> GenerateIsotopePrecursorLabels(ReactiveList <SearchModification> labelModifications = null)
{
var ions = new ReactiveList <LabeledIonViewModel> {
ChangeTrackingEnabled = true
};
if (this.SelectedPrSm.Sequence.Count == 0)
{
return(ions);
}
var sequence = this.SelectedPrSm.Sequence;
if (labelModifications != null)
{
sequence = IonUtils.GetHeavySequence(sequence, labelModifications.ToArray());
}
#pragma warning disable 0618
var precursorIonType = new IonType("Precursor", Composition.H2O, this.SelectedPrSm.Charge, false);
#pragma warning restore 0618
var composition = sequence.Aggregate(Composition.Zero, (current, aa) => current + aa.Composition);
var relativeIntensities = composition.GetIsotopomerEnvelope();
var indices = new List <int> {
-1
};
for (int i = 0; i < relativeIntensities.Envelope.Length; i++)
{
if (relativeIntensities.Envelope[i] >= IcParameters.Instance.PrecursorRelativeIntensityThreshold ||
i == 0)
{
indices.Add(i);
}
}
ions.AddRange(indices.Select(index => new LabeledIonViewModel(composition, precursorIonType, false, this.lcms, null, false, index)));
return(ions);
}
/// <summary>
/// Calculate fragment ion labels.
/// </summary>
/// <param name="ionTypes">List of IonTypes.</param>
/// <param name="labelModifications">The heavy/light labels.</param>
/// <returns>A list of fragment labeled ions.</returns>
public List <LabeledIonViewModel> GetFragmentLabels(IList <IonType> ionTypes, SearchModification[] labelModifications = null)
{
var fragmentLabelList = new List <LabeledIonViewModel> {
Capacity = Sequence.Count * ionTypes.Count * Charge
};
if (Sequence.Count < 1 || LcMsRun == null)
{
return(fragmentLabelList);
}
var sequence = labelModifications == null ? Sequence : IonUtils.GetHeavySequence(Sequence, labelModifications);
var precursorIon = IonUtils.GetPrecursorIon(sequence, Charge);
var tasks = new List <Task <object> >();
// Define a delegate that prints and returns the system tick count
Func <object, List <LabeledIonViewModel> > action = (object type) =>
{
IonType iType = (IonType)type;
var ionFragments = new List <LabeledIonViewModel>();
for (var i = 1; i < Sequence.Count; i++)
{
var startIndex = iType.IsPrefixIon ? 0 : i;
var length = iType.IsPrefixIon ? i : sequence.Count - i;
var fragment = new Sequence(Sequence.GetRange(startIndex, length));
var ions = iType.GetPossibleIons(fragment);
foreach (var ion in ions)
{
lock (cacheLock)
{
var labeledIonViewModel = fragmentCache.Get(new Tuple <Composition, IonType>(ion.Composition, iType));
labeledIonViewModel.Index = length;
labeledIonViewModel.PrecursorIon = precursorIon;
ionFragments.Add(labeledIonViewModel);
}
}
if (!iType.IsPrefixIon)
{
ionFragments.Reverse();
}
}
return(ionFragments);
};
foreach (var ionType in ionTypes)
{
tasks.Add(Task <object> .Factory.StartNew(action, ionType));
}
Task.WaitAll(tasks.ToArray());
foreach (Task <object> task in tasks)
{
List <LabeledIonViewModel> list = (List <LabeledIonViewModel>)task.Result;
fragmentLabelList.AddRange(list);
}
return(fragmentLabelList);
}