public TransitionLossKey(TransitionGroupDocNode parent, TransitionDocNode transition, TransitionLosses losses)
{
Transition = transition.Transition;
Losses = losses;
if (Transition.IsCustom())
{
if (!string.IsNullOrEmpty(transition.PrimaryCustomIonEquivalenceKey))
CustomIonEquivalenceTestValue = transition.PrimaryCustomIonEquivalenceKey;
else if (!string.IsNullOrEmpty(transition.SecondaryCustomIonEquivalenceKey))
CustomIonEquivalenceTestValue = transition.SecondaryCustomIonEquivalenceKey;
else if (Transition.IsNonReporterCustomIon())
CustomIonEquivalenceTestValue = "_mzSortIndex_" + parent.Children.IndexOf(transition); // Not L10N
else
CustomIonEquivalenceTestValue = null;
}
else
{
CustomIonEquivalenceTestValue = null;
}
}
public static int CalcProductCharge(double productPrecursorMass,
int precursorCharge,
double[,] productMasses,
IList<IList<ExplicitLoss>> potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType? ionType,
out int? ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double minDelta = double.MaxValue, minDeltaNs = double.MaxValue;
int bestCharge = 0, bestChargeNs = 0;
IonType? bestIonType = null, bestIonTypeNs = null;
int? bestOrdinal = null, bestOrdinalNs = null;
TransitionLosses bestLosses = null, bestLossesNs = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
double productMass = productPrecursorMass - (lossesTrial != null ? lossesTrial.Mass : 0);
int potentialMassShift;
int nearestCharge;
int? charge = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (charge.HasValue && charge.Value == precursorCharge)
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge.Value) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (potentialMassShift == 0 && minDeltaNs > delta)
{
bestChargeNs = charge.Value;
bestIonTypeNs = IonType.precursor;
bestOrdinalNs = len + 1;
bestLossesNs = lossesTrial;
minDeltaNs = delta;
}
else if (potentialMassShift != 0 && minDelta > delta)
{
bestCharge = charge.Value;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
foreach (IonType type in Transition.ALL_TYPES)
{
// Types have priorities. If moving to a lower priority type, and there is already a
// suitable answer stop looking.
if ((type == Transition.ALL_TYPES[2] || type == Transition.ALL_TYPES[2]) &&
(MatchMz(minDelta, tolerance) || MatchMz(minDeltaNs, tolerance)))
break;
for (int offset = 0; offset < len; offset++)
{
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
double productMass = productMasses[(int) type, offset];
if (lossesTrial != null)
productMass -= lossesTrial.Mass;
int potentialMassShift;
int nearestCharge;
int? chargeFound = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (chargeFound.HasValue)
{
int charge = chargeFound.Value;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (potentialMassShift == 0 && minDeltaNs > delta)
{
bestChargeNs = charge;
bestIonTypeNs = type;
// The peptide length is 1 longer than the mass array
bestOrdinalNs = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLossesNs = lossesTrial;
minDeltaNs = delta;
}
else if (potentialMassShift != 0 && minDelta > delta)
{
bestCharge = charge;
bestIonType = type;
// The peptide length is 1 longer than the mass array
bestOrdinal = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
// Pefer no-shift to shift, even if the shift value is closer
if (MatchMz(minDelta, tolerance) && !MatchMz(minDeltaNs, tolerance))
{
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return bestCharge;
}
ionType = bestIonTypeNs;
ordinal = bestOrdinalNs;
losses = bestLossesNs;
massShift = 0;
return bestChargeNs;
}
public static double CalcMass(double massH, TransitionLosses losses)
{
return massH - (losses != null ? losses.Mass : 0);
}
/// <summary>
/// In the case of small molecule transitions specified by mass only, position within
/// the parent's list of transitions is the only meaningful key. So we need to know our parent.
/// </summary>
public TransitionLossEquivalentKey(TransitionGroupDocNode parent, TransitionDocNode transition, TransitionLosses losses)
{
Key = new TransitionEquivalentKey(parent, transition);
Losses = losses;
}
/// <summary>
/// From a transition loss perspective, losses with equall masses
/// are equal. It is not necessary to compare the exact losses.
/// </summary>
public bool Equals(TransitionLosses other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return other.Mass == Mass;
}
private string GetLabel(IonType type, int ordinal, TransitionLosses losses, int charge, double mz, int rank, bool showMz)
{
var label = new StringBuilder(type.GetLocalizedString());
if (!Transition.IsPrecursor(type))
label.Append(ordinal.ToString(LocalizationHelper.CurrentCulture));
if (losses != null)
{
label.Append(" -"); // Not L10N
label.Append(Math.Round(losses.Mass, 1));
}
string chargeIndicator = (charge == 1 ? string.Empty : Transition.GetChargeIndicator(charge));
label.Append(chargeIndicator);
if (showMz)
label.Append(string.Format(" = {0:F01}", mz)); // Not L10N
if (rank > 0 && ShowRanks)
label.Append(TextUtil.SEPARATOR_SPACE).Append(string.Format("({0})",string.Format(Resources.AbstractSpectrumGraphItem_GetLabel_rank__0__, rank))); // Not L10N
return label.ToString();
}
public TransitionKey(TransitionKey key, IsotopeLabelType labelType)
{
_ionType = key._ionType;
_customIonEquivalenceTestValue = key._customIonEquivalenceTestValue;
_ionOrdinal = key._ionOrdinal;
_massIndex = key._massIndex;
_decoyMassShift = key._decoyMassShift;
_charge = key._charge;
_precursorCharge = key._precursorCharge;
_losses = key._losses;
_labelType = labelType;
}
public TransitionKey(TransitionGroupDocNode nodeGroup, TransitionLossKey tranLossKey, IsotopeLabelType labelType)
{
var transition = tranLossKey.Transition;
_ionType = transition.IonType;
_customIonEquivalenceTestValue = tranLossKey.CustomIonEquivalenceTestValue;
_ionOrdinal = transition.Ordinal;
_massIndex = transition.MassIndex;
_decoyMassShift = transition.DecoyMassShift;
_charge = transition.Charge;
_precursorCharge = nodeGroup.TransitionGroup.PrecursorCharge;
_losses = tranLossKey.Losses;
_labelType = labelType;
}
public ProductExp(int productCharge, IonType ionType, int fragmentOrdinal, TransitionLosses losses, int massShift)
{
Charge = productCharge;
IonType = ionType;
FragmentOrdinal = fragmentOrdinal;
Losses = losses;
MassShift = null;
if (massShift != 0)
MassShift = massShift;
}
