private bool MatchNext(RankingState rankingState, double ionMz, MatchedFragmentIon match, bool filter, int end, int start, double startMz, ref RankedMI rankedMI)
{
// Unless trying to match everything, stop looking outside the instrument range
if (!rankingState.matchAll && !HasLosses && ionMz > MaxMz)
{
return(false);
}
// Check filter properties, if appropriate
if ((rankingState.matchAll || ionMz >= MinMz) && Math.Abs(ionMz - rankedMI.ObservedMz) < Libraries.IonMatchTolerance)
{
// Make sure each m/z value is only used for the most intense peak
// that is within the tolerance range.
if (rankingState.IsSeen(ionMz))
{
return(true); // Keep looking
}
rankingState.Seen(ionMz);
// If this m/z already matched a different ion, just remember the second ion.
if (rankedMI.MatchedIons != null)
{
// If first type was excluded from causing a ranking, but second does, then make it the first
// Otherwise, this can cause very mysterious failures to rank transitions that appear in the
// document.
if (rankedMI.Rank == 0 && ApplyRanking(rankingState, ionMz, match, filter, start, end, startMz, ref rankedMI))
{
rankedMI = rankedMI.ChangeMatchedIons(rankedMI.MatchedIons.Prepend(match));
}
else
{
rankedMI = rankedMI.ChangeMatchedIons(rankedMI.MatchedIons.Append(match));
}
if (rankedMI.MatchedIons.Count < MAX_MATCH)
{
return(true);
}
rankingState.matched = true;
return(false);
}
double predictedMz = match.PredictedMz;
// Avoid using the same predicted m/z on two different peaks
if (predictedMz == ionMz || !rankingState.IsSeen(predictedMz))
{
rankingState.Seen(predictedMz);
ApplyRanking(rankingState, ionMz, match, filter, start, end, startMz, ref rankedMI);
rankedMI = rankedMI.ChangeMatchedIons(ImmutableList.Singleton(match));
rankingState.matched = !rankingState.matchAll;
return(rankingState.matchAll);
}
}
// Stop looking once the mass has been passed, unless there are losses to consider
if (HasLosses)
{
return(true);
}
return(ionMz <= rankedMI.ObservedMz);
}
private bool ApplyRanking(RankingState rankingState, double ionMz, MatchedFragmentIon match, bool filter, int start, int end, double startMz, ref RankedMI rankedMI)
{
// Avoid ranking precursor ions without losses, if the precursor isotopes will
// not be taken from product ions
if (!ExcludePrecursorIsotopes || match.IonType != IonType.precursor || match.Losses != null)
{
int offset = OrdinalToOffset(match.IonType, match.Ordinal);
var type = match.IonType;
if (filter)
{
if (TargetInfoObj.LookupMods == null || !TargetInfoObj.LookupMods.HasCrosslinks)
{
if (!TransitionSettings.Accept(Sequence, MoleculeMassesObj.precursorMz, type, offset, ionMz, start,
end, startMz))
{
return(false);
}
}
}
if (rankingState.matchAll)
{
if (MinMz > ionMz || ionMz > MaxMz)
{
return(false);
}
if (!RankTypes.Contains(type))
{
return(false);
}
if (RankLimit.HasValue && rankingState.Ranked >= RankLimit)
{
return(false);
}
if (type != IonType.precursor)
{
// CONSIDER(bspratt) we may eventually want adduct-level control for small molecules, not just abs charge
if (!RankCharges.Contains(Math.Abs(match.Charge.AdductCharge)))
{
return(false);
}
}
}
rankedMI = rankedMI.ChangeRank(rankingState.RankNext());
return(true);
}
return(false);
}
private MoleculeMasses GetCrosslinkMasses(SrmSettings settings)
{
var predictDocNode = MakeTransitionGroupWithAllPossibleChildren(settings, TargetInfoObj.TransitionGroupDocNode.LabelType);
TransitionGroupDocNode matchDocNode;
if (Equals(TargetInfoObj.TransitionGroupDocNode.LabelType, TargetInfoObj.SpectrumLabelType))
{
matchDocNode = predictDocNode;
}
else
{
matchDocNode = MakeTransitionGroupWithAllPossibleChildren(settings, TargetInfoObj.SpectrumLabelType);
}
var matchTransitions = matchDocNode.Transitions.ToDictionary(child => child.Key(matchDocNode));
var predictFragments = new List <MatchedFragmentIon>();
var matchFragments = new List <MatchedFragmentIon>();
foreach (var predictedTransition in predictDocNode.Transitions)
{
var key = predictedTransition.Key(null);
TransitionDocNode matchTransition;
if (!matchTransitions.TryGetValue(key, out matchTransition))
{
continue;
}
var complexFragmentIonName = predictedTransition.ComplexFragmentIon.GetName();
var ionType = DecideIonType(complexFragmentIonName);
string fragmentName = predictedTransition.ComplexFragmentIon.GetFragmentIonName();
var predictedIon = new MatchedFragmentIon(ionType, predictFragments.Count + 1,
predictedTransition.Transition.Adduct, fragmentName, predictedTransition.Losses,
predictedTransition.Mz)
.ChangeComplexFragmentIonName(complexFragmentIonName);
predictFragments.Add(predictedIon);
matchFragments.Add(predictedIon.ChangePredictedMz(matchTransition.Mz));
}
var matchMasses = new IonMasses(
SequenceMassCalc.GetMH(matchDocNode.PrecursorMz, matchDocNode.PrecursorAdduct,
MassType.MonoisotopicMassH), IonTable <TypedMass> .EMPTY)
.ChangeKnownFragments(matchFragments);
var predictMasses = new IonMasses(
SequenceMassCalc.GetMH(predictDocNode.PrecursorMz, predictDocNode.PrecursorAdduct,
MassType.MonoisotopicMassH), IonTable <TypedMass> .EMPTY)
.ChangeKnownFragments(predictFragments);
return(new MoleculeMasses(predictDocNode.PrecursorMz, matchMasses).ChangePredictIonMasses(predictMasses));
}
private bool MatchNext(RankParams rp, IonType type, int offset, TransitionLosses losses, Adduct adduct, string fragmentName, int len, bool filter, int end, int start, double startMz)
{
bool isFragment = !Transition.IsPrecursor(type);
var ionMass = isFragment ? rp.massesMatch[type, offset] : rp.massPreMatch;
if (losses != null)
{
ionMass -= losses.Mass;
}
double ionMz = SequenceMassCalc.GetMZ(ionMass, adduct);
// Unless trying to match everything, stop looking outside the instrument range
if (!rp.matchAll && !rp.HasLosses && ionMz > rp.maxMz)
{
return(false);
}
// Check filter properties, if apropriate
if ((rp.matchAll || ionMz >= rp.minMz) && Math.Abs(ionMz - ObservedMz) < rp.tolerance)
{
// Make sure each m/z value is only used for the most intense peak
// that is within the tolerance range.
if (rp.IsSeen(ionMz))
{
return(true); // Keep looking
}
rp.Seen(ionMz);
int ordinal = Transition.OffsetToOrdinal(type, offset, len + 1);
// If this m/z aready matched a different ion, just remember the second ion.
var predictedMass = isFragment ? rp.massesPredict[type, offset] : rp.massPrePredict;
if (losses != null)
{
predictedMass -= losses.Mass;
}
double predictedMz = SequenceMassCalc.GetMZ(predictedMass, adduct);
if (MatchedIons != null)
{
// If first type was excluded from causing a ranking, but second does, then make it the first
// Otherwise, this can cause very mysterious failures to rank transitions that appear in the
// document.
var match = new MatchedFragmentIon(type, ordinal, adduct, fragmentName, losses, predictedMz);
if (Rank == 0 && ApplyRanking(rp, type, offset, losses, adduct, filter, start, end, startMz, ionMz))
{
MatchedIons.Insert(0, match);
}
else
{
MatchedIons.Add(match);
}
if (MatchedIons.Count < RankParams.MAX_MATCH)
{
return(true);
}
rp.matched = true;
return(false);
}
// Avoid using the same predicted m/z on two different peaks
if (predictedMz == ionMz || !rp.IsSeen(predictedMz))
{
rp.Seen(predictedMz);
ApplyRanking(rp, type, offset, losses, adduct, filter, start, end, startMz, ionMz);
MatchedIons = new List <MatchedFragmentIon> {
new MatchedFragmentIon(type, ordinal, adduct, fragmentName, losses, predictedMz)
};
rp.matched = !rp.matchAll;
return(rp.matchAll);
}
}
// Stop looking once the mass has been passed, unless there are losses to consider
if (rp.HasLosses)
{
return(true);
}
return(ionMz <= ObservedMz);
}
