private static int OrderIntensityDesc(RankedMI mi1, RankedMI mi2)
{
float i1 = mi1.Intensity, i2 = mi2.Intensity;
if (i1 > i2)
{
return(-1);
}
if (i1 < i2)
{
return(1);
}
return(-OrderMz(mi1, mi2));
}
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 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 RankedMI CalculateRank(RankingState rankingState, RankedMI rankedMI)
{
// Rank based on filtered range, if the settings use it in picking
bool filter = (Pick == TransitionLibraryPick.filter);
var knownFragments = MoleculeMassesObj.MatchIonMasses.KnownFragments;
if (knownFragments != null)
{
// Small molecule work - we only know about the fragments we're given, we can't predict others
foreach (IonType type in Types)
{
if (Transition.IsPrecursor(type))
{
var matchedFragmentIon = MakeMatchedFragmentIon(type, 0, PrecursorAdduct, null, out double matchMz);
if (!MatchNext(rankingState, matchMz, matchedFragmentIon, filter, 0, 0, 0, ref rankedMI))
{
// If matched return. Otherwise look for other ion types.
if (rankingState.matched)
{
rankingState.Clean();
return(rankedMI);
}
}
}
else
{
for (var i = 0; i < knownFragments.Count; i++)
{
var fragment = knownFragments[i];
double matchMz = MoleculeMassesObj.PredictIonMasses.KnownFragments[i].PredictedMz;
if (!MatchNext(rankingState, matchMz, fragment, filter, 0, 0, fragment.PredictedMz, ref rankedMI))
{
// If matched return. Otherwise look for other ion types.
if (rankingState.matched)
{
rankingState.Clean();
return(rankedMI);
}
}
}
}
}
return(rankedMI);
}
// Look for a predicted match within the acceptable tolerance
int len = MoleculeMassesObj.MatchIonMasses.FragmentMasses.GetLength(1);
foreach (IonType type in Types)
{
if (Transition.IsPrecursor(type))
{
foreach (var losses in TransitionGroup.CalcTransitionLosses(type, 0, MassType, PotentialLosses))
{
var matchedFragmentIon =
MakeMatchedFragmentIon(type, 0, PrecursorAdduct, losses, out double matchMz);
if (!MatchNext(rankingState, matchMz, matchedFragmentIon, filter, len, len, 0, ref rankedMI))
{
// If matched return. Otherwise look for other ion types.
if (rankingState.matched)
{
rankingState.Clean();
return(rankedMI);
}
}
}
continue;
}
foreach (var adduct in Adducts)
{
// Precursor charge can never be lower than product ion charge.
if (Math.Abs(PrecursorAdduct.AdductCharge) < Math.Abs(adduct.AdductCharge))
{
continue;
}
int start = 0, end = 0;
double startMz = 0;
if (filter)
{
start = TransitionSettings.Filter.FragmentRangeFirst.FindStartFragment(
MoleculeMassesObj.MatchIonMasses.FragmentMasses, type, adduct,
MoleculeMassesObj.precursorMz, TransitionSettings.Filter.PrecursorMzWindow, out startMz);
end = TransitionSettings.Filter.FragmentRangeLast.FindEndFragment(type, start, len);
if (Transition.IsCTerminal(type))
{
Helpers.Swap(ref start, ref end);
}
}
// These inner loops are performance bottlenecks, and the following
// code duplication proved the fastest implementation under a
// profiler. Apparently .NET failed to inline an attempt to put
// the loop contents in a function.
if (Transition.IsCTerminal(type))
{
for (int i = len - 1; i >= 0; i--)
{
foreach (var losses in TransitionGroup.CalcTransitionLosses(type, i, MassType, PotentialLosses))
{
var matchedFragmentIon =
MakeMatchedFragmentIon(type, i, adduct, losses, out double matchMz);
if (!MatchNext(rankingState, matchMz, matchedFragmentIon, filter, end, start, startMz, ref rankedMI))
{
if (rankingState.matched)
{
rankingState.Clean();
return(rankedMI);
}
i = -1; // Terminate loop on i
break;
}
}
}
}
else
{
for (int i = 0; i < len; i++)
{
foreach (var losses in TransitionGroup.CalcTransitionLosses(type, i, MassType, PotentialLosses))
{
var matchedFragmentIon =
MakeMatchedFragmentIon(type, i, adduct, losses, out double matchMz);
if (!MatchNext(rankingState, matchMz, matchedFragmentIon, filter, end, start, startMz, ref rankedMI))
{
if (rankingState.matched)
{
rankingState.Clean();
return(rankedMI);
}
i = len; // Terminate loop on i
break;
}
}
}
}
}
}
return(rankedMI);
}
private static int OrderMz(RankedMI mi1, RankedMI mi2)
{
return(mi1.ObservedMz.CompareTo(mi2.ObservedMz));
}
public LibraryRankedSpectrumInfo RankSpectrum(SpectrumPeaksInfo info, int minPeaks, double?score)
{
var ionsToReturn = FragmentFilterObj.FragmentMatchCount;
RankingState rankingState = new RankingState()
{
matchAll = MatchAll,
};
// Get the library spectrum mass-intensity pairs
IList <SpectrumPeaksInfo.MI> listMI = info.Peaks;
// Because sorting and matching observed ions with predicted
// ions appear as bottlenecks in a profiler, a minimum number
// of peaks may be supplied to allow the use of a 2-phase linear
// filter that can significantly reduce the number of peaks
// needing the O(n*log(n)) sorting and the O(n*m) matching.
int len = listMI.Count;
float intensityCutoff = 0;
if (minPeaks != -1)
{
// Start searching for good cut-off at mean intensity.
double totalIntensity = info.Intensities.Sum();
FindIntensityCutoff(listMI, 0, (float)(totalIntensity / len) * 2, minPeaks, 1, ref intensityCutoff, ref len);
}
// Create filtered peak array storing original index for m/z ordering
// to avoid needing to sort to return to this order.
RankedMI[] arrayRMI = new RankedMI[len];
// Detect when m/z values are out of order, and use the expensive sort
// by m/z to correct this.
double lastMz = double.MinValue;
bool sortMz = false;
for (int i = 0, j = 0, lenOrig = listMI.Count; i < lenOrig; i++)
{
SpectrumPeaksInfo.MI mi = listMI[i];
if (mi.Intensity >= intensityCutoff || intensityCutoff == 0)
{
arrayRMI[j] = new RankedMI(mi, j);
j++;
}
if (!ionsToReturn.HasValue)
{
if (mi.Mz < lastMz)
{
sortMz = true;
}
lastMz = mi.Mz;
}
}
// The one expensive sort is used to determine rank order
// by intensity, or m/z in case of a tie.
Array.Sort(arrayRMI, OrderIntensityDesc);
RankedMI[] arrayResult = new RankedMI[ionsToReturn.HasValue ? ionsToReturn.Value : arrayRMI.Length];
foreach (RankedMI rmi in arrayRMI)
{
var rankedRmi = CalculateRank(rankingState, rmi);
// If not filtering for only the highest ionMatchCount ranks
if (!ionsToReturn.HasValue)
{
// Put the ranked record back where it started in the
// m/z ordering to avoid a second sort.
arrayResult[rmi.IndexMz] = rankedRmi;
}
// Otherwise, if this ion was ranked, add it to the result array
else if (rankedRmi.Rank > 0)
{
int countRanks = rankedRmi.Rank;
arrayResult[countRanks - 1] = rankedRmi;
// And stop when the array is full
if (countRanks == ionsToReturn.Value)
{
break;
}
}
}
// Is this a theoretical library with no intensity variation? If so it can't be ranked.
// If it has any interesting peak annotations, pass those through
if (rankingState.Ranked == 0 && arrayRMI.All(rmi => rmi.Intensity == arrayRMI[0].Intensity))
{
// Only do this if we have been asked to limit the ions matched, and there are any annotations
if (ionsToReturn.HasValue && arrayRMI.Any(rmi => rmi.HasAnnotations))
{
// Pass through anything with an annotation as being of probable interest
arrayResult = arrayRMI.Where(rmi => rmi.HasAnnotations).ToArray();
ionsToReturn = null;
}
}
// If not enough ranked ions were found, fill the rest of the results array
if (ionsToReturn.HasValue)
{
for (int i = rankingState.Ranked; i < ionsToReturn.Value; i++)
{
arrayResult[i] = RankedMI.EMPTY;
}
}
// If all ions are to be included, and some were found out of order, then
// the expensive full sort by m/z is necessary.
else if (sortMz)
{
Array.Sort(arrayResult, OrderMz);
}
double?spectrumScore;
if (score == null && GroupDocNode.HasLibInfo && GroupDocNode.LibInfo is BiblioSpecSpectrumHeaderInfo libInfo)
{
spectrumScore = libInfo.Score;
}
else
{
spectrumScore = score;
}
return(new LibraryRankedSpectrumInfo(PredictLabelType, Libraries.IonMatchTolerance, arrayResult, spectrumScore));
}