public void CalculateRank(RankParams rp)
{
// Rank based on filtered range, if the settings use it in picking
bool filter = (rp.pick == TransitionLibraryPick.filter);
if (rp.knownFragments != null)
{
// Small molecule work - we only know about the fragments we're given, we can't predict others
foreach (IonType type in rp.types)
{
if (Transition.IsPrecursor(type))
{
if (!MatchNext(rp, type, 0, null, rp.precursorAdduct, null, 0, filter, 0, 0, 0))
{
// If matched return. Otherwise look for other ion types.
if (rp.matched)
{
rp.Clean();
return;
}
}
}
else
{
for (var i = 0; i < rp.knownFragments.Count; i++)
{
var fragment = rp.knownFragments[i];
if (!MatchNext(rp, IonType.custom, i, null, fragment.Adduct, fragment.Name, 0, filter, 0, 0, fragment.Mz))
{
// If matched return. Otherwise look for other ion types.
if (rp.matched)
{
rp.Clean();
return;
}
}
}
}
}
return;
}
// Look for a predicted match within the acceptable tolerance
int len = rp.massesMatch.GetLength(1);
foreach (IonType type in rp.types)
{
if (Transition.IsPrecursor(type))
{
foreach (var losses in TransitionGroup.CalcTransitionLosses(type, 0, rp.massType, rp.potentialLosses))
{
if (!MatchNext(rp, type, len, losses, rp.precursorAdduct, null, len + 1, filter, len, len, 0))
{
// If matched return. Otherwise look for other ion types.
if (rp.matched)
{
rp.Clean();
return;
}
}
}
continue;
}
foreach (var adduct in rp.adducts)
{
// Precursor charge can never be lower than product ion charge.
if (Math.Abs(rp.precursorAdduct.AdductCharge) < Math.Abs(adduct.AdductCharge))
{
continue;
}
int start = 0, end = 0;
double startMz = 0;
if (filter)
{
start = rp.startFinder.FindStartFragment(rp.massesMatch, type, adduct,
rp.precursorMz, rp.filter.PrecursorMzWindow, out startMz);
end = rp.endFinder.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, rp.massType, rp.potentialLosses))
{
if (!MatchNext(rp, type, i, losses, adduct, null, len, filter, end, start, startMz))
{
if (rp.matched)
{
rp.Clean();
return;
}
i = -1; // Terminate loop on i
break;
}
}
}
}
else
{
for (int i = 0; i < len; i++)
{
foreach (var losses in TransitionGroup.CalcTransitionLosses(type, i, rp.massType, rp.potentialLosses))
{
if (!MatchNext(rp, type, i, losses, adduct, null, len, filter, end, start, startMz))
{
if (rp.matched)
{
rp.Clean();
return;
}
i = len; // Terminate loop on i
break;
}
}
}
}
}
}
}
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);
}