/// <summary>
/// Returns a LibraryRankedSpectrumInfo
/// </summary>
/// <param name="info">The spectrum to be ranked</param>
/// <param name="labelType">The IsotopeLabelType for the peptide in the library. This might be different from the
/// LabelType on the GroupDocNode.</param>
/// <param name="groupDocNode">The Transition Group from the user's document</param>
/// <param name="settings"></param>
/// <param name="lookupSequence"></param>
/// <param name="lookupMods"></param>
/// <param name="charges">The set of charges that the user is choosing to show in the spectrum viewer.</param>
/// <param name="types">The set of ion types to be displayed</param>
/// <param name="rankCharges">The set of charges that are enabled in the document's Transition Settings</param>
/// <param name="rankTypes">The set of ion types in the user's transition settings</param>
/// <param name="score">the score to assign to the spectrum. If it is null, then the spectrum gets the score from transition group's LibInfo</param>
/// <param name="useFilter">true if this list is being generated in order to show the filtered list of potential transitions</param>
/// <param name="matchAll">true if peaks matched peaks should be given a list of all of the ion types that they match, instead
/// of only being annotated with the first matching one</param>
/// <param name="minPeaks">The minimum number of peaks to match, or -1 to match as many as possible</param>
/// <returns></returns>
public static LibraryRankedSpectrumInfo RankSpectrum(SpectrumPeaksInfo info,
IsotopeLabelType labelType,
TransitionGroupDocNode groupDocNode, SrmSettings settings,
Target lookupSequence, ExplicitMods lookupMods,
IEnumerable <Adduct> charges, IEnumerable <IonType> types,
IEnumerable <Adduct> rankCharges, IEnumerable <IonType> rankTypes,
double?score, bool useFilter, bool matchAll, int minPeaks)
{
var targetInfo = new TargetInfo(labelType, groupDocNode, lookupSequence, lookupMods);
var fragmentFilter = new FragmentFilter(settings.TransitionSettings, rankCharges, rankTypes).ChangeMatchAll(matchAll);
if (!useFilter)
{
bool isProteomic = groupDocNode.TransitionGroup.IsProteomic;
fragmentFilter = fragmentFilter.ChangeUseFilter(false);
fragmentFilter = fragmentFilter
.ChangeAdductsToDisplay(charges ?? GetRanked(fragmentFilter.RankedAdducts,
isProteomic
? Transition.DEFAULT_PEPTIDE_CHARGES
: Transition.DEFAULT_MOLECULE_CHARGES));
fragmentFilter = fragmentFilter.ChangeIonTypesToDisplay(
types ?? GetRanked(fragmentFilter.RankedIonTypes,
isProteomic ? Transition.PEPTIDE_ION_TYPES : Transition.MOLECULE_ION_TYPES));
fragmentFilter = fragmentFilter.ChangeMatchAll(true);
}
else
{
if (null != charges)
{
fragmentFilter = fragmentFilter.ChangeAdductsToDisplay(charges);
}
if (null != types)
{
fragmentFilter = fragmentFilter.ChangeIonTypesToDisplay(types);
}
}
bool limitRanks =
groupDocNode.IsCustomIon && // For small molecules, cap the number of ranked ions displayed if we don't have any peak metadata
groupDocNode.Transitions.Any(t => string.IsNullOrEmpty(t.FragmentIonName));
if (limitRanks)
{
fragmentFilter = fragmentFilter.ChangeRankLimit(settings.TransitionSettings.Libraries.IonCount);
}
// If no library filtering will happen, return all rankings for view in the UI
if (!useFilter || fragmentFilter.LibraryPick == TransitionLibraryPick.none)
{
if (fragmentFilter.LibraryPick == TransitionLibraryPick.none)
{
fragmentFilter = fragmentFilter.ChangeLibraryPick(TransitionLibraryPick.all);
}
fragmentFilter = fragmentFilter.ChangeFragmentMatchCount(null);
}
var spectrumRanker = new SpectrumRanker(targetInfo, settings, fragmentFilter);
return(spectrumRanker.RankSpectrum(info, minPeaks, score));
}
private static LibraryRankedSpectrumInfo MakeLibraryRankedSpectrumInfo(SpectrumPeaksInfo info,
IsotopeLabelType labelType,
TransitionGroupDocNode groupDocNode, SrmSettings settings,
Target lookupSequence, ExplicitMods lookupMods,
IEnumerable <Adduct> charges, IEnumerable <IonType> types,
IEnumerable <Adduct> rankCharges, IEnumerable <IonType> rankTypes,
double?score, bool useFilter, bool matchAll, int minPeaks)
{
return(SpectrumRanker.RankSpectrum(info, labelType, groupDocNode, settings, lookupSequence, lookupMods,
charges, types, rankCharges, rankTypes, score, useFilter, matchAll, minPeaks));
}
