public override bool TryLoadSpectrum(LibKey key, out SpectrumPeaksInfo spectrum)
{
spectrum = null;
DbSpectrum[] spectra;
if (!key.IsPrecursorKey)
{
spectra = GetSpectraByPeptide(null, key).ToArray();
}
else
{
spectra = GetSpectraByPrecursor(null, key.PrecursorMz.GetValueOrDefault()).ToArray();
var keyRt = key.RetentionTime;
if (keyRt.HasValue)
{
spectra = spectra.Where(s => Equals(keyRt.Value, s.RetentionTime)).ToArray();
}
}
if (!spectra.Any())
{
return(false);
}
var spec = spectra.First();
var mi = spec.Mzs.Select((t, i) => new SpectrumPeaksInfo.MI {
Mz = spec.Mzs[i], Intensity = (float)spec.Intensities[i]
}); // CONSIDER(bspratt): annotation?
spectrum = new SpectrumPeaksInfo(mi.ToArray());
return(true);
}
/// <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));
}
public LibraryRankedSpectrumInfo(SpectrumPeaksInfo info,
IsotopeLabelType labelType, TransitionGroup group,
SrmSettings settings, string lookupSequence, ExplicitMods lookupMods,
IEnumerable <int> charges, IEnumerable <IonType> types,
IEnumerable <int> rankCharges, IEnumerable <IonType> rankTypes)
: this(info, labelType, group, settings, lookupSequence, lookupMods,
charges, types, rankCharges, rankTypes, false, true, -1)
{
}
public LibraryRankedSpectrumInfo(SpectrumPeaksInfo info,
IsotopeLabelType labelType, TransitionGroupDocNode group,
SrmSettings settings, Target lookupSequence, ExplicitMods lookupMods,
IEnumerable <Adduct> charges, IEnumerable <IonType> types,
IEnumerable <Adduct> rankCharges, IEnumerable <IonType> rankTypes, double?score)
: this(info, labelType, group, settings, lookupSequence, lookupMods,
charges, types, rankCharges, rankTypes, score, false, true, -1)
{
}
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));
}
public LibraryRankedSpectrumInfo(SpectrumPeaksInfo info, IsotopeLabelType labelType,
TransitionGroup group, SrmSettings settings, ExplicitMods lookupMods,
bool useFilter, int minPeaks)
: this(info, labelType, group, settings, group.Peptide.Sequence, lookupMods,
null, // charges
null, // types
// ReadOnlyCollection enumerators are too slow, and show under a profiler
settings.TransitionSettings.Filter.ProductCharges.ToArray(),
settings.TransitionSettings.Filter.IonTypes.ToArray(),
useFilter, false, minPeaks)
{
}
public LibraryRankedSpectrumInfo(SpectrumPeaksInfo info, IsotopeLabelType labelType,
TransitionGroupDocNode group, SrmSettings settings, ExplicitMods lookupMods,
bool useFilter, int minPeaks)
: this(info, labelType, group, settings, group.Peptide.Target, lookupMods,
null, // charges
null, // types
// ReadOnlyCollection enumerators are too slow, and show under a profiler
group.IsCustomIon ? settings.TransitionSettings.Filter.SmallMoleculeFragmentAdducts.ToArray() : settings.TransitionSettings.Filter.PeptideProductCharges.ToArray(),
group.IsCustomIon ? settings.TransitionSettings.Filter.SmallMoleculeIonTypes.ToArray() : settings.TransitionSettings.Filter.PeptideIonTypes.ToArray(),
null, useFilter, false, minPeaks)
{
}
public override bool TryLoadSpectrum(LibKey key, out SpectrumPeaksInfo spectrum)
{
BiblioSpectrumInfo info;
if (_dictLibrary != null && _dictLibrary.TryGetValue(key, out info))
{
spectrum = new SpectrumPeaksInfo(ReadSpectrum(info));
return(true);
}
spectrum = null;
return(false);
}
public override bool TryLoadSpectrum(LibKey key, out SpectrumPeaksInfo spectrum)
{
if (_dictLibrary != null)
{
foreach (var item in _dictLibrary.ItemsMatching(key.LibraryKey, true))
{
spectrum = new SpectrumPeaksInfo(ReadSpectrum(item));
return(true);
}
}
spectrum = null;
return(false);
}
public PrositMS2Spectrum(SrmSettings settings, PrositIntensityModel.PeptidePrecursorNCE peptidePrecursorNCE,
int precursorIndex, PrositIntensityModel.PrositIntensityOutput prositIntensityOutput, IsotopeLabelType labelTypeOverride = null)
{
PeptidePrecursorNCE = peptidePrecursorNCE;
Settings = settings;
var precursor = peptidePrecursorNCE.NodeGroup;
var peptide = peptidePrecursorNCE.NodePep;
var calc = settings.GetFragmentCalc(IsotopeLabelType.light, peptide.ExplicitMods);
var ionTable = calc.GetFragmentIonMasses(peptide.Target); // TODO: get mods and pass them as explicit mods above?
var ions = ionTable.GetLength(1);
var mis = new List <SpectrumPeaksInfo.MI>(ions * PrositConstants.IONS_PER_RESIDUE);
for (int i = 0; i < ions; ++i)
{
var intensities = prositIntensityOutput.OutputRows[precursorIndex].Intensities[i].Intensities
.Select(ReLu).ToArray();
var yMIs = CalcMIs(ionTable[IonType.y, ions - i - 1], intensities, 0);
var bMIs = CalcMIs(ionTable[IonType.b, i], intensities, PrositConstants.IONS_PER_RESIDUE / 2);
mis.AddRange(yMIs);
mis.AddRange(bMIs);
}
var maxIntensity = mis.Max(mi => mi.Intensity);
// Max Norm
for (int i = 0; i < mis.Count; ++i)
{
mis[i] = new SpectrumPeaksInfo.MI {
Mz = mis[i].Mz, Intensity = mis[i].Intensity / maxIntensity
}
}
;
SpectrumPeaks = new SpectrumPeaksInfo(mis.ToArray());
}
public bool TryLoadSpectrum(string sequence, int charge, ExplicitMods mods,
out IsotopeLabelType type, out SpectrumPeaksInfo spectrum)
{
var libraries = PeptideSettings.Libraries;
foreach (var typedSequence in GetTypedSequences(sequence, mods))
{
var key = new LibKey(typedSequence.ModifiedSequence, charge);
if (libraries.TryLoadSpectrum(key, out spectrum))
{
type = typedSequence.LabelType;
return true;
}
}
type = IsotopeLabelType.light;
spectrum = null;
return false;
}
private void GetSmallMoleculeFragments(LibKey key, TransitionGroupDocNode nodeGroupMatched, SpectrumPeaksInfo spectrum,
IList <DocNode> transitionDocNodes)
{
// We usually don't know actual charge of fragments in the library, so just note + or - if
// there are no peak annotations containing that info
var fragmentCharge = key.Adduct.AdductCharge < 0 ? Adduct.M_MINUS : Adduct.M_PLUS;
// Get list of possible transitions based on library spectrum
var transitionsUnranked = new List <DocNode>();
foreach (var peak in spectrum.Peaks)
{
transitionsUnranked.Add(TransitionFromPeakAndAnnotations(key, nodeGroupMatched, fragmentCharge, peak, null));
}
var nodeGroupUnranked = (TransitionGroupDocNode)nodeGroupMatched.ChangeChildren(transitionsUnranked);
// Filter again, retain only those with rank info, or at least an interesting name
SpectrumHeaderInfo groupLibInfo = null;
var transitionRanks = new Dictionary <double, LibraryRankedSpectrumInfo.RankedMI>();
nodeGroupUnranked.GetLibraryInfo(Settings, ExplicitMods.EMPTY, true, ref groupLibInfo, transitionRanks);
foreach (var ranked in transitionRanks)
{
transitionDocNodes.Add(TransitionFromPeakAndAnnotations(key, nodeGroupMatched, fragmentCharge, ranked.Value.MI, ranked.Value.Rank));
}
// And add any unranked that have names to display
foreach (var unrankedT in nodeGroupUnranked.Transitions)
{
var unranked = unrankedT;
if (!string.IsNullOrEmpty(unranked.Transition.CustomIon.Name) &&
!transitionDocNodes.Any(t => t is TransitionDocNode && unranked.Transition.Equivalent(((TransitionDocNode)t).Transition)))
{
transitionDocNodes.Add(unranked);
}
}
}
public override bool TryLoadSpectrum(LibKey key, out SpectrumPeaksInfo spectrum)
{
BiblioSpectrumInfo info;
if (_dictLibrary != null && _dictLibrary.TryGetValue(key, out info))
{
spectrum = new SpectrumPeaksInfo(ReadSpectrum(info));
return true;
}
spectrum = null;
return false;
}
public static ICollection <DbRefSpectraPeakAnnotations> Create(DbRefSpectra refSpectra, SpectrumPeaksInfo peaks)
{
List <DbRefSpectraPeakAnnotations> resultList = null;
// Each peak may have more than one annotation
if (peaks.Peaks.Any(p => p.Annotations != null && p.Annotations.Any(a => !SpectrumPeakAnnotation.IsNullOrEmpty(a))))
{
resultList = new List <DbRefSpectraPeakAnnotations>();
var i = 0;
foreach (var peak in peaks.Peaks)
{
if (peak.Annotations != null)
{
foreach (var annotation in peak.Annotations.Where(a => !SpectrumPeakAnnotation.IsNullOrEmpty(a)))
{
var result = new DbRefSpectraPeakAnnotations
{
RefSpectra = refSpectra,
PeakIndex = i,
Name = annotation.Ion.Name,
Formula = annotation.Ion.NeutralFormula,
InchiKey = annotation.Ion.AccessionNumbers.GetInChiKey(),
OtherKeys = annotation.Ion.AccessionNumbers.GetNonInChiKeys(),
Adduct = annotation.Ion.Adduct.ToString(),
Charge = annotation.Ion.Adduct.AdductCharge,
Comment = annotation.Comment,
mzTheoretical = annotation.Ion.MonoisotopicMassMz,
mzObserved = peak.Mz
};
resultList.Add(result);
}
}
i++;
}
}
return(resultList);
}
private static byte[] MZsToBytes(SpectrumPeaksInfo.MI[] peaks)
{
const int sizeMz = sizeof(double);
byte[] peakMZs = new byte[peaks.Length * sizeMz];
for (int i = 0; i < peaks.Length; i++)
{
int offset = i * sizeMz;
Array.Copy(BitConverter.GetBytes(peaks[i].Mz), 0, peakMZs, offset, sizeMz);
}
return peakMZs.Compress();
}
private static byte[] IntensitiesToBytes(SpectrumPeaksInfo.MI[] peaks)
{
const int sizeInten = sizeof(float);
byte[] peakIntens = new byte[peaks.Length * sizeInten];
for (int i = 0; i < peaks.Length; i++)
{
int offset = i*sizeInten;
Array.Copy(BitConverter.GetBytes(peaks[i].Intensity), 0, peakIntens, offset, sizeInten);
}
return peakIntens.Compress();
}
public bool TryLoadSpectrum(LibKey key, out SpectrumPeaksInfo spectrum)
{
Assume.IsTrue(IsLoaded);
foreach (Library lib in _libraries)
{
if (lib != null && lib.TryLoadSpectrum(key, out spectrum))
return true;
}
spectrum = null;
return false;
}
private LibraryRankedSpectrumInfo(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)
{
LabelType = labelType;
// Avoid ReSharper multiple enumeration warning
var rankChargesArray = rankCharges.ToArray();
var rankTypesArray = rankTypes.ToArray();
TransitionGroup group = groupDocNode.TransitionGroup;
bool isProteomic = group.IsProteomic;
if (score == null && groupDocNode.HasLibInfo && groupDocNode.LibInfo is BiblioSpecSpectrumHeaderInfo libInfo)
{
Score = libInfo.Score;
}
else
{
Score = score;
}
if (!useFilter)
{
if (charges == null)
{
charges = GetRanked(rankChargesArray, isProteomic ? Transition.DEFAULT_PEPTIDE_CHARGES : Transition.DEFAULT_MOLECULE_CHARGES);
}
if (types == null)
{
types = GetRanked(rankTypesArray, isProteomic ? Transition.PEPTIDE_ION_TYPES : Transition.MOLECULE_ION_TYPES);
}
matchAll = true;
}
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));
RankParams rp = new RankParams
{
sequence = lookupSequence,
precursorAdduct = group.PrecursorAdduct,
adducts = charges ?? rankCharges,
types = types ?? rankTypes,
matchAll = matchAll,
rankCharges = rankChargesArray.Select(a => Math.Abs(a.AdductCharge)).ToArray(),
rankTypes = rankTypesArray,
// Precursor isotopes will not be included in MS/MS, if they will be filtered
// from MS1
excludePrecursorIsotopes = settings.TransitionSettings.FullScan.IsEnabledMs,
tranSettings = settings.TransitionSettings,
rankLimit = limitRanks ? settings.TransitionSettings.Libraries.IonCount : (int?)null
};
// Get necessary mass calculators and masses
var calcMatchPre = settings.GetPrecursorCalc(labelType, lookupMods);
var calcMatch = isProteomic ? settings.GetFragmentCalc(labelType, lookupMods) : settings.GetDefaultFragmentCalc();
var calcPredict = isProteomic ? settings.GetFragmentCalc(group.LabelType, lookupMods) : calcMatch;
if (isProteomic && rp.sequence.IsProteomic)
{
rp.precursorMz = SequenceMassCalc.GetMZ(calcMatchPre.GetPrecursorMass(rp.sequence), rp.precursorAdduct);
rp.massPreMatch = calcMatch.GetPrecursorFragmentMass(rp.sequence);
rp.massesMatch = calcMatch.GetFragmentIonMasses(rp.sequence);
rp.knownFragments = null;
}
else if (!isProteomic && !rp.sequence.IsProteomic)
{
string isotopicForumla;
rp.precursorMz = SequenceMassCalc.GetMZ(calcMatchPre.GetPrecursorMass(rp.sequence.Molecule, null, rp.precursorAdduct, out isotopicForumla), rp.precursorAdduct);
rp.massPreMatch = calcMatch.GetPrecursorFragmentMass(rp.sequence);
// rp.massesMatch = calcMatch.GetFragmentIonMasses(rp.molecule); CONSIDER, for some molecule types someday?
// For small molecules we can't predict fragmentation, so just use those we have
// Older Resharper code inspection implementations insist on warning here
// Resharper disable PossibleMultipleEnumeration
var existing = groupDocNode.Transitions.Where(tran => tran.Transition.IsNonPrecursorNonReporterCustomIon()).Select(t => t.Transition.CustomIon.GetMass(MassType.Monoisotopic)).ToArray();
rp.massesMatch = new IonTable <TypedMass>(IonType.custom, existing.Length);
for (var i = 0; i < existing.Length; i++)
{
rp.massesMatch[IonType.custom, i] = existing[i];
}
// Resharper restore PossibleMultipleEnumeration
rp.knownFragments = groupDocNode.Transitions.Where(tran => tran.Transition.IsNonPrecursorNonReporterCustomIon()).Select(t =>
new KnownFragment
{
Adduct = t.Transition.Adduct,
Name = t.GetFragmentIonName(CultureInfo.CurrentCulture, settings.TransitionSettings.Libraries.IonMatchTolerance),
Mz = t.Mz
}).ToList();
}
else
{
rp.precursorMz = 0.0;
rp.massPreMatch = TypedMass.ZERO_MONO_MASSH;
rp.massesMatch = IonTable <TypedMass> .EMPTY;
rp.knownFragments = null;
}
rp.massPrePredict = rp.massPreMatch;
rp.massesPredict = rp.massesMatch;
if (!ReferenceEquals(calcPredict, calcMatch))
{
rp.massPrePredict = calcPredict.GetPrecursorFragmentMass(rp.sequence);
if (rp.sequence.IsProteomic) // CONSIDER - eventually we may be able to predict fragments for small molecules?
{
rp.massesPredict = calcPredict.GetFragmentIonMasses(rp.sequence);
}
}
// Get values of interest from the settings.
var tranSettings = settings.TransitionSettings;
var predict = tranSettings.Prediction;
var filter = tranSettings.Filter;
var libraries = tranSettings.Libraries;
var instrument = tranSettings.Instrument;
// Get potential losses to all fragments in this peptide
rp.massType = predict.FragmentMassType;
rp.potentialLosses = TransitionGroup.CalcPotentialLosses(rp.sequence,
settings.PeptideSettings.Modifications, lookupMods,
rp.massType);
// Create arrays because ReadOnlyCollection enumerators are too slow
// In some cases these collections must be enumerated for every ion
// allowed in the library specturm.
rp.startFinder = filter.FragmentRangeFirst;
rp.endFinder = filter.FragmentRangeLast;
// Get library settings
Tolerance = libraries.IonMatchTolerance;
rp.tolerance = Tolerance;
rp.pick = tranSettings.Libraries.Pick;
int ionMatchCount = libraries.IonCount;
// If no library filtering will happen, return all rankings for view in the UI
if (!useFilter || rp.pick == TransitionLibraryPick.none)
{
if (rp.pick == TransitionLibraryPick.none)
{
rp.pick = TransitionLibraryPick.all;
}
ionMatchCount = -1;
}
// Get instrument settings
rp.minMz = instrument.MinMz;
rp.maxMz = instrument.MaxMz;
// 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 (ionMatchCount == -1)
{
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[ionMatchCount != -1 ? ionMatchCount : arrayRMI.Length];
foreach (RankedMI rmi in arrayRMI)
{
rmi.CalculateRank(rp);
// If not filtering for only the highest ionMatchCount ranks
if (ionMatchCount == -1)
{
// Put the ranked record back where it started in the
// m/z ordering to avoid a second sort.
arrayResult[rmi.IndexMz] = rmi;
}
// Otherwise, if this ion was ranked, add it to the result array
else if (rmi.Rank > 0)
{
int countRanks = rmi.Rank;
arrayResult[countRanks - 1] = rmi;
// And stop when the array is full
if (countRanks == ionMatchCount)
{
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 (rp.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 (ionMatchCount != -1 && arrayRMI.Any(rmi => rmi.HasAnnotations))
{
// Pass through anything with an annotation as being of probable interest
arrayResult = arrayRMI.Where(rmi => rmi.HasAnnotations).ToArray();
ionMatchCount = -1;
}
}
// If not enough ranked ions were found, fill the rest of the results array
if (ionMatchCount != -1)
{
for (int i = rp.Ranked; i < ionMatchCount; 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 necesary.
else if (sortMz)
{
Array.Sort(arrayResult, OrderMz);
}
_spectrum = MakeReadOnly(arrayResult);
}
private LibraryRankedSpectrumInfo(SpectrumPeaksInfo info, IsotopeLabelType labelType,
TransitionGroup group, SrmSettings settings,
string lookupSequence, ExplicitMods lookupMods,
IEnumerable <int> charges, IEnumerable <IonType> types,
IEnumerable <int> rankCharges, IEnumerable <IonType> rankTypes,
bool useFilter, bool matchAll, int minPeaks)
{
LabelType = labelType;
// Avoid ReSharper multiple enumeration warning
var rankChargesArray = rankCharges.ToArray();
var rankTypesArray = rankTypes.ToArray();
if (!useFilter)
{
if (charges == null)
{
charges = GetRanked(rankChargesArray, Transition.ALL_CHARGES);
}
if (types == null)
{
types = GetRanked(rankTypesArray, Transition.ALL_TYPES);
}
matchAll = true;
}
RankParams rp = new RankParams
{
sequence = lookupSequence,
precursorCharge = group.PrecursorCharge,
charges = charges ?? rankCharges,
types = types ?? rankTypes,
matchAll = matchAll,
rankCharges = rankChargesArray,
rankTypes = rankTypesArray,
// Precursor isotopes will not be included in MS/MS, if they will be filtered
// from MS1
excludePrecursorIsotopes = settings.TransitionSettings.FullScan.IsEnabledMs,
tranSettings = settings.TransitionSettings
};
// Get necessary mass calculators and masses
var calcMatchPre = settings.GetPrecursorCalc(labelType, lookupMods);
var calcMatch = settings.GetFragmentCalc(labelType, lookupMods);
var calcPredict = settings.GetFragmentCalc(group.LabelType, lookupMods);
if (!string.IsNullOrEmpty(rp.sequence))
{
rp.precursorMz = SequenceMassCalc.GetMZ(calcMatchPre.GetPrecursorMass(rp.sequence), rp.precursorCharge);
rp.massPreMatch = calcMatch.GetPrecursorFragmentMass(rp.sequence);
rp.massesMatch = calcMatch.GetFragmentIonMasses(rp.sequence);
}
else
{
rp.precursorMz = 0.0;
rp.massPreMatch = 0.0;
rp.massesMatch = new double[0, 0];
}
rp.massPrePredict = rp.massPreMatch;
rp.massesPredict = rp.massesMatch;
if (!ReferenceEquals(calcPredict, calcMatch) && !string.IsNullOrEmpty(rp.sequence))
{
rp.massPrePredict = calcPredict.GetPrecursorFragmentMass(rp.sequence);
rp.massesPredict = calcPredict.GetFragmentIonMasses(rp.sequence);
}
// Get values of interest from the settings.
var tranSettings = settings.TransitionSettings;
var predict = tranSettings.Prediction;
var filter = tranSettings.Filter;
var libraries = tranSettings.Libraries;
var instrument = tranSettings.Instrument;
// Get potential losses to all fragments in this peptide
rp.massType = predict.FragmentMassType;
rp.potentialLosses = TransitionGroup.CalcPotentialLosses(rp.sequence,
settings.PeptideSettings.Modifications, lookupMods,
rp.massType);
// Create arrays because ReadOnlyCollection enumerators are too slow
// In some cases these collections must be enumerated for every ion
// allowed in the library specturm.
rp.startFinder = filter.FragmentRangeFirst;
rp.endFinder = filter.FragmentRangeLast;
// Get library settings
Tolerance = libraries.IonMatchTolerance;
rp.tolerance = Tolerance;
rp.pick = tranSettings.Libraries.Pick;
int ionMatchCount = libraries.IonCount;
// If no library filtering will happen, return all rankings for view in the UI
if (!useFilter || rp.pick == TransitionLibraryPick.none)
{
if (rp.pick == TransitionLibraryPick.none)
{
rp.pick = TransitionLibraryPick.all;
}
ionMatchCount = -1;
}
// Get instrument settings
rp.minMz = instrument.MinMz;
rp.maxMz = instrument.MaxMz;
// 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 (ionMatchCount == -1)
{
if (mi.Mz < lastMz)
{
sortMz = true;
}
lastMz = mi.Mz;
}
}
// The one expensive sort is used to determine rank order
// by intensity.
Array.Sort(arrayRMI, OrderIntensityDesc);
RankedMI[] arrayResult = new RankedMI[ionMatchCount != -1 ? ionMatchCount : arrayRMI.Length];
foreach (RankedMI rmi in arrayRMI)
{
rmi.CalculateRank(rp);
// If not filtering for only the highest ionMatchCount ranks
if (ionMatchCount == -1)
{
// Put the ranked record back where it started in the
// m/z ordering to avoid a second sort.
arrayResult[rmi.IndexMz] = rmi;
}
// Otherwise, if this ion was ranked, add it to the result array
else if (rmi.Rank > 0)
{
int countRanks = rmi.Rank;
arrayResult[countRanks - 1] = rmi;
// And stop when the array is full
if (countRanks == ionMatchCount)
{
break;
}
}
}
// If not enough ranked ions were found, fill the rest of the results array
if (ionMatchCount != -1)
{
for (int i = rp.Ranked; i < ionMatchCount; 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 necesary.
else if (sortMz)
{
Array.Sort(arrayResult, OrderMz);
}
_spectrum = MakeReadOnly(arrayResult);
}
public void UpdateUI(bool selectionChanged = true)
{
// Only worry about updates, if the graph is visible
// And make sure it is not disposed, since rendering happens on a timer
if (!Visible || IsDisposed)
{
return;
}
// Clear existing data from the graph pane
var graphPane = (MSGraphPane)graphControl.MasterPane[0];
graphPane.CurveList.Clear();
graphPane.GraphObjList.Clear();
GraphItem = null;
GraphHelper.FormatGraphPane(graphControl.GraphPane);
GraphHelper.FormatFontSize(graphControl.GraphPane, Settings.Default.SpectrumFontSize);
// Try to find a tree node with spectral library info associated
// with the current selection.
var nodeTree = _stateProvider.SelectedNode as SrmTreeNode;
var nodeGroupTree = nodeTree as TransitionGroupTreeNode;
var nodeTranTree = nodeTree as TransitionTreeNode;
if (nodeTranTree != null)
{
nodeGroupTree = nodeTranTree.Parent as TransitionGroupTreeNode;
}
var nodeGroup = (nodeGroupTree != null ? nodeGroupTree.DocNode : null);
PeptideTreeNode nodePepTree;
if (nodeGroup == null)
{
nodePepTree = nodeTree as PeptideTreeNode;
if (nodePepTree != null)
{
var listInfoGroups = GetLibraryInfoChargeGroups(nodePepTree);
if (listInfoGroups.Length == 1)
{
nodeGroup = listInfoGroups[0];
}
else if (listInfoGroups.Length > 1)
{
_nodeGroup = null;
toolBar.Visible = false;
_graphHelper.SetErrorGraphItem(new NoDataMSGraphItem(
Resources.GraphSpectrum_UpdateUI_Multiple_charge_states_with_library_spectra));
return;
}
}
}
else
{
nodePepTree = nodeGroupTree.Parent as PeptideTreeNode;
}
// Check for appropriate spectrum to load
SrmSettings settings = DocumentUI.Settings;
PeptideLibraries libraries = settings.PeptideSettings.Libraries;
bool available = false;
if (nodeGroup == null || (!nodeGroup.HasLibInfo && !libraries.HasMidasLibrary))
{
_spectra = null;
}
else
{
TransitionGroup group = nodeGroup.TransitionGroup;
TransitionDocNode transition = (nodeTranTree == null ? null : nodeTranTree.DocNode);
var lookupSequence = group.Peptide.Target;// Sequence or custom ion id
ExplicitMods lookupMods = null;
if (nodePepTree != null)
{
lookupSequence = nodePepTree.DocNode.SourceUnmodifiedTarget;
lookupMods = nodePepTree.DocNode.SourceExplicitMods;
}
try
{
// Try to load a list of spectra matching the criteria for
// the current node group.
if (libraries.HasLibraries && libraries.IsLoaded)
{
if (NodeGroupChanged(nodeGroup))
{
try
{
UpdateSpectra(nodeGroup, lookupSequence, lookupMods);
UpdateToolbar();
}
catch (Exception)
{
_spectra = null;
UpdateToolbar();
throw;
}
_nodeGroup = nodeGroup;
if (settings.TransitionSettings.Instrument.IsDynamicMin)
{
ZoomSpectrumToSettings();
}
}
var spectrum = SelectedSpectrum;
if (spectrum != null)
{
IsotopeLabelType typeInfo = spectrum.LabelType;
var types = _stateProvider.ShowIonTypes(group.IsProteomic);
var adducts = (group.IsProteomic ?
Transition.DEFAULT_PEPTIDE_LIBRARY_CHARGES :
nodeGroup.InUseAdducts).ToArray();
var charges = _stateProvider.ShowIonCharges(adducts);
var rankTypes = group.IsProteomic ? settings.TransitionSettings.Filter.PeptideIonTypes : settings.TransitionSettings.Filter.SmallMoleculeIonTypes;
var rankAdducts = group.IsProteomic ? settings.TransitionSettings.Filter.PeptideProductCharges : settings.TransitionSettings.Filter.SmallMoleculeFragmentAdducts;
var rankCharges = Adduct.OrderedAbsoluteChargeValues(rankAdducts);
// Make sure the types and charges in the settings are at the head
// of these lists to give them top priority, and get rankings correct.
int i = 0;
foreach (IonType type in rankTypes)
{
if (types.Remove(type))
{
types.Insert(i++, type);
}
}
i = 0;
var showAdducts = new List <Adduct>();
foreach (var charge in rankCharges)
{
if (charges.Remove(charge))
{
charges.Insert(i++, charge);
}
// NB for all adducts we just look at abs value of charge
// CONSIDER(bspratt): we may want finer per-adduct control for small molecule use
showAdducts.AddRange(adducts.Where(a => charge == Math.Abs(a.AdductCharge)));
}
showAdducts.AddRange(adducts.Where(a => charges.Contains(Math.Abs(a.AdductCharge)) && !showAdducts.Contains(a)));
SpectrumPeaksInfo spectrumInfo = spectrum.SpectrumPeaksInfo;
var spectrumInfoR = new LibraryRankedSpectrumInfo(spectrumInfo,
typeInfo,
nodeGroup,
settings,
lookupSequence,
lookupMods,
showAdducts,
types,
rankAdducts,
rankTypes);
GraphItem = new SpectrumGraphItem(nodeGroup, transition, spectrumInfoR, spectrum.LibName)
{
ShowTypes = types,
ShowCharges = charges,
ShowRanks = Settings.Default.ShowRanks,
ShowMz = Settings.Default.ShowIonMz,
ShowObservedMz = Settings.Default.ShowObservedMz,
ShowDuplicates = Settings.Default.ShowDuplicateIons,
FontSize = Settings.Default.SpectrumFontSize,
LineWidth = Settings.Default.SpectrumLineWidth
};
LibraryChromGroup chromatogramData = null;
if (Settings.Default.ShowLibraryChromatograms)
{
chromatogramData = spectrum.LoadChromatogramData();
}
if (null == chromatogramData)
{
_graphHelper.ResetForSpectrum(new[] { nodeGroup.TransitionGroup });
_graphHelper.AddSpectrum(GraphItem);
_graphHelper.ZoomSpectrumToSettings(DocumentUI, nodeGroup);
}
else
{
_graphHelper.ResetForChromatograms(new[] { nodeGroup.TransitionGroup });
var displayType = GraphChromatogram.GetDisplayType(DocumentUI, nodeGroup);
IList <TransitionDocNode> displayTransitions =
GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).ToArray();
int numTrans = displayTransitions.Count;
var allChromDatas =
chromatogramData.ChromDatas.Where(
chromData => DisplayTypeMatches(chromData, displayType)).ToList();
var chromDatas = new List <LibraryChromGroup.ChromData>();
for (int iTran = 0; iTran < numTrans; iTran++)
{
var displayTransition = displayTransitions[iTran];
var indexMatch =
allChromDatas.IndexOf(chromData => IonMatches(displayTransition.Transition, chromData));
if (indexMatch >= 0)
{
chromDatas.Add(allChromDatas[indexMatch]);
allChromDatas.RemoveAt(indexMatch);
}
else
{
chromDatas.Add(null);
}
}
allChromDatas.Sort((chromData1, chromData2) => chromData1.Mz.CompareTo(chromData2.Mz));
chromDatas.AddRange(allChromDatas);
double maxHeight = chromDatas.Max(chromData => null == chromData ? double.MinValue : chromData.Height);
int iChromDataPrimary = chromDatas.IndexOf(chromData => null != chromData && maxHeight == chromData.Height);
int colorOffset = displayType == DisplayTypeChrom.products
? GraphChromatogram.GetDisplayTransitions(nodeGroup,
DisplayTypeChrom.
precursors).Count()
: 0;
for (int iChromData = 0; iChromData < chromDatas.Count; iChromData++)
{
var chromData = chromDatas[iChromData];
if (chromData == null)
{
continue;
}
string label;
var pointAnnotation = GraphItem.AnnotatePoint(new PointPair(chromData.Mz, 1.0));
if (null != pointAnnotation)
{
label = pointAnnotation.Label;
}
else
{
label = chromData.Mz.ToString(@"0.####");
}
TransitionDocNode matchingTransition;
Color color;
if (iChromData < numTrans)
{
matchingTransition = displayTransitions[iChromData];
color =
GraphChromatogram.COLORS_LIBRARY[
(iChromData + colorOffset) % GraphChromatogram.COLORS_LIBRARY.Count];
}
else
{
matchingTransition = null;
color =
GraphChromatogram.COLORS_GROUPS[
iChromData % GraphChromatogram.COLORS_GROUPS.Count];
}
TransitionChromInfo tranPeakInfo;
ChromatogramInfo chromatogramInfo;
MakeChromatogramInfo(nodeGroup.PrecursorMz, chromatogramData, chromData, out chromatogramInfo, out tranPeakInfo);
var graphItem = new ChromGraphItem(nodeGroup, matchingTransition, chromatogramInfo, iChromData == iChromDataPrimary ? tranPeakInfo : null, null,
new[] { iChromData == iChromDataPrimary }, null, 0, false, false, null, 0,
color, Settings.Default.ChromatogramFontSize, 1);
LineItem curve = (LineItem)_graphHelper.AddChromatogram(PaneKey.DEFAULT, graphItem);
if (matchingTransition == null)
{
curve.Label.Text = label;
}
curve.Line.Width = Settings.Default.ChromatogramLineWidth;
if (null != transition)
{
if (IonMatches(transition.Transition, chromData))
{
color = ChromGraphItem.ColorSelected;
}
}
curve.Color = color;
}
graphPane.Title.IsVisible = false;
graphPane.Legend.IsVisible = true;
_graphHelper.FinishedAddingChromatograms(chromatogramData.StartTime, chromatogramData.EndTime, false);
graphControl.Refresh();
}
graphControl.IsEnableVPan = graphControl.IsEnableVZoom =
!Settings.Default.LockYAxis;
available = true;
}
}
}
catch (Exception)
{
_graphHelper.SetErrorGraphItem(new NoDataMSGraphItem(
Resources.GraphSpectrum_UpdateUI_Failure_loading_spectrum__Library_may_be_corrupted));
return;
}
}
// Show unavailable message, if no spectrum loaded
if (!available)
{
UpdateToolbar();
_nodeGroup = null;
_graphHelper.SetErrorGraphItem(new UnavailableMSGraphItem());
}
}
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));
}
