private static void AddOptimizationStepAreas(TransitionDocNode nodeTran, int iResult, TReg regression,
IDictionary <int, OptimizationStep <TReg> > optTotals)
{
var results = (nodeTran.HasResults ? nodeTran.Results[iResult] : null);
// Skip the result set if it only has step 0, the predicted value. This happens
// when someone mistakenly sets "Optimizing" on a data set that does not contain
// optimization steps.
if (results == null || results.All(c => c.OptimizationStep == 0 || c.IsEmpty))
{
return;
}
foreach (var chromInfo in results)
{
if (chromInfo.Area == 0)
{
continue;
}
int step = chromInfo.OptimizationStep;
OptimizationStep <TReg> optStep;
if (!optTotals.TryGetValue(step, out optStep))
{
optTotals.Add(step, optStep = new OptimizationStep <TReg>(regression, step));
}
optStep.AddArea(chromInfo.Area);
}
}
private bool OtherLabelTypesAllowed(SrmSettings settings, double minMz, double maxMz, int start, int end, double startMz, bool accept,
TransitionGroupDocNode nodeGroupMatching,
TransitionDocNode nodeTran,
IEnumerable <Tuple <TransitionGroupDocNode, IFragmentMassCalc> > listOtherTypes)
{
foreach (var otherType in listOtherTypes)
{
var nodeGroupOther = otherType.Item1;
var tranGroupOther = nodeGroupOther.TransitionGroup;
var nodeTranMatching = tranGroupOther.GetMatchingTransition(settings,
nodeGroupMatching, nodeTran, otherType.Item2);
if (minMz > nodeTranMatching.Mz || nodeTranMatching.Mz > maxMz)
{
return(false);
}
if (accept && !settings.TransitionSettings.Accept(Peptide.Sequence,
nodeGroupOther.PrecursorMz,
nodeTranMatching.Transition.IonType,
nodeTranMatching.Transition.CleavageOffset,
nodeTranMatching.Mz,
start,
end,
startMz))
{
return(false);
}
}
return(true);
}
private TransitionDocNode GetMatchingTransition(SrmSettings settings,
TransitionGroupDocNode nodeGroupMatching,
TransitionDocNode nodeTran,
IFragmentMassCalc calc)
{
var transition = nodeTran.Transition;
var losses = nodeTran.Losses;
var libInfo = nodeTran.LibInfo;
int?decoyMassShift = transition.IsPrecursor() ? DecoyMassShift : transition.DecoyMassShift;
var tranNew = new Transition(this,
transition.IonType,
transition.CleavageOffset,
transition.MassIndex,
transition.Charge,
decoyMassShift,
transition.CustomIon ?? CustomIon); // Handle reporter ions as well as small molecules
var isotopeDist = nodeGroupMatching.IsotopeDist;
double massH;
if (tranNew.IsCustom())
{
massH = tranNew.CustomIon.GetMass(settings.TransitionSettings.Prediction.FragmentMassType);
}
else
{
massH = calc.GetFragmentMass(tranNew, isotopeDist);
}
var isotopeDistInfo = TransitionDocNode.GetIsotopeDistInfo(tranNew, losses, isotopeDist);
var nodeTranMatching = new TransitionDocNode(tranNew, losses, massH, isotopeDistInfo, libInfo);
return(nodeTranMatching);
}
public TransitionLossKey(TransitionGroupDocNode parent, TransitionDocNode transition, TransitionLosses losses)
{
Transition = transition.Transition;
Losses = losses;
if (Transition.IsCustom())
{
if (!string.IsNullOrEmpty(transition.PrimaryCustomIonEquivalenceKey))
{
CustomIonEquivalenceTestValue = transition.PrimaryCustomIonEquivalenceKey;
}
else if (!string.IsNullOrEmpty(transition.SecondaryCustomIonEquivalenceKey))
{
CustomIonEquivalenceTestValue = transition.SecondaryCustomIonEquivalenceKey;
}
else if (Transition.IsNonReporterCustomIon())
{
CustomIonEquivalenceTestValue = @"_mzSortIndex_" + parent.Children.IndexOf(transition);
}
else
{
CustomIonEquivalenceTestValue = null;
}
}
else
{
CustomIonEquivalenceTestValue = null;
}
}
public void Add(TransitionDocNode nodeTran, float abundance)
{
string ion = nodeTran.FragmentIonName;
float current = !_abundances.ContainsKey(ion) ? 0 : _abundances[ion];
_abundances[ion] = current + abundance;
}
private TransitionDocNode GetMatchingTransition(SrmSettings settings,
TransitionGroupDocNode nodeGroupMatching,
TransitionDocNode nodeTran,
IFragmentMassCalc calc)
{
var transition = nodeTran.Transition;
var losses = nodeTran.Losses;
var libInfo = nodeTran.LibInfo;
int?decoyMassShift = transition.IsPrecursor() ? DecoyMassShift : transition.DecoyMassShift;
var tranNew = new Transition(this,
transition.IonType,
transition.CleavageOffset,
transition.MassIndex,
transition.Adduct,
decoyMassShift,
transition.CustomIon ?? CustomMolecule); // Handle reporter ions as well as small molecules
var isotopeDist = nodeGroupMatching.IsotopeDist;
TypedMass massH;
var massType = calc.MassType;
if (tranNew.IsCustom())
{
massH = tranNew.CustomIon.GetMass(massType);
}
else
{
massH = calc.GetFragmentMass(tranNew, isotopeDist);
}
var isotopeDistInfo = TransitionDocNode.GetIsotopeDistInfo(tranNew, losses, isotopeDist);
var nodeTranMatching = new TransitionDocNode(tranNew, losses, massH, new TransitionDocNode.TransitionQuantInfo(isotopeDistInfo, libInfo, nodeTran.IsQuantitative(settings)), nodeTran.ExplicitValues);
return(nodeTranMatching);
}
private TransitionDocNode CreateTransitionNode(IonType type, int cleavageOffset, int charge, double massH,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, CustomIon customIon = null)
{
Transition transition = new Transition(this, type, cleavageOffset, 0, charge, null, customIon);
var info = TransitionDocNode.GetLibInfo(transition, Transition.CalcMass(massH, losses), transitionRanks);
return(new TransitionDocNode(transition, losses, massH, null, info));
}
private TransitionDocNode CreateTransitionNode(int massIndex, double precursorMassH, TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, CustomIon customIon = null)
{
Transition transition = new Transition(this, massIndex, customIon);
var info = isotopeDistInfo == null?TransitionDocNode.GetLibInfo(transition, Transition.CalcMass(precursorMassH, losses), transitionRanks) : null;
return(new TransitionDocNode(transition, losses, precursorMassH, isotopeDistInfo, info));
}
public static int CompareTransitions(TransitionDocNode node1, TransitionDocNode node2)
{
int result = CompareTransitionIds(node1.Transition, node2.Transition);
if (result == 0)
{
result = node1.LostMass.CompareTo(node2.LostMass);
}
return(result);
}
public static double FindOptimizedValue(SrmSettings settings,
PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
TransitionDocNode nodeTran,
OptimizedMethodType methodType,
TReg regressionDocument,
GetRegressionValue getRegressionValue)
{
double?optimizedValue = FindOptimizedValueFromResults(settings, nodePep, nodeGroup, nodeTran, methodType, getRegressionValue);
return(optimizedValue.HasValue ? optimizedValue.Value : getRegressionValue(settings, nodePep, nodeGroup, regressionDocument, 0));
}
private TransitionDocNode CreateTransitionNode(int massIndex, TypedMass precursorMassH, TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, CustomMolecule customMolecule = null)
{
Transition transition = new Transition(this, massIndex, customMolecule);
var quantInfo = TransitionDocNode.TransitionQuantInfo.GetLibTransitionQuantInfo(transition, losses,
Transition.CalcMass(precursorMassH, losses), transitionRanks).ChangeIsotopeDistInfo(isotopeDistInfo);
var transitionDocNode = new TransitionDocNode(transition, losses, precursorMassH, quantInfo);
if (massIndex < 0)
{
transitionDocNode = transitionDocNode.ChangeQuantitative(false);
}
return(transitionDocNode);
}
public TransitionDocNode MergeUserInfo(SrmSettings settings, TransitionDocNode nodeTranMerge)
{
var result = this;
var annotations = Annotations.Merge(nodeTranMerge.Annotations);
if (!ReferenceEquals(annotations, Annotations))
{
result = (TransitionDocNode)result.ChangeAnnotations(annotations);
}
var resultsInfo = MergeResultsUserInfo(settings, nodeTranMerge.Results);
if (!ReferenceEquals(resultsInfo, Results))
{
result = result.ChangeResults(resultsInfo);
}
return(result);
}
public bool Equals(TransitionDocNode obj)
{
if (ReferenceEquals(null, obj))
{
return(false);
}
if (ReferenceEquals(this, obj))
{
return(true);
}
var equal = base.Equals(obj) && obj.Mz == Mz &&
Equals(obj.IsotopeDistInfo, IsotopeDistInfo) &&
Equals(obj.LibInfo, LibInfo) &&
Equals(obj.Results, Results);
return(equal); // For debugging convenience
}
public static int CompareTransitions(TransitionDocNode node1, TransitionDocNode node2)
{
Transition tran1 = node1.Transition, tran2 = node2.Transition;
int diffType = GetOrder(tran1.IonType) - GetOrder(tran2.IonType);
if (diffType != 0)
{
return(diffType);
}
int diffCharge = tran1.Charge - tran2.Charge;
if (diffCharge != 0)
{
return(diffCharge);
}
int diffOffset = tran1.CleavageOffset - tran2.CleavageOffset;
if (diffOffset != 0)
{
return(diffOffset);
}
return(Comparer <double> .Default.Compare(node1.LostMass, node2.LostMass));
}
public static FragmentedMolecule GetFragmentedMolecule(SrmSettings settings, PeptideDocNode peptideDocNode,
TransitionGroupDocNode transitionGroupDocNode, TransitionDocNode transitionDocNode)
{
FragmentedMolecule fragmentedMolecule = EMPTY
.ChangePrecursorMassShift(0, settings.TransitionSettings.Prediction.PrecursorMassType)
.ChangeFragmentMassShift(0, settings.TransitionSettings.Prediction.FragmentMassType);
if (peptideDocNode == null)
{
return(fragmentedMolecule);
}
var labelType = transitionGroupDocNode == null
? IsotopeLabelType.light
: transitionGroupDocNode.TransitionGroup.LabelType;
if (peptideDocNode.IsProteomic)
{
fragmentedMolecule = fragmentedMolecule.ChangeModifiedSequence(
ModifiedSequence.GetModifiedSequence(settings, peptideDocNode, labelType));
if (transitionGroupDocNode != null)
{
fragmentedMolecule = fragmentedMolecule
.ChangePrecursorCharge(transitionGroupDocNode.PrecursorCharge);
}
if (transitionDocNode == null || transitionDocNode.IsMs1)
{
return(fragmentedMolecule);
}
var transition = transitionDocNode.Transition;
fragmentedMolecule = fragmentedMolecule
.ChangeFragmentIon(transition.IonType, transition.Ordinal)
.ChangeFragmentCharge(transition.Charge);
var transitionLosses = transitionDocNode.Losses;
if (transitionLosses != null)
{
var fragmentLosses = transitionLosses.Losses.Select(transitionLoss => transitionLoss.Loss);
fragmentedMolecule = fragmentedMolecule.ChangeFragmentLosses(fragmentLosses);
}
return(fragmentedMolecule);
}
if (transitionGroupDocNode == null)
{
return(fragmentedMolecule
.ChangePrecursorFormula(
Molecule.Parse(peptideDocNode.CustomMolecule.Formula ?? string.Empty)));
}
var customMolecule = transitionGroupDocNode.CustomMolecule;
fragmentedMolecule =
fragmentedMolecule.ChangePrecursorCharge(transitionGroupDocNode.TransitionGroup
.PrecursorCharge);
if (customMolecule.Formula != null)
{
var ionInfo = new IonInfo(customMolecule.Formula,
transitionGroupDocNode.PrecursorAdduct);
fragmentedMolecule = fragmentedMolecule
.ChangePrecursorFormula(Molecule.Parse(ionInfo.FormulaWithAdductApplied));
}
else
{
fragmentedMolecule = fragmentedMolecule.ChangePrecursorMassShift(
transitionGroupDocNode.PrecursorAdduct.MassFromMz(
transitionGroupDocNode.PrecursorMz, transitionGroupDocNode.PrecursorMzMassType),
transitionGroupDocNode.PrecursorMzMassType);
}
if (transitionDocNode == null || transitionDocNode.IsMs1)
{
return(fragmentedMolecule);
}
var customIon = transitionDocNode.Transition.CustomIon;
if (customIon.Formula != null)
{
fragmentedMolecule = fragmentedMolecule.ChangeFragmentFormula(
Molecule.Parse(customIon.FormulaWithAdductApplied));
}
else
{
fragmentedMolecule = fragmentedMolecule.ChangeFragmentMassShift(
transitionDocNode.Transition.Adduct.MassFromMz(
transitionDocNode.Mz, transitionDocNode.MzMassType),
transitionDocNode.MzMassType);
}
fragmentedMolecule = fragmentedMolecule
.ChangeFragmentCharge(transitionDocNode.Transition.Charge);
return(fragmentedMolecule);
}
public Chromatogram[] GetChromatograms(DocumentLocation documentLocation)
{
if (documentLocation == null)
{
return(new Chromatogram[0]);
}
var result = new List <Chromatogram>();
SrmDocument document = Program.MainWindow.Document;
Bookmark bookmark = Bookmark.ToBookmark(documentLocation, document);
IdentityPath identityPath = bookmark.IdentityPath;
var nodeList = GetDocNodes(identityPath, document);
TransitionDocNode transitionDocNode = null;
if (nodeList.Count > 3)
{
transitionDocNode = (TransitionDocNode)nodeList[3];
}
var measuredResults = document.Settings.MeasuredResults;
var nodePep = (PeptideDocNode)(nodeList.Count > 1 ? nodeList[1] : null);
if (null == nodePep)
{
return(result.ToArray());
}
int iColor = 0;
foreach (var chromatogramSet in measuredResults.Chromatograms)
{
foreach (var msDataFileInfo in chromatogramSet.MSDataFileInfos)
{
if (bookmark.ChromFileInfoId != null && !ReferenceEquals(msDataFileInfo.FileId, bookmark.ChromFileInfoId))
{
continue;
}
foreach (var nodeGroup in nodePep.TransitionGroups)
{
if (nodeList.Count > 2 && !Equals(nodeGroup, nodeList[2]))
{
continue;
}
ChromatogramGroupInfo[] arrayChromInfo;
measuredResults.TryLoadChromatogram(
chromatogramSet,
nodePep,
nodeGroup,
(float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance,
true,
out arrayChromInfo);
foreach (var transition in nodeGroup.Transitions)
{
if (transitionDocNode != null && !Equals(transitionDocNode, transition))
{
continue;
}
foreach (var chromatogramGroup in arrayChromInfo)
{
for (int iTransition = 0; iTransition < chromatogramGroup.NumTransitions; iTransition++)
{
ChromatogramInfo transitionInfo = chromatogramGroup.GetTransitionInfo(iTransition);
if (Math.Abs(transitionInfo.ProductMz - transition.Mz) >
document.Settings.TransitionSettings.Instrument.MzMatchTolerance)
{
continue;
}
Color color = GraphChromatogram.COLORS_LIBRARY[iColor % GraphChromatogram.COLORS_LIBRARY.Count];
iColor++;
result.Add(new Chromatogram
{
Intensities = transitionInfo.Intensities.ToArray(),
ProductMz = transitionInfo.ProductMz.RawValue, // For negative ion mode data this will be a negative value
PrecursorMz = chromatogramGroup.PrecursorMz.RawValue, // For negative ion mode data this will be a negative value
Times = transitionInfo.Times.ToArray(),
Color = color
});
}
}
}
}
}
}
if (result.Count == 1)
{
result[0].Color = ChromGraphItem.ColorSelected;
}
return(result.ToArray());
}
/// <summary>
/// In the case of small molecule transitions specified by mass only, position within
/// the parent's list of transitions is the only meaningful key. So we need to know our parent.
/// </summary>
public TransitionLossEquivalentKey(TransitionGroupDocNode parent, TransitionDocNode transition, TransitionLosses losses)
{
Key = new TransitionEquivalentKey(parent, transition);
Losses = losses;
}
protected virtual bool SkipTransition(PeptideGroupDocNode nodePepGroup, PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup, TransitionGroupDocNode nodeGroupPrimary, TransitionDocNode nodeTran)
{
return(false);
}
private readonly string _customIonEquivalenceTestText; // For use with small molecules
public TransitionEquivalentKey(TransitionGroupDocNode parent, TransitionDocNode nodeTran)
{
_nodeTran = nodeTran.Transition;
_customIonEquivalenceTestText = new TransitionLossKey(parent, nodeTran, null).CustomIonEquivalenceTestValue;
}
public static double?FindOptimizedValueFromResults(SrmSettings settings,
PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
TransitionDocNode nodeTran,
OptimizedMethodType methodType,
GetRegressionValue getRegressionValue)
{
// Collect peak area for
var dictOptTotals = new Dictionary <TReg, Dictionary <int, OptimizationStep <TReg> > >();
if (settings.HasResults)
{
var chromatograms = settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatograms.Count; i++)
{
var chromSet = chromatograms[i];
var regression = chromSet.OptimizationFunction as TReg;
if (regression == null)
{
continue;
}
Dictionary <int, OptimizationStep <TReg> > stepAreas;
if (!dictOptTotals.TryGetValue(regression, out stepAreas))
{
dictOptTotals.Add(regression, stepAreas = new Dictionary <int, OptimizationStep <TReg> >());
}
if (methodType == OptimizedMethodType.Precursor)
{
TransitionGroupDocNode[] listGroups = FindCandidateGroups(nodePep, nodeGroup);
foreach (var nodeGroupCandidate in listGroups)
{
AddOptimizationStepAreas(nodeGroupCandidate, i, regression, stepAreas);
}
}
else if (methodType == OptimizedMethodType.Transition)
{
IEnumerable <TransitionDocNode> listTransitions = FindCandidateTransitions(nodePep, nodeGroup, nodeTran);
foreach (var nodeTranCandidate in listTransitions)
{
AddOptimizationStepAreas(nodeTranCandidate, i, regression, stepAreas);
}
}
}
}
// If no candidate values were found, use the document regressor.
if (dictOptTotals.Count == 0)
{
return(null);
}
// Get the CE value with the maximum total peak area
double maxArea = 0;
double bestValue = 0;
foreach (var optTotals in dictOptTotals.Values)
{
foreach (var optStep in optTotals.Values)
{
if (maxArea < optStep.TotalArea)
{
maxArea = optStep.TotalArea;
bestValue = getRegressionValue(settings, nodePep, nodeGroup, optStep.Regression, optStep.Step);
}
}
}
// Use value for candidate with the largest area
return(bestValue);
}
private static IEnumerable <TransitionDocNode> FindCandidateTransitions(PeptideDocNode nodePep, TransitionGroupDocNode nodeGroup, TransitionDocNode nodeTran)
{
var candidateGroups = FindCandidateGroups(nodePep, nodeGroup);
if (candidateGroups.Length < 2)
{
return new[] { nodeTran }
}
;
Debug.Assert(ReferenceEquals(nodeGroup, candidateGroups[0]));
var listCandidates = new List <TransitionDocNode> {
nodeTran
};
var transition = nodeTran.Transition;
for (int i = 1; i < candidateGroups.Length; i++)
{
foreach (TransitionDocNode nodeTranCandidate in candidateGroups[i].Children)
{
var transitionCandidate = nodeTranCandidate.Transition;
if (transition.Charge == transitionCandidate.Charge &&
transition.Ordinal == transitionCandidate.Ordinal &&
transition.IonType == transitionCandidate.IonType)
{
listCandidates.Add(nodeTranCandidate);
break;
}
}
}
return(listCandidates.ToArray());
}
public static ExplicitTransitionValues Get(TransitionDocNode node)
{
return(node == null ? EMPTY : node.ExplicitValues);
} // Convenience function
public IEnumerable <TransitionDocNode> GetTransitions(SrmSettings settings,
TransitionGroupDocNode groupDocNode,
ExplicitMods mods,
double precursorMz,
IsotopeDistInfo isotopeDist,
SpectrumHeaderInfo libInfo,
IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks,
bool useFilter)
{
Assume.IsTrue(ReferenceEquals(groupDocNode.TransitionGroup, this));
// Get necessary mass calculators and masses
var calcFilterPre = settings.GetPrecursorCalc(IsotopeLabelType.light, mods);
var calcFilter = settings.GetFragmentCalc(IsotopeLabelType.light, mods);
var calcPredict = settings.GetFragmentCalc(LabelType, mods);
string sequence = Peptide.Sequence;
// Save the true precursor m/z for TranstionSettings.Accept() now that all isotope types are
// checked. This is more correct than just using the light precursor m/z for precursor window
// exclusion.
double precursorMzAccept = precursorMz;
if (!ReferenceEquals(calcFilter, calcPredict))
{
// Get the normal precursor m/z for filtering, so that light and heavy ion picks will match.
precursorMz = IsCustomIon ?
BioMassCalc.CalculateIonMz(calcFilterPre.GetPrecursorMass(groupDocNode.CustomIon), groupDocNode.TransitionGroup.PrecursorCharge) :
SequenceMassCalc.GetMZ(calcFilterPre.GetPrecursorMass(sequence), groupDocNode.TransitionGroup.PrecursorCharge);
}
if (!IsAvoidMismatchedIsotopeTransitions)
{
precursorMzAccept = precursorMz;
}
var tranSettings = settings.TransitionSettings;
var filter = tranSettings.Filter;
var charges = filter.ProductCharges;
var startFinder = filter.FragmentRangeFirst;
var endFinder = filter.FragmentRangeLast;
double precursorMzWindow = filter.PrecursorMzWindow;
var types = filter.IonTypes;
MassType massType = tranSettings.Prediction.FragmentMassType;
int minMz = tranSettings.Instrument.GetMinMz(precursorMzAccept);
int maxMz = tranSettings.Instrument.MaxMz;
var pepMods = settings.PeptideSettings.Modifications;
var potentialLosses = CalcPotentialLosses(sequence, pepMods, mods, massType);
// A start m/z will need to be calculated if the start fragment
// finder uses m/z and their are losses to consider. If the filter
// is set to only consider fragments with m/z greater than the
// precursor, the code below needs to also prevent loss fragments
// from being under that m/z.
double startMz = 0;
// Get library settings
var pick = tranSettings.Libraries.Pick;
if (!useFilter)
{
pick = TransitionLibraryPick.all;
var listAll = Transition.ALL_CHARGES.ToList();
listAll.AddRange(charges.Where(c => !Transition.ALL_CHARGES.Contains(c)));
listAll.Sort();
charges = listAll.ToArray();
types = Transition.ALL_TYPES;
}
// If there are no libraries or no library information, then
// picking cannot use library information
else if (!settings.PeptideSettings.Libraries.HasLibraries || libInfo == null)
{
pick = TransitionLibraryPick.none;
}
// If filtering without library picking
if (potentialLosses != null)
{
if (pick == TransitionLibraryPick.none)
{
// Only include loss combinations where all losses are included always
potentialLosses = potentialLosses.Where(losses =>
losses.All(loss => loss.TransitionLoss.Loss.Inclusion == LossInclusion.Always)).ToArray();
}
else if (useFilter)
{
// Exclude all losses which should never be included by default
potentialLosses = potentialLosses.Where(losses =>
losses.All(loss => loss.TransitionLoss.Loss.Inclusion != LossInclusion.Never)).ToArray();
}
if (!potentialLosses.Any())
{
potentialLosses = null;
}
}
// Return precursor ions
if (!useFilter || types.Contains(IonType.precursor))
{
bool libraryFilter = (pick == TransitionLibraryPick.all || pick == TransitionLibraryPick.filter);
foreach (var nodeTran in GetPrecursorTransitions(settings, mods, calcFilterPre, calcPredict,
precursorMz, isotopeDist, potentialLosses, transitionRanks, libraryFilter, useFilter))
{
if (minMz <= nodeTran.Mz && nodeTran.Mz <= maxMz)
{
yield return(nodeTran);
}
}
}
// Return special ions from settings, if this is a peptide
if (!IsCustomIon)
{
// This is a peptide, but it may have custom transitions (reporter ions), check those
foreach (var measuredIon in tranSettings.Filter.MeasuredIons.Where(m => m.IsCustom))
{
if (useFilter && measuredIon.IsOptional)
{
continue;
}
var tran = new Transition(this, measuredIon.Charge, null, measuredIon.CustomIon);
double mass = settings.GetFragmentMass(IsotopeLabelType.light, null, tran, null);
var nodeTran = new TransitionDocNode(tran, null, mass, null, null);
if (minMz <= nodeTran.Mz && nodeTran.Mz <= maxMz)
{
yield return(nodeTran);
}
}
}
// For small molecules we can't generate new nodes, so just mz filter those we have
foreach (var nodeTran in groupDocNode.Transitions.Where(tran => tran.Transition.IsNonPrecursorNonReporterCustomIon()))
{
if (minMz <= nodeTran.Mz && nodeTran.Mz <= maxMz)
{
yield return(nodeTran);
}
}
if (sequence == null) // Completely custom
{
yield break;
}
// If picking relies on library information
if (useFilter && pick != TransitionLibraryPick.none)
{
// If it is not yet loaded, or nothing got ranked, return an empty enumeration
if (!settings.PeptideSettings.Libraries.IsLoaded ||
(transitionRanks != null && transitionRanks.Count == 0))
{
yield break;
}
}
double[,] massesPredict = calcPredict.GetFragmentIonMasses(sequence);
int len = massesPredict.GetLength(1);
if (len == 0)
{
yield break;
}
double[,] massesFilter = massesPredict;
if (!ReferenceEquals(calcFilter, calcPredict))
{
// Get the normal m/z values for filtering, so that light and heavy
// ion picks will match.
massesFilter = calcFilter.GetFragmentIonMasses(sequence);
}
// Get types other than this to make sure matches are possible for all types
var listOtherTypes = new List <Tuple <TransitionGroupDocNode, IFragmentMassCalc> >();
foreach (var labelType in settings.PeptideSettings.Modifications.GetModificationTypes())
{
if (Equals(labelType, LabelType))
{
continue;
}
var calc = settings.GetFragmentCalc(labelType, mods);
if (calc == null)
{
continue;
}
var tranGroupOther = new TransitionGroup(Peptide, PrecursorCharge, labelType, false, DecoyMassShift);
var nodeGroupOther = new TransitionGroupDocNode(tranGroupOther, Annotations.EMPTY, settings, mods,
libInfo, ExplicitTransitionGroupValues.EMPTY, null, new TransitionDocNode[0], false);
listOtherTypes.Add(new Tuple <TransitionGroupDocNode, IFragmentMassCalc>(nodeGroupOther, calc));
}
// Loop over potential product ions picking transitions
foreach (IonType type in types)
{
// Precursor type is handled above.
if (type == IonType.precursor)
{
continue;
}
foreach (int charge in charges)
{
// Precursor charge can never be lower than product ion charge.
if (Math.Abs(PrecursorCharge) < Math.Abs(charge))
{
continue;
}
int start = 0, end = 0;
if (pick != TransitionLibraryPick.all)
{
start = startFinder.FindStartFragment(massesFilter, type, charge,
precursorMz, precursorMzWindow, out startMz);
end = endFinder.FindEndFragment(type, start, len);
if (Transition.IsCTerminal(type))
{
Helpers.Swap(ref start, ref end);
}
}
for (int i = 0; i < len; i++)
{
// Get the predicted m/z that would be used in the transition
double massH = massesPredict[(int)type, i];
foreach (var losses in CalcTransitionLosses(type, i, massType, potentialLosses))
{
double ionMz = SequenceMassCalc.GetMZ(Transition.CalcMass(massH, losses), charge);
// Make sure the fragment m/z value falls within the valid instrument range.
// CONSIDER: This means that a heavy transition might excede the instrument
// range where a light one is accepted, leading to a disparity
// between heavy and light transtions picked.
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
TransitionDocNode nodeTranReturn = null;
bool accept = true;
if (pick == TransitionLibraryPick.all || pick == TransitionLibraryPick.all_plus)
{
if (!useFilter)
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
accept = false;
}
else
{
if (IsMatched(transitionRanks, ionMz, type, charge, losses))
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
accept = false;
}
// If allowing library or filter, check the filter to decide whether to accept
else if (pick == TransitionLibraryPick.all_plus &&
tranSettings.Accept(sequence, precursorMzAccept, type, i, ionMz, start, end, startMz))
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
}
}
}
else if (tranSettings.Accept(sequence, precursorMzAccept, type, i, ionMz, start, end, startMz))
{
if (pick == TransitionLibraryPick.none)
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
}
else
{
if (IsMatched(transitionRanks, ionMz, type, charge, losses))
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
}
}
}
if (nodeTranReturn != null)
{
if (IsAvoidMismatchedIsotopeTransitions &&
!OtherLabelTypesAllowed(settings, minMz, maxMz, start, end, startMz, accept,
groupDocNode, nodeTranReturn, listOtherTypes))
{
continue;
}
Assume.IsTrue(minMz <= nodeTranReturn.Mz && nodeTranReturn.Mz <= maxMz);
yield return(nodeTranReturn);
}
}
}
}
}
}
