private PeptideDocNode Refine(PeptideDocNode nodePep,
SrmDocument document,
int bestResultIndex,
List<int> acceptedCharges)
{
int minTrans = MinTransitionsPepPrecursor ?? 0;
bool addedGroups = false;
var listGroups = new List<TransitionGroupDocNode>();
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (acceptedCharges != null && !acceptedCharges.Contains(nodeGroup.TransitionGroup.PrecursorCharge))
continue;
if (!AddLabelType && RefineLabelType != null && Equals(RefineLabelType, nodeGroup.TransitionGroup.LabelType))
continue;
double? peakFoundRatio = nodeGroup.GetPeakCountRatio(bestResultIndex);
if (!peakFoundRatio.HasValue)
{
if (RemoveMissingResults)
continue;
}
else
{
if (MinPeakFoundRatio.HasValue)
{
if (peakFoundRatio < MinPeakFoundRatio.Value)
continue;
}
if (MaxPeakFoundRatio.HasValue)
{
if (peakFoundRatio > MaxPeakFoundRatio.Value)
continue;
}
}
TransitionGroupDocNode nodeGroupRefined = nodeGroup;
if (AutoPickTransitionsAll && nodeGroup.AutoManageChildren == AutoPickChildrenOff)
{
nodeGroupRefined = (TransitionGroupDocNode) nodeGroupRefined.ChangeAutoManageChildren(!AutoPickChildrenOff);
var settings = document.Settings;
if (!settings.TransitionSettings.Filter.AutoSelect && !AutoPickChildrenOff)
settings = settings.ChangeTransitionFilter(filter => filter.ChangeAutoSelect(!AutoPickChildrenOff));
nodeGroupRefined = nodeGroupRefined.ChangeSettings(settings, nodePep, nodePep.ExplicitMods,
new SrmSettingsDiff(false, false, false, false, true, false));
}
nodeGroupRefined = Refine(nodeGroupRefined, bestResultIndex);
if (nodeGroupRefined.Children.Count < minTrans)
continue;
if (peakFoundRatio.HasValue)
{
if (DotProductThreshold.HasValue)
{
float? dotProduct = nodeGroupRefined.GetLibraryDotProduct(bestResultIndex);
if (dotProduct.HasValue && dotProduct.Value < DotProductThreshold.Value)
continue;
}
if (IdotProductThreshold.HasValue)
{
float? idotProduct = nodeGroupRefined.GetIsotopeDotProduct(bestResultIndex);
if (idotProduct.HasValue && idotProduct.Value < IdotProductThreshold.Value)
continue;
}
}
// If this precursor node is going to be added, check to see if it
// should be added with another matching isotope label type.
var explicitMods = nodePep.ExplicitMods;
if (IsLabelTypeRequired(nodePep, nodeGroup, listGroups) &&
document.Settings.TryGetPrecursorCalc(RefineLabelType, explicitMods) != null)
{
// CONSIDER: This is a lot like some code in PeptideDocNode.ChangeSettings
Debug.Assert(RefineLabelType != null); // Keep ReSharper from warning
var tranGroup = new TransitionGroup(nodePep.Peptide,
nodeGroup.TransitionGroup.PrecursorCharge,
RefineLabelType,
false,
nodeGroup.TransitionGroup.DecoyMassShift);
var settings = document.Settings;
// string sequence = nodePep.Peptide.Sequence;
TransitionDocNode[] transitions = nodePep.GetMatchingTransitions(
tranGroup, settings, explicitMods);
var nodeGroupMatch = new TransitionGroupDocNode(tranGroup,
Annotations.EMPTY,
settings,
explicitMods,
nodeGroup.LibInfo,
nodeGroup.ExplicitValues,
null, // results
transitions,
transitions == null);
nodeGroupMatch = nodeGroupMatch.ChangeSettings(settings, nodePep, explicitMods, SrmSettingsDiff.ALL);
// Make sure it is measurable before adding it
if (settings.TransitionSettings.IsMeasurablePrecursor(nodeGroupMatch.PrecursorMz))
{
listGroups.Add(nodeGroupMatch);
addedGroups = true;
}
}
listGroups.Add(nodeGroupRefined);
}
// If groups were added, make sure everything is in the right order.
if (addedGroups)
listGroups.Sort(Peptide.CompareGroups);
// Change the children, but only change auto-management, if the child
// identities have changed, not if their contents changed.
var childrenNew = listGroups.ToArray();
bool updateAutoManage = !PeptideDocNode.AreEquivalentChildren(nodePep.Children, childrenNew);
return (PeptideDocNode) nodePep.ChangeChildrenChecked(childrenNew, updateAutoManage);
}
public PeptideDocNode UpdateResults(PeptideDocNode nodePeptide)
{
var listChromInfoList = _listResultCalcs.ConvertAll(calc =>
calc.CalcChromInfoList(TransitionGroupCount));
var results = Results<PeptideChromInfo>.Merge(nodePeptide.Results, listChromInfoList);
if (!ReferenceEquals(results, nodePeptide.Results))
nodePeptide = nodePeptide.ChangeResults(results);
var listGroupsNew = new List<DocNode>();
foreach (TransitionGroupDocNode nodeGroup in nodePeptide.Children)
{
// Update transition group ratios
var nodeGroupConvert = nodeGroup;
bool isMatching = nodeGroup.RelativeRT == RelativeRT.Matching;
var listGroupInfoList = _listResultCalcs.ConvertAll(
calc => calc.UpdateTransitonGroupRatios(nodeGroupConvert,
nodeGroupConvert.HasResults
? nodeGroupConvert.Results[calc.ResultsIndex]
: null,
isMatching));
var resultsGroup = Results<TransitionGroupChromInfo>.Merge(nodeGroup.Results, listGroupInfoList);
var nodeGroupNew = nodeGroup;
if (!ReferenceEquals(resultsGroup, nodeGroup.Results))
nodeGroupNew = nodeGroup.ChangeResults(resultsGroup);
var listTransNew = new List<DocNode>();
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
// Update transition ratios
var nodeTranConvert = nodeTran;
var listTranInfoList = _listResultCalcs.ConvertAll(
calc => calc.UpdateTransitionRatios(nodeGroup,
nodeTranConvert,
nodeTranConvert.Results[calc.ResultsIndex], isMatching));
var resultsTran = Results<TransitionChromInfo>.Merge(nodeTran.Results, listTranInfoList);
listTransNew.Add(ReferenceEquals(resultsTran, nodeTran.Results)
? nodeTran
: nodeTran.ChangeResults(resultsTran));
}
listGroupsNew.Add(nodeGroupNew.ChangeChildrenChecked(listTransNew));
}
return (PeptideDocNode) nodePeptide.ChangeChildrenChecked(listGroupsNew);
}
