// ReSharper restore SuggestBaseTypeForParameter
// ReSharper disable SuggestBaseTypeForParameter
private TransitionGroupDocNode Refine(TransitionGroupDocNode nodeGroup, int bestResultIndex)
{
var listTrans = new List<TransitionDocNode>();
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
double? peakFoundRatio = nodeTran.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;
}
}
listTrans.Add(nodeTran);
}
TransitionGroupDocNode nodeGroupRefined = (TransitionGroupDocNode)
nodeGroup.ChangeChildrenChecked(listTrans.ToArray(), true);
if (MaxPeakRank.HasValue)
{
// Calculate the average peak area for each transition
int countTrans = nodeGroupRefined.Children.Count;
var listAreaIndexes = new List<AreaSortInfo>();
for (int i = 0; i < countTrans; i++)
{
var nodeTran = (TransitionDocNode) nodeGroupRefined.Children[i];
var sortInfo = new AreaSortInfo(nodeTran.GetPeakArea(bestResultIndex) ?? 0,
nodeTran.Transition.Ordinal,
nodeTran.Mz > nodeGroup.PrecursorMz,
i);
listAreaIndexes.Add(sortInfo);
}
// Sort to area order descending
if (PreferLargeIons)
{
// If prefering large ions, then larger ions get a slight area
// advantage over smaller ones
listAreaIndexes.Sort((p1, p2) =>
{
float areaAdjusted1 = p1.Area;
// If either transition is below the precursor m/z value,
// apply the fragment size correction.
if (!p1.AbovePrecusorMz || !p2.AbovePrecusorMz)
{
int deltaOrdinal = Math.Max(-5, Math.Min(5, p1.Ordinal - p2.Ordinal));
if (deltaOrdinal != 0)
deltaOrdinal += (deltaOrdinal > 0 ? 1 : -1);
areaAdjusted1 += areaAdjusted1 * 0.05f * deltaOrdinal;
}
return Comparer.Default.Compare(p2.Area, areaAdjusted1);
});
}
else
{
listAreaIndexes.Sort((p1, p2) => Comparer.Default.Compare(p2.Area, p1.Area));
}
// Store area ranks by transition index
var ranks = new int[countTrans];
for (int i = 0, iRank = 1; i < countTrans; i++)
{
var areaIndex = listAreaIndexes[i];
// Never keep a transition with no peak area
ranks[areaIndex.Index] = (areaIndex.Area > 0 ? iRank++ : int.MaxValue);
}
// Add back all transitions with low enough rank.
listTrans.Clear();
for (int i = 0; i < countTrans; i++)
{
if (ranks[i] > MaxPeakRank.Value)
continue;
listTrans.Add((TransitionDocNode) nodeGroupRefined.Children[i]);
}
nodeGroupRefined = (TransitionGroupDocNode)
nodeGroupRefined.ChangeChildrenChecked(listTrans.ToArray(), true);
}
return nodeGroupRefined;
}