public int ComparePeakLists(PeptideChromDataPeakList p1, PeptideChromDataPeakList p2)
{
// TODO: Do we want to keep this?
// All identified peaks come first
if (p1.IsIdentified != p2.IsIdentified)
{
return(p1.IsIdentified ? -1 : 1);
}
// Then order by CombinedScore descending
return(Comparer <double> .Default.Compare(p2.CombinedScore, p1.CombinedScore));
}
/// <summary>
/// Given a high scoring peak precursor peak group, find other lower scoring precursor peak
/// groups from different precursors for the same peptide, which overlap in time with the
/// high scoring peak.
/// </summary>
/// <param name="dataSets">Chromatogram data sets from which to create peptide peaks</param>
/// <param name="dataPeakMax">High scoring precursor peak group</param>
/// <param name="allPeakGroups">List of all lower scoring precursor peak groups for the same peptide</param>
/// <returns>A list of coeluting precursor peak groups for this peptide</returns>
private PeptideChromDataPeakList FindCoelutingPeptidePeaks(IEnumerable <ChromDataSet> dataSets,
PeptideChromDataPeak dataPeakMax,
IList <PeptideChromDataPeak> allPeakGroups)
{
TransitionGroupDocNode nodeGroupMax = dataPeakMax.Data.NodeGroup;
int startMax = dataPeakMax.StartIndex;
int endMax = dataPeakMax.EndIndex;
int timeMax = dataPeakMax.TimeIndex;
// Initialize the collection of peaks with this peak
var listPeaks = new PeptideChromDataPeakList(NodePep, FileInfo, dataPeakMax);
// Enumerate the precursors for this peptide
foreach (var chromData in dataSets)
{
// Skip the precursor for the max peak itself
if (ReferenceEquals(chromData, dataPeakMax.Data))
{
continue;
}
int iPeakBest = -1;
double bestProduct = 0;
// Find nearest peak in remaining set that is less than 1/4 length
// from the primary peak's center
for (int i = 0, len = allPeakGroups.Count; i < len; i++)
{
var peakGroup = allPeakGroups[i];
// Consider only peaks for the current precursor
if (!ReferenceEquals(peakGroup.Data, chromData))
{
continue;
}
// Exclude peaks that do not overlap with the maximum peak
TransitionGroupDocNode nodeGroup = peakGroup.Data.NodeGroup;
int startPeak = peakGroup.StartIndex;
int endPeak = peakGroup.EndIndex;
if (Math.Min(endPeak, endMax) - Math.Max(startPeak, startMax) <= 0)
{
continue;
}
int timeIndex = peakGroup.TimeIndex;
if ((nodeGroup.RelativeRT == RelativeRT.Matching && nodeGroupMax.RelativeRT == RelativeRT.Matching) ||
// Matching label types (i.e. different charge states of same label type should always match)
ReferenceEquals(nodeGroup.TransitionGroup.LabelType, nodeGroupMax.TransitionGroup.LabelType))
{
// If the peaks are supposed to have the same elution time,
// then be more strict about how they overlap
if (startMax >= timeIndex || timeIndex >= endMax)
{
continue;
}
}
else if (nodeGroup.RelativeRT == RelativeRT.Matching && nodeGroupMax.RelativeRT == RelativeRT.Preceding)
{
// If the maximum is supposed to precede this, look for any
// indication that this relationship holds, by testing the peak apex
// and the peak center.
if (timeIndex < timeMax && (startPeak + endPeak) / 2 < (startMax + endMax) / 2)
{
continue;
}
}
else if (nodeGroup.RelativeRT == RelativeRT.Preceding && nodeGroupMax.RelativeRT == RelativeRT.Matching)
{
// If this peak is supposed to precede the maximum, look for any
// indication that this relationship holds, by testing the peak apex
// and the peak center.
if (timeIndex > timeMax && (startPeak + endPeak) / 2 > (startMax + endMax) / 2)
{
continue;
}
}
// Choose the next best peak that overlaps
if (peakGroup.PeakGroup.CombinedScore > bestProduct)
{
iPeakBest = i;
bestProduct = peakGroup.PeakGroup.CombinedScore;
}
}
// If no coeluting peaks found, add an empty peak group
if (iPeakBest == -1)
{
listPeaks.Add(new PeptideChromDataPeak(chromData, null));
}
// Otherwise, add the found coeluting peak group, and remove it from the full list
else
{
listPeaks.Add(new PeptideChromDataPeak(chromData, allPeakGroups[iPeakBest].PeakGroup));
allPeakGroups.RemoveAt(iPeakBest);
}
}
return(listPeaks);
}
