/// <summary>
/// Set this peak based on another best peak for a peak group
/// </summary>
public void SetBestPeak(PeptideChromDataPeak peakBest, int indexSet)
{
PeakGroup = Data.SetBestPeak(PeakGroup, peakBest, indexSet);
}
private List <PeptideChromDataPeakList> PickPeptidePeaks(ICollection <ChromDataSet> dataSets)
{
var listPeakSets = new List <PeptideChromDataPeakList>();
// Only possible to improve upon individual precursor peak picking,
// if there are more than one precursor
if (dataSets.Count == 0)
{
return(listPeakSets);
}
if (dataSets.Count == 1)
{
// Create peptide peak group data structures for scoring only
var dataSet = dataSets.First();
// Truncate to maximum peak groups, unless this is a summary chromatogram
// where we want to leave more annotated peaks
listPeakSets.AddRange(dataSet.PeakSets.Select(p =>
new PeptideChromDataPeakList(NodePep, FileInfo, new PeptideChromDataPeak(dataSet, p))));
return(listPeakSets);
}
// Merge all the peaks into a single set
var allPeakGroups = MergePeakGroups(dataSets);
if (allPeakGroups.Count == 0)
{
return(listPeakSets);
}
// Create coeluting groups
while (allPeakGroups.Count > 0)
{
var peakNext = allPeakGroups[0];
allPeakGroups.RemoveAt(0);
var peakSetNext = FindCoelutingPeptidePeaks(dataSets, peakNext, allPeakGroups);
listPeakSets.Add(peakSetNext);
}
// Reset best picked peaks and reintegrate if necessary
for (int i = 0; i < listPeakSets.Count; i++)
{
var peakSet = listPeakSets[i];
PeptideChromDataPeak peakBest = null, peakNarrowest = null;
int minLength = int.MaxValue;
foreach (var peak in peakSet.OrderedPeaks)
{
peak.SetBestPeak(peakBest, i);
// The first peak seen is the best peak
if (peakBest == null)
{
peakBest = peak;
}
int lenPeak = peak.Length;
if (0 < lenPeak && lenPeak < minLength)
{
peakNarrowest = peak;
minLength = lenPeak;
}
}
// If any peak trunctation occurred in peaks that should be matching
if (peakNarrowest != null && !ReferenceEquals(peakBest, peakNarrowest))
{
foreach (var peak in peakSet)
{
if (peak.PeakGroup == null || peak.Length == peakNarrowest.Length)
{
continue;
}
peak.Data.NarrowPeak(peak.PeakGroup, peakNarrowest, i);
}
}
}
// Discard peaks not included in a peptide peak list
foreach (var chromDataSet in dataSets)
{
chromDataSet.TruncatePeakSets(listPeakSets.Count);
}
return(listPeakSets);
}
/// <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);
}
/// <summary>
/// Returns true if the apex for the given peak is contained in this peak
/// </summary>
public bool IsContained(PeptideChromDataPeak peak)
{
return(StartIndex <= peak.TimeIndex && peak.TimeIndex <= EndIndex);
}
