public void NarrowPeak(ChromDataPeakList peakSet, PeptideChromDataPeak narrowestPeptidePeak, int indexSet)
{
var peak = peakSet[0].Peak;
if (peak != null)
{
int len = narrowestPeptidePeak.Length;
if (narrowestPeptidePeak.IsRightBound)
peak.ResetBoundaries(peak.EndIndex - len + 1, peak.EndIndex);
else // if (narrowestPeptidePeak.IsLeftBound) Need to make sure they are the same length
peak.ResetBoundaries(peak.StartIndex, peak.StartIndex + len - 1);
}
}
public ChromDataPeakList SetBestPeak(ChromDataPeakList peakSet, PeptideChromDataPeak bestPeptidePeak, int indexSet)
{
ChromDataPeakList peakSetAdd = null;
int startIndex, endIndex;
// TODO: Need to do something more reasonable for Deuterium elution time shifts
bool matchBounds = GetLocalPeakBounds(bestPeptidePeak, out startIndex, out endIndex);
if (peakSet != null)
{
// If the peak ranked by peptide matching is not in its proper position,
// then move it there
if (!ReferenceEquals(peakSet, _listPeakSets[indexSet]))
{
_listPeakSets.Remove(peakSet);
_listPeakSets.Insert(indexSet, peakSet);
}
// If there is a different best peptide peak, and it should have
// the same retention time charachteristics, then reset the integration
// boundaries of this peak set
if (matchBounds)
{
var peak = peakSet[0].Peak;
// If this peak and the best peak for this peptide are allowed to be shifted in
// relationship to each other, then make that shift be the delta between the apex
// times of the two peaks. They still need to be the same width.
if (!IsSameRT(bestPeptidePeak.Data))
{
int deltaBounds = GetLocalIndex(bestPeptidePeak.TimeIndex) - peak.TimeIndex;
startIndex = Math.Max(0, startIndex + deltaBounds);
endIndex = Math.Min(Times.Length - 1, endIndex + deltaBounds);
}
// Reset the range of the best peak, if the chromatograms for this peak group
// overlap with the best peptide peak at all. Resetting the range of the best
// peak for this peak group will cause it and all other peaks in the peak group
// to be reintegrated to this range
if (startIndex < endIndex)
{
peak.ResetBoundaries(startIndex, endIndex);
}
// In a peak set with mutiple charge states and light-heavy pairs, it is
// possible that a peak may not overlap with the best peak in its
// charge group. If this is the case, and the best peak is completely
// outside the bounds of the current chromatogram, then insert an
// empty peak.
else
{
var peakAdd = new ChromDataPeak(BestChromatogram, null);
peakSetAdd = new ChromDataPeakList(peakAdd, _listChromData) { IsForcedIntegration = true };
}
}
}
// If no peak was found at the peptide level for this data set,
// but there is a best peak for the peptide
else if (bestPeptidePeak != null && matchBounds)
{
// And the chromatograms for this transition group overlap with the best peptide
// peak, then create a peak with the same extents as the best peak. This peak will
// appear as missing, if Integrate All is not selected.
ChromDataPeak peakAdd;
if (startIndex < endIndex)
{
// CONSIDER: Not that great for peaks that are expected to be shifted in relationship
// to each other, since this will force them to have the same boundaries,
// but if no evidence of a peak was found, it is hard to understand what
// could be done better.
var chromData = BestChromatogram;
peakAdd = new ChromDataPeak(chromData, chromData.CalcPeak(startIndex, endIndex));
}
// Otherwise, create an empty peak
else
{
peakAdd = new ChromDataPeak(BestChromatogram, null);
}
peakSetAdd = new ChromDataPeakList(peakAdd, _listChromData) {IsForcedIntegration = true};
}
else
{
// Otherwise, insert an empty peak
var peakAdd = new ChromDataPeak(BestChromatogram, null);
peakSetAdd = new ChromDataPeakList(peakAdd, _listChromData) { IsForcedIntegration = true };
}
if (peakSetAdd != null)
{
if (indexSet < _listPeakSets.Count)
_listPeakSets.Insert(indexSet, peakSetAdd);
else
_listPeakSets.Add(peakSetAdd);
peakSet = peakSetAdd;
}
return peakSet;
}
/// <summary>
/// Returns true if the peak boundaries should be reset to the startIndex and endIndex
/// values output from this function.
/// </summary>
/// <param name="bestPeptidePeak">The best peak for this peptide, which will be in its own scale</param>
/// <param name="startIndex">The start index this peak should have, if return is true</param>
/// <param name="endIndex">The end index this peak should have, if return is false</param>
/// <returns>True if peak bounds should be reset</returns>
private bool GetLocalPeakBounds(PeptideChromDataPeak bestPeptidePeak, out int startIndex, out int endIndex)
{
if (bestPeptidePeak == null)
{
startIndex = endIndex = -1;
return false;
}
startIndex = Math.Max(0, GetLocalIndex(bestPeptidePeak.StartIndex));
endIndex = Math.Min(Times.Length - 1, GetLocalIndex(bestPeptidePeak.EndIndex));
return IsSameRT(bestPeptidePeak.Data) || IsShiftedRT(bestPeptidePeak.Data);
}
