//assumes peaks are sorted by peakrt
void mark_overlaps_by_peak_rt(IList <PeaksUsedOrNot> peaks, PeakCoordSet peak_set, PeaksUsedOrNot p)
{
var overlap_bounds = peak_set.find_overlap_bounds_by_peak_rt_idx(p.p);
for (int i = overlap_bounds.leftmost; i <= overlap_bounds.rightmost; i++)
{
peaks[i].used = true;
}
}
///this takes the set of peaks and extends them, based on potential shoulder peaks which have odd alignments
void extend_peak_set(IList <SlimCrawPeak> in_peaks, IList <SlimCrawPeak> out_peaks, bool start_at_peak = false)
{
if (in_peaks.Count == 0)
{
return;
}
List <SlimCrawPeak> peak_ptrs_by_rt = new List <SlimCrawPeak>(in_peaks);
peak_ptrs_by_rt.Sort(crawutils.CompByPeakRTIdx);
List <PeaksUsedOrNot> peaks_by_rt = new List <PeaksUsedOrNot>(peak_ptrs_by_rt.Select(p => new PeaksUsedOrNot(p)));
List <PeaksUsedOrNot> peaks_by_I = new List <PeaksUsedOrNot>(peaks_by_rt);
peaks_by_I.Sort(crawutils.CompByPeakRawHeight);
PeakCoordSet peak_coords = new PeakCoordSet(peak_ptrs_by_rt);
int intensity_index = peaks_by_I.Count - 1;
do
{
intensity_index--;
PeaksUsedOrNot here = peaks_by_I[intensity_index];
if (!here.used)
{
//extend peak
extend_to_1d_zero(here.p, pf.method.extend_from_peak_rt);
if (pf.method.ratchet_back_to_frac_maxval > -1)
{
ratchet_back_to_frac_maxval(here.p, pf.method.ratchet_back_to_frac_maxval);
}
//exclude overlappers -- find peaks from my start to my end
//TODO -- deal with overlappers... or convert to linear walk algorithm
//safe, since push_back will copy the dereferenced SlimCrawPeakPtr
if (pf.method.exclude_extension_overlaps_by_peakrt)
{
mark_overlaps_by_peak_rt(peaks_by_rt, peak_coords, here);
}
out_peaks.Add(here.p);
here.used = true;
}
} while (intensity_index > 0);
}
