void InitPriorityQueue(Dictionary <string, List <IGlycan> > candidate,
Dictionary <double, PeakNode> peak_nodes_map, PriorityQueue <PeakNode> queue)
{
foreach (var peptide in candidate.Keys)
{
// Y1 mass
double mass = ComputePeptideMass(peptide) + util.mass.Glycan.kHexNAc;
// node matches
if (!peak_nodes_map.ContainsKey(mass))
{
PeakNode node = new PeakNode();
// set mass
node.set_mass(mass);
// set matches
if (ComplexInclude)
{
node.Add(peptide, kY1, new List <int>());
}
if (HybridInclude)
{
node.Add(peptide, kY1_hybrid, new List <int>());
}
if (HighMannoseInclude)
{
node.Add(peptide, kY1_mannose, new List <int>());
}
// add node
peak_nodes_map[mass] = node;
// enqueue
queue.Enqueue(mass, peak_nodes_map[mass]);
}
else
{
// update glycopeptide match
if (ComplexInclude)
{
peak_nodes_map[mass].Add(peptide, kY1, new List <int>());
}
if (HybridInclude)
{
peak_nodes_map[mass].Add(peptide, kY1_hybrid, new List <int>());
}
if (HighMannoseInclude)
{
peak_nodes_map[mass].Add(peptide, kY1_mannose, new List <int>());
}
}
}
}
List <PeakNode> DynamicProgramming(List <IPeak> peaks,
Dictionary <double, PeakNode> peak_nodes_map, PriorityQueue <PeakNode> queue)
{
List <PeakNode> matched_nodes = new List <PeakNode>();
while (queue.Count > 0)
{
// get node
PeakNode node = queue.Dequeue();
// // match peaks
double target = node.Mass();
List <int> matched = searcher_.Search(target);
// max if matched a peak
node.Max(peaks);
// update matches
if (matched.Count > 0)
{
node.Add(matched);
node.set_miss(0);
matched_nodes.Add(node);
}
if (node.Missing() > kMissing)
{
continue;
}
// extending queue
Dictionary <string, Dictionary <string, HashSet <int> > > peakMatch = node.Matches();
foreach (var peptide in peakMatch.Keys.ToList())
{
foreach (var glycan_id in peakMatch[peptide].Keys.ToList())
{
List <int> peak_indexes = peakMatch[peptide][glycan_id].ToList();
IGlycan glycan = glycans_map_[glycan_id];
foreach (var g in glycan.Children())
{
double mass = g.Mass() + util.mass.Peptide.To.Compute(peptide);
if (!peak_nodes_map.ContainsKey(mass))
{
PeakNode next = new PeakNode();
// set mass
next.set_mass(mass);
// set matches
next.Add(peptide, g.ID(), peak_indexes);
// set missing
next.set_miss(node.Missing() + 1);
// add node
peak_nodes_map[mass] = next;
// enqueue
queue.Enqueue(mass, peak_nodes_map[mass]);
}
else
{
// std::cout << "here" << std::endl;
PeakNode next = peak_nodes_map[mass];
// set missing
next.set_miss(Math.Min(next.Missing(), node.Missing() + 1));
// set matches
next.Add(peptide, g.ID(), peak_indexes);
}
}
}
}
}
return(matched_nodes);
}
