public void Init(List <string> peptides, Dictionary <string, model.glycan.IGlycan> glycans)
{
foreach (var it in peptides)
{
algorithm.Point <string> seq = new algorithm.Point <string>(util.mass.Peptide.To.Compute(it), it);
peptides_.Add(seq);
}
foreach (var it in glycans.Values)
{
glycans_.Add(it);
}
searcher_.Init(peptides_);
}
protected void InitSearch(Dictionary <string, List <model.glycan.IGlycan> > candidate)
{
List <algorithm.Point <string> > peptides_points = new List <algorithm.Point <string> >();
foreach (var peptide in candidate.Keys)
{
// get glycan mass
double glycan_mean_mass = SearchHelper.ComputeGlycanMass(candidate[peptide]);
// create points
foreach (int pos in protein.ProteinPTM.FindNGlycanSite(peptide))
{
string table_key = SearchHelper.MakeKeySequence(peptide, pos);
//init table
if (!mass_table_.ContainsKey(table_key))
{
List <double> mass_list = SearchHelper.ComputeNonePTMPeptideMass(peptide, pos);
mass_table_[table_key] = new List <double>(mass_list);
mass_list = SearchHelper.ComputePTMPeptideMass(peptide, pos);
ptm_mass_table_[table_key] = new List <double>(mass_list);
}
// retreive table
foreach (double mass in mass_table_[table_key])
{
algorithm.Point <string> point = new algorithm.Point <string>(mass, table_key);
peptides_points.Add(point);
}
foreach (double mass in ptm_mass_table_[table_key])
{
algorithm.Point <string> point = new algorithm.Point <string>(mass + glycan_mean_mass, table_key);
peptides_points.Add(point);
}
}
}
searcher_.Init(peptides_points);
}
