public PrecursorMatcherByBinSearchOnGlycansTemplate(List <IPeptide> peptides, List <IGlycan> glycans, double tol)
{
matcher = new BinarySearch();
parameter = new PrecursorParameter(tol);
glycanPoints = new List <Point>();
calculator = UtilMass.Instance;
option = UtilMassOption.Instance;
this.peptides = peptides;
// build points on glycans
Dictionary <double, PrecursorPoint <IGlycan> > seen = new Dictionary <double, PrecursorPoint <IGlycan> >();
foreach (IGlycan glycan in glycans)
{
double mass = calculator.CalcGlycanMass(glycan, option);
if (!seen.ContainsKey(mass))
{
PrecursorPoint <IGlycan> pt = new PrecursorPoint <IGlycan>(mass);
seen[mass] = pt;
glycanPoints.Add(pt);
}
seen[mass].Add(glycan);
}
matcher.SetPoints(glycanPoints);
}
public PrecursorMatcherByBinSearchOnPeptidesTemplate(List <IPeptide> peptides, List <IGlycan> glycans,
PrecursorParameter parameter)
{
matcher = new BinarySearch();
this.parameter = parameter;
peptidePoints = new List <Point>();
calculator = UtilMass.Instance;
option = UtilMassOption.Instance;
this.glycans = glycans;
// build points on peptides
Dictionary <double, PrecursorPoint <IPeptide> > seen = new Dictionary <double, PrecursorPoint <IPeptide> >();
foreach (IPeptide peptide in peptides)
{
double mass = calculator.CalcPeptideMass(peptide, option);
if (!seen.ContainsKey(mass))
{
PrecursorPoint <IPeptide> pt = new PrecursorPoint <IPeptide>(mass);
seen[mass] = pt;
peptidePoints.Add(pt);
}
seen[mass].Add(peptide);
}
matcher.SetPoints(peptidePoints);
}
protected void MatchPrecursorMass(double precusorMass, List <T> glycoPeptides)
{
HashSet <string> seen = new HashSet <string>();
List <Point> matches = new List <Point>();
foreach (IGlycan glycan in glycans)
{
//search on glycans for a peptide
double target = precusorMass - calculator.CalcGlycanMass(glycan, option);
if (target <= 0)
{
continue;
}
PrecursorPoint <IPeptide> p = new PrecursorPoint <IPeptide>(target);
matches.AddRange(matcher.GetSearchResult(p, parameter));
//build glycopeptide
foreach (Point pt in matches)
{
foreach (IPeptide peptide in (pt as PrecursorPoint <IPeptide>).GetObjects())
{
//check redundant
string s = peptide.GetSequence();
if (!seen.Contains(s))
{
glycoPeptides.AddRange(GenerateNewGlycoPeptide(peptide, glycan));
seen.Add(s);
}
}
}
matches.Clear();
seen.Clear();
}
}
public void SetPeptides(List <IPeptide> peptides)
{
// build points on peptides
Dictionary <double, PrecursorPoint <IPeptide> > seen = new Dictionary <double, PrecursorPoint <IPeptide> >();
foreach (IPeptide peptide in peptides)
{
double mass = calculator.CalcPeptideMass(peptide, option);
if (!seen.ContainsKey(mass))
{
PrecursorPoint <IPeptide> pt = new PrecursorPoint <IPeptide>(mass);
seen[mass] = pt;
peptidePoints.Add(pt);
}
seen[mass].Add(peptide);
}
matcher.SetPoints(peptidePoints);
}