protected List <IGlycoPeptide> MatchPoints(IPeak peak, int parentCharge)
{
HashSet <IGlycoPeptide> g = new HashSet <IGlycoPeptide>();
for (int i = 1; i <= parentCharge; i++)
{
double mass = calculator.CalcChargeMass(peak.GetMZ(), i, option);
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
foreach (Point pt in matcher.GetSearchResult(p, parameter as BinarySearchParameter))
{
g.UnionWith((pt as BinSearchAnnotatedPoint).GetGlycoPeptide());
}
}
return(g.ToList());
}
protected void InitMatcher(IGlycoPeptide glycoPeptide)
{
List <Point> points = new List <Point>();
List <ITableNGlycan> glycans = glycansTable[
glycoPeptide.GetGlycan().GetName()];
IPeptide peptide = glycoPeptide.GetPeptide();
string seq = peptide.GetSequence();
int pos = glycoPeptide.GetPosition();
Dictionary <double, BinSearchAnnotatedPoint> seen =
new Dictionary <double, BinSearchAnnotatedPoint>();
//glycanfrag
foreach (ITableNGlycan g in glycans)
{
double glycanMass = calculator.CalcGlycanMass(g, option);
double mass = calculator.CalcPeptideMass(seq, option) + glycanMass;
if (!seen.ContainsKey(mass))
{
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
seen[mass] = p;
points.Add(p);
}
seen[mass].AddGlycoPeptide(
new GeneralPeptide(peptide.GetID(), seq), g, pos);
//n-peptidefrag
for (int i = 0; i < pos; i++)
{
mass = calculator.CalcPeptideIonMass(
seq.Substring(0, i + 1), IonType.cIon, option) + glycanMass;
if (!seen.ContainsKey(mass))
{
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
seen[mass] = p;
points.Add(p);
}
seen[mass].AddGlycoPeptide(
new GeneralPeptide(peptide.GetID(), seq.Substring(0, i + 1)),
g, pos);
}
//c-peptidefrag
for (int i = pos + 1; i < seq.Length; i++)
{
mass = calculator.CalcPeptideIonMass(
seq.Substring(i, seq.Length - i), IonType.zIon, option) + glycanMass;
if (!seen.ContainsKey(mass))
{
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
seen[mass] = p;
points.Add(p);
}
seen[mass].AddGlycoPeptide(
new GeneralPeptide(peptide.GetID(), seq.Substring(i, seq.Length - i)),
g, pos);
}
}
points.Sort();
matcher.SetPoints(points);
}
