protected override List <IGlycoPeptide> GenerateNewGlycoPeptide(IPeptide peptide, IGlycan glycan)
{
List <IGlycoPeptide> glycos = new List <IGlycoPeptide>();
glycos.Add(new GeneralGlycoPeptide(peptide, glycan, -1));
return(glycos);
}
public SpecialGlycoPeptide(
IPeptide peptide, T glycan, int pos)
{
this.peptide = peptide;
this.glycan = glycan;
this.position = pos;
}
public IGlycoPeptideProxy Generate(IGlycan glycan, IPeptide peptide, int modifySite)
{
if (glycan is ITableNGlycanMassProxy)
{
IGlycoPeptide glycoPeptide = new GeneralGlycoPeptide(glycan, peptide, modifySite);
IGlycoPeptideMassProxy glycoPeptideMassProxy = new GeneralGlycoPeptideMassProxy(glycoPeptide);
foreach (double glycanMass in (glycan as ITableNGlycanMassProxy).GetMass())
{
glycoPeptideMassProxy.AddMass(glycanMass +
PeptideCalcMass.Instance.Compute(glycoPeptide.GetPeptide()), MassType.Branch);
}
foreach (double glycanMass in (glycan as ITableNGlycanMassProxy).GetCoreMass())
{
glycoPeptideMassProxy.AddMass(glycanMass +
PeptideCalcMass.Instance.Compute(glycoPeptide.GetPeptide()), MassType.Core);
}
glycoPeptideMassProxy.AddRangeMass(SingaturePeakCalcMass.Instance.ComputeComplex(glycan), MassType.Glycan);
double mass = GlycanCalcMass.Instance.Compute(glycan);
foreach (double peptideMass in PTMPeptideCalcMass.Compute(peptide.GetSequence(), modifySite))
{
glycoPeptideMassProxy.AddMass(mass + peptideMass, MassType.Peptide);
}
return(glycoPeptideMassProxy);
}
else
{
throw new InvalidCastException("Can not cast to ITableNGlycanMassProxy");
}
}
public NGlycoPeptideNode(ITableNGlycan nGlycan, IPeptide peptide, IScore score)
{
glycan = nGlycan.TableClone();
this.peptide = peptide.Clone();
this.score = score.Clone();
calculator = UtilMass.Instance;
option = UtilMassOption.Instance;
mass = calculator.CalcGlycanMass(glycan, option) + calculator.CalcPeptideMass(peptide, option);
}
public List <IGlycoPeptide> Create(IGlycan glycan, IPeptide peptide)
{
List <IGlycoPeptide> glycoPeptides = new List <IGlycoPeptide>();
foreach (int pos in FindPTMPosition.FindNGlycanSite(peptide.GetSequence()))
{
glycoPeptides.Add(new GeneralGlycoPeptide(peptide, glycan, pos));
}
return(glycoPeptides);
}
GenerateNewGlycoPeptide(IPeptide peptide, IGlycan glycan)
{
List <IAccumulatedGlycoPeptideMassProxy> glycos = new List <IAccumulatedGlycoPeptideMassProxy>();
foreach (int pos in FindPTMPosition.FindNGlycanSite(peptide.GetSequence()))
{
SpecialGlycoPeptide <IAccumulatedGlycanMassProxy> g =
new SpecialGlycoPeptide <IAccumulatedGlycanMassProxy>(peptide, glycan as IAccumulatedGlycanMassProxy, pos);
glycos.Add(new GeneralAccumulatedGlycoPeptideMassProxy(g));
}
return(glycos);
}
public List <IGlycoPeptide> Create(IGlycan glycan, IPeptide peptide)
{
List <IGlycoPeptide> glycoPeptides = new List <IGlycoPeptide>();
foreach (int pos in FindPTMPosition.FindNGlycanSite(peptide.GetSequence()))
{
try
{
IGlycoPeptideProxy glycoPeptideProxy = generator.Generate(glycan, peptide, pos);
glycoPeptides.Add(glycoPeptideProxy);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
}
return(glycoPeptides);
}
public void SetPeptide(IPeptide peptide)
{
glycoPeptide.SetPeptide(peptide);
}
public GeneralGlycoPeptide(IPeptide peptide, IGlycan glycan, int pos)
{
this.peptide = peptide;
this.glycan = glycan;
this.position = pos;
}
protected abstract List <T> GenerateNewGlycoPeptide(IPeptide peptide, IGlycan glycan);
public GlycoPeptideTemplate(IPeptide peptide, IGlycan glycan, int pos)
{
this.peptide = peptide;
this.glycan = glycan;
this.position = pos;
}
public double Compute(IPeptide peptide, IonType type)
{
return(ComputePeptide(peptide.GetSequence(), type));
}
public double Compute(IPeptide peptide)
{
return(Compute(peptide.GetSequence()));
}
public double CalcPeptideIonMass(IPeptide peptide, IonType type, ICalcMassOption option)
{
return(CalcPeptideIonMass(peptide.GetSequence(), type, option));
}
public void AddGlycoPeptide(IPeptide peptide, IGlycan glycan, int pos)
{
glycoPeptides.Add(new GeneralGlycoPeptide(peptide, glycan, pos));
}
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);
}
public void SetPeptide(IPeptide peptide)
{
this.peptide = peptide;
}
public double CalcPeptideMass(IPeptide peptide, ICalcMassOption option)
{
string sequence = peptide.GetSequence();
return(CalcPeptideMass(sequence, option));
}
