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 <string> Generate(string sequence)
{
List <string> peptideList = new List <string>();
foreach (string s in generator.Generate(sequence))
{
if (FindPTMPosition.ContainsOGlycanSite(s))
{
peptideList.Add(s);
}
}
return(peptideList);
}
public List <IPeptide> Create(IProtein protein)
{
List <string> pepList = new List <string>();
foreach (string sequence in creator.GeneratePeptideSequences(protein))
{
if (FindPTMPosition.ContainsOGlycanSite(sequence))
{
pepList.Add(sequence);
}
}
List <IPeptide> peptideList = creator.CreateNewPeptides(protein.GetID(), pepList);
protein.SetPeptides(peptideList);
return(peptideList);
}
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);
}
