public List <IPeptide> Create(IProtein protein)
{
List <IPeptide> peptideList = new List <IPeptide>();
List <string> sequences = generator.Generate(protein.GetSequence());
foreach (string seq in sequences)
{
GeneralPeptide peptide = new GeneralPeptide(protein.GetID(), seq);
peptideList.Add(peptide);
}
protein.SetPeptides(peptideList);
return(peptideList);
}
public override List <string> GeneratePeptideSequences(IProtein protein)
{
if (protein.GetPeptides().Count == 0)
{
List <string> sequences =
GeneratePeptideSequence.Generate(
protein.GetSequence(), parameter.GetProtease(),
parameter.GetMissCleavage(), parameter.GetMiniLength());
return(sequences);
}
List <IPeptide> peptides = protein.GetPeptides();
HashSet <string> seqList = new HashSet <string>();
foreach (IPeptide peptide in peptides)
{
string seq = peptide.GetSequence();
seqList.UnionWith(GeneratePeptideSequence.Generate(
seq, parameter.GetProtease(), parameter.GetMissCleavage(),
parameter.GetMiniLength()));
}
return(seqList.ToList());
}
public override List <string> GeneratePeptideSequences(IProtein protein)
{
return(GeneratePeptideSequence.Generate(
protein.GetSequence(), parameter.GetProtease(),
parameter.GetMissCleavage(), parameter.GetMiniLength()));
}