public List <IPeptide> Run(string fileName)
{
List <IPeptide> peptideList = new List <IPeptide>();
HashSet <string> sequenceSeen = new HashSet <string>();
List <IProtein> proteins = fastaReader.Create(fileName);
foreach (IPeptideCreatorParameter parameter in parameters)
{
pepRunner.SetParameter(parameter);
foreach (IProtein protein in proteins)
{
pepRunner.Create(protein);
}
}
foreach (IProtein protein in proteins)
{
foreach (IPeptide pep in protein.GetPeptides())
{
string seq = pep.GetSequence();
if (!sequenceSeen.Contains(seq))
{
peptideList.Add(pep);
sequenceSeen.Add(seq);
//Console.WriteLine(seq);
}
}
}
return(peptideList);
}
public List <IPeptide> Run(string fileName)
{
List <IProtein> proteins = fastaReader.Create(fileName);
List <IPeptide> peptideList = new List <IPeptide>();
HashSet <string> sequenceSeen = new HashSet <string>();
foreach (IProtein p in proteins)
{
List <IPeptide> peptides = pepRunner.Create(p);
foreach (IPeptide pep in peptides)
{
string seq = pep.GetSequence();
if (!sequenceSeen.Contains(seq))
{
peptideList.Add(pep);
sequenceSeen.Add(seq);
}
}
}
return(peptideList);
}
public void Init(string spectrumFileLocation, string peptideFileLocation, string outputLocation)
{
spectrumFactory.Init(spectrumFileLocation);
proteins = proteinCreator.Create(peptideFileLocation);
HashSet <string> seen = new HashSet <string>();
peptides = new List <IPeptide>();
foreach (IProtein protein in proteins)
{
foreach (IPeptide peptide in peptideCreator.Create(protein))
{
if (!seen.Contains(peptide.GetSequence()))
{
seen.Add(peptide.GetSequence());
peptides.Add(peptide);
}
}
}
glycans = glycanCreator.Create();
precursorMatcher.SetPeptides(peptides);
precursorMatcher.SetGlycans(glycans);
reportProducer.SetOutputLocation(outputLocation);
}