protected override IIdentifiedResult GetIdentifiedResult(string fileName)
{
format = new MascotPeptideTextFormat();
var spectra = format.ReadFromFile(fileName);
IIdentifiedResult result;
if (isSiteLevel)
{
result = IdentifiedSpectrumUtils.BuildGroupByPeptide(spectra);
}
else
{
result = IdentifiedSpectrumUtils.BuildGroupByUniquePeptide(spectra);
}
var map = SequenceUtils.ReadAccessNumberReferenceMap(new FastaFormat(), this.fastaFile, this.parser);
foreach (var group in result)
{
var proteins = group[0].Description.Split('/');
group[0].Description = (from p in proteins
let ac = parser.GetValue(p)
select map[ac]).ToList().Merge(" ! ");
}
return(result);
}