private IIdentifiedProteinGroup ReadNextProteinGroup(StreamReader filein,
Dictionary <string, IIdentifiedSpectrum> peptideMap,
ref string lastLine)
{
while (!IsProteinLine(lastLine) && (lastLine = filein.ReadLine()) != null)
{
}
if (lastLine == null)
{
return(null);
}
IIdentifiedProteinGroup result = new IdentifiedProteinGroup();
while (IsProteinLine(lastLine))
{
IIdentifiedProtein protein = new IdentifiedProtein();
this.proteinConverter.SetProperty(protein, lastLine);
result.Add(protein);
lastLine = filein.ReadLine();
}
var peptides = new List <IIdentifiedSpectrum>();
while (!IsProteinLine(lastLine))
{
IIdentifiedSpectrum mphit = new IdentifiedSpectrum();
this.peptideConverter.SetProperty(mphit, lastLine);
string id = mphit.Query.FileScan.LongFileName + "-" + mphit.Rank;
if (!peptideMap.ContainsKey(id))
{
peptideMap[id] = mphit;
}
else
{
mphit = peptideMap[id];
}
peptides.Add(mphit);
lastLine = filein.ReadLine();
if (lastLine == null || lastLine.Trim().Length == 0)
{
break;
}
}
peptides.Sort();
result.AddIdentifiedSpectra(peptides);
return(result);
}
