public List <IIdentifiedSpectrum> ReadFromFile(string fileName)
{
var result = new MascotPeptideTextFormat().ReadFromFile(fileName);
FilterSpectra(result);
UpdateModifications(result);
foreach (var peptide in result)
{
peptide.Peptide.AssignProteins((peptide.Annotations[PROTEIN_KEY] as string).Split(';'));
peptide.Annotations.Remove(PROTEIN_KEY);
peptide.TheoreticalMass = peptide.ExperimentalMass;
}
var i = 0;
while (i < result.Count - 1)
{
var ititle = result[i].Annotations[TITLE_KEY] as string;
while (i < result.Count - 1)
{
var jtitle = result[i + 1].Annotations[TITLE_KEY] as string;
if (!ititle.Equals(jtitle))
{
i++;
break;
}
for (int l = result[i + 1].Peptides.Count - 1; l >= 0; l--)
{
result[i].AddPeptide(result[i + 1].Peptides[l]);
}
result.RemoveAt(i + 1);
}
}
foreach (var peptide in result)
{
var title = peptide.Annotations[TITLE_KEY] as string;
peptide.Annotations.Remove(TITLE_KEY);
var oldCharge = peptide.Query.FileScan.Charge;
peptide.Query.FileScan = TitleParser.GetValue(title);
peptide.Query.FileScan.Charge = oldCharge;
if (string.IsNullOrEmpty(peptide.Query.FileScan.Experimental))
{
peptide.Query.FileScan.Experimental = Path.GetFileNameWithoutExtension(fileName);
}
var rtstr = peptide.Annotations[RT_KEY] as string;
if (!string.IsNullOrWhiteSpace(rtstr))
{
peptide.Query.FileScan.RetentionTime = double.Parse(rtstr.StringBefore("-"));
}
peptide.Annotations.Remove(RT_KEY);
}
return(result);
}
