public override IEnumerable<PeptideSpectralMatch> ReadNextPsm()
{
Protein prot;
MSDataFile dataFile;
foreach (OmssaPeptideSpectralMatch omssaPSM in _reader.GetRecords<OmssaPeptideSpectralMatch>())
{
Peptide peptide = new Peptide(omssaPSM.Sequence.ToUpper());
SetFixedMods(peptide);
SetDynamicMods(peptide, omssaPSM.Modifications);
peptide.StartResidue = omssaPSM.StartResidue;
peptide.EndResidue = omssaPSM.StopResidue;
if (_proteins.TryGetValue(omssaPSM.Defline, out prot))
{
peptide.Parent = prot;
}
PeptideSpectralMatch psm = new PeptideSpectralMatch();
if (_extraColumns.Count > 0)
{
foreach(string name in _extraColumns) {
psm.AddExtraData(name, _reader.GetField<string>(name));
}
}
psm.Peptide = peptide;
psm.Score = omssaPSM.EValue;
psm.Charge = omssaPSM.Charge;
psm.ScoreType = PeptideSpectralMatchScoreType.EValue;
psm.IsDecoy = omssaPSM.Defline.StartsWith("DECOY");
psm.SpectrumNumber = omssaPSM.SpectrumNumber;
psm.FileName = omssaPSM.FileName;
string[] filenameparts = psm.FileName.Split('.');
if (_dataFiles.TryGetValue(filenameparts[0], out dataFile))
{
if (!dataFile.IsOpen)
dataFile.Open();
psm.Spectrum = dataFile[psm.SpectrumNumber] as MsnDataScan;
}
yield return psm;
}
}
