public override IEnumerable <string> Process(string filename)
{
List <string> result = new List <string>();
Dictionary <IFilter <IIdentifiedSpectrum>, SpectrumEntry> map = new Dictionary <IFilter <IIdentifiedSpectrum>, SpectrumEntry>();
foreach (IFilter <IIdentifiedSpectrum> filter in filterMap.Keys)
{
string resultFile = filename + "." + filterMap[filter];
result.Add(resultFile);
map[filter] = new SpectrumEntry(resultFile, isProteinFile);
}
return(DoProcess(filename, result, map));
}
protected override IEnumerable <string> DoProcess(string filename, List <string> result, Dictionary <IFilter <IIdentifiedSpectrum>, SpectrumEntry> map)
{
try
{
var format = new MascotPeptideTextFormat();
var spectra = format.ReadFromFile(filename);
foreach (IFilter <IIdentifiedSpectrum> filter in map.Keys)
{
SpectrumEntry entry = map[filter];
foreach (IIdentifiedSpectrum spectrum in spectra)
{
if (filter.Accept(spectrum))
{
entry.Spectra.Add(spectrum);
}
}
if (entry.Spectra.Count > 0)
{
entry.ResultWriter.WriteLine(format.PeptideFormat.GetHeader());
entry.Spectra.ForEach(m => entry.ResultWriter.WriteLine(format.PeptideFormat.GetString(m)));
}
}
return(result);
}
finally
{
foreach (SpectrumEntry entry in map.Values)
{
entry.Dispose();
}
}
}
protected override IEnumerable <string> DoProcess(string filename, List <string> result, Dictionary <IFilter <IIdentifiedSpectrum>, SpectrumEntry> map)
{
string database = filename + ".fasta";
if (!File.Exists(database))
{
throw new Exception("Fasta file not exists : " + database);
}
IAccessNumberParser acParser = AccessNumberParserFactory.GuessParser(database);
Dictionary <string, Sequence> seqMap = DatabaseUtils.GetAccessNumberMap(database, acParser);
try
{
using (IdentifiedProteinGroupEnumerator iter = new IdentifiedProteinGroupEnumerator(filename))
{
foreach (IFilter <IIdentifiedSpectrum> filter in map.Keys)
{
SpectrumEntry entry = map[filter];
entry.ResultWriter.WriteLine(iter.ProteinFormat.GetHeader());
entry.ResultWriter.WriteLine(iter.PeptideFormat.GetHeader());
}
while (iter.MoveNext())
{
IIdentifiedProteinGroup group = iter.Current;
List <IIdentifiedSpectrum> spectra = group[0].GetSpectra();
foreach (IFilter <IIdentifiedSpectrum> filter in map.Keys)
{
SpectrumEntry entry = map[filter];
entry.Spectra.Clear();
foreach (IIdentifiedSpectrum spectrum in spectra)
{
if (filter.Accept(spectrum))
{
entry.Spectra.Add(spectrum);
}
}
if (entry.Spectra.Count > 0)
{
for (int i = 0; i < group.Count; i++)
{
entry.ResultWriter.WriteLine("${0}-{1}{2}", group.Index, i + 1, iter.ProteinFormat.GetString(group[i]));
string ac = acParser.GetValue(group[i].Name);
Sequence seq = seqMap[ac];
entry.FastaWriter.WriteLine(">" + seq.Reference);
entry.FastaWriter.WriteLine(seq.SeqString);
}
foreach (IIdentifiedSpectrum spectrum in entry.Spectra)
{
entry.ResultWriter.WriteLine(iter.PeptideFormat.GetString(spectrum));
}
}
}
}
return(result);
}
}
finally
{
foreach (SpectrumEntry entry in map.Values)
{
entry.Dispose();
}
}
}
