public override IEnumerable <string> Process()
{
var searchEngine = EnumUtils.StringToEnum <SearchEngineType>(options.EngineType, SearchEngineType.Unknown);
var factory = searchEngine.GetFactory();
string suffix = options.Rank2 ? ".rank2" : string.Empty;
var result = new List <string>();
foreach (var inputfile in options.InputFiles)
{
ISpectrumParser parser = factory.GetParser(inputfile, options.Rank2);
if (!string.IsNullOrEmpty(options.TitleType))
{
parser.TitleParser = TitleParserUtils.FindByName(options.TitleType);
}
parser.Progress = this.Progress;
Progress.SetMessage("Parsing " + inputfile + "...");
var spectra = parser.ReadFromFile(inputfile);
var format = factory.GetPeptideFormat(true);
var outputFile = string.IsNullOrEmpty(options.OutputFile) ? inputfile + suffix + ".peptides" : options.OutputFile;
Progress.SetMessage("Writing {0} PSMs to {1}...", spectra.Count, outputFile);
format.WriteToFile(outputFile, spectra);
result.Add(outputFile);
}
return(result);
}
public PercolatorFileParser(ISpectrumParser baseParser)
{
this.baseParser = baseParser;
}
