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 List <IIdentifiedSpectrum> ReadFromFile(string fileName)
{
var result = baseParser.ReadFromFile(fileName);
var resultMap = result.ToDictionary(m => m.Id.ToString());
var input = GetInputFile(fileName);
using (var sr = new StreamReader(input))
{
string line;
while ((line = sr.ReadLine()) != null)
{
if (line.Contains("<fragSpectrumScan"))
{
var scanNumber = line.StringAfter("scanNumber=\"").StringBefore("\"");
IIdentifiedSpectrum spec;
if (resultMap.TryGetValue(scanNumber, out spec))
{
line = sr.ReadLine();
spec.Tag = line.StringAfter("id=\"").StringBefore("\"");
}
else
{
Console.WriteLine("Cannot find {0} in database", scanNumber);
}
}
}
}
result.ForEach(m =>
{
if (string.IsNullOrEmpty(m.Tag))
{
Console.WriteLine("Cannot find query {0} at input file, score {1}", m.Query.FileScan.LongFileName, m.Score);
}
});
var inputMap = result.Where(m => !string.IsNullOrEmpty(m.Tag)).ToDictionary(m => m.Tag);
var output = GetOutputFile(fileName);
XElement root = XElement.Load(output);
var psms = root.FindElement("psms").FindElements("psm");
foreach (var psm in psms)
{
var id = psm.FindAttribute("psm_id").Value;
IIdentifiedSpectrum spec;
if (inputMap.TryGetValue(id, out spec))
{
spec.SpScore = double.Parse(psm.FindElement("svm_score").Value);
}
}
return(result);
}