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 override bool PrepareOptions()
{
foreach (var inputfile in this.InputFiles)
{
if (!File.Exists(inputfile))
{
ParsingErrors.Add(string.Format("Input file not exists {0}.", inputfile));
}
}
var engine = GetSearchEngineType();
if (engine == SearchEngineType.Unknown)
{
if (!this.EngineType.ToLower().Equals("help"))
{
ParsingErrors.Add(string.Format("Unknown search engine type {0}", this.EngineType));
}
ParsingErrors.Add(string.Format(" Those engines are valid: {0}", (GetValidEngines()).Merge(", ")));
}
if (!string.IsNullOrEmpty(TitleType) && TitleParserUtils.FindByName(TitleType) == null)
{
if (!this.TitleType.ToLower().Equals("help"))
{
ParsingErrors.Add(string.Format("Unknown title type {0}.", this.TitleType));
}
ParsingErrors.Add(" Those titles are valid:");
(from t in TitleParserUtils.GetTitleParsers()
select t.FormatName).ToList().ForEach(m => ParsingErrors.Add(" " + m));
}
if (Rank2 && engine != SearchEngineType.Unknown)
{
foreach (var inputfile in InputFiles)
{
try
{
var parser = engine.GetFactory().GetParser(inputfile, this.Rank2);
}
catch (Exception ex)
{
ParsingErrors.Add(ex.Message);
break;
}
}
}
return(ParsingErrors.Count == 0);
}
public PeptideSpectrumMatchDistillerUI()
{
InitializeComponent();
this.searchResultFiles.FileArgument = new OpenFileArgument("Search Result", "*");
var parsers = TitleParserUtils.GetTitleParsers().ToArray();
this.titleParsers = new RcpaComboBox <ITitleParser>(this.cbTitleFormat, "TitleFormat", parsers, parsers.Length - 1, true);
AddComponent(this.titleParsers);
var engineNames = PeptideSpectrumMatchDistillerOptions.GetValidEngines();
this.engines = new RcpaComboBox <string>(this.cbEngines, "Engine", engineNames, 0);
AddComponent(this.engines);
this.Text = Constants.GetSQHTitle(Title, Version);
}