private Task Process()
{
Counter readerCounter = new Counter();
Counter searchCounter = new Counter();
readerCounter.progressChange += ReadProgressChanged;
searchCounter.progressChange += SearchProgressChanged;
// build pepeptides
Peptide.To.SetCysteine(ConfigureParameters.Access.Cysteine);
IProteinReader proteinReader = new FastaReader();
List <IProtein> proteins = proteinReader.Read(SearchingParameters.Access.FastaFile);
List <IProtein> decoyProteins = new List <IProtein>();
foreach (IProtein protein in proteins)
{
IProtein p = new BaseProtein();
p.SetSequence(MultiThreadingSearchHelper.Reverse(protein.Sequence()));
decoyProteins.Add(p);
}
List <string> peptides =
MultiThreadingSearchHelper.GeneratePeptides(proteins);
List <string> decoyPeptides =
MultiThreadingSearchHelper.GeneratePeptides(decoyProteins);
// build glycans
GlycanBuilder glycanBuilder = new GlycanBuilder(
SearchingParameters.Access.HexNAc,
SearchingParameters.Access.Hex,
SearchingParameters.Access.Fuc,
SearchingParameters.Access.NeuAc,
SearchingParameters.Access.NeuGc,
SearchingParameters.Access.ComplexInclude,
SearchingParameters.Access.HybridInclude,
SearchingParameters.Access.MannoseInclude);
glycanBuilder.Build();
int index = 1;
foreach (string file in SearchingParameters.Access.MSMSFiles)
{
ReadingCounter = 0;
ProgressCounter = 0;
UpdateProgress(100);
Readingprogress(100);
UpdateSignal($"Searching...({index++}/{SearchingParameters.Access.MSMSFiles.Count})");
MultiThreadingSearch search =
new MultiThreadingSearch(file, readerCounter, searchCounter,
peptides, decoyPeptides, glycanBuilder);
search.Run();
UpdateSignal("Analyzing...");
Analyze(file, search.Target(), search.Decoy(), glycanBuilder);
}
UpdateSignal("Done");
return(Task.CompletedTask);
}
private void Analyze(string msPath, List <SearchResult> targets, List <SearchResult> decoys,
GlycanBuilder glycanBuilder)
{
FDRFilter filter = new FDRFilter(SearchingParameters.Access.FDRValue);
filter.set_data(targets, decoys);
filter.Init();
List <SearchResult> results = filter.Filter();
string path = System.IO.Path.Combine(System.IO.Path.GetDirectoryName(msPath),
System.IO.Path.GetFileNameWithoutExtension(msPath) + ".csv");
MultiThreadingSearchHelper.ReportResults(path, results, glycanBuilder.GlycanMaps());
}
