public void Run(string path, Counter counter, ISpectrumReader spectrumReader, NormalizerEngine normalizer) { NGlycanTheoryPeaksBuilder builder = new NGlycanTheoryPeaksBuilder(); builder.SetBuildType(true, false, false); List <IGlycanPeak> glycans = builder.Build(); spectrumReader.Init(path); IResultSelect resultSelect = new ResultMaxSelect(SearchingParameters.Access.Threshold, SearchingParameters.Access.PeakCutoff); List <IResult> final = new List <IResult>(); int start = spectrumReader.GetFirstScan(); int end = spectrumReader.GetLastScan(); Parallel.For(start, end, (i) => { if (spectrumReader.GetMSnOrder(i) < 2) { IResultFactory factory = new NGlycanResultFactory(); EnvelopeProcess envelopeProcess = new EnvelopeProcess( SearchingParameters.Access.Tolerance, SearchingParameters.Access.ToleranceBy); MonoisotopicSearcher monoisotopicSearcher = new MonoisotopicSearcher(factory); IProcess spectrumProcess = new LocalNeighborPicking(); ISpectrumSearch spectrumSearch = new NGlycanSpectrumSearch(glycans, spectrumProcess, envelopeProcess, monoisotopicSearcher, SearchingParameters.Access.MaxCharage, SearchingParameters.Access.Cutoff); ISpectrum spectrum = spectrumReader.GetSpectrum(i); List <IResult> results = spectrumSearch.Search(spectrum); lock (resultLock) { resultSelect.Add(results); final.AddRange(results); } } counter.Add(end - start); }); //original string outputPath = Path.Combine(Path.GetDirectoryName(path), Path.GetFileNameWithoutExtension(path) + "_one_quant.csv"); List <string> outputString = new List <string>(); foreach (IResult present in final.OrderBy(r => r.GetRetention())) { int scan = present.GetScan(); double rt = present.GetRetention(); double index = Math.Round(normalizer.Normalize(rt), 2); TIQ3XIC xicer = new TIQ3XIC(spectrumReader); double area = xicer.OneArea(present); List <string> output; if (!normalizer.Initialized()) { output = new List <string>() { scan.ToString(), rt.ToString(), present.Glycan().GetGlycan().Name(), present.GetMZ().ToString(), area.ToString(), }; } else { output = new List <string>() { scan.ToString(), rt.ToString(), index > 0? index.ToString():"0", present.Glycan().GetGlycan().Name(), present.GetMZ().ToString(), area.ToString(), }; } outputString.Add(string.Join(",", output)); } using (FileStream ostrm = new FileStream(outputPath, FileMode.OpenOrCreate, FileAccess.Write)) { using (StreamWriter writer = new StreamWriter(ostrm)) { if (!normalizer.Initialized()) { writer.WriteLine("scan,time,glycan,mz,area"); } else { writer.WriteLine("scan,time,GUI,glycan,mz,area"); } foreach (string output in outputString) { writer.WriteLine(output); } writer.Flush(); } } // merged string outputPathMerge = Path.Combine(Path.GetDirectoryName(path), Path.GetFileNameWithoutExtension(path) + "_quant.csv"); List <string> outputStringMerge = new List <string>(); Dictionary <string, List <SelectResult> > resultContainer = resultSelect.Produce(); foreach (string name in resultContainer.Keys) { List <SelectResult> selectResults = resultContainer[name]; foreach (SelectResult select in selectResults) { IResult present = select.Present; int scan = present.GetScan(); double rt = present.GetRetention(); double index = Math.Round(normalizer.Normalize(rt), 2); IXIC xicer = new TIQ3XIC(spectrumReader); double area = xicer.Area(select); List <string> output; if (!normalizer.Initialized()) { output = new List <string>() { scan.ToString(), rt.ToString(), name, present.GetMZ().ToString(), area.ToString(), }; } else { output = new List <string>() { scan.ToString(), rt.ToString(), index.ToString(), name, present.GetMZ().ToString(), area.ToString(), }; } outputStringMerge.Add(string.Join(",", output)); } } using (FileStream ostrm = new FileStream(outputPathMerge, FileMode.OpenOrCreate, FileAccess.Write)) { using (StreamWriter writer = new StreamWriter(ostrm)) { if (!normalizer.Initialized()) { writer.WriteLine("scan,time,glycan,mz,area"); } else { writer.WriteLine("scan,time,GUI,glycan,mz,area"); } foreach (string output in outputStringMerge) { writer.WriteLine(output); } writer.Flush(); } } }