static List <GUI> Init(ref ICurveFitting Fitter, ISpectrumReader reader) { double ppm = 5; object resultLock = new object(); List <double> Retention = new List <double>(); List <double> Guis = new List <double>(); IGUIFinder finder = new BinarySearchFinder(ppm); IProcess picking = new LocalNeighborPicking(); Dictionary <int, List <GUI> > pointMaps = new Dictionary <int, List <GUI> >(); int start = reader.GetFirstScan(); int end = reader.GetLastScan(); Parallel.For(start, end, (i) => { if (reader.GetMSnOrder(i) < 2) { ISpectrum spectrum = picking.Process(reader.GetSpectrum(i)); lock (resultLock) { pointMaps[i] = finder.FindGlucoseUnits(spectrum); } } }); List <List <GUI> > points = pointMaps.OrderBy(p => p.Key).Select(p => p.Value).ToList(); IGUISequencer sequencer = new DynamicProgrammingSequencer(); List <GUI> GuiPoints = sequencer.Choose(points); Fitter = new PolynomialFitting(); Dictionary <int, GUI> guiSelected = new Dictionary <int, GUI>(); foreach (GUI gui in GuiPoints) { if (guiSelected.ContainsKey(gui.Unit)) { if (guiSelected[gui.Unit].Peak.GetIntensity() < gui.Peak.GetIntensity()) { guiSelected[gui.Unit] = gui; } } else { guiSelected[gui.Unit] = gui; } } Retention.Clear(); Guis.Clear(); List <GUI> guiChoice = guiSelected.Values.OrderBy(g => g.Scan).ToList(); foreach (GUI gui in guiChoice) { int scan = gui.Scan; double time = reader.GetRetentionTime(scan); Retention.Add(time); Guis.Add(gui.Unit); } Fitter.Fit(Retention, Guis); return(GuiPoints); }
static void Main(string[] args) { string dir = @"C:\Users\iruiz\Downloads\GUI\compare\data"; string[] files = Directory.GetFiles(dir); List <double> ions = new List <double>(); ions.Add(Calculator.proton); Calculator.To.SetChargeIons(ions); foreach (string path in files) { Stopwatch stopWatch = new Stopwatch(); stopWatch.Start(); NGlycanTheoryPeaksBuilder builder = new NGlycanTheoryPeaksBuilder(); builder.SetBuildType(true, false, false); List <IGlycanPeak> glycans = builder.Build(); IResultFactory factory = new NGlycanResultFactory(); EnvelopeProcess envelopeProcess = new EnvelopeProcess(10, ToleranceBy.PPM); MonoisotopicSearcher monoisotopicSearcher = new MonoisotopicSearcher(factory); IProcess spectrumProcess = new LocalNeighborPicking(); ISpectrumSearch spectrumSearch = new NGlycanSpectrumSearch(glycans, spectrumProcess, envelopeProcess, monoisotopicSearcher); ISpectrumReader spectrumReader = new ThermoRawSpectrumReader(); spectrumReader.Init(path); ICurveFitting Fitter = new PolynomialFitting(); IResultSelect resultSelect = new ResultMaxSelect(); List <GUI> GuiPoints = Init(ref Fitter, spectrumReader); List <IResult> final = new List <IResult>(); for (int scan = spectrumReader.GetFirstScan(); scan <= spectrumReader.GetLastScan(); scan++) { if (spectrumReader.GetMSnOrder(scan) != 1) { continue; } ISpectrum spectrum = spectrumReader.GetSpectrum(scan); List <IResult> results = spectrumSearch.Search(spectrum); resultSelect.Add(results); final.AddRange(results); } // original List <string> outputString = new List <string>(); foreach (IResult present in final) { int scan = present.GetScan(); double rt = present.GetRetention(); double index = Math.Round(Normalize(Fitter, rt), 2); TIQ3XIC xicer = new TIQ3XIC(spectrumReader); double area = xicer.OneArea(present); List <string> 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)); } string outputPath = Path.Combine(Path.GetDirectoryName(path), Path.GetFileNameWithoutExtension(path) + "_one_quant.csv"); using (FileStream ostrm = new FileStream(outputPath, FileMode.OpenOrCreate, FileAccess.Write)) { using (StreamWriter writer = new StreamWriter(ostrm)) { writer.WriteLine("scan,time,GUI,glycan,mz,area"); foreach (string output in outputString) { writer.WriteLine(output); } writer.Flush(); } } // merged List <string> outputStringMerge = new List <string>(); Dictionary <string, List <SelectResult> > resultContainer = resultSelect.Produce(); foreach (string name in resultContainer.Keys) { //if (name == "5-6-1-2-0") // Console.WriteLine("here"); List <SelectResult> selectResults = resultContainer[name]; foreach (SelectResult select in selectResults) { if (select.Results.Count == 0) { continue; } IResult present = select.Present; int scan = present.GetScan(); double rt = present.GetRetention(); double index = Math.Round(Normalize(Fitter, rt), 2); IXIC xicer = new TIQ3XIC(spectrumReader); double area = xicer.Area(select); List <string> output = new List <string>() { scan.ToString(), rt.ToString(), index > 0? index.ToString():"0", name, present.GetMZ().ToString(), area.ToString() }; outputStringMerge.Add(string.Join(",", output)); } } string outputPathMerge = Path.Combine(Path.GetDirectoryName(path), Path.GetFileNameWithoutExtension(path) + "_quant.csv"); using (FileStream ostrm = new FileStream(outputPathMerge, FileMode.OpenOrCreate, FileAccess.Write)) { using (StreamWriter writer = new StreamWriter(ostrm)) { writer.WriteLine("scan,time,GUI,glycan,mz,area"); foreach (string output in outputStringMerge) { writer.WriteLine(output); } writer.Flush(); } } stopWatch.Stop(); TimeSpan ts = stopWatch.Elapsed; string elapsedTime = String.Format("{0:00}:{1:00}:{2:00}.{3:00}", ts.Hours, ts.Minutes, ts.Seconds, ts.Milliseconds / 10); Console.WriteLine("RunTime " + elapsedTime); } }