public TIQ3XIC(ISpectrumReader spectrumReader, double tol = 0.1, ToleranceBy by = ToleranceBy.Dalton) { this.spectrumReader = spectrumReader; this.tol = tol; this.by = by; }
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); }
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(); } } }
public GeneralSpectrumFactory(ISpectrumReader reader) { this.reader = reader; }
public void Run(string path, Counter counter, ISpectrumReader reader) { reader.Init(path); 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); } } counter.Add(end - start); }); List <List <GUI> > points = pointMaps.OrderBy(p => p.Key).Select(p => p.Value).ToList(); IGUISequencer sequencer = new DynamicProgrammingSequencer(); List <GUI> guiPoints = sequencer.Choose(points); 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> looped = guiSelected.Values.OrderBy(g => g.Scan).ToList(); string output = Path.Combine(Path.GetDirectoryName(path), Path.GetFileNameWithoutExtension(path) + ".csv"); using (FileStream ostrm = new FileStream(output, FileMode.OpenOrCreate, FileAccess.Write)) { using (StreamWriter writer = new StreamWriter(ostrm)) { writer.WriteLine("scan,time,gui,peak,intensity"); foreach (GUI gui in looped) { int scan = gui.Scan; double time = reader.GetRetentionTime(scan); Retention.Add(time); Guis.Add(gui.Unit); writer.WriteLine(scan.ToString() + "," + time.ToString() + "," + gui.Unit.ToString() + "," + gui.Peak.GetMZ().ToString() + "," + gui.Peak.GetIntensity().ToString()); } writer.Flush(); } } Fitter.Fit(Retention, Guis); initialized = true; }
public ThermoRawSearchRunSpectrum() { spectrumReader = new ThermoRawSpectrumReader(); }