public virtual void Read(string peptideFileLocation, string spectrumFileLocation) { List <IPeptide> peptides = initializer.GetPeptides(peptideFileLocation); spectrumRunner = initializer.GetSpectrumReader(spectrumFileLocation); int lastScan = spectrumRunner.GetLastScan(); resultTable = new IGlycoPeptideScoreResultProduct[lastScan + 1]; glycanGenerator = new BruteForceNGlycanCreator(initializer.GetGlycanCreatorParameter()); glycans = glycanGenerator.Generate(); // data process specProcessor = initializer.GetSpectrumProcessing(); monoRunner = new BinSearchMonoMassSpectrumRun(); // precursor double preTol = initializer.GetParameter().GetMS1Tolereance(); precursorMatcher = new Y1PeptidesFilterPrecursorMatcher( new GlycoPeptidePrecursorMatcher(peptides, glycans, preTol), peptides); // search spectrum double tol = initializer.GetParameter().GetMSMSTolereance(); searchWorker = new DPSearchSpectrumCID(tol); //result analyzer = new GeneralGlycoPeptideScoreResultAnalyzer(); }
public virtual void Read(string peptideFileLocation, string spectrumFileLocation) { List <IPeptide> peptides = initializer.GetPeptides(peptideFileLocation); spectrumRunner = initializer.GetSpectrumReader(spectrumFileLocation); int lastScan = spectrumRunner.GetLastScan(); resultTable = new IGlycoPeptideScoreResultProduct[lastScan + 1]; resultFDRTable = new IGlycoPeptideScoreResultProduct[lastScan + 1]; glycanGenerator = new AccumulatedMSBruteForceNGlycanCreator(initializer.GetGlycanCreatorParameter()); glycans = glycanGenerator.Generate(); // data process specProcessor = initializer.GetSpectrumProcessing(); monoRunner = new BinSearchMonoMassSpectrumRun(); // precursor double preTol = initializer.GetParameter().GetMS1Tolereance(); precursorMatcher = new Y1PeptidesFilterPrecursorMatcher( new AccumulatedMSNGlycoPeptidePrecursorMatcher(peptides, glycans, preTol), peptides); //precursorMatcher = new AccumulatedMSNGlycoPeptidePrecursorMatcher(peptides, glycans, preTol); // search spectrum double tol = initializer.GetParameter().GetMSMSTolereance(); searchWorker = new BinSearchSpectrumEThcD(tol); (searchWorker as BinSearchSpectrumEThcD).SetAlphaValue(initializer.GetParameter().GetAlphaFactor()); (searchWorker as BinSearchSpectrumEThcD).SetBetaValue(initializer.GetParameter().GetBetaFactor()); //result fdr = initializer.GetParameter().GetFDRlevel(); discover = new GeneralGlycoPeptideScoreResultFDR(fdr); }
public ISpectrumSearchRun GetSpectrumReader(string file) { ISpectrumSearchRun specRunner = null; string pext = Path.GetExtension(file); switch (pext) { case ".raw": specRunner = new ThermoRawSearchRunSpectrum(); specRunner.Run(file); return(specRunner); } return(specRunner); }