Esempio n. 1
0
        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);
        }
Esempio n. 2
0
        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();
        }