Exemplo n.º 1
0
        public void Run()
        {
            ITableNGlycan glycan = new ComplexNGlycan(new int[24]);

            Console.WriteLine(glycan.GetName());
            //glycan.SetNGlycanTable(0, 1);
            ITableNGlycanProxy glycanProxy = new GeneralTableNGlycanMassProxy(glycan);

            ITableNGlycanProxyGenerator generator = new GeneralTableNGlycanMassProxyGenerator();
            IGlycanCreator glycanCreator          = new GeneralTableNGlycanCreator(generator, glycanProxy);
            List <IGlycan> glycans = glycanCreator.Create();
            //foreach(IGlycan g in glycans)
            //{
            //    Console.WriteLine(string.Join(" ", g.GetStructure()));
            //}

            IGlycoPeptideProxyGenerator glycoPeptideProxyGenerator = new GeneralTableNGlycoPeptideMassProxyGenerator();
            IGlycoPeptideCreator        glycoPeptideCreator        = new GeneralNGlycoPeptideSingleSiteCreator(glycoPeptideProxyGenerator);

            IPeptide peptide = new GeneralPeptide("test3", "ILGGHLDAKGSFPWQAKMVSHHNLTTGATLINEQWLLTTAK");

            foreach (IGlycan g in glycans)
            {
                List <IGlycoPeptide> glycoPeptides = glycoPeptideCreator.Create(g, peptide);
                //Console.WriteLine(glycoPeptides.Count);

                foreach (IGlycoPeptide glyco in glycoPeptides)
                {
                    //Console.WriteLine(glyco.GetGlycan().GetName());
                    //Console.WriteLine(glyco.GetPosition());
                }
            }

            Console.Read();
        }
Exemplo n.º 2
0
 protected override void Load(ContainerBuilder builder)
 {
     builder.Register(c =>
     {
         ITableNGlycanProxyGenerator tableNGlycanProxyGenerator =
             new GeneralTableNGlycanMassProxyGenerator(HexNAcBound, HexBound, FucBound, NeuAcBound, NeuGcBound);
         int[] structTable       = new int[24];
         structTable[0]          = 1;
         ITableNGlycanProxy root = new GeneralTableNGlycanMassProxy(new ComplexNGlycan(structTable));
         return(new GeneralTableNGlycanCreator(tableNGlycanProxyGenerator, root));
     }).As <IGlycanCreator>();
 }
Exemplo n.º 3
0
        public void Run()
        {
            var watch = new System.Diagnostics.Stopwatch();

            watch.Start();
            // protein
            IProteinDataBuilder proteinBuilder = new GeneralFastaDataBuilder();
            IProteinCreator     proteinCreator = new GeneralProteinCreator(proteinBuilder);
            List <IProtein>     proteins       = proteinCreator.Create(@"C:\Users\iruiz\Desktop\app\HP.fasta");
            // peptides
            List <IPeptideSequencesGenerator>   generatorList = new List <IPeptideSequencesGenerator>();
            IPeptideSequencesGeneratorParameter parameter     = new GeneralPeptideGeneratorParameter();

            parameter.SetProtease(Proteases.GluC);
            NGlycosylatedPeptideSequencesGenerator generatorGluc = new NGlycosylatedPeptideSequencesGenerator(parameter);

            generatorList.Add(generatorGluc);
            parameter = new GeneralPeptideGeneratorParameter();
            parameter.SetProtease(Proteases.Trypsin);
            NGlycosylatedPeptideSequencesGenerator generatorTrypsin = new NGlycosylatedPeptideSequencesGenerator(parameter);

            generatorList.Add(generatorTrypsin);
            IPeptideSequencesGenerator peptideSequencesGenerator = new DoubleDigestionPeptideSequencesGeneratorProxy(generatorList);
            IPeptideCreator            peptideCreator            = new GeneralPeptideCreator(peptideSequencesGenerator);
            List <IPeptide>            peptides = new List <IPeptide>();
            HashSet <string>           seen     = new HashSet <string>();

            foreach (IProtein protein in proteins)
            {
                foreach (IPeptide peptide in peptideCreator.Create(protein))
                {
                    if (!seen.Contains(peptide.GetSequence()))
                    {
                        seen.Add(peptide.GetSequence());
                        peptides.Add(peptide);
                    }
                }
            }
            // glycans
            ITableNGlycanProxyGenerator tableNGlycanProxyGenerator = new GeneralTableNGlycanMassProxyGenerator(12, 12, 5, 4, 0);

            int[] structTable = new int[24];
            structTable[0] = 1;
            ITableNGlycanProxy root          = new GeneralTableNGlycanMassProxy(new ComplexNGlycan(structTable));
            IGlycanCreator     glycanCreator = new GeneralTableNGlycanCreator(tableNGlycanProxyGenerator, root);
            List <IGlycan>     glycans       = glycanCreator.Create();



            // precursor
            List <IPoint> points = new List <IPoint>();

            foreach (IGlycan glycan in glycans)
            {
                points.Add(new GlycanPoint(glycan));
            }
            IComparer <IPoint> comparer = new ToleranceComparer(0.01);
            ISearch            matcher  = new BucketSearch(comparer, 0.01);

            matcher.setData(points);
            IGlycoPeptideProxyGenerator glycoPeptideProxyGenerator = new GeneralTableNGlycoPeptideMassProxyGenerator();
            IGlycoPeptideCreator        glycoPeptideCreator        = new GeneralNGlycoPeptideSingleSiteCreator(glycoPeptideProxyGenerator);
            IPrecursorMatcher           precursorMatcher           = new GeneralPrecursorMatcher(matcher, glycoPeptideCreator);

            precursorMatcher.SetGlycans(glycans);
            precursorMatcher.SetPeptides(peptides);

            // spectrum
            ISpectrumReader spectrumReader = new ThermoRawSpectrumReader();

            spectrumReader.Init(@"C:\Users\iruiz\Desktop\app\ZC_20171218_H95_R1.raw");
            ISpectrumFactory spectrumFactory = new GeneralSpectrumFactory(spectrumReader);

            ISpectrum            spectrum      = spectrumFactory.GetSpectrum(7039);
            List <IGlycoPeptide> glycoPeptides = precursorMatcher.Match(spectrum);

            watch.Stop();

            Console.WriteLine(glycoPeptides.Count);
            foreach (IGlycoPeptide glycoPeptide in glycoPeptides)
            {
                Console.WriteLine(glycoPeptide.GetType());
            }

            Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
            Console.Read();
        }