Exemplo n.º 1
0
        private static void MapSequencesToSpectra(List <MSFeatureLight> features, string path)
        {
            var reader = new MsgfReader {
                Delimiter = '\t'
            };
            var peptides = reader.ReadFile(path);

            var scanMap = new Dictionary <int, Peptide>();

            foreach (var p in peptides)
            {
                if (!scanMap.ContainsKey(p.Scan))
                {
                    scanMap.Add(p.Scan, p);
                }
            }

            foreach (var feature in features)
            {
                foreach (var spectrum in feature.MSnSpectra)
                {
                    var hasScan = scanMap.ContainsKey(spectrum.Scan);
                    if (hasScan)
                    {
                        spectrum.Peptides.Add(scanMap[spectrum.Scan]);
                    }
                }
            }
        }
Exemplo n.º 2
0
        public static ISequenceFileReader CreateReader(SequenceFileType type)
        {
            ISequenceFileReader reader = null;

            switch (type)
            {
            case SequenceFileType.SEQUESTFirstHit:
                break;

            case SequenceFileType.MSGF:
                reader = new MsgfReader();
                break;

            case SequenceFileType.SkylineTransitionFile:
                reader = new SkylineTransitionFileReader();
                break;
            }

            return(reader);
        }
Exemplo n.º 3
0
        private static void MapSequencesToSpectra(List<MSFeatureLight> features, string path)
        {
            var reader = new MsgfReader { Delimiter = '\t' };
            var peptides = reader.ReadFile(path);

            var scanMap = new Dictionary<int, Peptide>();
            foreach (var p in peptides)
            {
                if (!scanMap.ContainsKey(p.Scan))
                {
                    scanMap.Add(p.Scan, p);
                }
            }

            foreach (var feature in features)
            {
                foreach (var spectrum in feature.MSnSpectra)
                {
                    var hasScan = scanMap.ContainsKey(spectrum.Scan);
                    if (hasScan)
                    {
                        spectrum.Peptides.Add(scanMap[spectrum.Scan]);
                    }
                }
            }
        }