コード例 #1
0
        public void InitializeByResult(IIdentifiedResult identifiedResult)
        {
            string oldProteinHeader = ProteinFormat == null?GetDefaultProteinHeader() : ProteinFormat.GetHeader();

            InitializeProteinFormat(identifiedResult, oldProteinHeader);

            string oldPeptideHeader = PeptideFormat == null?GetDefaultPeptideHeader() : PeptideFormat.GetHeader();

            InitializePeptideFormat(identifiedResult, oldPeptideHeader);
        }
        public override void WriteToFile(string fileName, IIdentifiedResult identifiedResult)
        {
            CheckFormat(identifiedResult);

            List <IIdentifiedSpectrum> allSpectra = identifiedResult.GetSpectra();

            for (int i = 0; i < allSpectra.Count; i++)
            {
                allSpectra[i].Id = i.ToString();
            }

            string linkFilename = GetLinkFileName(fileName);

            HashSet <IIdentifiedSpectrum> spectra = new HashSet <IIdentifiedSpectrum>();

            using (var linkWriter = new StreamWriter(linkFilename))
            {
                linkWriter.WriteLine("PeptideId\tGroupId");
                using (var sw = new StreamWriter(fileName))
                {
                    sw.WriteLine(ProteinFormat.GetHeader());

                    var groups = GetValidGroups(identifiedResult);

                    foreach (IIdentifiedProteinGroup mpg in groups)
                    {
                        GroupWriter.WriteToStream(sw, mpg);

                        var validSpectra = GetValidSpectra(mpg.GetSortedPeptides());

                        foreach (var spectrum in validSpectra)
                        {
                            linkWriter.WriteLine(spectrum.Id + "\t" + mpg.Index);
                        }

                        spectra.UnionWith(validSpectra);
                    }
                }
            }

            var finalSpectra = from s in spectra
                               orderby s.Id
                               select s;

            string peptideFile = GetPeptideFileName(fileName);

            if (!PeptideFormat.GetHeader().Contains("Id\t"))
            {
                PeptideFormat = new PeptideLineFormat("Id\t" + PeptideFormat.GetHeader());
            }

            using (var sw = new StreamWriter(peptideFile))
            {
                WritePeptideHeader(sw);

                foreach (IIdentifiedSpectrum mph in finalSpectra)
                {
                    WritePeptide(sw, mph);
                }
            }

            if (identifiedResult.Count > 0 && identifiedResult[0][0].Sequence != null)
            {
                string fastaFilename = fileName + ".fasta";
                WriteFastaFile(fastaFilename, identifiedResult);
            }
        }