Coon.Compass.ProteinHoarder.ProteinHoarder.Herd C# (CSharp) Method

        public void Herd()
        {
            // Keep track of how long the hoarding takes
            _startTime = DateTime.Now;

            try
            {
                // 1) Get the unique peptides from all csv files
                Peptides = GetAllUniquePeptides(CsvFiles);

                // 2) Digest Proteins in the Fasta and compare with the Unique Peptides
                List<Protein> proteins = GetMappedProteinsFromFasta(FastaFile, Peptides, Proteases.ToList(), SemiDigestion);

                // 3) Group the proteins together into protein groups
                _proteinGroups = GroupProteins(proteins);

                // 4) Groups the proteins to experiments
                Dictionary<string, ExperimentGroup> expgroups = GroupExperiments(CsvFiles, UseQuant);

                // 5) Write out the peptide level data
                WritePeptides(expgroups, OutputDirectory);

                // 6) Write out the peptide level data
                WriteGroups(expgroups, OutputDirectory);

                // 7) Write out the summary document
                if (DuplexQuantitation)
                    WriteSummary(expgroups, OutputDirectory);

                // 8) Write the proteins per minute file
                if (ProteinsPerMinute)
                    WriteProteinsPerMinute(Peptides.Values.ToList(), proteins, OutputDirectory);

                // 9) Write the sequence maps out
                if (SequenceCoverageMap)
                {
                    WriteSequenceMaps(_proteinGroups, OutputDirectory);
                    ExtraInfo(_proteinGroups, OutputDirectory);
                }

            }
            catch (Exception e)
            {
                Log("[ERROR]\t{0}", e.Message);
            }
            finally
            {
                CleanUp();
            }
        }