private static Database databaseSetUp(String fasta_file_name) { FastaFile f = Loader.parseFasta(fasta_file_name); DigestedFastaFile df = PerformDigestion.performDigest(f, GlobalVar.NUM_MISSED_CLEAVAGES); int numberOfProteinsInFasta = f.getAccessionToFullSequence().Count; int numberOfPeptidesInDigestedFasta = df.getDigestedPeptideArray().Count; log.Info("Fasta file: " + fasta_file_name); log.Info("Num missed cleavages: " + GlobalVar.NUM_MISSED_CLEAVAGES); log.Info("Number of proteins: " + numberOfProteinsInFasta); log.Info("Number of peptides: " + numberOfPeptidesInDigestedFasta); log.Debug("Constructing graph..."); Database g; if (GlobalVar.isSimulationForFeatureExtraction == true) { g = new Database(f, df, true, false); } else { g = new Database(f, df, true, true); } log.Debug(g); return(g); }
public Database(FastaFile fastaFile, DigestedFastaFile digestedFastaFile, bool _includeCarbamidoModification, bool _includeRetentionTime, double _retentionTimeWindow) { includeCarbamidoModification = _includeCarbamidoModification; includeRetentionTime = _includeRetentionTime; retentionTimeWindow = _retentionTimeWindow; log.Debug("Constructing graph..."); SequenceToPeptide = new Dictionary <String, Peptide>(); peptides = new List <Peptide>(); AccesstionToProtein = fastaFile.getAccessionToFullSequence(); addPeptides(digestedFastaFile.getDigestedPeptideArray()); log.Debug("Done constructing graph."); }