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 static Database loadExclusionDatabase(String fasta_file_name, int missedCleavages) { FastaFile fasta; DigestedFastaFile digestedFasta; // Load fasta file fasta = Loader.parseFasta(fasta_file_name); // Digest the fasta file using peptide chainsaw digestedFasta = PerformDigestion.performDigest(fasta, missedCleavages); return(loadExclusionDatabase(fasta, digestedFasta)); }