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));
}