+ if query == nil
+ query = own.query
+ qlen = own.qlen
+ else
+ raise StandardError, "failed sanity check" if query != own.query || qlen != own.qlen
+ raise StandardError, "failed sanity check: qlen != own.qlen" if qlen != own.qlen
+ end
+ end
+
+ species = nil
+ ll = nil
+ if msa != nil
+ seq = get_sequence( query, msa )
+ species = get_species( seq )
+ raise StandardError, "could not get species" if species == nil || species.empty?
+ if x_models != nil && x_models.length > 0
+ ll = extract_linker( hmmscan_results_per_protein_filtered, x_models, seq, extraction_output_file )
+ end