+ overall_target_length_sum += length
+ if length > overall_target_length_max
+ overall_target_length_max = length
+ end
+ if length < overall_target_length_min
+ overall_target_length_min = length
+ end
+
+ if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
+ ( ( length_threshold <= 0 ) || ( length >= length_threshold.to_f ) ) )
+ hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value )
+ passing_target_length_sum += length
+ if length > passing_target_length_max
+ passing_target_length_max = length
+ end
+ if length < passing_target_length_min
+ passing_target_length_min = length
+ end
+ if ( number > max_domain_copy_number_per_protein )
+ max_domain_copy_number_sequence = sequence
+ max_domain_copy_number_per_protein = number
+ end
+ else # no pass
+ log << domain_fail_counter.to_s + ": " + sequence.to_s + " fails threshold(s)"
+ if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
+ log << " iE=" + i_e_value.to_s
+ end
+ if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
+ le = env_to - env_from + 1
+ log << " l=" + le.to_s
+ end
+ log << ld
+ domain_fail_counter += 1
+ end
+
+ if number > out_of
+ error_msg = "number > out_of (this should not have happened)"
+ raise StandardError, error_msg
+ end
+
+ if number == out_of
+ if !hmmscan_datas.empty?
+ process_hmmscan_datas( hmmscan_datas,
+ in_msa,
+ add_position,
+ add_domain_number,
+ add_species,
+ out_msa,
+ out_msa_singles,
+ out_msa_pairs,
+ out_msa_isolated,
+ min_linker,
+ out_msa_single_domains_protein_seqs,
+ out_msa_close_pairs_protein_seqs,
+ out_msa_close_pairs_only_protein_seqs,
+ out_msa_isolated_protein_seqs,
+ out_msa_isolated_only_protein_seqs,
+ out_msa_isolated_and_close_pair_protein_seqs )
+ domain_pass_counter += hmmscan_datas.length
+ if passed_seqs.find_by_name_start( sequence, true ).length < 1
+ add_sequence( sequence, in_msa, passed_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg