+
+ def process_hmmscan_datas( hmmscan_datas,
+ in_msa,
+ add_position,
+ add_domain_number,
+ trim_name ,
+ add_species,
+ out_msa )
+
+ actual_out_of = hmmscan_datas.size
+
+ domain_pass_counter = 0;
+
+ hmmscan_datas.each_with_index do |hmmscan_data, index|
+ if hmmscan_data.number < ( index + 1 )
+ error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)"
+ raise StandardError, error_msg
+ end
+
+ extract_domain( hmmscan_data.seq_name,
+ index + 1,
+ actual_out_of,
+ hmmscan_data.env_from,
+ hmmscan_data.env_to,
+ in_msa,
+ out_msa,
+ add_position,
+ add_domain_number,
+ trim_name ,
+ add_species )
+ domain_pass_counter += 1
+
+ # if passed_seqs.find_by_name_start( hmmscan_data.seq_name, true ).length < 1
+ # add_sequence( hmmscan_data.seq_name, in_msa, passed_seqs )
+ # proteins_with_passing_domains += 1
+ # end
+
+=begin
+ if min_linker
+ if out_of == 1
+ extract_domain( sequence,
+ number,
+ out_of,
+ env_from,
+ env_to,
+ in_msa,
+ out_msa_singlets,
+ false,
+ true,
+ false,
+ false,
+ trim_name,
+ add_species )
+ singlets_counter += 1
+ elsif prev_sequence
+ if sequence != prev_sequence
+ prev_is_pair = false
+ else
+ if ( env_from - prev_env_to ) <= min_linker
+ extract_domain( sequence,
+ prev_number.to_s + "+" + number.to_s,
+ out_of,
+ prev_env_from,
+ env_to,
+ in_msa,
+ out_msa_pairs,
+ false,
+ true,
+ false,
+ false,
+ trim_name,
+ add_species )
+ prev_is_pair = true
+ close_pairs_counter += 2
+ else
+ if !prev_is_pair
+ extract_domain( sequence,
+ prev_number,
+ out_of,
+ prev_env_from,
+ prev_env_to,
+ in_msa,
+ out_msa_distant_partners,
+ false,
+ true,
+ false,
+ false,
+ trim_name,
+ add_species )
+ distant_pairs_counter += 1
+ end
+ if number == out_of
+ extract_domain( sequence,
+ number,
+ out_of,
+ env_from,
+ env_to,
+ in_msa,
+ out_msa_distant_partners,
+ false,
+ true,
+ false,
+ false,
+ trim_name,
+ add_species )
+ distant_pairs_counter += 1
+ end
+ prev_is_pair = false
+ end
+ end # sequence != prev_sequence else
+ end
+ prev_sequence = sequence
+ prev_number = number
+ prev_env_from = env_from
+ prev_env_to = env_to
+ #prev_i_e_value = i_e_value
+ end # if min_linker
+=end
+
+ end # each
+ domain_pass_counter
+ end # def process_hmmscan_data
+
+