+ if saw_isolated
+ if out_msa_isolated_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_isolated_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ end
+ if saw_close_pair
+ if out_msa_close_pairs_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_close_pairs_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ end
+ if saw_close_pair && saw_isolated
+ if out_msa_isolated_and_close_pair_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_isolated_and_close_pair_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ elsif saw_close_pair
+ if out_msa_close_pairs_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_close_pairs_only_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ elsif saw_isolated
+ if out_msa_isolated_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_isolated_only_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ end