Embrace structured bindings

source/ct_cluster/cath/cluster/cath_cluster_mapper.cpp

@@ -24,6 +24,8 @@
 #include <fstream>
 #include <functional>
 
+#include <boost/range/adaptor/indexed.hpp>
+
 #include "cath/cluster/clustmap_options.hpp"
 #include "cath/cluster/detail/mapping_job.hpp"
 #include "cath/cluster/file/cluster_membership_file.hpp"
@@ -45,6 +47,7 @@ using namespace ::cath::clust::detail;
 using namespace ::cath::common;
 using namespace ::cath::opts;
 
+using ::boost::adaptors::indexed;
 using ::std::filesystem::path;
 using ::std::ifstream;
 using ::std::istream;
@@ -130,12 +133,10 @@ void cath::clust::perform_map_clusters(const clustmap_input_spec   &prm_input_sp
 		path_vec{ { prm_output_spec.get_output_to_file().value_or( out_list.get_flag() ) } }
 	);
 
-	// \TODO Come C++17 and structured bindings, use here
-	for (const size_t &job_idx : indices( jobs.size() ) ) {
-		const mapping_job &job                    = jobs[ job_idx ];
-		const auto        &job_batch_id           = job.get_batch_id();
-		const auto        &job_new_clustmemb_file = job.get_new_cluster_membership_file();
-		const auto        &job_old_clustmemb_file = job.get_old_cluster_membership_file();
+	for ( const auto &[ job_idx, job ] : jobs | indexed() ) {
+		const auto &job_batch_id           = job.get_batch_id();
+		const auto &job_new_clustmemb_file = job.get_new_cluster_membership_file();
+		const auto &job_old_clustmemb_file = job.get_old_cluster_membership_file();
 
 		id_of_str_bidirnl seq_ider;
 

source/ct_cluster/cath/cluster/cluster_info_test.cpp

@@ -36,29 +36,28 @@ using ::std::vector;
 
 namespace {
 
-		/// \brief The cluster_info_test_suite_fixture to assist in testing cluster_info
-		struct cluster_info_test_suite_fixture {
-		protected:
-			~cluster_info_test_suite_fixture() noexcept = default;
-
-			/// \brief Type alias for a pair of string and seq_seg_run_opt
-			using str_seq_seg_run_opt_pair     = pair  < string, seq_seg_run_opt  >;
-
-			/// \brief Type alias for a vector of str_seq_seg_run_opt_pair
-			using str_seq_seg_run_opt_pair_vec = vector< str_seq_seg_run_opt_pair >;
-
-			/// \brief Make a cluster_info from the specified str_seq_seg_run_opt_pair_vec
-			cluster_info make_cluster_info(const str_seq_seg_run_opt_pair_vec &prm_data ///< The data from which to build the cluster_info
-			                               ) {
-				cluster_info result{};
-
-				// \TODO Come C++17 and structured bindings, use here
-				for (const pair<string, seq_seg_run_opt> &datum : prm_data) {
-					result.add_entry( datum.first, datum.second );
-				}
-				return result;
+	/// \brief The cluster_info_test_suite_fixture to assist in testing cluster_info
+	struct cluster_info_test_suite_fixture {
+	  protected:
+		~cluster_info_test_suite_fixture() noexcept = default;
+
+		/// \brief Type alias for a pair of string and seq_seg_run_opt
+		using str_seq_seg_run_opt_pair = pair<string, seq_seg_run_opt>;
+
+		/// \brief Type alias for a vector of str_seq_seg_run_opt_pair
+		using str_seq_seg_run_opt_pair_vec = vector<str_seq_seg_run_opt_pair>;
+
+		/// \brief Make a cluster_info from the specified str_seq_seg_run_opt_pair_vec
+		cluster_info make_cluster_info( const str_seq_seg_run_opt_pair_vec &prm_data ///< The data from which to build the cluster_info
+		                                ) {
+			cluster_info result{};
+
+			for ( const auto &[ name, segments ] : prm_data ) {
+				result.add_entry( name, segments );
 			}
-		};
+			return result;
+		}
+	};
 
 } // namespace
 

source/ct_cluster/cath/cluster/map/map_clusters.cpp

@@ -127,9 +127,7 @@ map_results cath::clust::map_clusters(const old_cluster_data_opt &prm_old_cluste
 					const domain_cluster_ids &new_dom_clust_ids = get_domain_cluster_ids_of_seq_id( prm_new_clusters, seq_id );
 
 					/// Loop over the old entries on the sequence
-					// \TODO Come C++17 and structured bindings, use here
-					for (const domain_cluster_id &old_dom_clust_id : old_dom_cluster_ids) {
-						const seq_seg_run_opt &old_segments_opt = old_dom_clust_id.segments;
+					for ( const auto &[ old_segments_opt, old_dom_clust_id ] : old_dom_cluster_ids ) {
 
 						// If the entry doesn't have segments then...
 						if ( ! old_segments_opt ) {
@@ -151,7 +149,7 @@ map_results cath::clust::map_clusters(const old_cluster_data_opt &prm_old_cluste
 									<< " "
 									<< prm_old_clusters->get_id_of_seq_name().get_name_of_id( seq_id )
 									<< " "
-									<< get_name_of_cluster_of_id( *prm_old_clusters, old_dom_clust_id.cluster_id )
+									<< get_name_of_cluster_of_id( *prm_old_clusters, old_dom_clust_id )
 									<< " 100 "
 									<< prm_old_clusters->get_id_of_seq_name().get_name_of_id( seq_id )
 									<< " "
@@ -167,7 +165,7 @@ map_results cath::clust::map_clusters(const old_cluster_data_opt &prm_old_cluste
 
 						if constexpr ( IS_IN_DEBUG_MODE ) {
 							// Check the old cluster ID is consistent
-							if ( old_cluster_idx != old_dom_clust_id.cluster_id ) {
+							if ( old_cluster_idx != old_dom_clust_id ) {
 								BOOST_THROW_EXCEPTION(
 								  out_of_range_exception( "Internal inconsistency detected in old cluster IDs" ) );
 							}
@@ -187,8 +185,11 @@ map_results cath::clust::map_clusters(const old_cluster_data_opt &prm_old_cluste
 						}
 
 						// Make a closure for calculating the domain overlap with *old_segments_opt
+						//
+						// TODO: Come C++20, drop this silly reference (needed in C++17 to allow a structured binding to be captured by a lambda)
+						const auto &old_segments_opt_ref = old_segments_opt;
 						const auto get_dom_ol_fn = [&] (const domain_cluster_id &x) {
-							return fraction_overlap_over_longer( *old_segments_opt, *x.segments );
+							return fraction_overlap_over_longer( *old_segments_opt_ref, *x.segments );
 						};
 
 						// Find the new entry that maps to the old domain best (and its overlap)
@@ -209,7 +210,7 @@ map_results cath::clust::map_clusters(const old_cluster_data_opt &prm_old_cluste
 								<< prm_old_clusters->get_id_of_seq_name().get_name_of_id( seq_id )
 								<< get_segments_suffix_string( old_segments_opt )
 								<< " "
-								<< get_name_of_cluster_of_id( *prm_old_clusters, old_dom_clust_id.cluster_id )
+								<< get_name_of_cluster_of_id( *prm_old_clusters, old_dom_clust_id )
 								<< " "
 								<< ( 100.0 * best_ol )
 								<< " "

source/ct_common/cath/common/boost_addenda/graph/spanning_tree.cpp

@@ -129,11 +129,8 @@ size_size_doub_tpl_vec cath::common::order_spanning_tree_from_start(const size_s
 		vector<size_set> edge_indcs( prm_spanning_tree.size() + 1 );
 		const auto non_starting_edge_indices = indices( prm_spanning_tree.size() )
 			| filtered( [&] (const size_t &x) { return x != prm_index; } );
-		// \TODO Come C++17 and structured bindings, use here
 		for (const size_t &non_starting_edge_index : non_starting_edge_indices) {
-			const auto   &the_edge = prm_spanning_tree[ non_starting_edge_index ];
-			const size_t &node_a   = get<0>( the_edge );
-			const size_t &node_b   = get<1>( the_edge );
+			const auto &[ node_a, node_b, val ] = prm_spanning_tree[ non_starting_edge_index ];
 			edge_indcs[ node_a ].insert( non_starting_edge_index );
 			edge_indcs[ node_b ].insert( non_starting_edge_index );
 		}

source/ct_uni/cath/alignment/residue_name_align/detail/residue_name_align_map.cpp

@@ -69,10 +69,9 @@ size_t residue_name_align_map::get_index_of_residue_name_string(const string &pr
 /// \brief Get a list of all the residue names (ie the keys)
 str_vec residue_name_align_map::get_residue_name_strings() const {
 	str_vec residue_names;
-	residue_names.reserve(index_of_residue_name.size());
-	/// TODO: Come C++17, use a structured binding to make the names clearer here
-	for (const auto &residue_name_index_pair : index_of_residue_name) {
-		residue_names.push_back(residue_name_index_pair.first);
+	residue_names.reserve( index_of_residue_name.size() );
+	for ( const auto &[ residue_name, index ] : index_of_residue_name ) {
+		residue_names.push_back( residue_name );
 	}
 	return residue_names;
 }

source/ct_uni/cath/display/viewer/chimera_viewer.cpp

@@ -293,17 +293,11 @@ void cath::detail::write_chimera_global_alignment(ostream                     &p
 		}
 		prm_os << join(
 			core_res_ids_of_entry_name
-				// \TODO Come C++17 and structured bindings, use here
 				| transformed( [] (const pair<const coreness, str_res_id_vec_map> &core_data) {
-					const coreness           &is_core               = core_data.first;
-					const str_res_id_vec_map &res_ids_of_entry_name = core_data.second;
+					const auto &[ is_core, res_ids_of_entry_name ] = core_data;
 
-					// \TODO Come C++17 and structured bindings, use here
 					str_vec selection_strings;
-					for (const pair<const string, residue_id_vec> &entry_name_and_res_ids : res_ids_of_entry_name) {
-						const string         &entry_name = entry_name_and_res_ids.first;
-						const residue_id_vec &res_ids    = entry_name_and_res_ids.second;
-
+					for ( const auto &[ entry_name, res_ids ] : res_ids_of_entry_name ) {
 						const size_t num_res_ids     = res_ids.size();
 						const size_t num_res_batches = num_batches( num_res_ids, chimera_viewer::RESIDUE_BATCH_SIZE, broken_batch_tol::PERMIT );
 						for (const size_t &batch_ctr : indices( num_res_batches ) ) {

source/ct_uni/cath/display/viewer/pymol_viewer.cpp

@@ -279,17 +279,11 @@ void cath::detail::write_pymol_global_alignment(ostream                     &prm
 		}
 		prm_os << join(
 			core_res_ids_of_entry_name
-				// \TODO Come C++17 and structured bindings, use here
 				| transformed( [] (const pair<const coreness, str_res_id_vec_map> &core_data) {
-					const coreness           &is_core               = core_data.first;
-					const str_res_id_vec_map &res_ids_of_entry_name = core_data.second;
+					const auto &[ is_core, res_ids_of_entry_name ] = core_data;
 
-					// \TODO Come C++17 and structured bindings, use here
 					str_vec selection_strings;
-					for (const pair<const string, residue_id_vec> &entry_name_and_res_ids : res_ids_of_entry_name) {
-						const string         &entry_name = entry_name_and_res_ids.first;
-						const residue_id_vec &res_ids    = entry_name_and_res_ids.second;
-
+					for ( const auto &[ entry_name, res_ids ] : res_ids_of_entry_name ) {
 						const size_t num_res_ids     = res_ids.size();
 						const size_t num_res_batches = num_batches( num_res_ids, pymol_viewer::RESIDUE_BATCH_SIZE, broken_batch_tol::PERMIT );
 						for (const size_t &batch_ctr : indices( num_res_batches ) ) {

source/ct_uni/cath/ssap/ssap.cpp

@@ -823,11 +823,10 @@ protein cath::read_protein_data_from_ssap_options_files(const data_dirs_spec
 		prm_protein_name
 	);
 
-	/// TODO: Come C++17, use a structured binding to make the names clearer here
-	for (const auto &filename_and_data_file : filename_of_data_file) {
-		const string file_str              = to_lower_copy( lexical_cast<string>( filename_and_data_file.first ) );
+	for ( const auto &[ data_file, filename ] : filename_of_data_file ) {
+		const string file_str              = to_lower_copy( lexical_cast<string>( data_file ) );
 		const string right_padded_file_str = string( max_data_file_str_length() - file_str.length(), ' ' );
-		::spdlog::debug( "Loading {}{} from {}", file_str, right_padded_file_str, filename_and_data_file.second.string() );
+		::spdlog::debug( "Loading {}{} from {}", file_str, right_padded_file_str, filename.string() );
 	}
 
 	// Create a protein object from the name, wolf file and sec file

source/ct_uni/cath/structure/geometry/detail/cross_covariance_matrix.cpp

@@ -40,11 +40,7 @@ gsl_matrix_wrp cath::geom::detail::cross_covariance_matrix(const coord_list &prm
 	gsl_matrix_wrp result{ 3, 3 };
 	gsl_matrix_set_zero( result.get_ptr() );
 
-	/// \TODO Come C++17 and structure bindings, use here
-	for (const auto &coord_pair : combine( prm_coords_a, prm_coords_b ) ) {
-		const coord &coord_a = coord_pair.get<0>();
-		const coord &coord_b = coord_pair.get<1>();
-
+	for ( const auto &[ coord_a, coord_b ] : combine( prm_coords_a, prm_coords_b ) ) {
 		gsl_matrix_wrp_increment( result, 0, 0, coord_a.get_x() * coord_b.get_x() );
 		gsl_matrix_wrp_increment( result, 0, 1, coord_a.get_x() * coord_b.get_y() );
 		gsl_matrix_wrp_increment( result, 0, 2, coord_a.get_x() * coord_b.get_z() );