Remove a bunch of unused using declarations

source/cath_assign_domains/options/cath_assign_domains_options.cpp

@@ -53,9 +53,7 @@ using namespace cath::opts;
 using namespace cath::sup;
 
 using boost::filesystem::path;
-using boost::lexical_cast;
 using boost::none;
-using boost::ptr_vector;
 using std::string;
 
 /// \brief The name of the program that uses this executable_options

source/cath_refine_align/cath_align_refiner.cpp

@@ -58,8 +58,6 @@ using namespace cath::opts;
 using namespace cath::score;
 using namespace std;
 
-using boost::ptr_vector;
-
 /// \brief Perform a cath-refine-align job as specified by the cath_superpose_options argument
 ///
 /// The input and output stream parameters default to cin and cout respectively but are configurable,

source/cath_refine_align/options/cath_refine_align_options.cpp

@@ -56,9 +56,7 @@ using namespace cath::common;
 using namespace cath::file;
 using namespace cath::opts;
 
-using boost::lexical_cast;
 using boost::none;
-using boost::ptr_vector;
 using std::istream;
 using std::string;
 using std::unique_ptr;

source/cath_score_align/cath_align_scorer.cpp

@@ -47,8 +47,6 @@ using namespace cath::opts;
 using namespace cath::score;
 using namespace std;
 
-using boost::ptr_vector;
-
 /// \brief Perform a cath-score-align job as specified by the cath_superpose_options argument
 ///
 /// The input and output stream parameters default to cin and cout respectively but are configurable,

source/cath_score_align/options/cath_score_align_options.cpp

@@ -51,9 +51,7 @@ using namespace cath::align;
 using namespace cath::common;
 using namespace cath::opts;
 
-using boost::lexical_cast;
 using boost::none;
-using boost::ptr_vector;
 using std::string;
 using std::unique_ptr;
 

source/cath_superpose/cath_superposer.cpp

@@ -50,7 +50,6 @@ using namespace cath::sup;
 using namespace std;
 
 using boost::filesystem::path;
-using boost::ptr_vector;
 
 /// \brief Perform a cath-superpose job as specified by the cath_superpose_options argument
 ///

source/chopping/chopping_format/simple_chopping_format.cpp

@@ -35,7 +35,6 @@ using namespace cath::chop;
 using namespace cath::common;
 
 using boost::string_ref;
-using std::distance;
 using std::find;
 using std::next;
 using std::string;

source/cluster/cath_cluster_mapper.cpp

@@ -50,7 +50,6 @@ using boost::filesystem::path;
 using std::ifstream;
 using std::istream;
 using std::ostream;
-using std::reference_wrapper;
 
 /// \brief Perform map-clusters according to the specified arguments strings with the specified i/o streams
 void cath::clust::perform_map_clusters(const str_vec &args,        ///< The arguments strings specifying the map-clusters action to perform

source/cluster/map/map_clusters.cpp

@@ -42,15 +42,11 @@ using namespace cath::seq;
 
 using boost::adaptors::filtered;
 using boost::algorithm::any_of;
-using boost::find_if;
 using boost::none;
 using boost::range::stable_partition;
-using boost::sub_range;
-using std::deque;
 using std::less;
 using std::max;
 using std::string;
-using std::vector;
 
 /// \brief Map old clusters to new clusters
 ///

source/cluster/map/map_results.cpp

@@ -43,8 +43,6 @@ using boost::adaptors::transformed;
 using boost::algorithm::join;
 using boost::filesystem::path;
 using boost::format;
-using boost::lexical_cast;
-using boost::numeric_cast;
 using std::ofstream;
 using std::string;
 

source/cluster/map/overlap_frac_distn.cpp

@@ -40,7 +40,6 @@ using boost::algorithm::join;
 using boost::format;
 using std::accumulate;
 using std::get;
-using std::make_pair;
 using std::max;
 using std::min;
 using std::string;

source/cluster/new_cluster_data.cpp

@@ -32,7 +32,6 @@ using namespace cath::common;
 using boost::adaptors::filtered;
 using boost::adaptors::transformed;
 using boost::algorithm::join;
-using std::pair;
 using std::string;
 
 /// \brief Generate a string describing the specified new_cluster_data

source/cluster/options/options_block/clustmap_input_options_block.cpp

@@ -29,7 +29,6 @@ using namespace cath::opts;
 using namespace std::literals::string_literals;
 
 using boost::filesystem::path;
-using boost::none;
 using boost::program_options::bool_switch;
 using boost::program_options::options_description;
 using boost::program_options::value;

source/executables/cath_assign_domains/cath_assign_domains.cpp

@@ -56,10 +56,8 @@ using boost::algorithm::is_space;
 using boost::algorithm::join;
 using boost::algorithm::starts_with;
 using boost::algorithm::token_compress_on;
-using boost::is_any_of;
 using boost::filesystem::path;
 using boost::is_space;
-using boost::lexical_cast;
 using boost::log::trivial::info;
 using boost::log::trivial::severity;
 using boost::make_optional;

source/executables/cath_check_pdb/cath_check_pdb.cpp

@@ -38,7 +38,6 @@ using namespace cath::opts;
 using boost::filesystem::path;
 using std::cerr;
 using std::cout;
-using std::endl;
 using std::ifstream;
 using std::string;
 

source/executables/cath_extract_pdb/cath_extract_pdb.cpp

@@ -33,7 +33,6 @@ using namespace cath::file;
 using namespace cath::opts;
 
 using boost::filesystem::path;
-using boost::make_optional;
 using std::cout;
 using std::string;
 

source/options/executable/executable_options.cpp

@@ -41,7 +41,6 @@ using namespace cath::common;
 using namespace cath::opts;
 using namespace std::literals::string_literals;
 
-using boost::ends_with;
 using boost::filesystem::path;
 using boost::program_options::command_line_parser;
 using boost::program_options::options_description;

source/options/options_block/extract_pdb_options_block_test.cpp

@@ -32,8 +32,6 @@ using namespace cath::common;
 using namespace cath::opts;
 using namespace std;
 
-using boost::filesystem::path;
-
 namespace cath {
 	namespace test {
 

source/options/options_block/ids_options_block.cpp

@@ -36,7 +36,6 @@ using namespace cath::common;
 using namespace cath::opts;
 using namespace std;
 
-using boost::lexical_cast;
 using boost::none;
 
 const string ids_options_block::PO_ID( "id" ); ///< The option name for the id option

source/options/options_block/options_block.cpp

@@ -39,7 +39,6 @@ using boost::adaptors::filtered;
 using boost::algorithm::any_of;
 using boost::filesystem::is_empty;
 using boost::filesystem::path;
-using boost::none;
 using boost::numeric_cast;
 
 /// \brief A string to use to separate (valid values and their descriptions) from each other

source/resolve_hits/algo/masked_bests_cacher.cpp

@@ -43,8 +43,6 @@ using boost::adaptors::transformed;
 using boost::algorithm::all_of;
 using boost::algorithm::any_of;
 using boost::range::max_element;
-using boost::range::upper_bound;
-using boost::sub_range;
 
 /// \brief Build a masked_bests_cacher to handle the caching of best results in the specified masked_bests_cache
 ///        whilst scanning from the specified start position with the specified hits and mask

source/resolve_hits/calc_hit_list.cpp

@@ -64,18 +64,13 @@ using namespace cath::rslv;
 using namespace cath::seq;
 
 using boost::adaptors::filtered;
-using boost::adaptors::transformed;
-using boost::algorithm::is_any_of;
-using boost::algorithm::is_space;
-using boost::contains;
 using boost::empty;
 using boost::filesystem::path;
 using boost::integer_range;
 using boost::irange;
 using boost::make_optional;
 using boost::none;
 using boost::numeric_cast;
-using boost::range::equal;
 using boost::range::lower_bound;
 using boost::range::max_element;
 using boost::range::reverse;
@@ -86,13 +81,10 @@ using boost::spirit::qi::omit;
 using boost::spirit::qi::parse;
 using boost::spirit::uint_;
 using boost::string_ref;
-using boost::sub_range;
-using boost::token_compress_on;
 using std::distance;
 using std::find_if;
 using std::ifstream;
 using std::istream;
-using std::make_pair;
 using std::ostream;
 using std::pair;
 using std::string;

source/resolve_hits/file/parse_hmmer_out.cpp

@@ -38,7 +38,6 @@ using namespace cath::seq;
 using boost::filesystem::path;
 using std::ifstream;
 using std::istream;
-using std::make_unique;
 
 /// \brief Parse HMMER output data from the specified file and pass the hits to the specified read_and_process_mgr
 void cath::rslv::parse_hmmer_out_file(read_and_process_mgr &arg_read_and_process_mgr, ///< The read_and_process_mgr to which the hits should be passed for processing

source/resolve_hits/full_hit_fns.cpp

@@ -34,7 +34,6 @@ using namespace cath::seq;
 using namespace std::literals::string_literals;
 
 using boost::format;
-using boost::lexical_cast;
 using boost::make_optional;
 using boost::none;
 using std::string;

source/resolve_hits/html_output/resolve_hits_html_outputter.cpp

@@ -65,12 +65,9 @@ using boost::format;
 using boost::irange;
 using boost::make_optional;
 using boost::none;
-using std::get;
 using std::make_pair;
 using std::string;
 using std::tie;
-using std::tuple;
-using std::vector;
 
 string upper_first_lower_rest(const string &arg_string
                               ) {

source/resolve_hits/html_output/resolve_hits_html_outputter_test.cpp

@@ -29,7 +29,6 @@
 #include "resolve_hits/options/spec/crh_segment_spec.hpp"
 #include "resolve_hits/resolve_hits_type_aliases.hpp"
 #include "resolve_hits/trim/trim_spec.hpp"
-// #include "common/file/spew.hpp"
 
 #include <cmath>
 #include <iostream>
@@ -42,9 +41,6 @@ using namespace cath::seq;
 using namespace cath::test;
 using namespace std::literals::string_literals;
 
-using std::log;
-using std::pow;
-
 namespace cath {
 	namespace test {
 

source/resolve_hits/options/crh_options.cpp

@@ -32,9 +32,7 @@ using boost::none;
 using boost::program_options::positional_options_description;
 using boost::program_options::variables_map;
 using std::map;
-using std::pair;
 using std::string;
-using std::vector;
 
 /// The name of the program that uses this executable_options
 const string crh_options::PROGRAM_NAME("cath-resolve-hits");

source/resolve_hits/options/options_block/crh_html_options_block.cpp

@@ -33,7 +33,6 @@ using namespace cath::common;
 using namespace cath::opts;
 using namespace cath::rslv;
 
-using boost::algorithm::any_of;
 using boost::none;
 using boost::program_options::bool_switch;
 using boost::program_options::options_description;

source/resolve_hits/options/options_block/crh_output_options_block.cpp

@@ -33,7 +33,6 @@ using namespace cath::opts;
 using namespace cath::rslv;
 
 using boost::filesystem::path;
-using boost::none;
 using boost::program_options::bool_switch;
 using boost::program_options::options_description;
 using boost::program_options::value;

source/resolve_hits/options/options_block/crh_segment_options_block.cpp

@@ -34,7 +34,6 @@ using namespace cath::seq;
 using namespace cath;
 
 using boost::none;
-using boost::program_options::bool_switch;
 using boost::program_options::options_description;
 using boost::program_options::value;
 using boost::program_options::variables_map;

source/resolve_hits/options/options_block/crh_single_output_options_block.cpp

@@ -28,7 +28,6 @@ using namespace cath::opts;
 using namespace cath::rslv;
 
 using boost::filesystem::path;
-using boost::none;
 using boost::program_options::bool_switch;
 using boost::program_options::options_description;
 using boost::program_options::value;

source/resolve_hits/options/spec/crh_html_spec.cpp

@@ -22,8 +22,6 @@
 
 using namespace cath::rslv;
 
-using boost::none;
-
 constexpr bool   crh_html_spec::DEFAULT_RESTRICT_HTML_WITHIN_BODY;
 constexpr size_t crh_html_spec::DEFAULT_MAX_NUM_NON_SOLN_HITS;
 constexpr bool   crh_html_spec::DEFAULT_EXCLUDE_REJECTED_HITS;

source/resolve_hits/options/spec/crh_single_output_spec.cpp

@@ -41,9 +41,7 @@ using boost::algorithm::join;
 using boost::filesystem::path;
 using boost::make_optional;
 using boost::none;
-using boost::range::count_if;
 using std::string;
-using std::vector;
 
 constexpr bool                crh_single_output_spec::DEFAULT_GENERATE_HTML_OUTPUT;
 constexpr bool                crh_single_output_spec::DEFAULT_JSON_OUTPUT;

source/resolve_hits/read_and_process_hits/hits_processor/summarise_hits_processor.cpp

@@ -36,7 +36,6 @@ using namespace cath::rslv::detail;
 using namespace std::literals::string_literals;
 
 using boost::format;
-using boost::lexical_cast;
 using boost::numeric_cast;
 using boost::range::max_element;
 using boost::range::min_element;

source/resolve_hits/read_and_process_hits/hits_processor/write_html_hits_processor.cpp

@@ -32,7 +32,6 @@ using namespace cath::rslv::detail;
 
 using std::move;
 using std::ostream;
-using std::reference_wrapper;
 using std::string;
 using std::unique_ptr;
 

source/resolve_hits/read_and_process_hits/hits_processor/write_json_hits_processor.cpp

@@ -32,10 +32,8 @@ using namespace cath::rslv::detail;
 
 using std::move;
 using std::ostream;
-using std::reference_wrapper;
 using std::string;
 using std::unique_ptr;
-using std::vector;
 
 /// \brief A standard do_clone method
 unique_ptr<hits_processor> write_json_hits_processor::do_clone() const {

source/resolve_hits/read_and_process_hits/read_and_process_mgr.cpp

@@ -41,13 +41,7 @@ using namespace cath::common;
 using namespace cath::rslv;
 using namespace cath::rslv::detail;
 
-using boost::size;
-using std::forward;
-using std::future;
-using std::launch;
-using std::move;
 using std::ostream;
-using std::ref;
 using std::string;
 
 constexpr bool read_and_process_mgr::DEFAULT_INPUT_HITS_ARE_GROUPED;

source/resolve_hits/resolve/hit_resolver.cpp

@@ -43,10 +43,6 @@ using namespace cath::rslv::detail;
 using namespace cath::seq;
 
 using boost::ignore_unused;
-using boost::none;
-using boost::range::sort;
-using boost::sub_range;
-using std::make_pair;
 using std::numeric_limits;
 
 // POSSIBLY TODO:

source/resolve_hits/resolve/naive_greedy_hit_resolver.cpp

@@ -30,8 +30,6 @@ using namespace cath::common;
 using namespace cath::rslv;
 using namespace cath::rslv::detail;
 
-using std::numeric_limits;
-
 /// \brief Naively, greedily resolve hits
 scored_hit_arch cath::rslv::naive_greedy_resolve_hits(const calc_hit_list &arg_hits ///< The hits to resolve
                                                       ) {