Remove a bunch of needless using namespace declrns

UCLOrengoGroup · Nov 22, 2017 · 33bfda3 · 33bfda3
1 parent 3ca6706
commit 33bfda3
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Showing 95 changed files with 118 additions and 166 deletions.
diff --git a/source/biocore/chain_label.cpp b/source/biocore/chain_label.cpp
@@ -24,7 +24,6 @@
 
 #include "common/exception/invalid_argument_exception.hpp"
 
-using namespace boost::algorithm;
 using namespace cath;
 using namespace cath::common;
 using namespace std;

diff --git a/source/biocore/residue_name.cpp b/source/biocore/residue_name.cpp
@@ -25,11 +25,12 @@
 
 #include "common/exception/invalid_argument_exception.hpp"
 
-using namespace boost::algorithm;
 using namespace cath;
 using namespace cath::common;
 using namespace std;
 
+using boost::algorithm::is_alnum;
+using boost::algorithm::is_digit;
 using boost::lexical_cast;
 using boost::optional;
 

diff --git a/source/cath_refine_align/options/cath_refine_align_options.cpp b/source/cath_refine_align/options/cath_refine_align_options.cpp
@@ -48,7 +48,6 @@
 #include "outputter/superposition_outputter/superposition_outputter_list.hpp"
 #include "superposition/superposition_context.hpp"
 
-using namespace boost::program_options;
 using namespace cath;
 using namespace cath::align;
 using namespace cath::chop;
@@ -57,6 +56,7 @@ using namespace cath::file;
 using namespace cath::opts;
 
 using boost::none;
+using boost::program_options::variables_map;
 using std::istream;
 using std::string;
 using std::unique_ptr;

diff --git a/source/cluster/file/cluster_membership_file.cpp b/source/cluster/file/cluster_membership_file.cpp
@@ -38,7 +38,6 @@
 #include <sstream>
 #include <string>
 
-using namespace boost::log;
 using namespace cath;
 using namespace cath::clust;
 using namespace cath::common;

diff --git a/source/display_colour/display_colour.cpp b/source/display_colour/display_colour.cpp
@@ -34,7 +34,6 @@
 
 #include <tuple>
 
-using namespace boost::algorithm;
 using namespace cath;
 using namespace cath::common;
 using namespace std;

diff --git a/source/display_colour/display_colour_gradient.cpp b/source/display_colour/display_colour_gradient.cpp
@@ -27,11 +27,11 @@
 #include "common/exception/invalid_argument_exception.hpp"
 #include "display_colour/display_colour.hpp"
 
-using namespace boost::algorithm;
 using namespace cath;
 using namespace cath::common;
 using namespace std;
 
+using boost::algorithm::clamp;
 using boost::lexical_cast;
 using boost::numeric_cast;
 

diff --git a/source/display_colour/display_colour_list.cpp b/source/display_colour/display_colour_list.cpp
@@ -31,7 +31,6 @@
 #include "display_colour/display_colour.hpp"
 #include "display_colour/display_colour_type_aliases.hpp"
 
-using namespace boost::algorithm;
 using namespace cath;
 using namespace cath::common;
 using namespace std;

diff --git a/source/executables/cath_ssap/cath_ssap.cpp b/source/executables/cath_ssap/cath_ssap.cpp
@@ -26,11 +26,13 @@
 #include "ssap/options/cath_ssap_options.hpp"
 #include "ssap/ssap.hpp"
 
-using namespace boost::log::trivial;
 using namespace cath::common;
 using namespace cath::opts;
 using namespace std;
 
+using boost::log::trivial::severity;
+using boost::log::trivial::trace;
+
 namespace cath {
 
 	/// \brief A concrete program_exception_wrapper that implements do_run_program() to parse the options and then pass them to call_ssap()

diff --git a/source/options/executable/env_var_option_name_handler.cpp b/source/options/executable/env_var_option_name_handler.cpp
@@ -25,13 +25,15 @@
 #include <boost/algorithm/string/predicate.hpp>
 #include <boost/algorithm/string/replace.hpp>
 
-using namespace boost::algorithm;
-using namespace boost::program_options;
 using namespace cath::opts;
 using namespace std;
 
 using boost::algorithm::replace_all_copy;
 using boost::algorithm::starts_with;
+using boost::erase_first_copy;
+using boost::program_options::options_description;
+using boost::to_lower_copy;
+using boost::to_upper_copy;
 
 /// \brief Ctor for env_var_option_name_handler
 env_var_option_name_handler::env_var_option_name_handler(string                     arg_prefix,        ///< The prefix string to strip off all environment variable names(eg "CATH_TOOLS_"

diff --git a/source/options/executable/env_var_option_name_handler_test.cpp b/source/options/executable/env_var_option_name_handler_test.cpp
@@ -22,10 +22,11 @@
 
 #include "options/executable/env_var_option_name_handler.hpp"
 
-using namespace boost::program_options;
 using namespace cath::opts;
 using namespace std;
 
+using boost::program_options::options_description;
+
 namespace cath {
 	namespace test {
 

diff --git a/source/options/options_block/check_pdb_options_block_test.cpp b/source/options/options_block/check_pdb_options_block_test.cpp
@@ -27,7 +27,6 @@
 #include "options/options_block/check_pdb_options_block.hpp"
 #include "options/options_block/options_block_tester.hpp"
 
-using namespace boost::program_options;
 using namespace cath::common;
 using namespace cath::opts;
 using namespace std;

diff --git a/source/options/options_block/detail_help_options_block_test.cpp b/source/options/options_block/detail_help_options_block_test.cpp
@@ -24,7 +24,6 @@
 #include "options/options_block/detail_help_options_block.hpp"
 #include "options/options_block/options_block_tester.hpp"
 
-using namespace boost::program_options;
 using namespace cath::common;
 using namespace cath::opts;
 using namespace std;

diff --git a/source/options/options_block/extract_pdb_options_block_test.cpp b/source/options/options_block/extract_pdb_options_block_test.cpp
@@ -27,7 +27,6 @@
 #include "options/options_block/extract_pdb_options_block.hpp"
 #include "options/options_block/options_block_tester.hpp"
 
-using namespace boost::program_options;
 using namespace cath::common;
 using namespace cath::opts;
 using namespace std;

diff --git a/source/options/options_block/ids_options_block.cpp b/source/options/options_block/ids_options_block.cpp
@@ -30,13 +30,15 @@
 
 #include <iostream>
 
-using namespace boost::program_options;
 using namespace cath;
 using namespace cath::common;
 using namespace cath::opts;
 using namespace std;
 
 using boost::none;
+using boost::program_options::options_description;
+using boost::program_options::value;
+using boost::program_options::variables_map;
 
 const string ids_options_block::PO_ID( "id" ); ///< The option name for the id option
 

diff --git a/source/options/options_block/misc_help_version_options_block_test.cpp b/source/options/options_block/misc_help_version_options_block_test.cpp
@@ -24,7 +24,6 @@
 #include "options/options_block/misc_help_version_options_block.hpp"
 #include "options/options_block/options_block_tester.hpp"
 
-using namespace boost::program_options;
 using namespace cath::opts;
 using namespace std;
 

diff --git a/source/options/options_block/options_block.cpp b/source/options/options_block/options_block.cpp
@@ -29,7 +29,6 @@
 #include "common/boost_addenda/program_options/variables_map_contains.hpp"
 #include "common/clone/check_uptr_clone_against_this.hpp"
 
-using namespace boost::program_options;
 using namespace cath;
 using namespace cath::common;
 using namespace cath::opts;
@@ -40,6 +39,8 @@ using boost::algorithm::any_of;
 using boost::filesystem::is_empty;
 using boost::filesystem::path;
 using boost::numeric_cast;
+using boost::program_options::options_description;
+using boost::program_options::variables_map;
 
 /// \brief A string to use to separate (valid values and their descriptions) from each other
 const string options_block::SUB_DESC_SEPARATOR = "\n   ";

diff --git a/source/options/options_block/options_block_test.cpp b/source/options/options_block/options_block_test.cpp
@@ -29,11 +29,14 @@
 #include "options/options_block/pdb_input_options_block.hpp"
 #include "test/boost_addenda/boost_check_no_throw_diag.hpp"
 
-using namespace boost::program_options;
 using namespace cath;
 using namespace cath::opts;
 using namespace std;
 
+using boost::program_options::options_description;
+using boost::program_options::unknown_option;
+using boost::program_options::variables_map;
+
 BOOST_TEST_DONT_PRINT_LOG_VALUE(type_info)
 
 /// \brief A type alias for a list of all the different types of options_blocks, so they can all be tested

diff --git a/source/options/options_block/options_block_tester.cpp b/source/options/options_block/options_block_tester.cpp
@@ -26,11 +26,14 @@
 #include "common/argc_argv_faker.hpp"
 #include "options/options_block/options_block.hpp"
 
-using namespace boost::program_options;
 using namespace cath;
 using namespace cath::opts;
 using namespace std;
 
+using boost::program_options::command_line_parser;
+using boost::program_options::options_description;
+using boost::program_options::variables_map;
+
 const string options_block_tester::UNKNOWN_OPT  ( "--it-does-not-know-me"            );
 const string options_block_tester::TEST_OPTION_1( "test_help_option_1"               );
 const string options_block_tester::TEST_OPTION_2( "test_help_option_2"               );

diff --git a/source/options/options_block/string_options_block.cpp b/source/options/options_block/string_options_block.cpp
@@ -24,13 +24,14 @@
 
 #include "common/clone/make_uptr_clone.hpp"
 
-using namespace boost::program_options;
 using namespace cath;
 using namespace cath::common;
 using namespace cath::opts;
 
 using boost::none;
 using boost::optional;
+using boost::program_options::options_description;
+using boost::program_options::variables_map;
 using std::string;
 using std::unique_ptr;
 

diff --git a/source/src_common/common/clone/clone_ptr_test.cpp b/source/src_common/common/clone/clone_ptr_test.cpp
@@ -40,8 +40,6 @@
 
 namespace cath { namespace test { } }
 
-using namespace boost::archive;
-using namespace boost::test_tools;
 using namespace cath::common;
 using namespace cath::common::detail;
 using namespace cath::test;

diff --git a/source/src_common/common/program_exception_wrapper.cpp b/source/src_common/common/program_exception_wrapper.cpp
@@ -27,12 +27,18 @@
 #include <boost/log/utility/setup/common_attributes.hpp>
 #include <boost/numeric/conversion/cast.hpp>
 
-using namespace boost::log;
-using namespace boost::log::expressions;
-using namespace boost::log::trivial;
 using namespace cath::common;
 using namespace std;
 
+using boost::log::expressions::format_date_time;
+using boost::log::expressions::message;
+using boost::log::expressions::smessage;
+using boost::log::expressions::stream;
+using boost::log::keywords::filter;
+using boost::log::keywords::format;
+using boost::log::trivial::severity;
+using boost::log::trivial::warning;
+
 /// \brief A simple private function to provide a standard way of outputting the context of a catch to a stream.
 void program_exception_wrapper::output_catch_context(ostream            &arg_os,
                                                      const char * const  arg_program_name
@@ -80,14 +86,14 @@ int program_exception_wrapper::run_program(int      arg_c,   ///< The main()-sty
 		// If using Boost Log, then add a sink that writes to stderr, rather than using the default stdout sink
 		boost_log_sink_sptr = boost::log::add_console_log(
 			cerr,
-			keywords::format = (
+			format = (
 				stream          << format_date_time< boost::posix_time::ptime >("TimeStamp", "%Y-%m-%d %H:%M:%S.%f")
 //	                   << "] [" << attr<boost::log::attributes::current_thread_id::value_type >("ThreadID")
 					   << " ["  << do_get_program_name()
-					   << "|\033[1m"  << left << setw( 7 ) << setfill(' ') << trivial::severity
+					   << "|\033[1m"  << left << setw( 7 ) << setfill(' ') << severity
 					   << "\033[0m] " << smessage
 			),
-			keywords::filter = ( severity >= warning )
+			filter = ( severity >= warning )
 		);
 		boost::log::add_common_attributes();
 

diff --git a/source/src_common/common/program_exception_wrapper_test.cpp b/source/src_common/common/program_exception_wrapper_test.cpp
@@ -31,11 +31,11 @@
 #include <sstream>
 #include <string>
 
-using namespace boost::test_tools;
 using namespace cath;
 using namespace cath::common;
 using namespace std;
 
+using boost::test_tools::output_test_stream;
 using boost::algorithm::contains;
 
 namespace cath {

diff --git a/source/uni/acquirer/pdbs_acquirer/domain_defn_pdbs_acquirer.cpp b/source/uni/acquirer/pdbs_acquirer/domain_defn_pdbs_acquirer.cpp
@@ -32,7 +32,6 @@
 #include "file/pdb/pdb_list.hpp"
 #include "file/pdb/pdb_residue.hpp"
 
-using namespace boost::log;
 using namespace cath::chop;
 using namespace cath::common;
 using namespace cath::file;

diff --git a/source/uni/alignment/alignment_action.cpp b/source/uni/alignment/alignment_action.cpp
@@ -29,7 +29,6 @@
 #include "common/exception/invalid_argument_exception.hpp"
 #include "common/exception/not_implemented_exception.hpp"
 
-using namespace boost::log;
 using namespace cath::align;
 using namespace cath::align::detail;
 using namespace cath::common;

diff --git a/source/uni/alignment/alignment_test.cpp b/source/uni/alignment/alignment_test.cpp
@@ -37,14 +37,14 @@
 
 #include <utility>
 
-using namespace boost::test_tools;
 using namespace cath;
 using namespace cath::align;
 using namespace cath::common;
 using namespace cath::common::test;
 using namespace std;
 
 using boost::none;
+using boost::test_tools::output_test_stream;
 
 namespace cath {
 	namespace test {

diff --git a/...nment/common_residue_selection_policy/common_residue_select_best_score_percent_policy.cpp b/...nment/common_residue_selection_policy/common_residue_select_best_score_percent_policy.cpp
@@ -40,7 +40,6 @@
 #include <algorithm>
 #include <numeric>
 
-using namespace boost::math;
 using namespace cath;
 using namespace cath::align;
 using namespace cath::common;

diff --git a/.../uni/alignment/common_residue_selection_policy/common_residue_select_min_score_policy.cpp b/.../uni/alignment/common_residue_selection_policy/common_residue_select_min_score_policy.cpp
@@ -27,7 +27,6 @@
 #include "common/clone/make_uptr_clone.hpp"
 #include "common/exception/invalid_argument_exception.hpp"
 
-using namespace boost::math;
 using namespace cath;
 using namespace cath::align;
 using namespace cath::common;

diff --git a/source/uni/alignment/dyn_prog_align/detail/string_aligner/string_aligner.cpp b/source/uni/alignment/dyn_prog_align/detail/string_aligner/string_aligner.cpp
@@ -45,7 +45,6 @@
 #include <algorithm>
 #include <string>
 
-using namespace boost::algorithm;
 using namespace cath;
 using namespace cath::align::detail;
 using namespace cath::align::gap;
@@ -57,6 +56,7 @@ using boost::algorithm::is_space;
 using boost::algorithm::is_upper;
 using boost::algorithm::token_compress_on;
 using boost::algorithm::trim_copy;
+using boost::empty_formatter;
 using boost::lexical_cast;
 using boost::numeric_cast;
 using boost::range::count;

diff --git a/source/uni/alignment/dyn_prog_align/dyn_prog_score_source/dyn_prog_score_source_test.cpp b/source/uni/alignment/dyn_prog_align/dyn_prog_score_source/dyn_prog_score_source_test.cpp
@@ -31,8 +31,8 @@
 #include "common/size_t_literal.hpp"
 #include "test/boost_addenda/boost_check_no_throw_diag.hpp"
 
- using namespace cath::align;
- using namespace cath::common;
+using namespace cath::align;
+using namespace cath::common;
 
 /// \brief TODOCUMENT
 ///

diff --git a/source/uni/alignment/gap/alignment_gap_test.cpp b/source/uni/alignment/gap/alignment_gap_test.cpp
@@ -30,13 +30,13 @@
 #include "common/size_t_literal.hpp"
 #include "common/type_aliases.hpp"
 
-using namespace boost::algorithm;
 using namespace cath;
 using namespace cath::align;
 using namespace cath::align::gap;
 using namespace cath::common;
 using namespace std;
 
+using boost::algorithm::erase_all_copy;
 using boost::none;
 using boost::numeric_cast;