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@tonyelewis
tonyelewis committed Nov 3, 2017
1 parent c51ce31 commit 9636a93
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Showing 135 changed files with 156 additions and 157 deletions.
2 changes: 1 addition & 1 deletion source/cath_assign_domains/options/cath_assign_domains_options.cpp
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#include "alignment/common_atom_selection_policy/common_atom_select_ca_policy.hpp"
#include "alignment/common_residue_selection_policy/common_residue_select_best_score_percent_policy.hpp"
#include "chopping/region/region.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/logger.hpp"
#include "common/type_aliases.hpp"
#include "display/options/display_spec.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "file/pdb/pdb.hpp"
#include "file/pdb/pdb_atom.hpp"
#include "file/pdb/pdb_list.hpp"
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2 changes: 1 addition & 1 deletion source/cath_refine_align/options/cath_refine_align_options.cpp
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#include "chopping/region/region.hpp"
#include "common/algorithm/transform_build.hpp"
#include "common/argc_argv_faker.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/exception/not_implemented_exception.hpp"
#include "common/exception/runtime_error_exception.hpp"
#include "common/type_aliases.hpp"
#include "file/pdb/pdb.hpp"
#include "file/pdb/pdb_atom.hpp"
#include "file/pdb/pdb_residue.hpp"
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2 changes: 1 addition & 1 deletion source/cath_score_align/options/cath_score_align_options.cpp
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#include "alignment/common_residue_selection_policy/common_residue_select_best_score_percent_policy.hpp"
#include "chopping/region/region.hpp"
#include "common/argc_argv_faker.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/exception/not_implemented_exception.hpp"
#include "common/exception/runtime_error_exception.hpp"
#include "common/type_aliases.hpp"
#include "file/pdb/pdb.hpp"
#include "file/pdb/pdb_atom.hpp"
#include "file/pdb/pdb_residue.hpp"
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2 changes: 1 addition & 1 deletion source/chopping/region/region.cpp
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#include <boost/program_options.hpp>

#include "chopping/chopping_format/sillitoe_chopping_format.hpp"
#include "common/optional/make_optional_if.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/optional/make_optional_if.hpp"

using namespace cath;
using namespace cath::chop;
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2 changes: 1 addition & 1 deletion source/chopping/region/regions_limiter.cpp
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#include "chopping/region/region.hpp"
#include "common/algorithm/transform_build.hpp"
#include "common/boost_addenda/range/indices.hpp"
#include "common/optional/make_optional_if.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/optional/make_optional_if.hpp"

using namespace cath;
using namespace cath::chop;
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2 changes: 1 addition & 1 deletion source/cluster/cluster_info.hpp
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#include <boost/operators.hpp>
#include <boost/utility/string_ref.hpp>

#include "common/exception/invalid_argument_exception.hpp"
#include "common/optional/make_optional_if.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "seq/seq_seg_run.hpp"

#include <string>
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2 changes: 1 addition & 1 deletion source/cluster/file/cluster_membership_file.cpp
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#include "cluster/old_cluster_data.hpp"
#include "common/boost_addenda/log/log_to_ostream_guard.hpp"
#include "common/debug_numeric_cast.hpp"
#include "common/exception/runtime_error_exception.hpp"
#include "common/file/open_fstream.hpp"
#include "common/optional/make_optional_if.hpp"
#include "common/string/string_parse_tools.hpp"
#include "common/exception/runtime_error_exception.hpp"
#include "seq/seq_seg_run_parser.hpp"

#include <fstream>
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2 changes: 1 addition & 1 deletion source/cluster/map/aggregate_map_results.cpp
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#include "cluster/map/map_results.hpp"
#include "cluster/new_cluster_data.hpp"
#include "cluster/old_cluster_data.hpp"
#include "common/file/open_fstream.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/file/open_fstream.hpp"

using namespace cath::clust;
using namespace cath::common;
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2 changes: 1 addition & 1 deletion source/cluster/map/map_results.cpp
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#include "cluster/new_cluster_data.hpp"
#include "cluster/old_cluster_data.hpp"
#include "common/boost_addenda/range/indices.hpp"
#include "common/file/open_fstream.hpp"
#include "common/exception/out_of_range_exception.hpp"
#include "common/file/open_fstream.hpp"

#include <fstream>

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2 changes: 1 addition & 1 deletion source/cluster/map/map_results_test.cpp
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#include <boost/test/auto_unit_test.hpp>

#include "cluster/map/map_results.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/size_t_literal.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"

using namespace cath;
using namespace cath::clust;
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2 changes: 1 addition & 1 deletion source/cluster/map/overlap_frac_distn.hpp
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#include <boost/range/combine.hpp>

#include "common/cpp14/cbegin_cend.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/size_t_literal.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"

using namespace cath::common::literals;

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2 changes: 1 addition & 1 deletion source/display_colour/display_colour.cpp
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#include <boost/numeric/conversion/cast.hpp>

#include "common/boost_addenda/string_algorithm/split_build.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/type_aliases.hpp"

#include <tuple>

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2 changes: 1 addition & 1 deletion source/display_colour/display_colour_gradient.cpp
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#include <boost/lexical_cast.hpp>
#include <boost/numeric/conversion/cast.hpp>

#include "display_colour/display_colour.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "display_colour/display_colour.hpp"

using namespace boost::algorithm;
using namespace cath;
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2 changes: 1 addition & 1 deletion source/display_colour/display_colour_gradient_test.cpp
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#include <boost/test/auto_unit_test.hpp>

#include "common/exception/invalid_argument_exception.hpp"
#include "display_colour/display_colour.hpp"
#include "display_colour/display_colour_gradient.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "test/boost_addenda/boost_check_no_throw_diag.hpp"

using namespace cath;
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2 changes: 1 addition & 1 deletion source/display_colour/display_colour_test.cpp
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#include <boost/lexical_cast.hpp>
#include <boost/test/auto_unit_test.hpp>

#include "common/exception/invalid_argument_exception.hpp"
#include "display_colour/display_colour.hpp"
#include "display_colour/display_colour_type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "test/boost_addenda/boost_check_no_throw_diag.hpp"
#include "test/global_test_constants.hpp"
#include "test/test_tools.hpp"
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2 changes: 1 addition & 1 deletion source/executables/cath_check_pdb/cath_check_pdb.cpp
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#include <boost/filesystem.hpp>

#include "common/exception/invalid_argument_exception.hpp"
#include "common/file/open_fstream.hpp"
#include "common/logger.hpp"
#include "common/program_exception_wrapper.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "file/pdb/pdb.hpp"
#include "file/pdb/pdb_atom.hpp"
#include "file/pdb/pdb_residue.hpp"
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2 changes: 1 addition & 1 deletion source/options/executable/executable_options.cpp
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#include <boost/optional.hpp>

#include "common/argc_argv_faker.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/file/find_file.hpp"
#include "common/file/open_fstream.hpp"
#include "common/optional/make_optional_if.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "options/executable/env_var_option_name_handler.hpp"
#include "options/options_block/misc_help_version_options_block.hpp"

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2 changes: 1 addition & 1 deletion source/resolve_hits/calc_hit.hpp
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#include "common/algorithm/append.hpp"
#include "common/algorithm/transform_build.hpp"
#include "common/cpp14/cbegin_cend.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/type_aliases.hpp"
#include "resolve_hits/resolve_hits_type_aliases.hpp"
#include "seq/seq_arrow.hpp"
#include "seq/seq_seg.hpp"
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4 changes: 2 additions & 2 deletions source/resolve_hits/cath_hit_resolver.cpp
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#include "cath_hit_resolver.hpp"

#include "common/exception/not_implemented_exception.hpp"
#include "common/exception/out_of_range_exception.hpp"
#include "common/file/ofstream_list.hpp"
#include "common/file/open_fstream.hpp"
#include "common/logger.hpp"
#include "common/exception/not_implemented_exception.hpp"
#include "common/exception/out_of_range_exception.hpp"
#include "resolve_hits/calc_hit_list.hpp"
#include "resolve_hits/file/parse_domain_hits_table.hpp"
#include "resolve_hits/file/parse_hmmer_out.hpp"
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2 changes: 1 addition & 1 deletion source/resolve_hits/file/detail/hmmer_aln.hpp
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#include <boost/utility/string_ref.hpp>

#include "common/boost_addenda/make_string_ref.hpp"
#include "common/string/string_parse_tools.hpp"
#include "common/exception/runtime_error_exception.hpp"
#include "common/string/string_parse_tools.hpp"
#include "resolve_hits/file/alnd_rgn.hpp"
#include "resolve_hits/resolve_hits_type_aliases.hpp"
#include "seq/seq_arrow.hpp"
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2 changes: 1 addition & 1 deletion source/resolve_hits/file/detail/hmmer_parser.hpp
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#include <boost/optional/optional_io.hpp>

#include "common/boost_addenda/make_string_ref.hpp"
#include "common/string/string_parse_tools.hpp"
#include "common/exception/out_of_range_exception.hpp"
#include "common/exception/runtime_error_exception.hpp"
#include "common/string/string_parse_tools.hpp"
#include "resolve_hits/file/cath_id_score_category.hpp"
#include "resolve_hits/file/detail/hmmer_aln.hpp"
#include "resolve_hits/file/hmmer_format.hpp"
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2 changes: 1 addition & 1 deletion source/resolve_hits/file/hits_input_format_tag.cpp
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#include <boost/algorithm/string/case_conv.hpp>

#include "common/program_options/validator.hpp"
#include "common/exception/out_of_range_exception.hpp"
#include "common/program_options/validator.hpp"

#include <map>

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2 changes: 1 addition & 1 deletion source/resolve_hits/html_output/resolve_hits_html_outputter_test.cpp
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#include <boost/algorithm/string/predicate.hpp>
#include <boost/test/auto_unit_test.hpp>

// #include "common/file/spew.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "resolve_hits/full_hit.hpp"
#include "resolve_hits/full_hit_list.hpp"
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#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>
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2 changes: 1 addition & 1 deletion source/resolve_hits/options/spec/crh_filter_spec.hpp
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#include <boost/utility/string_ref.hpp>

#include "common/algorithm/contains.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/type_aliases.hpp"
#include "resolve_hits/hit_score_type.hpp"
#include "resolve_hits/resolve_hits_type_aliases.hpp"

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2 changes: 1 addition & 1 deletion source/resolve_hits/read_and_process_hits/read_and_process_mgr.hpp
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#include <boost/utility/string_ref.hpp>

#include "common/algorithm/sort_uniq_build.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/runtime_error_exception.hpp"
#include "common/type_aliases.hpp"
#include "resolve_hits/calc_hit.hpp"
#include "resolve_hits/calc_hit_list.hpp"
#include "resolve_hits/detail/full_hit_prune_builder.hpp"
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2 changes: 1 addition & 1 deletion source/resolve_hits/trim/trim_spec.cpp
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#include "common/algorithm/transform_build.hpp"
#include "common/boost_addenda/string_algorithm/split_build.hpp"
#include "common/debug_numeric_cast.hpp"
#include "common/program_options/validator.hpp"
#include "common/exception/runtime_error_exception.hpp"
#include "common/program_options/validator.hpp"

#include <string>

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2 changes: 1 addition & 1 deletion source/seq/seq_seg.hpp
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#include "common/boost_addenda/range/indices.hpp"
#include "common/cpp14/constexpr_min_max.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/json_style.hpp"
#include "common/rapidjson_addenda/rapidjson_writer.hpp"
#include "common/size_t_literal.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "seq/seq_arrow.hpp"

using namespace cath::common::literals;
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2 changes: 1 addition & 1 deletion source/src_common/common/argc_argv_faker_test.cpp
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#include "common/argc_argv_faker.hpp"
#include "common/boost_addenda/range/indices.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/type_aliases.hpp"

using namespace cath;
using namespace cath::common;
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2 changes: 1 addition & 1 deletion source/src_common/common/boost_addenda/graph/spanning_tree.hpp
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#include "common/boost_addenda/range/range_concept_type_aliases.hpp"
#include "common/boost_addenda/range/stable_sort_proj.hpp"
#include "common/cpp14/cbegin_cend.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/type_aliases.hpp"

#include <tuple>
#include <vector>
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2 changes: 1 addition & 1 deletion source/src_common/common/container/id_of_str_bidirnl.hpp
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#include "common/boost_addenda/range/max_proj_element.hpp"
#include "common/boost_addenda/range/range_concept_type_aliases.hpp"
#include "common/container/id_of_string_view.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/out_of_range_exception.hpp"
#include "common/type_aliases.hpp"

#include <string>

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2 changes: 1 addition & 1 deletion source/src_common/common/file/simple_file_read_write.hpp
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#include "common/cpp14/cbegin_cend.hpp"
#include "common/cpp17/apply.hpp"
#include "common/exception/out_of_range_exception.hpp"
#include "common/file/open_fstream.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/out_of_range_exception.hpp"

#include <fstream>

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2 changes: 1 addition & 1 deletion source/src_common/common/file/temp_file.cpp
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#include <boost/algorithm/string/replace.hpp>
#include <boost/filesystem.hpp>

#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/type_aliases.hpp"

#include <iostream> // *** TEMPORARY ***

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2 changes: 1 addition & 1 deletion source/src_common/common/file/temp_file_test.cpp
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#include <boost/filesystem.hpp>

#include "common/file/open_fstream.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/file/open_fstream.hpp"
#include "common/file/temp_file.hpp"

#include <fstream>
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2 changes: 1 addition & 1 deletion source/src_common/common/gsl/get_determinant.hpp
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#ifndef _CATH_TOOLS_SOURCE_COMMON_GSL_GET_DETERMINANT_H
#define _CATH_TOOLS_SOURCE_COMMON_GSL_GET_DETERMINANT_H

#include "common/exception/invalid_argument_exception.hpp"
#include "common/gsl/gsl_matrix_wrp.hpp"
#include "common/gsl/gsl_permutation_wrp.hpp"
#include "common/exception/invalid_argument_exception.hpp"

#include <gsl/gsl_linalg.h>
#include <gsl/gsl_vector.h>
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2 changes: 1 addition & 1 deletion source/src_common/common/program_exception_wrapper_test.cpp
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#include <boost/test/output_test_stream.hpp>

#include "common/argc_argv_faker.hpp"
#include "common/program_exception_wrapper.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/program_exception_wrapper.hpp"

#include <sstream>
#include <string>
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2 changes: 1 addition & 1 deletion source/src_common/common/string/string_parse_tools.hpp
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#include "common/boost_addenda/make_string_ref.hpp"
#include "common/cpp14/cbegin_cend.hpp"
#include "common/debug_numeric_cast.hpp"
#include "common/type_aliases.hpp"
#include "common/exception/invalid_argument_exception.hpp"
#include "common/exception/runtime_error_exception.hpp"
#include "common/type_aliases.hpp"

#include <string>

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