From 30494954e699ae7847913125ac2ff060e651caed Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Mon, 28 Mar 2022 17:45:22 +0200 Subject: [PATCH] [WIP] core_language adapt header --- include/seqan3/alignment/configuration/align_config_output.hpp | 2 +- .../seqan3/alignment/configuration/align_config_score_type.hpp | 2 +- include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp | 2 +- include/seqan3/alignment/matrix/detail/alignment_optimum.hpp | 2 +- .../matrix/detail/alignment_score_matrix_one_column.hpp | 2 +- .../matrix/detail/alignment_score_matrix_one_column_base.hpp | 2 +- .../alignment/matrix/detail/alignment_score_matrix_proxy.hpp | 2 +- .../matrix/detail/combined_score_and_trace_matrix.hpp | 2 +- include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp | 2 +- .../alignment/matrix/detail/score_matrix_single_column.hpp | 2 +- include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp | 2 +- .../alignment/pairwise/detail/alignment_algorithm_state.hpp | 2 +- include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp | 2 +- .../alignment/pairwise/policy/simd_affine_gap_policy.hpp | 2 +- include/seqan3/alignment/scoring/scoring_scheme_base.hpp | 2 +- include/seqan3/alphabet/composite/alphabet_tuple_base.hpp | 1 - include/seqan3/alphabet/concept.hpp | 2 +- include/seqan3/alphabet/detail/alphabet_proxy.hpp | 3 ++- include/seqan3/argument_parser/validators.hpp | 2 +- include/seqan3/core/concept/all.hpp | 2 +- include/seqan3/io/detail/misc_input.hpp | 2 +- include/seqan3/io/detail/misc_output.hpp | 2 +- include/seqan3/io/sam_file/sam_tag_dictionary.hpp | 1 - include/seqan3/search/configuration/max_error_common.hpp | 2 +- include/seqan3/utility/char_operations/transform.hpp | 2 +- include/seqan3/utility/simd/views/iota_simd.hpp | 2 +- include/seqan3/utility/views/convert.hpp | 2 +- ...@_implicit_conversion_from_@source_alphabet@_inherit.cpp.in | 2 +- .../dna15_implicit_conversion_from_rna15_inherit.cpp | 2 +- .../nucleotide/dna4_implicit_conversion_from_rna4_inherit.cpp | 2 +- .../nucleotide/dna5_implicit_conversion_from_rna5_inherit.cpp | 2 +- .../rna15_implicit_conversion_from_dna15_inherit.cpp | 2 +- .../nucleotide/rna4_implicit_conversion_from_dna4_inherit.cpp | 2 +- .../nucleotide/rna5_implicit_conversion_from_dna5_inherit.cpp | 2 +- test/unit/alphabet/semi_alphabet_test_template.hpp | 2 +- test/unit/std/concept/object_test.cpp | 2 +- 36 files changed, 35 insertions(+), 36 deletions(-) diff --git a/include/seqan3/alignment/configuration/align_config_output.hpp b/include/seqan3/alignment/configuration/align_config_output.hpp index 94db194084..dfeb25aca8 100644 --- a/include/seqan3/alignment/configuration/align_config_output.hpp +++ b/include/seqan3/alignment/configuration/align_config_output.hpp @@ -15,7 +15,7 @@ #include #include #include -#include +#include namespace seqan3::align_cfg { diff --git a/include/seqan3/alignment/configuration/align_config_score_type.hpp b/include/seqan3/alignment/configuration/align_config_score_type.hpp index b1478c15fd..22fbdb5171 100644 --- a/include/seqan3/alignment/configuration/align_config_score_type.hpp +++ b/include/seqan3/alignment/configuration/align_config_score_type.hpp @@ -14,7 +14,7 @@ #include #include -#include +#include namespace seqan3::align_cfg { diff --git a/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp b/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp index 37bb6b8155..39079b074b 100644 --- a/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp +++ b/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp @@ -18,7 +18,7 @@ #include #include -#include +#include #include #include diff --git a/include/seqan3/alignment/matrix/detail/alignment_optimum.hpp b/include/seqan3/alignment/matrix/detail/alignment_optimum.hpp index 7d59b5f8d9..4993a11423 100644 --- a/include/seqan3/alignment/matrix/detail/alignment_optimum.hpp +++ b/include/seqan3/alignment/matrix/detail/alignment_optimum.hpp @@ -17,7 +17,7 @@ #include #include -#include +#include #include #include #include diff --git a/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp b/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp index cfbd077bd5..5c726a93d5 100644 --- a/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp +++ b/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp @@ -19,7 +19,7 @@ #include #include #include -#include +#include #include namespace seqan3::detail diff --git a/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp b/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp index 08728d154e..692ac456d8 100644 --- a/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp +++ b/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp @@ -17,7 +17,7 @@ #include #include -#include +#include #include namespace seqan3::detail diff --git a/include/seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp b/include/seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp index 788669e588..4c28255d80 100644 --- a/include/seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp +++ b/include/seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp @@ -12,7 +12,7 @@ #pragma once -#include +#include #include namespace seqan3::detail diff --git a/include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp b/include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp index 839df4300f..3a9cf983b5 100644 --- a/include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp +++ b/include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp @@ -17,7 +17,7 @@ #include #include #include -#include +#include #include namespace seqan3::detail diff --git a/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp b/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp index b6460941a8..2e24be9f01 100644 --- a/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp +++ b/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp @@ -16,7 +16,7 @@ #include #include -#include +#include #include #include diff --git a/include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp b/include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp index d079364737..a423d3dfd5 100644 --- a/include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp +++ b/include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp @@ -17,7 +17,7 @@ #include #include -#include +#include #include #include #include diff --git a/include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp b/include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp index 378a2530b4..c75d26af78 100644 --- a/include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp +++ b/include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp @@ -21,7 +21,7 @@ #include #include #include -#include +#include #include #include #include diff --git a/include/seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp b/include/seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp index a460da1230..37a4fec06f 100644 --- a/include/seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp +++ b/include/seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp @@ -13,7 +13,7 @@ #pragma once #include -#include +#include #include namespace seqan3::detail diff --git a/include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp b/include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp index c8980ef35e..ce64703ee2 100644 --- a/include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp +++ b/include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp @@ -15,7 +15,7 @@ #include #include #include -#include +#include namespace seqan3::detail { diff --git a/include/seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp b/include/seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp index f8aaa07b98..64a5cc138c 100644 --- a/include/seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp +++ b/include/seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp @@ -20,7 +20,7 @@ #include #include #include -#include +#include #include #include #include diff --git a/include/seqan3/alignment/scoring/scoring_scheme_base.hpp b/include/seqan3/alignment/scoring/scoring_scheme_base.hpp index ebe2dc5d1a..a5d2c281dd 100644 --- a/include/seqan3/alignment/scoring/scoring_scheme_base.hpp +++ b/include/seqan3/alignment/scoring/scoring_scheme_base.hpp @@ -18,7 +18,7 @@ #include #include #include -#include +#include #if SEQAN3_WITH_CEREAL #include diff --git a/include/seqan3/alphabet/composite/alphabet_tuple_base.hpp b/include/seqan3/alphabet/composite/alphabet_tuple_base.hpp index 31fac8d9c6..44713086bf 100644 --- a/include/seqan3/alphabet/composite/alphabet_tuple_base.hpp +++ b/include/seqan3/alphabet/composite/alphabet_tuple_base.hpp @@ -20,7 +20,6 @@ #include #include #include -#include #include #include #include diff --git a/include/seqan3/alphabet/concept.hpp b/include/seqan3/alphabet/concept.hpp index 9caf796ebe..5f2d6605a4 100644 --- a/include/seqan3/alphabet/concept.hpp +++ b/include/seqan3/alphabet/concept.hpp @@ -17,7 +17,7 @@ #include #include #include -#include +#include #include #include diff --git a/include/seqan3/alphabet/detail/alphabet_proxy.hpp b/include/seqan3/alphabet/detail/alphabet_proxy.hpp index 775c0bc391..a08c0f40b9 100644 --- a/include/seqan3/alphabet/detail/alphabet_proxy.hpp +++ b/include/seqan3/alphabet/detail/alphabet_proxy.hpp @@ -15,10 +15,11 @@ #include #include +#include #include #include #include -#include +#include #include namespace seqan3 diff --git a/include/seqan3/argument_parser/validators.hpp b/include/seqan3/argument_parser/validators.hpp index 45bc16d013..92e2ab9e70 100644 --- a/include/seqan3/argument_parser/validators.hpp +++ b/include/seqan3/argument_parser/validators.hpp @@ -25,7 +25,7 @@ #include #include #include -#include +#include #include #include #include diff --git a/include/seqan3/core/concept/all.hpp b/include/seqan3/core/concept/all.hpp index 57ca046aca..6f5d03f1db 100644 --- a/include/seqan3/core/concept/all.hpp +++ b/include/seqan3/core/concept/all.hpp @@ -13,7 +13,7 @@ #pragma once #include -#include +#include #include /*!\defgroup core_concept Concept diff --git a/include/seqan3/io/detail/misc_input.hpp b/include/seqan3/io/detail/misc_input.hpp index c3a09cbcd2..667793e985 100644 --- a/include/seqan3/io/detail/misc_input.hpp +++ b/include/seqan3/io/detail/misc_input.hpp @@ -31,7 +31,7 @@ #endif #include #include -#include +#include namespace seqan3::detail { diff --git a/include/seqan3/io/detail/misc_output.hpp b/include/seqan3/io/detail/misc_output.hpp index 1610d65aeb..5a2e61731d 100644 --- a/include/seqan3/io/detail/misc_output.hpp +++ b/include/seqan3/io/detail/misc_output.hpp @@ -26,7 +26,7 @@ #include #endif #include -#include +#include namespace seqan3::detail { diff --git a/include/seqan3/io/sam_file/sam_tag_dictionary.hpp b/include/seqan3/io/sam_file/sam_tag_dictionary.hpp index 919dbeca75..f32744b707 100644 --- a/include/seqan3/io/sam_file/sam_tag_dictionary.hpp +++ b/include/seqan3/io/sam_file/sam_tag_dictionary.hpp @@ -18,7 +18,6 @@ #include #include -#include #include namespace seqan3::detail diff --git a/include/seqan3/search/configuration/max_error_common.hpp b/include/seqan3/search/configuration/max_error_common.hpp index a705ae0756..8fb49a8784 100644 --- a/include/seqan3/search/configuration/max_error_common.hpp +++ b/include/seqan3/search/configuration/max_error_common.hpp @@ -16,7 +16,7 @@ #include #include -#include +#include namespace seqan3::search_cfg { diff --git a/include/seqan3/utility/char_operations/transform.hpp b/include/seqan3/utility/char_operations/transform.hpp index 013e920029..ca2cb0a6aa 100644 --- a/include/seqan3/utility/char_operations/transform.hpp +++ b/include/seqan3/utility/char_operations/transform.hpp @@ -14,7 +14,7 @@ #include -#include +#include #include namespace seqan3::detail diff --git a/include/seqan3/utility/simd/views/iota_simd.hpp b/include/seqan3/utility/simd/views/iota_simd.hpp index 4ba261a44a..4b5fe1940c 100644 --- a/include/seqan3/utility/simd/views/iota_simd.hpp +++ b/include/seqan3/utility/simd/views/iota_simd.hpp @@ -14,7 +14,7 @@ #include -#include +#include #include #include #include diff --git a/include/seqan3/utility/views/convert.hpp b/include/seqan3/utility/views/convert.hpp index 6406cc2aab..1c8a74bb1e 100644 --- a/include/seqan3/utility/views/convert.hpp +++ b/include/seqan3/utility/views/convert.hpp @@ -15,7 +15,7 @@ #include #include -#include +#include namespace seqan3::views { diff --git a/test/snippet/alphabet/nucleotide/@target_alphabet@_implicit_conversion_from_@source_alphabet@_inherit.cpp.in b/test/snippet/alphabet/nucleotide/@target_alphabet@_implicit_conversion_from_@source_alphabet@_inherit.cpp.in index e4148bc234..92fd6cac48 100644 --- a/test/snippet/alphabet/nucleotide/@target_alphabet@_implicit_conversion_from_@source_alphabet@_inherit.cpp.in +++ b/test/snippet/alphabet/nucleotide/@target_alphabet@_implicit_conversion_from_@source_alphabet@_inherit.cpp.in @@ -21,7 +21,7 @@ int main() } //![main] -#include +#include static_assert(seqan3::implicitly_convertible_to); static_assert(!seqan3::implicitly_convertible_to); diff --git a/test/snippet/alphabet/nucleotide/dna15_implicit_conversion_from_rna15_inherit.cpp b/test/snippet/alphabet/nucleotide/dna15_implicit_conversion_from_rna15_inherit.cpp index b825cf4386..342358e629 100644 --- a/test/snippet/alphabet/nucleotide/dna15_implicit_conversion_from_rna15_inherit.cpp +++ b/test/snippet/alphabet/nucleotide/dna15_implicit_conversion_from_rna15_inherit.cpp @@ -21,7 +21,7 @@ int main() } //![main] -#include +#include static_assert(seqan3::implicitly_convertible_to); static_assert(!seqan3::implicitly_convertible_to); diff --git a/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_inherit.cpp b/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_inherit.cpp index 0ee801814f..b2bc4af6f0 100644 --- a/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_inherit.cpp +++ b/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_inherit.cpp @@ -21,7 +21,7 @@ int main() } //![main] -#include +#include static_assert(seqan3::implicitly_convertible_to); static_assert(!seqan3::implicitly_convertible_to); diff --git a/test/snippet/alphabet/nucleotide/dna5_implicit_conversion_from_rna5_inherit.cpp b/test/snippet/alphabet/nucleotide/dna5_implicit_conversion_from_rna5_inherit.cpp index 23aa292185..6c5f3c68aa 100644 --- a/test/snippet/alphabet/nucleotide/dna5_implicit_conversion_from_rna5_inherit.cpp +++ b/test/snippet/alphabet/nucleotide/dna5_implicit_conversion_from_rna5_inherit.cpp @@ -21,7 +21,7 @@ int main() } //![main] -#include +#include static_assert(seqan3::implicitly_convertible_to); static_assert(!seqan3::implicitly_convertible_to); diff --git a/test/snippet/alphabet/nucleotide/rna15_implicit_conversion_from_dna15_inherit.cpp b/test/snippet/alphabet/nucleotide/rna15_implicit_conversion_from_dna15_inherit.cpp index d1d8bf23cc..9267fb292c 100644 --- a/test/snippet/alphabet/nucleotide/rna15_implicit_conversion_from_dna15_inherit.cpp +++ b/test/snippet/alphabet/nucleotide/rna15_implicit_conversion_from_dna15_inherit.cpp @@ -21,7 +21,7 @@ int main() } //![main] -#include +#include static_assert(seqan3::implicitly_convertible_to); static_assert(!seqan3::implicitly_convertible_to); diff --git a/test/snippet/alphabet/nucleotide/rna4_implicit_conversion_from_dna4_inherit.cpp b/test/snippet/alphabet/nucleotide/rna4_implicit_conversion_from_dna4_inherit.cpp index 2a5ccd0454..aca2dfb162 100644 --- a/test/snippet/alphabet/nucleotide/rna4_implicit_conversion_from_dna4_inherit.cpp +++ b/test/snippet/alphabet/nucleotide/rna4_implicit_conversion_from_dna4_inherit.cpp @@ -21,7 +21,7 @@ int main() } //![main] -#include +#include static_assert(seqan3::implicitly_convertible_to); static_assert(!seqan3::implicitly_convertible_to); diff --git a/test/snippet/alphabet/nucleotide/rna5_implicit_conversion_from_dna5_inherit.cpp b/test/snippet/alphabet/nucleotide/rna5_implicit_conversion_from_dna5_inherit.cpp index 6f3d6e2dfd..fc8e901f42 100644 --- a/test/snippet/alphabet/nucleotide/rna5_implicit_conversion_from_dna5_inherit.cpp +++ b/test/snippet/alphabet/nucleotide/rna5_implicit_conversion_from_dna5_inherit.cpp @@ -21,7 +21,7 @@ int main() } //![main] -#include +#include static_assert(seqan3::implicitly_convertible_to); static_assert(!seqan3::implicitly_convertible_to); diff --git a/test/unit/alphabet/semi_alphabet_test_template.hpp b/test/unit/alphabet/semi_alphabet_test_template.hpp index 52dea639b9..245026df3c 100644 --- a/test/unit/alphabet/semi_alphabet_test_template.hpp +++ b/test/unit/alphabet/semi_alphabet_test_template.hpp @@ -11,7 +11,7 @@ #include #include #include -#include +#include template using semi_alphabet_test = ::testing::Test; diff --git a/test/unit/std/concept/object_test.cpp b/test/unit/std/concept/object_test.cpp index 33ba68ff15..675801aa58 100644 --- a/test/unit/std/concept/object_test.cpp +++ b/test/unit/std/concept/object_test.cpp @@ -10,7 +10,7 @@ #include #include -#include +#include #include "auxiliary.hpp"