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Merge pull request #2265 from joergi-w/refactor/type_traits
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Move the type traits submodule to utility
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@eseiler
eseiler authored Nov 23, 2020
2 parents b6e8e19 + f8cafc2 commit 9dbfcb4
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Showing 158 changed files with 2,223 additions and 1,999 deletions.
2 changes: 1 addition & 1 deletion include/seqan3/alignment/configuration/align_config_scoring_scheme.hpp
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#include <seqan3/std/concepts>

#include <seqan3/alignment/configuration/detail.hpp>
#include <seqan3/core/type_traits/basic.hpp>
#include <seqan3/alignment/scoring/scoring_scheme_concept.hpp>
#include <seqan3/core/algorithm/pipeable_config_element.hpp>
#include <seqan3/utility/type_traits/basic.hpp>

namespace seqan3::align_cfg
{
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6 changes: 3 additions & 3 deletions include/seqan3/alignment/matrix/alignment_coordinate.hpp
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#pragma once

#include <seqan3/std/concepts>
#include <seqan3/std/iterator>
#include <type_traits>

#include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
#include <seqan3/core/detail/debug_stream_tuple.hpp>
#include <seqan3/core/detail/debug_stream_type.hpp>
#include <seqan3/core/detail/strong_type.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/std/concepts>
#include <seqan3/std/iterator>
#include <seqan3/core/detail/template_inspection.hpp>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/alignment_optimum.hpp
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#include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
#include <seqan3/core/concept/core_language.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/core/simd/concept.hpp>
#include <seqan3/core/simd/simd_algorithm.hpp>
#include <seqan3/core/simd/simd_traits.hpp>
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/debug_matrix.hpp
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#include <seqan3/core/detail/debug_stream_range.hpp>
#include <seqan3/core/detail/debug_stream_type.hpp>
#include <seqan3/core/detail/debug_stream_optional.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/core/detail/template_inspection.hpp>

namespace seqan3::detail
{
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9 changes: 5 additions & 4 deletions include/seqan3/alignment/matrix/detail/aligned_sequence_builder.hpp
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#pragma once

#include <seqan3/std/concepts>
#include <seqan3/std/ranges>
#include <type_traits>
#include <vector>

#include <seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp>
#include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
#include <seqan3/alignment/matrix/trace_directions.hpp>
#include <seqan3/alphabet/gap/gapped.hpp>
#include <seqan3/core/type_traits/concept.hpp>
#include <seqan3/core/type_traits/lazy.hpp>
#include <seqan3/core/detail/is_class_template_declarable.hpp>
#include <seqan3/range/decorator/gap_decorator.hpp>
#include <seqan3/range/views/convert.hpp>
#include <seqan3/range/views/slice.hpp>
#include <seqan3/range/views/type_reduce.hpp>
#include <seqan3/range/views/to.hpp>
#include <seqan3/std/concepts>
#include <seqan3/std/ranges>
#include <seqan3/utility/type_traits/concept.hpp>
#include <seqan3/utility/type_traits/lazy_conditional.hpp>

namespace seqan3::detail
{
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5 changes: 3 additions & 2 deletions include/seqan3/alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp
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#pragma once

#include <seqan3/core/type_traits/basic.hpp>
#include <seqan3/core/type_traits/range.hpp>
#include <seqan3/std/iterator>
#include <seqan3/std/ranges>
#include <seqan3/std/span>

#include <seqan3/core/range/type_traits.hpp>
#include <seqan3/utility/type_traits/basic.hpp>

namespace seqan3::detail
{

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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/alignment_trace_matrix_proxy.hpp
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#include <seqan3/alignment/matrix/trace_directions.hpp>
#include <seqan3/core/simd/concept.hpp>
#include <seqan3/core/type_traits/basic.hpp>
#include <seqan3/utility/type_traits/basic.hpp>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp
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#include <seqan3/alignment/matrix/detail/affine_cell_proxy.hpp>
#include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
#include <seqan3/core/concept/core_language.hpp>
#include <seqan3/core/type_traits/range.hpp>
#include <seqan3/core/range/type_traits.hpp>
#include <seqan3/range/views/zip.hpp>

namespace seqan3::detail
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4 changes: 2 additions & 2 deletions include/seqan3/alignment/matrix/detail/coordinate_matrix.hpp
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#include <seqan3/std/ranges>

#include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/core/simd/concept.hpp>
#include <seqan3/core/simd/simd_algorithm.hpp>
#include <seqan3/core/simd/simd_traits.hpp>
#include <seqan3/core/simd/view_iota_simd.hpp>
#include <seqan3/core/type_traits/lazy.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/range/container/aligned_allocator.hpp>
#include <seqan3/utility/type_traits/lazy_conditional.hpp>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp
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#include <seqan3/alignment/matrix/detail/two_dimensional_matrix.hpp>
#include <seqan3/alignment/matrix/trace_directions.hpp>
#include <seqan3/core/concept/core_language.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/range/container/aligned_allocator.hpp>
#include <seqan3/range/views/repeat_n.hpp>
#include <seqan3/range/views/zip.hpp>
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10 changes: 5 additions & 5 deletions include/seqan3/alignment/matrix/detail/two_dimensional_matrix.hpp
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#pragma once

#include <seqan3/std/algorithm>
#include <memory>
#include <seqan3/std/ranges>
#include <vector>

#include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
#include <seqan3/alignment/matrix/detail/two_dimensional_matrix_iterator_base.hpp>
#include <seqan3/core/type_traits/deferred_crtp_base.hpp>
#include <seqan3/core/type_traits/range.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/std/algorithm>
#include <seqan3/std/ranges>
#include <seqan3/core/detail/deferred_crtp_base.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/core/range/type_traits.hpp>

namespace seqan3::detail
{
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8 changes: 4 additions & 4 deletions include/seqan3/alignment/matrix/detail/two_dimensional_matrix_iterator_base.hpp
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#pragma once

#include <seqan3/std/concepts>
#include <seqan3/std/ranges>
#include <type_traits>

#include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
#include <seqan3/core/type_traits/basic.hpp>
#include <seqan3/core/type_traits/iterator.hpp>
#include <seqan3/std/concepts>
#include <seqan3/std/ranges>
#include <seqan3/core/detail/iterator_traits.hpp>
#include <seqan3/utility/type_traits/basic.hpp>

namespace seqan3::detail
{
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6 changes: 3 additions & 3 deletions include/seqan3/alignment/pairwise/align_pairwise.hpp
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#pragma once

#include <seqan3/std/concepts>
#include <functional>
#include <iostream>
#include <seqan3/std/ranges>
#include <tuple>
#include <type_traits>

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#include <seqan3/core/parallel/execution.hpp>
#include <seqan3/core/simd/simd_traits.hpp>
#include <seqan3/core/simd/simd.hpp>
#include <seqan3/core/type_traits/basic.hpp>
#include <seqan3/range/views/persist.hpp>
#include <seqan3/std/concepts>
#include <seqan3/std/ranges>
#include <seqan3/utility/type_traits/basic.hpp>

namespace seqan3
{
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10 changes: 5 additions & 5 deletions include/seqan3/alignment/pairwise/align_result_selector.hpp
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#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/alphabet/gap/gapped.hpp>
#include <seqan3/core/algorithm/configuration.hpp>
#include <seqan3/core/type_traits/basic.hpp>
#include <seqan3/core/type_traits/lazy.hpp>
#include <seqan3/core/type_traits/range.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/core/type_traits/transformation_trait_or.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/core/range/type_traits.hpp>
#include <seqan3/range/decorator/gap_decorator.hpp>
#include <seqan3/range/views/type_reduce.hpp>
#include <seqan3/utility/type_traits/basic.hpp>
#include <seqan3/utility/type_traits/detail/transformation_trait_or.hpp>
#include <seqan3/utility/type_traits/lazy_conditional.hpp>

namespace seqan3::detail
{
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9 changes: 4 additions & 5 deletions include/seqan3/alignment/pairwise/alignment_algorithm.hpp
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#pragma once

#include <seqan3/std/iterator>
#include <memory>
#include <optional>
#include <seqan3/std/ranges>
#include <type_traits>

#include <seqan3/alignment/configuration/align_config_band.hpp>
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#include <seqan3/alignment/pairwise/detail/concept.hpp>
#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/alignment/matrix/detail/aligned_sequence_builder.hpp>

#include <seqan3/core/detail/deferred_crtp_base.hpp>
#include <seqan3/core/detail/empty_type.hpp>
#include <seqan3/core/simd/concept.hpp>
#include <seqan3/core/simd/simd.hpp>
#include <seqan3/core/simd/simd_traits.hpp>
#include <seqan3/core/simd/view_to_simd.hpp>
#include <seqan3/core/type_traits/deferred_crtp_base.hpp>
#include <seqan3/core/type_traits/function.hpp>
#include <seqan3/range/container/aligned_allocator.hpp>
#include <seqan3/range/views/drop.hpp>
#include <seqan3/range/views/get.hpp>
#include <seqan3/range/views/take.hpp>
#include <seqan3/std/iterator>
#include <seqan3/std/ranges>
#include <seqan3/utility/type_traits/function_traits.hpp>

namespace seqan3::detail
{
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6 changes: 3 additions & 3 deletions include/seqan3/alignment/pairwise/alignment_configurator.hpp
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#include <seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp>
#include <seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp>
#include <seqan3/core/concept/tuple.hpp>
#include <seqan3/core/detail/deferred_crtp_base.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/core/simd/simd.hpp>
#include <seqan3/core/type_traits/deferred_crtp_base.hpp>
#include <seqan3/core/type_traits/lazy.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/range/views/type_reduce.hpp>
#include <seqan3/range/views/zip.hpp>
#include <seqan3/utility/type_traits/lazy_conditional.hpp>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/alignment_result.hpp
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#include <seqan3/core/algorithm/configuration.hpp>
#include <seqan3/core/detail/debug_stream_type.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/core/detail/template_inspection.hpp>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/detail/policy_affine_gap_recursion.hpp
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#include <seqan3/alignment/configuration/align_config_gap_cost_affine.hpp>
#include <seqan3/alignment/matrix/detail/affine_cell_proxy.hpp>
#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/core/simd/concept.hpp>
#include <seqan3/core/simd/simd_algorithm.hpp>

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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/detail/policy_alignment_matrix.hpp
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#include <seqan3/alignment/matrix/detail/coordinate_matrix.hpp>
#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/core/algorithm/configuration.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/core/detail/template_inspection.hpp>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/detail/policy_alignment_result_builder.hpp
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#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/core/algorithm/configuration.hpp>
#include <seqan3/core/detail/empty_type.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/core/detail/template_inspection.hpp>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/detail/policy_optimum_tracker.hpp
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#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/core/algorithm/configuration.hpp>
#include <seqan3/core/concept/tuple.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/core/detail/template_inspection.hpp>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/detail/policy_optimum_tracker_simd.hpp
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#include <seqan3/core/simd/simd.hpp>
#include <seqan3/core/simd/simd_algorithm.hpp>
#include <seqan3/core/simd/simd_traits.hpp>
#include <seqan3/core/type_traits/lazy.hpp>
#include <seqan3/range/views/zip.hpp>
#include <seqan3/utility/type_traits/lazy_conditional.hpp>

namespace seqan3::detail
{
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8 changes: 4 additions & 4 deletions include/seqan3/alignment/pairwise/detail/type_traits.hpp
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Expand Up @@ -12,6 +12,7 @@

#pragma once

#include <seqan3/std/ranges>
#include <type_traits>

#include <seqan3/alignment/configuration/align_config_result_type.hpp>
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#include <seqan3/core/algorithm/configuration.hpp>
#include <seqan3/core/bit_manipulation.hpp>
#include <seqan3/core/detail/empty_type.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/core/simd/simd_traits.hpp>
#include <seqan3/core/simd/simd.hpp>
#include <seqan3/core/type_traits/function.hpp>
#include <seqan3/core/type_traits/lazy.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/range/views/chunk.hpp>
#include <seqan3/range/views/zip.hpp>
#include <seqan3/std/ranges>
#include <seqan3/utility/type_traits/function_traits.hpp>
#include <seqan3/utility/type_traits/lazy_conditional.hpp>

namespace seqan3::detail
{
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7 changes: 4 additions & 3 deletions include/seqan3/alignment/pairwise/edit_distance_fwd.hpp
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#pragma once

#include <seqan3/std/concepts>
#include <seqan3/std/ranges>

#include <seqan3/alignment/configuration/align_config_min_score.hpp>
#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/alignment/pairwise/align_result_selector.hpp>
#include <seqan3/core/bit_manipulation.hpp>
#include <seqan3/core/detail/deferred_crtp_base.hpp>
#include <seqan3/core/platform.hpp>
#include <seqan3/core/type_traits/deferred_crtp_base.hpp>
#include <seqan3/std/concepts>
#include <seqan3/std/ranges>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/policy/alignment_matrix_policy.hpp
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Expand Up @@ -17,9 +17,9 @@

#include <seqan3/alignment/configuration/align_config_band.hpp>
#include <seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp>
#include <seqan3/core/type_traits/basic.hpp>
#include <seqan3/range/views/slice.hpp>
#include <seqan3/range/views/zip.hpp>
#include <seqan3/utility/type_traits/basic.hpp>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/policy/scoring_scheme_policy.hpp
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Expand Up @@ -14,7 +14,7 @@

#include <seqan3/alphabet/concept.hpp>
#include <seqan3/core/simd/concept.hpp>
#include <seqan3/core/type_traits/basic.hpp>
#include <seqan3/utility/type_traits/basic.hpp>

namespace seqan3::detail
{
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2 changes: 1 addition & 1 deletion include/seqan3/alphabet/aminoacid/concept.hpp
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Expand Up @@ -16,7 +16,7 @@
#include <type_traits>

#include <seqan3/alphabet/concept.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/core/detail/template_inspection.hpp>

// ============================================================================
// aminoacid_empty_base
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