[FIX] adjust all all.hpp files

seqan · Nov 1, 2021 · 2c80957 · 2c80957
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diff --git a/include/seqan3/alignment/aligned_sequence/all.hpp b/include/seqan3/alignment/aligned_sequence/all.hpp
@@ -10,13 +10,13 @@
  * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>
  */
 
-#pragma once
-
-#include <seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp>
-#include <seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp>
-
 /*!\defgroup alignment_aligned_sequence Aligned Sequence
  * \ingroup alignment
  * \brief Provides seqan3::aligned_sequence, as well as various ranges that model it.
  * \see alignment
  */
+
+#pragma once
+
+#include <seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp>
+#include <seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp>
diff --git a/include/seqan3/alignment/all.hpp b/include/seqan3/alignment/all.hpp
@@ -24,11 +24,13 @@
  * is described in \ref alignment_pairwise.
  */
 
- #pragma once
+#pragma once
 
- #include <seqan3/alignment/aligned_sequence/all.hpp>
- #include <seqan3/alignment/configuration/all.hpp>
- #include <seqan3/alignment/exception.hpp>
- #include <seqan3/alignment/matrix/all.hpp>
- #include <seqan3/alignment/pairwise/all.hpp>
- #include <seqan3/alignment/scoring/all.hpp>
+#include <seqan3/alignment/aligned_sequence/all.hpp>
+#include <seqan3/alignment/configuration/all.hpp>
+#include <seqan3/alignment/decorator/all.hpp>
+#include <seqan3/alignment/detail/pairwise_alignment_concept.hpp>
+#include <seqan3/alignment/exception.hpp>
+#include <seqan3/alignment/matrix/all.hpp>
+#include <seqan3/alignment/pairwise/all.hpp>
+#include <seqan3/alignment/scoring/all.hpp>
diff --git a/include/seqan3/alignment/configuration/all.hpp b/include/seqan3/alignment/configuration/all.hpp
@@ -10,6 +10,22 @@
  * \author Rene Rahn <rene.rahn AT fu-berlin.de>
  */
 
+/*!\namespace seqan3::align_cfg
+ * \brief A special sub namespace for the alignment configurations.
+ */
+
+ /*!\if DEV
+  * \namespace seqan3::align_cfg::detail
+  * \copydoc seqan3::detail
+  * \endif
+  */
+
+/*!\defgroup alignment_configuration Configuration
+ * \ingroup alignment
+ * \brief Provides configuration elements for the pairwise alignment configuration.
+ * \see alignment
+ */
+
 #pragma once
 
 #include <seqan3/alignment/configuration/align_config_band.hpp>
@@ -26,19 +42,3 @@
 #include <seqan3/alignment/configuration/align_config_scoring_scheme.hpp>
 #include <seqan3/alignment/configuration/align_config_vectorised.hpp>
 #include <seqan3/alignment/configuration/detail.hpp>
-
-/*!\namespace seqan3::align_cfg
- * \brief A special sub namespace for the alignment configurations.
- */
-
- /*!\if DEV
-  * \namespace seqan3::align_cfg::detail
-  * \copydoc seqan3::detail
-  * \endif
-  */
-
-/*!\defgroup alignment_configuration Configuration
- * \ingroup alignment
- * \brief Provides configuration elements for the pairwise alignment configuration.
- * \see alignment
- */
diff --git a/include/seqan3/alignment/decorator/all.hpp b/include/seqan3/alignment/decorator/all.hpp
@@ -10,12 +10,12 @@
  * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>
  */
 
-#pragma once
-
-#include <seqan3/alignment/decorator/gap_decorator.hpp>
-
 /*!\defgroup alignment_decorator Decorator
  * \brief The decorator submodule contains special SeqAn decorators.
  * \ingroup alignment
  * \see alignment
  */
+
+#pragma once
+
+#include <seqan3/alignment/decorator/gap_decorator.hpp>
diff --git a/include/seqan3/alignment/matrix/all.hpp b/include/seqan3/alignment/matrix/all.hpp
@@ -10,8 +10,6 @@
  * \author Marcel Ehrhardt <marcel.ehrhardt AT fu-berlin.de>
  */
 
-#pragma once
-
 //!\cond DEV
 
 /*!\defgroup alignment_matrix Matrix
@@ -21,4 +19,6 @@
  */
 //!\endcond
 
-#include <seqan3/core/platform.hpp> // make header test happy
+#pragma once
+
+#include <seqan3/alignment/matrix/detail/all.hpp>
diff --git a/include/seqan3/alignment/pairwise/all.hpp b/include/seqan3/alignment/pairwise/all.hpp
@@ -10,16 +10,6 @@
  * \author Rene Rahn <rene.rahn AT fu-berlin.de>
  */
 
-#pragma once
-
-#include <seqan3/alignment/pairwise/align_pairwise.hpp>
-#include <seqan3/alignment/pairwise/align_result_selector.hpp>
-#include <seqan3/alignment/pairwise/alignment_algorithm.hpp>
-#include <seqan3/alignment/pairwise/alignment_configurator.hpp>
-#include <seqan3/alignment/pairwise/alignment_result.hpp>
-#include <seqan3/alignment/pairwise/edit_distance_unbanded.hpp>
-#include <seqan3/alignment/pairwise/policy/all.hpp>
-
 /*!\defgroup alignment_pairwise Pairwise
  * \ingroup alignment
  * \brief Provides the algorithmic components for the computation of pairwise alignments.
@@ -272,3 +262,29 @@
  *  - [lecture script - pairwise alignment](https://www.mi.fu-berlin.de/en/inf/groups/abi/teaching/lectures/lectures_past/WS0910/V___Algorithmen_und_Datenstrukturen/scripts/alignment.pdf)\n
  *  - alignment
  */
+
+#pragma once
+
+#include <seqan3/alignment/pairwise/align_pairwise.hpp>
+#include <seqan3/alignment/pairwise/align_result_selector.hpp>
+#include <seqan3/alignment/pairwise/alignment_algorithm.hpp>
+#include <seqan3/alignment/pairwise/alignment_configurator.hpp>
+#include <seqan3/alignment/pairwise/alignment_result.hpp>
+#include <seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp>
+#include <seqan3/alignment/pairwise/detail/concept.hpp>
+#include <seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm.hpp>
+#include <seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm_banded.hpp>
+#include <seqan3/alignment/pairwise/detail/policy_affine_gap_recursion.hpp>
+#include <seqan3/alignment/pairwise/detail/policy_affine_gap_recursion_banded.hpp>
+#include <seqan3/alignment/pairwise/detail/policy_affine_gap_with_trace_recursion.hpp>
+#include <seqan3/alignment/pairwise/detail/policy_affine_gap_with_trace_recursion_banded.hpp>
+#include <seqan3/alignment/pairwise/detail/policy_alignment_matrix.hpp>
+#include <seqan3/alignment/pairwise/detail/policy_alignment_result_builder.hpp>
+#include <seqan3/alignment/pairwise/detail/policy_optimum_tracker.hpp>
+#include <seqan3/alignment/pairwise/detail/policy_optimum_tracker_simd.hpp>
+#include <seqan3/alignment/pairwise/detail/policy_scoring_scheme.hpp>
+#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
+#include <seqan3/alignment/pairwise/edit_distance_algorithm.hpp>
+#include <seqan3/alignment/pairwise/edit_distance_fwd.hpp>
+#include <seqan3/alignment/pairwise/edit_distance_unbanded.hpp>
+#include <seqan3/alignment/pairwise/policy/all.hpp>
diff --git a/include/seqan3/alignment/pairwise/policy/all.hpp b/include/seqan3/alignment/pairwise/policy/all.hpp
@@ -12,16 +12,6 @@
  */
 //!\endcond
 
-#pragma once
-
-#include <seqan3/alignment/pairwise/policy/affine_gap_init_policy.hpp>
-#include <seqan3/alignment/pairwise/policy/affine_gap_policy.hpp>
-#include <seqan3/alignment/pairwise/policy/alignment_matrix_policy.hpp>
-#include <seqan3/alignment/pairwise/policy/find_optimum_policy.hpp>
-#include <seqan3/alignment/pairwise/policy/scoring_scheme_policy.hpp>
-#include <seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp>
-#include <seqan3/alignment/pairwise/policy/simd_find_optimum_policy.hpp>
-
 //!\cond DEV
 /*!\defgroup alignment_pairwise_policy Alignment policies
  * \ingroup alignment_pairwise
@@ -134,3 +124,13 @@
  *  - seqan3::detail::find_optimum_policy
  */
 //!\endcond
+
+#pragma once
+
+#include <seqan3/alignment/pairwise/policy/affine_gap_init_policy.hpp>
+#include <seqan3/alignment/pairwise/policy/affine_gap_policy.hpp>
+#include <seqan3/alignment/pairwise/policy/alignment_matrix_policy.hpp>
+#include <seqan3/alignment/pairwise/policy/find_optimum_policy.hpp>
+#include <seqan3/alignment/pairwise/policy/scoring_scheme_policy.hpp>
+#include <seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp>
+#include <seqan3/alignment/pairwise/policy/simd_find_optimum_policy.hpp>
diff --git a/include/seqan3/alignment/scoring/all.hpp b/include/seqan3/alignment/scoring/all.hpp
@@ -10,15 +10,17 @@
  * \author Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>
  */
 
-#pragma once
-
 /*!\defgroup alignment_scoring Scoring
  * \brief Provides the data structures used for scoring alphabets and sequences.
  * \ingroup alignment
  * \see alignment
  */
 
+#pragma once
+
 #include <seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp>
+#include <seqan3/alignment/scoring/detail/simd_match_mismatch_scoring_scheme.hpp>
+#include <seqan3/alignment/scoring/detail/simd_matrix_scoring_scheme.hpp>
 #include <seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp>
 #include <seqan3/alignment/scoring/scoring_scheme_base.hpp>
 #include <seqan3/alignment/scoring/scoring_scheme_concept.hpp>
diff --git a/include/seqan3/alphabet/adaptation/all.hpp b/include/seqan3/alphabet/adaptation/all.hpp
@@ -10,13 +10,13 @@
  * \brief Meta-header for the \link alphabet_adaptation Alphabet / Adaptation submodule \endlink.
  */
 
-#pragma once
-
-#include <seqan3/alphabet/adaptation/char.hpp>
-#include <seqan3/alphabet/adaptation/uint.hpp>
-
 /*!\defgroup alphabet_adaptation Adaptation
  * \brief Provides alphabet adaptions of some standard char and uint types.
  * \ingroup alphabet
  * \see alphabet
  */
+
+#pragma once
+
+#include <seqan3/alphabet/adaptation/char.hpp>
+#include <seqan3/alphabet/adaptation/uint.hpp>
diff --git a/include/seqan3/alphabet/all.hpp b/include/seqan3/alphabet/all.hpp
@@ -181,11 +181,21 @@
 #pragma once
 
 #include <seqan3/alphabet/adaptation/all.hpp>
+#include <seqan3/alphabet/alphabet_base.hpp>
 #include <seqan3/alphabet/aminoacid/all.hpp>
+#include <seqan3/alphabet/cigar/all.hpp>
 #include <seqan3/alphabet/composite/all.hpp>
 #include <seqan3/alphabet/concept.hpp>
+#include <seqan3/alphabet/container/all.hpp>
+#include <seqan3/alphabet/detail/alphabet_proxy.hpp>
+#include <seqan3/alphabet/detail/convert.hpp>
+#include <seqan3/alphabet/detail/debug_stream_alphabet.hpp>
+#include <seqan3/alphabet/exception.hpp>
 #include <seqan3/alphabet/gap/all.hpp>
+#include <seqan3/alphabet/hash.hpp>
 #include <seqan3/alphabet/mask/all.hpp>
 #include <seqan3/alphabet/nucleotide/all.hpp>
 #include <seqan3/alphabet/quality/all.hpp>
+#include <seqan3/alphabet/range/all.hpp>
 #include <seqan3/alphabet/structure/all.hpp>
+#include <seqan3/alphabet/views/all.hpp>
diff --git a/include/seqan3/alphabet/aminoacid/all.hpp b/include/seqan3/alphabet/aminoacid/all.hpp
@@ -9,16 +9,6 @@
  * \author Sara Hetzel <sara.hetzel AT fu-berlin.de>
  * \brief Meta-header for the \link alphabet_aminoacid Alphabet / Aminoacid submodule \endlink.
  */
-#pragma once
-
-#include <seqan3/alphabet/aminoacid/aa10li.hpp>
-#include <seqan3/alphabet/aminoacid/aa10murphy.hpp>
-#include <seqan3/alphabet/aminoacid/aa20.hpp>
-#include <seqan3/alphabet/aminoacid/aa27.hpp>
-#include <seqan3/alphabet/aminoacid/concept.hpp>
-#include <seqan3/alphabet/aminoacid/translation.hpp>
-#include <seqan3/alphabet/aminoacid/translation_details.hpp>
-#include <seqan3/alphabet/aminoacid/translation_genetic_code.hpp>
 
 /*!\defgroup alphabet_aminoacid Aminoacid
  * \brief Provides the amino acid alphabets and functionality for translation from nucleotide.
@@ -74,3 +64,15 @@
  * no benefits in regard to space consumption (both need 5bits).
  * Use it only when you know you need to interface with other software of formats that only support the canonical set.
  */
+
+#pragma once
+
+#include <seqan3/alphabet/aminoacid/aa10li.hpp>
+#include <seqan3/alphabet/aminoacid/aa10murphy.hpp>
+#include <seqan3/alphabet/aminoacid/aa20.hpp>
+#include <seqan3/alphabet/aminoacid/aa27.hpp>
+#include <seqan3/alphabet/aminoacid/aminoacid_base.hpp>
+#include <seqan3/alphabet/aminoacid/concept.hpp>
+#include <seqan3/alphabet/aminoacid/translation.hpp>
+#include <seqan3/alphabet/aminoacid/translation_details.hpp>
+#include <seqan3/alphabet/aminoacid/translation_genetic_code.hpp>
diff --git a/include/seqan3/alphabet/cigar/all.hpp b/include/seqan3/alphabet/cigar/all.hpp
@@ -10,10 +10,6 @@
  * \brief Meta-header for the \link alphabet_cigar Alphabet / CIGAR submodule \endlink.
  */
 
- #pragma once
-
- #include <seqan3/alphabet/cigar/cigar.hpp>
-
  /*!\defgroup alphabet_cigar CIGAR
   * \brief Provides (semi-)alphabets for representing elements in CIGAR strings.
   * \ingroup alphabet
@@ -34,3 +30,8 @@
   *
   * \copydoc seqan3::doxygen::cigar_operation_table
   */
+
+#pragma once
+
+#include <seqan3/alphabet/cigar/cigar.hpp>
+#include <seqan3/alphabet/cigar/exposition_only/cigar_operation.hpp>
diff --git a/include/seqan3/alphabet/composite/all.hpp b/include/seqan3/alphabet/composite/all.hpp
@@ -9,11 +9,6 @@
  * \author Marcel Ehrhardt <marcel.ehrhardt AT fu-berlin.de>
  * \brief Meta-header for the \link alphabet_composite Alphabet / Composite submodule \endlink.
  */
-#pragma once
-
-#include <seqan3/alphabet/composite/alphabet_tuple_base.hpp>
-#include <seqan3/alphabet/composite/alphabet_variant.hpp>
-#include <seqan3/alphabet/composite/semialphabet_any.hpp>
 
 /*!\defgroup alphabet_composite Composite
  * \brief Provides templates for combining existing alphabets into new alphabet types.
@@ -36,3 +31,10 @@
  * * seqan3::semialphabet_any which type erases other alphabets of the same size and allows again transformation to
  *   alphabets of the same size by copying the rank.
  */
+
+#pragma once
+
+#include <seqan3/alphabet/composite/alphabet_tuple_base.hpp>
+#include <seqan3/alphabet/composite/alphabet_variant.hpp>
+#include <seqan3/alphabet/composite/detail.hpp>
+#include <seqan3/alphabet/composite/semialphabet_any.hpp>
diff --git a/include/seqan3/alphabet/container/all.hpp b/include/seqan3/alphabet/container/all.hpp
@@ -9,13 +9,14 @@
  * \author Marcel Ehrhardt <marcel.ehrhardt AT fu-berlin.de>
  * \brief Meta-header for the \link alphabet_container Alphabet / Container submodule \endlink.
  */
-#pragma once
-
-#include <seqan3/alphabet/container/bitpacked_sequence.hpp>
-#include <seqan3/alphabet/container/concatenated_sequences.hpp>
 
 /*!\defgroup alphabet_container Container
  * \brief Alphabet related container.
  * \ingroup alphabet
  * \see alphabet
  */
+
+#pragma once
+
+#include <seqan3/alphabet/container/bitpacked_sequence.hpp>
+#include <seqan3/alphabet/container/concatenated_sequences.hpp>
diff --git a/include/seqan3/alphabet/gap/all.hpp b/include/seqan3/alphabet/gap/all.hpp
@@ -10,11 +10,6 @@
  * \brief Meta-header for the \link alphabet_gap Alphabet / Gap submodule \endlink.
  */
 
-#pragma once
-
-#include <seqan3/alphabet/gap/gap.hpp>
-#include <seqan3/alphabet/gap/gapped.hpp>
-
 /*!\defgroup alphabet_gap Gap
  * \brief Provides the gap alphabet and functionality to make an alphabet a gapped alphabet.
  * \ingroup alphabet
@@ -32,3 +27,8 @@
  * seqan3::gapped<> template which transforms any other alphabet to be a composite of that alphabet + the gap
  * character.
  */
+
+#pragma once
+
+#include <seqan3/alphabet/gap/gap.hpp>
+#include <seqan3/alphabet/gap/gapped.hpp>
diff --git a/include/seqan3/alphabet/mask/all.hpp b/include/seqan3/alphabet/mask/all.hpp
@@ -11,11 +11,6 @@
  * \author Lydia Buntrock <lydia.buntrock AT fu-berlin.de>
  */
 
-#pragma once
-
-#include <seqan3/alphabet/mask/mask.hpp>
-#include <seqan3/alphabet/mask/masked.hpp>
-
 /*!\defgroup alphabet_mask Mask
  * \brief Provides the mask alphabet and functionality for creating masked composites.
  * \ingroup alphabet
@@ -46,3 +41,8 @@
  * denoted by lowercase characters. Note that larger repeats, such as segmental duplications, large tandem repeats and
  * whole gene duplications are generally not masked.
  */
+
+#pragma once
+
+#include <seqan3/alphabet/mask/mask.hpp>
+#include <seqan3/alphabet/mask/masked.hpp>