API Stability of Alignment Module

[marehr]

• ./alignment/aligned_sequence
  • ./alignment/aligned_sequence/aligned_sequence_concept.hpp
    • aligned_sequence
    • writable_aligned_sequence (TODO: is this really stable or should be marked experimental)
    • insert_gap
    • erase_gap
    • assign_unaligned
  • ./alignment/aligned_sequence/all.hpp
  • ./alignment/aligned_sequence/debug_stream_alignment.hpp
• ./alignment/all.hpp
• ./alignment/band
  • ./alignment/band/all.hpp
  • ./alignment/band/static_band.hpp, [INFRA] Remove algorithm/bound.hpp & alignment/band/static_band.hpp seqan3#2272
• ./alignment/configuration Alignment Configuration and Interface #55
  • ./alignment/configuration/align_config_band.hpp
  • ./alignment/configuration/align_config_debug.hpp
  • ./alignment/configuration/align_config_edit.hpp
  • ./alignment/configuration/align_config_gap_cost_affine.hpp
  • ./alignment/configuration/align_config_method.hpp
  • ./alignment/configuration/align_config_min_score.hpp
  • ./alignment/configuration/align_config_on_result.hpp
  • ./alignment/configuration/align_config_output.hpp
  • ./alignment/configuration/align_config_parallel.hpp
  • ./alignment/configuration/align_config_result_type.hpp
  • ./alignment/configuration/align_config_score_type.hpp
  • ./alignment/configuration/align_config_scoring_scheme.hpp
  • ./alignment/configuration/align_config_vectorised.hpp
  • ./alignment/configuration/all.hpp
  • ./alignment/configuration/detail.hpp
• ./alignment/exception.hpp
  • gap_erase_failure
  • invalid_alignment_configuration
• ./alignment/matrix
  • ./alignment/matrix/alignment_coordinate.hpp
    • alignment_coordinate
  • ./alignment/matrix/alignment_optimum.hpp
  • ./alignment/matrix/all.hpp
  • ./alignment/matrix/debug_matrix.hpp (detail, except for operator<<)
  • ./alignment/matrix/detail
    • ./alignment/matrix/detail/affine_cell_proxy.hpp
    • ./alignment/matrix/detail/aligned_sequence_builder.hpp
    • ./alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp
    • ./alignment/matrix/detail/alignment_score_matrix_one_column_banded.hpp
    • ./alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp
    • ./alignment/matrix/detail/alignment_score_matrix_one_column.hpp
    • ./alignment/matrix/detail/alignment_score_matrix_proxy.hpp
    • ./alignment/matrix/detail/alignment_trace_matrix_base.hpp
    • ./alignment/matrix/detail/alignment_trace_matrix_full_banded.hpp
    • ./alignment/matrix/detail/alignment_trace_matrix_full.hpp
    • ./alignment/matrix/detail/alignment_trace_matrix_proxy.hpp
    • ./alignment/matrix/detail/all.hpp
    • ./alignment/matrix/detail/combined_score_and_trace_matrix.hpp
    • ./alignment/matrix/detail/coordinate_matrix.hpp
    • ./alignment/matrix/detail/matrix_coordinate.hpp
    • ./alignment/matrix/detail/score_matrix_single_column.hpp
    • ./alignment/matrix/detail/trace_iterator_banded.hpp
    • ./alignment/matrix/detail/trace_iterator_base.hpp
    • ./alignment/matrix/detail/trace_iterator.hpp
    • ./alignment/matrix/detail/trace_matrix_full.hpp
    • ./alignment/matrix/detail/two_dimensional_matrix.hpp
    • ./alignment/matrix/detail/two_dimensional_matrix_iterator_base.hpp
    • ./alignment/matrix/detail/two_dimensional_matrix_iterator_concept.hpp
  • ./alignment/matrix/edit_distance_score_matrix_full.hpp
  • ./alignment/matrix/edit_distance_trace_matrix_full.hpp
  • ./alignment/matrix/matrix_concept.hpp
  • ./alignment/matrix/row_wise_matrix.hpp
  • ./alignment/matrix/trace_directions.hpp (detail, except for operator<<)
• ./alignment/pairwise
  • ./alignment/pairwise/alignment_algorithm.hpp
  • ./alignment/pairwise/alignment_configurator.hpp
  • ./alignment/pairwise/alignment_result.hpp (detail, except for operator<<)
  • ./alignment/pairwise/align_pairwise.hpp
    • align_pairwise
  • ./alignment/pairwise/align_result_selector.hpp
  • ./alignment/pairwise/all.hpp
  • ./alignment/pairwise/detail
    • ./alignment/pairwise/detail/alignment_algorithm_state.hpp
    • ./alignment/pairwise/detail/concept.hpp
    • ./alignment/pairwise/detail/pairwise_alignment_algorithm_banded.hpp
    • ./alignment/pairwise/detail/pairwise_alignment_algorithm.hpp
    • ./alignment/pairwise/detail/policy_affine_gap_recursion_banded.hpp
    • ./alignment/pairwise/detail/policy_affine_gap_recursion.hpp
    • ./alignment/pairwise/detail/policy_affine_gap_with_trace_recursion_banded.hpp
    • ./alignment/pairwise/detail/policy_affine_gap_with_trace_recursion.hpp
    • ./alignment/pairwise/detail/policy_alignment_matrix.hpp
    • ./alignment/pairwise/detail/policy_alignment_result_builder.hpp
    • ./alignment/pairwise/detail/policy_optimum_tracker.hpp
    • ./alignment/pairwise/detail/policy_optimum_tracker_simd.hpp
    • ./alignment/pairwise/detail/policy_scoring_scheme.hpp
    • ./alignment/pairwise/detail/type_traits.hpp
  • ./alignment/pairwise/edit_distance_algorithm.hpp
  • ./alignment/pairwise/edit_distance_fwd.hpp
  • ./alignment/pairwise/edit_distance_unbanded.hpp
  • ./alignment/pairwise/policy
    • ./alignment/pairwise/policy/affine_gap_init_policy.hpp
    • ./alignment/pairwise/policy/affine_gap_policy.hpp
    • ./alignment/pairwise/policy/alignment_matrix_policy.hpp
    • ./alignment/pairwise/policy/all.hpp
    • ./alignment/pairwise/policy/find_optimum_policy.hpp
    • ./alignment/pairwise/policy/scoring_scheme_policy.hpp
    • ./alignment/pairwise/policy/simd_affine_gap_policy.hpp
    • ./alignment/pairwise/policy/simd_find_optimum_policy.hpp
• ./alignment/scoring
  • ./alignment/scoring/all.hpp
  • ./alignment/scoring/aminoacid_scoring_scheme.hpp
    • aminoacid_similarity_matrix
    • aminoacid_scoring_scheme
    • lower case member constants (BLOSUM45 -> blosum45)
    • aminoacid_scoring_scheme: lower case member constants #317
  • ./alignment/scoring/detail
    • ./alignment/scoring/detail/simd_match_mismatch_scoring_scheme.hpp
    • ./alignment/scoring/detail/simd_matrix_scoring_scheme.hpp
  • ./alignment/scoring/gap_scheme.hpp (is implemented via alignment/configuration/align_config_gap_cost_affine.hpp)
    • gap_score
    • gap_open_score
  • ./alignment/scoring/nucleotide_scoring_scheme.hpp
    • nucleotide_scoring_scheme
  • ./alignment/scoring/scoring_scheme_base.hpp
    • match_score
    • mismatch_score
    • scoring_scheme_base
  • ./alignment/scoring/scoring_scheme_concept.hpp
    • scoring_scheme_for

[smehringer]

Core Meeting 18.01.2021

Todos:

High Priority

• scoring schemes: scoring schemes must be supplied for seqan3::align_pairwise. If we mark seqan3::align_pairwise as api-stable but scoring schemes as experimental, seqan3::align_pairwise cannot really be used in a stable way. Discussing scoring schemes has a high priority!
  • MOVED TO 3.2: [Alignment] API Stability of Alignment Module #391
• Concern: Is the the naming of seqan3::alignment_result maybe not compatible with later changes, when we introduce the multiple alignment. Possible alternatives: seqan3::align_pairwise_result seqan3::sequence_alignment_result (and later seqan3::align_multiple_result, seqan3::multiple_sequence_alignment_result)
  • MOVED TO 3.2: [Alignment] API Stability of Alignment Module #391

Lower Priority

• Add deprecate documentation to seqan3::static_band (only the whole header has a doxygen deprecated documentation not the entity itself) ([DOC] Deprecate seqan3::static_band documentation. seqan3#2345)
• Deprecate seqan3::alignment_coordinate ([Alignment] Deprecate seqan3::alignment_coordinate #282)
• Deprecate seqan3::gap_scheme and it's utilities ([Alignment] Deprecate seqan3::gap_scheme #283)
• seqan3::align_cfg::scoring_sheme is in the wrong documentation group. fix the \ingroup command ([DOC] Put scoring scheme config into correct doxygen group. seqan3#2344)
• Is writeable_aligned_sequence concept really stable, or should it be experimental since the functions insert_gap, ... are not stable yet
  • MOVED TO 3.2: [Alignment] API Stability of Alignment Module #391

[marehr]

Open todos were collected in epic #391.