Provides data structures for representing alignment coordinates and alignments as a matrix.
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class | seqan3::detail::advanceable_alignment_coordinate< state > |
| Implements an internal alignment coordinate that can be used as an argument to the std::ranges::iota_view. More...
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class | seqan3::detail::affine_cell_proxy< tuple_t > |
| A proxy for an affine score matrix cell. More...
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interface | affine_score_and_trace_cell |
| The concept for a type that models an affine cell of the combined score and trace matrix. More...
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interface | affine_score_cell |
| The concept for a type that models an affine cell of the score matrix. More...
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interface | affine_trace_cell |
| The concept for a type that models an affine cell of the trace matrix. More...
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class | seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t > |
| Builds the alignment for a given pair of sequences and the respective trace. More...
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class | seqan3::detail::alignment_matrix_column_major_range_base< derived_t > |
| Provides a range interface for alignment matrices. More...
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struct | seqan3::detail::alignment_optimum< score_t > |
| Stores the current optimum of the alignment algorithm. More...
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class | seqan3::detail::alignment_score_matrix_one_column< score_t > |
| An alignment score matrix storing only a single column for the computation. More...
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class | seqan3::detail::alignment_score_matrix_one_column_banded< score_t > |
| A banded alignment score matrix storing only a single banded column for the computation. More...
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struct | seqan3::detail::alignment_score_matrix_one_column_base< score_t > |
| A base class for alignment score matrices using only one column to compute the matrix. More...
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struct | seqan3::detail::alignment_score_matrix_proxy< score_type > |
| A proxy type for a unified access to the score matrix during alignment computation. More...
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struct | seqan3::detail::alignment_trace_matrix_base< trace_t > |
| A crtp-base class for alignment traceback matrices. More...
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class | seqan3::detail::alignment_trace_matrix_full< trace_t, coordinate_only > |
| An alignment traceback matrix storing the entire traceback matrix. More...
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class | seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only > |
| An alignment traceback matrix storing the entire banded traceback matrix. More...
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struct | seqan3::detail::alignment_trace_matrix_proxy< coordinate_type, trace_type > |
| A proxy type for a unified access to the traceback matrix during alignment computation. More...
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interface | arithmetic_or_simd |
| The concept for a type that models either seqan3::arithmetic or seqan3::simd::simd_concept. More...
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struct | seqan3::detail::column_index_type< index_type > |
| A strong type for designated initialisation of the column index of a matrix. More...
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class | seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t > |
| An alignment matrix that combines a score matrix with a trace matrix into a common interface. More...
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class | seqan3::detail::coordinate_matrix< index_t > |
| A matrix over coordinates. More...
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class | seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t > |
| A debug matrix to wrap alignment matrices and sequences and make them printable together. More...
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class | seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors > |
| The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the score matrix. More...
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class | seqan3::detail::edit_distance_trace_matrix_full< word_t, is_semi_global, use_max_errors > |
| The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the trace matrix. More...
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struct | seqan3::detail::make_aligned_sequence_type< range_t > |
| A transformation trait that returns the correct aligned sequence type for a given sequence type. More...
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struct | seqan3::detail::make_pairwise_alignment_type< first_sequence_t, second_sequence_t > |
| A transformation trait that returns the correct pairwise alignment type for two given sequence types. More...
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interface | seqan3::detail::matrix< matrix_t > |
| Defines the requirements of a matrix (e.g. score matrices, trace matrices). More...
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struct | seqan3::detail::matrix_index< index_t > |
| A representation of a location or offset within a two-dimensional matrix. More...
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struct | seqan3::detail::number_cols |
| Strong type for setting the column dimension of a matrix. More...
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struct | seqan3::detail::number_rows |
| Strong type for setting the row dimension of a matrix. More...
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struct | seqan3::detail::row_index_type< index_type > |
| A strong type for designated initialisation of the row index of a matrix. More...
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class | seqan3::detail::score_matrix_single_column< score_t > |
| Score matrix for the pairwise alignment using only a single column. More...
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class | seqan3::detail::trace_iterator< matrix_iter_t > |
| A trace iterator an unbanded trace matrix. More...
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class | seqan3::detail::trace_iterator_banded< matrix_iter_t > |
| A trace iterator for banded trace matrices. More...
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class | seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t > |
| A CRTP-base class for trace iterator implementations for the alignment algorithms. More...
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class | seqan3::detail::trace_matrix_full< trace_t > |
| Trace matrix for the pairwise alignment using the full trace matrix. More...
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interface | tracedirections_or_simd |
| The concept for a type that either is the same type as seqan3::detail::trace_directions or models the seqan3::simd::simd_concept. More...
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class | seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order > |
| A two dimensional matrix used inside of alignment algorithms. More...
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interface | seqan3::detail::two_dimensional_matrix_iterator< iter_t > |
| A concept for iterators over a two dimensional matrix, e.g. seqan3::detail::two_dimensional_matrix. More...
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class | seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order > |
| A crtp-base class for iterators over seqan3::detail::two_dimensional_matrix. More...
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Provides data structures for representing alignment coordinates and alignments as a matrix.