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using | align_config_type = std::remove_reference_t< align_config_t > |
| The type of the alignment config.
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using | alignment_result_type = typename alignment_traits_type::alignment_result_type |
| The alignment result type generated by the algorithm.
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using | alignment_traits_type = alignment_configuration_traits< align_config_type > |
| The alignment algorithm traits over the alignment configuration type.
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using | database_iterator = std::ranges::iterator_t< database_type > |
| The type of an iterator of the database sequence.
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using | database_type = std::remove_reference_t< database_t > |
| The type of the database sequence.
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using | query_alphabet_type = std::remove_reference_t< std::ranges::range_reference_t< query_type > > |
| The alphabet type of the query sequence.
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using | query_type = std::remove_reference_t< query_t > |
| The type of the query sequence.
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using | result_value_type = typename alignment_result_value_type_accessor< alignment_result_type >::type |
| The alignment result value type.
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using | score_matrix_type = edit_distance_score_matrix_full< word_type, score_type, is_semi_global, use_max_errors > |
| The type of the score matrix.
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using | score_type = typename alignment_traits_type::original_score_type |
| The type of the score.
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using | trace_matrix_type = edit_distance_trace_matrix_full< word_type, is_semi_global, use_max_errors > |
| The type of the trace matrix.
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using | word_type = word_t |
| The type of one machine word.
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static constexpr bool | compute_begin_positions |
| Whether the alignment configuration indicates to compute and/or store the begin positions.
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static constexpr bool | compute_end_positions |
| Whether the alignment configuration indicates to compute and/or store the end positions.
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static constexpr bool | compute_matrix = compute_score_matrix || compute_trace_matrix |
| Whether the alignment configuration indicates to compute and/or store the score or trace matrix.
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static constexpr bool | compute_score = true |
| Whether the alignment configuration indicates to compute and/or store the score.
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static constexpr bool | compute_score_matrix = false |
| Whether the alignment configuration indicates to compute and/or store the score matrix.
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static constexpr bool | compute_sequence_alignment = alignment_traits_type::compute_sequence_alignment |
| Whether the alignment configuration indicates to compute and/or store the alignment of the sequences.
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static constexpr bool | compute_trace_matrix = compute_begin_positions || compute_sequence_alignment |
| Whether the alignment configuration indicates to compute and/or store the trace matrix.
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static constexpr bool | is_global = !is_semi_global |
| Whether the alignment is a global alignment or not.
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static constexpr bool | is_semi_global = is_semi_global_t::value |
| Whether the alignment is a semi-global alignment or not.
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static constexpr bool | use_max_errors = align_config_type::template exists<align_cfg::min_score>() |
| When true the computation will use the ukkonen trick with the last active cell and bounds the error to config.max_errors.
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static constexpr uint8_t | word_size = bits_of<word_type> |
| The size of one machine word.
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Protected Types inherited from seqan3::detail::edit_distance_unbanded_semi_global_policy< derived_t, edit_traits > |
using | base_t = edit_distance_unbanded_global_policy< derived_t, edit_traits > |
| The base policy of this policy.
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Protected Member Functions inherited from seqan3::detail::edit_distance_unbanded_global_policy< derived_t, edit_traits > |
| edit_distance_unbanded_global_policy () noexcept=default |
| Defaulted.
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| edit_distance_unbanded_global_policy (edit_distance_unbanded_global_policy const &) noexcept=default |
| Defaulted.
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| edit_distance_unbanded_global_policy (edit_distance_unbanded_global_policy &&) noexcept=default |
| Defaulted.
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edit_distance_unbanded_global_policy & | operator= (edit_distance_unbanded_global_policy const &) noexcept=default |
| Defaulted.
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edit_distance_unbanded_global_policy & | operator= (edit_distance_unbanded_global_policy &&) noexcept=default |
| Defaulted.
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| ~edit_distance_unbanded_global_policy () noexcept=default |
| Defaulted.
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void | score_init () noexcept |
| Initialises global policy.
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bool | is_valid () const noexcept |
| Returns true if the computation produced a valid alignment.
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seqan3::detail::advanceable_alignment_coordinate | invalid_coordinate () const noexcept |
| Returns an invalid_coordinate for this alignment.
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void | update_best_score () noexcept |
| Update the current best known score if the current score is better.
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size_t | end_positions_first () const noexcept |
| Returns the first component of the end_positions.
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Protected Member Functions inherited from seqan3::detail::edit_distance_unbanded_semi_global_policy< derived_t, edit_traits > |
| edit_distance_unbanded_semi_global_policy () noexcept=default |
| Defaulted.
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| edit_distance_unbanded_semi_global_policy (edit_distance_unbanded_semi_global_policy const &) noexcept=default |
| Defaulted.
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| edit_distance_unbanded_semi_global_policy (edit_distance_unbanded_semi_global_policy &&) noexcept=default |
| Defaulted.
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edit_distance_unbanded_semi_global_policy & | operator= (edit_distance_unbanded_semi_global_policy const &) noexcept=default |
| Defaulted.
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edit_distance_unbanded_semi_global_policy & | operator= (edit_distance_unbanded_semi_global_policy &&) noexcept=default |
| Defaulted.
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| ~edit_distance_unbanded_semi_global_policy () noexcept=default |
| Defaulted.
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void | score_init () noexcept |
| Initialises semi-global policy.
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void | update_best_score () noexcept |
| Update the current best known score if the current score is better.
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size_t | end_positions_first () const noexcept |
| Returns the first component of the end_positions.
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Protected Member Functions inherited from seqan3::detail::edit_distance_unbanded_score_matrix_policy< derived_t, edit_traits > |
| edit_distance_unbanded_score_matrix_policy () noexcept=default |
| Defaulted.
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| edit_distance_unbanded_score_matrix_policy (edit_distance_unbanded_score_matrix_policy const &) noexcept=default |
| Defaulted.
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| edit_distance_unbanded_score_matrix_policy (edit_distance_unbanded_score_matrix_policy &&) noexcept=default |
| Defaulted.
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edit_distance_unbanded_score_matrix_policy & | operator= (edit_distance_unbanded_score_matrix_policy const &) noexcept=default |
| Defaulted.
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edit_distance_unbanded_score_matrix_policy & | operator= (edit_distance_unbanded_score_matrix_policy &&) noexcept=default |
| Defaulted.
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| ~edit_distance_unbanded_score_matrix_policy () noexcept=default |
| Defaulted.
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void | score_matrix_init () |
| Initialises score-matrix policy.
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Protected Member Functions inherited from seqan3::detail::edit_distance_unbanded_trace_matrix_policy< derived_t, edit_traits > |
| edit_distance_unbanded_trace_matrix_policy () noexcept=default |
| Defaulted.
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| edit_distance_unbanded_trace_matrix_policy (edit_distance_unbanded_trace_matrix_policy const &) noexcept=default |
| Defaulted.
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| edit_distance_unbanded_trace_matrix_policy (edit_distance_unbanded_trace_matrix_policy &&) noexcept=default |
| Defaulted.
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edit_distance_unbanded_trace_matrix_policy & | operator= (edit_distance_unbanded_trace_matrix_policy const &) noexcept=default |
| Defaulted.
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edit_distance_unbanded_trace_matrix_policy & | operator= (edit_distance_unbanded_trace_matrix_policy &&) noexcept=default |
| Defaulted.
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| ~edit_distance_unbanded_trace_matrix_policy () noexcept=default |
| Defaulted.
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void | trace_matrix_init (size_t block_count) |
| Initialises trace-matrix policy.
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Protected Member Functions inherited from seqan3::detail::edit_distance_unbanded_max_errors_policy< derived_t, edit_traits > |
| edit_distance_unbanded_max_errors_policy () noexcept=default |
| Defaulted.
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| edit_distance_unbanded_max_errors_policy (edit_distance_unbanded_max_errors_policy const &) noexcept=default |
| Defaulted.
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| edit_distance_unbanded_max_errors_policy (edit_distance_unbanded_max_errors_policy &&) noexcept=default |
| Defaulted.
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edit_distance_unbanded_max_errors_policy & | operator= (edit_distance_unbanded_max_errors_policy const &) noexcept=default |
| Defaulted.
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edit_distance_unbanded_max_errors_policy & | operator= (edit_distance_unbanded_max_errors_policy &&) noexcept=default |
| Defaulted.
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| ~edit_distance_unbanded_max_errors_policy () noexcept=default |
| Defaulted.
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void | max_errors_init (size_t block_count) noexcept |
| Initialises max_errors policy.
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bool | is_last_active_cell_within_last_row () const noexcept |
| Returns true if the current active cell is within the last row.
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bool | prev_last_active_cell () noexcept |
| Decrement the last active cell position.
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void | next_last_active_cell () noexcept |
| Increment the last active cell position.
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bool | update_last_active_cell () noexcept |
| Use the ukkonen trick and update the last active cell.
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Static Protected Member Functions inherited from seqan3::detail::edit_distance_unbanded_max_errors_policy< derived_t, edit_traits > |
static size_t | max_rows (word_type const score_mask, unsigned const last_block, score_type const score, score_type const max_errors) noexcept |
| Computes the number of max rows in the current column.
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Protected Attributes inherited from seqan3::detail::edit_distance_unbanded_global_policy< derived_t, edit_traits > |
friend | derived_t |
| Befriends the derived type.
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score_type | _best_score {} |
| The best score of the alignment in the last row (if is_semi_global = true) or the last entry in the score matrix (if is_global = true).
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Protected Attributes inherited from seqan3::detail::edit_distance_unbanded_semi_global_policy< derived_t, edit_traits > |
friend | derived_t |
| Befriends the derived type.
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database_iterator | _best_score_col {} |
| In which column the best score of the alignment is located. Will only be tracked if is_semi_global is true.
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Protected Attributes inherited from seqan3::detail::edit_distance_unbanded_score_matrix_policy< derived_t, edit_traits > |
friend | derived_t |
| Befriends the derived type.
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score_matrix_type | _score_matrix {} |
| The score matrix of the edit distance alignment.
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Protected Attributes inherited from seqan3::detail::edit_distance_unbanded_trace_matrix_policy< derived_t, edit_traits > |
friend | derived_t |
| Befriends the derived type.
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std::vector< word_type > | hp {} |
| The machine word which stores the positive horizontal differences.
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std::vector< word_type > | db {} |
| The machine word which stores if trace_directions::diagonal is true.
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trace_matrix_type | _trace_matrix {} |
| The trace matrix of the edit distance alignment.
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Protected Attributes inherited from seqan3::detail::edit_distance_unbanded_max_errors_policy< derived_t, edit_traits > |
friend | derived_t |
| Befriends the derived type.
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score_type | max_errors {255} |
| Which score value is considered as a hit?
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size_t | last_block {0u} |
| The block containing the last active cell.
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word_type | last_score_mask {} |
| A mask with a bit set on the position of the last row.
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template<std::ranges::viewable_range database_t, std::ranges::viewable_range query_t, typename align_config_t, typename edit_traits>
class seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
This calculates an alignment using the edit distance and without a band.
- Template Parameters
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database_t | The type of the database sequence. |
query_t | The type of the query sequence. |
align_config_t | The configuration type; must be of type seqan3::configuration. |