This calculates an alignment using the edit distance and without a band. More...
#include <seqan3/alignment/pairwise/edit_distance_unbanded.hpp>
Classes | |
struct | compute_state |
The internal state needed to compute the alignment. More... | |
struct | compute_state_trace_matrix |
The internal state needed to compute the trace matrix. More... | |
Public Types | |
using | align_config_type = std::remove_reference_t< align_config_t > |
The type of the alignment config. | |
using | align_config_type = std::remove_reference_t< align_config_t > |
The type of the alignment config. | |
using | align_config_type = std::remove_reference_t< align_config_t > |
The type of the alignment config. | |
using | align_config_type = std::remove_reference_t< align_config_t > |
The type of the alignment config. | |
using | align_config_type = std::remove_reference_t< align_config_t > |
The type of the alignment config. | |
using | alignment_result_type = typename alignment_traits_type::alignment_result_type |
The alignment result type generated by the algorithm. | |
using | alignment_result_type = typename alignment_traits_type::alignment_result_type |
The alignment result type generated by the algorithm. | |
using | alignment_result_type = typename alignment_traits_type::alignment_result_type |
The alignment result type generated by the algorithm. | |
using | alignment_result_type = typename alignment_traits_type::alignment_result_type |
The alignment result type generated by the algorithm. | |
using | alignment_result_type = typename alignment_traits_type::alignment_result_type |
The alignment result type generated by the algorithm. | |
using | alignment_traits_type = alignment_configuration_traits< align_config_type > |
The alignment algorithm traits over the alignment configuration type. | |
using | alignment_traits_type = alignment_configuration_traits< align_config_type > |
The alignment algorithm traits over the alignment configuration type. | |
using | alignment_traits_type = alignment_configuration_traits< align_config_type > |
The alignment algorithm traits over the alignment configuration type. | |
using | alignment_traits_type = alignment_configuration_traits< align_config_type > |
The alignment algorithm traits over the alignment configuration type. | |
using | alignment_traits_type = alignment_configuration_traits< align_config_type > |
The alignment algorithm traits over the alignment configuration type. | |
using | database_iterator = std::ranges::iterator_t< database_type > |
The type of an iterator of the database sequence. | |
using | database_iterator = std::ranges::iterator_t< database_type > |
The type of an iterator of the database sequence. | |
using | database_iterator = std::ranges::iterator_t< database_type > |
The type of an iterator of the database sequence. | |
using | database_iterator = std::ranges::iterator_t< database_type > |
The type of an iterator of the database sequence. | |
using | database_iterator = std::ranges::iterator_t< database_type > |
The type of an iterator of the database sequence. | |
using | database_type = std::remove_reference_t< database_t > |
The type of the database sequence. | |
using | database_type = std::remove_reference_t< database_t > |
The type of the database sequence. | |
using | database_type = std::remove_reference_t< database_t > |
The type of the database sequence. | |
using | database_type = std::remove_reference_t< database_t > |
The type of the database sequence. | |
using | database_type = std::remove_reference_t< database_t > |
The type of the database sequence. | |
using | query_alphabet_type = std::remove_reference_t< std::ranges::range_reference_t< query_type > > |
The alphabet type of the query sequence. | |
using | query_alphabet_type = std::remove_reference_t< std::ranges::range_reference_t< query_type > > |
The alphabet type of the query sequence. | |
using | query_alphabet_type = std::remove_reference_t< std::ranges::range_reference_t< query_type > > |
The alphabet type of the query sequence. | |
using | query_alphabet_type = std::remove_reference_t< std::ranges::range_reference_t< query_type > > |
The alphabet type of the query sequence. | |
using | query_alphabet_type = std::remove_reference_t< std::ranges::range_reference_t< query_type > > |
The alphabet type of the query sequence. | |
using | query_type = std::remove_reference_t< query_t > |
The type of the query sequence. | |
using | query_type = std::remove_reference_t< query_t > |
The type of the query sequence. | |
using | query_type = std::remove_reference_t< query_t > |
The type of the query sequence. | |
using | query_type = std::remove_reference_t< query_t > |
The type of the query sequence. | |
using | query_type = std::remove_reference_t< query_t > |
The type of the query sequence. | |
using | result_value_type = typename alignment_result_value_type_accessor< alignment_result_type >::type |
The alignment result value type. | |
using | result_value_type = typename alignment_result_value_type_accessor< alignment_result_type >::type |
The alignment result value type. | |
using | result_value_type = typename alignment_result_value_type_accessor< alignment_result_type >::type |
The alignment result value type. | |
using | result_value_type = typename alignment_result_value_type_accessor< alignment_result_type >::type |
The alignment result value type. | |
using | result_value_type = typename alignment_result_value_type_accessor< alignment_result_type >::type |
The alignment result value type. | |
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. | |
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. | |
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. | |
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. | |
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. | |
using | score_type = typename alignment_traits_type::original_score_type |
The type of the score. | |
using | score_type = typename alignment_traits_type::original_score_type |
The type of the score. | |
using | score_type = typename alignment_traits_type::original_score_type |
The type of the score. | |
using | score_type = typename alignment_traits_type::original_score_type |
The type of the score. | |
using | score_type = typename alignment_traits_type::original_score_type |
The type of the score. | |
using | trace_matrix_type = edit_distance_trace_matrix_full< word_type, is_semi_global, use_max_errors > |
The type of the trace matrix. | |
using | trace_matrix_type = edit_distance_trace_matrix_full< word_type, is_semi_global, use_max_errors > |
The type of the trace matrix. | |
using | trace_matrix_type = edit_distance_trace_matrix_full< word_type, is_semi_global, use_max_errors > |
The type of the trace matrix. | |
using | trace_matrix_type = edit_distance_trace_matrix_full< word_type, is_semi_global, use_max_errors > |
The type of the trace matrix. | |
using | trace_matrix_type = edit_distance_trace_matrix_full< word_type, is_semi_global, use_max_errors > |
The type of the trace matrix. | |
using | word_type = word_t |
The type of one machine word. | |
using | word_type = word_t |
The type of one machine word. | |
using | word_type = word_t |
The type of one machine word. | |
using | word_type = word_t |
The type of one machine word. | |
using | word_type = word_t |
The type of one machine word. | |
Public Member Functions | |
template<typename callback_t > | |
void | operator() ([[maybe_unused]] size_t const idx, callback_t &&callback) |
Generic invocable interface. More... | |
Constructors, destructor and assignment | |
edit_distance_unbanded ()=delete | |
The class template parameter may resolve to an lvalue reference which prohibits default constructibility. More... | |
edit_distance_unbanded (edit_distance_unbanded const &)=default | |
Defaulted. | |
edit_distance_unbanded (edit_distance_unbanded &&)=default | |
Defaulted. | |
edit_distance_unbanded & | operator= (edit_distance_unbanded const &)=default |
Defaulted. | |
edit_distance_unbanded & | operator= (edit_distance_unbanded &&)=default |
Defaulted. | |
~edit_distance_unbanded ()=default | |
Defaulted. | |
edit_distance_unbanded (database_t _database, query_t _query, align_config_t _config, edit_traits const &_traits) | |
Constructor. More... | |
Global Policy: Public Member Functions | |
Allows seqan3::detail::edit_distance_unbanded_global_policy to access this class. | |
std::optional< score_type > | score () const noexcept |
Return the score of the alignment. Only available if default_edit_distance_trait_type::compute_score is true. | |
alignment_coordinate | end_positions () const noexcept |
Return the end position of the alignment Only available if default_edit_distance_trait_type::compute_end_positions is true. | |
std::optional< score_type > | score () const noexcept |
Return the score of the alignment. Only available if default_edit_distance_trait_type::compute_score is true. | |
alignment_coordinate | end_positions () const noexcept |
Return the end position of the alignment Only available if default_edit_distance_trait_type::compute_end_positions is true. | |
Score Matrix Policy: Public Member Functions | |
Allows seqan3::detail::edit_distance_unbanded_score_matrix_policy to access this class. | |
score_matrix_type const & | score_matrix () const noexcept |
Return the score matrix of the alignment. Only available if default_edit_distance_trait_type::compute_score_matrix is true. | |
Trace matrix Policy: Public Member Functions | |
Allows seqan3::detail::edit_distance_unbanded_trace_matrix_policy to access this class. | |
trace_matrix_type const & | trace_matrix () const noexcept |
Return the trace matrix of the alignment. | |
alignment_coordinate | begin_positions () const noexcept |
Return the begin position of the alignment. Only available if default_edit_distance_trait_type::compute_begin_positions is true. | |
auto | alignment () const noexcept |
Return the alignment, i.e. the actual base pair matching. Only available if default_edit_distance_trait_type::compute_sequence_alignment is true. | |
Static Public Attributes | |
static constexpr bool | compute_begin_positions |
Whether the alignment configuration indicates to compute and/or store the begin positions. More... | |
static constexpr bool | compute_begin_positions |
Whether the alignment configuration indicates to compute and/or store the begin positions. More... | |
static constexpr bool | compute_begin_positions |
Whether the alignment configuration indicates to compute and/or store the begin positions. More... | |
static constexpr bool | compute_begin_positions |
Whether the alignment configuration indicates to compute and/or store the begin positions. More... | |
static constexpr bool | compute_begin_positions |
Whether the alignment configuration indicates to compute and/or store the begin positions. More... | |
static constexpr bool | compute_end_positions |
Whether the alignment configuration indicates to compute and/or store the end positions. More... | |
static constexpr bool | compute_end_positions |
Whether the alignment configuration indicates to compute and/or store the end positions. More... | |
static constexpr bool | compute_end_positions |
Whether the alignment configuration indicates to compute and/or store the end positions. More... | |
static constexpr bool | compute_end_positions |
Whether the alignment configuration indicates to compute and/or store the end positions. More... | |
static constexpr bool | compute_end_positions |
Whether the alignment configuration indicates to compute and/or store the end positions. More... | |
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. | |
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. | |
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. | |
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. | |
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. | |
static constexpr bool | compute_score = true |
Whether the alignment configuration indicates to compute and/or store the score. | |
static constexpr bool | compute_score = true |
Whether the alignment configuration indicates to compute and/or store the score. | |
static constexpr bool | compute_score = true |
Whether the alignment configuration indicates to compute and/or store the score. | |
static constexpr bool | compute_score = true |
Whether the alignment configuration indicates to compute and/or store the score. | |
static constexpr bool | compute_score = true |
Whether the alignment configuration indicates to compute and/or store the score. | |
static constexpr bool | compute_score_matrix = false |
Whether the alignment configuration indicates to compute and/or store the score matrix. | |
static constexpr bool | compute_score_matrix = false |
Whether the alignment configuration indicates to compute and/or store the score matrix. | |
static constexpr bool | compute_score_matrix = false |
Whether the alignment configuration indicates to compute and/or store the score matrix. | |
static constexpr bool | compute_score_matrix = false |
Whether the alignment configuration indicates to compute and/or store the score matrix. | |
static constexpr bool | compute_score_matrix = false |
Whether the alignment configuration indicates to compute and/or store the score matrix. | |
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. | |
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. | |
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. | |
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. | |
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. | |
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. | |
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. | |
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. | |
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. | |
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. | |
static constexpr bool | is_global = !is_semi_global |
Whether the alignment is a global alignment or not. | |
static constexpr bool | is_global = !is_semi_global |
Whether the alignment is a global alignment or not. | |
static constexpr bool | is_global = !is_semi_global |
Whether the alignment is a global alignment or not. | |
static constexpr bool | is_global = !is_semi_global |
Whether the alignment is a global alignment or not. | |
static constexpr bool | is_global = !is_semi_global |
Whether the alignment is a global alignment or not. | |
static constexpr bool | is_semi_global = is_semi_global_t::value |
Whether the alignment is a semi-global alignment or not. | |
static constexpr bool | is_semi_global = is_semi_global_t::value |
Whether the alignment is a semi-global alignment or not. | |
static constexpr bool | is_semi_global = is_semi_global_t::value |
Whether the alignment is a semi-global alignment or not. | |
static constexpr bool | is_semi_global = is_semi_global_t::value |
Whether the alignment is a semi-global alignment or not. | |
static constexpr bool | is_semi_global = is_semi_global_t::value |
Whether the alignment is a semi-global alignment or not. | |
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. | |
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. | |
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. | |
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. | |
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. | |
static constexpr uint8_t | word_size = bits_of<word_type> |
The size of one machine word. | |
static constexpr uint8_t | word_size = bits_of<word_type> |
The size of one machine word. | |
static constexpr uint8_t | word_size = bits_of<word_type> |
The size of one machine word. | |
static constexpr uint8_t | word_size = bits_of<word_type> |
The size of one machine word. | |
static constexpr uint8_t | word_size = bits_of<word_type> |
The size of one machine word. | |
Protected Types | |
using | base_t = edit_distance_unbanded_global_policy< derived_t, edit_traits > |
The base policy of this policy. | |
Protected Member Functions | |
Global Policy: Protected Member Functions | |
Allows seqan3::detail::edit_distance_unbanded_global_policy to access this class. | |
void | score_init () noexcept |
Initialises global policy. | |
bool | is_valid () const noexcept |
Returns true if the computation produced a valid alignment. | |
alignment_coordinate | invalid_coordinate () const noexcept |
Returns an invalid_coordinate for this alignment. | |
void | update_best_score () noexcept |
Update the current best known score if the current score is better. | |
size_t | end_positions_first () const noexcept |
Returns the first component of the end_positions. | |
bool | is_valid () const noexcept |
Returns true if the computation produced a valid alignment. | |
alignment_coordinate | invalid_coordinate () const noexcept |
Returns an invalid_coordinate for this alignment. | |
Semi-Global Policy: Protected Member Functions | |
Allows seqan3::detail::edit_distance_unbanded_semi_global_policy to access this class. | |
void | score_init () noexcept |
Initialises semi-global policy. | |
void | update_best_score () noexcept |
Update the current best known score if the current score is better. More... | |
size_t | end_positions_first () const noexcept |
Returns the first component of the end_positions. More... | |
Score Matrix Policy: Protected Member Functions | |
Allows seqan3::detail::edit_distance_unbanded_score_matrix_policy to access this class. | |
void | score_matrix_init () |
Initialises score-matrix policy. More... | |
Trace matrix Policy: Protected Member Functions | |
Allows seqan3::detail::edit_distance_unbanded_trace_matrix_policy to access this class. | |
void | trace_matrix_init (size_t block_count) |
Initialises trace-matrix policy. More... | |
Max Error Policy: Protected Member Functions | |
Allows seqan3::detail::edit_distance_unbanded_max_errors_policy to access this class. | |
void | max_errors_init (size_t block_count) noexcept |
Initialises max_errors policy. | |
bool | is_last_active_cell_within_last_row () const noexcept |
Returns true if the current active cell is within the last row. | |
bool | prev_last_active_cell () noexcept |
Decrement the last active cell position. | |
void | next_last_active_cell () noexcept |
Increment the last active cell position. | |
bool | update_last_active_cell () noexcept |
Use the ukkonen trick and update the last active cell. More... | |
Static Protected Member Functions | |
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. More... | |
Protected Attributes | |
friend | derived_t |
Befriends the derived type. | |
friend | derived_t |
Befriends the derived type. | |
friend | derived_t |
Befriends the derived type. | |
friend | derived_t |
Befriends the derived type. | |
friend | derived_t |
Befriends the derived type. | |
Global Policy: Protected Attributes | |
Allows seqan3::detail::edit_distance_unbanded_global_policy to access this class. | |
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). | |
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). | |
Semi-Global Policy: Protected Attributes | |
Allows seqan3::detail::edit_distance_unbanded_semi_global_policy to access this class. | |
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. More... | |
Score Matrix Policy: Protected Attributes | |
Allows seqan3::detail::edit_distance_unbanded_score_matrix_policy to access this class. | |
score_matrix_type | _score_matrix {} |
The score matrix of the edit distance alignment. | |
Trace matrix Policy: Protected Attributes | |
Allows seqan3::detail::edit_distance_unbanded_trace_matrix_policy to access this class. | |
std::vector< word_type > | hp {} |
The machine word which stores the positive horizontal differences. More... | |
std::vector< word_type > | db {} |
The machine word which stores if trace_directions::diagonal is true. More... | |
trace_matrix_type | _trace_matrix {} |
The trace matrix of the edit distance alignment. | |
Max Error Policy: Protected Attributes | |
Allows seqan3::detail::edit_distance_unbanded_max_errors_policy to access this class. | |
score_type | max_errors {255} |
Which score value is considered as a hit? | |
size_t | last_block {0u} |
The block containing the last active cell. | |
word_type | last_score_mask {} |
A mask with a bit set on the position of the last row. | |
Private Member Functions | |
void | add_state () |
Add a computation step. | |
void | advance_score (word_type P, word_type N, word_type mask) noexcept |
Increase or decrease the score. | |
void | compute () |
Compute the alignment. | |
void | compute_empty_query_sequence () |
Special case if query sequence is empty. | |
template<bool with_carry> | |
void | compute_kernel (compute_state &state, size_t const block_offset, size_t const current_block) noexcept |
A single compute step in the current column at a given position. | |
bool | large_patterns () |
Pattern is larger than one machine word. Use overflow aware computation. | |
bool | on_hit () noexcept |
Will be called if a hit was found (e.g., score <= max_errors). | |
bool | small_patterns () |
Pattern is small enough that it fits into one machine word. Use faster computation with less overhead. | |
Static Private Member Functions | |
template<bool with_carry> | |
static void | compute_step (compute_state &state) noexcept |
A single compute step in the current column. | |
Private Attributes | |
score_type | _score {} |
The score of the current column. | |
std::vector< word_type > | bit_masks {} |
The machine words which translate a letter of the query into a bit mask. More... | |
align_config_t | config |
The configuration. | |
database_t | database |
The horizontal/database sequence. | |
database_iterator | database_it {} |
The current position in the database. | |
database_iterator | database_it_end {} |
The end position of the database. | |
query_t | query |
The vertical/query sequence. | |
word_type | score_mask {0u} |
The mask with a bit set at the position where the score change. More... | |
std::vector< word_type > | vn {} |
The machine word which stores the negative vertical differences. More... | |
std::vector< word_type > | vp {} |
The machine word which stores the positive vertical differences. More... | |
Static Private Attributes | |
static constexpr word_type | hn0 = 0u |
How to pre-initialise hn. | |
static constexpr word_type | hp0 = is_global ? 1u : 0u |
How to pre-initialise hp. | |
static constexpr word_type | vn0 = 0u |
How to pre-initialise vn. | |
static constexpr word_type | vp0 = ~word_type{0u} |
How to pre-initialise vp. | |
Friends | |
template<typename other_derived_t , typename other_edit_traits > | |
class | edit_distance_unbanded_global_policy |
Allows seqan3::detail::edit_distance_unbanded_global_policy to access this class. | |
template<typename other_derived_t , typename other_edit_traits > | |
class | edit_distance_unbanded_max_errors_policy |
Allows seqan3::detail::edit_distance_unbanded_max_errors_policy to access this class. | |
template<typename other_derived_t , typename other_edit_traits > | |
class | edit_distance_unbanded_score_matrix_policy |
Allows seqan3::detail::edit_distance_unbanded_score_matrix_policy to access this class. | |
template<typename other_derived_t , typename other_edit_traits > | |
class | edit_distance_unbanded_semi_global_policy |
Allows seqan3::detail::edit_distance_unbanded_semi_global_policy to access this class. | |
template<typename other_derived_t , typename other_edit_traits > | |
class | edit_distance_unbanded_trace_matrix_policy |
Allows seqan3::detail::edit_distance_unbanded_trace_matrix_policy to access this class. | |
Related Functions | |
(Note that these are not member functions.) | |
Type deduction guides | |
template<typename database_t , typename query_t , typename config_t , typename traits_t > | |
edit_distance_unbanded (database_t &&database, query_t &&query, config_t config, traits_t) -> edit_distance_unbanded< database_t, query_t, config_t, traits_t > | |
Deduce the type from the provided arguments. | |
This calculates an alignment using the edit distance and without a band.
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. |
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delete |
The class template parameter may resolve to an lvalue reference which prohibits default constructibility.
Defaulted.
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inline |
Constructor.
[in] | _database | The horizontal/database sequence. |
[in] | _query | The vertical/query sequence. |
[in] | _config | The configuration. |
[in] | _traits | The traits object. Only the type information will be used. |
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inlineprotectednoexceptinherited |
Returns the first component of the end_positions.
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inlinestaticprotectednoexceptinherited |
Computes the number of max rows in the current column.
score_type | The type of the score. |
score_mask | The mask with a bit set at the position where the score change. |
last_block | The block containing the last active cell. |
score | The score of the current column. |
max_errors | Which score value is considered as a hit? |
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inline |
Generic invocable interface.
[in] | idx | The index of the currently processed sequence pair. |
[in] | callback | The callback function to be invoked with the alignment result. |
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inlineprotectedinherited |
Initialises score-matrix policy.
Strong exception guarantee.
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inlineprotectedinherited |
Initialises trace-matrix policy.
Strong exception guarantee.
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inlineprotectednoexceptinherited |
Update the current best known score if the current score is better.
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inlineprotectednoexceptinherited |
Use the ukkonen trick and update the last active cell.
true
if computation should be aborted, false
if computation should continue.
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protectedinherited |
In which column the best score of the alignment is located. Will only be tracked if is_semi_global is true.
If is_global is true this is always at the last entry in the score matrix, i.e. at position (|query|
, |database|
).
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private |
The machine words which translate a letter of the query into a bit mask.
Each bit position which is true (= 1) corresponds to a match of a letter in the query at this position.
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staticconstexprinherited |
Whether the alignment configuration indicates to compute and/or store the begin positions.
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staticconstexprinherited |
Whether the alignment configuration indicates to compute and/or store the begin positions.
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staticconstexprinherited |
Whether the alignment configuration indicates to compute and/or store the begin positions.
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staticconstexprinherited |
Whether the alignment configuration indicates to compute and/or store the begin positions.
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staticconstexprinherited |
Whether the alignment configuration indicates to compute and/or store the begin positions.
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staticconstexprinherited |
Whether the alignment configuration indicates to compute and/or store the end positions.
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staticconstexprinherited |
Whether the alignment configuration indicates to compute and/or store the end positions.
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staticconstexprinherited |
Whether the alignment configuration indicates to compute and/or store the end positions.
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staticconstexprinherited |
Whether the alignment configuration indicates to compute and/or store the end positions.
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staticconstexprinherited |
Whether the alignment configuration indicates to compute and/or store the end positions.
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protectedinherited |
The machine word which stores if trace_directions::diagonal is true.
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protectedinherited |
The machine word which stores the positive horizontal differences.
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private |
The mask with a bit set at the position where the score change.
If use_max_errors is true this corresponds to the last active cell.
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private |
The machine word which stores the negative vertical differences.
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private |
The machine word which stores the positive vertical differences.