Algorithm

Provides core functionality used to configure algorithms. More...

Collaboration diagram for Algorithm:

Classes
class	seqan3::detail::algorithm_executor_blocking< resource_t, algorithm_t, algorithm_result_t, execution_handler_t >
	A blocking algorithm executor for algorithms. More...
class	seqan3::algorithm_result_generator_range< algorithm_executor_type >
	An input range over the algorithm results generated by the underlying algorithm executor. More...
interface	config_element
	Concept for an algorithm configuration element. More...
interface	config_element_pipeable_with
	Concept to check if one configuration element can be combined with another configuration element. More...
class	seqan3::configuration< configs_t >
	Collection of elements to configure an algorithm. More...
class	seqan3::detail::debug_mode< wrapped_config_id_t >
	A global configuration type used to enabled debugging of algorithms. More...
class	seqan3::detail::execution_handler_parallel
	Handles the parallel execution of algorithms. More...
struct	seqan3::detail::execution_handler_sequential
	Handles the sequential execution of algorithms. More...
struct	seqan3::detail::is_configuration_valid< query_t, compare_types >
	Checks if a given type is compatible with a list of other types. More...
struct	seqan3::detail::is_same_configuration_f< query_t >
	Helper meta function to check if a template type is contained in a seqan3::configuration. More...
class	seqan3::detail::parallel_mode< wrapped_config_id_t >
	A global configuration type used to enable parallel execution of algorithms. More...
class	seqan3::pipeable_config_element< derived_t >
	Adds pipe interface to configuration elements. More...
struct	std::tuple_element< pos, seqan3::configuration< configs_t... > >
	Returns the type of the element at the specified position within seqan3::configuration. More...
struct	std::tuple_size< seqan3::configuration< configs_t... > >
	Returns the number of elements stored in seqan3::configuration. More...

Variables
template<typename algorithm_id_type >
constexpr std::array< std::array< void *, 0 >, 0 >	seqan3::detail::compatibility_table {}
	Declaration of algorithm specific compatibility table. More...
template<>
constexpr std::array< std::array< bool, static_cast< uint8_t >align_config_id::SIZE)>, static_cast< uint8_t >align_config_id::SIZE)>	seqan3::detail::compatibility_table< align_config_id >
	Declaration of algorithm specific compatibility table. More...
template<typename config1_t , typename config2_t >
constexpr bool	seqan3::is_config_element_combineable_v = detail::config_element_pipeable_with<config1_t, config2_t>
	Helper variable template to test if a configuration element is combineable with another configuration element or configuration. More...
template<typename query_t , typename ... compare_types>
constexpr bool	is_configuration_valid_v = is_configuration_valid<query_t, compare_types...>::value
	Helper variable template to check for valid configuration composites (unary_type_trait shortcut).

Tuple interface
template<template< typename ... > class query_t, typename ... configs_t>
constexpr auto &	get (configuration< configs_t... > &config) noexcept
	Returns the stored element. More...

Detailed Description

Provides core functionality used to configure algorithms.

Function Documentation

get()

template<template< typename ... > class query_t, typename ... configs_t>

constexpr auto & get ( configuration< configs_t... > &  config )

related

Returns the stored element.

Template Parameters

query_t

A template template.

Parameters

[in]

config

The configuration to get the element for.

Extends the position-based and type based get interface for the configuration type, with a version that also accepts template-template types (types that are itself templates), such that the exact template definition must not be known.

Example

The following snippet demonstrates the various versions of get that can be used.

#include <seqan3/alignment/configuration/align_config_band.hpp>
#include <seqan3/alignment/configuration/align_config_gap_cost_affine.hpp>
#include <seqan3/core/algorithm/pipeable_config_element.hpp>
#include <seqan3/core/configuration/configuration.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::get;
 
    seqan3::configuration my_cfg = seqan3::align_cfg::gap_cost_affine{seqan3::align_cfg::open_score{-10},
                                                                      seqan3::align_cfg::extension_score{-1}} |
                                   seqan3::align_cfg::band_fixed_size{seqan3::align_cfg::lower_diagonal{-4},
                                                                      seqan3::align_cfg::upper_diagonal{4}};
    // my_cfg is now of type configuration<gap_cost_affine, band_fixed_size>
 
    seqan3::debug_stream << get<1>(my_cfg).lower_diagonal << '\n'; // prints -4
    seqan3::debug_stream << get<seqan3::align_cfg::band_fixed_size>(my_cfg).upper_diagonal << '\n';  // prints 4
    seqan3::debug_stream << get<seqan3::align_cfg::gap_cost_affine>(my_cfg).extension_score << '\n';  // prints -1
}

Exception

no-throw guarantee.

Complexity

Constant time.

Variable Documentation

compatibility_table

template<typename algorithm_id_type >

constexpr std::array<std::array<void *, 0>, 0> seqan3::detail::compatibility_table {}

inlineconstexpr

Declaration of algorithm specific compatibility table.

Template Parameters

algorithm_id_type

The type of the algorithm specific id. Algorithm configurations must maintain this table to allow validation checks.

compatibility_table< align_config_id >

template<>

constexpr std::array<std::array<bool, static_cast<uint8_t>align_config_id::SIZE)>, static_cast<uint8_t>align_config_id::SIZE)> seqan3::detail::compatibility_table< align_config_id >

inlineconstexpr

Declaration of algorithm specific compatibility table.

Template Parameters

algorithm_id_type

The type of the algorithm specific id. Algorithm configurations must maintain this table to allow validation checks.

is_config_element_combineable_v

template<typename config1_t , typename config2_t >

constexpr bool seqan3::is_config_element_combineable_v = detail::config_element_pipeable_with<config1_t, config2_t>

inlineconstexpr

Helper variable template to test if a configuration element is combineable with another configuration element or configuration.

Template Parameters

config1_t	Either the type of a configuration element or a configuration.
config2_t	Either the type of a configuration element or a configuration.

This helper variable template checks if config1_t fulfills the concept requirements seqan3::detail::config_element_pipeable_with config2_t. If config2_t is a seqan3::configuration, the check will be expanded to every configuration element contained in the configuration type. Only if config1_t is combineable with every element stored inside of the given configuration, this helper variable template evaluates to true, otherwise false. If config1_t is a seqan3::configuration the same applies in combination with the configuration element config2_t. If both config1_t and config2_t are seqan3::configuration types, then the cartesian product between the configuration elements of the first configuration and the second configuration are tested.

This entity is not part of the SeqAn API. Do not rely on it in your applications. This entity is exposition only!