An alignment traceback matrix storing the entire banded traceback matrix. More...

#include <seqan3/alignment/matrix/detail/alignment_trace_matrix_full_banded.hpp>

Inheritance diagram for seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >:

Public Types
Associated types
using	value_type = alignment_trace_matrix_proxy< coordinate_type, std::conditional_t< coordinate_only, detail::ignore_t const, trace_t > >
	The proxy type of an alignment matrix.

using	reference = value_type
	Same as value type.

using	iterator = typename range_base_t::iterator
	The type of the iterator.

using	sentinel = typename range_base_t::sentinel
	The type of sentinel.

using	size_type = size_t
	The size type.

Public Member Functions
auto	trace_path (matrix_coordinate const &trace_begin)
	Returns a trace path starting from the given coordinate and ending in the cell with seqan3::detail::trace_directions::none.

Constructors, destructor and assignment
constexpr	alignment_trace_matrix_full_banded ()=default
	Defaulted.

constexpr	alignment_trace_matrix_full_banded (alignment_trace_matrix_full_banded const &)=default
	Defaulted.

constexpr	alignment_trace_matrix_full_banded (alignment_trace_matrix_full_banded &&)=default
	Defaulted.

constexpr alignment_trace_matrix_full_banded &	operator= (alignment_trace_matrix_full_banded const &)=default
	Defaulted.

constexpr alignment_trace_matrix_full_banded &	operator= (alignment_trace_matrix_full_banded &&)=default
	Defaulted.

	~alignment_trace_matrix_full_banded ()=default
	Defaulted.

template<std::ranges::forward_range first_sequence_t, std::ranges::forward_range second_sequence_t>
constexpr	alignment_trace_matrix_full_banded (first_sequence_t &&first, second_sequence_t &&second, align_cfg::band_fixed_size const &band, trace_t const initial_value=trace_t{})
	Construction from two ranges and a band.

Public Member Functions inherited from seqan3::detail::alignment_matrix_column_major_range_base< derived_t >
constexpr iterator	begin () noexcept
	Returns an iterator to the first column of the matrix.

constexpr iterator	begin () const noexcept=delete
	Deleted begin for const-qualified alignment matrix.

constexpr sentinel	end () noexcept
	Returns a sentinel marking the end of the matrix.

constexpr sentinel	end () const noexcept=delete
	Deleted end for const-qualified alignment matrix.

Public Attributes
int32_t	band_col_index {}
	The column index where the upper bound of the band passes through.

int32_t	band_row_index {}
	The row index where the lower bound of the band passes through.

int32_t	band_size {}
	The size of the band.

Protected Types
using	column_data_view_type = std::conditional_t< coordinate_only, decltype(std::views::iota(coordinate_type{}, coordinate_type{})), decltype(views::zip(std::declval< std::span< element_type > >(), std::declval< std::span< element_type > >(), std::views::iota(coordinate_type{}, coordinate_type{})))>
	The view over the current alignment-column; must model std::ranges::view and std::ranges::input_range.

using	coordinate_type = advanceable_alignment_coordinate< advanceable_alignment_coordinate_state::row >
	The coordinate type.

using	element_type = trace_t
	The actual element type.

Protected Types inherited from seqan3::detail::alignment_trace_matrix_base< trace_t >
using	allocator_type = std::conditional_t< detail::simd_concept< trace_t >, aligned_allocator< element_type, sizeof(element_type)>, std::allocator< element_type > >
	The allocator type. Uses seqan3::aligned_allocator if storing seqan3::detail::simd_concepttypes.

using	coordinate_type = advanceable_alignment_coordinate< advanceable_alignment_coordinate_state::row >
	The coordinate type.

using	element_type = trace_t
	The actual element type.

using	pool_type = two_dimensional_matrix< element_type, allocator_type, matrix_major_order::column >
	The type of the underlying memory pool.

using	size_type = size_t
	The size type.

Private Types
using	matrix_base_t = alignment_trace_matrix_base< trace_t >
	The base class for data storage.

using	range_base_t = alignment_matrix_column_major_range_base< alignment_trace_matrix_full_banded< trace_t, coordinate_only > >
	The base class for iterating over the matrix.

Private Member Functions
constexpr alignment_column_type	initialise_column (size_type const column_index) noexcept
	Returns the current alignment-column at the given `column_index`.

template<std::random_access_iterator iter_t>
constexpr value_type	make_proxy (iter_t host_iter) noexcept
	Creates the proxy value returned when dereferencing the alignment-column-iterator.

Private Attributes
friend	range_base_t
	Befriend the range base class.

Additional Inherited Members
Protected Member Functions inherited from seqan3::detail::alignment_matrix_column_major_range_base< derived_t >
constexpr iterator	begin () noexcept
	Returns an iterator to the first column of the matrix.

constexpr iterator	begin () const noexcept=delete
	Deleted begin for const-qualified alignment matrix.

constexpr sentinel	end () noexcept
	Returns a sentinel marking the end of the matrix.

constexpr sentinel	end () const noexcept=delete
	Deleted end for const-qualified alignment matrix.

Protected Attributes inherited from seqan3::detail::alignment_trace_matrix_base< trace_t >
std::vector< element_type, allocator_type >	cache_left {}
	Internal cache for the trace values to the left.

element_type	cache_up {}
	Internal cache for the last trace value above.

pool_type	data {}
	The linearised matrix storing the trace data in column-major-order.

size_type	num_cols {}
	The number of columns.

size_type	num_rows {}
	The number of num_rows.

Detailed Descriptionno-api

template<typename trace_t, bool coordinate_only = false>
class seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >

An alignment traceback matrix storing the entire banded traceback matrix.

Template Parameters

trace_t	The type of the trace directions.
coordinate_only	A boolean flag indicating if only a seqan3::detail::advanceable_alignment_coordinate should be generated.

This implementation allocates the full banded traceback matrix using k*m memory, where k is the band size and m the number of columns to store. The matrix allows access to the underlying values through a range based interface. An iterator over the traceback matrix iterates in column-major-order over the traceback matrix. Dereferencing an iterator returns a slice over the current matrix column. The value type is a pair over a seqan3::detail::advanceable_alignment_coordinate and the seqan3::detail::alignment_trace_matrix_proxy, which gives a unified access to the respective matrix cells as needed by the standard alignment algorithm. The matrix is modelled as std::ranges::input_range since the alignment algorithm iterates only once over the complete matrix to calculate the values.

Only computing the coordinates

Sometimes it is desired to only get access to the alignment coordinates. This can be achieved by setting coordinate_only = true. In this case no memory will be allocated and only an internal state is maintained to generate the alignment coordinates. The coordinates are relative to the banded matrix, i.e. they do not represent the corresponding row indices of the actual (unbanded) matrix.

Member Typedef Documentation

◆ column_data_view_type [no-api]

template<typename trace_t , bool coordinate_only = false>

using seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >::column_data_view_type = std::conditional_t<coordinate_only, decltype(std::views::iota(coordinate_type{}, coordinate_type{})), decltype(views::zip(std::declval<std::span<element_type> >(), std::declval<std::span<element_type> >(), std::views::iota(coordinate_type{}, coordinate_type{})))>

no-apiprotected

The view over the current alignment-column; must model std::ranges::view and std::ranges::input_range.

Note: This type must be defined by the derived type.

◆ iterator [no-api]

using seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >::iterator = typename range_base_t::iterator

no-api

The type of the iterator.

◆ sentinel [no-api]

using seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >::sentinel = typename range_base_t::sentinel

no-api

The type of sentinel.

◆ value_type [no-api]

using seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >::value_type = alignment_trace_matrix_proxy<coordinate_type, std::conditional_t<coordinate_only, detail::ignore_t const, trace_t> >

no-api

The proxy type of an alignment matrix.

Note: This type must be defined by the derived type.

Constructor & Destructor Documentation

◆ alignment_trace_matrix_full_banded() [no-api]

template<typename trace_t , bool coordinate_only = false>

template<std::ranges::forward_range first_sequence_t, std::ranges::forward_range second_sequence_t>

constexpr seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >::alignment_trace_matrix_full_banded	(	first_sequence_t &&	first,
		second_sequence_t &&	second,
		align_cfg::band_fixed_size const &	band,
		trace_t const	initial_value = `trace_t{}`
	)

no-apiinlineconstexpr

Construction from two ranges and a band.

Template Parameters

first_sequence_t	The first range type; must model std::ranges::forward_range.
second_sequence_t	The second range type; must model std::ranges::forward_range.

Parameters

[in]	first	The first range.
[in]	second	The second range.
[in]	band	The seqan3::align_cfg::band_fixed_size in which to calculate the alignment.
[in]	initial_value	The value to initialise the matrix with. Default initialised if not specified.

Obtains the sizes of the passed ranges in order to allocate the traceback matrix. Only allocates memory to store the banded matrix. If coordinate_only is set to true, nothing will be allocated.

Member Function Documentation

◆ initialise_column() [no-api]

template<typename trace_t , bool coordinate_only = false>

constexpr alignment_column_type seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >::initialise_column ( size_type const column_index )

no-apiinlineconstexprprivatenoexcept

Returns the current alignment-column at the given column_index.

Parameters

[in] column_index The current column position of the outer matrix iterator.

Returns: A view representing the current alignment-column (seqan3::detail::alignment_matrix_column_major_range_base::alignment_column_type)

Creates a new seqan3::detail::alignment_matrix_column_major_range_base::alignment_column_type initialised with the current column of the alignment matrix depending on the given column_index. The alignment_column_type stores a column view as defined by the derived class using the seqan3::detail::alignment_matrix_column_major_range_base::column_data_view_type type definition.

◆ make_proxy() [no-api]

template<typename trace_t , bool coordinate_only = false>

template<std::random_access_iterator iter_t>

constexpr value_type seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >::make_proxy ( iter_t host_iter )

no-apiinlineconstexprprivatenoexcept

Creates the proxy value returned when dereferencing the alignment-column-iterator.

Parameters

[in] host_iter The wrapped iterator to the actual memory storage.

Returns: A proxy for the current matrix position, which must be of type seqan3::detail::alignment_matrix_column_major_range_base::value_type.

◆ trace_path() [no-api]

template<typename trace_t , bool coordinate_only = false>

auto seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >::trace_path ( matrix_coordinate const & trace_begin )

no-apiinline

Returns a trace path starting from the given coordinate and ending in the cell with seqan3::detail::trace_directions::none.

Parameters

[in] trace_begin A seqan3::matrix_coordinate pointing to the begin of the trace to follow.

Returns: A std::ranges::subrange over the corresponding trace path.

Exceptions

std::invalid_argument if the specified coordinate is out of range.

The documentation for this class was generated from the following file:

alignment_trace_matrix_full_banded.hpp

Public Types

Public Member Functions

Public Attributes

Protected Types

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Descriptionno-api

Only computing the coordinates

Member Typedef Documentation

◆ column_data_view_type [no-api]

◆ iterator [no-api]

◆ sentinel [no-api]

◆ value_type [no-api]

Constructor & Destructor Documentation

◆ alignment_trace_matrix_full_banded() [no-api]

Member Function Documentation

◆ initialise_column() [no-api]

◆ make_proxy() [no-api]

◆ trace_path() [no-api]