Manages the alignment and score matrix. More...

#include <seqan3/alignment/pairwise/policy/alignment_matrix_policy.hpp>

Private Attributes
friend	alignment_algorithm_t
	Allow alignment algorithm to instantiate this crtp base class.

Constructors, destructor and assignment
score_matrix_t	score_matrix {}
	The scoring matrix.

trace_matrix_t	trace_matrix {}
	The trace matrix if needed.

score_matrix_t::iterator	score_matrix_iter {}
	The matrix iterator over the score matrix.

trace_matrix_t::iterator	trace_matrix_iter {}
	The matrix iterator over the trace matrix.

size_t	seq1_slice_offset {}
	The offset of the first sequence slice.

size_t	seq2_slice_offset {}
	The offset of the second sequence slice;.

constexpr	alignment_matrix_policy ()=default
	Defaulted.

constexpr	alignment_matrix_policy (alignment_matrix_policy const &)=default
	Defaulted.

constexpr	alignment_matrix_policy (alignment_matrix_policy &&)=default
	Defaulted.

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

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

	~alignment_matrix_policy ()=default
	Defaulted.

template<typename configuration_t >
	alignment_matrix_policy (configuration_t const &)
	Initialise the policy.

template<typename sequence1_t , typename sequence2_t >
constexpr void	allocate_matrix (sequence1_t &&sequence1, sequence2_t &&sequence2)
	}

template<typename sequence1_t , typename sequence2_t , typename score_t >
constexpr void	allocate_matrix (sequence1_t &&sequence1, sequence2_t &&sequence2, align_cfg::band_fixed_size const &band, alignment_algorithm_state< score_t > const &state)
	Allocates the memory of the underlying matrices.

constexpr void	initialise_matrix_iterator () noexcept
	Initialises the score and trace matrix iterator after allocating the matrices.

template<typename sequence1_t , typename sequence2_t >
constexpr auto	slice_sequences (sequence1_t &sequence1, sequence2_t &sequence2, align_cfg::band_fixed_size const &band) noexcept
	Slices the sequences according to the band parameters.

constexpr auto	current_alignment_column () noexcept
	Returns the current alignment column.

constexpr void	next_alignment_column () noexcept
	Moves to the next alignment column.

constexpr size_t	to_original_sequence1_position (size_t position) const noexcept
	Converts a sliced position in the alignment matrix to the corresponding position in the original sequence 1.

constexpr size_t	to_original_sequence2_position (size_t position) const noexcept
	Converts a sliced position in the alignment matrix to the corresponding position in the original sequence 2.

Detailed Descriptionno-api

template<typename alignment_algorithm_t, typename score_matrix_t, typename trace_matrix_t>
class seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >

Manages the alignment and score matrix.

Template Parameters

alignment_algorithm_t	The derived type (seqan3::detail::alignment_algorithm) to be augmented with this CRTP-policy.
score_matrix_t	The type of the alignment score matrix.
trace_matrix_t	The type of the alignment trace matrix.

This policy is used to manage the score and trace matrix of the alignment algorithm. On invocation of an alignment instance the necessary memory is allocated and the corresponding matrix iterators are initialised. These iterators are used as a global state within this particular alignment instance and are accessed from the alignment algorithm.

Remarks: The template parameters of this CRTP-policy are selected in the seqan3::detail::alignment_configurator::select_matrix_policy when selecting the alignment for the given configuration.

Member Function Documentation

◆ allocate_matrix() [1/2] [no-api]

template<typename alignment_algorithm_t , typename score_matrix_t , typename trace_matrix_t >

template<typename sequence1_t , typename sequence2_t >

constexpr void seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >::allocate_matrix	(	sequence1_t &&	sequence1,
		sequence2_t &&	sequence2
	)

no-apiinlineconstexprprivate

}

Allocates the memory of the underlying matrices.

Template Parameters

sequence1_t	The type of the first sequence to align; must model std::forward_ranges.
sequence2_t	The type of the second sequence to align; must model std::forward_ranges.

Parameters

[in]	sequence1	The first sequence to align.
[in]	sequence2	The second sequence to align.

Initialises the underlying score and trace matrices and sets the respective matrix iterators to the begin of the corresponding matrix.

◆ allocate_matrix() [2/2] [no-api]

template<typename alignment_algorithm_t , typename score_matrix_t , typename trace_matrix_t >

template<typename sequence1_t , typename sequence2_t , typename score_t >

constexpr void seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >::allocate_matrix	(	sequence1_t &&	sequence1,
		sequence2_t &&	sequence2,
		align_cfg::band_fixed_size const &	band,
		alignment_algorithm_state< score_t > const &	state
	)

no-apiinlineconstexprprivate

Allocates the memory of the underlying matrices.

Template Parameters

sequence1_t	The type of the first sequence to align; must model std::forward_ranges.
sequence2_t	The type of the second sequence to align; must model std::forward_ranges.
score_t	The score type used inside of the alignment algorithm.

Parameters

[in]	sequence1	The first sequence to align.
[in]	sequence2	The second sequence to align.
[in]	band	The band used to initialise the matrices.
[in]	state	The current state used by the alignment algorithm.

Initialises the underlying banded score and trace matrices and sets the respective matrix iterators to the begin of the corresponding matrix. Using the additional band parameter the actual dimensions are reduced according to the matrix implementation. For the banded case, one additional cell per column is stored such that we can read from it without introducing a case distinction inside of the algorithm implementation. However, this cell needs to be properly initialised with an infinity value. To emulate the infinity for integral values we use the smallest representable value and subtract the gap extension score (assumed to be always negative) from it. In the algorithm we never write to this cell and only add the extension costs to the read value. This way we can get the smallest possible value as an infinity.

◆ current_alignment_column() [no-api]

template<typename alignment_algorithm_t , typename score_matrix_t , typename trace_matrix_t >

constexpr auto seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >::current_alignment_column ( )

no-apiinlineconstexprprivatenoexcept

Returns the current alignment column.

Returns: The current alignment column as a zipped view over the score matrix and trace matrix column.

The current alignment column is a zipped view over the current score matrix column and trace matrix column. These columns are managed by the corresponding alignment matrix policy.

◆ next_alignment_column() [no-api]

template<typename alignment_algorithm_t , typename score_matrix_t , typename trace_matrix_t >

constexpr void seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >::next_alignment_column ( )

no-apiinlineconstexprprivatenoexcept

Moves to the next alignment column.

Increments the underlying matrix iterators for the score matrix and the trace matrix.

◆ slice_sequences() [no-api]

template<typename alignment_algorithm_t , typename score_matrix_t , typename trace_matrix_t >

template<typename sequence1_t , typename sequence2_t >

constexpr auto seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >::slice_sequences	(	sequence1_t &	sequence1,
		sequence2_t &	sequence2,
		align_cfg::band_fixed_size const &	band
	)

no-apiinlineconstexprprivatenoexcept

Slices the sequences according to the band parameters.

Template Parameters

sequence1_t	The type of the first sequence to align; must model std::forward_ranges.
sequence2_t	The type of the second sequence to align; must model std::forward_ranges.

Parameters

[in]	sequence1	The first sequence to align.
[in]	sequence2	The second sequence to align.
[in]	band	The seqan3::align_cfg::band_fixed_size used to limit the alignment space.

If the band does not intersect with the origin or the sink of the matrix the sequences are sliced such that the band starts in the origin and ends in the sink.

◆ to_original_sequence1_position() [no-api]

template<typename alignment_algorithm_t , typename score_matrix_t , typename trace_matrix_t >

constexpr size_t seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >::to_original_sequence1_position ( size_t position ) const

no-apiinlineconstexprprivatenoexcept

Converts a sliced position in the alignment matrix to the corresponding position in the original sequence 1.

Parameters

position The position in the sliced alignment matrix.

Returns: The corresponding position in the original sequence 1.

Only changes the position if the sequence was sliced due to band configuration.

◆ to_original_sequence2_position() [no-api]

template<typename alignment_algorithm_t , typename score_matrix_t , typename trace_matrix_t >

constexpr size_t seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >::to_original_sequence2_position ( size_t position ) const

no-apiinlineconstexprprivatenoexcept

Converts a sliced position in the alignment matrix to the corresponding position in the original sequence 2.

Parameters

position The position in the sliced alignment matrix.

Returns: The corresponding position in the original sequence 2.

Only changes the position if the sequence was sliced due to band configuration.

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

alignment_matrix_policy.hpp

Private Attributes

Constructors, destructor and assignment

Detailed Descriptionno-api

Member Function Documentation

◆ allocate_matrix() [1/2] [no-api]

◆ allocate_matrix() [2/2] [no-api]

◆ current_alignment_column() [no-api]

◆ next_alignment_column() [no-api]

◆ slice_sequences() [no-api]

◆ to_original_sequence1_position() [no-api]

◆ to_original_sequence2_position() [no-api]