seqan3::detail::alignment_matrix_column_major_range_base< derived_t > Class Template Reference

Provides a range interface for alignment matrices. More...

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

Inheritance diagram for seqan3::detail::alignment_matrix_column_major_range_base< derived_t >:

Classes
class	alignment_column_type
	Represents a column within an alignment matrix. More...
class	iterator_type
	A column iterator over the alignment matrix. More...

Public Member Functions
Iterators
The matrix type is not const-iterable.
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.

Private Types
using	iterator = iterator_type
	The type of the iterator.
using	sentinel = std::default_sentinel_t
	The type of sentinel.

Private Member Functions
Constructors, destructor and assignment
constexpr	alignment_matrix_column_major_range_base ()=default
	Defaulted.
constexpr	alignment_matrix_column_major_range_base (alignment_matrix_column_major_range_base const &)=default
	Defaulted.
constexpr	alignment_matrix_column_major_range_base (alignment_matrix_column_major_range_base &&)=default
	Defaulted.
constexpr alignment_matrix_column_major_range_base &	operator= (alignment_matrix_column_major_range_base const &)=default
	Defaulted.
constexpr alignment_matrix_column_major_range_base &	operator= (alignment_matrix_column_major_range_base &&)=default
	Defaulted.
	~alignment_matrix_column_major_range_base ()=default
	Defaulted.
Required interfaces
The derived class must implement the following methods.
value_type	make_proxy (iter_t host_iter) noexcept
	Creates the proxy value returned when dereferencing the alignment-column-iterator.
alignment_column_type	initialise_column (size_t column_index)
	Returns the current alignment-column at the given column_index.
template<typename iter_t >
constexpr void	on_column_iterator_creation (iter_t host_iter) noexcept
	Allows additional initialisations when calling begin on an alignment-column.
template<typename iter_t >
constexpr void	before_column_iterator_increment (iter_t host_iter) noexcept
	Allows to perform additional steps before incrementing the alignment-column-iterator.
template<typename iter_t >
constexpr void	after_column_iterator_increment (iter_t host_iter) noexcept
	Allows to perform additional steps after incrementing the alignment-column-iterator.

Private Attributes
friend	derived_t
	Befriend the derived type.
Required types
The derived class must implement the following types.
typedef	value_type
	The proxy type of an alignment matrix.
typedef	column_data_view_type
	The view over the current alignment-column; must model std::ranges::view and std::ranges::input_range.

Detailed Description

template<typename derived_t>
class seqan3::detail::alignment_matrix_column_major_range_base< derived_t >

Provides a range interface for alignment matrices.

Template Parameters

derived_t

The derived type implementing the data model of the matrix (see details for more information).

This crtp-base class provides a range based interface for alignment matrices. It generates a range of ranges, where both the outer range and the inner ranges model std::ranges::input_range. The interface uses a column-major-order to iterate over the matrix, i.e. the outer range iterates over the columns and the inner range over the num_rows of each column. In addition, the inner range type, also referred to as alignment-column, must model std::ranges::view. It is a shallow wrapper around the actual column stored in the derived_t, who implements the corresponding data model. The current alignment-column is created within the derived_t when the iterator over the outer range is dereferenced. The iterator over the resulting alignment-column is further refined by the derived_t to implement the actual behavior of the underlying alignment matrix.

Requirements of the derived type

This base class requires the following functions and types defined within the derived type in order to customise the returned type over the underlying matrix.

• seqan3::detail::alignment_matrix_column_major_range_base::value_type
• seqan3::detail::alignment_matrix_column_major_range_base::alignment_column_type
• seqan3::detail::alignment_matrix_column_major_range_base::make_proxy
• seqan3::detail::alignment_matrix_column_major_range_base::initialise_column

The following functions are not mandatory but can be overriden by the derived type:

• seqan3::detail::alignment_matrix_column_major_range_base::on_column_iterator_creation
• seqan3::detail::alignment_matrix_column_major_range_base::before_column_iterator_increment
• seqan3::detail::alignment_matrix_column_major_range_base::after_column_iterator_increment

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <span>
#include <vector>
 
#include <seqan3/alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp>
#include <seqan3/core/debug_stream.hpp>
 
class my_matrix : public seqan3::detail::alignment_matrix_column_major_range_base<my_matrix>
{
public:
    // Alias the base class
    using base_t = seqan3::detail::alignment_matrix_column_major_range_base<my_matrix>;
 
    friend base_t;
 
    // Inherit the alignment column type defined in the base class. This type is returned in initialise_column.
    using typename base_t::alignment_column_type;
 
    // The following types are required by the base type since they cannot be inferred within the base.
 
    using column_data_view_type = std::span<int>; //This type is the underlying view over the actual memory location.
    using value_type = int;                       // The actual value type.
    using reference = int &;                      // The actual reference type.
 
    my_matrix() = default;
    my_matrix(my_matrix const &) = default;
    my_matrix(my_matrix &&) = default;
    my_matrix & operator=(my_matrix const &) = default;
    my_matrix & operator=(my_matrix &&) = default;
    ~my_matrix() = default;
 
    my_matrix(size_t const num_rows, size_t const num_cols) : num_rows{num_rows}, num_cols{num_cols}
    {
        data.resize(num_rows * num_cols);
    }
 
protected:
    std::vector<int> data{};
    size_t num_rows{};
    size_t num_cols{};
 
    //Required for the base class. Initialises the current column given the column index.
    alignment_column_type initialise_column(size_t const column_index) noexcept
    {
        return alignment_column_type{*this,
                                     column_data_view_type{std::addressof(data[num_rows * column_index]), num_rows}};
    }
 
    //Required for the base class. Initialises the proxy for the current iterator over the current column.
    template <std::random_access_iterator iter_t>
    constexpr reference make_proxy(iter_t iter) noexcept
    {
        return *iter;
    }
};
 
int main()
{
    my_matrix matrix{3, 5};
 
    // Fill the matrix with
    int val = 0;
    for (auto col : matrix)     // Iterate over the columns
        for (auto & cell : col) // Iterate over the cells in one column.
            cell = val++;
 
    // Print the matrix column by column
    for (auto col : matrix)
        seqan3::debug_stream << col << '\n';
}

Member Function Documentation

after_column_iterator_increment()

template<typename derived_t >

template<typename iter_t >

constexpr void seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::after_column_iterator_increment ( iter_t  host_iter )

inlineconstexprprivatenoexcept

Allows to perform additional steps after incrementing the alignment-column-iterator.

Template Parameters

iter_t

The iterator type of the host iterator.

Parameters

[in]

host_iter

The wrapped iterator to the actual memory storage.

before_column_iterator_increment()

template<typename derived_t >

template<typename iter_t >

constexpr void seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::before_column_iterator_increment ( iter_t  host_iter )

inlineconstexprprivatenoexcept

Allows to perform additional steps before incrementing the alignment-column-iterator.

Template Parameters

iter_t

The iterator type of the host iterator.

Parameters

[in]

host_iter

The wrapped iterator to the actual memory storage.

initialise_column()

template<typename derived_t >

alignment_column_type seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::initialise_column ( size_t  column_index )

inlineprivate

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()

template<typename derived_t >

value_type seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::make_proxy ( iter_t  host_iter )

inlineprivatenoexcept

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.

on_column_iterator_creation()

template<typename derived_t >

template<typename iter_t >

constexpr void seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::on_column_iterator_creation ( iter_t  host_iter )

inlineconstexprprivatenoexcept

Allows additional initialisations when calling begin on an alignment-column.

Template Parameters

iter_t

The iterator type of the host iterator.

Parameters

[in]

host_iter

The wrapped iterator to the actual memory storage.

Member Data Documentation

column_data_view_type

template<typename derived_t >

typedef seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::column_data_view_type

private

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.

value_type

template<typename derived_t >

typedef seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::value_type

private

The proxy type of an alignment matrix.

Note

This type must be defined by the derived type.

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

• alignment_matrix_column_major_range_base.hpp