SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
seqan3::semialphabet_any< size > Class Template Reference

A semi-alphabet that type erases all other semi-alphabets of the same size. More...

#include <seqan3/alphabet/composite/semialphabet_any.hpp>

+ Inheritance diagram for seqan3::semialphabet_any< size >:

Public Member Functions

template<semialphabet other_alph_t>
 operator other_alph_t () const
 Enable conversion of semialphabet_any into other (semi-)alphabet of the same size. More...
 
Constructors, destructor and assignment
constexpr semialphabet_any () noexcept=default
 Defaulted.
 
constexpr semialphabet_any (semialphabet_any const &) noexcept=default
 Defaulted.
 
constexpr semialphabet_any (semialphabet_any &&) noexcept=default
 Defaulted.
 
constexpr semialphabet_anyoperator= (semialphabet_any const &) noexcept=default
 Defaulted.
 
constexpr semialphabet_anyoperator= (semialphabet_any &&) noexcept=default
 Defaulted.
 
 ~semialphabet_any () noexcept=default
 Defaulted.
 
template<semialphabet other_alph_t>
 semialphabet_any (other_alph_t const other)
 Construct semialphabet_any from alphabet of the same size. More...
 
- Public Member Functions inherited from seqan3::alphabet_base< semialphabet_any< size >, size, void >
constexpr alphabet_base () noexcept=default
 Defaulted.
 
constexpr alphabet_base (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_base (alphabet_base &&) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (alphabet_base &&) noexcept=default
 Defaulted.
 
 ~alphabet_base () noexcept=default
 Defaulted.
 
constexpr char_type to_char () const noexcept
 Return the letter as a character of char_type. More...
 
constexpr rank_type to_rank () const noexcept
 Return the letter's numeric value (rank in the alphabet). More...
 
constexpr semialphabet_any< size > & assign_char (char_type const chr) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr semialphabet_any< size > & assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 

Additional Inherited Members

- Static Public Attributes inherited from seqan3::alphabet_base< semialphabet_any< size >, size, void >
static constexpr detail::min_viable_uint_t< size > alphabet_size
 The size of the alphabet, i.e. the number of different values it can take. More...
 
- Protected Types inherited from seqan3::alphabet_base< semialphabet_any< size >, size, void >
using char_type = std::conditional_t< std::same_as< void, void >, char, void >
 The char representation; conditional needed to make semi alphabet definitions legal. More...
 
using rank_type = detail::min_viable_uint_t< size - 1 >
 The type of the alphabet when represented as a number (e.g. via to_rank()). More...
 

Detailed Description

template<size_t size>
class seqan3::semialphabet_any< size >

A semi-alphabet that type erases all other semi-alphabets of the same size.

This alphabet provides a generic representation for different alphabets of the same size by erasing the type of the alphabet it is constructed from. This enables the usage of a single type although assigning different alphabets. The semialphabet_any can also be converted to any other (semi-)alphabet of the same size. It is therefore possible to convert the semialphabet_any into an alphabet type that is not the original alphabet type. However, this should either be avoided or used with care as no warnings are given when attempting to convert the semialphabet_any into a type that is not comparable to the original alphabet type. The main advantage of using this data structure is to reduce instantiation of templates when using multiple alphabets of the same size and either their character representation is not important or they are reified at a later point in the program.

See also
https://en.wikipedia.org/wiki/Type_erasure
https://en.wikipedia.org/wiki/Reification_(computer_science)

Example

// This example illustrates how we can reduce the usage of templates (or the amount of different instantiations) via
// type erasure. Having only one function generated for `algorithm()` is the only benefit of using `semialphabet_any`
// here. Of course this only makes sense for your application if the part of the program that is agnostic of the
// character representation (your equivalent of `algorithm()`) is substantially larger than the specific parts – and
// if compile-time and/or size of the exectuble are a concern.
#include <iostream>
using namespace seqan3::literals;
// Print is a template and gets instantiated two times because the behaviour is different for both types
template <typename rng_t>
void print(rng_t && r)
{
seqan3::debug_stream << r << '\n';
}
// Algorithm is not a template, only one instance is generated by the compiler
// Type information is encoded via a run-time parameter
void algorithm(std::vector<seqan3::semialphabet_any<10> > & r, bool is_murphy)
{
// Algorithm example that replaces rank 0 with rank 1
for (auto & v : r)
if (seqan3::to_rank(v) == 0)
// Here we reify the type for printing
if (is_murphy)
print(r | std::views::transform([] (auto const & in) { return static_cast<seqan3::aa10murphy>(in); }));
else
print(r | std::views::transform([] (auto const & in) { return static_cast<seqan3::aa10li>(in); }));
}
// Two instances of algo_pre exist
// They type erase the different arguments to the same type and encode the type information as a run-time parameter
void algo_pre(seqan3::aa10li_vector const & v)
{
| std::views::transform([] (auto const & in)
{
return static_cast<seqan3::semialphabet_any<10>>(in);
})
| seqan3::views::to<std::vector>;
algorithm(tmp, false);
}
void algo_pre(seqan3::aa10murphy_vector const & v)
{
| std::views::transform([] (auto const & in)
{
return static_cast<seqan3::semialphabet_any<10>>(in);
})
| seqan3::views::to<std::vector>;
algorithm(tmp, true);
}
int main()
{
seqan3::aa10li_vector v1{"AVRSTXOUB"_aa10li};
algo_pre(v1); // BIKBBBKCB
seqan3::aa10murphy_vector v2{"AVRSTXOUB"_aa10murphy};
algo_pre(v2); // BIKSSSKCB
}
Meta-header for the aminoacid submodule; includes all headers from alphabet/aminoacid/.
The reduced Li amino acid alphabet.
Definition: aa10li.hpp:83
The reduced Murphy amino acid alphabet.
Definition: aa10murphy.hpp:82
A semi-alphabet that type erases all other semi-alphabets of the same size.
Definition: semialphabet_any.hpp:48
Provides seqan3::debug_stream and related types.
constexpr auto assign_rank_to
Assign a rank to an alphabet object.
Definition: concept.hpp:291
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition: concept.hpp:155
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
decltype(detail::transform< trait_t >(list_t{})) transform
Apply a transformation trait to every type in the list and return a seqan3::type_list of the results.
Definition: traits.hpp:444
The SeqAn namespace for literals.
Provides seqan3::semialphabet_any.
Provides seqan3::views::to.

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

◆ semialphabet_any()

template<size_t size>
template<semialphabet other_alph_t>
seqan3::semialphabet_any< size >::semialphabet_any ( other_alph_t const  other)
inlineexplicit

Construct semialphabet_any from alphabet of the same size.

This entity is stable. Since version 3.1.

Member Function Documentation

◆ operator other_alph_t()

template<size_t size>
template<semialphabet other_alph_t>
seqan3::semialphabet_any< size >::operator other_alph_t ( ) const
inlineexplicit

Enable conversion of semialphabet_any into other (semi-)alphabet of the same size.

This entity is stable. Since version 3.1.


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