SeqAn3
The Modern C++ library for sequence analysis.
seqan3::structure_file_input_traits Interface Reference

The requirements a traits_type for seqan3::structure_file_input must meet. More...

#include <seqan3/io/structure_file/input.hpp>

+ Inheritance diagram for seqan3::structure_file_input_traits:

Related Functions

(Note that these are not member functions.)

Requirements for seqan3::structure_file_input_traits

You can expect these member types of all types that satisfy seqan3::structure_file_input_traits.

Note that the alphabet type of the seqan3::field::structured_seq is a combined alphabet, i.e. either seqan3::structured_rna<sequence_alphabet, structure_alphabet> or seqan3::structured_aa<sequence_alphabet, structure_alphabet> and the container type templates for the field are those of seqan3::field::seq and seqan3::field::structure, respectively.

using seq_alphabet
 Alphabet of the characters for the seqan3::field::seq; must satisfy seqan3::alphabet.
 
using seq_legal_alphabet
 Intermediate alphabet for seqan3::field::seq; must satisfy seqan3::alphabet and be convertible to seq_alphabet. More...
 
using seq_container
 Type template of the seqan3::field::seq, a container template over seq_alphabet; must satisfy seqan3::sequence_container.
 
using id_alphabet
 Alphabet of the characters for the seqan3::field::id; must satisfy seqan3::alphabet.
 
using id_container
 Type template of the seqan3::field::id, a container template over id_alphabet; must satisfy seqan3::sequence_container.
 
using bpp_prob
 Data type for the base pair probabilities in seqan3::field::bpp; must satisfy std::is_floating_point.
 
using bpp_partner
 Data type for the partner index of an interaction in seqan3::field::bpp; must satisfy std::numeric_limits::is_integer.
 
using bpp_queue
 A container template representing a set of interactions of type bpp_item, which are (comparable) tuples of bpp_prob and bpp_partner; must satisfy seqan3::container and must provide an std::emplace(bpp_prob, bpp_partner) function.
 
using bpp_container
 Type template of the seqan3::field::bpp, a container template over a set (bpp_queue) of interactions; must satisfy seqan3::sequence_container.
 
using structure_alphabet
 Alphabet of the characters for the seqan3::field::structure; must satisfy seqan3::rna_structure_alphabet.
 
using structure_container
 Type template of the seqan3::field::structure, a container template over structure_alphabet; must satisfy seqan3::sequence_container.
 
using energy_type
 Type template of the seqan3::field::energy; must be std::optional of a type satisfying std::is_floating_point. More...
 
using react_type
 Data type for the reactivity and reactivity error in seqan3::field::react and seqan3::field::react_err, respectively; must satisfy std::is_floating_point.
 
using react_container
 Type template of the seqan3::field::react and seqan3::field::react_err, a container template over react_type; must satisfy seqan3::sequence_container.
 
using comment_alphabet
 Alphabet of the characters for the seqan3::field::comment; must satisfy seqan3::alphabet.
 
using comment_container
 Type template of the seqan3::field::comment, a container template over comment_alphabet; must satisfy seqan3::sequence_container.
 
using offset_type
 Type template of the seqan3::field::offset; must statisfy std::numeric_limits::is_integer.
 

Detailed Description

The requirements a traits_type for seqan3::structure_file_input must meet.

Friends And Related Function Documentation

◆ energy_type()

using energy_type
related

Type template of the seqan3::field::energy; must be std::optional of a type satisfying std::is_floating_point.

If the file record contains an energy, the value can be obtained through dereference or std::optional::value. Otherwise, operator bool or std::optional::has_value return false.

◆ seq_legal_alphabet()

using seq_legal_alphabet
related

Intermediate alphabet for seqan3::field::seq; must satisfy seqan3::alphabet and be convertible to seq_alphabet.

This alphabet can be a superset of seq_alphabet to allow conversion of some characters without producing an error, e.g. if this is set to seqan3::rna15 and seq_alphabet is set to seqan3::rna5, 'M' will be an accepted character and automatically converted to 'N', while 'Z' will still be an illegal character and produce an error.


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