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 structure_file_input_traits:

Related Symbols
(Note that these are not member symbols.)
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.
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 a 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.
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 Symbol 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.

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

• structure_file/input.hpp