The requirements a traits_type for seqan3::structure_file_input must meet. More...
#include <seqan3/io/structure_file/input.hpp>
Related Functions | |
(Note that these are not member functions.) | |
Requirements for seqan3::StructureFileInputTraits | |
You can expect these member types of all types that satisfy seqan3::StructureFileInputTraits. 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::SequenceContainer. | |
using | seq_container_container |
Type template of a column of seqan3::field::SEQ, a container template that can hold multiple seq_container ; must satisfy seqan3::SequenceContainer. | |
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::SequenceContainer. | |
using | id_container_container |
Type template of a column of seqan3::field::ID, a container template that can hold multiple id_container ; must satisfy seqan3::SequenceContainer. | |
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::SequenceContainer. | |
using | bpp_container_container |
Type template of a column of seqan3::field::BPP, a container template that can hold multiple bpp_container ; must satisfy seqan3::SequenceContainer. | |
using | structure_alphabet |
Alphabet of the characters for the seqan3::field::STRUCTURE; must satisfy seqan3::RnaStructureAlphabet. | |
using | structure_container |
Type template of the seqan3::field::STRUCTURE, a container template over structure_alphabet ; must satisfy seqan3::SequenceContainer. | |
using | structure_container_container |
Type template of a column of seqan3::field::STRUCTURE, a container template that can hold multiple structure_container ; must satisfy seqan3::SequenceContainer. | |
using | energy_type |
Type template of the seqan3::field::ENERGY; must be std::optional of a type satisfying std::is_floating_point. More... | |
using | energy_container |
Type template of a column of seqan3::field::ENERGY, a container template that can hold multiple energy_type ; must satisfy seqan3::SequenceContainer. | |
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::SequenceContainer. | |
using | react_container_container |
Type template of a column of seqan3::field::REACT and seqan3::field::REACT_ERR, a container template that can hold multiple react_container ; must satisfy seqan3::SequenceContainer. | |
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::SequenceContainer. | |
using | comment_container_container |
Type template of a column of seqan3::field::COMMENT, a container template that can hold multiple comment_container ; must satisfy seqan3::SequenceContainer. | |
using | offset_type |
Type template of the seqan3::field::OFFSET; must statisfy std::numeric_limits::is_integer. | |
using | offset_container |
Type template of a column of seqan3::field::OFFSET, a container template that can hold multiple offset_type ; must satisfy seqan3::SequenceContainer. | |
The requirements a traits_type for seqan3::structure_file_input must meet.
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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.
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related |
Intermediate alphabet for seqan3::field::SEQ; must satisfy seqan3::Alphabet and be convertible to seq_alphabet
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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.