The default traits for seqan3::structure_file_input. More...
#include <seqan3/io/structure_file/input.hpp>
Public Types | |
Member types | |
Definitions to satisfy seqan3::structure_file_input_traits. | |
using | seq_alphabet = rna5 |
The sequence alphabet is seqan3::rna5. | |
using | seq_legal_alphabet = rna15 |
The legal sequence alphabet for parsing is seqan3::rna15. | |
template<typename _seq_alphabet > | |
using | seq_container = std::vector< _seq_alphabet > |
The type of an RNA sequence is std::vector. | |
using | id_alphabet = char |
The alphabet for an identifier string is char. | |
template<typename _id_alphabet > | |
using | id_container = std::basic_string< _id_alphabet > |
The string type for an identifier is std::basic_string. | |
using | bpp_prob = double |
The type for a base pair probability is double. | |
using | bpp_partner = size_t |
The type for the partner position of a base pair probability is size_t. | |
template<typename _bpp_prob , typename _bpp_partner > | |
using | bpp_item = std::pair< _bpp_prob, _bpp_partner > |
The type of a base pair item is std::pair<double, size_t>. | |
template<typename _bpp_item > | |
using | bpp_queue = std::set< _bpp_item > |
A queue of base pair items sorted by probability is realised with std::set. | |
template<typename _bpp_queue > | |
using | bpp_container = std::vector< _bpp_queue > |
A string over all bases containing the respective interaction queues is represented as std::vector. | |
using | structure_alphabet = wuss51 |
The alphabet for a structure annotation is seqan3::phred42. | |
template<typename _structure_alphabet > | |
using | structure_container = std::vector< _structure_alphabet > |
The string type for a structure annotation is std::vector. | |
template<typename _seq_alphabet , typename _structure_alphabet > | |
using | structured_seq_alphabet = structured_rna< _seq_alphabet, _structure_alphabet > |
The combined structured sequence alphabet is seqan3::structured_rna<seqan3::rna5, seqan3::wuss51>. | |
template<typename _structured_seq_alphabet > | |
using | structured_seq_container = std::vector< _structured_seq_alphabet > |
The type of a structured RNA sequence is std::vector. | |
using | energy_type = std::optional< double > |
The type of the energy is std::optional<double>. | |
using | react_type = double |
The type of the reactivity and reactivity error is double. | |
template<typename _react_type > | |
using | react_container = std::vector< _react_type > |
The type of a string of reactivity values is std::vector. | |
using | comment_alphabet = char |
The alphabet for a comment string is char. | |
template<typename _comment_alphabet > | |
using | comment_container = std::basic_string< _comment_alphabet > |
The string type for a comment is std::basic_string. | |
using | offset_type = size_t |
The type of the offset is size_t. | |
The default traits for seqan3::structure_file_input.
If you wish to change a single or a few types from the default, just inherit from this class and "overwrite" the respective type definitions.
This example will make the file read into a smaller alphabet: