SeqAn3
seqan3::structure_file_input_default_traits_rna Struct Reference

The default traits for seqan3::structure_file_in. More...

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

Inheritance diagram for seqan3::structure_file_input_default_traits_rna:
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Public Types

Member types
using seq_alphabet = rna5
 
using seq_legal_alphabet = rna15
 
template<typename _seq_alphabet >
using seq_container = std::vector< _seq_alphabet >
 
template<typename _seq_container >
using seq_container_container = concatenated_sequences< _seq_container >
 
using id_alphabet = char
 
template<typename _id_alphabet >
using id_container = std::basic_string< _id_alphabet >
 
template<typename _id_container >
using id_container_container = concatenated_sequences< _id_container >
 
using bpp_prob = double
 
using bpp_partner = size_t
 
template<typename _bpp_prec , typename _bpp_partner >
using bpp_item = std::pair< _bpp_prec, _bpp_partner >
 
template<typename _bpp_item >
using bpp_queue = std::set< _bpp_item >
 
template<typename _bpp_queue >
using bpp_container = std::vector< _bpp_queue >
 
template<typename _bpp_container >
using bpp_container_container = std::vector< _bpp_container >
 
using structure_alphabet = wuss51
 
template<typename _structure_alphabet >
using structure_container = std::vector< _structure_alphabet >
 
template<typename _structure_container >
using structure_container_container = concatenated_sequences< _structure_container >
 
template<typename _seq_alphabet , typename _structure_alphabet >
using structured_seq_alphabet = structured_rna< _seq_alphabet, _structure_alphabet >
 
template<typename _structured_seq_alphabet >
using structured_seq_container = std::vector< _structured_seq_alphabet >
 
template<typename _structured_seq_container >
using structured_seq_container_container = concatenated_sequences< _structured_seq_container >
 
using energy_type = std::optional< double >
 
template<typename _energy_type >
using energy_container = std::vector< _energy_type >
 
using react_type = double
 
template<typename _react_type >
using react_container = std::vector< _react_type >
 
template<typename _react_container >
using react_container_container = std::vector< _react_container >
 
using comment_alphabet = char
 
template<typename _comment_alphabet >
using comment_container = std::basic_string< _comment_alphabet >
 
template<typename _comment_container >
using comment_container_container = concatenated_sequences< _comment_container >
 
using offset_type = size_t
 
template<typename _offset_type >
using offset_container = std::vector< _offset_type >
 

Detailed Description

The default traits for seqan3::structure_file_in.

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:

struct my_traits : structure_file_input_default_traits_rna
{
using seq_alphabet = rna4; // instead of rna5
};
structure_file_in<my_traits> fin{filename.get_path()};

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