seqan3::structure_file_input_default_traits_rna Struct Reference

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

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

Inheritance diagram for seqan3::structure_file_input_default_traits_rna:

Public Types
Member types
Definitions to satisfy seqan3::StructureFileInputTraits.
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.
template<typename _seq_container >
using	seq_container_container = concatenated_sequences< _seq_container >
	The container for sequences is seqan3::concatenated_sequences.
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.
template<typename _id_container >
using	id_container_container = concatenated_sequences< _id_container >
	The container for identifier strings is seqan3::concatenated_sequences.
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.
template<typename _bpp_container >
using	bpp_container_container = std::vector< _bpp_container >
	The container for interaction strings is 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 _structure_container >
using	structure_container_container = concatenated_sequences< _structure_container >
	The container for structure annotation strings is seqan3::concatenated_sequences.
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.
template<typename _structured_seq_container >
using	structured_seq_container_container = concatenated_sequences< _structured_seq_container >
	The container for sequences is seqan3::concatenated_sequences.
using	energy_type = std::optional< double >
	The type of the energy is std::optional<double>.
template<typename _energy_type >
using	energy_container = std::vector< _energy_type >
	The type of a container of energy values is std::vector.
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.
template<typename _react_container >
using	react_container_container = std::vector< _react_container >
	The type of a container of reactivity strings 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.
template<typename _comment_container >
using	comment_container_container = concatenated_sequences< _comment_container >
	The container for comments is seqan3::concatenated_sequences.
using	offset_type = size_t
	The type of the offset is size_t.
template<typename _offset_type >
using	offset_container = std::vector< _offset_type >
	The type of a container of offset values is std::vector.

Detailed Description

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:

    struct my_traits : structure_file_input_default_traits_rna
    {
        using seq_alphabet = rna4; // instead of rna5
    };

    structure_file_input<my_traits> fin{filename.get_path()};

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

• seqan3/io/structure_file/input.hpp