SeqAn3
seqan3::sequence_file_input_default_traits_dna Struct Reference

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

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

Inheritance diagram for seqan3::sequence_file_input_default_traits_dna:
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Public Types

Member types
using sequence_alphabet = dna5
 
using sequence_legal_alphabet = dna15
 
template<typename _sequence_alphabet >
using sequence_container = std::vector< _sequence_alphabet >
 
template<typename _sequence_container >
using sequence_container_container = concatenated_sequences< _sequence_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 quality_alphabet = phred42
 
template<typename _quality_alphabet >
using quality_container = std::vector< _quality_alphabet >
 
template<typename _quality_container >
using quality_container_container = concatenated_sequences< _quality_container >
 

Detailed Description

The default traits for seqan3::sequence_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 and a compressed container:

struct my_traits : sequence_file_input_default_traits_dna
{
using sequence_alphabet = dna4; // instead of dna5
template <typename alph>
using sequence_container = bitcompressed_vector<alph>; // must be defined as a template!
};
sequence_file_input<my_traits> fin{"/tmp/my.fasta"};
//...

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