SeqAn3
The Modern C++ library for sequence analysis.
seqan3::alignment_file_input_traits Interface Reference

The requirements a traits_type for seqan3::alignment_file_input must meet. More...

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

+ Inheritance diagram for seqan3::alignment_file_input_traits:

Related Functions

(Note that these are not member functions.)

Requirements for seqan3::alignment_file_input_traits

You can expect these member types of all types that model seqan3::alignment_file_input_traits.

using sequence_alphabet
 Alphabet of the characters for the seqan3::field::seq; must model seqan3::alphabet.
 
using sequence_legal_alphabet
 Intermediate alphabet for seqan3::field::seq; must model seqan3::alphabet and be convertible to sequence_alphabet. More...
 
using sequence_container
 Type template of the seqan3::field::seq, a container template over sequence_alphabet; must model seqan3::sequence_container.
 
using id_container
 Type template of the seqan3::field::id, a container template over char; must model seqan3::sequence_container.
 
using quality_alphabet
 Alphabet of the characters for the seqan3::field::qual; must model seqan3::writable_quality_alphabet.
 
using quality_container
 Type template of the seqan3::field::qual, a container template over quality_alphabet; must model seqan3::sequence_container.
 
using ref_sequences
 The type of range over reference sequences; must model std::ranges::forward_range, the value_type must also model std::ranges::forward_range, and the value type of the value type must model seqan3::alphabet (e.g. std::vector<std::vector<dna4>>). More...
 
using ref_ids
 The type of range over reference sequences; must model std::ranges::forward_range, the value_type must also model std::ranges::forward_range, and the value type of the value type must model seqan3::alphabet (e.g. std::vector<string>). More...
 

Detailed Description

The requirements a traits_type for seqan3::alignment_file_input must meet.

Friends And Related Function Documentation

◆ ref_ids()

using ref_ids
related

The type of range over reference sequences; must model std::ranges::forward_range, the value_type must also model std::ranges::forward_range, and the value type of the value type must model seqan3::alphabet (e.g. std::vector<string>).

Attention
This type is the second template parameter of the alignment_file_default_traits and should not be manually configured in order to allow for automatic type deduction from reference information input on construction.

◆ ref_sequences()

using ref_sequences
related

The type of range over reference sequences; must model std::ranges::forward_range, the value_type must also model std::ranges::forward_range, and the value type of the value type must model seqan3::alphabet (e.g. std::vector<std::vector<dna4>>).

Attention
This type is the first template parameter of the alignment_file_default_traits and should not be manually configured in order to allow for automatic type deduction from reference information input on construction.

◆ sequence_legal_alphabet()

using sequence_legal_alphabet
related

Intermediate alphabet for seqan3::field::seq; must model seqan3::alphabet and be convertible to sequence_alphabet.

This alphabet can be a superset of sequence_alphabet to allow conversion of some characters without producing an error, e.g. if this is set to seqan3::dna15 and sequence_alphabet is set to seqan3::dna5, 'M' will be an accepted character and automatically converted to 'N', while 'Z' will still be an illegal character and produce an error.


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