seqan3::format_genbank Class Reference

The GenBank format. More...

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

Inheritance diagram for seqan3::format_genbank:

Public Member Functions
Constructors, destructor and assignment
	format_genbank () noexcept=default
	Defaulted.
	format_genbank (format_genbank const &) noexcept=default
	Defaulted.
format_genbank &	operator= (format_genbank const &) noexcept=default
	Defaulted.
	format_genbank (format_genbank &&) noexcept=default
	Defaulted.
format_genbank &	operator= (format_genbank &&) noexcept=default
	Defaulted.
	~format_genbank () noexcept=default
	Defaulted.

Static Public Attributes
static std::vector< std::string >	file_extensions
	The valid file extensions for this format; note that you can modify this value. More...

Protected Member Functions
template<typename stream_type , typename seq_legal_alph_type , bool seq_qual_combined, typename seq_type , typename id_type , typename qual_type >
void	read_sequence_record (stream_type &stream, sequence_file_input_options< seq_legal_alph_type, seq_qual_combined > const &options, seq_type &sequence, id_type &id, qual_type &qualities)
	Read from the specified stream and back-insert into the given field buffers. More...
template<typename stream_type , typename seq_type , typename id_type , typename qual_type >
void	write_sequence_record (stream_type &stream, sequence_file_output_options const &options, seq_type &&sequence, id_type &&id, qual_type &&qualities)
	Write the given fields to the specified stream. More...

Additional Inherited Members
Related Functions inherited from sequence_file_input_format
void	read_sequence_record (stream_type &stream, seqan3::sequence_file_input_options const &options, seq_type &sequence, id_type &id, qual_type &qualities)
	Read from the specified stream and back-insert into the given field buffers. More...
static inline std::vector< std::string >	file_extensions
	The format type is required to provide a vector of all supported file extensions.
Related Functions inherited from sequence_file_output_format
static inline std::vector< std::string >	file_extensions
	The format type is required to provide a vector of all supported file extensions.

Detailed Descriptionno-api

The GenBank format.

Introduction

genbank is the format used in the GenBank sequence database. See this example record at NCBI for more details about the format.

fields_specialisation

The genbank format provides the fields seqan3::field::seq and seqan3::field::id. Both fields are required when writing.

Implementation notes

There is no truncate_ids option while reading because the GenBank format has no (FASTA-like) idbuffer. Instead, there is the option "complete_header" to indicate whether the whole header is to be read (embl_genbank_complete_header=true) or only the "LOCUS" information should be stored.

Qualities passed to the write function are ignored.

Member Function Documentation

read_sequence_record()

template<typename stream_type , typename seq_legal_alph_type , bool seq_qual_combined, typename seq_type , typename id_type , typename qual_type >

void seqan3::format_genbank::read_sequence_record ( stream_type &  stream, sequence_file_input_options< seq_legal_alph_type, seq_qual_combined > const &  options, seq_type &  sequence, id_type &  id, qual_type &  qualities  )

no-apiinlineprotected

Read from the specified stream and back-insert into the given field buffers.

Template Parameters

stream_type	Input stream, must satisfy seqan3::input_stream_over with char.
seq_type	Type of the seqan3::field::seq input; must satisfy std::ranges::output_range over a seqan3::alphabet.
id_type	Type of the seqan3::field::id input; must satisfy std::ranges::output_range over a seqan3::alphabet.
qual_type	Type of the seqan3::field::qual input; must satisfy std::ranges::output_range over a seqan3::writable_quality_alphabet.

Parameters

[in,out]	stream	The input stream to read from.
[in]	options	File specific options passed to the format.
[out]	sequence	The buffer for seqan3::field::seq input, i.e. the "sequence".
[out]	id	The buffer for seqan3::field::id input, e.g. the header line in FastA.
[out]	qualities	The buffer for seqan3::field::qual input.

Additional requirements

• The function must also accept std::ignore as parameter for any of the fields. [This is enforced by the concept checker!]
• In this case the data read for that field shall be discarded by the format.

write_sequence_record()

template<typename stream_type , typename seq_type , typename id_type , typename qual_type >

void seqan3::format_genbank::write_sequence_record ( stream_type &  stream, sequence_file_output_options const &  options, seq_type &&  sequence, id_type &&  id, qual_type &&  qualities  )

no-apiinlineprotected

Write the given fields to the specified stream.

Template Parameters

stream_type	Output stream, must satisfy seqan3::output_stream_over with char.
seq_type	Type of the seqan3::field::seq output; must satisfy std::ranges::output_range over a seqan3::alphabet.
id_type	Type of the seqan3::field::id output; must satisfy std::ranges::output_range over a seqan3::alphabet.
qual_type	Type of the seqan3::field::qual output; must satisfy std::ranges::output_range over a seqan3::quality_alphabet.

Parameters

[in,out]	stream	The output stream to write into.
[in]	options	File specific options passed to the format.
[in]	sequence	The data for seqan3::field::seq, i.e. the "sequence".
[in]	id	The data for seqan3::field::id, e.g. the header line in FastA.
[in]	qualities	The data for seqan3::field::qual.

Additional requirements

• The format must also accept std::ignore as parameter for any of the fields, however it shall throw an exception if one of the fields required for writing the format is marked as such. [this shall be checked inside the function]

Implements sequence_file_output_format.

Member Data Documentation

file_extensions

std::vector<std::string> seqan3::format_genbank::file_extensions

no-apiinlinestatic

Initial value:

{
        { "genbank" },
        { "gb" },
        { "gbk" },
    }

The valid file extensions for this format; note that you can modify this value.

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

• seqan3/io/sequence_file/format_genbank.hpp