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 Description

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  )

inlineprotected

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  )

inlineprotected

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

inlinestatic

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