seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::selected_sequence_format< format_t > Struct Template Reference

The specific selected format to read the records from. More...

Inheritance diagram for seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::selected_sequence_format< format_t >:

Public Member Functions
void	read_sequence_record (std::istream &instream, record_type &record_buffer, std::streampos &position_buffer, sequence_file_input_options_type const &options) override
	Reads the next format specific record from the given istream.
Constructors, destructor and assignment
	selected_sequence_format ()=default
	Default.
	selected_sequence_format (selected_sequence_format const &)=default
	Default.
	selected_sequence_format (selected_sequence_format &&)=default
	Default.
selected_sequence_format &	operator= (selected_sequence_format const &)=default
	Default.
selected_sequence_format &	operator= (selected_sequence_format &&)=default
	Default.
	~selected_sequence_format ()=default
Public Member Functions inherited from seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::sequence_format_base
	sequence_format_base ()=default
	Default.
	sequence_format_base (sequence_format_base const &)=default
	Default.
	sequence_format_base (sequence_format_base &&)=default
	Default.
sequence_format_base &	operator= (sequence_format_base const &)=default
	Default.
sequence_format_base &	operator= (sequence_format_base &&)=default
	Default.
virtual	~sequence_format_base ()=default

Public Attributes
detail::sequence_file_input_format_exposer< format_t >	_format {}
	The selected format stored as a format exposer object.

Detailed Descriptionno-api

template<sequence_file_input_traits traits_type_ = sequence_file_input_default_traits_dna, detail::fields_specialisation selected_field_ids_ = fields<field::seq, field::id, field::qual>, detail::type_list_of_sequence_file_input_formats valid_formats_ = type_list<format_embl, format_fasta, format_fastq, format_genbank, format_sam>>
template<typename format_t>
struct seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::selected_sequence_format< format_t >

The specific selected format to read the records from.

Template Parameters

format_t

The user specific format type to store.

This class implements the format specific read operation based on the instantiated format type. The specfic format type is selected at runtime and stored through a pointer to the abstract seqan3::sequence_file_input::sequence_format_base class. A virtual function call then ensures that the specific read record function of the selected format is invoked.

Constructor & Destructor Documentation

~selected_sequence_format() [no-api]

template<sequence_file_input_traits traits_type_ = sequence_file_input_default_traits_dna, detail::fields_specialisation selected_field_ids_ = fields<field::seq, field::id, field::qual>, detail::type_list_of_sequence_file_input_formats valid_formats_ = type_list<format_embl, format_fasta, format_fastq, format_genbank, format_sam>>

template<typename format_t >

seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::selected_sequence_format< format_t >::~selected_sequence_format ( )

no-apidefault

Default.

Member Function Documentation

read_sequence_record() [no-api]

template<sequence_file_input_traits traits_type_ = sequence_file_input_default_traits_dna, detail::fields_specialisation selected_field_ids_ = fields<field::seq, field::id, field::qual>, detail::type_list_of_sequence_file_input_formats valid_formats_ = type_list<format_embl, format_fasta, format_fastq, format_genbank, format_sam>>

template<typename format_t >

void seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::selected_sequence_format< format_t >::read_sequence_record ( std::istream &  instream, record_type &  record_buffer, std::streampos &  position_buffer, sequence_file_input_options_type const &  options  )

no-apiinlineoverridevirtual

Reads the next format specific record from the given istream.

Parameters

[in,out]	instream	The input stream to extract the next record from.
[in,out]	record_buffer	The record buffer to fill.
[in,out]	position_buffer	The buffer to store the position of the current record.
[in]	options	User specific format options set from outside.

Invokes the actual read sequence record function for the selected format and fills the record accordingly.

Implements seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::sequence_format_base.

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

• sequence_file/input.hpp