seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::sequence_format_base Struct Reference

An abstract base class to store the selected input format. More...

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

Public Member Functions
virtual void	read_sequence_record (std::istream &instream, record_type &record_buffer, std::streampos &position_buffer, sequence_file_input_options_type const &options)=0
	Reads the next format specific record from the given istream.
Constructors, destructor and assignment
	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

Detailed Description

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>>
struct seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::sequence_format_base

An abstract base class to store the selected input format.

This abstract base class is used to store the user given input format as a type-erased base class in a std::unique_ptr. There is exactly one derived type that implements this abstract base class called seqan3::sequence_file_input::selected_sequence_format which is a private subclass of seqan3::sequence_file_input. It is not exposed to the user and allows to hide the implementation detail of storing a specfic format instance which is first known at runtime.

Constructor & Destructor Documentation

~sequence_format_base()

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>>

virtual seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::sequence_format_base::~sequence_format_base ( )

virtualdefault

Virtual default.

Member Function Documentation

read_sequence_record()

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>>

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

pure virtual

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.

Implemented in seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::selected_sequence_format< format_t >.

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

• sequence_file/input.hpp