SeqAn3
input.hpp File Reference

Provides seqan3::structure_file_in and corresponding traits classes. More...

#include <cassert>
#include <fstream>
#include <limits>
#include <optional>
#include <string>
#include <type_traits>
#include <utility>
#include <variant>
#include <vector>
#include <range/v3/algorithm/equal.hpp>
#include <seqan3/alphabet/adaptation/char.hpp>
#include <seqan3/alphabet/aminoacid/all.hpp>
#include <seqan3/alphabet/nucleotide/rna5.hpp>
#include <seqan3/alphabet/structure/all.hpp>
#include <seqan3/core/metafunction/basic.hpp>
#include <seqan3/io/stream/concept.hpp>
#include <seqan3/io/exception.hpp>
#include <seqan3/io/filesystem.hpp>
#include <seqan3/io/record.hpp>
#include <seqan3/io/detail/in_file_iterator.hpp>
#include <seqan3/io/detail/record.hpp>
#include <seqan3/io/structure_file/input_format_concept.hpp>
#include <seqan3/io/structure_file/input_options.hpp>
#include <seqan3/io/structure_file/format_vienna.hpp>
#include <seqan3/range/container/concatenated_sequences.hpp>
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Classes

class  seqan3::structure_file_in< traits_type_, selected_field_ids_, valid_formats_, stream_type_ >
 A class for reading structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ... More...
 
struct  seqan3::structure_file_input_default_traits_aa
 A traits type that specifies input as amino acids. More...
 
struct  seqan3::structure_file_input_default_traits_rna
 The default traits for seqan3::structure_file_in. More...
 
struct  std::tuple_element< elem_no, seqan3::structure_file_in< traits_type, selected_field_ids, valid_formats, stream_type > >
 std::tuple_element overload for column-like access. [metafunction specialisation for seqan3::structure_file_in] More...
 
struct  std::tuple_size< seqan3::structure_file_in< traits_type, selected_field_ids, valid_formats, stream_type > >
 std::tuple_size overload for column-like access. [metafunction specialisation for seqan3::structure_file_in] More...
 

Namespaces

 seqan3
 The main SeqAn3 namespace.
 
 std
 SeqAn specific customisations in the standard namespace.
 

Detailed Description

Provides seqan3::structure_file_in and corresponding traits classes.

Author
Jörg Winkler <j.winkler AT fu-berlin.de>