Alignment

namespace seqan3

The main SeqAn3 namespace.

Helpers for seqan3::semi_alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::semi_alphabet_concept.

Helpers for seqan3::alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::alphabet_concept.

Helpers for seqan3::nucleotide_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::nucleotide_concept.

Alphabet aliases

Other names (typedefs) for seqan3::nucl16

Range concepts

Adapted from the Ranges TS.

Container concepts

Container concepts as defined by the standard library (or very close).

Container-of-container concepts

Shortcuts for multi-dimensional container concepts.

Enums

enum align_record_fields

Values:

RAW_SCORE

BIT_SCORE

EDIT_DISTANCE

PERCENT_IDENTITY

Variables

concept bool seqan3::align_file_traits_concept = requires (t v) { t::stream_type; t::valid_formats; t::valid_compression_formats; t::query_seqs_type; t::query_ids_type; t::subject_seqs_type; t::subject_ids_type; t::qry_gaps_type; t::sbj_gaps_type; }

char align_record_fields_sam_bam_tags[2][] = { "AS", "BS", "NM", ... }

std::string align_record_field_labels[] = { "raw score" "bit score", "edit distance", ... }

namespace seqan3

The main SeqAn3 namespace.

Helpers for seqan3::semi_alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::semi_alphabet_concept.

Helpers for seqan3::alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::alphabet_concept.

Helpers for seqan3::nucleotide_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::nucleotide_concept.

Alphabet aliases

Other names (typedefs) for seqan3::nucl16

Range concepts

Adapted from the Ranges TS.

Container concepts

Container concepts as defined by the standard library (or very close).

Container-of-container concepts

Shortcuts for multi-dimensional container concepts.

Functions

template <typename record_type>

requires seqan3::align_record_concept< record_type >(requires container_concept < record_type > &&requires align_record_concept< typename record_type::value_type >)

template <typename align_file_in_traits = align_file_in_default_dna_traits>

class align_file_in

Inherits from seqan3::detail::align_file< align_file_in_traits >

Public Functions

align_file_in(std::string const &_file_name)

align_file_in(align_file_in const&)

align_file_in &operator=(align_file_in const&)

align_file_in(align_file_in&&)

align_file_in &operator=(align_file_in&&)

template <typename record_type>

requires seqan3::align_file_in::align_record_concept(requires container_concept < record_type > &&requires align_record_concept< typename record_type::value_type >)

template <typename... types>

void read_raw(...)

void set_store(std::tuple<subject_seqs_type const&, subject_ids_type const&> const&)

template <typename... arg_types>

void read_raw(arg_types&&... args)

Protected Functions

~align_file_in()

Protected Attributes

store_type store

struct store_type

Public Members

template<>
align_file_in_traits::query_seqs_type *qry_seqs = {nullptr}

template<>
align_file_in_traits::query_ids_type *qry_ids = {nullptr}

template<>
align_file_in_traits::subject_seqs_type *sbj_seqs = {nullptr}

template<>
align_file_in_traits::subject_ids_type *sbj_ids = {nullptr}

template<>
align_file_in_traits::query_seqs_type qry_seqs_from_file

template<>
align_file_in_traits::query_ids_type qry_ids_from_file

template<>
align_file_in_traits::subject_seqs_type sbj_seqs_from_file

template<>
align_file_in_traits::subject_ids_type sbj_ids_from_file

template<>
align_file_in_traits::query_id_map_type query_id_map

template<>
align_file_in_traits::subject_id_map_type subject_id_map

struct align_file_in_default_aa_traits

Inherits from seqan3::align_file_in_default_dna_traits

Public Types

using query_seqs_type = std::vector<aa27_vector>

using subject_seqs_type = std::vector<aa27_vector>

using stream_type = std::ifstream

using valid_formats = std::variant<align_file_in_format_sam, align_file_in_format_bam, align_file_in_format_blast_tabular align_file_in_format_blast_tabular_comments>

using query_ids_type = std::vector<std::string>

using subject_ids_type = std::vector<std::string>

Public Static Attributes

constexpr std::vector<std::pair<std::string, void>> valid_compression_formats = {}

struct align_file_in_default_dna_traits

Subclassed by seqan3::align_file_in_default_aa_traits

Public Types

using stream_type = std::ifstream

using valid_formats = std::variant<align_file_in_format_sam, align_file_in_format_bam, align_file_in_format_blast_tabular align_file_in_format_blast_tabular_comments>

using query_seqs_type = std::vector<dna_vector>

using query_ids_type = std::vector<std::string>

using subject_seqs_type = std::vector<dna_vector>

using subject_ids_type = std::vector<std::string>

Public Static Attributes

constexpr std::vector<std::pair<std::string, void>> valid_compression_formats = {}

namespace seqan3

The main SeqAn3 namespace.

Helpers for seqan3::semi_alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::semi_alphabet_concept.

Helpers for seqan3::alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::alphabet_concept.

Helpers for seqan3::nucleotide_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::nucleotide_concept.

Alphabet aliases

Other names (typedefs) for seqan3::nucl16

Range concepts

Adapted from the Ranges TS.

Container concepts

Container concepts as defined by the standard library (or very close).

Container-of-container concepts

Shortcuts for multi-dimensional container concepts.

template <typename align_file_out_traits = align_file_out_default_dna_traits>

class align_file_out

Inherits from seqan3::detail::align_file< align_file_out_traits >

Public Functions

align_file_out(std::string const &_file_name)

align_file_out(align_file_out const&)

align_file_out &operator=(align_file_out const&)

align_file_out(align_file_out&&)

align_file_out &operator=(align_file_out&&)

template <typename record_type>

requires seqan3::align_file_out::align_record_concept(requires container_concept < record_type > &&requires align_record_concept< typename record_type::value_type >)

template <typename... types>

void write_raw(...)

template <typename... arg_types>

void write_raw(arg_types&&... args)

Protected Functions

~align_file_out()

Protected Attributes

store_type store

struct store_type

Public Members

template<>
align_file_out_traits::query_seqs_type *qry_seqs = {nullptr}

template<>
align_file_out_traits::query_ids_type *qry_ids = {nullptr}

template<>
align_file_out_traits::subject_seqs_type *sbj_seqs = {nullptr}

template<>
align_file_out_traits::subject_ids_type *sbj_ids = {nullptr}

struct align_file_out_default_aa_traits

Inherits from seqan3::align_file_out_default_dna_traits

Public Types

using query_seqs_type = std::vector<aa27_vector>

using subject_seqs_type = std::vector<aa27_vector>

using stream_type = std::ifstream

using valid_formats = std::variant<align_file_out_format_sam, align_file_out_format_bam, align_file_out_format_blast_tabular align_file_out_format_blast_tabular_comments, align_file_out_format_blast_report>

using query_ids_type = std::vector<std::string>

using subject_ids_type = std::vector<std::string>

Public Static Attributes

constexpr std::vector<std::pair<std::string, void>> valid_compression_formats = {}

struct align_file_out_default_dna_traits

Subclassed by seqan3::align_file_out_default_aa_traits

Public Types

using stream_type = std::ifstream

using valid_formats = std::variant<align_file_out_format_sam, align_file_out_format_bam, align_file_out_format_blast_tabular align_file_out_format_blast_tabular_comments, align_file_out_format_blast_report>

using query_seqs_type = std::vector<dna_vector>

using query_ids_type = std::vector<std::string>

using subject_seqs_type = std::vector<dna_vector>

using subject_ids_type = std::vector<std::string>

Public Static Attributes

constexpr std::vector<std::pair<std::string, void>> valid_compression_formats = {}