API Reference (Modules)

Here is a list of all modules:

[detail level 123]

▼Alignment	The alignment module contains concepts, algorithms and classes that are related to the computation of pairwise and multiple sequence alignments
Aligned Sequence	Provides seqan3::aligned_sequence, as well as various ranges that model it
Band	Data structures for computing banded sequence alignments
Configuration	Provides configuration elements for the pairwise alignment configuration
Matrix	Provides data structures for representing alignment coordinates and alignments as a matrix
Pairwise	Provides the algorithmic components for the computation of pairwise alignments
Scoring	Provides the data structures used for scoring alphabets and sequences
▼Alphabet
Adaptation	Provides alphabet adaptions of some standard char and uint types
Aminoacid	Provides the amino acid alphabets and functionality for translation from nucleotide
CIGAR	Provides (semi-)alphabets for representing elements in CIGAR strings
Composite	Provides templates for combining existing alphabets into new alphabet types
Gap	Provides the gap alphabet and functionality to make an alphabet a gapped alphabet
Mask	Provides the mask alphabet and functionality for creating masked composites
Nucleotide	Provides the different DNA and RNA alphabet types
Quality	Provides the various quality score types
Structure	Provides types to represent single elements of RNA and protein structures
Argument Parser	The Argument Parser Module
▼Core	Provides core functionality used by multiple modules
Algorithm	Provides core functionality used to configure algorithms
Configuration	Provides core functionality used to configure configurations
▼IO	The IO module provides stream handling formatted I/O
SAM File	Provides files and formats for handling alignment data
Sequence File	Provides files and formats for handling sequence data
Stream	The stream sub-module contains data structures and functions for streaming and tokenization
Structure File	Provides files and formats for handling structure data
▼Range	The range module provides general purpose containers, decorators and views
Container	The container submodule contains special SeqAn containers and generic container concepts
Decorator	The decorator submodule contains special SeqAn decorators and generic decorator concepts
Views	Views are "lazy range combinators" that offer modified views onto other ranges
▼Search	Data structures and algorithms for the search of query sequences in a large collection of text
Configuration	Data structures and utility functions for configuring search algorithm
DREAM Index	Provides seqan3:interleaved_bloom_filter
FM Index	Provides seqan3:fm_index and seqan3:bi_fm_index as well as respective cursors
k-mer Index	Implementation of shapes for a k-mer Index
▼std	A subset of the C++20 standard library made available in pre-C++20 contexts
algorithm	The <algorithm> header with additional ranges algorithm from C++20's standard library
bit	A workaround for __cpp_lib_bitops for gcc version 9.x (in C++20 mode). Those versions implemented std::countl_zero, etc, but did not define that feature detection macro
concepts	The <concepts> header from C++20's standard library
iterator	The <iterator> header from C++20's standard library
memory	A workaround for __cpp_lib_to_address for gcc version >=8.0 and < 9.4 (in C++20 mode). Those versions implemented std::to_address, but did not define that feature detection macro
new	The <new> header from C++17's standard library
ranges	The <ranges> header from C++20's standard library
type_traits	The <concepts> header from C++20's standard library
▼Utility	Provides additional utility functionality used by multiple modules
Concept
Builtin Character Operations	Provides various operations on character types
▼Parallel	This module contains types and utilities for concurrent execution of algorithms in SeqAn
execution	Adopts the STL execution policies
Tuple	Additional helper utilities for "tuple" types like std::tuple, std::pair, seqan3::pod_tuple that are not specific to a SeqAn module
Type List	Provides seqan3::type_list and metaprogramming utilities for working on type lists
Type Pack	Provides metaprogramming utilities for working on template parameter packs
Type Traits	Provides various type traits and their shortcuts