▼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::AlignedSequence, 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 the CIGAR operation alphabet, along with the CIGAR cartesian composition |
Composite | Provides data structures joining multiple alphabets into a single alphabet |
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 | The structure module contains alphabets for RNA and protein structure |
Argument Parser | The Argument Parser Module |
▼Core | Provides core functionality used by multiple modules |
Algorithm | Provides core functionality used to configure algorithms |
Char operations | Provides various operations on character types |
Concept | Additional concepts that are not specific to a SeqAn3 module |
▼Parallel | This module contains types and utilities for concurrent execution of algorithms in SeqAn |
execution | Adopts the STL execution policies |
Type Traits | Provides various type traits and their shortcuts |
▼IO | The IO module provides stream handling formatted I/O |
Alignment 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 SeqAn3 containers and generic container concepts |
Decorator | The decorator submodule contains special SeqAn3 decorators and generic decorator concepts |
View | Views are "lazy range combinators" that offer modified views onto other ranges |
▼Search | Contains datastructures and algorithms for searching |
Algorithm | Provides seqan3::search |
Configuration | Data structures and utility functions for configuring search algorithm |
FM Index | Provides seqan3:fm_index and seqan3:bi_fm_index as well as respective cursors |
▼std | A subset of the C++20 standard library made available in pre-C++20 contexts |
Algorithm | Provides core functionality used to configure algorithms |
charconv | The <charconv> header from C++17's standard library |
concepts | The <concepts> header from C++20's standard library |
iterator | The <iterator> header from C++20's standard library |
new | The <new> header from C++17's standard library |
ranges | The <ranges> header from C++20's standard library |
Type Traits | Provides various type traits and their shortcuts |