This is the core library of the BioC++ project. It provides the following modules:
- Alphabet: data structures that represent single biological compounds like DNA, RNA and amino acids.
- Ranges: containers, views and utilities for storing and manipulating sequences of biological compounds.
- Meta: metaprogramming utilities and auxilliary data structures.
The design of this module is heavily influenced by C++ Ranges and C++ Concepts. A short introduction into the topic can be found here.
General information on the BioC++ project can be found in the main repository. The full documention (all BioC++ modules) can found here.
Attention: this library is currently a work-in-progress. Getting it into a stable state is of highest priority, but until then all kinds of changes are still possible.
std::vector seq = "GATTACATATA"_dna4;
auto translated = seq | bio::views::translate;
fmt::print("The six protein frames of '{}' are:\n{}\n", seq, translated);
/*
The six protein frames of 'GATTACATATA' are:
[DYI, ITY, LHI, YM*, ICN, YVI]
*/
fmt::print("The third frame's second amino acid is: {}\n", translated[2][1]);
/*
The third frame's second amino acid is: H
*/Here translated appears like a vector of protein sequences, however, it is actually a "view", i.e. a light-weight,
lazy-evaluated data structure. Its elements are computed on-the-fly and occupy no memory. It still supports
constant-time random access like a vector.
- Header-only → just drop it in your source code or include it as a git submodule!
- Zero dependencies → keep complexity low!
- No build-system and no configure steps required.
- Optional CMake support available.
- Integrates well with the standard library and {fmt}.
- Clone the repository:
git clone https://github.com/biocpp/biocpp-core.git - Add the include directory of BioC++, activate C++20 and you are good to go:
g++-10 -O3 -DNDEBUG -Wall -Wextra -std=c++20 -I /path/to/biocpp-core/include your_file.cpp- If you want to use {fmt}, add
-I /path/to/fmt/include -D FMT_HEADER_ONLY=1.
Currently, GCC ≥ 10 is the only supported compiler. Clang support is planned.