codes.hpp

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#ifndef GENESIS_SEQUENCE_FUNCTIONS_CODES_H_
#define GENESIS_SEQUENCE_FUNCTIONS_CODES_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2023 Lucas Czech
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include <map>
#include <string>
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
namespace genesis {
namespace utils {
 
    class Color;
 
}
}
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Codes
// =================================================================================================
 
// ---------------------------------------------------------------------
//     Nucleic Acids
// ---------------------------------------------------------------------
 
std::string nucleic_acid_codes_plain();
 
std::string nucleic_acid_codes_degenerated();
 
std::string nucleic_acid_codes_undetermined();
 
std::string nucleic_acid_codes_undetermined_letters();
 
std::string nucleic_acid_codes_all();
 
std::string nucleic_acid_codes_all_letters();
 
// ---------------------------------------------------------------------
//     Amino Acids
// ---------------------------------------------------------------------
 
std::string amino_acid_codes_plain();
 
std::string amino_acid_codes_degenerated();
 
std::string amino_acid_codes_undetermined();
 
std::string amino_acid_codes_all();
 
// ---------------------------------------------------------------------
//     Misc
// ---------------------------------------------------------------------
 
std::string normalize_code_alphabet( std::string const& alphabet );
 
char normalize_nucleic_acid_code( char code, bool accept_degenerated = true );
 
char normalize_amino_acid_code( char code, bool accept_degenerated = true );
 
std::string reverse_complement( std::string const& sequence, bool accept_degenerated = true );
 
char nucleic_acid_transition( char code );
 
bool nucleic_acid_code_containment( char a, char b, bool undetermined_matches_all = true );
 
// =================================================================================================
//     Color Codes
// =================================================================================================
 
std::map<char, std::string> nucleic_acid_text_colors();
 
std::map<char, std::string> amino_acid_text_colors();
 
std::map<char, utils::Color> nucleic_acid_colors();
 
std::map<char, utils::Color> amino_acid_colors();
 
// =================================================================================================
//     Code Names
// =================================================================================================
 
std::string nucleic_acid_name( char code );
 
std::string amino_acid_name( char code );
 
std::string nucleic_acid_ambiguities( char code );
 
char        nucleic_acid_ambiguity_code( std::string codes );
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard