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) 2014-2019 Lucas Czech and HITS gGmbH

    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 <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/

#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_all();

// ---------------------------------------------------------------------
//     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 );

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