1 #ifndef GENESIS_SEQUENCE_FUNCTIONS_CODES_H_ 2 #define GENESIS_SEQUENCE_FUNCTIONS_CODES_H_ 157 std::string
reverse_complement( std::string
const& sequence,
bool accept_degenerated =
true );
355 #endif // include guard std::string amino_acid_codes_all()
Return all valid amino acid codes. Those are "ACDEFGHIKLMNOPQRSTUVWYBJZX*-?".
std::string amino_acid_codes_degenerated()
Return all degenerated amino acid codes. Those are "BJZ".
std::string amino_acid_codes_plain()
Return all plain amino acid codes. Those are "ACDEFGHIKLMNOPQRSTUVWY".
std::string nucleic_acid_codes_all()
Return all valid nucleic acid codes. Those are "ACGTUWSMKRYBDHVNOX.-?".
std::string nucleic_acid_name(char code)
Get the name of a nucleic acid given its IUPAC code.
std::string normalize_code_alphabet(std::string const &alphabet)
Normalize an alphabet set of Sequence codes, i.e., make them upper case, sort them, and remove duplicates.
std::string nucleic_acid_codes_plain()
Return all plain nucleic acid codes. Those are "ACGTU".
Container namespace for all symbols of genesis in order to keep them separate when used as a library...
std::string nucleic_acid_codes_degenerated()
Return all degenerated nucleic acid codes. Those are "WSMKRYBDHV".
std::string nucleic_acid_codes_undetermined()
Return all undetermined nucleic acid codes. Those are "NOX.-?".
std::map< char, std::string > nucleic_acid_text_colors()
Return a map of text colors for each nucleic acid code.
std::string reverse_complement(std::string const &sequence, bool accept_degenerated)
Get the reverse complement of a nucleic acid sequence.
std::string amino_acid_name(char code)
Get the name of a amino acid given its IUPAC code.
char normalize_amino_acid_code(char code, bool accept_degenerated)
Normalize an amino acid code.
std::map< char, utils::Color > amino_acid_colors()
Return a map of Colors for each amino acid code.
std::map< char, std::string > amino_acid_text_colors()
Return a map of text colors for each amino acid code.
char normalize_nucleic_acid_code(char code, bool accept_degenerated)
Normalize a nucleic acide code.
bool nucleic_acid_code_containment(char a, char b, bool undetermined_matches_all)
Compare two nucleic acid codes and check if they are equal, taking degenerated/ambiguous characters i...
std::string nucleic_acid_ambiguities(char code)
Return the possible ambiguous nucleic acid codes for a given code char.
std::string amino_acid_codes_undetermined()
Return all undetermined amino acid codes. Those are "X*-?".
std::map< char, utils::Color > nucleic_acid_colors()
Return a map of Colors for each nucleic acid code.
char nucleic_acid_ambiguity_code(std::string codes)
Return the nucleic acid code that represents all given codes.