A toolkit for working with phylogenetic data.
v0.19.0
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codes.hpp File Reference
#include <map>
#include <string>

Go to the source code of this file.

Namespaces

 genesis
 Container namespace for all symbols of genesis in order to keep them separate when used as a library.
 
 genesis::sequence
 
 genesis::utils
 

Functions

std::string amino_acid_codes_all ()
 Return all valid amino acid codes. Those are "ACDEFGHIKLMNOPQRSTUVWYBJZX*-?". More...
 
std::string amino_acid_codes_degenerated ()
 Return all degenerated amino acid codes. Those are "BJZ". More...
 
std::string amino_acid_codes_plain ()
 Return all plain amino acid codes. Those are "ACDEFGHIKLMNOPQRSTUVWY". More...
 
std::string amino_acid_codes_undetermined ()
 Return all undetermined amino acid codes. Those are "X*-?". More...
 
std::map< char, utils::Color > amino_acid_colors ()
 Return a map of Colors for each amino acid code. More...
 
std::string amino_acid_name (char code)
 Get the name of a amino acid given its IUPAC code. More...
 
std::map< char, std::string > amino_acid_text_colors ()
 Return a map of text colors for each amino acid code. More...
 
char normalize_amino_acid_code (char code, bool accept_degenerated=true)
 Normalize an amino acid code. More...
 
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. More...
 
char normalize_nucleic_acid_code (char code, bool accept_degenerated=true)
 Normalize a nucleic acide code. More...
 
std::string nucleic_acid_ambiguities (char code)
 Return the possible ambiguous nucleic acid codes for a given code char. More...
 
char nucleic_acid_ambiguity_code (std::string codes)
 Return the nucleic acid code that represents all given codes. More...
 
std::string nucleic_acid_codes_all ()
 Return all valid nucleic acid codes. Those are "ACGTUWSMKRYBDHVNOX.-?". More...
 
std::string nucleic_acid_codes_degenerated ()
 Return all degenerated nucleic acid codes. Those are "WSMKRYBDHV". More...
 
std::string nucleic_acid_codes_plain ()
 Return all plain nucleic acid codes. Those are "ACGTU". More...
 
std::string nucleic_acid_codes_undetermined ()
 Return all undetermined nucleic acid codes. Those are "NOX.-?". More...
 
std::map< char, utils::Color > nucleic_acid_colors ()
 Return a map of Colors for each nucleic acid code. More...
 
std::string nucleic_acid_name (char code)
 Get the name of a nucleic acid given its IUPAC code. More...
 
std::map< char, std::string > nucleic_acid_text_colors ()
 Return a map of text colors for each nucleic acid code. More...
 
std::string reverse_complement (std::string const &sequence, bool accept_degenerated=true)
 Get the reverse complement of a nucleic acid sequence. More...