43 #ifndef _PROTEICALPHABET_H_ 44 #define _PROTEICALPHABET_H_ 86 throw (IndexOutOfBoundsException)
94 throw (IndexOutOfBoundsException)
161 #endif // _PROTEICALPHABET_H_ LetterAlphabet & operator=(const LetterAlphabet &bia)
const ProteicAlphabetState & getState(const std::string &letter) const
Get a state by its letter.
An alphabet exception thrown when trying to specify a bad char to the alphabet.
std::vector< int > getAlias(int state) const
Get all resolved states that match a generic state.
bool isUnresolved(int state) const
This alphabet is used to deal NumericAlphabet.
const ProteicAlphabetState & getStateAt(size_t pos) const
Get a state at a position in the alphabet_ vector.
ProteicAlphabet * clone() const
int getGeneric(const std::vector< int > &states) const
Get the generic state that match a set of states.
ProteicAlphabetState & getStateAt(size_t pos)
Get a state at a position in the alphabet_ vector.
ProteicAlphabet & operator=(const ProteicAlphabet &bia)
Specialized partial implementation of Alphabet using single letters.
const AlphabetState & getState(const std::string &letter) const
Get a state by its letter.
std::string getAlphabetType() const
Identification method.
virtual ~ProteicAlphabet()
This alphabet is used to deal with proteins.
std::string getAbbr(const std::string &aa) const
Get the abbreviation (3 letter code) for a state coded as char.
This is the base class to describe states in a ProteicAlphabet.
unsigned int getNumberOfTypes() const
Get the number of distinct states in alphabet (e.g. return 15 for DNA alphabet). This is the number o...
const ProteicAlphabetState & getState(int num) const
Get a state by its num.
The alphabet exception base class.
int getUnknownCharacterCode() const
bool isUnresolved(const std::string &state) const
An alphabet exception thrown when trying to specify a bad int to the alphabet.
unsigned int getSize() const
Get the number of resolved states in the alphabet (e.g. return 4 for DNA alphabet). This is the method you'll need in most cases.
virtual AlphabetState & getStateAt(size_t stateIndex)
Get a state at a position in the alphabet_ vector.
int charToInt(const std::string &state) const
Give the int description of a state given its string description.
ProteicAlphabet(const ProteicAlphabet &bia)