40 #ifndef _WORDFREQUENCIESSET_H_ 41 #define _WORDFREQUENCIESSET_H_ 43 #include <Bpp/Seq/Alphabet/WordAlphabet.h> 68 virtual size_t getSizeFromVector(
const std::vector<FrequenciesSet*>& freqVector) = 0;
71 #ifndef NO_VIRTUAL_COV 101 #ifndef NO_VIRTUAL_COV 117 #ifndef NO_VIRTUAL_COV 151 WordFromIndependentFrequenciesSet(
const WordAlphabet* pWA,
const std::vector<FrequenciesSet*>& freqVector,
const std::string& prefix =
"",
const std::string& name=
"WordFromIndependent");
172 virtual void setFrequencies(
const std::vector<double>& frequencies);
223 virtual void setFrequencies(
const std::vector<double>& frequencies);
241 #endif // _WORDFREQUENCIESSET_H_ virtual const FrequenciesSet & getFrequenciesSetForLetter(size_t i) const =0
virtual size_t getLength() const
virtual size_t getLength() const =0
virtual void updateFrequencies()
const WordAlphabet * getAlphabet() const =0
WordFromUniqueFrequenciesSet(const WordAlphabet *pWA, FrequenciesSet *pabsfreq, const std::string &prefix="", const std::string &name="WordFromUnique")
Constructor from a WordAlphabet* and a FrequenciesSet* repeated as many times as the length of the wo...
AbstractWordFrequenciesSet & operator=(const AbstractWordFrequenciesSet &af)
WordFromIndependentFrequenciesSet * clone() const
const FrequenciesSet & getFrequenciesSetForLetter(size_t i) const
size_t getSizeFromVector(const std::vector< FrequenciesSet *> &freqVector)
const WordAlphabet * getAlphabet() const
Parametrize a set of state frequencies.
void setNamespace(const std::string &prefix)
virtual void updateFrequencies()
WordFromIndependentFrequenciesSet & operator=(const WordFromIndependentFrequenciesSet &iwfs)
std::vector< FrequenciesSet * > vFreq_
AbstractWordFrequenciesSet * clone() const =0
std::string NestedPrefix_
const FrequenciesSet & getFrequenciesSetForLetter(size_t i) const
Frequencies in words computed from the frequencies on letters. The parameters are the parameters of t...
virtual void setFrequencies(const std::vector< double > &frequencies)
virtual void fireParameterChanged(const ParameterList &pl)
WordFromUniqueFrequenciesSet * clone() const
WordFromIndependentFrequenciesSet(const WordAlphabet *pWA, const std::vector< FrequenciesSet *> &freqVector, const std::string &prefix="", const std::string &name="WordFromIndependent")
Constructor from a WordAlphabet* and a vector of different FrequenciesSet*. Throws an Exception if th...
virtual size_t getSizeFromVector(const std::vector< FrequenciesSet *> &freqVector)=0
const Alphabet * getAlphabet() const
virtual void setFrequencies(const std::vector< double > &frequencies)
AbstractWordFrequenciesSet(const AbstractWordFrequenciesSet &af)
std::string getDescription() const
virtual ~AbstractWordFrequenciesSet()
std::string getDescription() const
the Frequencies in words are the product of Independent Frequencies in letters
std::vector< std::string > vNestedPrefix_
~WordFromIndependentFrequenciesSet()
AbstractWordFrequenciesSet(StateMap *stateMap, const std::string &prefix="", const std::string &name="")
WordFrequenciesSet * clone() const =0
Map the states of a given alphabet which have a model state.
void setNamespace(const std::string &prefix)
AbstractFrequenciesSet & operator=(const AbstractFrequenciesSet &af)
void fireParameterChanged(const ParameterList &pl)
WordFromUniqueFrequenciesSet & operator=(const WordFromUniqueFrequenciesSet &iwfs)
~WordFromUniqueFrequenciesSet()
Basic implementation of the FrequenciesSet interface.