bpp-seq
2.2.0
bpp::WordAlphabet Member List
This is the complete list of members for
bpp::WordAlphabet
, including all inherited members.
AbstractAlphabet
()
bpp::AbstractAlphabet
inline
AbstractAlphabet
(const AbstractAlphabet &alph)
bpp::AbstractAlphabet
inline
Alphabet
()
bpp::Alphabet
inline
build_
()
bpp::WordAlphabet
private
charList_
bpp::AbstractAlphabet
mutable
protected
charToInt
(const std::string &state) const
bpp::WordAlphabet
inline
virtual
clone
() const
bpp::WordAlphabet
inline
virtual
containsGap
(const std::string &state) const
bpp::WordAlphabet
private
containsUnresolved
(const std::string &state) const
bpp::WordAlphabet
private
equals
(const Alphabet &alphabet) const
bpp::AbstractAlphabet
inline
protected
virtual
getAlias
(int state) const
bpp::WordAlphabet
virtual
getAlias
(const std::string &state) const
bpp::WordAlphabet
virtual
getAlphabetType
() const
bpp::WordAlphabet
virtual
getCharCodeAt
(size_t stateIndex) const
bpp::AbstractAlphabet
inline
virtual
getGapCharacterCode
() const
bpp::AbstractAlphabet
inline
virtual
getGeneric
(const std::vector< int > &states) const
bpp::WordAlphabet
virtual
getGeneric
(const std::vector< std::string > &states) const
bpp::WordAlphabet
virtual
getIntCodeAt
(size_t stateIndex) const
bpp::AbstractAlphabet
inline
virtual
getLength
() const
bpp::WordAlphabet
inline
getNAlphabet
(size_t n) const
bpp::WordAlphabet
inline
getName
(const std::string &state) const
bpp::WordAlphabet
virtual
bpp::AbstractAlphabet::getName
(int state) const
bpp::AbstractAlphabet
virtual
getNPosition
(int word, size_t n) const
bpp::WordAlphabet
inline
getNPosition
(const std::string &word, size_t n) const
bpp::WordAlphabet
inline
getNumberOfChars
() const
bpp::AbstractAlphabet
inline
virtual
getNumberOfStates
() const
bpp::AbstractAlphabet
inline
virtual
getNumberOfTypes
() const
bpp::WordAlphabet
inline
virtual
getPositions
(int word) const
bpp::WordAlphabet
inline
getPositions
(const std::string &word) const
bpp::WordAlphabet
inline
getSize
() const
bpp::WordAlphabet
inline
virtual
getState
(const std::string &letter) const
bpp::AbstractAlphabet
virtual
getState
(const std::string &letter)
bpp::AbstractAlphabet
getState
(int num) const
bpp::AbstractAlphabet
virtual
getState
(int num)
bpp::AbstractAlphabet
getStateAt
(size_t stateIndex)
bpp::AbstractAlphabet
virtual
getStateAt
(size_t stateIndex) const
bpp::AbstractAlphabet
virtual
getStateCodingSize
() const
bpp::WordAlphabet
inline
virtual
getStateIndex
(int state) const
bpp::AbstractAlphabet
virtual
getStateIndex
(const std::string &state) const
bpp::AbstractAlphabet
virtual
getSupportedChars
() const
bpp::AbstractAlphabet
virtual
getSupportedInts
() const
bpp::AbstractAlphabet
virtual
getUnknownCharacterCode
() const
bpp::WordAlphabet
inline
virtual
getWord
(const std::vector< int > &vint, size_t pos=0) const
bpp::WordAlphabet
virtual
getWord
(const std::vector< std::string > &vpos, size_t pos=0) const
bpp::WordAlphabet
virtual
hasUniqueAlphabet
() const
bpp::WordAlphabet
intList_
bpp::AbstractAlphabet
mutable
protected
intToChar
(int state) const
bpp::AbstractAlphabet
virtual
isCharInAlphabet
(const std::string &state) const
bpp::AbstractAlphabet
virtual
isGap
(int state) const
bpp::AbstractAlphabet
inline
virtual
isGap
(const std::string &state) const
bpp::AbstractAlphabet
inline
virtual
isIntInAlphabet
(int state) const
bpp::AbstractAlphabet
virtual
isUnresolved
(int state) const
bpp::WordAlphabet
inline
virtual
isUnresolved
(const std::string &state) const
bpp::WordAlphabet
inline
virtual
operator=
(const WordAlphabet &bia)
bpp::WordAlphabet
inline
bpp::AbstractAlphabet::operator=
(const AbstractAlphabet &alph)
bpp::AbstractAlphabet
inline
registerState
(AlphabetState *st)
bpp::AbstractAlphabet
protected
virtual
remap
()
bpp::AbstractAlphabet
inline
protected
resize
(size_t size)
bpp::AbstractAlphabet
inline
protected
reverse
(const Sequence &sequence) const
bpp::WordAlphabet
setState
(size_t pos, AlphabetState *st)
bpp::AbstractAlphabet
protected
virtual
translate
(const Sequence &sequence, size_t=0) const
bpp::WordAlphabet
vAbsAlph_
bpp::WordAlphabet
protected
WordAlphabet
(const std::vector< const Alphabet *> &vAlpha)
bpp::WordAlphabet
WordAlphabet
(const Alphabet *pAlpha, unsigned int num)
bpp::WordAlphabet
WordAlphabet
(const WordAlphabet &bia)
bpp::WordAlphabet
inline
~AbstractAlphabet
()
bpp::AbstractAlphabet
inline
virtual
~Alphabet
()
bpp::Alphabet
inline
virtual
~WordAlphabet
()
bpp::WordAlphabet
inline
virtual
Generated on Sat May 23 2020 12:00:23 for bpp-seq by
1.8.14