bpp-seq
2.2.0
bpp::CaseMaskedAlphabet Member List
This is the complete list of members for
bpp::CaseMaskedAlphabet
, including all inherited members.
AbstractAlphabet
()
bpp::AbstractAlphabet
inline
AbstractAlphabet
(const AbstractAlphabet &alph)
bpp::AbstractAlphabet
inline
Alphabet
()
bpp::Alphabet
inline
CaseMaskedAlphabet
(const LetterAlphabet *nocaseAlphabet)
bpp::CaseMaskedAlphabet
CaseMaskedAlphabet
(const CaseMaskedAlphabet &cma)
bpp::CaseMaskedAlphabet
inline
charList_
bpp::AbstractAlphabet
mutable
protected
charToInt
(const std::string &state) const
bpp::LetterAlphabet
inline
virtual
clone
() const
bpp::CaseMaskedAlphabet
inline
virtual
equals
(const Alphabet &alphabet) const
bpp::AbstractAlphabet
inline
protected
virtual
getAlias
(int state) const
bpp::AbstractAlphabet
virtual
getAlias
(const std::string &state) const
bpp::AbstractAlphabet
virtual
getAlphabetType
() const
bpp::CaseMaskedAlphabet
inline
virtual
getCharCodeAt
(size_t stateIndex) const
bpp::AbstractAlphabet
inline
virtual
getGapCharacterCode
() const
bpp::AbstractAlphabet
inline
virtual
getGeneric
(const std::vector< int > &states) const
bpp::AbstractAlphabet
virtual
getGeneric
(const std::vector< std::string > &states) const
bpp::AbstractAlphabet
virtual
getIntCodeAt
(size_t stateIndex) const
bpp::AbstractAlphabet
inline
virtual
getMaskedEquivalentState
(int state) const
bpp::CaseMaskedAlphabet
getMaskedEquivalentState
(const std::string &state) const
bpp::CaseMaskedAlphabet
getName
(const std::string &state) const
bpp::AbstractAlphabet
virtual
getName
(int state) const
bpp::AbstractAlphabet
virtual
getNumberOfChars
() const
bpp::AbstractAlphabet
inline
virtual
getNumberOfStates
() const
bpp::AbstractAlphabet
inline
virtual
getNumberOfTypes
() const
bpp::CaseMaskedAlphabet
inline
virtual
getSize
() const
bpp::CaseMaskedAlphabet
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::AbstractAlphabet
inline
protected
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::CaseMaskedAlphabet
inline
virtual
getUnmaskedAlphabet
() const
bpp::CaseMaskedAlphabet
inline
intList_
bpp::AbstractAlphabet
mutable
protected
intToChar
(int state) const
bpp::AbstractAlphabet
virtual
isCharInAlphabet
(char state) const
bpp::LetterAlphabet
inline
isCharInAlphabet
(const std::string &state) const
bpp::LetterAlphabet
inline
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
isMasked
(int state) const
bpp::CaseMaskedAlphabet
inline
isMasked
(const std::string &state) const
bpp::CaseMaskedAlphabet
inline
isMasked
(char state) const
bpp::CaseMaskedAlphabet
inline
isUnresolved
(int state) const
bpp::CaseMaskedAlphabet
inline
virtual
isUnresolved
(const std::string &state) const
bpp::CaseMaskedAlphabet
inline
virtual
LetterAlphabet
(bool caseSensitive=false)
bpp::LetterAlphabet
inline
LetterAlphabet
(const LetterAlphabet &bia)
bpp::LetterAlphabet
inline
nocaseAlphabet_
bpp::CaseMaskedAlphabet
operator=
(const CaseMaskedAlphabet &cma)
bpp::CaseMaskedAlphabet
inline
bpp::LetterAlphabet::operator=
(const LetterAlphabet &bia)
bpp::LetterAlphabet
inline
bpp::AbstractAlphabet::operator=
(const AbstractAlphabet &alph)
bpp::AbstractAlphabet
inline
registerState
(AlphabetState *st)
bpp::LetterAlphabet
inline
protected
virtual
remap
()
bpp::AbstractAlphabet
inline
protected
resize
(size_t size)
bpp::AbstractAlphabet
inline
protected
setState
(size_t pos, AlphabetState *st)
bpp::LetterAlphabet
inline
protected
virtual
~AbstractAlphabet
()
bpp::AbstractAlphabet
inline
virtual
~Alphabet
()
bpp::Alphabet
inline
virtual
~LetterAlphabet
()
bpp::LetterAlphabet
inline
virtual
Generated on Sat May 23 2020 12:00:22 for bpp-seq by
1.8.14