bpp-seq  2.2.0
bpp::CodonAlphabet Member List

This is the complete list of members for bpp::CodonAlphabet, including all inherited members.

AbstractAlphabet()bpp::AbstractAlphabetinline
AbstractAlphabet(const AbstractAlphabet &alph)bpp::AbstractAlphabetinline
Alphabet()bpp::Alphabetinline
charList_bpp::AbstractAlphabetmutableprotected
charToInt(const std::string &state) constbpp::WordAlphabetinlinevirtual
clone() constbpp::CodonAlphabetinlinevirtual
CodonAlphabet(const NucleicAlphabet *alpha)bpp::CodonAlphabetinline
CodonAlphabet(const CodonAlphabet &bia)bpp::CodonAlphabetinline
equals(const Alphabet &alphabet) constbpp::AbstractAlphabetinlineprotectedvirtual
getAlias(int state) constbpp::WordAlphabetvirtual
getAlias(const std::string &state) constbpp::WordAlphabetvirtual
getAlphabetType() constbpp::CodonAlphabetinlinevirtual
getCharCodeAt(size_t stateIndex) constbpp::AbstractAlphabetinlinevirtual
getCodon(int pos1, int pos2, int pos3) constbpp::CodonAlphabetvirtual
getCodon(const std::string &pos1, const std::string &pos2, const std::string &pos3) constbpp::CodonAlphabetvirtual
getFirstPosition(int codon) constbpp::CodonAlphabetvirtual
getFirstPosition(const std::string &codon) constbpp::CodonAlphabetvirtual
getGapCharacterCode() constbpp::AbstractAlphabetinlinevirtual
getGeneric(const std::vector< int > &states) constbpp::WordAlphabetvirtual
getGeneric(const std::vector< std::string > &states) constbpp::WordAlphabetvirtual
getIntCodeAt(size_t stateIndex) constbpp::AbstractAlphabetinlinevirtual
getLength() constbpp::WordAlphabetinline
getNAlphabet(size_t n) constbpp::WordAlphabetinline
getName(const std::string &state) constbpp::WordAlphabetvirtual
bpp::AbstractAlphabet::getName(int state) constbpp::AbstractAlphabetvirtual
getNPosition(int word, size_t n) constbpp::WordAlphabetinline
getNPosition(const std::string &word, size_t n) constbpp::WordAlphabetinline
getNucleicAlphabet() constbpp::CodonAlphabetinlinevirtual
getNumberOfChars() constbpp::AbstractAlphabetinlinevirtual
getNumberOfStates() constbpp::AbstractAlphabetinlinevirtual
getNumberOfTypes() constbpp::WordAlphabetinlinevirtual
getPositions(int word) constbpp::WordAlphabetinline
getPositions(const std::string &word) constbpp::WordAlphabetinline
getSecondPosition(int codon) constbpp::CodonAlphabetvirtual
getSecondPosition(const std::string &codon) constbpp::CodonAlphabetvirtual
getSize() constbpp::WordAlphabetinlinevirtual
getState(const std::string &letter) constbpp::AbstractAlphabetvirtual
getState(const std::string &letter)bpp::AbstractAlphabet
getState(int num) constbpp::AbstractAlphabetvirtual
getState(int num)bpp::AbstractAlphabet
getStateAt(size_t stateIndex)bpp::AbstractAlphabetvirtual
getStateAt(size_t stateIndex) constbpp::AbstractAlphabetvirtual
getStateCodingSize() constbpp::WordAlphabetinlinevirtual
getStateIndex(int state) constbpp::AbstractAlphabetvirtual
getStateIndex(const std::string &state) constbpp::AbstractAlphabetvirtual
getSupportedChars() constbpp::AbstractAlphabetvirtual
getSupportedInts() constbpp::AbstractAlphabetvirtual
getThirdPosition(int codon) constbpp::CodonAlphabetvirtual
getThirdPosition(const std::string &codon) constbpp::CodonAlphabetvirtual
getUnknownCharacterCode() constbpp::WordAlphabetinlinevirtual
getWord(const std::vector< int > &vint, size_t pos=0) constbpp::WordAlphabetvirtual
getWord(const std::vector< std::string > &vpos, size_t pos=0) constbpp::WordAlphabetvirtual
hasUniqueAlphabet() constbpp::WordAlphabet
intList_bpp::AbstractAlphabetmutableprotected
intToChar(int state) constbpp::AbstractAlphabetvirtual
isCharInAlphabet(const std::string &state) constbpp::AbstractAlphabetvirtual
isGap(int state) constbpp::AbstractAlphabetinlinevirtual
isGap(const std::string &state) constbpp::AbstractAlphabetinlinevirtual
isIntInAlphabet(int state) constbpp::AbstractAlphabetvirtual
isUnresolved(int state) constbpp::WordAlphabetinlinevirtual
isUnresolved(const std::string &state) constbpp::WordAlphabetinlinevirtual
operator=(const CodonAlphabet &bia)bpp::CodonAlphabetinline
bpp::WordAlphabet::operator=(const WordAlphabet &bia)bpp::WordAlphabetinline
bpp::AbstractAlphabet::operator=(const AbstractAlphabet &alph)bpp::AbstractAlphabetinline
registerState(AlphabetState *st)bpp::AbstractAlphabetprotectedvirtual
remap()bpp::AbstractAlphabetinlineprotected
resize(size_t size)bpp::AbstractAlphabetinlineprotected
reverse(const Sequence &sequence) constbpp::WordAlphabet
setState(size_t pos, AlphabetState *st)bpp::AbstractAlphabetprotectedvirtual
translate(const Sequence &sequence, size_t=0) constbpp::WordAlphabet
vAbsAlph_bpp::WordAlphabetprotected
WordAlphabet(const std::vector< const Alphabet *> &vAlpha)bpp::WordAlphabet
WordAlphabet(const Alphabet *pAlpha, unsigned int num)bpp::WordAlphabet
WordAlphabet(const WordAlphabet &bia)bpp::WordAlphabetinline
~AbstractAlphabet()bpp::AbstractAlphabetinlinevirtual
~Alphabet()bpp::Alphabetinlinevirtual
~CodonAlphabet()bpp::CodonAlphabetinlinevirtual
~WordAlphabet()bpp::WordAlphabetinlinevirtual