bpp-seq3  3.0.0
bpp::WordAlphabet Member List

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

AbstractAlphabet()bpp::AbstractAlphabetinline
AbstractAlphabet(const AbstractAlphabet &alph)bpp::AbstractAlphabetinline
Alphabet()bpp::Alphabetinline
alphabet_bpp::AbstractAlphabetprivate
build_()bpp::WordAlphabetprivate
charList_bpp::AbstractAlphabetmutableprotected
charToInt(const std::string &state) const overridebpp::WordAlphabetinlinevirtual
clone() const overridebpp::WordAlphabetinlinevirtual
containsGap(const std::string &state) const overridebpp::WordAlphabetprivatevirtual
containsUnresolved(const std::string &state) const overridebpp::WordAlphabetprivatevirtual
CoreWordAlphabet()bpp::CoreWordAlphabetinline
equals(const Alphabet &alphabet) constbpp::AbstractAlphabetinlineprotectedvirtual
getAlias(int state) const overridebpp::WordAlphabetvirtual
getAlias(const std::string &state) const overridebpp::WordAlphabetvirtual
getAlphabetType() const overridebpp::WordAlphabetvirtual
getCharCodeAt(size_t stateIndex) constbpp::AbstractAlphabetinlinevirtual
getGapCharacterCode() constbpp::AbstractAlphabetinlinevirtual
getGeneric(const std::vector< int > &states) const overridebpp::WordAlphabetvirtual
getGeneric(const std::vector< std::string > &states) const overridebpp::WordAlphabetvirtual
getIntCodeAt(size_t stateIndex) constbpp::AbstractAlphabetinlinevirtual
getLength() const overridebpp::WordAlphabetinlinevirtual
getNAlphabet(size_t n) const overridebpp::WordAlphabetinlinevirtual
getName(const std::string &state) const overridebpp::WordAlphabetvirtual
bpp::AbstractAlphabet::getName(int state) constbpp::AbstractAlphabetvirtual
getNPosition(int word, size_t n) const overridebpp::WordAlphabetinlinevirtual
getNPosition(const std::string &word, size_t n) const overridebpp::WordAlphabetinlinevirtual
getNumberOfChars() constbpp::AbstractAlphabetinlinevirtual
getNumberOfStates() constbpp::AbstractAlphabetinlinevirtual
getNumberOfTypes() const overridebpp::WordAlphabetinlinevirtual
getPositions(int word) const overridebpp::WordAlphabetinlinevirtual
getPositions(const std::string &word) const overridebpp::WordAlphabetinlinevirtual
getResolvedChars() constbpp::AbstractAlphabetvirtual
getSize() const overridebpp::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() const overridebpp::WordAlphabetinlinevirtual
getStateIndex(int state) constbpp::AbstractAlphabetvirtual
getStateIndex(const std::string &state) constbpp::AbstractAlphabetvirtual
getSupportedChars() constbpp::AbstractAlphabetvirtual
getSupportedInts() constbpp::AbstractAlphabetvirtual
getUnknownCharacterCode() const overridebpp::WordAlphabetinlinevirtual
getWord(const Sequence &seq, size_t pos=0) const overridebpp::WordAlphabetvirtual
getWord(const std::vector< int > &vint, size_t pos=0) const overridebpp::WordAlphabetvirtual
getWord(const std::vector< std::string > &vpos, size_t pos=0) const overridebpp::WordAlphabetvirtual
hasUniqueAlphabet() const overridebpp::WordAlphabetvirtual
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
isResolvedIn(int state1, int state2) const overridebpp::WordAlphabetvirtual
isUnresolved(int state) const overridebpp::WordAlphabetinlinevirtual
isUnresolved(const std::string &state) const overridebpp::WordAlphabetinlinevirtual
letters_bpp::AbstractAlphabetprivate
nums_bpp::AbstractAlphabetprivate
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 SequenceInterface &sequence) const overridebpp::WordAlphabetvirtual
setState(size_t pos, AlphabetState *st)bpp::AbstractAlphabetprotectedvirtual
translate(const SequenceInterface &sequence, size_t=0) const overridebpp::WordAlphabetvirtual
updateMaps_(size_t pos, const AlphabetState &st)bpp::AbstractAlphabetprivate
vAbsAlph_bpp::WordAlphabetprotected
WordAlphabet(const std::vector< std::shared_ptr< const Alphabet >> &vAlpha)bpp::WordAlphabet
WordAlphabet(std::shared_ptr< const Alphabet > pAlpha, size_t num)bpp::WordAlphabet
WordAlphabet(const WordAlphabet &bia)bpp::WordAlphabetinline
~AbstractAlphabet()bpp::AbstractAlphabetinlinevirtual
~Alphabet()=defaultbpp::Alphabetvirtual
~Clonable()=defaultbpp::Clonablevirtual
~CoreWordAlphabet()bpp::CoreWordAlphabetinlinevirtual
~WordAlphabet()bpp::WordAlphabetinlinevirtual