bpp-seq3  3.0.0
bpp::IntegerAlphabet Member List

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

AbstractAlphabet()bpp::AbstractAlphabetinline
AbstractAlphabet(const AbstractAlphabet &alph)bpp::AbstractAlphabetinline
Alphabet()bpp::Alphabetinline
alphabet_bpp::AbstractAlphabetprivate
charList_bpp::AbstractAlphabetmutableprotected
charToInt(const std::string &state) constbpp::AbstractAlphabetvirtual
clone() constbpp::IntegerAlphabetinlinevirtual
equals(const Alphabet &alphabet) constbpp::AbstractAlphabetinlineprotectedvirtual
getAlias(int state) constbpp::AbstractAlphabetvirtual
getAlias(const std::string &state) constbpp::AbstractAlphabetvirtual
getAlphabetType() constbpp::IntegerAlphabetinlinevirtual
getCharCodeAt(size_t stateIndex) constbpp::AbstractAlphabetinlinevirtual
getGapCharacterCode() constbpp::AbstractAlphabetinlinevirtual
getGeneric(const std::vector< int > &states) constbpp::AbstractAlphabetvirtual
getGeneric(const std::vector< std::string > &states) constbpp::AbstractAlphabetvirtual
getIntCodeAt(size_t stateIndex) constbpp::AbstractAlphabetinlinevirtual
getName(const std::string &state) constbpp::AbstractAlphabetvirtual
getName(int state) constbpp::AbstractAlphabetvirtual
getNumberOfChars() constbpp::AbstractAlphabetinlinevirtual
getNumberOfStates() constbpp::AbstractAlphabetinlinevirtual
getNumberOfTypes() constbpp::IntegerAlphabetinlinevirtual
getResolvedChars() constbpp::AbstractAlphabetvirtual
getSize() constbpp::IntegerAlphabetinlinevirtual
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::AbstractAlphabetinlineprotectedvirtual
getStateIndex(int state) constbpp::AbstractAlphabetvirtual
getStateIndex(const std::string &state) constbpp::AbstractAlphabetvirtual
getSupportedChars() constbpp::AbstractAlphabetvirtual
getSupportedInts() constbpp::AbstractAlphabetvirtual
getUnknownCharacterCode() constbpp::IntegerAlphabetinlinevirtual
IntegerAlphabet(unsigned int max)bpp::IntegerAlphabet
IntegerAlphabet(const IntegerAlphabet &bia)bpp::IntegerAlphabetinline
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) constbpp::AbstractAlphabetvirtual
isUnresolved(int state) constbpp::IntegerAlphabetinlinevirtual
isUnresolved(const std::string &state) constbpp::IntegerAlphabetinlinevirtual
letters_bpp::AbstractAlphabetprivate
MAX_bpp::IntegerAlphabetprivate
nums_bpp::AbstractAlphabetprivate
operator=(const IntegerAlphabet &bia)bpp::IntegerAlphabetinline
bpp::AbstractAlphabet::operator=(const AbstractAlphabet &alph)bpp::AbstractAlphabetinline
registerState(AlphabetState *st)bpp::AbstractAlphabetprotectedvirtual
remap()bpp::AbstractAlphabetinlineprotected
resize(size_t size)bpp::AbstractAlphabetinlineprotected
setState(size_t pos, AlphabetState *st)bpp::AbstractAlphabetprotectedvirtual
updateMaps_(size_t pos, const AlphabetState &st)bpp::AbstractAlphabetprivate
~AbstractAlphabet()bpp::AbstractAlphabetinlinevirtual
~Alphabet()=defaultbpp::Alphabetvirtual
~Clonable()=defaultbpp::Clonablevirtual
~IntegerAlphabet()bpp::IntegerAlphabetinlinevirtual