| AbstractAlphabet() | bpp::AbstractAlphabet | inline |
| AbstractAlphabet(const AbstractAlphabet &alph) | bpp::AbstractAlphabet | inline |
| Alphabet() | bpp::Alphabet | inline |
| alphabet_ | bpp::AbstractAlphabet | private |
| binCodes_ | bpp::NucleicAlphabet | private |
| caseSensitive_ | bpp::LetterAlphabet | private |
| charList_ | bpp::AbstractAlphabet | mutableprotected |
| charToInt(const std::string &state) const | bpp::LetterAlphabet | inlinevirtual |
| clone() const | bpp::DNA | inlinevirtual |
| DNA(bool exclamationMarkCountsAsGap=false) | bpp::DNA | |
| DNA(const DNA &bia) | bpp::DNA | inline |
| equals(const Alphabet &alphabet) const | bpp::AbstractAlphabet | inlineprotectedvirtual |
| getAlias(int state) const | bpp::DNA | virtual |
| getAlias(const std::string &state) const | bpp::DNA | virtual |
| getAlphabetType() const | bpp::DNA | inlinevirtual |
| getCharCodeAt(size_t stateIndex) const | bpp::AbstractAlphabet | inlinevirtual |
| getGapCharacterCode() const | bpp::AbstractAlphabet | inlinevirtual |
| getGeneric(const std::vector< int > &states) const | bpp::DNA | virtual |
| getGeneric(const std::vector< std::string > &states) const | bpp::DNA | virtual |
| getIntCodeAt(size_t stateIndex) const | bpp::AbstractAlphabet | inlinevirtual |
| getName(const std::string &state) const | bpp::AbstractAlphabet | virtual |
| getName(int state) const | bpp::AbstractAlphabet | virtual |
| getNumberOfChars() const | bpp::AbstractAlphabet | inlinevirtual |
| getNumberOfStates() const | bpp::AbstractAlphabet | inlinevirtual |
| getNumberOfTypes() const | bpp::NucleicAlphabet | inlinevirtual |
| getOverlap(int s1, int s2) const | bpp::NucleicAlphabet | inline |
| getOverlap(const std::string &s1, const std::string &s2) const | bpp::NucleicAlphabet | inline |
| getResolvedChars() const | bpp::AbstractAlphabet | virtual |
| getSize() const | bpp::NucleicAlphabet | inlinevirtual |
| getState(const std::string &letter) const | bpp::NucleicAlphabet | inlinevirtual |
| getState(int num) const | bpp::NucleicAlphabet | inlinevirtual |
| bpp::LetterAlphabet::getState(const std::string &letter) | bpp::AbstractAlphabet | |
| bpp::LetterAlphabet::getState(int num) | bpp::AbstractAlphabet | |
| getStateAt(size_t stateIndex) const | bpp::NucleicAlphabet | inlinevirtual |
| getStateAt(size_t stateIndex) | bpp::NucleicAlphabet | inlinevirtual |
| getStateByBinCode(int code) const | bpp::NucleicAlphabet | inline |
| getStateCodingSize() const | bpp::AbstractAlphabet | inlineprotectedvirtual |
| 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::NucleicAlphabet | inlinevirtual |
| intList_ | bpp::AbstractAlphabet | mutableprotected |
| intToChar(int state) const | bpp::AbstractAlphabet | virtual |
| isCharInAlphabet(char state) const | bpp::LetterAlphabet | inline |
| isCharInAlphabet(const std::string &state) const | bpp::LetterAlphabet | inlinevirtual |
| isGap(int state) const | bpp::AbstractAlphabet | inlinevirtual |
| isGap(const std::string &state) const | bpp::AbstractAlphabet | inlinevirtual |
| isIntInAlphabet(int state) const | bpp::AbstractAlphabet | virtual |
| isResolvedIn(int state1, int state2) const | bpp::DNA | virtual |
| isUnresolved(int state) const | bpp::NucleicAlphabet | inlinevirtual |
| isUnresolved(const std::string &state) const | bpp::NucleicAlphabet | inlinevirtual |
| LETTER_UNDEF_VALUE | bpp::LetterAlphabet | privatestatic |
| LetterAlphabet(bool caseSensitive=false) | bpp::LetterAlphabet | inline |
| LetterAlphabet(const LetterAlphabet &bia) | bpp::LetterAlphabet | inline |
| letters_ | bpp::LetterAlphabet | private |
| NucleicAlphabet() | bpp::NucleicAlphabet | inline |
| NucleicAlphabet(const NucleicAlphabet &bia) | bpp::NucleicAlphabet | inline |
| nums_ | bpp::AbstractAlphabet | private |
| operator=(const DNA &bia) | bpp::DNA | inline |
| bpp::NucleicAlphabet::operator=(const NucleicAlphabet &bia) | bpp::NucleicAlphabet | inline |
| bpp::LetterAlphabet::operator=(const LetterAlphabet &bia) | bpp::LetterAlphabet | inline |
| bpp::AbstractAlphabet::operator=(const AbstractAlphabet &alph) | bpp::AbstractAlphabet | inline |
| registerState(AlphabetState *st) | bpp::NucleicAlphabet | inlineprotectedvirtual |
| remap() | bpp::AbstractAlphabet | inlineprotected |
| resize(size_t size) | bpp::AbstractAlphabet | inlineprotected |
| setState(size_t pos, AlphabetState *st) | bpp::NucleicAlphabet | inlineprotectedvirtual |
| subtract(int s1, int s2) const | bpp::NucleicAlphabet | inline |
| subtract(const std::string &s1, const std::string &s2) const | bpp::NucleicAlphabet | inline |
| updateBinMaps_(size_t pos, const NucleicAlphabetState &st) | bpp::NucleicAlphabet | inlineprivate |
| updateMaps_(size_t pos, const AlphabetState &st) | bpp::AbstractAlphabet | private |
| ~AbstractAlphabet() | bpp::AbstractAlphabet | inlinevirtual |
| ~Alphabet()=default | bpp::Alphabet | virtual |
| ~Clonable()=default | bpp::Clonable | virtual |
| ~DNA() | bpp::DNA | inlinevirtual |
| ~LetterAlphabet() | bpp::LetterAlphabet | inlinevirtual |
| ~NucleicAlphabet() | bpp::NucleicAlphabet | inlinevirtual |
1.9.1 
