bpp-seq3  3.0.0
bpp::CaseMaskedAlphabet Member List

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

AbstractAlphabet()bpp::AbstractAlphabetinline
AbstractAlphabet(const AbstractAlphabet &alph)bpp::AbstractAlphabetinline
Alphabet()bpp::Alphabetinline
alphabet_bpp::AbstractAlphabetprivate
CaseMaskedAlphabet(std::shared_ptr< const LetterAlphabet > nocaseAlphabet)bpp::CaseMaskedAlphabet
CaseMaskedAlphabet(const CaseMaskedAlphabet &cma)bpp::CaseMaskedAlphabetinline
caseSensitive_bpp::LetterAlphabetprivate
charList_bpp::AbstractAlphabetmutableprotected
charToInt(const std::string &state) constbpp::LetterAlphabetinlinevirtual
clone() const overridebpp::CaseMaskedAlphabetinlinevirtual
equals(const Alphabet &alphabet) constbpp::AbstractAlphabetinlineprotectedvirtual
getAlias(int state) constbpp::AbstractAlphabetvirtual
getAlias(const std::string &state) constbpp::AbstractAlphabetvirtual
getAlphabetType() const overridebpp::CaseMaskedAlphabetinlinevirtual
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
getMaskedEquivalentState(int state) constbpp::CaseMaskedAlphabet
getMaskedEquivalentState(const std::string &state) constbpp::CaseMaskedAlphabet
getName(const std::string &state) constbpp::AbstractAlphabetvirtual
getName(int state) constbpp::AbstractAlphabetvirtual
getNumberOfChars() constbpp::AbstractAlphabetinlinevirtual
getNumberOfStates() constbpp::AbstractAlphabetinlinevirtual
getNumberOfTypes() const overridebpp::CaseMaskedAlphabetinlinevirtual
getResolvedChars() constbpp::AbstractAlphabetvirtual
getSize() const overridebpp::CaseMaskedAlphabetinlinevirtual
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() const overridebpp::CaseMaskedAlphabetinlinevirtual
getUnmaskedAlphabet() constbpp::CaseMaskedAlphabetinline
intList_bpp::AbstractAlphabetmutableprotected
intToChar(int state) constbpp::AbstractAlphabetvirtual
isCharInAlphabet(char state) constbpp::LetterAlphabetinline
isCharInAlphabet(const std::string &state) constbpp::LetterAlphabetinlinevirtual
isGap(int state) constbpp::AbstractAlphabetinlinevirtual
isGap(const std::string &state) constbpp::AbstractAlphabetinlinevirtual
isIntInAlphabet(int state) constbpp::AbstractAlphabetvirtual
isMasked(int state) constbpp::CaseMaskedAlphabetinline
isMasked(const std::string &state) constbpp::CaseMaskedAlphabetinline
isMasked(char state) constbpp::CaseMaskedAlphabetinline
isResolvedIn(int state1, int state2) constbpp::AbstractAlphabetvirtual
isUnresolved(int state) const overridebpp::CaseMaskedAlphabetinlinevirtual
isUnresolved(const std::string &state) const overridebpp::CaseMaskedAlphabetinlinevirtual
LETTER_UNDEF_VALUEbpp::LetterAlphabetprivatestatic
LetterAlphabet(bool caseSensitive=false)bpp::LetterAlphabetinline
LetterAlphabet(const LetterAlphabet &bia)bpp::LetterAlphabetinline
letters_bpp::LetterAlphabetprivate
nocaseAlphabet_bpp::CaseMaskedAlphabet
nums_bpp::AbstractAlphabetprivate
operator=(const CaseMaskedAlphabet &cma)bpp::CaseMaskedAlphabetinline
bpp::LetterAlphabet::operator=(const LetterAlphabet &bia)bpp::LetterAlphabetinline
bpp::AbstractAlphabet::operator=(const AbstractAlphabet &alph)bpp::AbstractAlphabetinline
registerState(AlphabetState *st)bpp::LetterAlphabetinlineprotectedvirtual
remap()bpp::AbstractAlphabetinlineprotected
resize(size_t size)bpp::AbstractAlphabetinlineprotected
setState(size_t pos, AlphabetState *st)bpp::LetterAlphabetinlineprotectedvirtual
updateMaps_(size_t pos, const AlphabetState &st)bpp::AbstractAlphabetprivate
~AbstractAlphabet()bpp::AbstractAlphabetinlinevirtual
~Alphabet()=defaultbpp::Alphabetvirtual
~Clonable()=defaultbpp::Clonablevirtual
~LetterAlphabet()bpp::LetterAlphabetinlinevirtual