bpp-seq3  3.0.0
bpp::DNA Member List

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

AbstractAlphabet()bpp::AbstractAlphabetinline
AbstractAlphabet(const AbstractAlphabet &alph)bpp::AbstractAlphabetinline
Alphabet()bpp::Alphabetinline
alphabet_bpp::AbstractAlphabetprivate
binCodes_bpp::NucleicAlphabetprivate
caseSensitive_bpp::LetterAlphabetprivate
charList_bpp::AbstractAlphabetmutableprotected
charToInt(const std::string &state) constbpp::LetterAlphabetinlinevirtual
clone() constbpp::DNAinlinevirtual
DNA(bool exclamationMarkCountsAsGap=false)bpp::DNA
DNA(const DNA &bia)bpp::DNAinline
equals(const Alphabet &alphabet) constbpp::AbstractAlphabetinlineprotectedvirtual
getAlias(int state) constbpp::DNAvirtual
getAlias(const std::string &state) constbpp::DNAvirtual
getAlphabetType() constbpp::DNAinlinevirtual
getCharCodeAt(size_t stateIndex) constbpp::AbstractAlphabetinlinevirtual
getGapCharacterCode() constbpp::AbstractAlphabetinlinevirtual
getGeneric(const std::vector< int > &states) constbpp::DNAvirtual
getGeneric(const std::vector< std::string > &states) constbpp::DNAvirtual
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::NucleicAlphabetinlinevirtual
getOverlap(int s1, int s2) constbpp::NucleicAlphabetinline
getOverlap(const std::string &s1, const std::string &s2) constbpp::NucleicAlphabetinline
getResolvedChars() constbpp::AbstractAlphabetvirtual
getSize() constbpp::NucleicAlphabetinlinevirtual
getState(const std::string &letter) constbpp::NucleicAlphabetinlinevirtual
getState(int num) constbpp::NucleicAlphabetinlinevirtual
bpp::LetterAlphabet::getState(const std::string &letter)bpp::AbstractAlphabet
bpp::LetterAlphabet::getState(int num)bpp::AbstractAlphabet
getStateAt(size_t stateIndex) constbpp::NucleicAlphabetinlinevirtual
getStateAt(size_t stateIndex)bpp::NucleicAlphabetinlinevirtual
getStateByBinCode(int code) constbpp::NucleicAlphabetinline
getStateCodingSize() constbpp::AbstractAlphabetinlineprotectedvirtual
getStateIndex(int state) constbpp::AbstractAlphabetvirtual
getStateIndex(const std::string &state) constbpp::AbstractAlphabetvirtual
getSupportedChars() constbpp::AbstractAlphabetvirtual
getSupportedInts() constbpp::AbstractAlphabetvirtual
getUnknownCharacterCode() constbpp::NucleicAlphabetinlinevirtual
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
isResolvedIn(int state1, int state2) constbpp::DNAvirtual
isUnresolved(int state) constbpp::NucleicAlphabetinlinevirtual
isUnresolved(const std::string &state) constbpp::NucleicAlphabetinlinevirtual
LETTER_UNDEF_VALUEbpp::LetterAlphabetprivatestatic
LetterAlphabet(bool caseSensitive=false)bpp::LetterAlphabetinline
LetterAlphabet(const LetterAlphabet &bia)bpp::LetterAlphabetinline
letters_bpp::LetterAlphabetprivate
NucleicAlphabet()bpp::NucleicAlphabetinline
NucleicAlphabet(const NucleicAlphabet &bia)bpp::NucleicAlphabetinline
nums_bpp::AbstractAlphabetprivate
operator=(const DNA &bia)bpp::DNAinline
bpp::NucleicAlphabet::operator=(const NucleicAlphabet &bia)bpp::NucleicAlphabetinline
bpp::LetterAlphabet::operator=(const LetterAlphabet &bia)bpp::LetterAlphabetinline
bpp::AbstractAlphabet::operator=(const AbstractAlphabet &alph)bpp::AbstractAlphabetinline
registerState(AlphabetState *st)bpp::NucleicAlphabetinlineprotectedvirtual
remap()bpp::AbstractAlphabetinlineprotected
resize(size_t size)bpp::AbstractAlphabetinlineprotected
setState(size_t pos, AlphabetState *st)bpp::NucleicAlphabetinlineprotectedvirtual
subtract(int s1, int s2) constbpp::NucleicAlphabetinline
subtract(const std::string &s1, const std::string &s2) constbpp::NucleicAlphabetinline
updateBinMaps_(size_t pos, const NucleicAlphabetState &st)bpp::NucleicAlphabetinlineprivate
updateMaps_(size_t pos, const AlphabetState &st)bpp::AbstractAlphabetprivate
~AbstractAlphabet()bpp::AbstractAlphabetinlinevirtual
~Alphabet()=defaultbpp::Alphabetvirtual
~Clonable()=defaultbpp::Clonablevirtual
~DNA()bpp::DNAinlinevirtual
~LetterAlphabet()bpp::LetterAlphabetinlinevirtual
~NucleicAlphabet()bpp::NucleicAlphabetinlinevirtual