AbstractSubstitutionCount(SubstitutionRegister *reg) | bpp::AbstractSubstitutionCount | inline |
AbstractSubstitutionCount(const AbstractSubstitutionCount &asc) | bpp::AbstractSubstitutionCount | inline |
AbstractWeightedSubstitutionCount(const AlphabetIndex2 *weights, bool ownWeights) | bpp::AbstractWeightedSubstitutionCount | inline |
AbstractWeightedSubstitutionCount(const AbstractWeightedSubstitutionCount &index) | bpp::AbstractWeightedSubstitutionCount | inline |
allowSelf_ | bpp::NaiveSubstitutionCount | private |
clone() const | bpp::NaiveSubstitutionCount | inlinevirtual |
getAllNumbersOfSubstitutions(double length, size_t type=1) const | bpp::NaiveSubstitutionCount | virtual |
getAlphabet() const | bpp::SubstitutionCount | inlinevirtual |
getNumberOfStates() const | bpp::SubstitutionCount | inlinevirtual |
getNumberOfSubstitutions(size_t initialState, size_t finalState, double length, size_t type=1) const | bpp::NaiveSubstitutionCount | inlinevirtual |
getNumberOfSubstitutionsForEachType(size_t initialState, size_t finalState, double length) const | bpp::NaiveSubstitutionCount | inlinevirtual |
getNumberOfSubstitutionTypes() const | bpp::SubstitutionCount | inlinevirtual |
getSubstitutionRegister() const | bpp::AbstractSubstitutionCount | inlinevirtual |
getSubstitutionRegister() | bpp::AbstractSubstitutionCount | inlinevirtual |
getWeights() const | bpp::AbstractWeightedSubstitutionCount | inlinevirtual |
hasSubstitutionRegister() const | bpp::AbstractSubstitutionCount | inlinevirtual |
hasWeights() const | bpp::AbstractWeightedSubstitutionCount | inlinevirtual |
NaiveSubstitutionCount(const SubstitutionModel *model, SubstitutionRegister *reg, bool allowSelf=false, const AlphabetIndex2 *weights=0) | bpp::NaiveSubstitutionCount | inline |
bpp::operator=(const AbstractSubstitutionCount &asc) | bpp::AbstractSubstitutionCount | inline |
bpp::AbstractWeightedSubstitutionCount::operator=(const AbstractWeightedSubstitutionCount &index) | bpp::AbstractWeightedSubstitutionCount | inline |
ownWeights_ | bpp::AbstractWeightedSubstitutionCount | protected |
register_ | bpp::AbstractSubstitutionCount | protected |
setSubstitutionModel(const SubstitutionModel *model) | bpp::NaiveSubstitutionCount | inlinevirtual |
setSubstitutionRegister(SubstitutionRegister *reg) | bpp::AbstractSubstitutionCount | inlinevirtual |
setWeights(const AlphabetIndex2 *weights, bool ownWeights) | bpp::AbstractWeightedSubstitutionCount | virtual |
SubstitutionCount() | bpp::SubstitutionCount | inline |
substitutionRegisterHasChanged() | bpp::NaiveSubstitutionCount | inlineprivatevirtual |
supportedChars_ | bpp::NaiveSubstitutionCount | private |
weights_ | bpp::AbstractWeightedSubstitutionCount | protected |
weightsHaveChanged() | bpp::NaiveSubstitutionCount | inlineprivatevirtual |
~AbstractSubstitutionCount() | bpp::AbstractSubstitutionCount | inline |
~AbstractWeightedSubstitutionCount() | bpp::AbstractWeightedSubstitutionCount | inlinevirtual |
~NaiveSubstitutionCount() | bpp::NaiveSubstitutionCount | inlinevirtual |
~SubstitutionCount() | bpp::SubstitutionCount | inlinevirtual |