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 |
bMatrices_ | bpp::UniformizationSubstitutionCount | private |
clone() const | bpp::UniformizationSubstitutionCount | inlinevirtual |
computeCounts_(double length) const | bpp::UniformizationSubstitutionCount | protected |
counts_ | bpp::UniformizationSubstitutionCount | mutableprivate |
currentLength_ | bpp::UniformizationSubstitutionCount | mutableprivate |
fillBMatrices_() | bpp::UniformizationSubstitutionCount | private |
getAllNumbersOfSubstitutions(double length, size_t type=1) const | bpp::UniformizationSubstitutionCount | 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::UniformizationSubstitutionCount | virtual |
getNumberOfSubstitutionsForEachType(size_t initialState, size_t finalState, double length) const | bpp::UniformizationSubstitutionCount | virtual |
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 |
initBMatrices_() | bpp::UniformizationSubstitutionCount | private |
miu_ | bpp::UniformizationSubstitutionCount | private |
model_ | bpp::UniformizationSubstitutionCount | private |
nbStates_ | bpp::UniformizationSubstitutionCount | private |
operator=(const UniformizationSubstitutionCount &usc) | bpp::UniformizationSubstitutionCount | inline |
bpp::AbstractSubstitutionCount::operator=(const AbstractSubstitutionCount &asc) | bpp::AbstractSubstitutionCount | inline |
bpp::AbstractWeightedSubstitutionCount::operator=(const AbstractWeightedSubstitutionCount &index) | bpp::AbstractWeightedSubstitutionCount | inline |
ownWeights_ | bpp::AbstractWeightedSubstitutionCount | protected |
power_ | bpp::UniformizationSubstitutionCount | mutableprivate |
register_ | bpp::AbstractSubstitutionCount | protected |
resetBMatrices_() | bpp::UniformizationSubstitutionCount | private |
s_ | bpp::UniformizationSubstitutionCount | mutableprivate |
setSubstitutionModel(const SubstitutionModel *model) | bpp::UniformizationSubstitutionCount | virtual |
setSubstitutionRegister(SubstitutionRegister *reg) | bpp::AbstractSubstitutionCount | inlinevirtual |
setWeights(const AlphabetIndex2 *weights, bool ownWeights) | bpp::AbstractWeightedSubstitutionCount | virtual |
SubstitutionCount() | bpp::SubstitutionCount | inline |
substitutionRegisterHasChanged() | bpp::UniformizationSubstitutionCount | protectedvirtual |
UniformizationSubstitutionCount(const SubstitutionModel *model, SubstitutionRegister *reg, const AlphabetIndex2 *weights=0) | bpp::UniformizationSubstitutionCount | |
UniformizationSubstitutionCount(const UniformizationSubstitutionCount &usc) | bpp::UniformizationSubstitutionCount | inline |
weights_ | bpp::AbstractWeightedSubstitutionCount | protected |
weightsHaveChanged() | bpp::UniformizationSubstitutionCount | protectedvirtual |
~AbstractSubstitutionCount() | bpp::AbstractSubstitutionCount | inline |
~AbstractWeightedSubstitutionCount() | bpp::AbstractWeightedSubstitutionCount | inlinevirtual |
~SubstitutionCount() | bpp::SubstitutionCount | inlinevirtual |
~UniformizationSubstitutionCount() | bpp::UniformizationSubstitutionCount | inlinevirtual |