bpp-phyl
2.2.0
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Partial implementation of the WeightedSubstitutionCount interface. More...
#include <Bpp/Phyl/Mapping/WeightedSubstitutionCount.h>
Public Member Functions | |
AbstractWeightedSubstitutionCount (const AlphabetIndex2 *weights, bool ownWeights) | |
AbstractWeightedSubstitutionCount (const AbstractWeightedSubstitutionCount &index) | |
AbstractWeightedSubstitutionCount & | operator= (const AbstractWeightedSubstitutionCount &index) |
virtual | ~AbstractWeightedSubstitutionCount () |
void | setWeights (const AlphabetIndex2 *weights, bool ownWeights) |
bool | hasWeights () const |
const AlphabetIndex2 * | getWeights () const |
virtual SubstitutionCount * | clone () const =0 |
virtual bool | hasSubstitutionRegister () const =0 |
virtual const SubstitutionRegister * | getSubstitutionRegister () const =0 |
virtual SubstitutionRegister * | getSubstitutionRegister ()=0 |
virtual void | setSubstitutionRegister (SubstitutionRegister *reg)=0 |
virtual size_t | getNumberOfSubstitutionTypes () const |
Short cut function, equivalent to getSubstitutionRegister().getNumberOfSubstitutionTypes(). More... | |
virtual const Alphabet * | getAlphabet () const |
Short cut function, equivalent to getSubstitutionRegister()->getAlphabet(). More... | |
virtual size_t | getNumberOfStates () const |
Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize(). More... | |
virtual double | getNumberOfSubstitutions (size_t initialState, size_t finalState, double length, size_t type) const =0 |
Get the number of susbstitutions on a branch, given the initial and final states, and the branch length. More... | |
virtual Matrix< double > * | getAllNumbersOfSubstitutions (double length, size_t type) const =0 |
Get the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length. More... | |
virtual std::vector< double > | getNumberOfSubstitutionsForEachType (size_t initialState, size_t finalState, double length) const =0 |
Get the numbers of susbstitutions on a branch for all types, for an initial and final states, given the branch length. More... | |
virtual void | setSubstitutionModel (const SubstitutionModel *model)=0 |
Set the substitution model associated with this count, if relevent. More... | |
Protected Member Functions | |
virtual void | weightsHaveChanged ()=0 |
Protected Attributes | |
const AlphabetIndex2 * | weights_ |
bool | ownWeights_ |
Partial implementation of the WeightedSubstitutionCount interface.
Definition at line 67 of file WeightedSubstitutionCount.h.
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inline |
Definition at line 75 of file WeightedSubstitutionCount.h.
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inline |
Definition at line 80 of file WeightedSubstitutionCount.h.
References ownWeights_, and weights_.
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inlinevirtual |
Definition at line 97 of file WeightedSubstitutionCount.h.
References ownWeights_, and weights_.
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pure virtualinherited |
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pure virtualinherited |
Get the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length.
length | The length of the branch. |
type | The type of susbstitution to count. |
Implemented in bpp::LabelSubstitutionCount, bpp::DecompositionSubstitutionCount, bpp::UniformizationSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::OneJumpSubstitutionCount.
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inlinevirtualinherited |
Short cut function, equivalent to getSubstitutionRegister()->getAlphabet().
Definition at line 112 of file SubstitutionCount.h.
References bpp::SubstitutionRegister::getAlphabet(), and bpp::SubstitutionCount::getSubstitutionRegister().
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inlinevirtualinherited |
Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize().
Definition at line 119 of file SubstitutionCount.h.
References bpp::SubstitutionRegister::getAlphabet(), and bpp::SubstitutionCount::getSubstitutionRegister().
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pure virtualinherited |
Get the number of susbstitutions on a branch, given the initial and final states, and the branch length.
initialState | The initial state. |
finalState | The final state. |
length | The length of the branch. |
type | The type of substitution to count. |
Implemented in bpp::LabelSubstitutionCount, bpp::DecompositionSubstitutionCount, bpp::UniformizationSubstitutionCount, bpp::LaplaceSubstitutionCount, bpp::NaiveSubstitutionCount, and bpp::OneJumpSubstitutionCount.
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pure virtualinherited |
Get the numbers of susbstitutions on a branch for all types, for an initial and final states, given the branch length.
initialState | The initial state. |
finalState | The final state. |
length | The length of the branch. |
Implemented in bpp::LabelSubstitutionCount, bpp::DecompositionSubstitutionCount, bpp::UniformizationSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::OneJumpSubstitutionCount.
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inlinevirtualinherited |
Short cut function, equivalent to getSubstitutionRegister().getNumberOfSubstitutionTypes().
Definition at line 105 of file SubstitutionCount.h.
References bpp::SubstitutionRegister::getNumberOfSubstitutionTypes(), and bpp::SubstitutionCount::getSubstitutionRegister().
Referenced by bpp::NaiveSubstitutionCount::getNumberOfSubstitutionsForEachType(), bpp::UniformizationSubstitutionCount::getNumberOfSubstitutionsForEachType(), bpp::DecompositionSubstitutionCount::getNumberOfSubstitutionsForEachType(), and bpp::ProbabilisticSubstitutionMapping::getNumberOfSubstitutionTypes().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionCount.
Referenced by bpp::SubstitutionCount::getAlphabet(), bpp::SubstitutionCount::getNumberOfStates(), and bpp::SubstitutionCount::getNumberOfSubstitutionTypes().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionCount.
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inlinevirtual |
Implements bpp::WeightedSubstitutionCount.
Definition at line 106 of file WeightedSubstitutionCount.h.
References weights_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionCount.
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inlinevirtual |
Implements bpp::WeightedSubstitutionCount.
Definition at line 105 of file WeightedSubstitutionCount.h.
References weights_.
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inline |
Definition at line 88 of file WeightedSubstitutionCount.h.
References ownWeights_, and weights_.
Referenced by bpp::UniformizationSubstitutionCount::operator=(), and bpp::DecompositionSubstitutionCount::operator=().
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pure virtualinherited |
Set the substitution model associated with this count, if relevent.
model | The substitution model to use with this count. |
Implemented in bpp::LabelSubstitutionCount, bpp::DecompositionSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::UniformizationSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::OneJumpSubstitutionCount.
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pure virtualinherited |
reg | The new SubstitutionRegister object to be associated to this instance. The register contains the description of the various substitutions types that are mapped. |
Implemented in bpp::AbstractSubstitutionCount, bpp::LabelSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::OneJumpSubstitutionCount.
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virtual |
Implements bpp::WeightedSubstitutionCount.
Definition at line 44 of file WeightedSubstitutionCount.cpp.
References ownWeights_, weights_, and weightsHaveChanged().
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protectedpure virtual |
Implemented in bpp::DecompositionSubstitutionCount, bpp::NaiveSubstitutionCount, and bpp::UniformizationSubstitutionCount.
Referenced by setWeights().
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protected |
Definition at line 72 of file WeightedSubstitutionCount.h.
Referenced by AbstractWeightedSubstitutionCount(), operator=(), setWeights(), and ~AbstractWeightedSubstitutionCount().
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protected |
Definition at line 71 of file WeightedSubstitutionCount.h.
Referenced by AbstractWeightedSubstitutionCount(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::NaiveSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::NaiveSubstitutionCount::getNumberOfSubstitutions(), getWeights(), hasWeights(), operator=(), setWeights(), bpp::UniformizationSubstitutionCount::weightsHaveChanged(), bpp::DecompositionSubstitutionCount::weightsHaveChanged(), and ~AbstractWeightedSubstitutionCount().