bpp-phyl3  3.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
bpp::AbstractSubstitutionCount Class Referenceabstract

Partial implementation of the SubstitutionCount interface. More...

#include <Bpp/Phyl/Mapping/SubstitutionCount.h>

+ Inheritance diagram for bpp::AbstractSubstitutionCount:
+ Collaboration diagram for bpp::AbstractSubstitutionCount:

Public Member Functions

 AbstractSubstitutionCount (std::shared_ptr< const SubstitutionRegisterInterface > reg)
 
virtual ~AbstractSubstitutionCount ()
 
bool hasSubstitutionRegister () const
 
void setSubstitutionRegister (std::shared_ptr< const SubstitutionRegisterInterface > reg)
 attribution of a SubstitutionRegister More...
 
std::shared_ptr< const SubstitutionRegisterInterface > getSubstitutionRegister () const
 
virtual SubstitutionCountInterface * clone () const =0
 
virtual size_t getNumberOfSubstitutionTypes () const
 Short cut function, equivalent to getSubstitutionRegister().getNumberOfSubstitutionTypes(). More...
 
virtual std::shared_ptr< 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 std::unique_ptr< 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 void storeAllNumbersOfSubstitutions (double length, size_t type, Eigen::MatrixXd &mat) const =0
 Stores the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length. More...
 
virtual std::vector< double > getNumberOfSubstitutionsPerType (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 (std::shared_ptr< const SubstitutionModelInterface > model)=0
 Set the substitution model associated with this count, if relevant. More...
 

Protected Member Functions

virtual void substitutionRegisterHasChanged ()=0
 

Protected Attributes

std::shared_ptr< const SubstitutionRegisterInterface > register_
 

Detailed Description

Partial implementation of the SubstitutionCount interface.

Definition at line 142 of file SubstitutionCount.h.

Constructor & Destructor Documentation

◆ AbstractSubstitutionCount()

bpp::AbstractSubstitutionCount::AbstractSubstitutionCount ( std::shared_ptr< const SubstitutionRegisterInterface >  reg)
inline

Definition at line 149 of file SubstitutionCount.h.

◆ ~AbstractSubstitutionCount()

virtual bpp::AbstractSubstitutionCount::~AbstractSubstitutionCount ( )
inlinevirtual

Definition at line 153 of file SubstitutionCount.h.

Member Function Documentation

◆ clone()

virtual SubstitutionCountInterface* bpp::SubstitutionCountInterface::clone ( ) const
pure virtualinherited

Implements bpp::Clonable.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

Referenced by bpp::SubstitutionMappingTools::computeCounts().

◆ getAllNumbersOfSubstitutions()

virtual std::unique_ptr< Matrix<double> > bpp::SubstitutionCountInterface::getAllNumbersOfSubstitutions ( double  length,
size_t  type 
) const
pure virtualinherited

Get the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length.

Parameters
lengthThe length of the branch.
typeThe type of susbstitution to count.
Returns
A matrix with all numbers of substitutions for each initial and final states.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

◆ getAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::SubstitutionCountInterface::getAlphabet ( ) const
inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister()->getAlphabet().

Returns
The alphabet associated to this substitution count.

Definition at line 78 of file SubstitutionCount.h.

References bpp::SubstitutionCountInterface::getSubstitutionRegister().

◆ getNumberOfStates()

virtual size_t bpp::SubstitutionCountInterface::getNumberOfStates ( ) const
inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize().

Returns
The number of states in the model/alphabet.

Definition at line 85 of file SubstitutionCount.h.

References bpp::SubstitutionCountInterface::getSubstitutionRegister().

◆ getNumberOfSubstitutions()

virtual double bpp::SubstitutionCountInterface::getNumberOfSubstitutions ( size_t  initialState,
size_t  finalState,
double  length,
size_t  type 
) const
pure virtualinherited

Get the number of susbstitutions on a branch, given the initial and final states, and the branch length.

Parameters
initialStateThe initial state.
finalStateThe final state.
lengthThe length of the branch.
typeThe type of substitution to count.
Returns
The number of substitutions on a branch of specified length and according to initial and final states.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

◆ getNumberOfSubstitutionsPerType()

virtual std::vector<double> bpp::SubstitutionCountInterface::getNumberOfSubstitutionsPerType ( size_t  initialState,
size_t  finalState,
double  length 
) const
pure virtualinherited

Get the numbers of susbstitutions on a branch for all types, for an initial and final states, given the branch length.

Parameters
initialStateThe initial state.
finalStateThe final state.
lengthThe length of the branch.
Returns
A matrix with all numbers of substitutions for each initial and final states.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

◆ getNumberOfSubstitutionTypes()

virtual size_t bpp::SubstitutionCountInterface::getNumberOfSubstitutionTypes ( ) const
inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister().getNumberOfSubstitutionTypes().

Returns
The number of substitution types supported by this instance.

Definition at line 71 of file SubstitutionCount.h.

References bpp::SubstitutionCountInterface::getSubstitutionRegister().

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::DecompositionSubstitutionCount::getNumberOfSubstitutionsPerType(), bpp::NaiveSubstitutionCount::getNumberOfSubstitutionsPerType(), and bpp::UniformizationSubstitutionCount::getNumberOfSubstitutionsPerType().

◆ getSubstitutionRegister()

std::shared_ptr<const SubstitutionRegisterInterface> bpp::AbstractSubstitutionCount::getSubstitutionRegister ( ) const
inlinevirtual
Returns
The SubstitutionRegister object associated to this instance. The register contains the description of the various substitutions types that are mapped.

Implements bpp::SubstitutionCountInterface.

Definition at line 170 of file SubstitutionCount.h.

References register_.

◆ hasSubstitutionRegister()

bool bpp::AbstractSubstitutionCount::hasSubstitutionRegister ( ) const
inlinevirtual
Returns
Tell if a substitution register has been attached to this class.

Implements bpp::SubstitutionCountInterface.

Definition at line 156 of file SubstitutionCount.h.

References register_.

◆ setSubstitutionModel()

virtual void bpp::SubstitutionCountInterface::setSubstitutionModel ( std::shared_ptr< const SubstitutionModelInterface >  model)
pure virtualinherited

Set the substitution model associated with this count, if relevant.

Parameters
modelThe substitution model to use with this count.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

◆ setSubstitutionRegister()

void bpp::AbstractSubstitutionCount::setSubstitutionRegister ( std::shared_ptr< const SubstitutionRegisterInterface >  reg)
inlinevirtual

attribution of a SubstitutionRegister

Parameters
regpointer to a SubstitutionRegister

Implements bpp::SubstitutionCountInterface.

Definition at line 164 of file SubstitutionCount.h.

References register_, and substitutionRegisterHasChanged().

◆ storeAllNumbersOfSubstitutions()

virtual void bpp::SubstitutionCountInterface::storeAllNumbersOfSubstitutions ( double  length,
size_t  type,
Eigen::MatrixXd &  mat 
) const
pure virtualinherited

Stores the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length.

Parameters
lengthThe length of the branch.
typeThe type of susbstitution to count.
matThe matrix filled with all numbers of substitutions for each initial and final states.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

◆ substitutionRegisterHasChanged()

virtual void bpp::AbstractSubstitutionCount::substitutionRegisterHasChanged ( )
protectedpure virtual

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

Referenced by setSubstitutionRegister().

Member Data Documentation

◆ register_

std::shared_ptr<const SubstitutionRegisterInterface> bpp::AbstractSubstitutionCount::register_
protected

Definition at line 146 of file SubstitutionCount.h.

Referenced by bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::distancesHaveChanged(), bpp::UniformizationSubstitutionCount::distancesHaveChanged(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::NaiveSubstitutionCount::getNumberOfSubstitutions(), getSubstitutionRegister(), hasSubstitutionRegister(), bpp::UniformizationSubstitutionCount::initBMatrices_(), bpp::DecompositionSubstitutionCount::initCounts_(), bpp::UniformizationSubstitutionCount::resetBMatrices_(), bpp::DecompositionSubstitutionCount::setDistanceBMatrices_(), bpp::UniformizationSubstitutionCount::setDistanceBMatrices_(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), setSubstitutionRegister(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::DecompositionSubstitutionCount::weightsHaveChanged(), and bpp::UniformizationSubstitutionCount::weightsHaveChanged().

The documentation for this class was generated from the following file: