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

Methods useful for analytical substitution count and rewards using the eigen decomposition method. More...

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

+ Inheritance diagram for bpp::DecompositionMethods:
+ Collaboration diagram for bpp::DecompositionMethods:

Public Member Functions

 DecompositionMethods (std::shared_ptr< const SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg)
 
 DecompositionMethods (std::shared_ptr< const SubstitutionRegisterInterface > reg)
 
 DecompositionMethods (std::shared_ptr< const SubstitutionModelInterface > model)
 
 DecompositionMethods (const StateMapInterface &stateMap)
 
 DecompositionMethods (const DecompositionMethods &dm)
 
DecompositionMethods & operator= (const DecompositionMethods &dm)
 
DecompositionMethods * clone () const
 
virtual ~DecompositionMethods ()
 
void setSubstitutionModel (std::shared_ptr< const SubstitutionModelInterface > model)
 Set the substitution model. More...
 

Protected Member Functions

void initStates_ ()
 
void initBMatrices_ ()
 
void computeProducts_ ()
 
void computeExpectations (RowMatrix< double > &mapping, double length) const
 
void computeExpectations (std::vector< RowMatrix< double > > &mappings, double length) const
 
void jFunction_ (const std::vector< double > &lambda, double t, RowMatrix< double > &result) const
 Compute the integral part of the computation. More...
 
void jFunction_ (const std::vector< double > &lambda, const std::vector< double > &ilambda, double t, RowMatrix< double > &result, RowMatrix< double > &iresult) const
 Compute the integral part of the computation, in complex numbers. More...
 

Protected Attributes

std::shared_ptr< const SubstitutionModelInterface > model_
 
size_t nbStates_
 
size_t nbTypes_
 
RowMatrix< double > jMat_
 
RowMatrix< double > jIMat_
 
ColMatrix< double > rightEigenVectors_
 Real and imaginary eigenvectors, for non-reversible computation. More...
 
ColMatrix< double > rightIEigenVectors_
 
RowMatrix< double > leftEigenVectors_
 
RowMatrix< double > leftIEigenVectors_
 
std::vector< RowMatrix< double > > bMatrices_
 computation matrices More...
 
std::vector< RowMatrix< double > > insideProducts_
 
std::vector< RowMatrix< double > > insideIProducts_
 

Detailed Description

Methods useful for analytical substitution count and rewards using the eigen decomposition method.

The code is adapted from the original R code by Paula Tataru and Asger Hobolth.

Author
Julien Dutheil, Laurent Guéguen

Definition at line 26 of file DecompositionMethods.h.

Constructor & Destructor Documentation

◆ DecompositionMethods() [1/5]

DecompositionMethods::DecompositionMethods ( std::shared_ptr< const SubstitutionModelInterface >  model,
std::shared_ptr< const SubstitutionRegisterInterface >  reg 
)

Definition at line 17 of file DecompositionMethods.cpp.

References initBMatrices_(), and setSubstitutionModel().

Referenced by clone().

◆ DecompositionMethods() [2/5]

DecompositionMethods::DecompositionMethods ( std::shared_ptr< const SubstitutionRegisterInterface >  reg)

Definition at line 37 of file DecompositionMethods.cpp.

References initBMatrices_().

◆ DecompositionMethods() [3/5]

DecompositionMethods::DecompositionMethods ( std::shared_ptr< const SubstitutionModelInterface >  model)

Definition at line 73 of file DecompositionMethods.cpp.

References setSubstitutionModel().

◆ DecompositionMethods() [4/5]

DecompositionMethods::DecompositionMethods ( const StateMapInterface &  stateMap)

Definition at line 55 of file DecompositionMethods.cpp.

References initBMatrices_().

◆ DecompositionMethods() [5/5]

bpp::DecompositionMethods::DecompositionMethods ( const DecompositionMethods &  dm)
inline

Definition at line 57 of file DecompositionMethods.h.

◆ ~DecompositionMethods()

virtual bpp::DecompositionMethods::~DecompositionMethods ( )
inlinevirtual

Definition at line 93 of file DecompositionMethods.h.

Member Function Documentation

◆ clone()

DecompositionMethods * bpp::DecompositionMethods::clone ( ) const
inline

Definition at line 91 of file DecompositionMethods.h.

References DecompositionMethods().

◆ computeExpectations() [1/2]

void DecompositionMethods::computeExpectations ( RowMatrix< double > &  mapping,
double  length 
) const
protected

Definition at line 166 of file DecompositionMethods.cpp.

References bpp::MatrixTools::hadamardMult(), insideIProducts_, insideProducts_, jFunction_(), jIMat_, jMat_, leftEigenVectors_, leftIEigenVectors_, model_, bpp::MatrixTools::mult(), nbStates_, rightEigenVectors_, and rightIEigenVectors_.

Referenced by bpp::DecompositionSubstitutionCount::computeCounts_(), and bpp::DecompositionReward::computeRewards_().

◆ computeExpectations() [2/2]

void DecompositionMethods::computeExpectations ( std::vector< RowMatrix< double > > &  mappings,
double  length 
) const
protected

Definition at line 196 of file DecompositionMethods.cpp.

References bpp::MatrixTools::hadamardMult(), insideIProducts_, insideProducts_, jFunction_(), jIMat_, jMat_, leftEigenVectors_, leftIEigenVectors_, model_, bpp::MatrixTools::mult(), nbStates_, nbTypes_, rightEigenVectors_, and rightIEigenVectors_.

◆ computeProducts_()

void DecompositionMethods::computeProducts_ ( )
protected

Definition at line 91 of file DecompositionMethods.cpp.

References bMatrices_, insideIProducts_, insideProducts_, leftEigenVectors_, leftIEigenVectors_, model_, bpp::MatrixTools::mult(), nbStates_, nbTypes_, rightEigenVectors_, and rightIEigenVectors_.

Referenced by bpp::DecompositionReward::alphabetIndexHasChanged(), bpp::DecompositionReward::DecompositionReward(), bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), bpp::DecompositionSubstitutionCount::distancesHaveChanged(), bpp::DecompositionReward::setSubstitutionModel(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), and bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged().

◆ initBMatrices_()

void DecompositionMethods::initBMatrices_ ( )
protected

Definition at line 306 of file DecompositionMethods.cpp.

References bMatrices_, insideProducts_, nbStates_, and nbTypes_.

Referenced by DecompositionMethods(), bpp::DecompositionReward::DecompositionReward(), bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), initStates_(), setSubstitutionModel(), and bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged().

◆ initStates_()

void DecompositionMethods::initStates_ ( )
protected

Definition at line 233 of file DecompositionMethods.cpp.

References initBMatrices_(), jMat_, nbStates_, and RowMatrix< double >::resize().

Referenced by bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged().

◆ jFunction_() [1/2]

void DecompositionMethods::jFunction_ ( const std::vector< double > &  lambda,
const std::vector< double > &  ilambda,
double  t,
RowMatrix< double > &  result,
RowMatrix< double > &  iresult 
) const
protected

Compute the integral part of the computation, in complex numbers.

Definition at line 135 of file DecompositionMethods.cpp.

References bpp::abs(), bpp::VectorTools::cos(), bpp::VectorTools::exp(), nbStates_, bpp::VectorTools::sin(), and bpp::NumConstants::TINY().

◆ jFunction_() [2/2]

void DecompositionMethods::jFunction_ ( const std::vector< double > &  lambda,
double  t,
RowMatrix< double > &  result 
) const
protected

Compute the integral part of the computation.

Definition at line 117 of file DecompositionMethods.cpp.

References bpp::abs(), bpp::VectorTools::exp(), nbStates_, and bpp::NumConstants::TINY().

Referenced by computeExpectations().

◆ operator=()

DecompositionMethods & bpp::DecompositionMethods::operator= ( const DecompositionMethods &  dm)
inline

Definition at line 72 of file DecompositionMethods.h.

References bMatrices_, insideIProducts_, insideProducts_, jIMat_, jMat_, leftEigenVectors_, leftIEigenVectors_, model_, nbStates_, nbTypes_, rightEigenVectors_, and rightIEigenVectors_.

Referenced by bpp::DecompositionReward::operator=(), and bpp::DecompositionSubstitutionCount::operator=().

◆ setSubstitutionModel()

void DecompositionMethods::setSubstitutionModel ( std::shared_ptr< const SubstitutionModelInterface >  model)

Set the substitution model.

Parameters
modelA pointer toward the substitution model to use.

Definition at line 241 of file DecompositionMethods.cpp.

References bpp::ColMatrix< class >::col(), bpp::VectorTools::fill(), bpp::ColMatrix< class >::getCol(), bpp::ColMatrix< class >::getNumberOfRows(), RowMatrix< double >::getRow(), initBMatrices_(), insideIProducts_, jIMat_, jMat_, leftEigenVectors_, leftIEigenVectors_, model_, nbStates_, nbTypes_, bpp::ColMatrix< class >::resize(), RowMatrix< double >::resize(), rightEigenVectors_, rightIEigenVectors_, and RowMatrix< double >::row().

Referenced by DecompositionMethods(), bpp::DecompositionReward::setSubstitutionModel(), and bpp::DecompositionSubstitutionCount::setSubstitutionModel().

Member Data Documentation

◆ bMatrices_

std::vector< RowMatrix<double> > bpp::DecompositionMethods::bMatrices_
protected

computation matrices

Definition at line 44 of file DecompositionMethods.h.

Referenced by computeProducts_(), bpp::DecompositionReward::fillBMatrice_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), initBMatrices_(), operator=(), and bpp::DecompositionSubstitutionCount::setDistanceBMatrices_().

◆ insideIProducts_

std::vector< RowMatrix<double> > bpp::DecompositionMethods::insideIProducts_
protected

Definition at line 44 of file DecompositionMethods.h.

Referenced by computeExpectations(), computeProducts_(), operator=(), and setSubstitutionModel().

◆ insideProducts_

std::vector< RowMatrix<double> > bpp::DecompositionMethods::insideProducts_
protected

Definition at line 44 of file DecompositionMethods.h.

Referenced by computeExpectations(), computeProducts_(), initBMatrices_(), and operator=().

◆ jIMat_

RowMatrix<double> bpp::DecompositionMethods::jIMat_
protected

Definition at line 32 of file DecompositionMethods.h.

Referenced by computeExpectations(), operator=(), and setSubstitutionModel().

◆ jMat_

RowMatrix<double> bpp::DecompositionMethods::jMat_
mutableprotected

Definition at line 32 of file DecompositionMethods.h.

Referenced by computeExpectations(), initStates_(), operator=(), and setSubstitutionModel().

◆ leftEigenVectors_

RowMatrix<double> bpp::DecompositionMethods::leftEigenVectors_
protected

Definition at line 39 of file DecompositionMethods.h.

Referenced by computeExpectations(), computeProducts_(), operator=(), and setSubstitutionModel().

◆ leftIEigenVectors_

RowMatrix<double> bpp::DecompositionMethods::leftIEigenVectors_
protected

Definition at line 39 of file DecompositionMethods.h.

Referenced by computeExpectations(), computeProducts_(), operator=(), and setSubstitutionModel().

◆ model_

std::shared_ptr<const SubstitutionModelInterface> bpp::DecompositionMethods::model_
protected

Definition at line 29 of file DecompositionMethods.h.

Referenced by bpp::DecompositionReward::alphabetIndexHasChanged(), bpp::DecompositionSubstitutionCount::computeCounts_(), computeExpectations(), computeProducts_(), bpp::DecompositionReward::computeRewards_(), bpp::DecompositionSubstitutionCount::distancesHaveChanged(), bpp::DecompositionReward::fillBMatrice_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::DecompositionReward::getAllRewards(), bpp::DecompositionSubstitutionCount::getNumberOfSubstitutions(), bpp::DecompositionSubstitutionCount::getNumberOfSubstitutionsPerType(), operator=(), bpp::DecompositionSubstitutionCount::setDistanceBMatrices_(), setSubstitutionModel(), bpp::DecompositionSubstitutionCount::storeAllNumbersOfSubstitutions(), bpp::DecompositionReward::storeAllRewards(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), and bpp::DecompositionSubstitutionCount::weightsHaveChanged().

◆ nbStates_

size_t bpp::DecompositionMethods::nbStates_
protected

Definition at line 30 of file DecompositionMethods.h.

Referenced by bpp::DecompositionSubstitutionCount::computeCounts_(), computeExpectations(), computeProducts_(), bpp::DecompositionReward::computeRewards_(), bpp::DecompositionReward::fillBMatrice_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), initBMatrices_(), bpp::DecompositionSubstitutionCount::initCounts_(), bpp::DecompositionReward::initRewards_(), initStates_(), jFunction_(), operator=(), bpp::DecompositionSubstitutionCount::setDistanceBMatrices_(), setSubstitutionModel(), bpp::DecompositionSubstitutionCount::storeAllNumbersOfSubstitutions(), and bpp::DecompositionReward::storeAllRewards().

◆ nbTypes_

size_t bpp::DecompositionMethods::nbTypes_
protected

Definition at line 31 of file DecompositionMethods.h.

Referenced by bpp::DecompositionSubstitutionCount::computeCounts_(), computeExpectations(), computeProducts_(), initBMatrices_(), operator=(), and setSubstitutionModel().

◆ rightEigenVectors_

ColMatrix<double> bpp::DecompositionMethods::rightEigenVectors_
protected

Real and imaginary eigenvectors, for non-reversible computation.

Definition at line 38 of file DecompositionMethods.h.

Referenced by computeExpectations(), computeProducts_(), operator=(), and setSubstitutionModel().

◆ rightIEigenVectors_

ColMatrix<double> bpp::DecompositionMethods::rightIEigenVectors_
protected

Definition at line 38 of file DecompositionMethods.h.

Referenced by computeExpectations(), computeProducts_(), operator=(), and setSubstitutionModel().

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