bpp::CoalaCore Class Reference

This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid substitution model. More...

#include <Bpp/Phyl/Model/Protein/CoalaCore.h>

Inheritance diagram for bpp::CoalaCore:

Collaboration diagram for bpp::CoalaCore:

Public Member Functions
	CoalaCore (size_t nbAxes=0, const std::string &exch="LG08")
virtual	~CoalaCore ()
CoalaCore *	clone () const
size_t	getNbrOfAxes () const
const RowMatrix< double > &	getTppalAxesMatrix () const
const RowMatrix< double > &	getRowCoordinates () const
const std::vector< double > &	getColumnWeights () const
void	setParamValues (const std::map< std::string, std::string > &valuesSettings)

Protected Member Functions
ParameterList	computeCOA (const SequenceContainer &data, bool param=true)
std::vector< double >	prodMatrixVector (RowMatrix< double > &P, std::vector< double > &V)

Protected Attributes
bool	init_
size_t	nbrOfAxes_
std::string	exch_
RowMatrix< double >	P_
RowMatrix< double >	R_
std::vector< double >	colWeights_
std::map< std::string, std::string >	paramValues_

Detailed Description

This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid substitution model.

This class allows to compute the COA from the alignment, to define the parameter (axis positions), and implements a function used to compute the equilibrium frequencies from a set of coordinates along the principal axes of the COA.

Author

Mathieu Groussin

Parameters

nbAxes	The number of principal axes of the COA that have to be taken into account to optimize the 20 branch-specific equilibrium frequencies. This number is common to all branches, as well as on the root, where frequencies are optimized with a MVAprotein object (See the ProteinFrequenciesSet class).
exch	The exchangeability matrix. The matrices currently available are DSO78, JTT92, WAG01 or LG08. A user-defined matrix can be specified with the 'file' argument.

Definition at line 66 of file CoalaCore.h.

Constructor & Destructor Documentation

CoalaCore()

CoalaCore::CoalaCore	(	size_t	nbAxes = 0,
		const std::string &	exch = "LG08"
	)

Definition at line 65 of file CoalaCore.cpp.

Referenced by clone().

~CoalaCore()

virtual bpp::CoalaCore::~CoalaCore ( )

inlinevirtual

Definition at line 80 of file CoalaCore.h.

Member Function Documentation

clone()

CoalaCore* bpp::CoalaCore::clone ( ) const

inline

Definition at line 82 of file CoalaCore.h.

References CoalaCore().

computeCOA()

ParameterList CoalaCore::computeCOA ( const SequenceContainer &  data, bool  param = true  )

protected

Definition at line 77 of file CoalaCore.cpp.

References colWeights_, nbrOfAxes_, P_, paramValues_, and R_.

Referenced by bpp::Coala::setFreqFromData().

getColumnWeights()

const std::vector<double>& bpp::CoalaCore::getColumnWeights ( ) const

inline

Definition at line 88 of file CoalaCore.h.

References colWeights_.

Referenced by bpp::MvaFrequenciesSet::initSet().

getNbrOfAxes()

size_t bpp::CoalaCore::getNbrOfAxes ( ) const

inline

Definition at line 85 of file CoalaCore.h.

References nbrOfAxes_.

Referenced by bpp::MvaFrequenciesSet::initSet(), and bpp::BppOSubstitutionModelFormat::write().

getRowCoordinates()

const RowMatrix<double>& bpp::CoalaCore::getRowCoordinates ( ) const

inline

Definition at line 87 of file CoalaCore.h.

References R_.

Referenced by bpp::MvaFrequenciesSet::initSet().

getTppalAxesMatrix()

const RowMatrix<double>& bpp::CoalaCore::getTppalAxesMatrix ( ) const

inline

Definition at line 86 of file CoalaCore.h.

References P_.

Referenced by bpp::MvaFrequenciesSet::initSet().

prodMatrixVector()

vector< double > CoalaCore::prodMatrixVector ( RowMatrix< double > &  P, std::vector< double > &  V  )

protected

Definition at line 176 of file CoalaCore.cpp.

Referenced by bpp::Coala::computeEquilibriumFrequencies().

setParamValues()

void bpp::CoalaCore::setParamValues ( const std::map< std::string, std::string > &  valuesSettings )

inline

Definition at line 89 of file CoalaCore.h.

References paramValues_.

Member Data Documentation

colWeights_

std::vector<double> bpp::CoalaCore::colWeights_

protected

Definition at line 74 of file CoalaCore.h.

Referenced by computeCOA(), bpp::Coala::computeEquilibriumFrequencies(), and getColumnWeights().

exch_

std::string bpp::CoalaCore::exch_

protected

Definition at line 71 of file CoalaCore.h.

init_

bool bpp::CoalaCore::init_

protected

Definition at line 69 of file CoalaCore.h.

nbrOfAxes_

size_t bpp::CoalaCore::nbrOfAxes_

protected

Definition at line 70 of file CoalaCore.h.

Referenced by computeCOA(), and getNbrOfAxes().

P_

RowMatrix<double> bpp::CoalaCore::P_

protected

Definition at line 72 of file CoalaCore.h.

Referenced by computeCOA(), bpp::Coala::computeEquilibriumFrequencies(), and getTppalAxesMatrix().

paramValues_

std::map<std::string, std::string> bpp::CoalaCore::paramValues_

protected

Definition at line 75 of file CoalaCore.h.

Referenced by computeCOA(), and setParamValues().

R_

RowMatrix<double> bpp::CoalaCore::R_

protected

Definition at line 73 of file CoalaCore.h.

Referenced by computeCOA(), and getRowCoordinates().

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

• Bpp/Phyl/Model/Protein/CoalaCore.h
• Bpp/Phyl/Model/Protein/CoalaCore.cpp