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)

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

Protected Member Functions
ParameterList	computeCOA (const SequenceDataInterface &data, double pseudoCount=0, bool param=true)
	Comoute COA from data and return the axis position parameters. More...

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

Protected Attributes
bool	init_

size_t	nbrOfAxes_

RowMatrix< double >	P_

RowMatrix< double >	R_

std::vector< double >	colWeights_

ParameterList	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 ProteinFrequencySet class).

Definition at line 31 of file CoalaCore.h.

Constructor & Destructor Documentation

◆ CoalaCore()

CoalaCore::CoalaCore ( size_t nbAxes = 0 )

Definition at line 29 of file CoalaCore.cpp.

Referenced by clone().

◆ ~CoalaCore()

virtual bpp::CoalaCore::~CoalaCore ( )

inlinevirtual

Definition at line 44 of file CoalaCore.h.

Member Function Documentation

◆ clone()

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

inline

Definition at line 46 of file CoalaCore.h.

References CoalaCore().

◆ computeCOA()

ParameterList CoalaCore::computeCOA	(	const SequenceDataInterface &	data,
		double	pseudoCount = `0`,
		bool	param = `true`
	)

protected

Comoute COA from data and return the axis position parameters.

Parameters

data	the Data used
pseudoCount	double pseudo-counts added to amino acids counts (default: 0). If set to 0, null counted amino acids are added 10e-6.
param	boolean true if new parameters must be built (default: true)

Definition at line 40 of file CoalaCore.cpp.

References bpp::ParameterList::addParameter(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), RowMatrix< double >::col(), colWeights_, bpp::ApplicationTools::displayWarning(), bpp::CorrespondenceAnalysis::getColumnWeights(), bpp::SequenceTools::getCounts(), bpp::CorrespondenceAnalysis::getNbOfKeptAxes(), bpp::ParameterList::getParameterValue(), bpp::CorrespondenceAnalysis::getPrincipalAxes(), bpp::CorrespondenceAnalysis::getRowCoordinates(), TemplateSequenceDataInterface< std::string >::getSequenceKeys(), bpp::ParameterList::hasParameter(), bpp::VectorTools::max(), bpp::VectorTools::min(), nbrOfAxes_, P_, paramValues_, R_, bpp::TemplateSequenceContainerInterface< class, class >::sequence(), bpp::TextTools::toString(), and bpp::MatrixTools::transpose().