#include <CMatrix.h>

Inheritance diagram for CMatrix< CType >:

Public Types
typedef CType	elementType

Public Member Functions
bool	applyPivot (const CVector< size_t > &pivot)

virtual CType *	array ()

virtual const CType *	array () const

	CMatrix (const CMatrix< CType > &src)

	CMatrix (size_t rows=0, size_t cols=0)

virtual size_t	numCols () const

virtual size_t	numRows () const

virtual elementType &	operator() (const size_t &row, const size_t &col)

virtual const elementType &	operator() (const size_t &row, const size_t &col) const

virtual CMatrix< CType > &	operator= (const CMatrix< CType > &rhs)

virtual CMatrix< CType > &	operator= (const CType &value)

virtual CType *	operator[] (size_t row)

virtual const CType *	operator[] (size_t row) const

virtual void	resize (size_t rows, size_t cols, const bool &copy=false)

virtual size_t	size () const

virtual	~CMatrix ()

Protected Attributes
size_t	mCols

CType *	mpBuffer

size_t	mRows

Friends
std::ostream &	operator<< (std::ostream &os, const CMatrix< CType > &A)

Detailed Description

template<class CType>
class CMatrix< CType >

Template class CMatrix < class CType > This template class is a simple matrix class allowing standard C-style and fortran style access to the elements. It also supplies an ostream operator.

Member Typedef Documentation

◆ elementType

template<class CType >

typedef CType CMatrix< CType >::elementType

Constructor & Destructor Documentation

◆ CMatrix() [1/2]

template<class CType >

CMatrix< CType >::CMatrix	(	size_t	rows = `0`,
		size_t	cols = `0`
	)

inline

Default constructor

Parameters

size_t	rows (default = 0)
size_t	cols (default = 0)

References CMatrix< CType >::resize().

◆ CMatrix() [2/2]

template<class CType >

CMatrix< CType >::CMatrix ( const CMatrix< CType > & src )

inline

Copy constructor

Parameters

const CMatrix <CType> & src

References CMatrix< CType >::mCols, CMatrix< CType >::mpBuffer, CMatrix< CType >::mRows, and CMatrix< CType >::resize().

◆ ~CMatrix()

template<class CType >

virtual CMatrix< CType >::~CMatrix ( )

inlinevirtual

Destructor.

References CMatrix< CType >::mpBuffer.

Member Function Documentation

◆ applyPivot()

template<class CType >

bool CMatrix< CType >::applyPivot ( const CVector< size_t > & pivot )

inline

Reorder the rows according to the provided pivots

Parameters

const CVector<size_t> & pivot

Returns: bool success

References CMatrix< CType >::mCols, CMatrix< CType >::mpBuffer, CMatrix< CType >::mRows, pdeletev, and CVectorCore< CType >::size().

Referenced by CExperiment::read().

◆ array() [1/2]

template<class CType >

virtual CType* CMatrix< CType >::array ( )

inlinevirtual

Retrieve the array of the matrix elements. This is suitable for interfacing with clapack routines.

Returns: CType * array

References CMatrix< CType >::mpBuffer.

Referenced by CLinkMatrix::applyColumnPivot(), CLinkMatrix::build(), CBitPatternMethod::buildFluxModes(), CBitPatternTreeMethod::buildFluxModes(), CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CSSAMethod::buildKineticMatrix(), CModel::buildMoieties(), CStochasticRungeKuttaRI5::buildStage1(), CStochasticRungeKuttaRI5::buildStage2(), CModel::buildStoi(), CSSAMethod::buildStoichiometry(), CFitProblem::calcCov(), CFitProblem::calcEigen(), CEigen::calcEigenValues(), CFitProblem::calculate(), CTimeSensMethod::calculate_dAssignments_dPar(), CTimeSensMethod::calculate_dAssignments_dState(), CTimeSensMethod::calculate_dInitialState_dPar(), CTimeSensMethod::calculate_dRate_dPar(), CLNAMethod::calculateCovarianceMatrixFull(), CLNAMethod::calculateCovarianceMatrixReduced(), CFitProblem::calculateCrossValidation(), CMathContainer::calculateJacobian(), CBitPatternMethod::CalculateKernel(), CBitPatternTreeMethod::CalculateKernel(), CMathContainer::calculateRootJacobian(), CStochasticRungeKuttaRI5::calculateStateVariables(), CExperiment::calculateStatistics(), CFitProblem::calculateStatistics(), CMCAMethod::calculateUnscaledConcentrationCC(), CMCAMethod::calculateUnscaledElasticities(), CMCAMethod::calculateUnscaledFluxCC(), CMCAMethod::checkSummationTheorems(), CFitProblem::createParameterSets(), CStepMatrix::CStepMatrix(), CSSAMethod::decomposeJacobian(), CSSAMethod::diag(), dgemm::eval(), CLyapWolfMethod::evalF(), CTimeSensLsodaMethod::evalF(), CStochasticRungeKuttaRI5::generateRandomNumbers(), CExperiment::getErrorMeanSD(), CExperiment::getErrorSum(), COptMethodSteepestDescent::gradient(), CModel::handleUnusedMetabolites(), COptMethodLevenbergMarquardt::hessian(), CExperiment::initializeScalingMatrix(), CEFMMethod::isValidProblem(), CLinkMatrix::leftMultiply(), CSparseMatrix::operator const CMatrix< C_FLOAT64 >(), CSparseMatrix::operator=(), COptMethodLevenbergMarquardt::optimise(), CBitPatternMethod::performRankTest(), CSteadyStateTask::process(), CFitProblem::restore(), CLinkMatrix::rightMultiply(), CMCAMethod::scaleMCA(), COptMethodTruncatedNewton::sFun(), CCSPMethod::sminverse(), CLeastSquareSolution::solve(), and CFitProblem::updateContainer().

◆ array() [2/2]

template<class CType >

virtual const CType* CMatrix< CType >::array ( ) const

inlinevirtual

Retrieve the array of the matrix elements. This is suitable for interfacing with clapack routines.

Returns: const CType * array

References CMatrix< CType >::mpBuffer.

◆ numCols()

template<class CType >

virtual size_t CMatrix< CType >::numCols ( ) const

inlinevirtual

The number of columns of the matrix

Returns: size_t cols

References CMatrix< CType >::mCols.

Referenced by CLinkMatrix::applyColumnPivot(), CLinkMatrix::applyRowPivot(), CLinkMatrix::build(), CBitPatternMethod::buildFluxModeMatrix(), CBitPatternMethod::buildFluxModes(), CBitPatternTreeMethod::buildFluxModes(), CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CModel::buildRedStoi(), CEigen::calcEigenValues(), CFitProblem::calcFIM(), CFitProblem::calcPartialFIM(), CFitProblem::calculate(), CLNAMethod::calculateCovarianceMatrixReduced(), CFitProblem::calculateCrossValidation(), CBitPatternMethod::CalculateKernel(), CBitPatternTreeMethod::CalculateKernel(), CMathContainer::calculateRootDerivatives(), CExperiment::calculateStatistics(), CMCAMethod::calculateUnscaledConcentrationCC(), CMCAMethod::checkSummationTheorems(), CBitPatternMethod::combine(), CExperiment::compile(), CModel::createEventsForTimeseries(), CMCAMethod::createLinkMatrix(), CStepMatrix::CStepMatrix(), CSSAMethod::decomposeJacobian(), CNewtonMethod::doNewtonStep(), dgemm::eval(), CExperiment::getErrorMeanSD(), CExperiment::getErrorSum(), CExperiment::getTotalValueCount(), CModel::handleUnusedMetabolites(), COptMethodLevenbergMarquardt::hessian(), CBitPatternMethod::initialize(), CBitPatternTreeMethod::initialize(), CExperiment::initializeScalingMatrix(), CEFMMethod::isValidProblem(), CLinkMatrix::leftMultiply(), LUfactor(), CLinkMatrixView::numCols(), CSparseMatrix::operator=(), CBitPatternMethod::performRankTest(), CExperiment::printResult(), CMCAMethod::resizeAllMatrices(), CLinkMatrix::rightMultiply(), CMCAMethod::scaleMCA(), CLeastSquareSolution::solve(), CExperiment::storeExtendedTimeSeriesData(), CExperiment::sumOfSquares(), CExperiment::sumOfSquaresStore(), CExperiment::updateFittedPointValues(), and CExperiment::updateFittedPointValuesFromExtendedTimeSeries().

◆ numRows()

template<class CType >

virtual size_t CMatrix< CType >::numRows ( ) const

inlinevirtual

The number of rows of the matrix.

Returns: size_t rows

References CMatrix< CType >::mRows.

Referenced by CLinkMatrix::applyColumnPivot(), CLinkMatrix::applyRowPivot(), CLinkMatrix::build(), CBitPatternMethod::buildFluxModeMatrix(), CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CFitProblem::calcCov(), CFitProblem::calcEigen(), CEigen::calcEigenValues(), CFitProblem::calcFIM(), CFitProblem::calcPartialFIM(), CLNAMethod::calculateCovarianceMatrixReduced(), CBitPatternMethod::CalculateKernel(), CBitPatternTreeMethod::CalculateKernel(), CExperiment::calculateStatistics(), CMCAMethod::calculateUnscaledConcentrationCC(), CMCAMethod::calculateUnscaledFluxCC(), CHybridMethod::checkModel(), CHybridMethodODE45::checkModel(), CMCAMethod::checkSummationTheorems(), CExperiment::compile(), CSSAMethod::decomposeJacobian(), dgemm::eval(), CExperiment::getErrorMeanSD(), CExperiment::getErrorSum(), CModel::handleUnusedMetabolites(), CBitPatternMethod::initialize(), CExperiment::initializeScalingMatrix(), CLinkMatrix::leftMultiply(), LUfactor(), CLinkMatrixView::numRows(), CSparseMatrix::operator=(), CMCAMethod::resizeAllMatrices(), CLinkMatrix::rightMultiply(), CLeastSquareSolution::solve(), and CModel::suitableForStochasticSimulation().

◆ operator()() [1/2]

template<class CType >

virtual elementType& CMatrix< CType >::operator()	(	const size_t &	row,
		const size_t &	col
	)

inlinevirtual

Retrieve a matrix element using c-style indexing.

Parameters

const	size_t & row
const	size_t & col

Returns: const elementType & element

References CMatrix< CType >::mCols, CMatrix< CType >::mpBuffer, and CMatrix< CType >::mRows.

◆ operator()() [2/2]

template<class CType >

virtual const elementType& CMatrix< CType >::operator()	(	const size_t &	row,
		const size_t &	col
	)		const

inlinevirtual

Retrieve a matrix element using c-style indexing.

Parameters

const	size_t & row
const	size_t & col

Returns: const elementType & element

References CMatrix< CType >::mCols, CMatrix< CType >::mpBuffer, and CMatrix< CType >::mRows.

◆ operator=() [1/2]

template<class CType >

virtual CMatrix<CType>& CMatrix< CType >::operator= ( const CMatrix< CType > & rhs )

inlinevirtual

Assignment operator

Parameters

const CMatrix <CType> & rhs

Returns: CMatrix <CType> & lhs

References CMatrix< CType >::mCols, CMatrix< CType >::mpBuffer, CMatrix< CType >::mRows, and CMatrix< CType >::resize().

◆ operator=() [2/2]

template<class CType >

virtual CMatrix<CType>& CMatrix< CType >::operator= ( const CType & value )

inlinevirtual

Assignment operator

Parameters

const CType & value

Returns: CMatrix <CType> & lhs

References CMatrix< CType >::mCols, CMatrix< CType >::mpBuffer, and CMatrix< CType >::mRows.

◆ operator[]() [1/2]

template<class CType >

virtual CType* CMatrix< CType >::operator[] ( size_t row )

inlinevirtual

Retrieve a row of the matrix using c-style indexing

Parameters

size_t row

Returns: CType * row

References CMatrix< CType >::mCols, and CMatrix< CType >::mpBuffer.

◆ operator[]() [2/2]

template<class CType >

virtual const CType* CMatrix< CType >::operator[] ( size_t row ) const

inlinevirtual

Retrieve a row of the matrix using c-style indexing

Parameters

size_t row

Returns: const CType * row

References CMatrix< CType >::mCols, and CMatrix< CType >::mpBuffer.

◆ resize()

template<class CType >

virtual void CMatrix< CType >::resize	(	size_t	rows,
		size_t	cols,
		const bool &	copy = `false`
	)

inlinevirtual

Resize the matrix. The previous content is lost

Parameters

size_t	rows
size_t	cols

References C_FLOAT64, CCopasiMessage::EXCEPTION, max, CMatrix< CType >::mCols, MCopasiBase, min, CMatrix< CType >::mpBuffer, and CMatrix< CType >::mRows.

Referenced by CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CSSAMethod::buildKineticMatrix(), CModel::buildRedStoi(), CModel::buildStoi(), CSSAMethod::buildStoichiometry(), CFitProblem::calcEigen(), CEigen::calcEigenValues(), CFitProblem::calcFIM(), CFitProblem::calcPartialFIM(), CTimeSensMethod::calculate_dAssignments_dPar(), CTimeSensMethod::calculate_dAssignments_dState(), CTimeSensMethod::calculate_dInitialState_dPar(), CTimeSensMethod::calculate_dRate_dPar(), CLNAMethod::calculateCovarianceMatrixFull(), CLNAMethod::calculateCovarianceMatrixReduced(), CMathContainer::calculateElasticityDependencies(), CMathContainer::calculateJacobian(), CMathContainer::calculateJacobianDependencies(), CBitPatternMethod::CalculateKernel(), CBitPatternTreeMethod::CalculateKernel(), CMathContainer::calculateRootJacobian(), CFitProblem::calculateStatistics(), CMCAMethod::calculateUnscaledConcentrationCC(), CTimeSeries::clear(), CMatrix< CType >::CMatrix(), CTimeSeries::compile(), CMCAMethod::createLinkMatrix(), CCSPMethod::CSPImportanceIndex(), CCSPMethod::CSPParticipationIndex(), CCSPMethod::CSPradicalPointer(), CCSPMethod::cspstep(), CSSAMethod::decomposeJacobian(), CSSAMethod::diag(), dgemm::eval(), CTimeSeries::increaseAllocation(), COptMethodLevenbergMarquardt::initialize(), COptMethodNelderMead::initialize(), COptMethodNL2SOL::initialize(), COptMethodPS::initialize(), CFitProblem::initialize(), CCSPMethod::initializeOutput(), CExperiment::initializeScalingMatrix(), CLinkMatrix::leftMultiply(), CTSSAMethod::mat_anal_fast_space(), CTSSAMethod::mat_anal_mod(), CTSSAMethod::mat_anal_mod_space(), CILDMMethod::newton(), CILDMModifiedMethod::newton_new(), CSparseMatrix::operator const CMatrix< C_FLOAT64 >(), CMatrix< CType >::operator=(), CExperiment::read(), CLNAMethod::resizeAllMatrices(), CMCAMethod::resizeAllMatrices(), CLinkMatrix::rightMultiply(), CCSPMethod::setAnnotationM(), CILDMMethod::setAnnotationM(), CILDMModifiedMethod::setAnnotationM(), CLyapWolfMethod::start(), CTimeSensLsodaMethod::start(), CStochasticRungeKuttaRI5::start(), CCSPMethod::start(), CILDMMethod::start(), CILDMModifiedMethod::start(), CCSPMethod::step(), CILDMMethod::step(), CILDMModifiedMethod::step(), CTSSAMethod::sylvester(), CSteadyStateTask::updateMatrices(), and CCSPMethod::yCorrection().

◆ size()

template<class CType >

virtual size_t CMatrix< CType >::size ( ) const

inlinevirtual

Friends And Related Function Documentation

◆ operator<<

template<class CType >

std::ostream& operator<<	(	std::ostream &	os,
		const CMatrix< CType > &	A
	)

friend

Output stream operator

Parameters

ostream	& os
const	CMatrix< CType > & A

Returns: ostream & os

Member Data Documentation

◆ mCols

template<class CType >

size_t CMatrix< CType >::mCols

protected

Number of columns in the matrix

Referenced by CMatrix< CType >::applyPivot(), CMatrix< CType >::CMatrix(), CMatrix< CType >::numCols(), CMatrix< CType >::operator()(), CMatrix< CType >::operator=(), CMatrix< CType >::operator[](), CMatrix< CType >::resize(), and CMatrix< CType >::size().

◆ mpBuffer

template<class CType >

CType* CMatrix< CType >::mpBuffer

protected

The array storing the matrix elements

Referenced by CMatrix< CType >::applyPivot(), CMatrix< CType >::array(), CMatrix< CType >::CMatrix(), CMatrix< CType >::operator()(), CMatrix< CType >::operator=(), CMatrix< CType >::operator[](), CMatrix< CType >::resize(), and CMatrix< CType >::~CMatrix().

◆ mRows

template<class CType >

size_t CMatrix< CType >::mRows

protected

Number of rows in the matrix.

Referenced by CMatrix< CType >::applyPivot(), CMatrix< CType >::CMatrix(), CMatrix< CType >::numRows(), CMatrix< CType >::operator()(), CMatrix< CType >::operator=(), CMatrix< CType >::resize(), and CMatrix< CType >::size().

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

CMatrix.h

Public Types

Public Member Functions

Protected Attributes

Friends

Detailed Description

template<class CType> class CMatrix< CType >

Member Typedef Documentation

◆ elementType

Constructor & Destructor Documentation

◆ CMatrix() [1/2]

◆ CMatrix() [2/2]

◆ ~CMatrix()

Member Function Documentation

◆ applyPivot()

◆ array() [1/2]

◆ array() [2/2]

◆ numCols()

◆ numRows()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ resize()

◆ size()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ mCols

◆ mpBuffer

◆ mRows

template<class CType>
class CMatrix< CType >