#include <CMCAMethod.h>

Inheritance diagram for CMCAMethod:

Public Member Functions
bool	CalculateMCA (C_FLOAT64 res)

bool	calculateUnscaledConcentrationCC ()

void	calculateUnscaledElasticities (C_FLOAT64 res)

bool	calculateUnscaledFluxCC (const bool &status)

bool	checkSummationTheorems (const C_FLOAT64 &resolution)

	CMCAMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::mcaMethodReder, const CTaskEnum::Task &taskType=CTaskEnum::Task::mca)

	CMCAMethod (const CMCAMethod &src, const CDataContainer *pParent)

virtual bool	elevateChildren ()

const CModel *	getModel () const

const CMatrix< C_FLOAT64 > &	getScaledConcentrationCC () const

const CDataArray *	getScaledConcentrationCCAnn () const

const CMatrix< C_FLOAT64 > &	getScaledElasticities () const

const CDataArray *	getScaledElasticitiesAnn () const

const CMatrix< C_FLOAT64 > &	getScaledFluxCC () const

const CDataArray *	getScaledFluxCCAnn () const

const CSteadyStateMethod::ReturnCode &	getSteadyStateStatus () const

const CMatrix< C_FLOAT64 > &	getUnscaledConcentrationCC () const

const CDataArray *	getUnscaledConcentrationCCAnn () const

const CMatrix< C_FLOAT64 > &	getUnscaledElasticities () const

const CDataArray *	getUnscaledElasticitiesAnn () const

const CMatrix< C_FLOAT64 > &	getUnscaledFluxCC () const

const CDataArray *	getUnscaledFluxCCAnn () const

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

C_INT32	load (CReadConfig &configBuffer)

virtual bool	process ()

virtual void	resizeAllMatrices ()

bool	scaleMCA (const bool &status, C_FLOAT64 res)

void	setFactor (C_FLOAT64 factor)

void	setSteadyStateResolution (C_FLOAT64 factor)

void	setSteadyStateTask (CSteadyStateTask *pSteadyStateTask)

virtual	~CMCAMethod ()

Public Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src, const CDataContainer *pParent)

virtual void	clearCallBack ()

const CProcessReportLevel &	getCallBack () const

CMathContainer *	getMathContainer () const

const CTaskEnum::Method &	getSubType () const

const CTaskEnum::Task &	getType () const

virtual void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)

CCopasiMethod &	operator= (const CCopasiMethod &rhs)

virtual void	print (std::ostream *ostream) const

virtual void	printResult (std::ostream *ostream) const

virtual bool	setCallBack (CProcessReportLevel callBack)

void	setMathContainer (CMathContainer *pContainer)

virtual	~CCopasiMethod ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

void	addParameter (CCopasiParameter *pParameter)

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)

CCopasiParameterGroup *	assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

template<class CType >
CType *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

index_iterator	beginIndex () const

const_name_iterator	beginName () const

	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL)

	CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup")

void	clear ()

virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const

index_iterator	endIndex () const

const_name_iterator	endName () const

CCopasiParameterGroup &	getElementTemplates ()

const CCopasiParameterGroup &	getElementTemplates () const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

virtual size_t	getIndex (const CDataObject *pObject) const

size_t	getIndex (const std::string &name) const

std::string	getKey (const size_t &index) const

std::string	getKey (const std::string &name) const

virtual const std::string &	getName (const size_t &index) const

virtual const CObjectInterface *	getObject (const CCommonName &cn) const

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

CCopasiParameter *	getParameter (std::string name)

const CCopasiParameter *	getParameter (std::string name) const

CCopasiParameter::Type	getType (const size_t &index) const

CCopasiParameter::Type	getType (const std::string &name) const

std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const

template<class CType >
CType &	getValue (const size_t &index)

template<class CType >
const CType &	getValue (const size_t &index) const

template<class CType >
CType &	getValue (const std::string &name)

template<class CType >
const CType &	getValue (const std::string &name) const

bool	haveTemplate () const

virtual CUndoObjectInterface *	insert (const CData &data)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

virtual bool	remove (CDataObject *pObject)

bool	removeParameter (CCopasiParameter *pParameter)

bool	removeParameter (const size_t &index)

bool	removeParameter (const std::string &name)

virtual void	setUserInterfaceFlag (const UserInterfaceFlag &flag)

template<class CType >
bool	setValue (const size_t &index, const CType &value)

template<class CType >
bool	setValue (const std::string &name, const CType &value)

size_t	size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const

bool	swap (const size_t &iFrom, const size_t &iTo)

bool	swap (index_iterator &from, index_iterator &to)

virtual CData	toData () const

virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent)

	CCopasiParameter (const std::string &name, const Type &type, const void pValue=NULL, const CDataContainer pParent=NO_PARENT, const std::string &objectType="Parameter")

virtual CCommonName	getCN () const override

template<class CType >
const CType &	getDefault () const

virtual const std::string &	getKey () const override

virtual std::string	getObjectDisplayName () const override

const CCopasiParameter::Type &	getType () const

const UserInterfaceFlag &	getUserInterfaceFlag () const

template<class CType >
std::vector< std::pair< CType, CType > > &	getValidValues ()

template<class CType >
const std::vector< std::pair< CType, CType > > &	getValidValues () const

void *	getValidValuesPointer () const

template<class CType >
CType &	getValue ()

template<class CType >
const CType &	getValue () const

virtual void *	getValuePointer () const override

CDataObject *	getValueReference () const

bool	hasValidValues () const

bool	isBasic () const

bool	isDefault () const

bool	isEditable () const

bool	isUnsupported () const

bool	isValidValue (const bool &value) const

bool	isValidValue (const C_FLOAT64 &value) const

bool	isValidValue (const C_INT32 &value) const

bool	isValidValue (const CCommonName &value) const

template<class CType >
bool	isValidValue (const CType &) const

bool	isValidValue (const std::string &value) const

bool	isValidValue (const std::vector< CCopasiParameter * > &value) const

bool	isValidValue (const unsigned C_INT32 &value) const

CCopasiParameter &	operator= (const CCopasiParameter &rhs)

template<class CType >
bool	setDefault (const CType &defaultValue)

bool	setDefault (const std::vector< CCopasiParameter * > &defaultValue)

virtual bool	setObjectParent (const CDataContainer *pParent) override

template<class CType , class Enum >
bool	setValidValues (const CEnumAnnotation< CType, Enum > &validValues)

template<class CType >
bool	setValidValues (const std::vector< std::pair< CType, CType > > &validValues)

template<class CType >
bool	setValue (const CType &value)

bool	setValue (const std::vector< CCopasiParameter * > &value)

virtual	~CCopasiParameter ()

Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)

virtual bool	appendDeletedDependentData (CUndoData &undoData) const

	CDataContainer (const CDataContainer &src, const CDataContainer *pParent)

	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

virtual std::string	getChildObjectUnits (const CDataObject *pObject) const

void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

void	objectRenamed (CDataObject *pObject, const std::string &oldName)

virtual	~CDataContainer ()

Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)

void	addReference (const CDataContainer *pReference)

virtual void	calculateValue () override

	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)

virtual void	destruct () override

virtual const CDataObject *	getDataObject () const override

CDataContainer *	getObjectAncestor (const std::string &type) const

CDataModel *	getObjectDataModel () const

const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const

const std::string &	getObjectName () const

CDataContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override

virtual const CValidity &	getValidity () const override

bool	hasFlag (const Flag &flag) const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override

bool	prerequisitsContains (const DataObjectSet &objects) const

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

void	validityChanged (const CValidity &changedValidity) override

void	validityRemoved (const CValidity &changedValidity)

virtual	~CDataObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

	CObjectInterface (const CObjectInterface &src)

virtual	~CObjectInterface ()

Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()

	CUndoObjectInterface (const CUndoObjectInterface &src)

bool	generateUuid ()

const xg::Guid &	getUuid () const

bool	setUuid (const std::string &uuid)

bool	setUuid (const xg::Guid &uuid)

virtual	~CUndoObjectInterface ()

Private Member Functions
	CMCAMethod ()

bool	createLinkMatrix (const bool &useSmallbone=false)

void	initializeParameter ()

void	initObjects ()

Private Attributes
CMatrix< C_INT32 >	mElasticityDependencies

C_FLOAT64	mFactor

CLinkMatrix	mLinkZero

CSteadyStateTask *	mpSteadyStateTask

bool *	mpUseReder

bool *	mpUseSmallbone

CMatrix< C_FLOAT64 >	mReducedStoichiometry

CMatrix< C_FLOAT64 >	mScaledConcCC

CDataArray *	mScaledConcCCAnn

CMatrix< C_FLOAT64 >	mScaledElasticities

CDataArray *	mScaledElasticitiesAnn

CMatrix< C_FLOAT64 >	mScaledFluxCC

CDataArray *	mScaledFluxCCAnn

C_INT16	mSSReder

CSteadyStateMethod::ReturnCode	mSSStatus

std::vector< C_FLOAT64 >	mSsx

C_FLOAT64	mSteadyStateResolution

CMatrix< C_FLOAT64 >	mUnscaledConcCC

CDataArray *	mUnscaledConcCCAnn

CMatrix< C_FLOAT64 >	mUnscaledElasticities

CDataArray *	mUnscaledElasticitiesAnn

CMatrix< C_FLOAT64 >	mUnscaledFluxCC

CDataArray *	mUnscaledFluxCCAnn

Additional Inherited Members
Public Types inherited from CCopasiParameterGroup
typedef CDataObjectMap::const_type_iterator< CCopasiParameter >	const_name_iterator

typedef std::vector< CCopasiParameter * >	elements

typedef elements::iterator	index_iterator

typedef CDataObjectMap::type_iterator< CCopasiParameter >	name_iterator

Public Types inherited from CCopasiParameter
enum class	eUserInterfaceFlag { editable , basic , unsupported , __SIZE }

enum class	Type { DOUBLE = 0 , UDOUBLE , INT , UINT , BOOL , GROUP , STRING , CN , KEY , FILE , EXPRESSION , INVALID , __SIZE }

typedef CFlags< eUserInterfaceFlag >	UserInterfaceFlag

Public Types inherited from CDataContainer
typedef CDataObjectMap	objectMap

Public Types inherited from CDataObject
typedef std::set< const CDataObject * >	DataObjectSet

enum	Flag { Container , Vector , Matrix , NameVector , Reference , ValueBool , ValueInt , ValueInt64 , ValueDbl , NonUniqueName , StaticString , ValueString , Separator , DisplayName , ModelEntity , Array , DataModel , Root , Gui , __SIZE }

Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * >	ContainerList

typedef std::set< const CObjectInterface * >	ObjectSet

Static Public Member Functions inherited from CCopasiParameter
static void	allocateValidValues (const Type &type, void *&pValidValues)

static void	allocateValue (const Type &type, void *&pValue)

static void	assignValue (const Type &type, void &pValue, const void pNewValue)

static void	deleteValidValues (const Type &type, void *&pValidValues)

static void	deleteValue (const Type &type, void *&pValue)

static CCopasiParameter *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataContainer
static CDataContainer *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataObject
static CDataObject *	fromData (const CData &data, CUndoObjectInterface *pParent)

static void	sanitizeObjectName (std::string &name)

Static Public Member Functions inherited from CObjectInterface
static const CDataObject *	DataObject (const CObjectInterface *pInterface)

static CObjectInterface *	GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)

Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)

Static Public Attributes inherited from CCopasiParameter
static const CEnumAnnotation< std::string, Type >	TypeName

static const CEnumAnnotation< std::string, Type >	XMLType

Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Protected Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src)

	CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType)

virtual void	signalMathContainerChanged ()

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src)

Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > *	addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataObjectReference< CType > *	addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataVectorReference< CType > *	addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

	CDataContainer (const CDataContainer &src)

void	initObjects ()

Protected Member Functions inherited from CDataObject
	CDataObject ()

	CDataObject (const std::string &name, const CDataContainer pParent=static_cast< CDataContainer >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

Protected Attributes inherited from CCopasiMethod
CMathContainer *	mpContainer

CProcessReportLevel	mProcessReport

Protected Attributes inherited from CCopasiParameter
std::string	mKey

void *	mpDefault

void *	mpValidValues

void *	mpValue

CDataObject *	mpValueReference

UserInterfaceFlag	mUserInterfaceFlag

Protected Attributes inherited from CDataContainer
objectMap	mObjects

Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits

std::set< CDataContainer * >	mReferences

Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Constructor & Destructor Documentation

◆ CMCAMethod() [1/3]

CMCAMethod::CMCAMethod ( )

private

Default constructor.

◆ CMCAMethod() [2/3]

CMCAMethod::CMCAMethod	(	const CDataContainer *	pParent,
		const CTaskEnum::Method &	methodType = `CTaskEnum::Method::mcaMethodReder`,
		const CTaskEnum::Task &	taskType = `CTaskEnum::Task::mca`
	)

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Method & methodType (default: mcaMethodReder)
const	CTaskEnum::Task & taskType (default: mca)

Default constructor

References initializeParameter(), and initObjects().

◆ CMCAMethod() [3/3]

CMCAMethod::CMCAMethod	(	const CMCAMethod &	src,
		const CDataContainer *	pParent
	)

Copy constructor

Parameters

const	CMCAMethod & src
const	CDataContainer * pParent (Default: NULL)

References initializeParameter(), and initObjects().

◆ ~CMCAMethod()

CMCAMethod::~CMCAMethod ( )

virtual

Destructor

Deconstructor

References DESTRUCTOR_TRACE.

Member Function Documentation

◆ CalculateMCA()

bool CMCAMethod::CalculateMCA ( C_FLOAT64 res )

the steady state MCA entry point

Parameters

ss_solution	refer to steady-state solution
refer	to the resolution

References calculateUnscaledConcentrationCC(), calculateUnscaledElasticities(), calculateUnscaledFluxCC(), checkSummationTheorems(), createLinkMatrix(), CSteadyStateMethod::found, MCMCA, mpUseReder, mpUseSmallbone, mSSStatus, mUnscaledConcCC, mUnscaledFluxCC, scaleMCA(), and CCopasiMessage::WARNING.

Referenced by process().

◆ calculateUnscaledConcentrationCC()

bool CMCAMethod::calculateUnscaledConcentrationCC ( )

◆ calculateUnscaledElasticities()

void CMCAMethod::calculateUnscaledElasticities ( C_FLOAT64 res )

◆ calculateUnscaledFluxCC()

bool CMCAMethod::calculateUnscaledFluxCC ( const bool & status )

References CMatrix< CType >::array(), C_FLOAT64, C_INT, dlaset_(), dgemm::eval(), mUnscaledConcCC, mUnscaledElasticities, mUnscaledFluxCC, and CMatrix< CType >::numRows().

Referenced by CalculateMCA().

◆ checkSummationTheorems()

bool CMCAMethod::checkSummationTheorems ( const C_FLOAT64 & resolution )

Check whether the summation theorems hold.

References CMatrix< CType >::array(), CVectorCore< CType >::array(), C_FLOAT64, max, min, mScaledConcCC, mScaledFluxCC, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CVector< CType >::resize(), and CMatrix< CType >::size().

Referenced by CalculateMCA().

◆ createLinkMatrix()

bool CMCAMethod::createLinkMatrix ( const bool & useSmallbone = false )

private

References CLinkMatrix::build(), CLinkMatrix::doRowPivot(), CSteadyStateTask::getJacobian(), CModel::getL0(), CMathContainer::getModel(), CLinkMatrix::getNumIndependent(), CModel::getNumIndependentReactionMetabs(), CModel::getRedStoi(), CModel::getStoi(), mLinkZero, CCopasiMethod::mpContainer, mpSteadyStateTask, mReducedStoichiometry, CMatrix< CType >::numCols(), and CMatrix< CType >::resize().

Referenced by CalculateMCA().

◆ elevateChildren()

bool CMCAMethod::elevateChildren ( )

virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns: bool success

Reimplemented from CCopasiParameterGroup.

References initializeParameter().

◆ getModel()

const CModel * CMCAMethod::getModel ( ) const

Get the Model

References CMathContainer::getModel(), and CCopasiMethod::mpContainer.

◆ getScaledConcentrationCC()

const CMatrix<C_FLOAT64>& CMCAMethod::getScaledConcentrationCC ( ) const

inline

References mScaledConcCC.

◆ getScaledConcentrationCCAnn()

const CDataArray* CMCAMethod::getScaledConcentrationCCAnn ( ) const

inline

References mScaledConcCCAnn.

Referenced by CMCATask::printResult().

◆ getScaledElasticities()

const CMatrix<C_FLOAT64>& CMCAMethod::getScaledElasticities ( ) const

inline

References mScaledElasticities.

◆ getScaledElasticitiesAnn()

const CDataArray* CMCAMethod::getScaledElasticitiesAnn ( ) const

inline

References mScaledElasticitiesAnn.

Referenced by CMCATask::printResult().

◆ getScaledFluxCC()

const CMatrix<C_FLOAT64>& CMCAMethod::getScaledFluxCC ( ) const

inline

References mScaledFluxCC.

◆ getScaledFluxCCAnn()

const CDataArray* CMCAMethod::getScaledFluxCCAnn ( ) const

inline

References mScaledFluxCCAnn.

Referenced by CMCATask::printResult().

◆ getSteadyStateStatus()

const CSteadyStateMethod::ReturnCode& CMCAMethod::getSteadyStateStatus ( ) const

inline

References mSSStatus.

Referenced by CMCATask::printResult().

◆ getUnscaledConcentrationCC()

const CMatrix<C_FLOAT64>& CMCAMethod::getUnscaledConcentrationCC ( ) const

inline

References mUnscaledConcCC.

◆ getUnscaledConcentrationCCAnn()

const CDataArray* CMCAMethod::getUnscaledConcentrationCCAnn ( ) const

inline

References mUnscaledConcCCAnn.

Referenced by CMCATask::printResult().

◆ getUnscaledElasticities()

const CMatrix<C_FLOAT64>& CMCAMethod::getUnscaledElasticities ( ) const

inline

References mUnscaledElasticities.

◆ getUnscaledElasticitiesAnn()

const CDataArray* CMCAMethod::getUnscaledElasticitiesAnn ( ) const

inline

References mUnscaledElasticitiesAnn.

Referenced by CMCATask::printResult().

◆ getUnscaledFluxCC()

const CMatrix<C_FLOAT64>& CMCAMethod::getUnscaledFluxCC ( ) const

inline

References mUnscaledFluxCC.

◆ getUnscaledFluxCCAnn()

const CDataArray* CMCAMethod::getUnscaledFluxCCAnn ( ) const

inline

References mUnscaledFluxCCAnn.

Referenced by CMCATask::printResult().

◆ initializeParameter()

void CMCAMethod::initializeParameter ( )

private

Initialize the method parameter

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), mpUseReder, mpUseSmallbone, CCopasiParameterGroup::removeParameter(), CCopasiParameterGroup::setValue(), and CCopasiParameter::UDOUBLE.

Referenced by CMCAMethod(), and elevateChildren().

◆ initObjects()

void CMCAMethod::initObjects ( )

private

References mScaledConcCC, mScaledConcCCAnn, mScaledElasticities, mScaledElasticitiesAnn, mScaledFluxCC, mScaledFluxCCAnn, mUnscaledConcCC, mUnscaledConcCCAnn, mUnscaledElasticities, mUnscaledElasticitiesAnn, mUnscaledFluxCC, mUnscaledFluxCCAnn, CDataArray::setDescription(), CDataArray::setDimensionDescription(), CDataArray::setMode(), and CDataArray::Vector.

Referenced by CMCAMethod().

◆ isValidProblem()

bool CMCAMethod::isValidProblem ( const CCopasiProblem * pProblem )

virtual

Check if the method is suitable for this problem

Returns: bool suitability of the method

Reimplemented from CCopasiMethod.

References CDataVector< CType >::begin(), CCore::Default, CDataVector< CType >::end(), CCopasiMessage::ERROR, CModel::getCompartments(), CMathContainer::getCountODEs(), CMathContainer::getMathObject(), CMathContainer::getModel(), CMathContainer::getStateObjects(), CMathContainer::getTransientDependencies(), CMathDependencyGraph::getUpdateSequence(), CCopasiMethod::isValidProblem(), CCopasiMethod::mpContainer, mpUseReder, mpUseSmallbone, and CMathUpdateSequence::size().

◆ load()

C_INT32 CMCAMethod::load ( CReadConfig & configBuffer )

Read SSMCAUnscaled from configuration file

References C_INT32, CReadConfig::getVariable(), CReadConfig::LOOP, and mSSReder.

◆ process()

bool CMCAMethod::process ( )

virtual

References CalculateMCA(), and mSteadyStateResolution.

Referenced by CMCATask::process().

◆ resizeAllMatrices()

void CMCAMethod::resizeAllMatrices ( )

virtual

Resizes all result matrices and updates the corresponding array annotations. This needs to be called before output initialization (in case the output references parts of the matrix) from the task initialization, but it also needs to be called before selecting elements of the matrices in the object selection dialog. The model needs to be set before calling this.

References CMathContainer::getCountDependentSpecies(), CMathContainer::getCountIndependentSpecies(), CModel::getMetabolitesX(), CMathContainer::getModel(), CMathContainer::getReactions(), CModel::getReactions(), mElasticityDependencies, CCopasiMethod::mpContainer, mScaledConcCC, mScaledConcCCAnn, mScaledElasticities, mScaledElasticitiesAnn, mScaledFluxCC, mScaledFluxCCAnn, mUnscaledConcCC, mUnscaledConcCCAnn, mUnscaledElasticities, mUnscaledElasticitiesAnn, mUnscaledFluxCC, mUnscaledFluxCCAnn, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CDataArray::resize(), CMatrix< CType >::resize(), CDataArray::setAnnotationString(), CDataArray::setCopasiVector(), and CVectorCore< CType >::size().