CModelAdd Class Reference

#include <CModelMerging.h>

Public Member Functions
	CModelAdd (CModel *pModel, CModel *mModel)
void	setModel (CModel *pModel, CModel *mModel)
void	simpleCall ()
	just a simple method to call during development More...

Protected Member Functions
bool	addCompartments (std::string name)
bool	addCompartmentsExpressions ()
bool	addEvents (std::string name)
bool	addMetabolites (std::string name)
bool	addMetabolitesExpressions ()
bool	addModelValues (std::string name)
bool	addModelValuesExpressions ()
bool	addReactions (std::string name)
bool	copyDelayExpression (const CEvent *sourceEvent, CEvent *newEvent)
bool	copyEventAssignmentExpression (const CEventAssignment *sourceAssignment, CEventAssignment *newAssignment)
bool	copyExpression (const CModelEntity *sourceEntity, CModelEntity *newEntity)
bool	copyInitialExpression (const CModelEntity *sourceEntity, CModelEntity *newEntity)
bool	copyTriggerExpression (const CEvent *sourceEvent, CEvent *newEvent)

Static Protected Member Functions
static bool	reactionInvolvesCompartment (const CReaction *reac, const CCompartment *comp)

Protected Attributes
std::map< std::string, std::string >	keyMap
CModel *	mmModel
CModel *	mpModel
std::map< std::string, std::string >	nameMap

Constructor & Destructor Documentation

CModelAdd()

CModelAdd::CModelAdd	(	CModel *	pModel,
		CModel *	mModel
	)

Member Function Documentation

addCompartments()

bool CModelAdd::addCompartments ( std::string  name )

protected

References CModel::createCompartment(), CModel::getCompartments(), CCompartment::getDimensionality(), CModelEntity::getInitialValue(), CModelEntity::getKey(), CDataObject::getObjectName(), CModelEntity::getStatus(), keyMap, mmModel, mpModel, nameMap, CCompartment::setDimensionality(), CModelEntity::setStatus(), and CDataVector< CType >::size().

Referenced by simpleCall().

addCompartmentsExpressions()

bool CModelAdd::addCompartmentsExpressions ( )

protected

References CModelEntity::ASSIGNMENT, copyExpression(), copyInitialExpression(), CModelEntity::FIXED, CKeyFactory::get(), CModel::getCompartments(), CModelEntity::getInitialExpression(), CModelEntity::getKey(), CRootContainer::getKeyFactory(), keyMap, mmModel, CModelEntity::ODE, and CDataVector< CType >::size().

Referenced by simpleCall().

addEvents()

bool CModelAdd::addEvents ( std::string  name )

protected

References CDataVectorN< CType >::add(), C_INVALID_INDEX, copyDelayExpression(), copyEventAssignmentExpression(), copyTriggerExpression(), CModel::createEvent(), CEvent::getAssignments(), CEvent::getDelayAssignment(), CEvent::getDelayExpressionPtr(), CModel::getEvents(), CEventAssignment::getExpressionPtr(), CDataVectorN< CType >::getIndex(), CDataObject::getObjectName(), CEvent::getTriggerExpressionPtr(), keyMap, mmModel, mpModel, CEvent::setDelayAssignment(), and CDataVector< CType >::size().

Referenced by simpleCall().

addMetabolites()

bool CModelAdd::addMetabolites ( std::string  name )

protected

References CModel::createMetabolite(), CMetab::getCompartment(), CMetab::getInitialConcentration(), CModelEntity::getKey(), CModel::getMetabolites(), CDataObject::getObjectName(), CModelEntity::getStatus(), keyMap, mmModel, mpModel, nameMap, CModelEntity::setStatus(), and CDataVector< CType >::size().

Referenced by simpleCall().

addMetabolitesExpressions()

bool CModelAdd::addMetabolitesExpressions ( )

protected

References CModelEntity::ASSIGNMENT, copyExpression(), copyInitialExpression(), CModelEntity::FIXED, CKeyFactory::get(), CModelEntity::getInitialExpression(), CModelEntity::getKey(), CRootContainer::getKeyFactory(), CModel::getMetabolites(), keyMap, mmModel, CModelEntity::ODE, CModelEntity::REACTIONS, and CDataVector< CType >::size().

Referenced by simpleCall().

addModelValues()

bool CModelAdd::addModelValues ( std::string  name )

protected

References CModel::createModelValue(), CModelEntity::getInitialValue(), CModelEntity::getKey(), CModel::getModelValues(), CDataObject::getObjectName(), CModelEntity::getStatus(), keyMap, mmModel, mpModel, nameMap, CModelEntity::setStatus(), and CDataVector< CType >::size().

Referenced by simpleCall().

addModelValuesExpressions()

bool CModelAdd::addModelValuesExpressions ( )

protected

References CModelEntity::ASSIGNMENT, copyExpression(), copyInitialExpression(), CModelEntity::FIXED, CKeyFactory::get(), CModelEntity::getInitialExpression(), CModelEntity::getKey(), CRootContainer::getKeyFactory(), CModel::getModelValues(), keyMap, mmModel, CModelEntity::ODE, and CDataVector< CType >::size().

Referenced by simpleCall().

addReactions()

bool CModelAdd::addReactions ( std::string  name )

protected

References CReaction::addModifier(), CReaction::addProduct(), CReaction::addSubstrate(), CModel::createReaction(), CReaction::getChemEq(), CModel::getCompartments(), CReaction::getFunction(), CReaction::getFunctionParameters(), CModelEntity::getKey(), CChemEqElement::getMetaboliteKey(), CChemEq::getModifiers(), CChemEqElement::getMultiplicity(), CDataObject::getObjectName(), CReaction::getParameterValue(), CChemEq::getProducts(), CModel::getReactions(), CChemEq::getSubstrates(), CReaction::isLocalParameter(), CReaction::isReversible(), keyMap, mmModel, CFunctionParameter::MODIFIER, mpModel, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, reactionInvolvesCompartment(), CReaction::setFunction(), CReaction::setParameterValue(), CReaction::setReversible(), CDataVector< CType >::size(), CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, CFunctionParameter::VFLOAT64, and CFunctionParameter::VOLUME.

Referenced by simpleCall().

copyDelayExpression()

bool CModelAdd::copyDelayExpression ( const CEvent *  sourceEvent, CEvent *  newEvent  )

protected

References CKeyFactory::get(), CDataObject::getCN(), CEvent::getDelayExpressionPtr(), CEvaluationTree::getInfix(), CRootContainer::getKeyFactory(), CEvaluationTree::getNodeList(), CDataContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CDataObject::hasFlag(), keyMap, mmModel, CEvaluationNode::OBJECT, CDataObject::Reference, CEvaluationNodeObject::setData(), CEvent::setDelayExpression(), and CEvaluationTree::updateTree().

Referenced by addEvents().

copyEventAssignmentExpression()

bool CModelAdd::copyEventAssignmentExpression ( const CEventAssignment *  sourceAssignment, CEventAssignment *  newAssignment  )

protected

References CKeyFactory::get(), CDataObject::getCN(), CEventAssignment::getExpressionPtr(), CEvaluationTree::getInfix(), CRootContainer::getKeyFactory(), CEvaluationTree::getNodeList(), CDataContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CDataObject::hasFlag(), keyMap, mmModel, CEvaluationNode::OBJECT, CDataObject::Reference, CEvaluationNodeObject::setData(), CEventAssignment::setExpression(), and CEvaluationTree::updateTree().

Referenced by addEvents().

copyExpression()

bool CModelAdd::copyExpression ( const CModelEntity *  sourceEntity, CModelEntity *  newEntity  )

protected

References CKeyFactory::get(), CDataObject::getCN(), CModelEntity::getExpressionPtr(), CEvaluationTree::getInfix(), CRootContainer::getKeyFactory(), CEvaluationTree::getNodeList(), CDataContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CDataObject::hasFlag(), keyMap, mmModel, CEvaluationNode::OBJECT, CDataObject::Reference, CEvaluationNodeObject::setData(), CModelEntity::setExpression(), and CEvaluationTree::updateTree().

Referenced by addCompartmentsExpressions(), addMetabolitesExpressions(), and addModelValuesExpressions().

copyInitialExpression()

bool CModelAdd::copyInitialExpression ( const CModelEntity *  sourceEntity, CModelEntity *  newEntity  )

protected

References CKeyFactory::get(), CDataObject::getCN(), CEvaluationTree::getInfix(), CModelEntity::getInitialExpressionPtr(), CRootContainer::getKeyFactory(), CEvaluationTree::getNodeList(), CDataContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CDataObject::hasFlag(), keyMap, mmModel, CEvaluationNode::OBJECT, CDataObject::Reference, CEvaluationNodeObject::setData(), CModelEntity::setInitialExpression(), and CEvaluationTree::updateTree().

Referenced by addCompartmentsExpressions(), addMetabolitesExpressions(), and addModelValuesExpressions().

copyTriggerExpression()

bool CModelAdd::copyTriggerExpression ( const CEvent *  sourceEvent, CEvent *  newEvent  )

protected

References CKeyFactory::get(), CDataObject::getCN(), CEvaluationTree::getInfix(), CRootContainer::getKeyFactory(), CEvaluationTree::getNodeList(), CDataContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CEvent::getTriggerExpressionPtr(), CDataObject::hasFlag(), keyMap, mmModel, CEvaluationNode::OBJECT, CDataObject::Reference, CEvaluationNodeObject::setData(), CEvent::setTriggerExpression(), and CEvaluationTree::updateTree().

Referenced by addEvents().

reactionInvolvesCompartment()

bool CModelAdd::reactionInvolvesCompartment ( const CReaction *  reac, const CCompartment *  comp  )

staticprotected

determine whether the one of the substrate, products, or modifiers of the reaction is located in the given compartment

References CReaction::getChemEq(), CChemEq::getModifiers(), CChemEq::getProducts(), CChemEq::getSubstrates(), and CDataVector< CType >::size().

Referenced by addReactions().

setModel()

void CModelAdd::setModel	(	CModel *	pModel,
		CModel *	mModel
	)

References mmModel, and mpModel.

simpleCall()

void CModelAdd::simpleCall

(

)

just a simple method to call during development

References addCompartments(), addCompartmentsExpressions(), addEvents(), addMetabolites(), addMetabolitesExpressions(), addModelValues(), addModelValuesExpressions(), addReactions(), CModel::compileIfNecessary(), CCopasiMessage::ERROR, fatalError, CModel::getKey(), keyMap, MCModelMerging, mmModel, and mpModel.

Member Data Documentation

keyMap

std::map<std::string, std::string> CModelAdd::keyMap

protected

Referenced by addCompartments(), addCompartmentsExpressions(), addEvents(), addMetabolites(), addMetabolitesExpressions(), addModelValues(), addModelValuesExpressions(), addReactions(), copyDelayExpression(), copyEventAssignmentExpression(), copyExpression(), copyInitialExpression(), copyTriggerExpression(), and simpleCall().

mmModel

CModel* CModelAdd::mmModel

protected

Referenced by addCompartments(), addCompartmentsExpressions(), addEvents(), addMetabolites(), addMetabolitesExpressions(), addModelValues(), addModelValuesExpressions(), addReactions(), copyDelayExpression(), copyEventAssignmentExpression(), copyExpression(), copyInitialExpression(), copyTriggerExpression(), setModel(), and simpleCall().

mpModel

CModel* CModelAdd::mpModel

protected

Referenced by addCompartments(), addEvents(), addMetabolites(), addModelValues(), addReactions(), setModel(), and simpleCall().

nameMap

std::map<std::string, std::string> CModelAdd::nameMap

protected

Referenced by addCompartments(), addMetabolites(), and addModelValues().

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

• CModelMerging.h
• CModelMerging.cpp