COPASI API
4.16.103
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#include <CModelMerging.h>
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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 |
Definition at line 30 of file CModelMerging.h.
Definition at line 28 of file CModelMerging.cpp.
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Definition at line 448 of file CModelMerging.cpp.
References CModel::createCompartment(), CModel::getCompartments(), CCompartment::getDimensionality(), CModelEntity::getInitialValue(), CModelEntity::getKey(), CCopasiObject::getObjectName(), CModelEntity::getStatus(), keyMap, mmModel, mpModel, nameMap, CCompartment::setDimensionality(), CModelEntity::setStatus(), and CCopasiVector< T >::size().
Referenced by simpleCall().
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Definition at line 478 of file CModelMerging.cpp.
References CModelEntity::ASSIGNMENT, copyExpression(), copyInitialExpression(), CModelEntity::FIXED, CKeyFactory::get(), CModel::getCompartments(), CModelEntity::getInitialExpression(), CModelEntity::getKey(), CCopasiRootContainer::getKeyFactory(), keyMap, mmModel, CModelEntity::ODE, and CCopasiVector< T >::size().
Referenced by simpleCall().
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Definition at line 75 of file CModelMerging.cpp.
References CCopasiVectorN< CType >::add(), C_INVALID_INDEX, copyDelayExpression(), copyEventAssignmentExpression(), copyTriggerExpression(), CModel::createEvent(), CEvent::getAssignments(), CEvent::getDelayAssignment(), CEvent::getDelayExpressionPtr(), CModel::getEvents(), CEventAssignment::getExpressionPtr(), CCopasiVectorN< CType >::getIndex(), CCopasiObject::getObjectName(), CEventAssignment::getTargetKey(), CEvent::getTriggerExpressionPtr(), keyMap, mmModel, mpModel, CEvent::setDelayAssignment(), CEventAssignment::setTargetKey(), and CCopasiVector< T >::size().
Referenced by simpleCall().
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Definition at line 530 of file CModelMerging.cpp.
References CModel::createMetabolite(), CMetab::getCompartment(), CMetab::getInitialConcentration(), CModelEntity::getKey(), CModel::getMetabolites(), CCopasiObject::getObjectName(), CModelEntity::getStatus(), keyMap, mmModel, mpModel, nameMap, CMetab::setStatus(), and CCopasiVector< T >::size().
Referenced by simpleCall().
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Definition at line 562 of file CModelMerging.cpp.
References CModelEntity::ASSIGNMENT, copyExpression(), copyInitialExpression(), CModelEntity::FIXED, CKeyFactory::get(), CModelEntity::getInitialExpression(), CModelEntity::getKey(), CCopasiRootContainer::getKeyFactory(), CModel::getMetabolites(), keyMap, mmModel, CModelEntity::ODE, CModelEntity::REACTIONS, and CCopasiVector< T >::size().
Referenced by simpleCall().
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Definition at line 616 of file CModelMerging.cpp.
References CModel::createModelValue(), CModelEntity::getInitialValue(), CModelEntity::getKey(), CModel::getModelValues(), CCopasiObject::getObjectName(), CModelEntity::getStatus(), keyMap, mmModel, mpModel, nameMap, CModelEntity::setStatus(), and CCopasiVector< T >::size().
Referenced by simpleCall().
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Definition at line 645 of file CModelMerging.cpp.
References CModelEntity::ASSIGNMENT, copyExpression(), copyInitialExpression(), CModelEntity::FIXED, CKeyFactory::get(), CModelEntity::getInitialExpression(), CModelEntity::getKey(), CCopasiRootContainer::getKeyFactory(), CModel::getModelValues(), keyMap, mmModel, CModelEntity::ODE, and CCopasiVector< T >::size().
Referenced by simpleCall().
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Definition at line 696 of file CModelMerging.cpp.
References CReaction::addModifier(), CReaction::addParameterMapping(), CReaction::addProduct(), CReaction::addSubstrate(), CReaction::clearParameterMapping(), CModel::createReaction(), CReaction::getChemEq(), CModel::getCompartments(), CReaction::getFunction(), CReaction::getFunctionParameters(), CModelEntity::getKey(), CChemEqElement::getMetaboliteKey(), CChemEq::getModifiers(), CChemEqElement::getMultiplicity(), CCopasiObject::getObjectName(), CReaction::getParameterMappings(), 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::setParameterMapping(), CReaction::setParameterValue(), CReaction::setReversible(), CFunctionParameters::size(), CCopasiVector< T >::size(), CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, CFunctionParameter::VFLOAT64, and CFunctionParameter::VOLUME.
Referenced by simpleCall().
Definition at line 224 of file CModelMerging.cpp.
References CKeyFactory::get(), CCopasiObject::getCN(), CEvent::getDelayExpressionPtr(), CEvaluationTree::getInfix(), CCopasiRootContainer::getKeyFactory(), CEvaluationTree::getNodeList(), CCopasiContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectName(), CCopasiObject::getObjectParent(), CCopasiObject::isReference(), keyMap, mmModel, CEvaluationNode::OBJECT, CEvaluationNodeObject::setData(), CEvent::setDelayExpression(), CEvaluationNode::type(), and CEvaluationTree::updateTree().
Referenced by addEvents().
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Definition at line 168 of file CModelMerging.cpp.
References CKeyFactory::get(), CCopasiObject::getCN(), CEventAssignment::getExpressionPtr(), CEvaluationTree::getInfix(), CCopasiRootContainer::getKeyFactory(), CEvaluationTree::getNodeList(), CCopasiContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectName(), CCopasiObject::getObjectParent(), CCopasiObject::isReference(), keyMap, mmModel, CEvaluationNode::OBJECT, CEvaluationNodeObject::setData(), CEventAssignment::setExpression(), CEvaluationNode::type(), and CEvaluationTree::updateTree().
Referenced by addEvents().
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Definition at line 336 of file CModelMerging.cpp.
References CKeyFactory::get(), CCopasiObject::getCN(), CModelEntity::getExpressionPtr(), CEvaluationTree::getInfix(), CCopasiRootContainer::getKeyFactory(), CEvaluationTree::getNodeList(), CCopasiContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectName(), CCopasiObject::getObjectParent(), CCopasiObject::isReference(), keyMap, mmModel, CEvaluationNode::OBJECT, CEvaluationNodeObject::setData(), CModelEntity::setExpression(), CEvaluationNode::type(), and CEvaluationTree::updateTree().
Referenced by addCompartmentsExpressions(), addMetabolitesExpressions(), and addModelValuesExpressions().
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Definition at line 392 of file CModelMerging.cpp.
References CKeyFactory::get(), CCopasiObject::getCN(), CEvaluationTree::getInfix(), CModelEntity::getInitialExpressionPtr(), CCopasiRootContainer::getKeyFactory(), CEvaluationTree::getNodeList(), CCopasiContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectName(), CCopasiObject::getObjectParent(), CCopasiObject::isReference(), keyMap, mmModel, CEvaluationNode::OBJECT, CEvaluationNodeObject::setData(), CModelEntity::setInitialExpression(), CEvaluationNode::type(), and CEvaluationTree::updateTree().
Referenced by addCompartmentsExpressions(), addMetabolitesExpressions(), and addModelValuesExpressions().
Definition at line 280 of file CModelMerging.cpp.
References CKeyFactory::get(), CCopasiObject::getCN(), CEvaluationTree::getInfix(), CCopasiRootContainer::getKeyFactory(), CEvaluationTree::getNodeList(), CCopasiContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectName(), CCopasiObject::getObjectParent(), CEvent::getTriggerExpressionPtr(), CCopasiObject::isReference(), keyMap, mmModel, CEvaluationNode::OBJECT, CEvaluationNodeObject::setData(), CEvent::setTriggerExpression(), CEvaluationNode::type(), and CEvaluationTree::updateTree().
Referenced by addEvents().
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determine whether the one of the substrate, products, or modifiers of the reaction is located in the given compartment
Definition at line 898 of file CModelMerging.cpp.
References CReaction::getChemEq(), CChemEq::getModifiers(), CChemEq::getProducts(), CChemEq::getSubstrates(), and CCopasiVector< T >::size().
Referenced by addReactions().
void CModelAdd::simpleCall | ( | ) |
just a simple method to call during development
Definition at line 39 of file CModelMerging.cpp.
References addCompartments(), addCompartmentsExpressions(), addEvents(), addMetabolites(), addMetabolitesExpressions(), addModelValues(), addModelValuesExpressions(), addReactions(), CModel::compileIfNecessary(), CCopasiMessage::ERROR, fatalError, CModel::getKey(), keyMap, MCModelMerging, mmModel, and mpModel.
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Definition at line 42 of file CModelMerging.h.
Referenced by addCompartments(), addCompartmentsExpressions(), addEvents(), addMetabolites(), addMetabolitesExpressions(), addModelValues(), addModelValuesExpressions(), addReactions(), copyDelayExpression(), copyEventAssignmentExpression(), copyExpression(), copyInitialExpression(), copyTriggerExpression(), and simpleCall().
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Definition at line 69 of file CModelMerging.h.
Referenced by addCompartments(), addCompartmentsExpressions(), addEvents(), addMetabolites(), addMetabolitesExpressions(), addModelValues(), addModelValuesExpressions(), addReactions(), copyDelayExpression(), copyEventAssignmentExpression(), copyExpression(), copyInitialExpression(), copyTriggerExpression(), setModel(), and simpleCall().
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Definition at line 68 of file CModelMerging.h.
Referenced by addCompartments(), addEvents(), addMetabolites(), addModelValues(), addReactions(), setModel(), and simpleCall().
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Definition at line 43 of file CModelMerging.h.
Referenced by addCompartments(), addMetabolites(), and addModelValues().