CModelEntity Class Reference

#include <CModelValue.h>

Inheritance diagram for CModelEntity:

Collaboration diagram for CModelEntity:

Public Types
enum	Status {   FIXED = 0, ASSIGNMENT, REACTIONS, ODE,   TIME }
Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap
Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet
typedef std::vector< Refresh * >	DataUpdateSequence
Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet
typedef std::vector < CObjectInterface * >	UpdateSequence
Public Types inherited from CAnnotation
typedef std::map< std::string, std::string >	UnsupportedAnnotation

Public Member Functions
virtual void	calculate ()
	CModelEntity (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="ModelEntity", const unsigned C_INT32 &flag=CCopasiObject::Container|CCopasiObject::ValueDbl)
	CModelEntity (const CModelEntity &src, const CCopasiContainer *pParent=NULL)
virtual bool	compile ()
virtual std::set< const CCopasiObject * >	getDeletedObjects () const
std::string	getExpression () const
const CExpression *	getExpressionPtr () const
CExpression *	getExpressionPtr ()
std::string	getInitialExpression () const
const CExpression *	getInitialExpressionPtr () const
CExpression *	getInitialExpressionPtr ()
const C_FLOAT64 &	getInitialValue () const
CCopasiObject *	getInitialValueReference () const
virtual const std::string &	getKey () const
const C_FLOAT64 &	getRate () const
CCopasiObject *	getRateReference () const
const std::string &	getSBMLId () const
const CModelEntity::Status &	getStatus () const
const C_FLOAT64 &	getValue () const
virtual const CCopasiObject *	getValueObject () const
virtual void *	getValuePointer () const
CCopasiObject *	getValueReference () const
bool	isFixed () const
const bool &	isUsed () const
virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const
virtual void	refreshInitialValue ()
bool	setExpression (const std::string &expression)
bool	setExpressionPtr (CExpression *pExpression)
bool	setInitialExpression (const std::string &expression)
bool	setInitialExpressionPtr (CExpression *pExpression)
virtual void	setInitialValue (const C_FLOAT64 &initialValue)
void	setInitialValuePtr (C_FLOAT64 *pInitialValue)
virtual bool	setObjectParent (const CCopasiContainer *pParent)
void	setRate (const C_FLOAT64 &rate)
void	setSBMLId (const std::string &id)
virtual void	setStatus (const CModelEntity::Status &status)
void	setUsed (const bool &used)
virtual void	setValue (const C_FLOAT64 &value)
void	setValuePtr (C_FLOAT64 *pValue)
	~CModelEntity ()
Public Member Functions inherited from CCopasiContainer
virtual bool	add (CCopasiObject *pObject, const bool &adopt=true)
	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)
	CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)
virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const
virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const
virtual const objectMap &	getObjects () const
virtual std::string	getUnits () const
virtual bool	remove (CCopasiObject *pObject)
virtual	~CCopasiContainer ()
Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)
	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)
void	clearDirectDependencies ()
void	clearRefresh ()
bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const
void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const
virtual CCopasiObjectName	getCN () const
virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
CCopasiContainer *	getObjectAncestor (const std::string &type) const
CCopasiDataModel *	getObjectDataModel ()
const CCopasiDataModel *	getObjectDataModel () const
virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const
const std::string &	getObjectName () const
CCopasiContainer *	getObjectParent () const
const std::string &	getObjectType () const
virtual const CObjectInterface::ObjectSet &	getPrerequisites () const
virtual Refresh *	getRefresh () const
UpdateMethod *	getUpdateMethod () const
bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const
bool	hasUpdateMethod () const
bool	isArray () const
bool	isContainer () const
bool	isDataModel () const
bool	isMatrix () const
bool	isNameVector () const
bool	isNonUniqueName () const
virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const
bool	isReference () const
bool	isRoot () const
bool	isSeparator () const
bool	isStaticString () const
bool	isValueBool () const
bool	isValueDbl () const
bool	isValueInt () const
bool	isValueInt64 () const
bool	isValueString () const
bool	isVector () const
virtual void	print (std::ostream *ostream) const
void	removeDirectDependency (const CCopasiObject *pObject)
void	setDirectDependencies (const DataObjectSet &directDependencies)
bool	setObjectName (const std::string &name)
void	setObjectValue (const C_FLOAT64 &value)
void	setObjectValue (const C_INT32 &value)
void	setObjectValue (const bool &value)
template<class CType >
void	setRefresh (CType *pType, void(CType::*method)(void))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const bool &))
virtual	~CCopasiObject ()
Public Member Functions inherited from CObjectInterface
	CObjectInterface ()
virtual	~CObjectInterface ()
Public Member Functions inherited from CAnnotation
bool	addUnsupportedAnnotation (const std::string &name, const std::string &xml)
	CAnnotation ()
	CAnnotation (const CAnnotation &src)
const std::string &	getMiriamAnnotation () const
const std::string &	getNotes () const
UnsupportedAnnotation &	getUnsupportedAnnotations ()
const UnsupportedAnnotation &	getUnsupportedAnnotations () const
bool	operator== (const CAnnotation &rhs) const
bool	removeUnsupportedAnnotation (const std::string &name)
bool	replaceUnsupportedAnnotation (const std::string &name, const std::string &xml)
void	setMiriamAnnotation (const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)
void	setNotes (const std::string &notes)
virtual	~CAnnotation ()

Static Public Attributes
static const std::string	StatusName []
static const char *	XMLStatus []
Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Attributes
CExpression *	mpExpression
CExpression *	mpInitialExpression
C_FLOAT64 *	mpIValue
CCopasiObjectReference < C_FLOAT64 > *	mpIValueReference
CModel *	mpModel
CCopasiObjectReference < C_FLOAT64 > *	mpRateReference
C_FLOAT64 *	mpValue
CCopasiObjectReference < C_FLOAT64 > *	mpValueReference
C_FLOAT64	mRate
std::string	mSBMLId
Protected Attributes inherited from CCopasiContainer
objectMap	mObjects
Protected Attributes inherited from CAnnotation
std::string	mKey

Private Member Functions
void	initObjects ()

Private Attributes
Status	mStatus
bool	mUsed

Additional Inherited Members
Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())
static void	setRenameHandler (CRenameHandler *rh)
Static Public Member Functions inherited from CAnnotation
static CAnnotation *	castObject (CCopasiObject *pObject)
static const CAnnotation *	castObject (const CCopasiObject *pObject)
Protected Types inherited from CCopasiObject
enum	Flag {   Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8,   Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80,   ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800,   Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000,   Root = 0x10000, Gui = 0x20000 }
Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
void	initObjects ()
Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()
	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

The base class for CCompartment, CMetab and CModelValue. CModelEntity is a base class for CCompartment, CMetab and CModelValue. These three classes have in common that (in the long run) they can each be model variables (subject to ODEs), constant, or subject to algebraic assignments. In addition, the CMetab objects can also be subject to reactions, and conservation rules.

Definition at line 39 of file CModelValue.h.

Member Enumeration Documentation

enum CModelEntity::Status

The valid states for metabolites

Enumerator
FIXED
ASSIGNMENT
REACTIONS
ODE
TIME

Definition at line 53 of file CModelValue.h.

  {
    FIXED = 0, //the entity is constant (for species even if they are part of a reaction)
    ASSIGNMENT, //the entity is changed by an assignment rule
    REACTIONS, //applies only for species, the species concentration is changed by reactions
    //      DEPENDENT, //applies only for species, the species concentration is determined by conservation rules
    //      UNUSED,
    ODE, //the entity is changed by an ordinary differential equation
    TIME
  };

Constructor & Destructor Documentation

CModelEntity::CModelEntity	(	const std::string &	name = "NoName",
		const CCopasiContainer *	pParent = NULL,
		const std::string &	type = "ModelEntity",
		const unsigned C_INT32 &	flag = CCopasiObject::Container | CCopasiObject::ValueDbl
	)

Default constructor

Parameters

const	std::string & name (default: "NoName")
const	CCopasiContainer * pParent (default: NULL)

Definition at line 62 of file CModelValue.cpp.

References CKeyFactory::add(), CONSTRUCTOR_TRACE, CCopasiRootContainer::getKeyFactory(), CCopasiObject::getObjectType(), initObjects(), CAnnotation::mKey, mpIValue, and mpValue.

                                                         :
  CCopasiContainer(name, pParent, type, (flag | CCopasiObject::Container | CCopasiObject::ValueDbl | CCopasiObject::ModelEntity)),
  CAnnotation(),
  mpValue(NULL),
  mpIValue(NULL),
  mRate(0.0),
  mpExpression(NULL),
  mpInitialExpression(NULL),
  mStatus(FIXED),
  mUsed(false),
  mpModel(NULL)
{
  mKey = CCopasiRootContainer::getKeyFactory()->add(getObjectType(), this);

  initObjects();

  *mpIValue = 1.0;
  *mpValue = std::numeric_limits<C_FLOAT64>::quiet_NaN();

  CONSTRUCTOR_TRACE;
}

CModelEntity::CModelEntity	(	const CModelEntity &	src,
		const CCopasiContainer *	pParent = NULL
	)

Copy constructor

Parameters

const	CModelValue & src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 87 of file CModelValue.cpp.

References CKeyFactory::add(), CCopasiRootContainer::getKeyFactory(), CAnnotation::getMiriamAnnotation(), CCopasiObject::getObjectType(), initObjects(), CAnnotation::mKey, mpIValue, mpValue, mStatus, CAnnotation::setMiriamAnnotation(), and setStatus().

                                                            :
  CCopasiContainer(src, pParent),
  CAnnotation(src),
  mpValue(NULL),
  mpIValue(NULL),
  mRate(src.mRate),
  mpExpression(src.mpExpression ? new CExpression(*src.mpExpression, this) : NULL),
  mpInitialExpression(src.mpInitialExpression ? new CExpression(*src.mpInitialExpression, this) : NULL),
  mStatus(FIXED),
  mUsed(false),
  mpModel(NULL)
{
  mKey = CCopasiRootContainer::getKeyFactory()->add(getObjectType(), this);

  initObjects();

  setStatus(src.mStatus);

  *mpValue = *src.mpValue;
  *mpIValue = *src.mpIValue;

  setMiriamAnnotation(src.getMiriamAnnotation(), mKey, src.mKey);
}

CModelEntity::~CModelEntity

(

)

Destructor.

Definition at line 112 of file CModelValue.cpp.

References DESTRUCTOR_TRACE, CModel::getStateTemplate(), mpIValue, mpModel, mpValue, pdelete, and CStateTemplate::remove().

{
  if (mpModel)
    mpModel->getStateTemplate().remove(this);

  // After the above call we definitely own the data and
  // therefore must destroy them.

  pdelete(mpValue);
  pdelete(mpIValue);
  // since the expressions now have the model entity as parent, they should
  // automatically be destroyed be the destructor of CCopasiContainer
  //pdelete(mpExpression);
  //pdelete(mpInitialExpression);

  DESTRUCTOR_TRACE;
}

Member Function Documentation

void CModelEntity::calculate ( void  )

virtual

Calculate the value or the rate depending whether we have an ASIGNMENT or ODE

Reimplemented in CMetab.

Definition at line 197 of file CModelValue.cpp.

References ASSIGNMENT, CExpression::calcValue(), mpExpression, mpValue, mRate, mStatus, and ODE.

Referenced by setStatus().

{
  switch (mStatus)
    {
      case ASSIGNMENT:
        *mpValue = mpExpression->calcValue();
        break;

      case ODE:
        mRate = mpExpression->calcValue();
        break;

      default:
        break;
    }
}

bool CModelEntity::compile ( )

virtual

Compile the model value. This is only needed for status ASIGNMENT and ODE.

Returns

bool success

Reimplemented in CModel, and CMetab.

Definition at line 143 of file CModelValue.cpp.

References CCopasiContainer::add(), CCopasiObject::addDirectDependency(), ASSIGNMENT, CExpression::calcValue(), CExpression::compile(), CExpression::createInitialExpression(), CCopasiObject::getDirectDependencies(), CEvaluationTree::getInfix(), CCopasiObject::getObjectDataModel(), CEvaluationTree::isUsable(), mpExpression, mpInitialExpression, mpIValue, mpIValueReference, mpModel, mpRateReference, mpValueReference, mStatus, ODE, pdelete, CCopasiObject::setDirectDependencies(), and CCopasiObject::setObjectName().

Referenced by CModel::buildSimulatedSequence(), CModel::buildStateTemplate(), setExpression(), setExpressionPtr(), setInitialExpression(), and setInitialExpressionPtr().

{
  bool success = true;

  std::set< const CCopasiObject * > NoDependencies;
  std::vector< CCopasiContainer * > listOfContainer;
  listOfContainer.push_back(mpModel);
  CCopasiDataModel* pDataModel = NULL;

  switch (mStatus)
    {
      case ASSIGNMENT:
        success &= mpExpression->compile(listOfContainer);
        mpValueReference->setDirectDependencies(mpExpression->getDirectDependencies());

        pdelete(mpInitialExpression);
        pDataModel = getObjectDataModel();
        assert(pDataModel != NULL);
        mpInitialExpression = CExpression::createInitialExpression(*mpExpression, pDataModel);
        mpInitialExpression->setObjectName("InitialExpression");
        add(mpInitialExpression, true);
        break;

      case ODE:
        mpValueReference->addDirectDependency(this);

        success &= mpExpression->compile(listOfContainer);
        mpRateReference->setDirectDependencies(mpExpression->getDirectDependencies());
        break;

      default:
        break;
    }

  // Here we handle initial expressions for all types.
  if (mpInitialExpression != NULL &&
      mpInitialExpression->getInfix() != "")
    {
      success &= mpInitialExpression->compile(listOfContainer);
      mpIValueReference->setDirectDependencies(mpInitialExpression->getDirectDependencies());

      // If we have a valid initial expression, we update the initial value.
      // In case the expression is constant this suffices other are updated lated again.
      if (mpInitialExpression->isUsable())
        *mpIValue = mpInitialExpression->calcValue();
    }
  else
    {
      mpIValueReference->setDirectDependencies(NoDependencies);
    }

  return success;
}

std::set< const CCopasiObject * > CModelEntity::getDeletedObjects ( ) const

virtual

Retrieve the list of deleted numeric child objects;

Returns

std::set< const CCopasiObject * > deletedObjects

Reimplemented in CMetab, and CCompartment.

Definition at line 587 of file CModelValue.cpp.

References mpIValueReference, mpRateReference, and mpValueReference.

Referenced by CModel::appendDependentModelObjects(), CModel::determineIsAutonomous(), CCompartment::getDeletedObjects(), CMetab::getDeletedObjects(), mustBeDeleted(), CModel::removeModelValue(), CQGlobalQuantityDM::removeRows(), and CQModelValue::slotBtnDelete().

{
  std::set< const CCopasiObject * > Deleted;

  Deleted.insert(this);
  Deleted.insert(mpIValueReference);
  Deleted.insert(mpValueReference);
  Deleted.insert(mpRateReference);

  return Deleted;
}

std::string CModelEntity::getExpression

(

)

const

Retrieve the expression for non FIXED model values.

Returns

std::string expression

Definition at line 236 of file CModelValue.cpp.

References CEvaluationTree::getInfix(), isFixed(), mpExpression, and CExpression::updateInfix().

Referenced by CModel::convert2NonReversible(), CMathObject::createExtensiveODERateExpression(), CSBMLExporter::createRule(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CQSpeciesDetail::load(), CQCompartment::load(), CQModelValue::load(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), and CCopasiXML::saveModel().

{
  if (isFixed() || mpExpression == NULL)
    return "";

  mpExpression->updateInfix();
  return mpExpression->getInfix();
}

const CExpression * CModelEntity::getExpressionPtr

(

)

const

Retrieve the pointer to the expression for non FIXED model values.

Returns

CExpression*

Definition at line 250 of file CModelValue.cpp.

References mpExpression.

Referenced by CSBMLExporter::checkForPiecewiseFunctions(), CSBMLExporter::checkForUnsupportedFunctionCalls(), CSBMLExporter::checkForUnsupportedObjectReferences(), CMathObject::compileRate(), CMathObject::compileValue(), CModelAdd::copyExpression(), CSBMLExporter::createRule(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportModelValuesExpressions(), SBMLImporter::importRuleForModelEntity(), CModelMerging::mergeMetabolites(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInModelEntity(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000027::test_hasOnlySubstanceUnits(), test000034::test_hasOnlySubstanceUnits(), test000023::test_hasOnlySubstanceUnits(), test000025::test_hasOnlySubstanceUnits(), test000033::test_hasOnlySubstanceUnits(), test000087::test_import_reaction_flux_reference_2(), test000075::test_import_time_dependent_function_definition(), test000087::test_simulate_reaction_flux_reference_1(), and CMMLOutput::writeRHS_ModelEntity().

{
  return mpExpression;
}

CExpression * CModelEntity::getExpressionPtr

(

)

Retrieve the pointer to the expression for non FIXED model values.

Returns

CExpression*

Definition at line 245 of file CModelValue.cpp.

References mpExpression.

{
  return mpExpression;
}

std::string CModelEntity::getInitialExpression

(

)

const

Retrieve the expression for ODE or REACTION model values.

Returns

std::string expression

Definition at line 350 of file CModelValue.cpp.

References ASSIGNMENT, CEvaluationTree::getInfix(), mpInitialExpression, mStatus, and CExpression::updateInfix().

Referenced by CModelAdd::addCompartmentsExpressions(), CModelAdd::addMetabolitesExpressions(), CModelAdd::addModelValuesExpressions(), CModel::buildInitialRefreshSequence(), CModel::convert2NonReversible(), CSBMLExporter::createCompartment(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CQGlobalQuantityDM::data(), CQSpecieDM::data(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), SliderDialog::fillSliderBox(), CQSimpleSelectionTree::filter(), CParticleReference::getDirectDependencies(), CQSpeciesDetail::load(), CQCompartment::load(), CQModelValue::load(), CModelMerging::mergeMetabolites(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), CCopasiXML::saveModel(), test000041::test_hasOnlySubstanceUnits(), and test000040::test_hasOnlySubstanceUnits().

{
  if (mStatus == ASSIGNMENT || mpInitialExpression == NULL)
    return "";

  mpInitialExpression->updateInfix();
  return mpInitialExpression->getInfix();
}

const CExpression * CModelEntity::getInitialExpressionPtr

(

)

const

Retrieve the pointer to the expression for non FIXED model values.

Returns

CExpression*

Definition at line 294 of file CModelValue.cpp.

References mpInitialExpression.

Referenced by CSBMLExporter::checkForUnsupportedFunctionCalls(), CSBMLExporter::checkForUnsupportedObjectReferences(), CMathObject::compileInitialValue(), CModelAdd::copyInitialExpression(), CSBMLExporter::createInitialAssignment(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), SBMLImporter::importInitialAssignments(), CModelMerging::mergeMetabolites(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInModelEntity(), test000093::test_bug1503_1(), test000040::test_hasOnlySubstanceUnits(), test000041::test_hasOnlySubstanceUnits(), and test000075::test_import_time_dependent_function_definition().

{
  return mpInitialExpression;
}

CExpression * CModelEntity::getInitialExpressionPtr

(

)

Retrieve the pointer to the expression for non FIXED model values.

Returns

CExpression*

Definition at line 289 of file CModelValue.cpp.

References mpInitialExpression.

{
  return mpInitialExpression;
}

const C_FLOAT64 & CModelEntity::getInitialValue

(

)

const

Retrieve the initial value

Definition at line 138 of file CModelValue.cpp.

References mpIValue.

Referenced by CModelAdd::addCompartments(), CModelAdd::addModelValues(), CFunctionAnalyzer::constructCallParametersActualValues(), CMetab::convertToConcentration(), CMetab::convertToNumber(), CSBMLExporter::createCompartment(), CModelParameterSet::createFromModel(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CCSPMethod::cspstep(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CODEExporter::exportCompartments(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportModelValues(), CModel::initializeAtolVector(), CQSpeciesDetail::load(), CQCompartment::load(), CQModelValue::load(), CReactionInterface::loadMappingAndValues(), CQUpdatesWidget::loadObjectsTable(), CModelParameter::refreshFromModel(), CMetab::refreshInitialConcentration(), CMetab::refreshInitialValue(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), CQSpecieDM::setData(), CQSpeciesDetail::slotCompartmentChanged(), CModel::suitableForStochasticSimulation(), test000091::test_delay_in_kinetic_law_local_parameter(), test000026::test_hasOnlySubstanceUnits(), test000087::test_simulate_reaction_flux_reference_1(), and ParameterTable::updateTable().

{return *mpIValue;}

CCopasiObject * CModelEntity::getInitialValueReference

(

)

const

Retrieve object referencing the initial value

Returns

CCopasiObject * initialValueReference

Definition at line 367 of file CModelValue.cpp.

References mpIValueReference.

Referenced by DataModelGUI::buildChangedObjects(), CModel::buildInitialRefreshSequence(), CMetab::compileInitialValueDependencies(), CMathObject::createExtensiveValueExpression(), CModelParameterSet::createFromModel(), CSBMLExporter::createInitialAssignment(), CExpression::createInitialExpression(), CMathObject::createIntensiveValueExpression(), test000097::createModel(), SliderDialog::determineCorrectObjectForSlider(), findObjectByDisplayName(), CMetab::getChildObjectUnits(), getInitialCNForSBase(), CModelParameter::getUnit(), SBMLImporter::importInitialAssignments(), CMathContainer::initializeObjects(), CQSimpleSelectionTree::populateTree(), SBMLImporter::replace_time_with_initial_time(), test000058::test_bug1025_10(), test000058::test_bug1025_2(), test000058::test_bug1025_4(), test000058::test_bug1025_5(), test000058::test_bug1025_7(), test000058::test_bug1025_9(), test000059::test_unique_id_1(), test000059::test_unique_id_12(), test000059::test_unique_id_14(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_20(), test000059::test_unique_id_21(), test000059::test_unique_id_21_2(), test000059::test_unique_id_3(), test000059::test_unique_id_6(), and test000059::test_unique_id_8().

{return mpIValueReference;}

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

virtual

Retrieve the key

Returns

std::string key

Reimplemented from CAnnotation.

Reimplemented in CModel.

Definition at line 131 of file CModelValue.cpp.

References CAnnotation::getKey().

Referenced by CModelAdd::addCompartments(), CModelAdd::addCompartmentsExpressions(), CModelAdd::addMetabolites(), CModelAdd::addMetabolitesExpressions(), CModelAdd::addModelValues(), CModelAdd::addModelValuesExpressions(), CModelAdd::addReactions(), CFixLocalReactionParameters::changeModel(), CQCompartment::copy(), CLayoutInitializer::createCompartmentGlyph(), CMathObject::createExtensiveReactionRateExpression(), CCopasiSpringLayout::createLayout(), CLayoutInitializer::createMetabGlyph(), test000097::createModel(), CSBMLExporter::createSBMLDocument(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), CODEExporter::exportExpression(), CODEExporter::exportKineticFunction(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportODEs(), CODEExporterBM::exportSingleCompartment(), CODEExporterXPPAUT::exportSingleCompartment(), CODEExporterC::exportSingleCompartment(), CODEExporterBM::exportSingleMetabolite(), CODEExporterXPPAUT::exportSingleMetabolite(), CODEExporterC::exportSingleMetabolite(), CODEExporterBM::exportSingleModelEntity(), CODEExporterXPPAUT::exportSingleModelEntity(), CODEExporterC::exportSingleModelEntity(), CODEExporterBM::exportSingleModVal(), CODEExporterXPPAUT::exportSingleModVal(), CODEExporterC::exportSingleModVal(), CODEExporterBM::exportSingleODE(), CODEExporterXPPAUT::exportSingleODE(), CODEExporterC::exportSingleODE(), CQSelectionWizardPage::fillTree(), getMetabGlyphForKey(), CMetabNameInterface::getMetaboliteKey(), CEFMTask::getSpeciesChanges(), SBMLImporter::importMIRIAM(), CCopasiSpringLayout::initFromLayout(), CQGlobalQuantityDM::insertRows(), CQCompartmentDM::insertRows(), CQSpecieDM::insertRows(), CODEExporterC::KineticFunction2ODEmember(), CModelMerging::mergeMetabolites(), CODEExporterC::preprocess(), CODEExporter::preprocess(), CCopasiSpringLayout::randomize(), CModelExpansion::replaceInReaction(), CCopasiXML::saveModel(), CQNewMainWindow::selectMetabolite(), CQGlobalQuantityDM::setData(), CQCompartmentDM::setData(), CQSpecieDM::setData(), CChemEq::setMultiplicity(), CModelMerging::simpleCall(), CModelExpansion::simpleCall(), CQEventWidget1::slotAddTarget(), CQSpeciesDetail::slotBtnNew(), CQCompartment::slotBtnNew(), CQModelValue::slotBtnNew(), CQEventWidget1::slotSelectObject(), CCopasiXMLParser::SourceParameterElement::start(), CCopasiXMLParser::ModifierElement::start(), CCopasiXMLParser::ProductElement::start(), CCopasiXMLParser::SubstrateElement::start(), CCopasiXMLParser::AssignmentElement::start(), CCopasiXMLParser::CompartmentGlyphElement::start(), CCopasiXMLParser::MetaboliteGlyphElement::start(), CCopasiXMLParser::TextGlyphElement::start(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000087::test_simulate_reaction_flux_reference_1(), CSBMLExporter::updateMIRIAMAnnotation(), and CMMLOutput::writeRHS().

{
  return CAnnotation::getKey();
}

const C_FLOAT64 & CModelEntity::getRate

(

)

const

Return rate of production of this entity

Definition at line 362 of file CModelValue.cpp.

References mRate.

Referenced by CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CQCompartment::load(), CQModelValue::load(), operator<<(), CMetab::refreshConcentrationRate(), and CQSpeciesDetail::setFramework().

{
  return mRate;
}

CCopasiObject * CModelEntity::getRateReference

(

)

const

Retrieve object referencing the rate

Returns

CCopasiObject * rateReference

Definition at line 373 of file CModelValue.cpp.

References mpRateReference.

Referenced by CMetab::compile(), CMathObject::createIntensiveRateExpression(), findObjectByDisplayName(), CMathContainer::initializeObjects(), and CQSimpleSelectionTree::populateTree().

{return mpRateReference;}

const std::string & CModelEntity::getSBMLId

(

)

const

Returns a reference to the SBML Id.

Definition at line 637 of file CModelValue.cpp.

References mSBMLId.

Referenced by SBMLImporter::applyStoichiometricExpressions(), CSBMLExporter::collectIds(), CSBMLExporter::createCompartment(), SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createInitialAssignment(), CSBMLExporter::createKineticLaw(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CSBMLExporter::createReaction(), CSBMLExporter::createRule(), CSBMLExporter::createRules(), CSBMLExporter::createSBMLDocument(), CSBMLExporter::createTimesTree(), SBMLImporter::replaceObjectNames(), CCopasiXML::saveModel(), test000055::test_bug1004(), test000057::test_bug1006(), test000103::test_bug1743_l2(), test000103::test_bug1743_l3(), and CEvaluationNodeObject::toAST().

{
  return this->mSBMLId;
}

const CModelEntity::Status & CModelEntity::getStatus

(

)

const

Retrieve the status of the entity.

Returns

const CModelEntity::Status & status

Definition at line 141 of file CModelValue.cpp.

References mStatus.

Referenced by CModelAdd::addCompartments(), CModelAdd::addMetabolites(), CModelAdd::addModelValues(), CModel::buildInitialRefreshSequence(), CMetab::calculate(), CLNAMethod::calculateCovarianceMatrixReduced(), CSBMLExporter::checkForODESpeciesInNonfixedCompartment(), CSBMLExporter::checkForPiecewiseFunctions(), CEventAssignment::compile(), CMetab::compile(), CMetab::compileInitialValueDependencies(), CFunctionAnalyzer::constructCallParametersActualValues(), CModel::convert2NonReversible(), CSBMLExporter::createCompartment(), CCopasiSpringLayout::createLayout(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CSBMLExporter::createRule(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CODEExporter::exportCompartments(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportModelValues(), CODEExporter::exportModelValuesExpressions(), CODEExporter::exportODEs(), CODEExporterBM::exportSingleCompartment(), CODEExporterXPPAUT::exportSingleCompartment(), CODEExporterC::exportSingleCompartment(), CODEExporterBM::exportSingleMetabolite(), CODEExporterXPPAUT::exportSingleMetabolite(), CODEExporterC::exportSingleMetabolite(), CODEExporterBM::exportSingleModelEntity(), CODEExporterXPPAUT::exportSingleModelEntity(), CODEExporterC::exportSingleModelEntity(), CODEExporterBM::exportSingleModVal(), CODEExporterXPPAUT::exportSingleModVal(), CODEExporterC::exportSingleModVal(), CQSimpleSelectionTree::filter(), CParticleReference::getDirectDependencies(), SBMLImporter::importRuleForModelEntity(), CSteadyStateTask::initialize(), CMathContainer::initializeObjects(), CSBMLExporter::isEventAssignmentSBMLCompatible(), CODEExporter::isModelEntityExpressionODEExporterCompatible(), CParticleReference::isPrerequisiteForContext(), CQSpeciesDetail::load(), CQCompartment::load(), CQModelValue::load(), CQUpdatesWidget::loadObjectsTable(), CModelMerging::mergeMetabolites(), CMetab::mustBeDeleted(), operator<<(), CQSimpleSelectionTree::populateTree(), CODEExporterC::preprocess(), CODEExporter::preprocess(), CMetab::refreshRate(), CMetab::refreshTransitionTime(), SBMLImporter::removeUnusedFunctions(), CSBMLExporter::replaceSpeciesReferences(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), CCopasiXML::saveModel(), CQSpeciesDetail::setFramework(), CMetab::setObjectParent(), CMetab::setStatus(), CHybridMethodODE45::setupBalances(), CHybridMethod::setupBalances(), CHybridMethodLSODA::setupBalances(), CHybridMethodODE45::setupMetab2React(), CTauLeapMethod::start(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), CTrajectoryMethodDsaLsodar::start(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000040::test_hasOnlySubstanceUnits(), test000023::test_hasOnlySubstanceUnits(), test000033::test_hasOnlySubstanceUnits(), test000025::test_hasOnlySubstanceUnits(), test000041::test_hasOnlySubstanceUnits(), test000026::test_hasOnlySubstanceUnits(), test000034::test_hasOnlySubstanceUnits(), test000027::test_hasOnlySubstanceUnits(), test000087::test_import_reaction_flux_reference_2(), test000075::test_import_time_dependent_function_definition(), CSteadyStateTask::updateMatrices(), CModelParameter::updateModel(), and ParameterTable::updateTable().

{return mStatus;}

const C_FLOAT64 & CModelEntity::getValue

(

)

const

Retrieve the value

Definition at line 136 of file CModelValue.cpp.

References mpValue.

Referenced by CMetab::calculate(), CModel::calculateElasticityMatrix(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CHybridMethod::fireReaction(), CHybridMethodLSODA::fireReaction(), CHybridMethodODE45::fireReaction(), CTSSAMethod::initializeAtol(), CSteadyStateMethod::isEquilibrium(), CQCompartment::load(), CQModelValue::load(), operator<<(), CMetab::refreshConcentration(), CMetab::refreshConcentrationRate(), CMetab::refreshNumber(), CSBMLExporter::replaceSpeciesReferences(), CMCAMethod::scaleMCA(), CQSpeciesDetail::setFramework(), CNewtonMethod::solveJacobianXeqB(), and CNewtonMethod::targetFunction().

{return *mpValue;}

const CCopasiObject * CModelEntity::getValueObject ( ) const

virtual

Retrieve the object representing the value;

Reimplemented from CCopasiContainer.

Reimplemented in CMetab.

Definition at line 484 of file CModelValue.cpp.

References mpValueReference.

Referenced by CEventAssignment::compile().

{
  return mpValueReference;
}

void * CModelEntity::getValuePointer ( ) const

virtual

Retrieve a pointer to the value;

Reimplemented from CCopasiObject.

Reimplemented in CMetab.

Definition at line 490 of file CModelValue.cpp.

References C_FLOAT64, and mpValue.

Referenced by CReaction::setScalingFactor().

{
  return const_cast<C_FLOAT64 *>(mpValue);
}

CCopasiObject * CModelEntity::getValueReference

(

)

const

Retrieve object referencing the value

Returns

CCopasiObject * valueReference

Definition at line 370 of file CModelValue.cpp.

References mpValueReference.

Referenced by CMathModel::buildDependendRefreshList(), CMetab::compile(), CPlotSpecification::createDefaultPlot(), CMathObject::createExtensiveODERateExpression(), CMathObject::createExtensiveValueExpression(), CExpression::createInitialExpression(), CMathObject::createIntensiveRateExpression(), CMathObject::createIntensiveValueExpression(), CSBMLExporter::createRule(), CSBMLExporter::exportEventAssignments(), findObjectByDisplayName(), CModel::getCorrespondingTransientObject(), SBMLImporter::importEvent(), SBMLImporter::importRuleForModelEntity(), CMathContainer::initializeObjects(), CQSimpleSelectionTree::populateTree(), CReaction::setScalingFactor(), CMetab::setStatus(), CHybridMethodODE45::setupMetab2React(), CTauLeapMethod::start(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), and CTrajectoryMethodDsaLsodar::start().

{return mpValueReference;}

void CModelEntity::initObjects ( )

private

Initialize the contained CCopasiObjects

Definition at line 495 of file CModelValue.cpp.

References CStateTemplate::add(), CCopasiContainer::addObjectReference(), C_FLOAT64, CCopasiObject::getObjectAncestor(), CModel::getStateTemplate(), mpIValueReference, mpModel, mpRateReference, mpValueReference, mRate, mSBMLId, refreshInitialValue(), setInitialValue(), setInitialValuePtr(), CCopasiObject::setRefresh(), CCopasiObject::setUpdateMethod(), setValue(), setValuePtr(), CCopasiObject::ValueDbl, and CCopasiObject::ValueString.

Referenced by CModelEntity().

{
  C_FLOAT64 Dummy;

  mpValueReference =
    static_cast<CCopasiObjectReference<C_FLOAT64> *>(addObjectReference("Value",
        Dummy,
        CCopasiObject::ValueDbl));
  mpValueReference->setUpdateMethod(this, &CModelEntity::setValue);

  mpIValueReference =
    static_cast<CCopasiObjectReference<C_FLOAT64> *>(addObjectReference("InitialValue",
        Dummy,
        CCopasiObject::ValueDbl));
  mpIValueReference->setUpdateMethod(this, &CModelEntity::setInitialValue);
  mpIValueReference->setRefresh(this, &CModelEntity::refreshInitialValue);

  mpRateReference =
    static_cast<CCopasiObjectReference<C_FLOAT64> *>(addObjectReference("Rate", mRate, CCopasiObject::ValueDbl));

  addObjectReference("SBMLId", mSBMLId, CCopasiObject::ValueString);

  mpModel = static_cast<CModel *>(getObjectAncestor("Model"));

  if (mpModel)
    {
      mpModel->getStateTemplate().add(this);
    }
  else
    {
      // This creates the needed values.
      setInitialValuePtr(NULL);
      setValuePtr(NULL);
    }
}

bool CModelEntity::isFixed ( ) const

inline

Check whether the entity is FIXED or not.

Returns

bool isFixed

Definition at line 124 of file CModelValue.h.

References FIXED, and mStatus.

Referenced by getExpression(), CMetab::refreshInitialConcentration(), CMetab::setConcentration(), setExpression(), and setExpressionPtr().

{return mStatus == FIXED;}

const bool & CModelEntity::isUsed

(

)

const

Retrieve whether the model value is used during simulation

Returns

const bool & used

Definition at line 645 of file CModelValue.cpp.

References mUsed.

Referenced by CModel::buildUserOrder(), and CQUpdatesWidget::loadObjectsTable().

{return mUsed;}

bool CModelEntity::mustBeDeleted ( const DataObjectSet &  deletedObjects ) const

virtual

Check whether an object must be deleted because its prerequisites can no longer be fulfilled due to the given deleted objects

Parameters

const

DataObjectSet & deletedObjects

Returns

bool mustBeDeleted

Reimplemented from CCopasiObject.

Reimplemented in CMetab.

Definition at line 600 of file CModelValue.cpp.

References getDeletedObjects().

{
  bool MustBeDeleted = false;

  DataObjectSet ChildObjects = getDeletedObjects();

  DataObjectSet::const_iterator it = ChildObjects.begin();
  DataObjectSet::const_iterator end = ChildObjects.end();

  for (; it != end; ++it)
    {
      if (*it == this)
        {
          if ((*it)->CCopasiObject::mustBeDeleted(deletedObjects))
            {
              MustBeDeleted = true;
              break;
            }

          continue;
        }

      if ((*it)->mustBeDeleted(deletedObjects))
        {
          MustBeDeleted = true;
          break;
        }
    }

  return MustBeDeleted;
}

void CModelEntity::refreshInitialValue ( )

virtual

Refresh the initial value

Reimplemented in CMetab.

Definition at line 214 of file CModelValue.cpp.

References CExpression::calcValue(), CEvaluationTree::getInfix(), mpInitialExpression, and mpIValue.

Referenced by initObjects().

{
  if (mpInitialExpression != NULL &&
      mpInitialExpression->getInfix() != "")
    *mpIValue = mpInitialExpression->calcValue();
}

bool CModelEntity::setExpression

(

const std::string &

expression

)

Set the expression for non FIXED model values

Parameters

const

std::string & expression

Returns

bool success

Definition at line 221 of file CModelValue.cpp.

References compile(), isFixed(), mpExpression, mpModel, CModel::setCompileFlag(), and CExpression::setInfix().

Referenced by CModel::convert2NonReversible(), CModelAdd::copyExpression(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CQEventWidget1::loadFromEvent(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), test000058::test_bug1025_10(), test000058::test_bug1025_5(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_20(), test000059::test_unique_id_21(), and test000059::test_unique_id_21_2().

{
  if (isFixed()) return false;

  if (mpExpression == NULL)
    mpExpression = new CExpression("Expression", this);

  if (mpModel)
    mpModel->setCompileFlag(true);

  if (!mpExpression->setInfix(expression)) return false;

  return compile();
}

bool CModelEntity::setExpressionPtr

(

CExpression *

pExpression

)

Set the expression for non FIXED model values

Parameters

CExpression*

Returns

bool success

Definition at line 255 of file CModelValue.cpp.

References CCopasiContainer::add(), compile(), isFixed(), mpExpression, mpModel, pdelete, CModel::setCompileFlag(), CCopasiObject::setObjectName(), and CCopasiObject::setObjectParent().

Referenced by SBMLImporter::importRuleForModelEntity().

{
  if (isFixed()) return false;

  if (pExpression == mpExpression) return true;

  if (pExpression == NULL) return false;

  if (mpModel != NULL)
    {
      mpModel->setCompileFlag(true);
    }

  CExpression * pOld = mpExpression;
  mpExpression = pExpression;

  mpExpression->setObjectName("Expression");
  add(mpExpression, true);

  if (compile())
    {
      pdelete(pOld);
      return true;
    }

  // If compile fails we do not take ownership
  // and we remove the object from the container
  remove(mpExpression);
  mpExpression->setObjectParent(NULL);
  mpExpression = pOld;

  return false;
}

bool CModelEntity::setInitialExpression

(

const std::string &

expression

)

Set the expression for ODE or REACTION model values

Parameters

const

std::string & expression

Returns

bool success

Definition at line 333 of file CModelValue.cpp.

References ASSIGNMENT, compile(), mpInitialExpression, mpModel, mStatus, CModel::setCompileFlag(), and CExpression::setInfix().

Referenced by CModel::convert2NonReversible(), CModelAdd::copyInitialExpression(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CCopasiXMLParser::ModelElement::end(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), CQMoietiesTaskResult::slotCreateGlobalQuantity(), and CModelParameter::updateModel().

{
  if (mStatus == ASSIGNMENT) return false;

  if (mpModel)
    mpModel->setCompileFlag(true);

  if (mpInitialExpression == NULL)
    {
      mpInitialExpression = new CExpression("InitialExpression", this);
    }

  if (!mpInitialExpression->setInfix(expression)) return false;

  return compile();
}

bool CModelEntity::setInitialExpressionPtr

(

CExpression *

pExpression

)

Set the expression for non FIXED model values

Parameters

CExpression*

Returns

bool success

Definition at line 299 of file CModelValue.cpp.

References CCopasiContainer::add(), ASSIGNMENT, compile(), mpInitialExpression, mpModel, mStatus, pdelete, CModel::setCompileFlag(), CCopasiObject::setObjectName(), and CCopasiObject::setObjectParent().

Referenced by SBMLImporter::importInitialAssignments().

{
  if (mStatus == ASSIGNMENT) return false;

  if (pExpression == mpInitialExpression) return true;

  if (pExpression == NULL) return false;

  if (mpModel != NULL)
    {
      mpModel->setCompileFlag(true);
    }

  CExpression * pOld = mpInitialExpression;
  mpInitialExpression = pExpression;

  mpInitialExpression->setObjectName("InitialExpression");
  add(mpInitialExpression, true);

  if (compile())
    {
      pdelete(pOld);
      return true;
    }

  // If compile fails we do not take ownership
  // and we remove the object from the container
  remove(mpInitialExpression);
  mpInitialExpression->setObjectParent(NULL);
  mpInitialExpression = pOld;

  return false;
}

void CModelEntity::setInitialValue ( const C_FLOAT64 &  initialValue )

virtual

Set the initial value

Parameters

const

C_FLOAT64 & initialValue

Definition at line 383 of file CModelValue.cpp.

References mpIValue.

Referenced by CModel::createCompartment(), CModel::createModelValue(), CModel::determineIsAutonomous(), initObjects(), CCompartment::load(), CMetab::operator=(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), CQGlobalQuantityDM::setData(), CQCompartmentDM::setData(), CQSpecieDM::setData(), CQSpeciesDetail::slotBtnNew(), and CModelParameter::updateModel().

{
  *mpIValue = initialValue;
}

void CModelEntity::setInitialValuePtr

(

C_FLOAT64 *

pInitialValue

)

Set the pointer to the initial value

Parameters

C_FLOAT64

* pInitialValue

Definition at line 531 of file CModelValue.cpp.

References C_FLOAT64, mpIValue, mpIValueReference, and CCopasiObjectReference< CType >::setReference().

Referenced by CStateTemplate::add(), initObjects(), and CStateTemplate::remove().

{
  mpIValue = pInitialValue;

  if (!mpIValue) mpIValue = new C_FLOAT64;

  mpIValueReference->setReference(*mpIValue);
}

bool CModelEntity::setObjectParent ( const CCopasiContainer *  pParent )

virtual

Set the object parent

Parameters

const

CCopasiContainer * pParent

Returns

bool success

Reimplemented from CCopasiObject.

Reimplemented in CMetab.

Definition at line 549 of file CModelValue.cpp.

References CStateTemplate::add(), C_FLOAT64, CCopasiObject::getObjectAncestor(), CModel::getStateTemplate(), mpIValue, mpModel, mpValue, pdelete, CStateTemplate::remove(), and CCopasiObject::setObjectParent().

Referenced by CCopasiDataModel::commonAfterLoad(), and CMetab::setObjectParent().

{
  CCopasiContainer::setObjectParent(pParent);
  CModel * pNewModel = static_cast<CModel *>(getObjectAncestor("Model"));

  if (mpModel == pNewModel) return true;

  C_FLOAT64 InitialValue = *mpIValue;
  C_FLOAT64 Value = *mpValue;

  if (mpModel)
    {
      // This allocates new objects for mpIValue and mpValueData
      mpModel->getStateTemplate().remove(this);
    }

  // We can safely remove the currently allocated objects as they
  // are not part of an CStateTemplate
  pdelete(mpIValue);
  pdelete(mpValue);

  if (pNewModel)
    {
      pNewModel->getStateTemplate().add(this);
    }
  else
    {
      mpValue = new C_FLOAT64;
      mpIValue = new C_FLOAT64;
    }

  mpModel = pNewModel;
  *mpIValue = InitialValue;
  *mpValue = Value;

  return true;
}

void CModelEntity::setRate

(

const C_FLOAT64 &

rate

)

Set the rate (dmValue/dt)

Parameters

const C_FLOAT64 &

rate

Definition at line 388 of file CModelValue.cpp.

References mRate.

{
  mRate = rate;
}

void CModelEntity::setSBMLId

(

const std::string &

id

)

Sets the SBMLId.

Definition at line 632 of file CModelValue.cpp.

References mSBMLId.

Referenced by SBMLImporter::createCCompartmentFromCompartment(), SBMLImporter::createCMetabFromSpecies(), SBMLImporter::createCModelFromSBMLDocument(), SBMLImporter::createCModelValueFromParameter(), CSBMLExporter::createCompartment(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CCopasiXMLParser::SBMLMapElement::start(), test000103::test_bug1743_l2(), and test000103::test_bug1743_l3().

{
  this->mSBMLId = id;
}

void CModelEntity::setStatus ( const CModelEntity::Status &  status )

virtual

Set the status

Parameters

const

CModelEntity::Status & status

Reimplemented in CMetab.

Definition at line 395 of file CModelValue.cpp.

References CCopasiContainer::add(), ASSIGNMENT, calculate(), CCopasiObject::clearRefresh(), CExpression::createInitialExpression(), FIXED, CCopasiObject::getDirectDependencies(), CCopasiObject::getObjectDataModel(), mpExpression, mpInitialExpression, mpIValueReference, mpModel, mpRateReference, mpValue, mpValueReference, mRate, mStatus, mUsed, ODE, pdelete, REACTIONS, CModel::setCompileFlag(), CCopasiObject::setDirectDependencies(), CCopasiObject::setObjectName(), CCopasiObject::setRefresh(), setValuePtr(), and TIME.

Referenced by CModelAdd::addCompartments(), CModelAdd::addModelValues(), CCompartment::CCompartment(), CModel::CModel(), CModelEntity(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), SBMLImporter::importRuleForModelEntity(), CQCompartment::save(), CQModelValue::save(), CQGlobalQuantityDM::setData(), CQCompartmentDM::setData(), CMetab::setStatus(), test000058::test_bug1025_10(), test000058::test_bug1025_5(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_20(), test000059::test_unique_id_21(), and test000059::test_unique_id_21_2().

{
  if (mStatus != status)
    {
      if (mpModel != NULL)
        mpModel->setCompileFlag(true);

      // An assignment may not have an initial expression.
      // However, internally we always create one, which need
      // to be deleted.
      if (mStatus == ASSIGNMENT)
        pdelete(mpInitialExpression);

      mStatus = status;
      this->setValuePtr(mpValue);

      if (mpModel != NULL)
        mpModel->setCompileFlag(true);

      std::set< const CCopasiObject * > NoDependencies;

      setDirectDependencies(NoDependencies);
      clearRefresh();

      mpIValueReference->setDirectDependencies(NoDependencies);

      mpValueReference->setDirectDependencies(NoDependencies);
      mpValueReference->clearRefresh();

      mpRateReference->setDirectDependencies(NoDependencies);
      mpRateReference->clearRefresh();
      CCopasiDataModel* pDataModel = NULL;

      switch (mStatus)
        {
          case ASSIGNMENT:

            if (mpExpression == NULL)
              mpExpression = new CExpression("Expression", this);

            pdelete(mpInitialExpression);
            pDataModel = getObjectDataModel();
            mpInitialExpression = CExpression::createInitialExpression(*mpExpression, pDataModel);
            mpInitialExpression->setObjectName("InitialExpression");
            add(mpInitialExpression, true);

            mpValueReference->setDirectDependencies(mpExpression->getDirectDependencies());
            mpValueReference->setRefresh(this, &CModelEntity::calculate);

            mRate = std::numeric_limits<C_FLOAT64>::quiet_NaN();

            mUsed = true;
            break;

          case ODE:

            if (mpExpression == NULL)
              mpExpression = new CExpression("Expression", this);

            mpRateReference->setDirectDependencies(mpExpression->getDirectDependencies());
            mpRateReference->setRefresh(this, &CModelEntity::calculate);

            mUsed = true;
            break;

          case REACTIONS:
            pdelete(mpExpression);

            mUsed = true;
            break;

          case TIME:
            pdelete(mpExpression);

            mUsed = true;
            break;

          case FIXED:
            pdelete(mpExpression);

            mRate = 0.0;

            mUsed = false;
            break;
        }
    }
}

void CModelEntity::setUsed

(

const bool &

used

)

Set whether the model entity is used during simulation

Parameters

const

bool & used

Definition at line 642 of file CModelValue.cpp.

References mUsed.

Referenced by CModel::buildStateTemplate(), and CModel::CModel().

{mUsed = used;}

void CModelEntity::setValue ( const C_FLOAT64 &  value )

virtual

Set the value

Parameters

const

C_FLOAT64 & value

Definition at line 378 of file CModelValue.cpp.

References mpValue.

Referenced by CHybridMethod::fireReaction(), CHybridMethodLSODA::fireReaction(), CHybridMethodODE45::fireReaction(), initObjects(), CQSpecieDM::setData(), and CStochMethod::updateSystemState().

{
  *mpValue = value;
}

void CModelEntity::setValuePtr

(

C_FLOAT64 *

pValue

)

Set the pointer to the value

Parameters

C_FLOAT64

* pValue

Definition at line 540 of file CModelValue.cpp.

References C_FLOAT64, mpValue, mpValueReference, and CCopasiObjectReference< CType >::setReference().

Referenced by CStateTemplate::add(), initObjects(), CStateTemplate::remove(), and setStatus().

{
  mpValue = pValue;

  if (!mpValue) mpValue = new C_FLOAT64;

  mpValueReference->setReference(*mpValue);
}

Member Data Documentation

CExpression* CModelEntity::mpExpression

protected

The infix expression for objects of type ASSIGNMENT or ODE

Definition at line 336 of file CModelValue.h.

Referenced by calculate(), CMetab::calculate(), compile(), CMetab::compile(), getExpression(), getExpressionPtr(), setExpression(), setExpressionPtr(), setStatus(), and CMetab::setStatus().

CExpression* CModelEntity::mpInitialExpression

protected

Optional initial expression

Definition at line 341 of file CModelValue.h.

Referenced by compile(), CMetab::compile(), CMetab::compileInitialValueDependencies(), getInitialExpression(), getInitialExpressionPtr(), CMetab::refreshInitialConcentration(), refreshInitialValue(), setInitialExpression(), setInitialExpressionPtr(), and setStatus().

C_FLOAT64* CModelEntity::mpIValue

protected

Pointer to the initial value of the model entity.

Definition at line 326 of file CModelValue.h.

Referenced by CCompartment::CCompartment(), CModel::CModel(), CModelEntity(), compile(), CModel::getInitialTime(), getInitialValue(), CModel::initObjects(), CModel::load(), operator<<(), CMetab::refreshInitialConcentration(), refreshInitialValue(), CMetab::refreshInitialValue(), CModel::setInitialTime(), setInitialValue(), setInitialValuePtr(), setObjectParent(), CModel::~CModel(), and ~CModelEntity().

CCopasiObjectReference<C_FLOAT64>* CModelEntity::mpIValueReference

protected

Definition at line 356 of file CModelValue.h.

Referenced by CMoiety::add(), compile(), CMetab::compileInitialValueDependencies(), CMetab::compileIsInitialConcentrationChangeAllowed(), CCompartment::getChildObjectUnits(), CMetab::getChildObjectUnits(), getDeletedObjects(), getInitialValueReference(), CCompartment::initObjects(), initObjects(), CMetab::initObjects(), CModel::initObjects(), setInitialValuePtr(), and setStatus().

CModel* CModelEntity::mpModel

protected

Definition at line 359 of file CModelValue.h.

Referenced by CMetab::calculate(), compile(), CMetab::compile(), CCompartment::getChildObjectUnits(), CMetab::getChildObjectUnits(), CMetab::getModel(), initObjects(), operator<<(), CMetab::operator=(), CMetab::refreshConcentration(), CMetab::refreshConcentrationRate(), CMetab::refreshInitialConcentration(), CMetab::refreshInitialValue(), CMetab::refreshNumber(), setExpression(), setExpressionPtr(), setInitialExpression(), setInitialExpressionPtr(), setObjectParent(), setStatus(), CMetab::setStatus(), and ~CModelEntity().

CCopasiObjectReference<C_FLOAT64>* CModelEntity::mpRateReference

protected

Definition at line 358 of file CModelValue.h.

Referenced by compile(), CMetab::compile(), CCompartment::getChildObjectUnits(), CMetab::getChildObjectUnits(), getDeletedObjects(), getRateReference(), initObjects(), CMetab::initObjects(), CMetab::mustBeDeleted(), setStatus(), and CMetab::setStatus().

C_FLOAT64* CModelEntity::mpValue

protected

Pointer to the value of the model entity.

Definition at line 321 of file CModelValue.h.

Referenced by calculate(), CMetab::calculate(), CModel::CModel(), CModelEntity(), CModel::getTime(), getValue(), getValuePointer(), CModel::initObjects(), operator<<(), CMetab::refreshConcentration(), CMetab::refreshNumber(), CMetab::refreshTransitionTime(), setObjectParent(), setStatus(), CModel::setTime(), setValue(), setValuePtr(), CModel::~CModel(), and ~CModelEntity().

CCopasiObjectReference<C_FLOAT64>* CModelEntity::mpValueReference

protected

Definition at line 357 of file CModelValue.h.

Referenced by CMoiety::add(), compile(), CMetab::compile(), CModel::compile(), CCompartment::getChildObjectUnits(), CMetab::getChildObjectUnits(), getDeletedObjects(), getValueObject(), getValueReference(), CCompartment::initObjects(), initObjects(), CMetab::initObjects(), CModel::initObjects(), setStatus(), CMetab::setStatus(), and setValuePtr().

C_FLOAT64 CModelEntity::mRate

protected

Rate of change/time.

Definition at line 331 of file CModelValue.h.

Referenced by calculate(), CMetab::calculate(), CMetab::compile(), getRate(), initObjects(), CModel::initObjects(), operator<<(), CMetab::operator=(), CMetab::refreshConcentrationRate(), CMetab::refreshRate(), CMetab::refreshTransitionTime(), setRate(), and setStatus().

std::string CModelEntity::mSBMLId

protected

The id of the corresponding parameter in an SBML file. This value is either set upon importing an SBML file, or when the object is first exported to an SBML file.

Definition at line 47 of file CModelValue.h.

Referenced by getSBMLId(), initObjects(), and setSBMLId().

Status CModelEntity::mStatus

private

Status of the model entity.

Definition at line 347 of file CModelValue.h.

Referenced by calculate(), CModelEntity(), compile(), getInitialExpression(), getStatus(), isFixed(), setInitialExpression(), setInitialExpressionPtr(), and setStatus().

bool CModelEntity::mUsed

private

Indicates whether the model value is used, i.e., must be calculated during the simulation

Definition at line 353 of file CModelValue.h.

Referenced by isUsed(), setStatus(), and setUsed().

const std::string CModelEntity::StatusName

static

Initial value:

=
{
  "fixed",
  "assignment",
  "reactions",
  "ode",
  "time",
  ""
}

String representation of the states

Definition at line 67 of file CModelValue.h.

Referenced by CQCompartment::CQCompartment(), CQCompartmentDM::CQCompartmentDM(), CQGlobalQuantityDM::CQGlobalQuantityDM(), CQSpecieDM::CQSpecieDM(), CQSpeciesDetail::CQSpeciesDetail(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CODEExporter::exportCompartments(), CODEExporter::exportMetabolites(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportModelValues(), CQGlobalQuantityDM::flags(), CQCompartmentDM::flags(), CQSpecieDM::flags(), CQModelValue::init(), CQSpeciesDetail::load(), CQCompartment::load(), CQModelValue::load(), StateSubwidget::loadCompartments(), StateSubwidget::loadMetabolites(), StateSubwidget::loadModelValues(), CQUpdatesWidget::loadObjectsTable(), CQGlobalQuantityDM::setData(), CQCompartmentDM::setData(), CQSpecieDM::setData(), and CQParameterOverviewDM::typeData().

const char * CModelEntity::XMLStatus

static

Initial value:

=
{
  "fixed",
  "assignment",
  "reactions",
  "ode",
  "time",
  NULL
}

XML representation of the states

Definition at line 72 of file CModelValue.h.

Referenced by CCopasiXML::saveModel(), CCopasiXML::saveModelParameter(), CCopasiXMLParser::ModelParameterElement::start(), CCopasiXMLParser::MetaboliteElement::start(), CCopasiXMLParser::CompartmentElement::start(), and CCopasiXMLParser::ModelValueElement::start().

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

• CModelValue.h
• CModelValue.cpp