#include <CExpression.h>

Inheritance diagram for CExpression:

Public Member Functions
virtual const C_FLOAT64 &	calcValue ()

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

	CExpression (const std::string &name="Expression", const CDataContainer *pParent=NO_PARENT)

virtual CIssue	compile (CObjectInterface::ContainerList listOfContainer=CDataContainer::EmptyList)

std::string	getBerkeleyMadonnaString () const

std::string	getCCodeString () const

const std::string &	getDisplayString () const

const CObjectInterface::ContainerList &	getListOfContainer () const

virtual const CObjectInterface *	getNodeObject (const CCommonName &CN) const override

std::string	getXPPString () const

void	refresh ()

virtual CIssue	setInfix (const std::string &infix) override

void	setIsBoolean (const bool &booleanRequired)

bool	updateInfix ()

void	writeMathML (std::ostream &out, bool fullExpand, size_t l) const

virtual	~CExpression ()

Public Member Functions inherited from CEvaluationTree
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)

bool	calls (std::set< std::string > &list) const

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

	CEvaluationTree (const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT, const Type &type=Function)

virtual CIssue	compile ()

bool	containsCN (const DataObjectSet &elements) const

std::string::size_type	getErrorPosition () const

const std::string &	getInfix () const

const std::vector< CEvaluationNode * > &	getNodeList () const

CEvaluationNode *	getRoot ()

const CEvaluationNode *	getRoot () const

const CEvaluationTree::Type &	getType () const

virtual size_t	getVariableIndex (const std::string &name) const

virtual const C_FLOAT64 &	getVariableValue (const size_t &index) const

bool	hasCircularDependency () const

bool	hasDiscontinuity () const

bool	isBoolean () const

bool	mapObjectNodes (const CDataContainer pSrc, const CDataContainer pTarget)

bool	operator== (const CEvaluationTree &rhs) const

virtual bool	setRoot (CEvaluationNode *pRootNode)

bool	setTree (const ASTNode &pRootNode, bool isFunction)

size_t	size () const

virtual ASTNode *	toAST (const CDataModel *pDataModel) const

virtual CData	toData () const

CIssue	updateTree ()

virtual	~CEvaluationTree ()

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

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

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

virtual size_t	getIndex (const CDataObject *pObject) const

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

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

virtual CUndoObjectInterface *	insert (const CData &data) override

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

virtual bool	remove (CDataObject *pObject)

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 CCommonName	getCN () const override

virtual const CDataObject *	getDataObject () const override

virtual const std::string &	getKey () const

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

CDataModel *	getObjectDataModel () const

virtual std::string	getObjectDisplayName () const override

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

virtual void *	getValuePointer () 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

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

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CDataContainer *pParent)

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

virtual	~CUndoObjectInterface ()

Static Public Member Functions
static CExpression *	createInitialExpression (const CExpression &expression, const CDataModel *pDataModel)

Static Public Member Functions inherited from CEvaluationTree
static CEvaluationTree *	copy (const CEvaluationTree &src)

static CEvaluationTree *	create (CEvaluationTree::Type type)

static CEvaluationNode *	fromAST (const ASTNode *pASTNode, bool isFunction)

static CEvaluationTree *	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 *)

Protected Attributes
std::string	mDisplayString

bool	mIsBoolean

const CObjectInterface::ContainerList *	mpListOfContainer

Protected Attributes inherited from CEvaluationTree
CVector< CEvaluationNode * >	mCalculationSequence

std::string	mInfix

std::vector< CEvaluationNode * > *	mpNodeList

const C_FLOAT64 *	mpRootValue

CEvaluationTree::Type	mType

C_FLOAT64	mValue

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

Private Member Functions
void	initObjects ()

Additional Inherited Members
Public Types inherited from CEvaluationTree
enum	Type { Function = 0 , MassAction , PreDefined , UserDefined , Expression , MathExpression }

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 Attributes inherited from CEvaluationTree
static const std::string	TypeName []

static const char *	XMLType []

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

Protected Member Functions inherited from CEvaluationTree
void	buildCalculationSequence ()

void	calculate ()

	CEvaluationTree (const CEvaluationTree &src)

void	clearNodes ()

CIssue	compileNodes ()

CIssue	parse ()

void	setType (const CEvaluationTree::Type &type)

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)

Constructor & Destructor Documentation

◆ CExpression() [1/2]

CExpression::CExpression	(	const std::string &	name = `"Expression"`,
		const CDataContainer *	pParent = `NO_PARENT`
	)

Default constructor

Parameters

const	std::string & name (default: "Expression")
const	CDataContainer * pParent (default: NULL)

References initObjects().

Referenced by createInitialExpression().

◆ CExpression() [2/2]

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

Copy constructor

Parameters

const CExpression &	src
const	CDataContainer * pParent (default: NULL)

References CEvaluationTree::compile(), and initObjects().

◆ ~CExpression()

CExpression::~CExpression ( )

virtual

Destructor

Member Function Documentation

◆ calcValue()

const C_FLOAT64 & CExpression::calcValue ( )

virtual

Calculates the value of the function

Returns: const C_FLOAT64 & result

References CEvaluationTree::calculate(), and CEvaluationTree::mValue.

Referenced by SBMLImporter::applyStoichiometricExpressions(), CModelEntity::calculate(), CEvaluationNodeCall::calculate(), CMetab::calculate(), CModelEntity::compile(), CMetab::compile(), and refresh().

◆ compile()

CIssue CExpression::compile ( CObjectInterface::ContainerList listOfContainer = CDataContainer::EmptyList )

virtual

Compile the evaluation tree.

Parameters

CObjectInterface::ContainerList listOfContainer (Default: CDataContainer::EmptyList)

Returns: CIssue issue

References CValidity::add(), CFlags< Enum >::All, CEvaluationNode::buildDisplayString(), CEvaluationNode::buildInfix(), CEvaluationTree::compileNodes(), CIssue::ExpressionDataTypeInvalid, CIssue::ExpressionInvalid, CDataObject::getObjectParent(), CEvaluationTree::getRoot(), CIssue::HasCircularDependency, CIssue::isSuccess(), mDisplayString, CEvaluationTree::mInfix, mpListOfContainer, CObjectInterface::mValidity, and CValidity::remove().

Referenced by CMathEvent::CTrigger::allocate(), SBMLImporter::applyStoichiometricExpressions(), CModelParameter::compile(), CModelEntity::compile(), CReaction::compile(), CMetab::compile(), CEventAssignment::compile(), CEvent::compile(), CMathEvent::CTrigger::compile(), CMathEvent::compile(), CMathEvent::CAssignment::compile(), CMathObject::compileFlux(), CModel::createEventsForTimeseries(), CMathObject::createExtensiveNoiseExpression(), CMathObject::createExtensiveODERateExpression(), CModelExpansion::duplicateEvent(), COptProblem::initialize(), CModel::prepareElasticity(), CEvent::setDelayExpressionPtr(), CMathObject::setExpression(), CEventAssignment::setExpressionPtr(), CEvent::setPriorityExpressionPtr(), and CEvent::setTriggerExpressionPtr().

◆ createInitialExpression()

CExpression * CExpression::createInitialExpression	(	const CExpression &	expression,
		const CDataModel *	pDataModel
	)

static

Creates the corresponding initial expression for the given expression by converting each transient value to the corresponding initial value.

Parameters

const CExpression & expression

Returns: CExpression * pInitialExpression

References CExpression(), CDataObject::getCN(), CMetab::getConcentrationReference(), CValidity::getFirstWorstIssue(), CMetab::getInitialConcentrationReference(), CModelEntity::getInitialValueReference(), CCopasiMessage::getLastMessage(), CEvaluationTree::getNodeList(), CDataContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CDataObject::getObjectParent(), CDataObject::getValidity(), CModelEntity::getValueReference(), CIssue::isError(), CEvaluationNodeObject::setData(), CCopasiMessage::size(), and CEvaluationTree::updateTree().

Referenced by CModelEntity::compile(), CMetab::compile(), and CModelEntity::setStatus().

◆ getBerkeleyMadonnaString()

std::string CExpression::getBerkeleyMadonnaString ( ) const

Retrieve the display string in Berkeley Madonna syntax.

References CEvaluationNode::buildBerkeleyMadonnaString(), and CEvaluationTree::getRoot().

◆ getCCodeString()

std::string CExpression::getCCodeString ( ) const

Retrieve the display string in C syntax.

References CEvaluationNode::buildCCodeString(), and CEvaluationTree::getRoot().

◆ getDisplayString()

const std::string & CExpression::getDisplayString ( ) const

Retrieve the human readable display string. Note, the expression must be compiled for this return a displayable string.

Returns: const std::string & displayString

References mDisplayString.

◆ getListOfContainer()

const CObjectInterface::ContainerList & CExpression::getListOfContainer ( ) const

Retrieve the list of container used for compile

Returns: const CObjectInterface::ContainerList & listOfContainer

References mpListOfContainer.

◆ getNodeObject()

const CObjectInterface * CExpression::getNodeObject ( const CCommonName & CN ) const

overridevirtual

Retrieve a pointer to the object defined by CN. This method may only be called during compile() since the list mpListOfContainer is only valid then.

Parameters

const CCommonName & CN

Returns: const CObjectInterface * value

Reimplemented from CEvaluationTree.

References CEvaluationTree::getNodeObject(), CObjectInterface::getObject(), CObjectInterface::GetObjectFromCN(), and mpListOfContainer.

◆ getXPPString()

std::string CExpression::getXPPString ( ) const

Retrieve the display string in XPPAUT syntax.

References CEvaluationNode::buildXPPString(), and CEvaluationTree::getRoot().

◆ initObjects()

void CExpression::initObjects ( )

private

Initialize the contained CDataObjects

References CDataContainer::getObject().

Referenced by CExpression().

◆ refresh()

void CExpression::refresh ( )

Refresh the value of the expression

References calcValue().

◆ setInfix()

CIssue CExpression::setInfix ( const std::string & infix )

overridevirtual

Set the infix description of the tree and compile it.

Parameters

const std::string & infix

Returns: CIssue issue

Reimplemented from CEvaluationTree.

References CValidity::add(), CIssue::Error, CIssue::ExpressionDataTypeInvalid, CEvaluationTree::getRoot(), CEvaluationTree::isBoolean(), mIsBoolean, CEvaluationTree::mpNodeList, CObjectInterface::mValidity, CEvaluationTree::setInfix(), CEvaluationNode::VARIABLE, and CIssue::VariableInExpression.

Referenced by CMathContainer::addAnalysisObject(), CMathEvent::CTrigger::allocate(), CMathEvent::CTrigger::compile(), CMathEvent::compile(), CMathEvent::CAssignment::compile(), CMathObject::compileFlux(), CMathObject::createExtensiveNoiseExpression(), CMathObject::createExtensiveODERateExpression(), FunctionHandler::processEnd(), CEvent::setDelayExpression(), CEventAssignment::setExpression(), CModelEntity::setExpression(), CMathObject::setExpression(), CModelEntity::setInitialExpression(), CModelParameter::setInitialExpression(), CModelEntity::setNoiseExpression(), CReaction::setNoiseExpression(), COptProblem::setObjectiveFunction(), CEvent::setPriorityExpression(), and CEvent::setTriggerExpression().

◆ setIsBoolean()

void CExpression::setIsBoolean ( const bool & booleanRequired )

Set whether this a boolean expression or not

Parameters

const bool & isBoolean

References CEvaluationTree::isBoolean(), and mIsBoolean.

Referenced by CMathEvent::CTrigger::allocate(), CMathEvent::CTrigger::compile(), SBMLImporter::importEvent(), CMathObject::setExpression(), and CEvent::setTriggerExpression().

◆ updateInfix()

bool CExpression::updateInfix ( )

This method performs an infix update if a referenced object has been renamed

Returns: bool success

References CEvaluationNode::buildInfix(), CEvaluationTree::getRoot(), and CEvaluationTree::mInfix.

Referenced by CEvent::getDelayExpression(), CEvent::getDelayExpressionPtr(), CEventAssignment::getExpression(), CModelEntity::getExpression(), CModelEntity::getExpressionPtr(), CEventAssignment::getExpressionPtr(), CModelParameter::getInitialExpression(), CModelEntity::getInitialExpression(), CModelEntity::getInitialExpressionPtr(), CModelEntity::getNoiseExpression(), CReaction::getNoiseExpression(), CModelEntity::getNoiseExpressionPtr(), CReaction::getNoiseExpressionPtr(), COptProblem::getObjectiveFunction(), CEvent::getPriorityExpression(), CEvent::getPriorityExpressionPtr(), CEvent::getTriggerExpression(), and CEvent::getTriggerExpressionPtr().

◆ writeMathML()

void CExpression::writeMathML	(	std::ostream &	out,
		bool	fullExpand,
		size_t	l
	)		const

Write display mathml of the expression into the ostream "out" level specifies indentation fullExpand==true means function calls are expanded

References CEvaluationNode::buildMMLString(), CEvaluationTree::getRoot(), and SPC.

Referenced by CMMLOutput::writeRHS_ModelEntity().

Member Data Documentation

◆ mDisplayString

std::string CExpression::mDisplayString

protected

Human readable display string.

Referenced by compile(), and getDisplayString().

◆ mIsBoolean

bool CExpression::mIsBoolean

protected

Indicates whether the expression is boolean or not.

Referenced by setInfix(), and setIsBoolean().

◆ mpListOfContainer

const CObjectInterface::ContainerList* CExpression::mpListOfContainer

protected

Pointer to the list of containers used for compilation.

Referenced by compile(), getListOfContainer(), and getNodeObject().

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

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ CExpression() [1/2]

◆ CExpression() [2/2]

◆ ~CExpression()

Member Function Documentation

◆ calcValue()

◆ compile()

◆ createInitialExpression()

◆ getBerkeleyMadonnaString()

◆ getCCodeString()

◆ getDisplayString()

◆ getListOfContainer()

◆ getNodeObject()

◆ getXPPString()

◆ initObjects()

◆ refresh()

◆ setInfix()

◆ setIsBoolean()

◆ updateInfix()

◆ writeMathML()

Member Data Documentation

◆ mDisplayString

◆ mIsBoolean

◆ mpListOfContainer