CMathExpression Class Reference

#include <CMathExpression.h>

Inheritance diagram for CMathExpression:

Public Member Functions
	CMathExpression (const CExpression &src, CMathContainer &container, const bool &replaceDiscontinuousNodes)
	CMathExpression (const CFunction &src, const CCallParameters< C_FLOAT64 > &callParameters, CMathContainer &container, const bool &replaceDiscontinuousNodes)
	CMathExpression (const std::string &name, CMathContainer &container)
virtual CIssue	compile () override
bool	convertToInitialExpression ()
virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override
void	relocate (const CMathContainer *pContainer, const std::vector< CMath::sRelocate > &relocations)
const C_FLOAT64 &	value ()
virtual	~CMathExpression ()
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)
bool	containsCN (const DataObjectSet &elements) const
std::string::size_type	getErrorPosition () const
const std::string &	getInfix () const
const std::vector< CEvaluationNode * > &	getNodeList () const
virtual const CObjectInterface *	getNodeObject (const CCommonName &CN) 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 CIssue	setInfix (const std::string &infix)
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 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 CMathExpression *	copy (const CMathExpression &src, CMathContainer &container)
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 *)

Private Member Functions
	CMathExpression ()
	CMathExpression (const CMathExpression &src)=delete
CEvaluationNode *	createMassActionPart (const C_FLOAT64 *pK, const CCallParameters< C_FLOAT64 > *pSpecies)
CEvaluationNode *	createNodeFromValue (const C_FLOAT64 *pDataValue)
virtual bool	setRoot (CEvaluationNode *pRootNode) override

Private Attributes
CObjectInterface::ObjectSet	mPrerequisites

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)
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

Constructor & Destructor Documentation

CMathExpression() [1/5]

CMathExpression::CMathExpression ( )

private

Hidden default constructor

Referenced by copy().

CMathExpression() [2/5]

CMathExpression::CMathExpression ( const CMathExpression &  src )

privatedelete

CMathExpression() [3/5]

CMathExpression::CMathExpression	(	const std::string &	name,
		CMathContainer &	container
	)

Specific constructor.

Parameters

const	std::string & name
CMathContainer	& container

CMathExpression() [4/5]

CMathExpression::CMathExpression	(	const CExpression &	src,
		CMathContainer &	container,
		const bool &	replaceDiscontinuousNodes
	)

Specific constructor. The src expression must have been successfully compiled in the context of the current model

Parameters

const	CExpression & src
CMathContainer	& container
const	bool & replaceDiscontinuousNodes

References CEvaluationTree::clearNodes(), compile(), CMathContainer::copyBranch(), CEvaluationTree::getRoot(), and setRoot().

CMathExpression() [5/5]

CMathExpression::CMathExpression	(	const CFunction &	src,
		const CCallParameters< C_FLOAT64 > &	callParameters,
		CMathContainer &	container,
		const bool &	replaceDiscontinuousNodes
	)

Specific constructor. The src function must have been successfully compiled in the context of the current model

Parameters

const	CFunction & src
const	CCallParameters< C_FLOAT64 > & callParameters
CMathContainer	& container
const	bool & replaceDiscontinuousNodes

References CCopasiNode< _Data >::addChild(), CCallParameters< Type >::begin(), C_FLOAT64, CEvaluationTree::clearNodes(), compile(), CMathContainer::copyBranch(), createMassActionPart(), createNodeFromValue(), CCallParameters< Type >::end(), CEvaluationTree::Expression, CEvaluationTree::Function, CEvaluationTree::getRoot(), CEvaluationTree::getType(), CEvaluationTree::MassAction, CEvaluationTree::MathExpression, CEvaluationNode::MINUS, pdelete, CEvaluationTree::PreDefined, setRoot(), CCallParameters< Type >::size(), and CEvaluationTree::UserDefined.

~CMathExpression()

CMathExpression::~CMathExpression ( )

virtual

Destructor

Member Function Documentation

compile()

CIssue CMathExpression::compile ( )

overridevirtual

Compile the evaluation tree.

Reimplemented from CEvaluationTree.

References CValidity::add(), CEvaluationTree::buildCalculationSequence(), CValidity::clear(), CEvaluationNodeObject::getObjectInterfacePtr(), CDataObject::getObjectParent(), CEvaluationTree::mCalculationSequence, CEvaluationTree::mInfix, CEvaluationTree::mpNodeList, mPrerequisites, CObjectInterface::mValidity, CEvaluationNode::POINTER, CVector< CType >::resize(), CEvaluationNode::RGAMMA, CEvaluationNode::RNORMAL, CEvaluationNode::RPOISSON, CEvaluationNode::RUNIFORM, CIssue::Success, and CEvaluationTree::updateTree().

Referenced by CMathExpression(), CMathObject::compileDependentMass(), CMathObject::compileParticleFlux(), CMathObject::compilePropensity(), CMathObject::compileReactionNoise(), CMathObject::compileTotalMass(), CMathObject::compileTransitionTime(), CMathObject::createExtensiveReactionNoiseExpression(), CMathObject::createExtensiveReactionRateExpression(), CMathObject::createExtensiveValueExpression(), CMathObject::createIntensiveRateExpression(), CMathObject::createIntensiveValueExpression(), and CMathObject::setExpressionPtr().

convertToInitialExpression()

bool CMathExpression::convertToInitialExpression

(

)

Convert to a corresponding initial expression.

Returns

bool success

References CEvaluationNode::buildInfix(), C_FLOAT64, CDataObject::getObjectName(), CEvaluationNodeObject::getObjectValuePtr(), CEvaluationTree::getRoot(), CEvaluationNode::getValuePointer(), CEvaluationTree::mInfix, CEvaluationTree::mpNodeList, mPrerequisites, CEvaluationTree::mpRootValue, CEvaluationNode::OBJECT, pMathContainer, CEvaluationNode::POINTER, CDataObject::setObjectName(), and CEvaluationNodeObject::setObjectValuePtr().

Referenced by CMathContainer::addAnalysisObject(), and CMathObject::compileExpression().

copy()

CMathExpression * CMathExpression::copy ( const CMathExpression &  src, CMathContainer &  container  )

static

Copy an expression with the given offsets

Parameters

const	CMathExpression & src
CMathContainer	& container

Returns

CMathExpression * copy

References CEvaluationTree::buildCalculationSequence(), CMathExpression(), CEvaluationNode::copyBranch(), CDataObject::getObjectName(), CEvaluationTree::getRoot(), mPrerequisites, and setRoot().

Referenced by CMathObject::copy(), and CMathObject::relocate().

createMassActionPart()

CEvaluationNode * CMathExpression::createMassActionPart ( const C_FLOAT64 *  pK, const CCallParameters< C_FLOAT64 > *  pSpecies  )

private

Create a part of Mass Action kinetics

Parameters

const	C_FLOAT64 * pK
const	CCallParameters< C_FLOAT64 > * pSpecies

Returns

CEvaluationNode * massActionPart

References CCopasiNode< _Data >::addChild(), CCallParameters< Type >::begin(), createNodeFromValue(), CCallParameters< Type >::end(), CEvaluationNode::MULTIPLY, CEvaluationNode::NaN, and CCallParameters< Type >::size().

Referenced by CMathExpression().

createNodeFromValue()

CEvaluationNode * CMathExpression::createNodeFromValue ( const C_FLOAT64 *  pDataValue )

private

Create a node based on the given pointer to a data value

Parameters

const

C_FLOAT64 * pDataValue

Returns

CEvaluationNode * pNode

References C_FLOAT64, CMathObject::getValuePointer(), CEvaluationNode::NaN, and pMathContainer.

Referenced by CMathExpression(), and createMassActionPart().

getPrerequisites()

const CObjectInterface::ObjectSet & CMathExpression::getPrerequisites ( ) const

overridevirtual

Retrieve the prerequisites, i.e., the objects which need to be evaluated before this.

Returns

const CObjectInterface::ObjectSet & prerequisites

Reimplemented from CDataObject.

References mPrerequisites.

Referenced by CMathObject::compileExpression(), and COptProblem::initialize().

relocate()

void CMathExpression::relocate	(	const CMathContainer *	pContainer,
		const std::vector< CMath::sRelocate > &	relocations
	)

Copy an expression with the given offsets

Parameters

const	CMathContainer * pContainer
const	std::vector< CMath::sRelocate > & relocations

References CEvaluationNode::buildInfix(), C_FLOAT64, CEvaluationTree::getRoot(), CEvaluationTree::mInfix, mPrerequisites, CEvaluationNode::OBJECT, CEvaluationNode::POINTER, CMathContainer::relocateObjectSet(), CMathContainer::relocateValue(), and stringToPointer().

Referenced by CMathContainer::createDelays(), and CMathObject::relocate().

setRoot()

bool CMathExpression::setRoot ( CEvaluationNode *  pRootNode )

overrideprivatevirtual

Sets the root node of the tree. Note: This is private to assure that only valid root node representing mathematical expressions are set.

Parameters

CEvaluationNode*

root node of the tree

Returns

bool success

Reimplemented from CEvaluationTree.

References CEvaluationTree::setRoot().

Referenced by CMathExpression(), and copy().

value()

const C_FLOAT64 & CMathExpression::value

(

)

Evaluate the expression

Returns

const C_FLOAT64 & value

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

Referenced by COptProblem::calculate(), and CMathObject::calculateExpression().

Member Data Documentation

mPrerequisites

CObjectInterface::ObjectSet CMathExpression::mPrerequisites

private

The prerequisites for calculating the expression.

Referenced by compile(), convertToInitialExpression(), copy(), getPrerequisites(), and relocate().

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

• CMathExpression.h
• CMathExpression.cpp