CEvaluationTree Class Reference

#include <CEvaluationTree.h>

Inheritance diagram for CEvaluationTree:

Public Types
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

Public Member Functions
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
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)
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 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 *)

Static Public Attributes
static const std::string	TypeName []
static const char *	XMLType []
Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Protected Member Functions
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
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 ()

Private Attributes
std::string::size_type	mErrorPosition
CEvaluationNode *	mpRootNode

Member Enumeration Documentation

Type

enum CEvaluationTree::Type

The valid types of a function

Enumerator
Function
MassAction
PreDefined
UserDefined
Expression
MathExpression

Constructor & Destructor Documentation

CEvaluationTree() [1/3]

CEvaluationTree::CEvaluationTree ( const CEvaluationTree &  src )

protected

CEvaluationTree() [2/3]

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

Default constructor

Parameters

const	std::string & name (default: "NoName")
const	CDataContainer * pParent (default: NULL)
const	CEvaluationTree::Type & type (default: Function)

References initObjects(), and setInfix().

CEvaluationTree() [3/3]

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

Copy constructor

Parameters

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

References initObjects(), mInfix, and setInfix().

~CEvaluationTree()

CEvaluationTree::~CEvaluationTree ( )

virtual

Destructor

References clearNodes().

Member Function Documentation

applyData()

bool CEvaluationTree::applyData ( const CData &  data, CUndoData::CChangeSet &  changes  )

virtual

Apply the provided data to the object

Parameters

const

CData & data

Returns

bool success

Reimplemented from CDataContainer.

Reimplemented in CFunction.

References CDataContainer::applyData().

Referenced by CFunction::applyData().

buildCalculationSequence()

void CEvaluationTree::buildCalculationSequence ( )

protected

Build the sequence of calculations required to determine the value of the expression.

References CVectorCore< CType >::begin(), CEvaluationNode::CONSTANT, CVectorCore< CType >::end(), CNodeContextIterator< Node, Context >::end(), mCalculationSequence, mpRootNode, CNodeContextIterator< Node, Context >::next(), CEvaluationNode::NUMBER, CEvaluationNode::OBJECT, CVector< CType >::resize(), and CEvaluationNode::UNIT.

Referenced by CMathExpression::compile(), compileNodes(), CMathExpression::copy(), and mapObjectNodes().

calculate()

void CEvaluationTree::calculate ( void  )

protected

Calculate the value

References CVectorCore< CType >::begin(), CVectorCore< CType >::end(), CValidity::getFirstWorstIssue(), CIssue::isSuccess(), mCalculationSequence, mpRootNode, mpRootValue, CObjectInterface::mValidity, and mValue.

Referenced by CExpression::calcValue(), CFunction::calcValue(), and CMathExpression::value().

calls()

bool CEvaluationTree::calls

(

std::set< std::string > &

list

)

const

Check whether the evaluation tree calls any tree in the list

Parameters

std::set<

std::string > & list

Returns

bool calls

References CEvaluationNode::CALL, CEvaluationNodeCall::calls(), CDataObject::getObjectName(), and mpNodeList.

Referenced by CEvaluationNodeCall::calls(), and hasCircularDependency().

clearNodes()

void CEvaluationTree::clearNodes ( )

protected

Convenient function to free the list of generated nodes.

References mpNodeList, mpRootNode, mpRootValue, mValue, and pdelete.

Referenced by CMathExpression::CMathExpression(), parse(), setRoot(), updateTree(), and ~CEvaluationTree().

compile()

CIssue CEvaluationTree::compile ( )

virtual

Compile the evaluation tree.

Reimplemented in CMathExpression, and CMassAction.

References compileNodes().

Referenced by CMathEvent::CTrigger::allocate(), CExpression::CExpression(), CFunction::CFunction(), SBMLImporter::createCFunctionFromFunctionTree(), SBMLImporter::importFunctionDefinitions(), CRootContainer::initializeChildren(), CFunctionDB::load(), CReaction::setFunctionFromExpressionTree(), and CFunction::splitFunction().

compileNodes()

CIssue CEvaluationTree::compileNodes ( )

protected

Compile the individual nodes.

Returns

CIssue issue

References CValidity::add(), CFlags< Enum >::All, buildCalculationSequence(), CEvaluationNode::CALL, CNodeContextIterator< Node, Context >::end(), CCopasiMessage::ERROR, CIssue::Error, CIssue::ExpressionDataTypeInvalid, CIssue::ExpressionInvalid, CEvaluationNodeCall::getCalledTree(), CValidity::getFirstWorstIssue(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CEvaluationNode::getValuePointer(), CIssue::HasCircularDependency, mCalculationSequence, MCFunction, mErrorPosition, mInfix, mpNodeList, CDataObject::mPrerequisits, mpRootNode, mpRootValue, CObjectInterface::mValidity, mValue, CNodeContextIterator< Node, Context >::next(), CValidity::remove(), CVector< CType >::resize(), and CIssue::StructureInvalid.

Referenced by compile(), CExpression::compile(), and CFunction::setInfix().

containsCN()

bool CEvaluationTree::containsCN

(

const DataObjectSet &

elements

)

const

Returns

true if any of the given CN's is used by this expression

References CEvaluationNode::CALL, CEvaluationNode::CN, containsCN(), CEvaluationNode::EXPRESSION, CEvaluationNode::FUNCTION, CEvaluationNodeCall::getCalledTree(), CEvaluationNodeObject::getObjectCN(), mpNodeList, and CEvaluationNode::OBJECT.

Referenced by containsCN(), and CEvent::getOriginFor().

copy()

CEvaluationTree * CEvaluationTree::copy ( const CEvaluationTree &  src )

static

Copy an EvaluationTree of the specified type. Note: the returned object has to be released after use with delete.

Parameters

const

EvaluationTree & src

Returns

EvaluationTree * pEvaluationTree

References Expression, fatalError, Function, getType(), MassAction, NO_PARENT, PreDefined, and UserDefined.

create()

CEvaluationTree * CEvaluationTree::create ( CEvaluationTree::Type  type )

static

Create an EvaluationTree of the specified type. Note: the returned object has to be released after use with delete.

Parameters

CEvaluationTree::Type

type

Returns

EvaluationTree * pEvaluationTree

References Expression, fatalError, Function, MassAction, PreDefined, setType(), and UserDefined.

Referenced by SBMLImporter::createExpressionFromFunction(), fromData(), SBMLImporter::importEvent(), and FunctionHandler::processStart().

fromAST()

CEvaluationNode * CEvaluationTree::fromAST ( const ASTNode *  pASTNode, bool  isFunction  )

static

Converts an SBML ASTNode to the corresponding CEvaluationNode tree.

Parameters

const	ASTNode * pASTNode
bool	isFunction

Returns

CEvaluationNode*

References CNodeContextIterator< Node, Context >::context(), CNodeContextIterator< Node, Context >::end(), CCopasiMessage::EXCEPTION, fatalError, CEvaluationNodeCall::fromAST(), CEvaluationNodeChoice::fromAST(), CEvaluationNodeConstant::fromAST(), CEvaluationNodeDelay::fromAST(), CEvaluationNodeFunction::fromAST(), CEvaluationNodeLogical::fromAST(), CEvaluationNodeNumber::fromAST(), CEvaluationNodeObject::fromAST(), CEvaluationNodeOperator::fromAST(), CEvaluationNodeVariable::fromAST(), MCMathML, CNodeContextIterator< Node, Context >::next(), and CNodeContextIterator< Node, Context >::parentContextPtr().

Referenced by SBMLImporter::createCReactionFromReaction(), and setTree().

fromData()

CEvaluationTree * CEvaluationTree::fromData ( const CData &  data, CUndoObjectInterface *  pParent  )

static

Static method to create a CDataObject based on the provided data

Parameters

const

CData & data

Returns

CEvaluationTree * pDataObject

References create(), CData::EVALUATION_TREE_TYPE, CData::getProperty(), CData::OBJECT_NAME, CDataObject::setObjectName(), CDataValue::toString(), and CDataValue::toUint().

Referenced by CFunction::fromData().

getErrorPosition()

std::string::size_type CEvaluationTree::getErrorPosition

(

)

const

Retrieve the position of the error in the string description. std::string::npos indicates no error.

Returns

std::string::size_type errorPosition

References mErrorPosition.

getInfix()

const std::string & CEvaluationTree::getInfix

(

)

const

Retrieve the infix description of the tree

Returns

const std::string & infix

References mInfix.

Referenced by CMathObject::calculateValue(), CModelEntity::compile(), CMetab::compile(), CMathObject::compileFlux(), CModelAdd::copyDelayExpression(), CModelAdd::copyEventAssignmentExpression(), CModelAdd::copyExpression(), CModelAdd::copyInitialExpression(), CModelAdd::copyTriggerExpression(), CMathContainer::createDelays(), CSBMLExporter::createEvent(), CReaction::createUndoData(), COptProblem::elevateChildren(), CSBMLExporter::exportEventAssignments(), CEvent::getDelayExpression(), CEventAssignment::getExpression(), CModelEntity::getExpression(), CReactionInterface::getFunctionDescription(), CModelParameter::getInitialExpression(), CModelEntity::getInitialExpression(), CModelEntity::getNoiseExpression(), CReaction::getNoiseExpression(), COptProblem::getObjectiveFunction(), CEvent::getPriorityExpression(), CEvent::getTriggerExpression(), COptProblem::initialize(), CMathDelay::modifyMathObject(), CCopasiXML::saveFunctionList(), CEvent::setDelayExpression(), CEventAssignment::setExpression(), CModelEntity::setExpression(), CModelEntity::setInitialExpression(), CReaction::setNoiseExpression(), CEvent::setPriorityExpression(), CEvent::setTriggerExpression(), and CReaction::toData().

getNodeList()

const std::vector< CEvaluationNode * > & CEvaluationTree::getNodeList

(

)

const

Retrieve the list of nodes

Returns

const std::vector< CEvaluationNode * > & nodeList;

References mpNodeList.

Referenced by CMathObject::appendDelays(), CSBMLExporter::checkForUnsupportedObjectReferences(), CFunction::completeFunctionList(), CModelAdd::copyDelayExpression(), CModelAdd::copyEventAssignmentExpression(), CModelAdd::copyExpression(), CModelAdd::copyInitialExpression(), CModelAdd::copyTriggerExpression(), CExpression::createInitialExpression(), CODEExporter::exportExpression(), CModelExpansion::expressionContainsObject(), CODEExporter::isModelEntityExpressionODEExporterCompatible(), CModelMerging::mergeInExpression(), CModelExpansion::replaceInExpression(), and CModelExpansion::updateExpression().

getNodeObject()

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

virtual

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 in CExpression.

References CRootContainer::getFunctionList(), CDataContainer::getObject(), and CDataObject::getObjectFromCN().

Referenced by CEvaluationNodeObject::compile(), and CExpression::getNodeObject().

getRoot() [1/2]

CEvaluationNode * CEvaluationTree::getRoot

(

)

Returns the root node of the tree.

References mpRootNode.

Referenced by CMathContainer::addAnalysisObject(), CMathEvent::CTrigger::allocate(), SBMLImporter::applyStoichiometricExpressions(), SBMLImporter::areEqualFunctions(), CSBMLExporter::checkForPiecewiseFunctions(), CSBMLExporter::checkForUnsupportedFunctionCalls(), CFunctionAnalyzer::checkKineticFunction(), CMathExpression::CMathExpression(), CExpression::compile(), CMathEvent::CTrigger::compile(), CMathExpression::convertToInitialExpression(), CMathExpression::copy(), CMathContainer::copyBranch(), SBMLImporter::createCFunctionFromFunctionTree(), CFunction::createCopy(), SBMLImporter::createCReactionFromReaction(), CMathContainer::createDiscontinuityEvents(), CSBMLExporter::createEvent(), SBMLImporter::createExpressionFromFunction(), CSBMLExporter::createInitialAssignment(), CKinFunction::createParameters(), CSBMLExporter::createRule(), CDerive::deriveBranch(), CFunctionAnalyzer::evaluateNode(), CSBMLExporter::exportEventAssignments(), CODEExporter::exportKineticFunction(), CODEExporterC::exportKineticFunctionGroup(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportModelValuesExpressions(), CODEExporter::exportSingleFunction(), CODEExporterC::exportSingleFunction(), SBMLImporter::findCorrespondingFunction(), SBMLImporter::findFunctionCalls(), CODEExporter::findFunctionsCalls(), CSBMLExporter::findUsedFunctions(), CExpression::getBerkeleyMadonnaString(), CExpression::getCCodeString(), CODEExporterBM::getDisplayExpressionString(), CODEExporterC::getDisplayExpressionString(), CODEExporterXPPAUT::getDisplayExpressionString(), CODEExporterBM::getDisplayFunctionString(), CODEExporterXPPAUT::getDisplayFunctionString(), CUnitValidator::getUnit(), CUnitValidator::getUnits(), CExpression::getXPPString(), SBMLImporter::importEvent(), SBMLImporter::importInitialAssignments(), SBMLImporter::importRuleForModelEntity(), CMathDerive::initOneVar(), SBMLImporter::isConstantFlux(), CSBMLExporter::isEventAssignmentSBMLCompatible(), CSBMLExporter::isEventSBMLCompatible(), CSBMLExporter::isExpressionSBMLCompatible(), SBMLImporter::isMassAction(), SBMLImporter::isMassActionFunction(), CSBMLExporter::isModelSBMLCompatible(), CMathObject::isPrerequisiteForContext(), CODEExporter::modifyTreeForMassAction(), CSBMLExporter::orderRules(), CModel::prepareElasticity(), CODEExporterC::preprocess(), CMathExpression::relocate(), SBMLImporter::removeUnusedFunctions(), CODEExporterC::setExportNameOfFunction(), CReaction::setFunctionFromExpressionTree(), CExpression::setInfix(), CUnitValidator::setUnits(), CFunction::splitFunction(), CExpression::updateInfix(), CModelParameter::updateModel(), CUnitValidator::validate(), CFunction::writeMathML(), and CExpression::writeMathML().

getRoot() [2/2]

const CEvaluationNode * CEvaluationTree::getRoot

(

)

const

Returns the root node of the tree.

References mpRootNode.

getType()

const CEvaluationTree::Type & CEvaluationTree::getType

(

)

const

Retrieves the type of the function

Returns

const CEvaluationTree::Type & type

References mType.

Referenced by CMathExpression::CMathExpression(), copy(), SBMLImporter::createCFunctionFromFunctionDefinition(), SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createKineticExpression(), CKinFunction::createParameters(), CUnitValidator::CUnitValidator(), CODEExporter::exportKineticFunction(), CODEExporterC::exportKineticFunctionGroup(), CODEExporterC::exportSingleFunction(), CODEExporter::findFunctionsCalls(), CReactionInterface::getFunction(), SBMLImporter::isMassAction(), CODEExporterC::KineticFunction2ODEmember(), CFunctionDB::load(), CODEExporter::modifyTreeForMassAction(), CODEExporterC::preprocess(), SBMLImporter::restoreFunctionDB(), CCopasiXML::saveFunctionList(), CODEExporterC::setExportNameOfFunction(), and CUnitValidator::validate().

getVariableIndex()

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

virtual

Retrieve the index to the value of the named variable.

Parameters

const

std::string & name

Returns

size_t

Reimplemented in CFunction.

References C_INVALID_INDEX.

Referenced by CEvaluationNodeVariable::compile().

getVariableValue()

const C_FLOAT64 & CEvaluationTree::getVariableValue ( const size_t &  index ) const

virtual

Retrieve the value of the indexed variable

Parameters

const

size_t & index

Returns

const C_FLOAT64 & variableValue

Reimplemented in CFunction.

References C_FLOAT64.

Referenced by CEvaluationNodeVariable::calculate().

hasCircularDependency()

bool CEvaluationTree::hasCircularDependency

(

)

const

Check whether the the tree has circular dependencies.

Returns

bool hasCircularDependency

References calls().

Referenced by parse().

hasDiscontinuity()

bool CEvaluationTree::hasDiscontinuity

(

)

const

Check whether tree may introduce discontinuities.

Returns

bool hasDiscontinuity

References CEvaluationNode::CALL, CEvaluationNode::CEIL, CEvaluationNode::CHOICE, CEvaluationNode::EXPRESSION, CEvaluationNode::FLOOR, CEvaluationNode::FUNCTION, CEvaluationNodeCall::getCalledTree(), hasDiscontinuity(), CEvaluationNode::IF, CEvaluationNode::MODULUS, mpNodeList, CEvaluationNode::OPERATOR, and CEvaluationNode::REMAINDER.

Referenced by hasDiscontinuity().

initObjects()

void CEvaluationTree::initObjects ( )

private

Initialize the contained CDataObjects

References CDataContainer::addObjectReference(), and mValue.

Referenced by CEvaluationTree().

isBoolean()

bool CEvaluationTree::isBoolean

(

)

const

Check whether this function evaluates to a boolean value.

Returns

bool isBoolean

References CEvaluationNode::isBoolean(), and mpRootNode.

Referenced by CEvaluationNodeCall::compile(), CEvaluationNodeCall::isBoolean(), CMathDelay::modifyMathObject(), CExpression::setInfix(), and CExpression::setIsBoolean().

mapObjectNodes()

bool CEvaluationTree::mapObjectNodes	(	const CDataContainer *	pSrc,
		const CDataContainer *	pTarget
	)

Map object nodes which are children of the src container to children of the target container

Parameters

const	CDataContainer * pSrc
const	CDataContainer * pTarget

Returns

bool success;

References buildCalculationSequence(), CEvaluationNode::CALL, CEvaluationNode::CN, CEvaluationNode::EXPRESSION, CEvaluationNode::FUNCTION, CEvaluationNodeCall::getCalledTree(), CDataObject::getCN(), CEvaluationNodeObject::getObjectInterfacePtr(), CDataObject::getPrerequisites(), CEvaluationNode::getValuePointer(), CEvaluationNodeObject::mapObject(), mapObjectNodes(), mCalculationSequence, mpNodeList, CDataObject::mPrerequisits, mpRootNode, mpRootValue, mValue, CEvaluationNode::OBJECT, and CVector< CType >::resize().

Referenced by COptProblem::initialize(), and mapObjectNodes().

operator==()

bool CEvaluationTree::operator==

(

const CEvaluationTree &

rhs

)

const

Comparison operator

Parameters

const

CEvaluationTree & rhs

Returns

bool equal

References mInfix, and mType.

parse()

CIssue CEvaluationTree::parse ( )

protected

Parse the description

Returns

CIssue issue

References CValidity::add(), CFlags< Enum >::All, clearNodes(), CCopasiMessage::ERROR, CIssue::Error, CIssue::ExpressionInvalid, CEvaluationParserBase::getErrorPosition(), CEvaluationParserBase::getNodeList(), CEvaluationParserBase::getRootNode(), CEvaluationNode::getValuePointer(), hasCircularDependency(), CIssue::HasCircularDependency, MassAction, MCFunction, mErrorPosition, mInfix, mpNodeList, mpRootNode, mpRootValue, mType, CObjectInterface::mValidity, mValue, CValidity::remove(), CEvaluationNode::setTree(), CIssue::Success, and CEvaluationParserBase::yyparse().

Referenced by setInfix().

setInfix()

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

virtual

Set the infix description of the tree and compile it.

Parameters

const

std::string & infix

Returns

CIssue issue

Reimplemented in CExpression, CMassAction, and CFunction.

References CValidity::clear(), CIssue::Error, mInfix, CObjectInterface::mValidity, parse(), and CIssue::Success.

Referenced by CEvaluationTree(), CMathObject::compileDependentMass(), CMathObject::compileParticleFlux(), CMathObject::compilePropensity(), CMathObject::compileReactionNoise(), CMathObject::compileTotalMass(), CMathObject::compileTransitionTime(), CMathContainer::createDelays(), CSBMLExporter::createEvent(), CMathObject::createExtensiveReactionNoiseExpression(), CMathObject::createExtensiveReactionRateExpression(), CMathObject::createExtensiveValueExpression(), CMathObject::createIntensiveRateExpression(), CMathObject::createIntensiveValueExpression(), CSBMLExporter::createRule(), CSBMLExporter::exportEventAssignments(), CFunction::setInfix(), and CExpression::setInfix().

setRoot()

bool CEvaluationTree::setRoot ( CEvaluationNode *  pRootNode )

virtual

Sets the root node of the tree.

Parameters

CEvaluationNode*

root node of the tree

Returns

bool success

Reimplemented in CMathExpression.

References clearNodes(), CCopasiNode< _Data >::getParent(), mpRootNode, CEvaluationNode::setTree(), and updateTree().

Referenced by CFunction::createCopy(), SBMLImporter::createCReactionFromReaction(), SBMLImporter::createExpressionFromFunction(), SBMLImporter::importEvent(), SBMLImporter::importInitialAssignments(), SBMLImporter::importRuleForModelEntity(), CModel::prepareElasticity(), CReaction::setFunctionFromExpressionTree(), CMathExpression::setRoot(), setTree(), and CFunction::splitFunction().

setTree()

bool CEvaluationTree::setTree	(	const ASTNode &	pRootNode,
		bool	isFunction
	)

Sets the complete tree from an SBML ASTNode.

Parameters

const	ASTNode& root node of the tree
bool	isFunction

Returns

bool success

References CCopasiNode< _Data >::addChild(), CEvaluationNode::Boolean, CNodeContextIterator< Node, Context >::end(), CIssue::Error, fromAST(), CCopasiNode< _Data >::getSibling(), CEvaluationNode::IF, mpRootNode, CNodeContextIterator< Node, Context >::next(), CEvaluationNode::Number, setRoot(), CEvaluationNode::setValueType(), CEvaluationNode::Unknown, updateTree(), and CIssue::ValueTypeMismatch.

Referenced by SBMLImporter::applyStoichiometricExpressions(), SBMLImporter::createCFunctionFromFunctionTree(), SBMLImporter::importEvent(), SBMLImporter::importInitialAssignments(), and SBMLImporter::importRuleForModelEntity().

setType()

void CEvaluationTree::setType ( const CEvaluationTree::Type &  type )

protected

Set the type of the function

Parameters

const

CEvaluationTree::Type & type

References mType.

Referenced by create(), and CFunction::load().

size()

size_t CEvaluationTree::size

(

)

const

Retrieve the number of node evaluations required to computate the value of the tree.

Returns

size_t size

References mCalculationSequence, and CVectorCore< CType >::size().

Referenced by SBMLImporter::findCorrespondingFunction(), and CModelMerging::mergeMetabolites().

toAST()

ASTNode * CEvaluationTree::toAST ( const CDataModel *  pDataModel ) const

virtual

Converts a CEvaluationTree to an ASTNode based tree.

Returns

ASTNode* root node of the tree.

References mpRootNode, and CEvaluationNode::toAST().

toData()

CData CEvaluationTree::toData ( ) const

virtual

Retrieve the data describing the object

Returns

CData data

Reimplemented from CDataContainer.

Reimplemented in CFunction.

References CDataContainer::toData().

Referenced by CFunction::toData().

updateTree()

CIssue CEvaluationTree::updateTree

(

)

Updates the infix and the nodeList

References CValidity::add(), CFlags< Enum >::All, CEvaluationNode::buildInfix(), clearNodes(), CIssue::Error, CIssue::ExpressionInvalid, CEvaluationNode::getValuePointer(), CIssue::HasCircularDependency, mInfix, mpNodeList, mpRootNode, mpRootValue, CObjectInterface::mValidity, mValue, CValidity::remove(), and CIssue::StructureInvalid.

Referenced by CMathExpression::compile(), CModelAdd::copyDelayExpression(), CModelAdd::copyEventAssignmentExpression(), CModelAdd::copyExpression(), CModelAdd::copyInitialExpression(), CModelAdd::copyTriggerExpression(), CExpression::createInitialExpression(), CModelMerging::mergeInExpression(), setRoot(), and setTree().

Member Data Documentation

mCalculationSequence

CVector< CEvaluationNode * > CEvaluationTree::mCalculationSequence

protected

A vector of nodes which need to be calculated in sequence

Referenced by buildCalculationSequence(), calculate(), CMathExpression::compile(), compileNodes(), mapObjectNodes(), and size().

mErrorPosition

std::string::size_type CEvaluationTree::mErrorPosition

private

The error position in case the compilation fails. std::string::npos indicates no error.

Referenced by compileNodes(), getErrorPosition(), and parse().

mInfix

std::string CEvaluationTree::mInfix

protected

The key of the function The infix representation of the expression

Referenced by CEvaluationTree(), CMathExpression::compile(), CExpression::compile(), compileNodes(), CMathExpression::convertToInitialExpression(), getInfix(), CFunction::initVariables(), operator==(), parse(), CMathExpression::relocate(), setInfix(), CFunction::setInfix(), CExpression::updateInfix(), and updateTree().

mpNodeList

std::vector< CEvaluationNode * >* CEvaluationTree::mpNodeList

protected

A vector of nodes containing the result of parse.

Referenced by calls(), clearNodes(), CMathExpression::compile(), compileNodes(), containsCN(), CMathExpression::convertToInitialExpression(), CKinFunction::createParameters(), getNodeList(), hasDiscontinuity(), CFunction::initVariables(), mapObjectNodes(), parse(), CFunction::setInfix(), CExpression::setInfix(), and updateTree().

mpRootNode

CEvaluationNode* CEvaluationTree::mpRootNode

private

The root node of the tree.

Referenced by buildCalculationSequence(), calculate(), clearNodes(), compileNodes(), getRoot(), isBoolean(), mapObjectNodes(), parse(), setRoot(), setTree(), toAST(), and updateTree().

mpRootValue

const C_FLOAT64* CEvaluationTree::mpRootValue

protected

Referenced by calculate(), clearNodes(), compileNodes(), CMathExpression::convertToInitialExpression(), mapObjectNodes(), parse(), and updateTree().

mType

CEvaluationTree::Type CEvaluationTree::mType

protected

The type of the function

Referenced by getType(), CFunction::isReadOnly(), operator==(), parse(), and setType().

mValue

C_FLOAT64 CEvaluationTree::mValue

protected

The last computed value of the tree;

Referenced by calculate(), CExpression::calcValue(), CFunction::calcValue(), CMassAction::calcValue(), clearNodes(), compileNodes(), initObjects(), mapObjectNodes(), parse(), updateTree(), and CMathExpression::value().

TypeName

const std::string CEvaluationTree::TypeName

static

Initial value:

=
{
  "userdefined",
  "predefined",
  "predefined",
  "userdefined",
  "userdefined",
  "userdefined",
  "internal",
  ""
}

The string representation of valid types of a function

XMLType

const char * CEvaluationTree::XMLType

static

Initial value:

=
{
  "Function",
  "MassAction",
  "PreDefined",
  "UserDefined",
  "Expression",
  "Boolean",
  "MathExpression",
  NULL
}

The string representation of valid types of a function

Referenced by FunctionHandler::processStart(), and CCopasiXML::saveFunctionList().

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

• CEvaluationTree.h
• CEvaluationTree.cpp