The class for handling a chemical kinetic function. More...

#include <CFunction.h>

Inheritance diagram for CFunction:

Public Member Functions
bool	addVariable (const std::string &name, CFunctionParameter::Role usage=CFunctionParameter::Role::VARIABLE, const CFunctionParameter::DataType &type=CFunctionParameter::DataType::FLOAT64)

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

virtual const C_FLOAT64 &	calcValue (const CCallParameters< C_FLOAT64 > &callParameters)

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

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

CFunction *	createCopy () const

void	createListOfParametersForMathML (std::vector< std::vector< std::string > > &env)

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

const std::string &	getKey () const

const std::string &	getSBMLId () const

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

CFunctionParameters &	getVariables ()

const CFunctionParameters &	getVariables () const

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

virtual bool	isReadOnly () const

const TriLogic &	isReversible () const

bool	isSuitable (const size_t noSubstrates, const size_t noProducts, const TriLogic reversible)

virtual void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)

bool	operator== (const CFunction &rhs) const

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

void	setReversible (const TriLogic &reversible)

void	setSBMLId (const std::string &id)

std::pair< CFunction , CFunction >	splitFunction (const CEvaluationNode *node, const std::string &name1, const std::string &name2) const

virtual CData	toData () const

virtual std::string	writeMathML (const std::vector< std::vector< std::string > > &variables, bool expand=true, bool fullExpand=true) const

virtual void	writeMathML (std::ostream &out, size_t l=0) const

virtual	~CFunction ()

Public Member Functions inherited from CEvaluationTree
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

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

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 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

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 ()

Public Member Functions inherited from CAnnotation
bool	addUnsupportedAnnotation (const std::string &name, const std::string &xml)

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

	CAnnotation ()

	CAnnotation (const CAnnotation &src)

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

const std::string &	getMiriamAnnotation () const

const std::string &	getNotes () const

UnsupportedAnnotation &	getUnsupportedAnnotations ()

const UnsupportedAnnotation &	getUnsupportedAnnotations () const

void	initMiriamAnnotation (const std::string &newId)

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)

CData	toData () const

virtual	~CAnnotation ()

Static Public Member Functions
static bool	completeFunctionList (std::vector< const CFunction * > &list, const size_t &added=0)

static CFunction *	fromData (const CData &data, CUndoObjectInterface *pParent)

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 *)

Static Public Member Functions inherited from CAnnotation
static CMIRIAMInfo *	allocateMiriamInfo (CDataContainer *pParent)

static CAnnotation *	castObject (CDataObject *pObject)

static const CAnnotation *	castObject (const CDataObject *pObject)

static void	freeMiriamInfo (CDataContainer *pParent)

Protected Member Functions
	CFunction (const CFunction &src)

CIssue	initVariables ()

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)

Private Attributes
CCallParameters< C_FLOAT64 >::const_iterator	mCallParametersBegin

TriLogic	mReversible

std::string	mSBMLId

CFunctionParameters	mVariables

Friends
std::ostream &	operator<< (std::ostream &os, const CFunction &f)

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

Public Types inherited from CAnnotation
typedef std::map< std::string, std::string >	UnsupportedAnnotation

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 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

Protected Attributes inherited from CAnnotation
std::string	mKey

Detailed Description

The class for handling a chemical kinetic function.

This class is designed to handle all about a given chemical kinetic function from editing and displaying (with help of MathML) the function to calculating the function value.

Constructor & Destructor Documentation

◆ CFunction() [1/3]

CFunction::CFunction ( const CFunction & src )

protected

Referenced by createCopy(), and splitFunction().

◆ CFunction() [2/3]

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

Default constructor

Parameters

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

References CKeyFactory::add(), CRootContainer::getKeyFactory(), CAnnotation::initMiriamAnnotation(), and CAnnotation::mKey.

◆ CFunction() [3/3]

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

Copy constructor

Parameters

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

References CKeyFactory::add(), CEvaluationTree::compile(), CRootContainer::getKeyFactory(), CAnnotation::getMiriamAnnotation(), CAnnotation::mKey, and CAnnotation::setMiriamAnnotation().

◆ ~CFunction()

CFunction::~CFunction ( )

virtual

Destructor

References CRootContainer::getKeyFactory(), CAnnotation::mKey, and CKeyFactory::remove().

Member Function Documentation

◆ addVariable()

bool CFunction::addVariable	(	const std::string &	name,
		CFunctionParameter::Role	usage = `CFunctionParameter::Role::VARIABLE`,
		const CFunctionParameter::DataType &	type = `CFunctionParameter::DataType::FLOAT64`
	)

Function to add the description of a variable.

Parameters

const	string & name
const	string & usage (Default: VARIABLE)
const	CFunctionParameters::DataType & type (Default: value)

Returns: bool success

References CFunctionParameters::add(), and mVariables.

Referenced by SBMLImporter::createCFunctionFromFunctionTree(), and CReaction::setFunctionFromExpressionTree().

◆ applyData()

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

virtual

Apply the provided data to the object

Parameters

const CData & data

Returns: bool success

Reimplemented from CEvaluationTree.

References CEvaluationTree::applyData(), and CAnnotation::applyData().

◆ calcValue()

const C_FLOAT64 & CFunction::calcValue ( const CCallParameters< C_FLOAT64 > & callParameters )

virtual

Function to calculate the value of the function

Parameters

const CCallParameters<C_FLOAT64> & callParameters

Returns: const C_FLOAT64 & result

Reimplemented in CMassAction.

References CCallParameters< Type >::begin(), CEvaluationTree::calculate(), mCallParametersBegin, and CEvaluationTree::mValue.

Referenced by CEvaluationNodeCall::calculate().

◆ completeFunctionList()

bool CFunction::completeFunctionList	(	std::vector< const CFunction * > &	list,
		const size_t &	added = `0`
	)

static

Complete the list of evaluation tree such that all called trees are includes.

Parameters

std::vector<	const CFunction * > & list
const	size_t & added (Default: list.size())

Returns: bool success

References C_INVALID_INDEX, CEvaluationNode::CALL, CRootContainer::getFunctionList(), CDataVectorN< CType >::getIndex(), CEvaluationTree::getNodeList(), and CFunctionDB::loadedFunctions().

Referenced by CFunctionDB::getUsedFunctions().

◆ createCopy()

CFunction * CFunction::createCopy ( ) const

Function to duplicate itself

References CFunction(), CEvaluationTree::getRoot(), mReversible, and CEvaluationTree::setRoot().

◆ createListOfParametersForMathML()

void CFunction::createListOfParametersForMathML ( std::vector< std::vector< std::string > > & env )

Function to create a list of the names of the function parameters in MathML format. This list can be passed as the env argument to the writeMathML() method.

Parameters

std::vector<std::vector<std::string> > & env

References CMathMl::fixName(), CDataObject::getObjectName(), getVariables(), and CFunctionParameters::size().

◆ createUndoData()

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

virtual

Create the undo data which represents the changes recording the differences between the provided oldData and the current data.

Parameters

CUndoData	& undoData
const	CUndoData::Type & type
const	CData & oldData (default: empty data)
const	CCore::Framework & framework (default: CCore::Framework::ParticleNumbers)

Returns: CUndoData undoData

Reimplemented from CDataContainer.

References CUndoData::CHANGE, CAnnotation::createUndoData(), and CDataContainer::createUndoData().

◆ fromData()

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

static

Static method to create a CDataObject based on the provided data

Parameters

const CData & data

Returns: CFunction * pDataObject

References CEvaluationTree::fromData(), and pdelete.

◆ getKey()

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

virtual

Retrieves the key of the EvaluationTree

Returns: const std::string & key

Reimplemented from CAnnotation.

References CAnnotation::getKey().

Referenced by CODEExporter::exportExpression(), CODEExporterC::exportSingleFunction(), SBMLImporter::importMIRIAM(), CODEExporterC::KineticFunction2ODEmember(), CODEExporterC::preprocess(), FunctionHandler::processEnd(), CCopasiXML::saveFunctionList(), CCopasiXML::saveModel(), and CODEExporterC::setExportNameOfFunction().

◆ getSBMLId()

const std::string & CFunction::getSBMLId ( ) const

Returns a reference to the SBML Id.

References mSBMLId.

Referenced by CSBMLExporter::collectIds(), SBMLImporter::createCFunctionFromFunctionDefinition(), SBMLImporter::createCModelFromSBMLDocument(), CCopasiXML::saveFunctionList(), CSBMLExporter::setFunctionSBMLIds(), and CEvaluationNodeCall::toAST().

◆ getVariableIndex()

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

virtual

Function to retrieve the index to the value of the named variable.

Parameters

const std::string & name

Returns: size_t index

Reimplemented from CEvaluationTree.

References CFunctionParameters::findParameterByName(), and mVariables.

Referenced by CODEExporter::exportKineticFunction(), and CODEExporter::exportSingleFunction().

◆ getVariables() [1/2]

CFunctionParameters & CFunction::getVariables ( )

Function to retrive the definition of the parameters

Returns: CFunctionParameters & variables

References mVariables.

Referenced by CMathEvent::CTrigger::allocate(), SBMLImporter::areEqualFunctions(), CFunctionAnalyzer::checkKineticFunction(), CEvaluationNodeCall::compile(), SBMLImporter::createCReactionFromReaction(), SBMLImporter::createExpressionFromFunction(), CReaction::createFunctionFromExpression(), CSBMLExporter::createKineticExpression(), createListOfParametersForMathML(), CKinFunction::createParameters(), CReaction::createUndoData(), SBMLImporter::doMapping(), CFunctionAnalyzer::evaluateNode(), CODEExporter::exportKineticFunction(), CODEExporterC::exportSingleFunction(), SBMLImporter::findCorrespondingFunction(), CReactionInterface::getDeletedParameters(), CReactionInterface::initMapping(), FunctionHandler::processEnd(), ParameterDescriptionHandler::processStart(), CCopasiXML::saveFunctionList(), CCopasiXML::saveModel(), SBMLImporter::setCorrectUsage(), CReaction::setFunction(), CReaction::setFunctionFromExpressionTree(), CMassAction::setInfix(), CReaction::setParameterValue(), splitFunction(), CReaction::toData(), CReactionInterface::writeBackToReaction(), and writeMathML().

◆ getVariables() [2/2]

const CFunctionParameters & CFunction::getVariables ( ) const

Function to retrive the definition of the parameters

Returns: const CFunctionParameters & variables

References mVariables.

◆ getVariableValue()

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

virtual

Function to retrieve the value of the indexed variable.

Note this function is only usable during calcValue, since the values of the call parameters are only defined during that time.

Parameters

const size_t & index

Returns: const C_FLOAT64 & variableValue

Reimplemented from CEvaluationTree.

References mCallParametersBegin.

◆ initVariables()

CIssue CFunction::initVariables ( )

protected

Function to initialize the parameters

Returns: CIssue issue;

References CFunctionParameters::add(), C_INVALID_INDEX, CIssue::Error, CFunctionParameters::findParameterByName(), CFunctionParameter::FLOAT64, CDataObject::getObjectName(), CEvaluationTree::mInfix, CEvaluationTree::mpNodeList, mVariables, CFunctionParameters::remove(), CFunctionParameters::size(), CIssue::StructureInvalid, CIssue::Success, CEvaluationNode::VARIABLE, and CFunctionParameter::VARIABLE.

Referenced by setInfix(), and splitFunction().

◆ isReadOnly()

bool CFunction::isReadOnly ( ) const

virtual

Check whether a function is read only

Returns: bool isReadOnly

References CEvaluationTree::MassAction, CEvaluationTree::mType, and CEvaluationTree::PreDefined.

◆ isReversible()

const TriLogic & CFunction::isReversible ( ) const

Function to retrieve whether it is reversible.

References mReversible.

Referenced by CMassAction::calcValue(), CFunctionAnalyzer::checkKineticFunction(), CModelAnalyzer::checkReaction(), CSBMLExporter::createKineticExpression(), CSBMLExporter::createKineticLaw(), CODEExporter::exportKineticFunction(), CReactionInterface::getFunction(), isSuitable(), CODEExporterC::KineticFunction2ODEmember(), CCopasiXML::saveFunctionList(), CReaction::setFunctionFromExpressionTree(), CMassAction::setInfix(), and CMassAction::writeMathML().

◆ isSuitable()

bool CFunction::isSuitable	(	const size_t	noSubstrates,
		const size_t	noProducts,
		const TriLogic	reversible
	)

Function to determine whether it is suitable for a reaction with the given number of substrates and products and reversibility

References C_INVALID_INDEX, CFunctionParameters::getNumberOfParametersByUsage(), isReversible(), CFunctionParameters::isVector(), mVariables, CFunctionParameter::PRODUCT, CFunctionParameter::SUBSTRATE, TriTrue, TriUnspecified, and CFunctionParameter::VARIABLE.

Referenced by SBMLImporter::createCReactionFromReaction(), and CFunctionDB::suitableFunctions().

◆ load()

void CFunction::load	(	CReadConfig &	configBuffer,
		CReadConfig::Mode	mode = `CReadConfig::SEARCH`
	)

virtual

Function to load an object with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters

CReadConfig &	configBuffer
CReadConfig::Mode	mode (default: CReadConfig::SEARCH)

Returns: Fail

References C_INT32, fatalError, CReadConfig::getVariable(), mReversible, CReadConfig::SEARCH, setInfix(), CDataObject::setObjectName(), CEvaluationTree::setType(), and CEvaluationTree::UserDefined.

Referenced by CFunctionDB::load().

◆ operator==()

bool CFunction::operator== ( const CFunction & rhs ) const

Comparison operator

Parameters

const CFunction & rhs

Returns: bool equal

References mVariables.

◆ setInfix()

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

virtual

Function to set the infix description of the tree and compile it.

Parameters

const std::string & infix

Returns: CIssue issue

Reimplemented from CEvaluationTree.

Reimplemented in CMassAction.

References CValidity::add(), CEvaluationNode::AVOGADRO, CEvaluationNode::CALL, CEvaluationTree::compileNodes(), CEvaluationNode::DELAY, CIssue::Error, CEvaluationNode::EXPRESSION, CRootContainer::functionDefinitionChanged(), initVariables(), CEvaluationTree::mInfix, CEvaluationTree::mpNodeList, CObjectInterface::mValidity, CEvaluationNode::OBJECT, CEvaluationTree::setInfix(), and CIssue::StructureInvalid.

Referenced by CMathEvent::CTrigger::allocate(), CReaction::createFunctionFromExpression(), CKinFunction::createParameters(), CReactionInterface::getFunction(), SBMLImporter::importFunctionDefinitions(), CRootContainer::initializeChildren(), load(), FunctionHandler::processEnd(), and CMassAction::setInfix().

◆ setReversible()

void CFunction::setReversible ( const TriLogic & reversible )

Function to set whether it is reversible.

References mReversible.

Referenced by SBMLImporter::createCReactionFromReaction(), FunctionHandler::processStart(), CReaction::setFunctionFromExpressionTree(), and CMassAction::setInfix().

◆ setSBMLId()

void CFunction::setSBMLId ( const std::string & id )

Sets the SBMLId.

References mSBMLId.

Referenced by SBMLImporter::createCFunctionFromFunctionDefinition(), SBMLImporter::createCModelFromSBMLDocument(), SBMLMapHandler::processStart(), and CSBMLExporter::setFunctionSBMLIds().

◆ splitFunction()

std::pair< CFunction , CFunction > CFunction::splitFunction	(	const CEvaluationNode *	node,
		const std::string &	name1,
		const std::string &	name2
	)		const

Function to split

Parameters

const	CEvaluationNode* node
const	std::string & name1
const	std::string & name2

References CFunction(), CEvaluationTree::compile(), CFunctionAnalyzer::constructCallParameters(), CEvaluationNode::findTopMinus(), CEvaluationTree::getRoot(), getVariables(), initVariables(), CFunctionParameter::MODIFIER, mReversible, mVariables, CFunctionParameter::PRODUCT, CDataObject::setObjectName(), CEvaluationTree::setRoot(), CFunctionParameters::size(), CEvaluationNode::splitBranch(), CFunctionParameter::SUBSTRATE, TriFalse, and TriTrue.

Referenced by CFunctionAnalyzer::checkKineticFunction(), and CModel::convert2NonReversible().

◆ toData()

CData CFunction::toData ( ) const

virtual

Retrieve the data describing the object

Returns: CData data

Reimplemented from CEvaluationTree.

References CData::appendData(), CEvaluationTree::toData(), and CAnnotation::toData().

◆ writeMathML() [1/2]

std::string CFunction::writeMathML	(	const std::vector< std::vector< std::string > > &	variables,
		bool	expand = `true`,
		bool	fullExpand = `true`
	)		const

virtual

Function to write the mathematical formula in format of MathML.

Parameters

std::ostream	& out
const	std::vector< std::vector< std::string > > & variables
bool	expand = true
bool	fullExpand

Returns: std::string

Reimplemented in CMassAction.

References CEvaluationNode::buildMMLString(), CMathMl::fixName(), CDataObject::getObjectName(), and CEvaluationTree::getRoot().

◆ writeMathML() [2/2]

void CFunction::writeMathML	(	std::ostream &	out,
		size_t	l = `0`
	)		const

virtual

This is an overloaded member function, provided for convenience. It behaves essentially like the above function.

Parameters

std::ostream	& out
size_t	l

References CMathMl::fixName(), CDataObject::getObjectName(), getVariables(), CFunctionParameters::size(), and SPC.

Referenced by CEvaluationNodeCall::getMMLString(), and CMMLOutput::writeRHS().

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const CFunction &	f
	)

friend

Insert operator

Member Data Documentation

◆ mCallParametersBegin

CCallParameters< C_FLOAT64 >::const_iterator CFunction::mCallParametersBegin

private

A pointer to the call parameters during calculation.

Referenced by calcValue(), and getVariableValue().

◆ mReversible

TriLogic CFunction::mReversible

private

Whether the function is reversible

Referenced by createCopy(), isReversible(), load(), setReversible(), and splitFunction().

◆ mSBMLId

std::string CFunction::mSBMLId

private

The id of the corresponding function 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.

Referenced by getSBMLId(), and setSBMLId().

◆ mVariables

CFunctionParameters CFunction::mVariables

private

The description of the variables of the function. It describes which variables need to be passed to the function for evaluation and its eventual type.

Referenced by addVariable(), getVariableIndex(), getVariables(), initVariables(), isSuitable(), operator==(), and splitFunction().

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CFunction() [1/3]

◆ CFunction() [2/3]

◆ CFunction() [3/3]

◆ ~CFunction()

Member Function Documentation

◆ addVariable()

◆ applyData()

◆ calcValue()

◆ completeFunctionList()

◆ createCopy()

◆ createListOfParametersForMathML()

◆ createUndoData()

◆ fromData()

◆ getKey()

◆ getSBMLId()

◆ getVariableIndex()

◆ getVariables() [1/2]

◆ getVariables() [2/2]

◆ getVariableValue()

◆ initVariables()

◆ isReadOnly()

◆ isReversible()

◆ isSuitable()

◆ load()

◆ operator==()

◆ setInfix()

◆ setReversible()

◆ setSBMLId()

◆ splitFunction()

◆ toData()

◆ writeMathML() [1/2]

◆ writeMathML() [2/2]

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ mCallParametersBegin

◆ mReversible

◆ mSBMLId

◆ mVariables