CMassAction Class Reference

#include <CMassAction.h>

Inheritance diagram for CMassAction:

Public Member Functions
virtual const C_FLOAT64 &	calcValue (const CCallParameters< C_FLOAT64 > &callParameters)
	CMassAction (const CFunction &src, const CDataContainer *pParent)
	CMassAction (const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT)
	CMassAction (const TriLogic &reversible, const CDataContainer *pParent=NO_PARENT)
virtual CIssue	compile ()
virtual CIssue	setInfix (const std::string &infix)
virtual std::string	writeMathML (const std::vector< std::vector< std::string > > &variables, bool expand=true, bool fullExpand=true) const
	~CMassAction ()
Public Member Functions inherited from CFunction
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)
	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
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 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)
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 Attributes
static const char *	Infix []
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
	CMassAction (const CMassAction &src)
Protected Member Functions inherited from CFunction
	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)

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 Member Functions inherited from CFunction
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 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

CMassAction

Created for Copasi by Stefan Hoops (C) Stefan Hoops 2001

Constructor & Destructor Documentation

CMassAction() [1/4]

CMassAction::CMassAction ( const CMassAction &  src )

protected

CMassAction() [2/4]

CMassAction::CMassAction	(	const std::string &	name = "NoName",
		const CDataContainer *	pParent = NO_PARENT
	)

Default constructor

Parameters

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

CMassAction() [3/4]

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

Copy constructor

Parameters

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

CMassAction() [4/4]

CMassAction::CMassAction	(	const TriLogic &	reversible,
		const CDataContainer *	pParent = NO_PARENT
	)

Specified constructor

Parameters

const

CDataContainer * pParent (default: NULL)

References CONSTRUCTOR_TRACE, CCopasiMessage::ERROR, Infix, MCMassAction, setInfix(), TriFalse, and TriTrue.

~CMassAction()

CMassAction::~CMassAction

(

)

Destructor

References DESTRUCTOR_TRACE.

Member Function Documentation

calcValue()

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

virtual

Calculates the value of the function

Parameters

const

CCallParameters<C_FLOAT64> & callParameters

Returns

const C_FLOAT64 & result

Reimplemented from CFunction.

References CCallParameters< Type >::begin(), C_FLOAT64, CCallParameters< Type >::end(), CFunction::isReversible(), CEvaluationTree::mValue, and TriFalse.

compile()

CIssue CMassAction::compile ( )

virtual

Compile the evaluation tree.

Reimplemented from CEvaluationTree.

References CValidity::getFirstWorstIssue(), and CObjectInterface::mValidity.

setInfix()

CIssue CMassAction::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 from CFunction.

References CFunctionParameters::add(), CValidity::add(), CFunctionParameters::cleanup(), CValidity::clear(), CIssue::Error, CIssue::ExpressionInvalid, CFunctionParameter::FLOAT64, CValidity::getFirstWorstIssue(), CFunction::getVariables(), CFunction::isReversible(), CObjectInterface::mValidity, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, CFunction::setInfix(), CFunction::setReversible(), CFunctionParameter::SUBSTRATE, TriFalse, TriTrue, and CFunctionParameter::VFLOAT64.

Referenced by CMassAction().

writeMathML()

std::string CMassAction::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 from CFunction.

References CFunction::isReversible(), and TriTrue.

Member Data Documentation

Infix

const char * CMassAction::Infix

static

Initial value:

=
{"k1*PRODUCT<substrate_i>-k2*PRODUCT<product_j>", "k1*PRODUCT<substrate_i>"}

CMassAction

Created for COPASI by Stefan Hoops (C) Stefan Hoops 2001

Referenced by CMassAction().

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

• CMassAction.h
• CMassAction.cpp