#include <CLReactionGlyph.h>

Inheritance diagram for CLMetabReferenceGlyph:

Public Types
enum	Role { UNDEFINED , SUBSTRATE , PRODUCT , SIDESUBSTRATE , SIDEPRODUCT , MODIFIER , ACTIVATOR , INHIBITOR }

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)

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

	CLMetabReferenceGlyph (const SpeciesReferenceGlyph &sbml, const std::map< std::string, std::string > &modelmap, std::map< std::string, std::string > &layoutmap, const CDataContainer *pParent=NO_PARENT)

	CLMetabReferenceGlyph (const std::string &name="MetabReferenceGlyph", const CDataContainer *pParent=NO_PARENT)

virtual CLGraphicalObject *	clone () const

virtual void	exportToSBML (SpeciesReferenceGlyph g, const std::map< const CDataObject , SBase * > &copasimodelmap, std::map< std::string, const SBase * > &sbmlIDs, const std::map< const CLBase , const SBase > &layoutmap) const

Role	getFunctionalRole () const

CLMetabGlyph *	getMetabGlyph () const

const std::string &	getMetabGlyphKey () const

Role	getRole () const

const std::string &	getRoleDisplayName () const

CLMetabReferenceGlyph &	operator= (const CLMetabReferenceGlyph &rhs)

void	print (std::ostream *ostream) const

void	setFunctionalRole (Role r)

void	setMetabGlyphKey (const std::string &k)

void	setRole (Role r)

virtual CData	toData () const

Public Member Functions inherited from CLGlyphWithCurve
	CLGlyphWithCurve (const CLGlyphWithCurve &src, const CDataContainer *pParent)

	CLGlyphWithCurve (const GraphicalObject &sbml, const std::map< std::string, std::string > &modelmap, std::map< std::string, std::string > &layoutmap, const CDataContainer *pParent=NO_PARENT)

	CLGlyphWithCurve (const std::string &name="ReferenceGlyph", const CDataContainer *pParent=NO_PARENT)

CLCurve &	getCurve ()

const CLCurve &	getCurve () const

virtual void	moveBy (const CLPoint &p)

CLGlyphWithCurve &	operator= (const CLGlyphWithCurve &rhs)

void	setCurve (const CLCurve &c)

Public Member Functions inherited from CLGraphicalObject
	CLGraphicalObject (const CLGraphicalObject &src, const CDataContainer *pParent)

	CLGraphicalObject (const GraphicalObject &sbml, std::map< std::string, std::string > &layoutmap, const CDataContainer *pParent=NO_PARENT)

	CLGraphicalObject (const std::string &name="GraphicalObject", const CDataContainer *pParent=NO_PARENT)

virtual void	exportToSBML (GraphicalObject sbmlobject, const std::map< const CDataObject , SBase * > &copasimodelmap, std::map< std::string, const SBase * > &sbmlIDs) const

CLBoundingBox &	getBoundingBox ()

const CLBoundingBox &	getBoundingBox () const

const CLDimensions &	getDimensions () const

const C_FLOAT64 &	getHeight () const

virtual const std::string &	getKey () const

CDataObject *	getModelObject () const

std::string	getModelObjectDisplayName (bool regular=true, bool richtext=false) const

const std::string &	getModelObjectKey () const

std::string	getModelObjectName () const

const std::string &	getObjectRole () const

const CLPoint &	getPosition () const

const C_FLOAT64 &	getWidth () const

const C_FLOAT64 &	getX () const

const C_FLOAT64 &	getY () const

bool	hasValidModelReference () const

CLGraphicalObject &	operator= (const CLGraphicalObject &rhs)

void	setBoundingBox (const CLBoundingBox &bb)

void	setDimensions (const CLDimensions &d)

void	setHeight (const C_FLOAT64 &h)

void	setModelObjectKey (const std::string &k)

void	setObjectRole (const std::string &role)

void	setPosition (const CLPoint &p)

void	setWidth (const C_FLOAT64 &w)

void	setX (const C_FLOAT64 &x)

void	setY (const C_FLOAT64 &y)

	~CLGraphicalObject ()

Public Member Functions inherited from CLBase
	CLBase ()

	CLBase (const CLBase &b)

	CLBase (const SBase &)

const std::string &	getTag () const

bool	hasTag () const

void	setTag (const std::string &tag)

virtual	~CLBase ()

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

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

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 CLMetabReferenceGlyph *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CLGraphicalObject
static CLGraphicalObject *	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	RoleName []

static const std::string	XMLRole []

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

Protected Member Functions
	CLMetabReferenceGlyph (const CLMetabReferenceGlyph &src)

Protected Member Functions inherited from CLGlyphWithCurve
	CLGlyphWithCurve (const CLGlyphWithCurve &src)

Protected Member Functions inherited from CLGraphicalObject
	CLGraphicalObject (const CLGraphicalObject &src)

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
Role	mFunctionalRole

std::string	mMetabGlyphKey

Role	mRole

Friends
std::ostream &	operator<< (std::ostream &os, const CLMetabReferenceGlyph &g)

Additional Inherited Members
Protected Attributes inherited from CLGlyphWithCurve
CLCurve	mCurve

Protected Attributes inherited from CLGraphicalObject
CLBoundingBox	mBBox

std::string	mKey

std::string	mModelObjectKey

std::string	mObjectRole

Protected Attributes inherited from CLBase
std::string	mTag

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

Detailed Description

Graphical representation of a CChemEqElement. This correspondents to the sbml SpeciesReferenceGlyph. The copasi equivalent is the CChemEqElement, however it has no key, so it cannot be referred to.

Member Enumeration Documentation

◆ Role

enum CLMetabReferenceGlyph::Role

Enum type for the role of the metab reference This enum must be synchronized with the corresponding enum in libsbml (sbml/layout/SpeciesReferenceRole.h)

Enumerator
UNDEFINED
SUBSTRATE
PRODUCT
SIDESUBSTRATE
SIDEPRODUCT
MODIFIER
ACTIVATOR
INHIBITOR

Constructor & Destructor Documentation

◆ CLMetabReferenceGlyph() [1/4]

CLMetabReferenceGlyph::CLMetabReferenceGlyph ( const CLMetabReferenceGlyph & src )

protected

Referenced by clone(), and fromData().

◆ CLMetabReferenceGlyph() [2/4]

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

◆ CLMetabReferenceGlyph() [3/4]

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

◆ CLMetabReferenceGlyph() [4/4]

CLMetabReferenceGlyph::CLMetabReferenceGlyph	(	const SpeciesReferenceGlyph &	sbml,
		const std::map< std::string, std::string > &	modelmap,
		std::map< std::string, std::string > &	layoutmap,
		const CDataContainer *	pParent = `NO_PARENT`
	)

constructor from libsbml object

References CLGlyphWithCurve::mCurve, mMetabGlyphKey, and CLGraphicalObject::setModelObjectKey().

Member Function Documentation

◆ applyData()

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

virtual

Apply the provided data to the object

Parameters

const CData & data

Returns: bool success

Reimplemented from CLGraphicalObject.

References fatalError.

◆ clone()

CLGraphicalObject * CLMetabReferenceGlyph::clone ( ) const

virtual

Reimplemented from CLGraphicalObject.

References CLMetabReferenceGlyph().

◆ exportToSBML()

void CLMetabReferenceGlyph::exportToSBML	(	SpeciesReferenceGlyph *	g,
		const std::map< const CDataObject , SBase > &	copasimodelmap,
		std::map< std::string, const SBase * > &	sbmlIDs,
		const std::map< const CLBase , const SBase > &	layoutmap
	)		const

virtual

This method writes the information of the COPASI layout object into the corresponding SBML object layoutmap contains a map from COPASI layout objects to libsbml layout objects. this is needed for resolving the reference to the metab glyph.

References CLCurve::exportToSBML(), CLGraphicalObject::exportToSBML(), getMetabGlyph(), CLGlyphWithCurve::mCurve, and mRole.

Referenced by CLReactionGlyph::exportToSBML().

◆ fromData()

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

static

Static method to create a CDataObject based on the provided data

Parameters

const CData & data

Returns: CLMetabReferenceGlyph * pDataObject

References CLMetabReferenceGlyph(), CData::getProperty(), NO_PARENT, CData::OBJECT_NAME, and CDataValue::toString().

◆ getFunctionalRole()

CLMetabReferenceGlyph::Role CLMetabReferenceGlyph::getFunctionalRole ( ) const

References getRole(), mFunctionalRole, and UNDEFINED.

Referenced by CCopasiSpringLayout::finalizeState().

◆ getMetabGlyph()

CLMetabGlyph * CLMetabReferenceGlyph::getMetabGlyph ( ) const

References CKeyFactory::get(), CRootContainer::getKeyFactory(), and mMetabGlyphKey.

Referenced by exportToSBML(), CCopasiSpringLayout::finalizeState(), CCopasiSpringLayout::potEdge(), and CCopasiSpringLayout::potSecondOrderEdge().

◆ getMetabGlyphKey()

const std::string & CLMetabReferenceGlyph::getMetabGlyphKey ( ) const

References mMetabGlyphKey.

Referenced by CLayout::CLayout(), CLayout::exportToDotFile(), CCopasiXML::saveLayoutList(), and CLLayoutRenderer::update_associations().

◆ getRole()

CLMetabReferenceGlyph::Role CLMetabReferenceGlyph::getRole ( ) const

References mRole.

Referenced by CLayout::exportToDotFile(), getFunctionalRole(), CCopasiSpringLayout::potEdge(), CLRenderResolver::resolveStyle(), and CCopasiXML::saveLayoutList().

◆ getRoleDisplayName()

const std::string & CLMetabReferenceGlyph::getRoleDisplayName ( ) const

References mRole, and RoleName.

◆ operator=()

CLMetabReferenceGlyph & CLMetabReferenceGlyph::operator= ( const CLMetabReferenceGlyph & rhs )

assignment operator.

References mMetabGlyphKey, mRole, and CLGlyphWithCurve::operator=().

◆ print()

void CLMetabReferenceGlyph::print ( std::ostream * ostream ) const

virtual

This is the output method for any object. The default implementation provided with CDataObject uses the ostream operator<< of the object to print the object.To override this default behavior one needs to reimplement the virtual print function.

Parameters

std::ostream * ostream

Reimplemented from CLGlyphWithCurve.

◆ setFunctionalRole()

void CLMetabReferenceGlyph::setFunctionalRole ( CLMetabReferenceGlyph::Role r )

References mFunctionalRole.

Referenced by CCopasiSpringLayout::createLayout().

◆ setMetabGlyphKey()

void CLMetabReferenceGlyph::setMetabGlyphKey ( const std::string & k )

References mMetabGlyphKey.

Referenced by CLayout::CLayout(), CCopasiSpringLayout::createLayout(), CLayoutInitializer::createReactionGlyph(), and MetaboliteReferenceGlyphHandler::processStart().

◆ setRole()

void CLMetabReferenceGlyph::setRole ( CLMetabReferenceGlyph::Role r )

References mRole.

Referenced by CCopasiSpringLayout::createLayout(), CLayoutInitializer::createReactionGlyph(), and MetaboliteReferenceGlyphHandler::processStart().

◆ toData()

CData CLMetabReferenceGlyph::toData ( ) const

virtual

Retrieve the data describing the object

Returns: CData data

Reimplemented from CLGraphicalObject.

References fatalError.

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const CLMetabReferenceGlyph &	g
	)

friend

insert operator

Member Data Documentation

◆ mFunctionalRole

Role CLMetabReferenceGlyph::mFunctionalRole

private

The role of the metab, logically. This may be used for automatic layout

Referenced by getFunctionalRole(), and setFunctionalRole().

◆ mMetabGlyphKey

std::string CLMetabReferenceGlyph::mMetabGlyphKey

private

Key of a CLMetabGlyph.

Referenced by CLMetabReferenceGlyph(), getMetabGlyph(), getMetabGlyphKey(), operator=(), and setMetabGlyphKey().

◆ mRole

Role CLMetabReferenceGlyph::mRole

private

The role of the metab, as used for rendering, this is also used in SBML

Referenced by exportToSBML(), getRole(), getRoleDisplayName(), operator=(), and setRole().

◆ RoleName

const std::string CLMetabReferenceGlyph::RoleName

static

Initial value:

=
{
  "undefined role",
  "substrate",
  "product",
  "side substrate",
  "side product",
  "modifier",
  "activator",
  "inhibitor"
  ""
}

String literals for the GUI to display the role of a metab reference

Referenced by getRoleDisplayName().

◆ XMLRole

const std::string CLMetabReferenceGlyph::XMLRole

static

Initial value:

=
{
  "undefinedRole",
  "substrate",
  "product",
  "sideSubstrate",
  "sideProduct",
  "modifier",
  "activator",
  "inhibitor",
  ""
}

XML type names of the roles. This is used in the XML importer and exporter

Referenced by MetaboliteReferenceGlyphHandler::processStart(), and CCopasiXML::saveLayoutList().

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

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ Role

Constructor & Destructor Documentation

◆ CLMetabReferenceGlyph() [1/4]

◆ CLMetabReferenceGlyph() [2/4]

◆ CLMetabReferenceGlyph() [3/4]

◆ CLMetabReferenceGlyph() [4/4]

Member Function Documentation

◆ applyData()

◆ clone()

◆ exportToSBML()

◆ fromData()

◆ getFunctionalRole()

◆ getMetabGlyph()

◆ getMetabGlyphKey()

◆ getRole()

◆ getRoleDisplayName()

◆ operator=()

◆ print()

◆ setFunctionalRole()

◆ setMetabGlyphKey()

◆ setRole()

◆ toData()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ mFunctionalRole

◆ mMetabGlyphKey

◆ mRole

◆ RoleName

◆ XMLRole