Inheritance diagram for LayoutSBMLDocumentPlugin:

Detailed Description

The LayoutSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin class, and codifies the extensions to the SBMLDocument class defined in the SBML Level 3 Layout (“layout”) package.

The LayoutSBMLDocumentPlugin defines a required flag named required, which indicates whether the 'fbc' constructs can be used to change the core mathematics of the <model> child of the <sbml> element. Because they can not, this attribute must be set false.

Public Member Functions
virtual LayoutSBMLDocumentPlugin *	clone () const
	Creates and returns a deep copy of this LayoutSBMLDocumentPlugin object. More...

virtual List *	getAllElements (ElementFilter *filter=NULL)
	Returns all child objects of this object. More...

virtual SBase *	getElementByMetaId (const std::string &metaid)
	Return the first child object found with a given meta identifier. More...

virtual SBase *	getElementBySId (const std::string &id)
	Return the first child object found with a given identifier. More...

const std::string &	getElementNamespace () const
	Returns the namespace URI of the package to which this plugin object belongs. More...

unsigned int	getLevel () const
	Returns the SBML Level of the package extension of this plugin object. More...

const std::string &	getPackageName () const
	Returns the short-form name of the package to which this plugin object belongs. More...

unsigned int	getPackageVersion () const
	Returns the package version of the package extension of this plugin object. More...

SBase *	getParentSBMLObject ()
	Returns the parent object to which this plugin object is connected. More...

const SBase *	getParentSBMLObject () const
	Returns the parent object to which this plugin object is connected. More...

const std::string &	getPrefix () const
	Returns the XML namespace prefix of the package to which this plugin object belongs. More...

virtual bool	getRequired () const
	Returns the value of the "required" attribute. More...

SBMLDocument *	getSBMLDocument ()
	Returns the SBMLDocument object containing this object instance. More...

const SBMLDocument *	getSBMLDocument () const
	Returns the SBMLDocument object containing this object instance. More...

std::string	getURI () const
	Returns the XML namespace URI for the package to which this object belongs. More...

unsigned int	getVersion () const
	Returns the Version within the SBML Level of the package extension of this plugin object. More...

virtual bool	isSetRequired () const
	Returns the value of the "required" attribute. More...

virtual bool	isValidTypeForList (SBase *item) const

	LayoutSBMLDocumentPlugin (const LayoutSBMLDocumentPlugin &orig)
	Copy constructor for LayoutSBMLDocumentPlugin. More...

	LayoutSBMLDocumentPlugin (const std::string &uri, const std::string &prefix, LayoutPkgNamespaces *layoutns)
	Creates a new LayoutSBMLDocumentPlugin object using the given parameters. More...

LayoutSBMLDocumentPlugin &	operator= (const LayoutSBMLDocumentPlugin &rhs)
	Assignment operator for LayoutSBMLDocumentPlugin. More...

virtual void	renameMetaIdRefs (const std::string &oldid, const std::string &newid)

virtual void	renameSIdRefs (const std::string &oldid, const std::string &newid)

virtual void	renameUnitSIdRefs (const std::string &oldid, const std::string &newid)

int	setElementNamespace (const std::string &uri)
	Sets the XML namespace to which this object belongs. More...

virtual int	setRequired (bool value)
	Sets the SBML "required" attribute value. More...

virtual int	unsetRequired ()
	Unsets the value of the "required" attribute of this SBMLDocumentPlugin. More...

virtual	~LayoutSBMLDocumentPlugin ()
	Destructor for LayoutSBMLDocumentPlugin. More...

Constructor & Destructor Documentation

◆ LayoutSBMLDocumentPlugin() [1/2]

LayoutSBMLDocumentPlugin::LayoutSBMLDocumentPlugin	(	const std::string &	uri,
		const std::string &	prefix,
		LayoutPkgNamespaces *	layoutns
	)

Creates a new LayoutSBMLDocumentPlugin object using the given parameters.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

: The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

uri	the URI of the SBML Level 3 package implemented by this libSBML package extension.
prefix	the XML namespace prefix being used for the package.
layoutns	the namespaces object for the package.

◆ LayoutSBMLDocumentPlugin() [2/2]

LayoutSBMLDocumentPlugin::LayoutSBMLDocumentPlugin ( const LayoutSBMLDocumentPlugin & orig )

Copy constructor for LayoutSBMLDocumentPlugin.

Parameters

orig	the LayoutSBMLDocumentPlugin instance to copy.

◆ ~LayoutSBMLDocumentPlugin()

LayoutSBMLDocumentPlugin::~LayoutSBMLDocumentPlugin ( )

virtual

Destructor for LayoutSBMLDocumentPlugin.

Member Function Documentation

◆ clone()

LayoutSBMLDocumentPlugin * LayoutSBMLDocumentPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this LayoutSBMLDocumentPlugin object.

Returns: a (deep) copy of this LayoutSBMLDocumentPlugin object.

Reimplemented from SBMLDocumentPlugin.

◆ getAllElements()

List * SBasePlugin::getAllElements ( ElementFilter * filter = NULL )

virtualinherited

Returns all child objects of this object.

This returns a List object containing all child SBase objects of this one, at any nesting depth. Optionally, callers can supply a filter that will establish the search criteria for matching objects.

Parameters

filter a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.

Returns: a List of pointers to all children objects.

Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, RenderListOfLayoutsPlugin, RenderLayoutPlugin, QualModelPlugin, MultiSpeciesReferencePlugin, MultiSpeciesPlugin, MultiSimpleSpeciesReferencePlugin, MultiModelPlugin, MultiCompartmentPlugin, LayoutModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcReactionPlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ getElementByMetaId()

SBase * SBasePlugin::getElementByMetaId ( const std::string & metaid )

virtualinherited

Return the first child object found with a given meta identifier.

This method searches all the subobjects under this one, compares their meta identifiers to metaid, and returns the first one that machines.

Parameters

metaid string, the metaid of the object to find.

Returns: pointer to the first object found with the given metaid.

Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, QualModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ getElementBySId()

SBase * SBasePlugin::getElementBySId ( const std::string & id )

virtualinherited

Return the first child object found with a given identifier.

This method searches all the subobjects under this one, compares their identifiers to id, and returns the first one that machines. It uses SBasePlugin::getAllElements(ElementFilter* filter) to get the list of identifiers, so the order in which identifiers are searched is the order in which they appear in the results returned by that method.

Normally, SId type identifier values are unique across a model in SBML. However, in some circumstances they may not be, such as if a model is invalid because of multiple objects having the same identifier.

Parameters

id	string representing the identifier of the object to find.

Returns: pointer to the first object with the given id.

Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, QualModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ getElementNamespace()

const std::string & SBasePlugin::getElementNamespace ( ) const

inherited

Returns the namespace URI of the package to which this plugin object belongs.

Returns: the XML namespace URI of the SBML Level 3 package implemented by this libSBML package extension.

◆ getLevel()

unsigned int SBasePlugin::getLevel ( ) const

inherited

Returns the SBML Level of the package extension of this plugin object.

Returns: the SBML Level.

See also: getVersion()

◆ getPackageName()

const std::string & SBasePlugin::getPackageName ( ) const

inherited

Returns the short-form name of the package to which this plugin object belongs.

Returns: the short-form package name (or nickname) of the SBML package implemented by this package extension.

◆ getPackageVersion()

unsigned int SBasePlugin::getPackageVersion ( ) const

inherited

Returns the package version of the package extension of this plugin object.

Returns: the package version of the package extension of this plugin object.

See also: getLevel(); getVersion()

◆ getParentSBMLObject() [1/2]

SBase * SBasePlugin::getParentSBMLObject ( )

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

◆ getParentSBMLObject() [2/2]

const SBase * SBasePlugin::getParentSBMLObject ( ) const

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

◆ getPrefix()

const std::string & SBasePlugin::getPrefix ( ) const

inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

Returns: the XML namespace prefix of the SBML Level 3 package implemented by this libSBML package extension.

◆ getRequired()

bool SBMLDocumentPlugin::getRequired ( ) const

virtualinherited

Returns the value of the "required" attribute.

: SBML Level 3 requires that every package defines an attribute named "required" on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Returns: the bool value of "required" attribute for the SBML package.

See also: setRequired(bool value); isSetRequired(); unsetRequired()

◆ getSBMLDocument() [1/2]

SBMLDocument * SBasePlugin::getSBMLDocument ( )

inherited

Returns the SBMLDocument object containing this object instance.

: LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

◆ getSBMLDocument() [2/2]

const SBMLDocument * SBasePlugin::getSBMLDocument ( ) const

inherited

Returns the SBMLDocument object containing this object instance.

: LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

◆ getURI()

std::string SBasePlugin::getURI ( ) const

inherited

Returns the XML namespace URI for the package to which this object belongs.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

This method first looks into the SBMLNamespaces object possessed by the parent SBMLDocument object of the current object. If this cannot be found, this method returns the result of getElementNamespace().

Returns: a string, the URI of the XML namespace to which this object belongs.

See also: getPackageName(); getElementNamespace(); getSBMLDocument()

◆ getVersion()

unsigned int SBasePlugin::getVersion ( ) const

inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns: the SBML Version.

See also: getLevel()

◆ isSetRequired()

bool SBMLDocumentPlugin::isSetRequired ( ) const

virtualinherited

Returns the value of the "required" attribute.

: SBML Level 3 requires that every package defines an attribute named "required" on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Returns: true if the "required" attribute of this SBMLDocument has been set to true, false otherwise.

◆ isValidTypeForList()

virtual bool SBasePlugin::isValidTypeForList ( SBase * item ) const

virtualinherited

◆ operator=()

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

Assignment operator for LayoutSBMLDocumentPlugin.

Parameters

rhs	the object whose values are used as the basis of the assignment.

◆ renameMetaIdRefs()

virtual void SBasePlugin::renameMetaIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

: Replaces all uses of a given meta identifier attribute value with another value.

: In SBML, object "meta" identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as "metaid refs", in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

◆ renameSIdRefs()

virtual void SBasePlugin::renameSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

: Replaces all uses of a given SIdRef type attribute value with another value.

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to an identifier", but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

Reimplemented in FbcReactionPlugin.

◆ renameUnitSIdRefs()

virtual void SBasePlugin::renameUnitSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

: Replaces all uses of a given UnitSIdRef type attribute value with another value.

: In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to a unit identifier", but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

◆ setElementNamespace()

int SBasePlugin::setElementNamespace ( const std::string & uri )

inherited

Sets the XML namespace to which this object belongs.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

Parameters

uri	the URI to assign to this object.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getElementNamespace()

Examples: convertLayout.cpp.

◆ setRequired()

int SBMLDocumentPlugin::setRequired ( bool value )

virtualinherited

Sets the SBML "required" attribute value.

: SBML Level 3 requires that every package defines an attribute named "required" on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Parameters

value the value to be assigned to the "required" attribute. The "required" attribute takes a Boolean value, either true or false.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getRequired(); isSetRequired(); unsetRequired()

Reimplemented in CompSBMLDocumentPlugin.

◆ unsetRequired()

int SBMLDocumentPlugin::unsetRequired ( )

virtualinherited

Unsets the value of the "required" attribute of this SBMLDocumentPlugin.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

◆ LayoutSBMLDocumentPlugin() [1/2]

◆ LayoutSBMLDocumentPlugin() [2/2]

◆ ~LayoutSBMLDocumentPlugin()

Member Function Documentation

◆ clone()

◆ getAllElements()

◆ getElementByMetaId()

◆ getElementBySId()

◆ getElementNamespace()

◆ getLevel()

◆ getPackageName()

◆ getPackageVersion()

◆ getParentSBMLObject() [1/2]

◆ getParentSBMLObject() [2/2]

◆ getPrefix()

◆ getRequired()

◆ getSBMLDocument() [1/2]

◆ getSBMLDocument() [2/2]

◆ getURI()

◆ getVersion()

◆ isSetRequired()

◆ isValidTypeForList()

◆ operator=()

◆ renameMetaIdRefs()

◆ renameSIdRefs()

◆ renameUnitSIdRefs()

◆ setElementNamespace()

◆ setRequired()

◆ unsetRequired()