libSBML Perl API  libSBML 5.17.2 Perl API
CompSBMLDocumentPlugin Class Reference
Inheritance diagram for CompSBMLDocumentPlugin:
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Detailed Description

{comp}

comp Extension of SBMLDocument.

The CompSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin class, and codifies the extensions to the SBMLDocument class defined in the SBML Level 3 Hierarchical Model Composition (“comp”) package. This extension allows multiple Model objects to be defined in a single SBMLDocument, stored in an optional child ListOfModelDefinitions object, as well as define references to Model objects in other files, stored in the optional child ListOfExternalModelDefinitions object. These model definitions, if present, allow Submodel objects to reference other Models to instantiate.

The presence of any ModelDefinition or ExternalModelDefinition in an SBMLDocument does not change the default Model in the file. If a SBMLDocument is submitted somewhere to be simulated, it is still the <model> child of the <sbml> element that should be simulated.

In addition, as all packages do, the CompSBMLDocumentPlugin defines a required flag named required, which indicates whether “comp” constructs can be used to change the core mathematics of the <model> child of the <sbml> element. Because they can, this attribute must be set true.

Public Member Functions

int addExternalModelDefinition (const ExternalModelDefinition *externalModelDefinition)
 Adds a copy of the given ExternalModelDefinition object to the ListOfExternalModelDefinitions. More...
 
int addModelDefinition (const ModelDefinition *modelDefinition)
 Adds a copy of the given ModelDefinition object to the ListOfModelDefinitions. More...
 
virtual CompSBMLDocumentPluginclone () const
 Creates and returns a deep copy of this CompSBMLDocumentPlugin object. More...
 
 CompSBMLDocumentPlugin (const std::string &uri, const std::string &prefix, CompPkgNamespaces *compns)
 Creates a new CompSBMLDocumentPlugin object using the given parameters. More...
 
 CompSBMLDocumentPlugin (const CompSBMLDocumentPlugin &orig)
 Copy constructor. More...
 
ExternalModelDefinitioncreateExternalModelDefinition ()
 Creates a ExternalModelDefinition object, adds it to the end of the ExternalModelDefinition objects list and returns a pointer to the newly created object. More...
 
ModelDefinitioncreateModelDefinition ()
 Creates a ModelDefinition object, adds it to the end of the ModelDefinition objects list and returns a pointer to the newly created object. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or NULL if no such object is found. More...
 
virtual SBasegetElementBySId (const std::string &id)
 Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More...
 
const std::string & getElementNamespace () const
 Returns the namespace URI of the package to which this plugin object belongs. More...
 
ExternalModelDefinitiongetExternalModelDefinition (unsigned int n)
 Returns the ExternalModelDefinition with the given index. More...
 
const ExternalModelDefinitiongetExternalModelDefinition (unsigned int n) const
 Returns the ExternalModelDefinition with the given index. More...
 
ExternalModelDefinitiongetExternalModelDefinition (const std::string &sid)
 Returns the model definition object based on its identifier. More...
 
const ExternalModelDefinitiongetExternalModelDefinition (const std::string &sid) const
 Returns the model definition object based on its identifier. More...
 
unsigned int getLevel () const
 Returns the SBML Level of the package extension of this plugin object. More...
 
const ListOfExternalModelDefinitionsgetListOfExternalModelDefinitions () const
 Returns the ListOf object that holds each ExternalModelDefinition. More...
 
ListOfExternalModelDefinitionsgetListOfExternalModelDefinitions ()
 Returns the ListOf object that holds each ExternalModelDefinition. More...
 
const ListOfModelDefinitionsgetListOfModelDefinitions () const
 Returns the ListOf object that holds each ModelDefinition. More...
 
ListOfModelDefinitionsgetListOfModelDefinitions ()
 Returns the ListOf object that holds each ModelDefinition. More...
 
const SBasegetModel (const std::string &sid) const
 Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier. More...
 
SBasegetModel (const std::string &sid)
 Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier. More...
 
ModelDefinitiongetModelDefinition (unsigned int n)
 Returns the ModelDefinition with the given index. More...
 
const ModelDefinitiongetModelDefinition (unsigned int n) const
 Returns the ModelDefinition with the given index. More...
 
ModelDefinitiongetModelDefinition (const std::string &sid)
 Returns the model definition object based on its identifier. More...
 
const ModelDefinitiongetModelDefinition (const std::string &sid) const
 Returns the model definition object based on its identifier. More...
 
unsigned int getNumExternalModelDefinitions () const
 Returns the number of ExternalModelDefinition objects for this SBMLDocumentPlugin. More...
 
unsigned int getNumModelDefinitions () const
 Returns the number of ModelDefinition objects for this SBMLDocumentPlugin. 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...
 
SBasegetParentSBMLObject ()
 Returns the parent object to which this plugin object is connected. More...
 
const SBasegetParentSBMLObject () 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...
 
SBMLDocumentgetSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
const SBMLDocumentgetSBMLDocument () 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
 
CompSBMLDocumentPluginoperator= (const CompSBMLDocumentPlugin &orig)
 Assignment operator for CompSBMLDocumentPlugin. More...
 
ExternalModelDefinitionremoveExternalModelDefinition (unsigned int index)
 Removes the ExternalModelDefinition with the given index. More...
 
ExternalModelDefinitionremoveExternalModelDefinition (std::string id)
 Removes the ExternalModelDefinition with the given id. More...
 
ModelDefinitionremoveModelDefinition (unsigned int index)
 Removes the ModelDefinition with the given index from the CompSBMLDocumentPlugin. More...
 
ModelDefinitionremoveModelDefinition (std::string id)
 Removes the ModelDefinition with the given id from the CompSBMLDocumentPlugin. 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 bool value of "required" attribute of corresponding package in SBMLDocument element. More...
 
virtual int unsetRequired ()
 Unsets the value of the "required" attribute of this SBMLDocumentPlugin. More...
 
virtual ~CompSBMLDocumentPlugin ()
 Destroy this object. More...
 

Friends

class ExternalModelDefinition
 

Constructor & Destructor Documentation

◆ CompSBMLDocumentPlugin() [1/2]

CompSBMLDocumentPlugin::CompSBMLDocumentPlugin ( const std::string &  uri,
const std::string &  prefix,
CompPkgNamespaces compns 
)

Creates a new CompSBMLDocumentPlugin 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
urithe URI of the SBML Level 3 package implemented by this libSBML package extension.
prefixthe XML namespace prefix being used for the package.
compnsthe namespaces object for the package.

◆ CompSBMLDocumentPlugin() [2/2]

CompSBMLDocumentPlugin::CompSBMLDocumentPlugin ( const CompSBMLDocumentPlugin orig)

Copy constructor.

Creates a copy of this CompSBMLDocumentPlugin object.

Parameters
origthe instance to copy.

◆ ~CompSBMLDocumentPlugin()

CompSBMLDocumentPlugin::~CompSBMLDocumentPlugin ( )
virtual

Destroy this object.

Member Function Documentation

◆ addExternalModelDefinition()

int CompSBMLDocumentPlugin::addExternalModelDefinition ( const ExternalModelDefinition externalModelDefinition)

Adds a copy of the given ExternalModelDefinition object to the ListOfExternalModelDefinitions.

Parameters
externalModelDefinitionthe ExternalModelDefinition object to be added to the ListOFExternalModelDefinitions. Fails if the added ExternalModelDefinition is NULL, does not match the level/version/package of the parent object, or cannot be added to the list of external model definitions.

◆ addModelDefinition()

int CompSBMLDocumentPlugin::addModelDefinition ( const ModelDefinition modelDefinition)

Adds a copy of the given ModelDefinition object to the ListOfModelDefinitions.

Parameters
modelDefinitionthe ModelDefinition object to be added to the ListOfModelDefinitions. Fails if the added ModelDefinition is NULL, does not match the level/version/package of the parent object, or cannot be added to the list of replaced elements.

◆ clone()

CompSBMLDocumentPlugin * CompSBMLDocumentPlugin::clone ( ) const
virtual

Creates and returns a deep copy of this CompSBMLDocumentPlugin object.

Returns
a (deep) copy of this CompSBMLDocumentPlugin object.

Reimplemented from SBMLDocumentPlugin.

◆ createExternalModelDefinition()

ExternalModelDefinition * CompSBMLDocumentPlugin::createExternalModelDefinition ( )

Creates a ExternalModelDefinition object, adds it to the end of the ExternalModelDefinition objects list and returns a pointer to the newly created object.

Returns
a newly created ExternalModelDefinition object.

◆ createModelDefinition()

ModelDefinition * CompSBMLDocumentPlugin::createModelDefinition ( )

Creates a ModelDefinition object, adds it to the end of the ModelDefinition objects list and returns a pointer to the newly created object.

Returns
a newly created ModelDefinition object.

◆ getAllElements()

List * CompSBMLDocumentPlugin::getAllElements ( ElementFilter filter = NULL)
virtual

Returns a List of all child SBase objects, including those nested to an arbitrary depth.

Parameters
filtera 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 from SBasePlugin.

◆ getElementByMetaId()

SBase * CompSBMLDocumentPlugin::getElementByMetaId ( const std::string &  metaid)
virtual

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or NULL if no such object is found.

Parameters
metaidstring representing the meta identifier of the object to find.
Returns
a pointer to the SBase element with the given metaid.

Reimplemented from SBasePlugin.

◆ getElementBySId()

SBase * CompSBMLDocumentPlugin::getElementBySId ( const std::string &  id)
virtual

Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.

Parameters
idstring representing the identifier of the object to find.
Returns
a pointer to the SBase element with the given id.
Note
The comp SBML document plugin has multiple model-wide SId namespaces, so a valid document may well contain multiple elements with the same SId that reside in separate models. It is not recommended to ever call this function—instead, call the function on the child ModelDefinition objects.

Reimplemented from SBasePlugin.

◆ 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.

◆ getExternalModelDefinition() [1/4]

ExternalModelDefinition * CompSBMLDocumentPlugin::getExternalModelDefinition ( unsigned int  n)

Returns the ExternalModelDefinition with the given index.

Parameters
nthe index number of the ExternalModelDefinition to get.
Returns
the nth ExternalModelDefinition in the ListOfExternalModelDefinitions. If the index is invalid, NULL is returned.

◆ getExternalModelDefinition() [2/4]

const ExternalModelDefinition * CompSBMLDocumentPlugin::getExternalModelDefinition ( unsigned int  n) const

Returns the ExternalModelDefinition with the given index.

Parameters
nthe index number of the ExternalModelDefinition to get.
Returns
the nth ExternalModelDefinition in the ListOfExternalModelDefinitions. If the index is invalid, NULL is returned.

◆ getExternalModelDefinition() [3/4]

ExternalModelDefinition * CompSBMLDocumentPlugin::getExternalModelDefinition ( const std::string &  sid)

Returns the model definition object based on its identifier.

Parameters
sida string representing the identifier of the model definition to get.
Returns
ExternalModelDefinition in the ListOfExternalModelDefinitions with the given sid or NULL if no such ExternalModelDefinition exists.
See also
getExternalModelDefinition(unsigned int n)
getListOfExternalModelDefinitions()

◆ getExternalModelDefinition() [4/4]

const ExternalModelDefinition * CompSBMLDocumentPlugin::getExternalModelDefinition ( const std::string &  sid) const

Returns the model definition object based on its identifier.

Parameters
sida string representing the identifier of the model definition to get.
Returns
ExternalModelDefinition in the ListOfExternalModelDefinitions with the given sid or NULL if no such ExternalModelDefinition exists.
See also
getExternalModelDefinition(unsigned int n)
getListOfExternalModelDefinitions()

◆ 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()

◆ getListOfExternalModelDefinitions() [1/2]

const ListOfExternalModelDefinitions * CompSBMLDocumentPlugin::getListOfExternalModelDefinitions ( ) const

Returns the ListOf object that holds each ExternalModelDefinition.

Returns
the ListOf object that each all ExternalModelDefinition.

◆ getListOfExternalModelDefinitions() [2/2]

ListOfExternalModelDefinitions * CompSBMLDocumentPlugin::getListOfExternalModelDefinitions ( )

Returns the ListOf object that holds each ExternalModelDefinition.

Returns
the ListOf object that each all ExternalModelDefinition.

◆ getListOfModelDefinitions() [1/2]

const ListOfModelDefinitions * CompSBMLDocumentPlugin::getListOfModelDefinitions ( ) const

Returns the ListOf object that holds each ModelDefinition.

Returns
the ListOf object that holds each ModelDefinition.

◆ getListOfModelDefinitions() [2/2]

ListOfModelDefinitions * CompSBMLDocumentPlugin::getListOfModelDefinitions ( )

Returns the ListOf object that holds each ModelDefinition.

Returns
the ListOf object that holds each ModelDefinition.

◆ getModel() [1/2]

const SBase * CompSBMLDocumentPlugin::getModel ( const std::string &  sid) const

Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier.

Parameters
sida string representing the identifier of the model definition to get.
Returns
The SBase* corresponding to the given sid or NULL if no such model exists. If no such model exists, this will return NULL.

◆ getModel() [2/2]

SBase * CompSBMLDocumentPlugin::getModel ( const std::string &  sid)

Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier.

Parameters
sida string representing the identifier of the model definition to get.
Returns
The SBase* corresponding to the given sid or NULL if no such model exists. If no such model exists, this will return NULL.

◆ getModelDefinition() [1/4]

ModelDefinition * CompSBMLDocumentPlugin::getModelDefinition ( unsigned int  n)

Returns the ModelDefinition with the given index.

Parameters
nthe index number of the ModelDefinition to get.
Returns
the nth ModelDefinition in the ListOfModelDefinitions. If the index is invalid, NULL is returned.

◆ getModelDefinition() [2/4]

const ModelDefinition * CompSBMLDocumentPlugin::getModelDefinition ( unsigned int  n) const

Returns the ModelDefinition with the given index.

Parameters
nthe index number of the ModelDefinition to get.
Returns
the nth ModelDefinition in the ListOfModelDefinitions. If the index n is invalid, NULL is returned.

◆ getModelDefinition() [3/4]

ModelDefinition * CompSBMLDocumentPlugin::getModelDefinition ( const std::string &  sid)

Returns the model definition object based on its identifier.

Parameters
sida string representing the identifier of the model definition to get.
Returns
ModelDefinition in the ListOfModelDefinitions with the given sid or NULL if no such ModelDefinition exists.
See also
getModelDefinition(unsigned int n)
getListOfModelDefinitions()

◆ getModelDefinition() [4/4]

const ModelDefinition * CompSBMLDocumentPlugin::getModelDefinition ( const std::string &  sid) const

Returns the model definition object based on its identifier.

Parameters
sida string representing the identifier of the model definition to get.
Returns
ModelDefinition in the ListOfModelDefinitions with the given sid or NULL if no such ModelDefinition exists.
See also
getModelDefinition(unsigned int n)
getListOfModelDefinitions()

◆ getNumExternalModelDefinitions()

unsigned int CompSBMLDocumentPlugin::getNumExternalModelDefinitions ( ) const

Returns the number of ExternalModelDefinition objects for this SBMLDocumentPlugin.

Returns
the number of ExternalModelDefinition objects for this SBMLDocumentPlugin.

◆ getNumModelDefinitions()

unsigned int CompSBMLDocumentPlugin::getNumModelDefinitions ( ) const

Returns the number of ModelDefinition objects for this SBMLDocumentPlugin.

Returns
the number of ModelDefinition objects.

◆ 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=()

CompSBMLDocumentPlugin & CompSBMLDocumentPlugin::operator= ( const CompSBMLDocumentPlugin orig)

Assignment operator for CompSBMLDocumentPlugin.

Parameters
origthe object whose values are used as the basis of the assignment.

◆ removeExternalModelDefinition() [1/2]

ExternalModelDefinition * CompSBMLDocumentPlugin::removeExternalModelDefinition ( unsigned int  index)

Removes the ExternalModelDefinition with the given index.

A pointer to the ExternalModelDefinition that was removed is returned. If no ExternalModelDefinition has been removed, NULL is returned.

Parameters
indexthe index of the ExternalModelDefinition object to remove.
Returns
the ExternalModelDefinition object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

◆ removeExternalModelDefinition() [2/2]

ExternalModelDefinition * CompSBMLDocumentPlugin::removeExternalModelDefinition ( std::string  id)

Removes the ExternalModelDefinition with the given id.

A pointer to the ExternalModelDefinition that was removed is returned. If no ExternalModelDefinition has been removed, NULL is returned.

Parameters
idthe id of the ExternalModelDefinition object to remove.
Returns
the ExternalModelDefinition object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

◆ removeModelDefinition() [1/2]

ModelDefinition * CompSBMLDocumentPlugin::removeModelDefinition ( unsigned int  index)

Removes the ModelDefinition with the given index from the CompSBMLDocumentPlugin.

A pointer to the ModelDefinition that was removed is returned. If no ModelDefinition has been removed, NULL is returned.

Parameters
indexthe index of the ModelDefinition object to remove.
Returns
the ModelDefinition object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

◆ removeModelDefinition() [2/2]

ModelDefinition * CompSBMLDocumentPlugin::removeModelDefinition ( std::string  id)

Removes the ModelDefinition with the given id from the CompSBMLDocumentPlugin.

A pointer to the ModelDefinition that was removed is returned. If no ModelDefinition has been removed, NULL is returned.

Parameters
idthe id of the ModelDefinition object to remove.
Returns
the ModelDefinition object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

◆ renameMetaIdRefs()

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

◆ renameSIdRefs()

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

Reimplemented in FbcReactionPlugin.

◆ renameUnitSIdRefs()

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

◆ 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
urithe URI to assign to this object.

◆ setRequired()

int CompSBMLDocumentPlugin::setRequired ( bool  value)
virtual

Sets the bool value of "required" attribute of corresponding package in SBMLDocument element.

The only legal value is 'true' for the Hierarchical Model Composition package.

Parameters
valuethe bool value of "required" attribute of corresponding package in SBMLDocument element.

Reimplemented from SBMLDocumentPlugin.

◆ unsetRequired()

int SBMLDocumentPlugin::unsetRequired ( )
virtualinherited

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

Friends And Related Function Documentation

◆ ExternalModelDefinition

friend class ExternalModelDefinition
friend