libSBML C++ API
5.18.0
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This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
The SBMLDocumentPlugin class is a specialization of SBasePlugin designed specifically for extending SBMLDocument. All package extensions must extend SBMLDocument to implement support for SBML Level 3 packages; these extensions can be subclasses of this class or from a derived class of this class.
All packages must additionally define a required flag named required
, which indicates whether that package's constructs can be used to change the core mathematics of the <model>
child of the <sbml>
element. If they can, this attribute must be set true
, and if they cannot, this attribute must be set false
.
The specification for a SBML Level 3 package will define the changes to the SBML <sbml>
element. Packages typically do not make any changes beyond adding an attribute named "required" (discussed below), so in most cases, the extension of SBMLDocument is very simple. However, some packages do more. For instance, the Hierarchical Model Composition package adds subobjects for lists of model definitions. SBMLDocumentPlugin supports all these cases.
A package extension will only define one subclass of SBMLDocumentPlugin. Below, we describe in detail the different parts of a subclass definition.
The derived class must override the constructor, copy constructor, assignment operator (operator=
) and clone()
methods from SBasePlugin.
At minimum, it is necessary for a package implementation to add the "required" attribute to the SBML <sbml>
element mandated by SBML for all Level 3 packages, and this is done using this class as a base. If the 'required' attribute is the only addition necessary for a particular SBML Level 3 package, then the subclass of SBMLDocumentPlugin for the package can have a very simple implementation. Some Level 3 packages add additional attributes or elements to <sbml>
, and their implementations would go into the subclassed SBMLDocumentPlugin.
SBMLDocumentPlugin provides methods with default implementations that support managing the "required" attribute, so package extension code does not need to provide implementations—they only need to set the correct value for the SBML Level 3 package based on its specification. The following are the virtual methods for working with the "required" attribute. Package extensions would only need to override them in special circumstances:
setRequired(bool value)
: This method sets the value of the flag.getRequired()
: This method gets the value of the "required" flag.isSetRequired()
: This method tests if the value has been set.unsetRequired()
: This method unsets the value of the "required" flag.An extended SBMLDocument object may need more than just the "required" attribute, depending on what is defined in the specification for the package being implemented. Data attributes on the extended <sbml>
object in an SBML package will have one of the data types std::string
, double
, int
, or bool
. Subelements/subobjects will normally be derived from the ListOf class or from SBase.
The additional data members must be properly initialized in the class constructor, and must be properly copied in the copy constructor and assignment operator.
If the extended component is defined by the SBML Level 3 package to have attributes, then the extended SBMLDocumentPlugin class definition needs to override the following internal methods that come from SBasePlugin (the base class of SBMLDocumentPlugin) and provide appropriate implementations:
addExpectedAttributes(ExpectedAttributes& attributes)
: This method should add the attributes that are expected to be found on this kind of extended component in an SBML file or data stream.readAttributes(XMLAttributes& attributes, ExpectedAttributes& expectedAttributes)
: This method should read the attributes expected to be found on this kind of extended component in an SBML file or data stream.hasRequiredAttributes()
: This method should return true
if all of the required attribute for this extended component are present on instance of the object.writeAttributes(XMLOutputStream& stream)
: This method should write out the attributes of an extended component. The implementation should use the different kinds of writeAttribute
methods defined by XMLOutputStream to achieve this.If the extended component is defined by the Level 3 package to have subcomponents (i.e., full XML elements rather than mere attributes), then the extended class definition needs to override the following internal methods on SBasePlugin (the base class of SBMLDocumentPlugin) and provide appropriate implementations:
createObject(XMLInputStream& stream)
: Subclasses must override this method to create, store, and then return an SBML object corresponding to the next XMLToken in the XMLInputStream. To do this, implementations can use methods like peek()
on XMLInputStream to test if the next object in the stream is something expected for the package. For example, LayoutModelPlugin uses peek()
to examine the next element in the input stream, then tests that element against the Layout namespace and the element name "listOfLayouts"
to see if it's the single subcomponent (ListOfLayouts) permitted on a Model object using the Layout package. If it is, it returns the appropriate object.connectToParent(SBase *sbase)
: This creates a parent-child relationship between a given extended component and its subcomponent(s).setSBMLDocument(SBMLDocument* d)
: This method should set the parent SBMLDocument object on the subcomponent object instances, so that the subcomponent instances know which SBMLDocument contains them.enablePackageInternal(std::string& pkgURI, std::string& pkgPrefix, bool flag)
: This method should enable or disable the subcomponent based on whether a given XML namespace is active.writeElements(XMLOutputStream& stream)
: This method must be overridden to provide an implementation that will write out the expected subcomponents/subelements to the XML output stream.readOtherXML(SBase* parentObject, XMLInputStream& stream)
: This function should be overridden if elements of annotation, notes, MathML content, etc., need to be directly parsed from the given XMLInputStream object.hasRequiredElements()
: This method should return true
if a given object contains all the required subcomponents defined by the specification for that SBML Level 3 package.If the package needs to add additional xmlns
attributes to declare additional XML namespace URIs, the extended class should override the following method coming from SBasePlugin (the parent class of SBMLDocumentPlugin):
writeXMLNS(XMLOutputStream& stream)
: This method should write out any additional XML namespaces that might be needed by a package implementation.Extended SBMLDocumentPlugin implementations can add whatever additional utility methods are useful for their implementation.
Public Member Functions | |
virtual SBMLDocumentPlugin * | clone () const |
Creates and returns a deep copy of this SBMLDocumentPlugin 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 |
SBMLDocumentPlugin & | operator= (const SBMLDocumentPlugin &rhs) |
Assignment operator for SBMLDocumentPlugin. More... | |
virtual void | renameMetaIdRefs (const std::string &oldid, const std::string &newid) |
Replaces all uses of a given meta identifier attribute value with another value. More... | |
virtual void | renameSIdRefs (const std::string &oldid, const std::string &newid) |
Replaces all uses of a given SIdRef type attribute value with another value. More... | |
virtual void | renameUnitSIdRefs (const std::string &oldid, const std::string &newid) |
Replaces all uses of a given UnitSIdRef type attribute value with another value. More... | |
SBMLDocumentPlugin (const std::string &uri, const std::string &prefix, SBMLNamespaces *sbmlns) | |
Creates a new SBMLDocumentPlugin object using the given parameters. More... | |
SBMLDocumentPlugin (const SBMLDocumentPlugin &orig) | |
Copy constructor. More... | |
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 | ~SBMLDocumentPlugin () |
Destroy this SBMLDocumentPlugin object. More... | |
SBMLDocumentPlugin::SBMLDocumentPlugin | ( | const std::string & | uri, |
const std::string & | prefix, | ||
SBMLNamespaces * | sbmlns | ||
) |
Creates a new SBMLDocumentPlugin object using the given parameters.
"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/"
.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. |
sbmlns | the SBMLNamespaces object for the package. |
SBMLDocumentPlugin::SBMLDocumentPlugin | ( | const SBMLDocumentPlugin & | orig | ) |
Copy constructor.
This creates a copy of this object.
orig | the SBMLDocumentPlugin instance to copy. |
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virtual |
Destroy this SBMLDocumentPlugin object.
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virtual |
Creates and returns a deep copy of this SBMLDocumentPlugin object.
Reimplemented from SBasePlugin.
Reimplemented in CompSBMLDocumentPlugin, RenderSBMLDocumentPlugin, LayoutSBMLDocumentPlugin, GroupsSBMLDocumentPlugin, QualSBMLDocumentPlugin, FbcSBMLDocumentPlugin, and MultiSBMLDocumentPlugin.
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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.
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. |
Reimplemented in GroupsModelPlugin, FbcModelPlugin, MultiCompartmentPlugin, LayoutModelPlugin, RenderListOfLayoutsPlugin, MultiSpeciesPlugin, FbcReactionPlugin, MultiSimpleSpeciesReferencePlugin, CompModelPlugin, CompSBasePlugin, CompSBMLDocumentPlugin, RenderLayoutPlugin, MultiSpeciesReferencePlugin, MultiModelPlugin, and QualModelPlugin.
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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.
metaid | string, the metaid of the object to find. |
metaid
. Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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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.
id | string representing the identifier of the object to find. |
id
. Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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inherited |
Returns the namespace URI of the package to which this plugin object belongs.
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inherited |
Returns the SBML Level of the package extension of this plugin object.
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inherited |
Returns the short-form name of the package to which this plugin object belongs.
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inherited |
Returns the package version of the package extension of this plugin object.
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inherited |
Returns the parent object to which this plugin object is connected.
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inherited |
Returns the parent object to which this plugin object is connected.
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inherited |
Returns the XML namespace prefix of the package to which this plugin object belongs.
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virtual |
Returns the value of the "required" attribute.
<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.
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inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
Returns the XML namespace URI for the package to which this object belongs.
"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().
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inherited |
Returns the Version within the SBML Level of the package extension of this plugin object.
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Returns the value of the "required" attribute.
<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.
true
if the "required" attribute of this SBMLDocument has been set to true
, false
otherwise.
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virtualinherited |
SBMLDocumentPlugin & SBMLDocumentPlugin::operator= | ( | const SBMLDocumentPlugin & | rhs | ) |
Assignment operator for SBMLDocumentPlugin.
rhs | the object whose values are used as the basis of the assignment. |
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virtualinherited |
Replaces all uses of a given meta identifier attribute value with another value.
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.
oldid | the old identifier. |
newid | the new identifier. |
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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.
oldid | the old identifier. |
newid | the new identifier. |
Reimplemented in FbcReactionPlugin.
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virtualinherited |
Replaces all uses of a given UnitSIdRef
type attribute value with another value.
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.
oldid | the old identifier. |
newid | the new identifier. |
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inherited |
Sets the XML namespace to which this object belongs.
"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/"
.uri | the URI to assign to this object. |
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Sets the SBML "required" attribute value.
<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.
value | the value to be assigned to the "required" attribute. The "required" attribute takes a Boolean value, either true or false . |
Reimplemented in CompSBMLDocumentPlugin.
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Unsets the value of the "required" attribute of this SBMLDocumentPlugin.