libSBML C# API
libSBML 5.8.0 C# API
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Representation of a plug-in object of SBML's package extension.
Additional attributes and/or elements of a package extension which are directly contained by some pre-defined element are contained/accessed by SBasePlugin class which is extended by package developers for each extension point. The extension point, which represents an element to be extended, is identified by a combination of a Package name and a typecode of the element, and is represented by SBaseExtensionPoint class.
For example, the layout extension defines <listOfLayouts> element which is directly contained in <model> element of the core package. In the layout package (provided as one of example packages in libSBML-5), the additional element for the model element is implemented as ListOfLayouts class (an SBase derived class) and the object is contained/accessed by a LayoutModelPlugin class (an SBasePlugin derived class).
SBasePlugin class defines basic virtual functions for reading/writing/checking additional attributes and/or top-level elements which should or must be overridden by subclasses like SBase class and its derived classes.
Package developers must implement an SBasePlugin exntended class for each element to be extended (e.g. SBMLDocument, Model, ...) in which additional attributes and/or top-level elements of the package extension are directly contained.
To implement reading/writing functions for attributes and/or top-level elements of the SBsaePlugin extended class, package developers should or must override the corresponding virtual functions below provided in the SBasePlugin class:
reading elements :
virtual SBase createObject (XMLInputStream& stream)
This function must be overridden if one or more additional elements are defined.
virtual bool readOtherXML (SBase parentObject, XMLInputStream& stream)
This function should be overridden if elements of annotation, notes, MathML, etc. need to be directly parsed from the given XMLInputStream object instead of the SBase::readAnnotation(XMLInputStream& stream) and/or SBase::readNotes(XMLInputStream& stream) functions.
reading attributes (must be overridden if additional attributes are defined) :
virtual void addExpectedAttributes(ExpectedAttributes& attributes)
virtual void readAttributes (XMLAttributes attributes, ExpectedAttributes& expectedAttributes)
writing elements (must be overridden if additional elements are defined) :
virtual void writeElements (XMLOutputStream& stream)
writing attributes :
virtual void writeAttributes (XMLOutputStream& stream)
This function must be overridden if one or more additional attributes are defined.
virtual void writeXMLNS (XMLOutputStream& stream)
This function must be overridden if one or more additional xmlns attributes are defined.
checking elements (should be overridden) :
virtual bool hasRequiredElements()
checking attributes (should be overridden) :
virtual bool hasRequiredAttributes()
To implement package-specific creating/getting/manipulating functions of the SBasePlugin derived class (e.g., getListOfLayouts(), createLyout(), getLayout(), and etc are implemented in LayoutModelPlugin class of the layout package), package developers must newly implement such functions (as they like) in the derived class.
SBasePlugin class defines other virtual functions of internal implementations such as:
virtual void setSBMLDocument(SBMLDocument d)
virtual void connectToParent(SBase sbase)
virtual void enablePackageInternal(string pkgURI, string pkgPrefix, bool flag)
These functions must be overridden by subclasses in which one or more top-level elements are defined.
For example, the following three SBasePlugin extended classes are implemented in the layout extension:
SBMLDocumentPlugin class for SBMLDocument element
(SBMLDocumentPlugin class is a common SBasePlugin extended class for SBMLDocument class. Package developers can use this class as-is if no additional elements/attributes (except for required attribute) is needed for the SBMLDocument class in their packages, otherwise package developers must implement a new SBMLDocumentPlugin derived class.)
LayoutModelPlugin class for Model element
<listOfLayouts> element is added to Model object.
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
createObject()
: (read elements) readOtherXML()
: (read elements in annotation of SBML L2) writeElements()
: (write elements) The following virtual functions of internal implementations are overridden: (type of arguments and return values are omitted)
setSBMLDocument()
connectToParent()
enablePackageInternal()
The following creating/getting/manipulating functions are newly implemented: (type of arguments and return values are omitted)
getListOfLayouts()
getLayout ()
addLayout()
createLayout()
removeLayout()
getNumLayouts()
LayoutSpeciesReferencePlugin class for SpeciesReference element (used only for SBML L2V1)
id attribute is internally added to SpeciesReference object only for SBML L2V1
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
readOtherXML()
writeAttributes()
Public Member Functions | |
SBasePlugin | clone () |
Creates and returns a deep copy of this SBasePlugin object. More... | |
void | connectToParent (SBase sbase) |
Sets the parent SBML object of this plugin object to this object and child elements (if any). More... | |
virtual void | Dispose () |
void | divideAssignmentsToSIdByFunction (string id, ASTNode function) |
If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More... | |
void | enablePackageInternal (string pkgURI, string pkgPrefix, bool flag) |
Enables/Disables the given package with child elements in this plugin object (if any). More... | |
long | getColumn () |
Returns the column number on which this object first appears in the XML representation of the SBML document. More... | |
SBase | getElementByMetaId (string metaid) |
Returns the first child element it can find with the given metaid , or null if no such object is found. More... | |
SBase | getElementBySId (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... | |
string | getElementNamespace () |
Returns the XML namespace (URI) of the package extension of this plugin object. More... | |
long | getLevel () |
Returns the SBML level of the package extension of this plugin object. More... | |
long | getLine () |
Returns the line number on which this object first appears in the XML representation of the SBML document. More... | |
SBaseList | getListOfAllElements () |
string | getPackageName () |
Returns the package name of this plugin object. More... | |
long | getPackageVersion () |
Returns the package version of the package extension of this plugin object. More... | |
SBase | getParentSBMLObject () |
Returns the parent SBase object to which this plugin object connected. More... | |
string | getPrefix () |
Returns the prefix of the package extension of this plugin object. More... | |
SBMLDocument | getSBMLDocument () |
Returns the parent SBMLDocument of this plugin object. More... | |
SBMLNamespaces | getSBMLNamespaces () |
Returns the column number on which this object first appears in the XML representation of the SBML document. More... | |
string | getURI () |
Gets the URI to which this element belongs to. More... | |
long | getVersion () |
Returns the SBML version of the package extension of this plugin object. More... | |
bool | hasIdentifierBeginningWith (string prefix) |
Check to see if the given prefix is used by any of the IDs defined by extension elements. More... | |
void | logUnknownElement (string element, long sbmlLevel, long sbmlVersion, long pkgVersion) |
Helper to log a common type of error for elements. More... | |
void | multiplyAssignmentsToSIdByFunction (string id, ASTNode function) |
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More... | |
int | prependStringToAllIdentifiers (string prefix) |
Add the given string to all identifiers in the object. More... | |
void | replaceSIDWithFunction (string id, ASTNode function) |
If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More... | |
int | setElementNamespace (string uri) |
Sets the XML namespace to which this element belongs to. More... | |
bool | stripPackage (string pkgPrefix, bool flag) |
Enables/Disables the given package with child elements in this plugin object (if any). More... | |
Protected Attributes | |
bool | swigCMemOwn |
SBasePlugin libsbmlcs.SBasePlugin.clone | ( | ) |
Creates and returns a deep copy of this SBasePlugin object.
void libsbmlcs.SBasePlugin.connectToParent | ( | SBase | sbase | ) |
Sets the parent SBML object of this plugin object to this object and child elements (if any).
(Creates a child-parent relationship by this plugin object)
This function is called when this object is created by the parent element. Subclasses must override this this function if they have one or more child elements. Also, SBasePlugin::connectToParent() must be called in the overridden function.
sbase | the SBase object to use |
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virtual |
void libsbmlcs.SBasePlugin.divideAssignmentsToSIdByFunction | ( | string | id, |
ASTNode | function | ||
) |
If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).
void libsbmlcs.SBasePlugin.enablePackageInternal | ( | string | pkgURI, |
string | pkgPrefix, | ||
bool | flag | ||
) |
Enables/Disables the given package with child elements in this plugin object (if any).
(This is an internal implementation invoked from SBase::enablePackageInternal() function)
Subclasses which contain one or more SBase derived elements should override this function if elements defined in them can be extended by some other package extension.
long libsbmlcs.SBasePlugin.getColumn | ( | ) |
Returns the column number on which this object first appears in the XML representation of the SBML document.
SBase libsbmlcs.SBasePlugin.getElementByMetaId | ( | string | metaid | ) |
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
. SBase libsbmlcs.SBasePlugin.getElementBySId | ( | 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.
id | string representing the id of objects to find |
id
. string libsbmlcs.SBasePlugin.getElementNamespace | ( | ) |
Returns the XML namespace (URI) of the package extension of this plugin object.
long libsbmlcs.SBasePlugin.getLevel | ( | ) |
Returns the SBML level of the package extension of this plugin object.
long libsbmlcs.SBasePlugin.getLine | ( | ) |
Returns the line number on which this object first appears in the XML representation of the SBML document.
SBaseList libsbmlcs.SBasePlugin.getListOfAllElements | ( | ) |
string libsbmlcs.SBasePlugin.getPackageName | ( | ) |
Returns the package name of this plugin object.
long libsbmlcs.SBasePlugin.getPackageVersion | ( | ) |
Returns the package version of the package extension of this plugin object.
SBase libsbmlcs.SBasePlugin.getParentSBMLObject | ( | ) |
string libsbmlcs.SBasePlugin.getPrefix | ( | ) |
Returns the prefix of the package extension of this plugin object.
SBMLDocument libsbmlcs.SBasePlugin.getSBMLDocument | ( | ) |
Returns the parent SBMLDocument of this plugin object.
SBMLNamespaces libsbmlcs.SBasePlugin.getSBMLNamespaces | ( | ) |
Returns the column number on which this object first appears in the XML representation of the SBML document.
string libsbmlcs.SBasePlugin.getURI | ( | ) |
Gets the URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace
long libsbmlcs.SBasePlugin.getVersion | ( | ) |
Returns the SBML version of the package extension of this plugin object.
bool libsbmlcs.SBasePlugin.hasIdentifierBeginningWith | ( | string | prefix | ) |
Check to see if the given prefix is used by any of the IDs defined by extension elements.
A package that defines its own 'id' attribute for a core element would check that attribute here.
void libsbmlcs.SBasePlugin.logUnknownElement | ( | string | element, |
long | sbmlLevel, | ||
long | sbmlVersion, | ||
long | pkgVersion | ||
) |
Helper to log a common type of error for elements.
void libsbmlcs.SBasePlugin.multiplyAssignmentsToSIdByFunction | ( | string | id, |
ASTNode | function | ||
) |
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).
int libsbmlcs.SBasePlugin.prependStringToAllIdentifiers | ( | string | prefix | ) |
Add the given string to all identifiers in the object.
If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.
void libsbmlcs.SBasePlugin.replaceSIDWithFunction | ( | string | id, |
ASTNode | function | ||
) |
If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.
int libsbmlcs.SBasePlugin.setElementNamespace | ( | string | uri | ) |
Sets the XML namespace to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
bool libsbmlcs.SBasePlugin.stripPackage | ( | string | pkgPrefix, |
bool | flag | ||
) |
Enables/Disables the given package with child elements in this plugin object (if any).
(This is an internal implementation invoked from SBase::enablePackageInternal() function)
Subclasses which contain one or more SBase derived elements should override this function if elements defined in them can be extended by some other package extension.
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