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libSBML C# API
5.18.0
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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 SBasePlugin class is libSBML's base class for extensions of core SBML component objects. SBasePlugin defines basic virtual methods for reading/writing/checking additional attributes and/or subobjects; these methods should be overridden by subclasses to implement the necessary features of an extended SBML object.
SBML Level 3's package structure permits modular extensions to the core SBML format. In libSBML, support for SBML Level 3 packages is provided through optional package extensions that can be plugged into libSBML at the time it is built/compiled. Users of libSBML can thus choose which extensions are enabled in their software applications.
LibSBML defines a number of classes that developers of package extensions can use to implement support for an SBML Level 3 package. These classes make it easier to extend libSBML objects with new attributes and/or subobjects as needed by a particular Level 3 package. Three overall categories of classes make up libSBML's facilities for implementing package extensions. There are (1) classes that serve as base classes meant to be subclassed, (2) template classes meant to be instantiated rather than subclassed, and (3) support classes that provide utility features. A given package implementation for libSBML will take the form of code using these and other libSBML classes, placed in a subdirectory of src/sbml/packages/.
The basic libSBML distribution includes a number of package extensions implementing support for officially-endorsed SBML Level 3 packages; among these are Flux Balance Constraints ('fbc'), Hierarchical Model Composition ('comp'), Layout ('layout'), and Qualitative Models ('qual'). They can serve as working examples for developers working to implement other packages.
Extensions in libSBML can currently only be implemented in C++ or C; there is no mechanism to implement them first in languages such as Java or Python. However, once implemented in C++ or C, language interfaces can be generated semi-automatically using the framework in place in libSBML. (The approach is based on using SWIG and facilities in libSBML's build system.)
Public Member Functions | |
| new SBasePlugin | clone () |
| Creates and returns a deep copy of this SBasePlugin object. More... | |
| virtual void | Dispose () |
| long | getColumn () |
| new SBase | getElementByMetaId (string metaid) |
| Return the first child object found with a given meta identifier. More... | |
| new SBase | getElementBySId (string id) |
| Return the first child object found with a given identifier. More... | |
| string | getElementNamespace () |
| Returns the namespace URI of the package to which this plugin object belongs. More... | |
| long | getLevel () |
| Returns the SBML Level of the package extension of this plugin object. More... | |
| long | getLine () |
| SBaseList | getListOfAllElements (ElementFilter filter) |
| SBaseList | getListOfAllElements () |
| string | getPackageName () |
| Returns the short-form name of the package to which this plugin object belongs. More... | |
| long | getPackageVersion () |
| 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... | |
| string | getPrefix () |
| Returns the XML namespace prefix of the package to which this plugin object belongs. More... | |
| SBMLDocument | getSBMLDocument () |
| Returns the SBMLDocument object containing this object instance. More... | |
| SBMLExtension | getSBMLExtension () |
| string | getURI () |
| Returns the XML namespace URI for the package to which this object belongs. More... | |
| long | getVersion () |
| Returns the Version within the SBML Level of the package extension of this plugin object. More... | |
| new bool | isValidTypeForList (SBase item) |
| new void | renameMetaIdRefs (string oldid, string newid) |
| Replaces all uses of a given meta identifier attribute value with another value. More... | |
| new void | renameSIdRefs (string oldid, string newid) |
Replaces all uses of a given SIdRef type attribute value with another value. More... | |
| new void | renameUnitSIdRefs (string oldid, string newid) |
Replaces all uses of a given UnitSIdRef type attribute value with another value. More... | |
| int | setElementNamespace (string uri) |
| Sets the XML namespace to which this object belongs. More... | |
Protected Attributes | |
| bool | swigCMemOwn |
| new SBasePlugin libsbmlcs.SBasePlugin.clone | ( | ) |
Creates and returns a deep copy of this SBasePlugin object.
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virtual |
Reimplemented in libsbmlcs.SBMLDocumentPlugin, libsbmlcs.FbcModelPlugin, libsbmlcs.FbcSpeciesPlugin, libsbmlcs.CompSBMLDocumentPlugin, libsbmlcs.CompSBasePlugin, libsbmlcs.MultiCompartmentPlugin, libsbmlcs.CompModelPlugin, libsbmlcs.FbcReactionPlugin, libsbmlcs.FbcSBMLDocumentPlugin, libsbmlcs.MultiSpeciesReferencePlugin, libsbmlcs.MultiSBMLDocumentPlugin, libsbmlcs.MultiSpeciesPlugin, libsbmlcs.QualModelPlugin, libsbmlcs.MultiSimpleSpeciesReferencePlugin, libsbmlcs.MultiModelPlugin, libsbmlcs.MultiListOfReactionsPlugin, libsbmlcs.RenderGraphicalObjectPlugin, libsbmlcs.RenderLayoutPlugin, libsbmlcs.RenderListOfLayoutsPlugin, libsbmlcs.GroupsModelPlugin, libsbmlcs.LayoutModelPlugin, and libsbmlcs.LayoutSpeciesReferencePlugin.
| long libsbmlcs.SBasePlugin.getColumn | ( | ) |
| new SBase libsbmlcs.SBasePlugin.getElementByMetaId | ( | string | metaid | ) |
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. | new SBase libsbmlcs.SBasePlugin.getElementBySId | ( | string | id | ) |
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.
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. | string libsbmlcs.SBasePlugin.getElementNamespace | ( | ) |
Returns the namespace URI of the package to which this plugin object belongs.
| long libsbmlcs.SBasePlugin.getLevel | ( | ) |
Returns the SBML Level of the package extension of this plugin object.
| long libsbmlcs.SBasePlugin.getLine | ( | ) |
| SBaseList libsbmlcs.SBasePlugin.getListOfAllElements | ( | ElementFilter | filter | ) |
| SBaseList libsbmlcs.SBasePlugin.getListOfAllElements | ( | ) |
| string libsbmlcs.SBasePlugin.getPackageName | ( | ) |
Returns the short-form name of the package to which this plugin object belongs.
| long libsbmlcs.SBasePlugin.getPackageVersion | ( | ) |
Returns the package version of the package extension of this plugin object.
| SBase libsbmlcs.SBasePlugin.getParentSBMLObject | ( | ) |
Returns the parent object to which this plugin object is connected.
| string libsbmlcs.SBasePlugin.getPrefix | ( | ) |
Returns the XML namespace prefix of the package to which this plugin object belongs.
| SBMLDocument libsbmlcs.SBasePlugin.getSBMLDocument | ( | ) |
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.
| SBMLExtension libsbmlcs.SBasePlugin.getSBMLExtension | ( | ) |
| string libsbmlcs.SBasePlugin.getURI | ( | ) |
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().
| long libsbmlcs.SBasePlugin.getVersion | ( | ) |
Returns the Version within the SBML Level of the package extension of this plugin object.
| new bool libsbmlcs.SBasePlugin.isValidTypeForList | ( | SBase | item | ) |
| new void libsbmlcs.SBasePlugin.renameMetaIdRefs | ( | string | oldid, |
| string | newid | ||
| ) |
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.
| oldid | the old identifier. |
| newid | the new identifier. |
| new void libsbmlcs.SBasePlugin.renameSIdRefs | ( | string | oldid, |
| string | newid | ||
| ) |
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. |
| new void libsbmlcs.SBasePlugin.renameUnitSIdRefs | ( | string | oldid, |
| string | newid | ||
| ) |
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.
| oldid | the old identifier. |
| newid | the new identifier. |
| int libsbmlcs.SBasePlugin.setElementNamespace | ( | string | uri | ) |
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/'.
| uri | the URI to assign to this object. |
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protected |