| libsbmlcs.LayoutSpeciesReferencePlugin.LayoutSpeciesReferencePlugin |
( |
string |
uri, |
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|
string |
prefix, |
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|
LayoutPkgNamespaces |
layoutns |
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) |
| |
Creates a new LayoutSpeciesReferencePlugin 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. |
| new SBase libsbmlcs.SBasePlugin.getElementBySId |
( |
string |
id | ) |
|
|
inherited |
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.
- Parameters
-
| id | string representing the identifier of the object to find. |
- Returns
- pointer to the first object with the given
id.
| SBMLDocument libsbmlcs.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()
| string libsbmlcs.SBasePlugin.getURI |
( |
| ) |
|
|
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()
| new void libsbmlcs.SBasePlugin.renameMetaIdRefs |
( |
string |
oldid, |
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|
string |
newid |
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) |
| |
|
inherited |
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. |
| new void libsbmlcs.SBasePlugin.renameSIdRefs |
( |
string |
oldid, |
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|
string |
newid |
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) |
| |
|
inherited |
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. |
| new void libsbmlcs.SBasePlugin.renameUnitSIdRefs |
( |
string |
oldid, |
|
|
string |
newid |
|
) |
| |
|
inherited |
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. |
