libSBML Python API  5.18.0
libsbml.RenderLayoutPlugin Class Reference
Inheritance diagram for libsbml.RenderLayoutPlugin:
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Detailed Description

render LibSBML implementation for the extension to the Layout class by the Render extension.

The Render package extends the Layout object from the Layout package with the addition of an optional ListOfLocalRenderInformation object.

Public Member Functions

def __init__ (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def addLocalRenderInformation (self, pLRI)
 Adds a copy of the given local render information object to the list of local render information objects. More...
 
def clone (self)
 Creates and returns a deep copy of this RenderLayoutPlugin object. More...
 
def createLocalRenderInformation (self)
 Creates a new local render information object and adds it to the list. More...
 
def getElementByMetaId (self, metaid)
 Return the first child object found with a given meta identifier. More...
 
def getElementBySId (self, id)
 Return the first child object found with a given identifier. More...
 
def getElementNamespace (self)
 Returns the namespace URI of the package to which this plugin object belongs. More...
 
def getLevel (self)
 Returns the SBML Level of the package extension of this plugin object. More...
 
def getListOfAllElements (self, filter=None)
 Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...
 
def getListOfLocalRenderInformation (self, args)
 Returns a pointer to the list object that contains local render information. More...
 
def getNumLocalRenderInformationObjects (self)
 Returns the number of local render information objects. More...
 
def getPackageName (self)
 Returns the short-form name of the package to which this plugin object belongs. More...
 
def getPackageVersion (self)
 Returns the package version of the package extension of this plugin object. More...
 
def getParentSBMLObject (self, args)
 Returns the parent object to which this plugin object is connected. More...
 
def getPrefix (self)
 Returns the XML namespace prefix of the package to which this plugin object belongs. More...
 
def getRenderInformation (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def getSBMLDocument (self, args)
 Returns the SBMLDocument object containing this object instance. More...
 
def getURI (self)
 Returns the XML namespace URI for the package to which this object belongs. More...
 
def getVersion (self)
 Returns the Version within the SBML Level of the package extension of this plugin object. More...
 
def isValidTypeForList (self, item)
 
def removeLocalRenderInformation (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def renameMetaIdRefs (self, oldid, newid)
 Replaces all uses of a given meta identifier attribute value with another value. More...
 
def renameSIdRefs (self, oldid, newid)
 Replaces all uses of a given SIdRef type attribute value with another value. More...
 
def renameUnitSIdRefs (self, oldid, newid)
 Replaces all uses of a given UnitSIdRef type attribute value with another value. More...
 
def setElementNamespace (self, uri)
 Sets the XML namespace to which this object belongs. More...
 

Constructor & Destructor Documentation

def libsbml.RenderLayoutPlugin.__init__ (   self,
  args 
)

This method has multiple variants; they differ in the arguments they accept.

__init__(string uri, string prefix, RenderPkgNamespaces groupsns)   RenderLayoutPlugin
__init__(RenderLayoutPlugin orig)   RenderLayoutPlugin

Each variant is described separately below.


Method variant with the following signature:
RenderLayoutPlugin(RenderLayoutPlugin orig)

Copy constructor. Creates a copy of this SBase object.


Method variant with the following signature:
RenderLayoutPlugin(string uri, string prefix, RenderPkgNamespaces groupsns)

Constructor

Member Function Documentation

def libsbml.RenderLayoutPlugin.addLocalRenderInformation (   self,
  pLRI 
)

Adds a copy of the given local render information object to the list of local render information objects.

addLocalRenderInformation(LocalRenderInformation pLRI)

If an object with the same id exists, it is replaced.

def libsbml.RenderLayoutPlugin.clone (   self)

Creates and returns a deep copy of this RenderLayoutPlugin object.

clone()   RenderLayoutPlugin
Returns
a (deep) copy of this RenderLayoutPlugin object
def libsbml.RenderLayoutPlugin.createLocalRenderInformation (   self)

Creates a new local render information object and adds it to the list.

createLocalRenderInformation()   LocalRenderInformation

The created object does not have a id and it is the responsibility of the calling code to ensure that it gets one. For constraints on the id, please consult the render information document.

def libsbml.SBasePlugin.getElementByMetaId (   self,
  metaid 
)
inherited

Return the first child object found with a given meta identifier.

getElementByMetaId(string metaid)   SBase

This method searches all the subobjects under this one, compares their meta identifiers to metaid, and returns the first one that machines.

Parameters
metaidstring, the metaid of the object to find.
Returns
pointer to the first object found with the given metaid.
def libsbml.SBasePlugin.getElementBySId (   self,
  id 
)
inherited

Return the first child object found with a given identifier.

getElementBySId(string id)   SBase

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
idstring representing the identifier of the object to find.
Returns
pointer to the first object with the given id.
def libsbml.SBasePlugin.getElementNamespace (   self)
inherited

Returns the namespace URI of the package to which this plugin object belongs.

getElementNamespace()   string
Returns
the XML namespace URI of the SBML Level 3 package implemented by this libSBML package extension.
def libsbml.SBasePlugin.getLevel (   self)
inherited

Returns the SBML Level of the package extension of this plugin object.

getLevel()   long
Returns
the SBML Level.
See also
getVersion()
def libsbml.SBasePlugin.getListOfAllElements (   self,
  filter = None 
)
inherited

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

getListOfAllElements(ElementFilter filter)   SBaseList
getListOfAllElements()   SBaseList
Returns
a list of all objects that are children of this object.
def libsbml.RenderLayoutPlugin.getListOfLocalRenderInformation (   self,
  args 
)

Returns a pointer to the list object that contains local render information.

getListOfLocalRenderInformation()   ListOfLocalRenderInformation
 
def libsbml.RenderLayoutPlugin.getNumLocalRenderInformationObjects (   self)

Returns the number of local render information objects.

getNumLocalRenderInformationObjects()   long
 
def libsbml.SBasePlugin.getPackageName (   self)
inherited

Returns the short-form name of the package to which this plugin object belongs.

getPackageName()   string
Returns
the short-form package name (or nickname) of the SBML package implemented by this package extension.
def libsbml.SBasePlugin.getPackageVersion (   self)
inherited

Returns the package version of the package extension of this plugin object.

getPackageVersion()   long
Returns
the package version of the package extension of this plugin object.
See also
getLevel()
getVersion()
def libsbml.SBasePlugin.getParentSBMLObject (   self,
  args 
)
inherited

Returns the parent object to which this plugin object is connected.

getParentSBMLObject()   SBase
Returns
the parent object of this object.
def libsbml.SBasePlugin.getPrefix (   self)
inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

getPrefix()   string
Returns
the XML namespace prefix of the SBML Level 3 package implemented by this libSBML package extension.
def libsbml.RenderLayoutPlugin.getRenderInformation (   self,
  args 
)

This method has multiple variants; they differ in the arguments they accept.

getRenderInformation(long  index)   LocalRenderInformation
getRenderInformation(string id)   LocalRenderInformation

Each variant is described separately below.


Method variant with the following signature:
getRenderInformation(long index)

Returns a pointer to the local render information object with the given index. If the index is invalid, None is returned.


Method variant with the following signature:
getRenderInformation(string id)

Returns a pointer to the local render information object with the given id. If no object with the given id exists, None is returned.

def libsbml.SBasePlugin.getSBMLDocument (   self,
  args 
)
inherited

Returns the SBMLDocument object containing this object instance.

getSBMLDocument()   SBMLDocument
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()
def libsbml.SBasePlugin.getURI (   self)
inherited

Returns the XML namespace URI for the package to which this object belongs.

getURI()   string
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()
def libsbml.SBasePlugin.getVersion (   self)
inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

getVersion()   long
Returns
the SBML Version.
See also
getLevel()
def libsbml.SBasePlugin.isValidTypeForList (   self,
  item 
)
inherited
isValidTypeForList(SBase item)   bool
 
def libsbml.RenderLayoutPlugin.removeLocalRenderInformation (   self,
  args 
)

This method has multiple variants; they differ in the arguments they accept.

removeLocalRenderInformation(long  index)   LocalRenderInformation
removeLocalRenderInformation(string id)   LocalRenderInformation

Each variant is described separately below.


Method variant with the following signature:
removeLocalRenderInformation(long index)

Removed the render information with the given index from the list. The removed object is returned. It is the responsibility of the calling code to delete the object. If the index is not valid, None is returned.


Method variant with the following signature:
removeLocalRenderInformation(string id)

Removed the render information with the given id from the list. The removed object is returned. It is the responsibility of the calling code to delete the object. If an object with the given id does not exist, None is returned.

def libsbml.SBasePlugin.renameMetaIdRefs (   self,
  oldid,
  newid 
)
inherited

Replaces all uses of a given meta identifier attribute value with another value.

renameMetaIdRefs(string oldid, string newid)
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
oldidthe old identifier.
newidthe new identifier.
def libsbml.SBasePlugin.renameSIdRefs (   self,
  oldid,
  newid 
)
inherited

Replaces all uses of a given SIdRef type attribute value with another value.

renameSIdRefs(string oldid, string newid)
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
oldidthe old identifier.
newidthe new identifier.
def libsbml.SBasePlugin.renameUnitSIdRefs (   self,
  oldid,
  newid 
)
inherited

Replaces all uses of a given UnitSIdRef type attribute value with another value.

renameUnitSIdRefs(string oldid, string newid)
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
oldidthe old identifier.
newidthe new identifier.
def libsbml.SBasePlugin.setElementNamespace (   self,
  uri 
)
inherited

Sets the XML namespace to which this object belongs.

setElementNamespace(string uri)   int
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.
Returns
integer value indicating success/failure of the function. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
See also
getElementNamespace()