libSBML Python API  5.11.0
libsbml.CompModelPlugin Class Reference
Inheritance diagram for libsbml.CompModelPlugin:
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Detailed Description

comp Extension of Model.

The CompModelPlugin class inherits from the SBMLSBasePlugin class, and codifies the extentions to the Model class defined in the SBML Level 3 Hierarchical Model Composition package (“comp”). This extention allows a Model to define Submodels (other Models that are instantiated as new parts of the parent Model), and Ports, a defined interface for including the given Model as a Submodel of a different Model.

Submodels are stored in an optional child ListOfSubmodels object, which, if present, must contain one or more Submodel objects. All of the Submodels present in the ListOfSubmodels are defined to be instantiated in the 'complete' Model.

Ports are stored in an optional child ListOfPorts object, which, if present, must contain one or more Port objects. All of the Ports present in the ListOfPorts collectively define the 'port interface' of the Model.

Public Member Functions

def __init__ (self, args)
 comp Extension of Model. More...
 
def addPort (self, port)
 Adds a copy of the given Port object to the list of ports. More...
 
def addReplacedElement (self, replacedElement)
 Adds a copy of the given ReplacedElement object to the list of ReplacedElements. More...
 
def addSubmodel (self, submodel)
 Adds a copy of the given Submodel object to the list of submodels. More...
 
def clearReplacedElements (self)
 Remove all ReplacedElements, if any exist. More...
 
def clone (self)
 Creates and returns a deep copy of this CompModelPlugin object. More...
 
def createPort (self)
 Creates a Port object, adds it to the end of the port objects list and returns a pointer to the newly created object. More...
 
def createReplacedBy (self)
 Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy. More...
 
def createReplacedElement (self)
 Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object. More...
 
def createSubmodel (self)
 Creates a Submodel object, adds it to the end of the submodel objects list and returns a pointer to the newly created object. More...
 
def getDivider (self)
 Get the string used as the divider between names when renaming and flattening models. More...
 
def getElementByMetaId (self, metaid)
 Returns the first child element it can find with the given meta identifier, or itself if it has the given metaid, or None if no such object is found. More...
 
def getElementBySId (self, id)
 Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found. More...
 
def getElementNamespace (self)
  Base class for extending SBML objects in packages. More...
 
def getLevel (self)
 Returns the SBML Level of the package extension of this plugin object. More...
 
def getListOfAllElements
 Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...
 
def getListOfPorts (self)
 Returns the ListOf object that holds all ports. More...
 
def getListOfReplacedElements (self)
 Returns the ListOf object that holds all replacedElements. More...
 
def getListOfSubmodels (self)
 Returns the ListOf object that holds all submodels. More...
 
def getNumPorts (self)
 Returns the number of ports for this CompModelPlugin. More...
 
def getNumReplacedElements (self)
 Returns the number of ReplacedElements for this CompSBasePlugin. More...
 
def getNumSubmodels (self)
 Returns the number of submodels for this CompModelPlugin. 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 getPort (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def getPrefix (self)
 Returns the XML namespace prefix of the package to which this plugin object belongs. More...
 
def getReplacedBy (self, args)
 Get the child ReplacedBy of this SBase. More...
 
def getReplacedElement (self, args)
 Returns the ReplacedElement with the given index. More...
 
def getSBMLDocument (self, args)
 Returns the SBMLDocument object containing this object instance. More...
 
def getSubmodel (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def getTransformer (self)
 
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 isSetReplacedBy (self)
 Predicate for testing whether the ReplacedBy for this SBase is set. More...
 
def isSetTransformer (self)
 
def logInvalidId (self, attribute, wrongattribute)
 Helper to log a common type of error. More...
 
def removePort (self, index)
 Removes the port with the given index. More...
 
def removeReplacedElement (self, index)
 Removes the ReplacedElement with the given index. More...
 
def removeSubmodel (self, index)
 Removes the submodel with the given index. More...
 
def setDivider (self, divider)
 Set the string used as the divider between names when renaming and flattening models. More...
 
def setElementNamespace (self, uri)
 Sets the XML namespace to which this object belongs. More...
 
def setReplacedBy (self, replacedBy)
 Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance. More...
 
def setTransformer (self, transformer)
 
def unsetReplacedBy (self)
 Unsets the child ReplacedBy of this SBase. More...
 
def unsetTransformer (self)
 Unsets any custom prefix transformers. More...
 

Member Function Documentation

def libsbml.CompModelPlugin.addPort (   self,
  port 
)

Adds a copy of the given Port object to the list of ports.

addPort(Port port)   int
Parameters
portthe Port object to be added to the list of ports. Fails if the added port is None, does not match the level/version/package of the parent object, or cannot be added to the list of ports.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.CompSBasePlugin.addReplacedElement (   self,
  replacedElement 
)
inherited

Adds a copy of the given ReplacedElement object to the list of ReplacedElements.

addReplacedElement(ReplacedElement replacedElement)   int
Parameters
replacedElementthe ReplacedElement object to be added to the list of ReplacedElements. Fails if the added ReplacedElement is None, does not match the level/version/package of the parent object, or cannot be added to the list of replaced elements.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.CompModelPlugin.addSubmodel (   self,
  submodel 
)

Adds a copy of the given Submodel object to the list of submodels.

addSubmodel(Submodel submodel)   int

Fails if the added submodel is None, does not match the level/version/package of the parent object, or cannot be added to the list of submodels.

Parameters
submodelthe Submodel object to be added to the list of submodels.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.CompSBasePlugin.clearReplacedElements (   self)
inherited

Remove all ReplacedElements, if any exist.

clearReplacedElements()
def libsbml.CompModelPlugin.clone (   self)

Creates and returns a deep copy of this CompModelPlugin object.

clone()   CompModelPlugin
Returns
a (deep) copy of this CompModelPlugin object
def libsbml.CompModelPlugin.createPort (   self)

Creates a Port object, adds it to the end of the port objects list and returns a pointer to the newly created object.

createPort()   Port
Returns
a newly created Port object
def libsbml.CompSBasePlugin.createReplacedBy (   self)
inherited

Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy.

createReplacedBy()   ReplacedBy
Returns
the newly created ReplacedBy object instance
def libsbml.CompSBasePlugin.createReplacedElement (   self)
inherited

Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object.

createReplacedElement()   ReplacedElement
Returns
a newly created ReplacedElement object
def libsbml.CompModelPlugin.createSubmodel (   self)

Creates a Submodel object, adds it to the end of the submodel objects list and returns a pointer to the newly created object.

createSubmodel()   Submodel
Returns
a newly created Submodel object
def libsbml.CompModelPlugin.getDivider (   self)

Get the string used as the divider between names when renaming and flattening models.

getDivider()   string

The divider string consists of two underscore characters ("__") by default, and can be overridden with the setDivider() function.

See also
setDivider()
def libsbml.CompModelPlugin.getElementByMetaId (   self,
  metaid 
)

Returns the first child element it can find with the given meta identifier, or itself if it has the given metaid, or None if no such object is found.

getElementByMetaId(string metaid)   SBase
Parameters
metaida string representing the metaid of objects to find.
Returns
a pointer to the SBase element with the given metaid.
def libsbml.CompModelPlugin.getElementBySId (   self,
  id 
)

Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.

getElementBySId(string id)   SBase
Parameters
ida string representing the id of objects to find.
Returns
a pointer to the SBase element with the given id.
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=None)   SBaseList
getListOfAllElements()   SBaseList
Returns
a list of all objects that are children of this object.
def libsbml.CompModelPlugin.getListOfPorts (   self)

Returns the ListOf object that holds all ports.

getListOfPorts()   ListOfPorts
Returns
the ListOf object that holds all ports.
def libsbml.CompSBasePlugin.getListOfReplacedElements (   self)
inherited

Returns the ListOf object that holds all replacedElements.

getListOfReplacedElements()   ListOfReplacedElements
Returns
the ListOf object that holds all replacedElements.
def libsbml.CompModelPlugin.getListOfSubmodels (   self)

Returns the ListOf object that holds all submodels.

getListOfSubmodels()   ListOfSubmodels
Returns
the ListOf object that holds all submodels.
def libsbml.CompModelPlugin.getNumPorts (   self)

Returns the number of ports for this CompModelPlugin.

getNumPorts()   long
Returns
the number of ports for this CompModelPlugin.
def libsbml.CompSBasePlugin.getNumReplacedElements (   self)
inherited

Returns the number of ReplacedElements for this CompSBasePlugin.

getNumReplacedElements()   long
Returns
the number of ReplacedElements for this CompSBasePlugin.
def libsbml.CompModelPlugin.getNumSubmodels (   self)

Returns the number of submodels for this CompModelPlugin.

getNumSubmodels()   long
Returns
the number of submodels for this CompModelPlugin.
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.CompModelPlugin.getPort (   self,
  args 
)

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

getPort(long n)   Port
getPort(string id)   Port

Each variant is described separately below.


Method variant with the following signature:
getPort(long n)

Returns the port with the given index.

Parameters
nthe index number of the Port to get.
Returns
the nth Port in the ListOfPorts. If the index n is invalid, None is returned.

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

Returns the port with the given identifier.

Parameters
idthe id of the Port to get.
Returns
the Port in the ListOfPorts with the given identifier. If the identifier is invalid, None is returned.
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.CompSBasePlugin.getReplacedBy (   self,
  args 
)
inherited

Get the child ReplacedBy of this SBase.

getReplacedBy()   ReplacedBy
Returns
the ReplacedBy child of this SBase
def libsbml.CompSBasePlugin.getReplacedElement (   self,
  args 
)
inherited

Returns the ReplacedElement with the given index.

getReplacedElement(long n)   ReplacedElement
Parameters
nthe index number of the ReplacedElement to get.
Returns
the nth ReplacedElement in the ListOfReplacedElements. If the index is invalid, 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.CompModelPlugin.getSubmodel (   self,
  args 
)

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

getSubmodel(long n)   Submodel
getSubmodel(string id)   Submodel

Each variant is described separately below.


Method variant with the following signature:
getSubmodel(long n)

Returns the submodel with the given index.

Parameters
nthe index number of the Submodel to get.
Returns
the nth Submodel in the ListOfSubmodels. If the index n is invalid, None is returned.

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

Returns the submodel with the given identifier.

Parameters
idthe identifier of the Submodel to get.
Returns
the Submodel in the ListOfSubmodels with the given identifier. If no submodel with identifier id exists, None is returned.
def libsbml.CompModelPlugin.getTransformer (   self)
getTransformer()   PrefixTransformer *
Returns
any custom transformer set for prefix operations, will be None by default.
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()
SBMLDocument.getSBMLNamespaces()
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.CompSBasePlugin.isSetReplacedBy (   self)
inherited

Predicate for testing whether the ReplacedBy for this SBase is set.

isSetReplacedBy()   bool
Returns
True if the ReplacedBy of this SBase is set, False otherwise.
def libsbml.CompModelPlugin.isSetTransformer (   self)
isSetTransformer()   bool
Returns
an indicator, whether a custom transformer has been set.
def libsbml.CompSBasePlugin.logInvalidId (   self,
  attribute,
  wrongattribute 
)
inherited

Helper to log a common type of error.

logInvalidId(string attribute, string wrongattribute)
def libsbml.CompModelPlugin.removePort (   self,
  index 
)

Removes the port with the given index.

removePort(long index)   Port
Parameters
indexthe index of the Port object to remove
Returns
the Port object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.CompSBasePlugin.removeReplacedElement (   self,
  index 
)
inherited

Removes the ReplacedElement with the given index.

removeReplacedElement(long index)   ReplacedElement

A pointer to the ReplacedElement that was removed is returned. If no ReplacedElement has been removed, None is returned.

Parameters
indexthe index of the ReplacedElement object to remove
Returns
the ReplacedElement object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.CompModelPlugin.removeSubmodel (   self,
  index 
)

Removes the submodel with the given index.

removeSubmodel(long index)   Submodel

A pointer to the submodel that was removed is returned.

Parameters
indexthe index of the Submodel object to remove
Returns
the Submodel object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range and no submodel has been removed, None is returned.
def libsbml.CompModelPlugin.setDivider (   self,
  divider 
)

Set the string used as the divider between names when renaming and flattening models.

setDivider(string divider)   int

The divider string consists of two underscore characters ("__") by default. This method will fail if called with an empty divider, or a divider that cannot be used internally as part of a valid SBML SId.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
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. The possible values returned by this function are:
See also
getElementNamespace()
def libsbml.CompSBasePlugin.setReplacedBy (   self,
  replacedBy 
)
inherited

Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance.

setReplacedBy(ReplacedBy replacedBy)   int

This method fails if the added ReplacedBy does not match the level/version/package of the parent object or if the added ReplacedBy cannot be copied.

Parameters
replacedBythe ReplacedBy object instance to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.CompModelPlugin.setTransformer (   self,
  transformer 
)
setTransformer(PrefixTransformer * transformer)
Sets the custom transformer that is to be used, instead of the standard
prefixing with the given divider. This makes it possible to finely control
how elements are altered.
If not set, only ids and meta ids will be prefixed.
NOTE: the model plugin only holds the pointer to the element it does not 
take ownership of it. Thus the calling program is responsible of 
freeing the transformer when no longer needed (i.e after the 
SBML document has been deleted)
 
def libsbml.CompSBasePlugin.unsetReplacedBy (   self)
inherited

Unsets the child ReplacedBy of this SBase.

unsetReplacedBy()   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.CompModelPlugin.unsetTransformer (   self)

Unsets any custom prefix transformers.

unsetTransformer()