libSBML Python API
5.11.0
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The CompSBasePlugin class inherits from the SBasePlugin class, and codifies the extentions to the SBase class defined in the Hierarchical Model Composition package (“comp”). This extention allows the modeler to define one or more submodel elements which the parent SBase object replaces, and/or a single submodel element which replaces the parent SBase object. This is accomplished through the addition of an optional ListOfReplacedElements child, which may contain one or more ReplacedElement objects, each of which references a submodel object to be replaced by the containing SBase object, and through the addition of a single optional ReplacedBy child, which references a submodel object which is to replace the containing SBase object. If a single SBase element both contains a ListOfReplacedElements and has a ReplacedBy child, it and all the referenced ReplacedElement objects are to be replaced by the object referenced by the ReplacedBy element.
Public Member Functions | |
def | __init__ (self, args) |
comp
Extension of SBase. More... | |
def | addReplacedElement (self, replacedElement) |
Adds a copy of the given ReplacedElement object to the list of ReplacedElements. More... | |
def | clearReplacedElements (self) |
Remove all ReplacedElements, if any exist. More... | |
def | clone (self) |
Creates and returns a deep copy of this CompSBasePlugin 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 | getElementByMetaId (self, metaid) |
Returns the first child element it can find with the given metaid , 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 | getListOfReplacedElements (self) |
Returns the ListOf object that holds all replacedElements. More... | |
def | getNumReplacedElements (self) |
Returns the number of ReplacedElements for this CompSBasePlugin. 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 | 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 | 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 | logInvalidId (self, attribute, wrongattribute) |
Helper to log a common type of error. More... | |
def | removeReplacedElement (self, index) |
Removes the ReplacedElement with the given index. 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 | unsetReplacedBy (self) |
Unsets the child ReplacedBy of this SBase. More... | |
def libsbml.CompSBasePlugin.addReplacedElement | ( | self, | |
replacedElement | |||
) |
Adds a copy of the given ReplacedElement object to the list of ReplacedElements.
addReplacedElement(ReplacedElement replacedElement) int
replacedElement | the 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. |
def libsbml.CompSBasePlugin.clearReplacedElements | ( | self | ) |
Remove all ReplacedElements, if any exist.
clearReplacedElements()
def libsbml.CompSBasePlugin.clone | ( | self | ) |
Creates and returns a deep copy of this CompSBasePlugin object.
clone() CompSBasePlugin
def libsbml.CompSBasePlugin.createReplacedBy | ( | self | ) |
Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy.
createReplacedBy() ReplacedBy
def libsbml.CompSBasePlugin.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.
createReplacedElement() ReplacedElement
def libsbml.CompSBasePlugin.getElementByMetaId | ( | self, | |
metaid | |||
) |
Returns the first child element it can find with the given metaid
, or itself if it has the given metaid
, or None
if no such object is found.
getElementByMetaId(string metaid) SBase
metaid | string representing the metaid of objects to find |
metaid
. def libsbml.CompSBasePlugin.getElementBySId | ( | self, | |
id | |||
) |
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inherited |
Returns the SBML Level of the package extension of this plugin object.
getLevel() long
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inherited |
Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.
getListOfAllElements(ElementFilter filter=None) SBaseList getListOfAllElements() SBaseList
def libsbml.CompSBasePlugin.getListOfReplacedElements | ( | self | ) |
Returns the ListOf object that holds all replacedElements.
getListOfReplacedElements() ListOfReplacedElements
def libsbml.CompSBasePlugin.getNumReplacedElements | ( | self | ) |
Returns the number of ReplacedElements for this CompSBasePlugin.
getNumReplacedElements() long
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inherited |
Returns the short-form name of the package to which this plugin object belongs.
getPackageName() string
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inherited |
Returns the package version of the package extension of this plugin object.
getPackageVersion() long
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inherited |
Returns the parent object to which this plugin object is connected.
getParentSBMLObject() SBase
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inherited |
Returns the XML namespace prefix of the package to which this plugin object belongs.
getPrefix() string
def libsbml.CompSBasePlugin.getReplacedBy | ( | self, | |
args | |||
) |
Get the child ReplacedBy of this SBase.
getReplacedBy() ReplacedBy
def libsbml.CompSBasePlugin.getReplacedElement | ( | self, | |
args | |||
) |
Returns the ReplacedElement with the given index.
getReplacedElement(long n) ReplacedElement
n | the index number of the ReplacedElement to get. |
None
is returned.
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inherited |
Returns the SBMLDocument object containing this object instance.
getSBMLDocument() SBMLDocument
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
Returns the XML namespace URI for the package to which this object belongs.
getURI() string
'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().
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inherited |
Returns the Version within the SBML Level of the package extension of this plugin object.
getVersion() long
def libsbml.CompSBasePlugin.isSetReplacedBy | ( | self | ) |
Predicate for testing whether the ReplacedBy for this SBase is set.
isSetReplacedBy() bool
True
if the ReplacedBy of this SBase is set, False
otherwise. def libsbml.CompSBasePlugin.logInvalidId | ( | self, | |
attribute, | |||
wrongattribute | |||
) |
Helper to log a common type of error.
logInvalidId(string attribute, string wrongattribute)
def libsbml.CompSBasePlugin.removeReplacedElement | ( | self, | |
index | |||
) |
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.
index | the index of the ReplacedElement object to remove |
None
is returned if the given index is out of range.
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inherited |
Sets the XML namespace to which this object belongs.
setElementNamespace(string uri) int
'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. |
def libsbml.CompSBasePlugin.setReplacedBy | ( | self, | |
replacedBy | |||
) |
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.
replacedBy | the ReplacedBy object instance to use. |
def libsbml.CompSBasePlugin.unsetReplacedBy | ( | self | ) |
Unsets the child ReplacedBy of this SBase.
unsetReplacedBy() int