libSBML Python API
5.18.0
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Public Member Functions | |
def | __init__ (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | addLayout (self, layout) |
Adds a copy of the layout object to the list of layouts. More... | |
def | clone (self) |
Creates and returns a deep copy of this LayoutModelPlugin object. More... | |
def | createLayout (self) |
Creates a new layout object and adds it to the list of layout objects and returns it. 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 | getLayout (self, args) |
This method has multiple variants; they differ in the arguments they accept. 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 | getListOfLayouts (self, args) |
Returns the ListOfLayouts object for this Model. More... | |
def | getNumLayouts (self) |
Returns the number of layout 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 | 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 | removeLayout (self, n) |
Removes the nth Layout object from this Model object and returns a pointer to it. 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... | |
def libsbml.LayoutModelPlugin.__init__ | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
__init__(string uri, string prefix, LayoutPkgNamespaces layoutns) LayoutModelPlugin __init__(LayoutModelPlugin orig) LayoutModelPlugin
Each variant is described separately below.
LayoutModelPlugin(LayoutModelPlugin orig)
Copy constructor. Creates a copy of this SBase object.
orig | the instance to copy. |
LayoutModelPlugin(string uri, string prefix, LayoutPkgNamespaces layoutns)
Creates a new LayoutModelPlugin object using the given parameters.
'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 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. |
def libsbml.LayoutModelPlugin.addLayout | ( | self, | |
layout | |||
) |
Adds a copy of the layout object to the list of layouts.
addLayout(Layout layout) int
layout | the layout object to be added. |
def libsbml.LayoutModelPlugin.clone | ( | self | ) |
Creates and returns a deep copy of this LayoutModelPlugin object.
clone() LayoutModelPlugin
def libsbml.LayoutModelPlugin.createLayout | ( | self | ) |
Creates a new layout object and adds it to the list of layout objects and returns it.
createLayout() Layout
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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.
metaid | string, the metaid of the object to find. |
metaid
.
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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.
id | string representing the identifier of the object to find. |
id
.
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inherited |
Returns the namespace URI of the package to which this plugin object belongs.
getElementNamespace() string
def libsbml.LayoutModelPlugin.getLayout | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getLayout(long index) Layout getLayout(string sid) Layout
Each variant is described separately below.
getLayout(long index)
Returns the layout object that belongs to the given index. If the index is invalid, None
is returned.
index | the index of list of layout objects. |
getLayout(string sid)
Returns the layout object with the given sid
attribute. If the id is invalid, None
is returned.
sid | the id attribute of the layout object. |
sid
attribute. None is returned if the given sid
is invalid.
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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) SBaseList getListOfAllElements() SBaseList
def libsbml.LayoutModelPlugin.getListOfLayouts | ( | self, | |
args | |||
) |
Returns the ListOfLayouts object for this Model.
getListOfLayouts() ListOfLayouts
def libsbml.LayoutModelPlugin.getNumLayouts | ( | self | ) |
Returns the number of layout objects.
getNumLayouts() int
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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
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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
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inherited |
isValidTypeForList(SBase item) bool
def libsbml.LayoutModelPlugin.removeLayout | ( | self, | |
n | |||
) |
Removes the nth Layout object from this Model object and returns a pointer to it.
removeLayout(long n) Layout
The caller owns the returned object and is responsible for deleting it.
n | the index of the Layout object to remove. |
None
is returned if the given index is out of range.
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inherited |
Replaces all uses of a given meta identifier attribute value with another value.
renameMetaIdRefs(string oldid, string newid)
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. |
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inherited |
Replaces all uses of a given SIdRef
type attribute value with another value.
renameSIdRefs(string oldid, string newid)
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. |
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inherited |
Replaces all uses of a given UnitSIdRef
type attribute value with another value.
renameUnitSIdRefs(string oldid, string newid)
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. |
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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. |