libsbml.Parameter Class Reference

Inheritance diagram for libsbml.Parameter:

Detailed Description

LibSBML implementation of SBML's Parameter construct.

A Parameter is used in SBML to define a symbol associated with a value; this symbol can then be used in mathematical formulas in a model. By default, parameters have constant value for the duration of a simulation, and for this reason are called parameters instead of variables in SBML, although it is crucial to understand that SBML parameters represent both concepts. Whether a given SBML parameter is intended to be constant or variable is indicated by the value of its 'constant' attribute.

SBML's Parameter has a required attribute, 'id', that gives the parameter a unique identifier by which other parts of an SBML model definition can refer to it. A parameter can also have an optional 'name' attribute of type string. Identifiers and names must be used according to the guidelines described in the SBML specifications.

The optional attribute 'value' determines the value (of type float) assigned to the parameter. A missing value for 'value' implies that the value either is unknown, or to be obtained from an external source, or determined by an initial assignment. The unit of measurement associated with the value of the parameter can be specified using the optional attribute 'units'. Here we only mention briefly some notable points about the possible unit choices, but readers are urged to consult the SBML specification documents for more information:

In SBML Level 3, there are no constraints on the units that can be assigned to parameters in a model; there are also no units to inherit from the enclosing Model object (unlike the case for, e.g., Species and Compartment).
In SBML Level 2, the value assigned to the parameter's 'units' attribute must be chosen from one of the following possibilities: one of the base unit identifiers defined in SBML; one of the built-in unit identifiers 'substance', 'time', 'volume', 'area' or 'length'; or the identifier of a new unit defined in the list of unit definitions in the enclosing Model structure. There are no constraints on the units that can be chosen from these sets. There are no default units for parameters.

The Parameter structure has another boolean attribute named 'constant' that is used to indicate whether the parameter's value can vary during a simulation. (In SBML Level 3, the attribute is mandatory and must be given a value; in SBML Levels below Level 3, the attribute is optional.) A value of true indicates the parameter's value cannot be changed by any construct except InitialAssignment. Conversely, if the value of 'constant' is false, other constructs in SBML, such as rules and events, can change the value of the parameter.

SBML Level 3 uses a separate object class, LocalParameter, for parameters that are local to a Reaction's KineticLaw. In Levels prior to SBML Level 3, the Parameter class is used both for definitions of global parameters, as well as reaction-local parameters stored in a list within KineticLaw objects. Parameter objects that are local to a reaction (that is, those defined within the KineticLaw structure of a Reaction) cannot be changed by rules and therefore are implicitly always constant; consequently, in SBML Level 2, parameter definitions within Reaction structures should not have their 'constant' attribute set to false.

What if a global parameter has its 'constant' attribute set to false, but the model does not contain any rules, events or other constructs that ever change its value over time? Although the model may be suspect, this situation is not strictly an error. A value of false for 'constant' only indicates that a parameter can change value, not that it must.

As with all other major SBML components, Parameter is derived from SBase, and the methods defined on SBase are available on Parameter.

Note:: The use of the term parameter in SBML sometimes leads to confusion among readers who have a particular notion of what something called 'parameter' should be. It has been the source of heated debate, but despite this, no one has yet found an adequate replacement term that does not have different connotations to different people and hence leads to confusion among some subset of users. Perhaps it would have been better to have two constructs, one called constants and the other called variables. The current approach in SBML is simply more parsimonious, using a single Parameter construct with the boolean flag 'constant' indicating which flavor it is. In any case, readers are implored to look past their particular definition of a parameter and simply view SBML's Parameter as a single mechanism for defining both constants and (additional) variables in a model. (We write additional because the species in a model are usually considered to be the central variables.) After all, software tools are not required to expose to users the actual names of particular SBML constructs, and thus tools can present to their users whatever terms their designers feel best matches their target audience.

See also:: ListOfParameters

Public Member Functions
def	addCVTerm
def	appendAnnotation
def	appendNotes
def	clone
def	disablePackage
def	enablePackage
def	getAncestorOfType
def	getAnnotation
def	getAnnotationString
def	getColumn
def	getConstant
def	getCVTerm
def	getCVTerms
def	getDerivedUnitDefinition
def	getElementByMetaId
def	getElementBySId
def	getElementName
def	getId
def	getLevel
def	getLine
def	getListOfAllElements
def	getListOfAllElementsFromPlugins
def	getMetaId
def	getModel
def	getModelHistory
def	getName
def	getNamespaces
def	getNotes
def	getNotesString
def	getNumCVTerms
def	getNumPlugins
def	getPackageName
def	getPackageVersion
def	getParentSBMLObject
def	getPlugin
def	getResourceBiologicalQualifier
def	getResourceModelQualifier
def	getSBMLDocument
def	getSBOTerm
def	getSBOTermID
def	getTypeCode
def	getUnits
def	getValue
def	getVersion
def	hasRequiredAttributes
def	hasValidLevelVersionNamespaceCombination
def	initDefaults
def	isPackageEnabled
def	isPackageURIEnabled
def	isPkgEnabled
def	isPkgURIEnabled
def	isSetAnnotation
def	isSetConstant
def	isSetId
def	isSetMetaId
def	isSetModelHistory
def	isSetName
def	isSetNotes
def	isSetSBOTerm
def	isSetUnits
def	isSetValue
def	matchesSBMLNamespaces
def	removeFromParentAndDelete
def	renameMetaIdRefs
def	renameSIdRefs
def	renameUnitSIdRefs
def	setAnnotation
def	setConstant
def	setId
def	setMetaId
def	setModelHistory
def	setName
def	setNamespaces
def	setNotes
def	setSBOTerm
def	setUnits
def	setValue
def	toSBML
def	unsetAnnotation
def	unsetCVTerms
def	unsetId
def	unsetMetaId
def	unsetModelHistory
def	unsetName
def	unsetNotes
def	unsetSBOTerm
def	unsetUnits
def	unsetValue

Member Function Documentation

def libsbml.SBase.addCVTerm	(	self,
		args
	)		`[inherited]`

Python method signature(s):

addCVTerm(CVTerm term, bool newBag = False)    int
addCVTerm(CVTerm term)    int

Adds a copy of the given CVTerm object to this SBML object.

Parameters:

	term	the CVTerm to assign
	newBag	if `true`, creates a new RDF bag with the same identifier as a previous bag, and if `false`, adds the term to an existing RDF bag with the same type of qualifier as the term being added.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS
LIBSBML_OPERATION_FAILED
LIBSBML_UNEXPECTED_ATTRIBUTE , if this object lacks a 'metaid' attribute
LIBSBML_INVALID_OBJECT

Note:: Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.

Warning:: The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

def libsbml.SBase.appendAnnotation	(	self,
		args
	)		`[inherited]`

Python method signature(s):

appendAnnotation(XMLNode annotation)    int
appendAnnotation(string annotation)    int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

appendAnnotation(XMLNode annotation)

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters:

annotation

an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See also:: getAnnotationString(); isSetAnnotation(); setAnnotation(); setAnnotation(); appendAnnotation(); unsetAnnotation()

Method variant with the following signature:

appendAnnotation(string annotation)

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters:

annotation

an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See also:: getAnnotationString(); isSetAnnotation(); setAnnotation(); setAnnotation(); appendAnnotation(); unsetAnnotation()

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

def libsbml.SBase.appendNotes	(	self,
		args
	)		`[inherited]`

Python method signature(s):

appendNotes(XMLNode notes)    int
appendNotes(string notes)    int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

appendNotes(string notes)

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters:

notes

an XML string that is to appended to the content of the 'notes' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See also:: getNotesString(); isSetNotes(); setNotes(); setNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:

appendNotes(XMLNode notes)

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters:

notes

an XML node structure that is to appended to the content of the 'notes' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See also:: getNotesString(); isSetNotes(); setNotes(); setNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.Parameter.clone ( self )

Python method signature(s):

clone()    Parameter

Creates and returns a deep copy of this Parameter.

Returns:: a (deep) copy of this Parameter.

Reimplemented from libsbml.SBase.

Reimplemented in libsbml.LocalParameter.

def libsbml.SBase.disablePackage	(	self,
		args
	)		`[inherited]`

Python method signature(s):

disablePackage(string pkgURI, string pkgPrefix)    int

Disables the given SBML Level 3 package

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters:

	pkgURI	the URI of the package
	pkgPrefix	the XML prefix of the package

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.SBase.enablePackage	(	self,
		args
	)		`[inherited]`

Python method signature(s):

enablePackage(string pkgURI, string pkgPrefix, bool flag)    int

Enables or disables the given SBML Level 3 package

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters:

	pkgURI	the URI of the package
	pkgPrefix	the XML prefix of the package
	flag	whether to enable (`true`) or disable (`false`) the package

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.SBase.getAncestorOfType	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getAncestorOfType(int type, string pkgName = "core")    SBase
getAncestorOfType(int type)    SBase
getAncestorOfType(int type, string pkgName = "core")    SBase
getAncestorOfType(int type)    SBase

Returns the first ancestor object that has the given SBML type code.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters:

	type	the SBML type code of the object sought
	pkgName	(optional) the short name of an SBML Level 3 package to which the sought-after object must belong

Returns:: the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or None if no ancestor exists.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

def libsbml.SBase.getAnnotation ( self ) [inherited]

Python method signature(s):

getAnnotation()    XMLNode

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns:: the annotation of this SBML object as a tree of XMLNode objects.

See also:: getAnnotationString(); isSetAnnotation(); setAnnotation(); setAnnotation(); appendAnnotation(); appendAnnotation(); unsetAnnotation()

def libsbml.SBase.getAnnotationString ( self ) [inherited]

Python method signature(s):

getAnnotationString()    string

Returns the content of the 'annotation' subelement of this object as a character string.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form.

Returns:: the annotation of this SBML object as a character string.

See also:: getAnnotation(); isSetAnnotation(); setAnnotation(); setAnnotation(); appendAnnotation(); appendAnnotation(); unsetAnnotation()

def libsbml.SBase.getColumn ( self ) [inherited]

Python method signature(s):

getColumn()    long

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns:: the column number of this SBML object.

Note:: The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also:: getLine()

def libsbml.Parameter.getConstant ( self )

Python method signature(s):

getConstant()    bool

Gets the value of the 'constant' attribute of this Parameter instance.

Returns:: true if this Parameter is declared as being constant, false otherwise.

Note:: Readers who view the documentation for LocalParameter may be confused about the presence of this method. LibSBML derives LocalParameter from Parameter; however, this does not precisely match the object hierarchy defined by SBML Level 3, where LocalParameter is derived directly from SBase and not Parameter. We believe this arrangement makes it easier for libSBML users to program applications that work with both SBML Level 2 and SBML Level 3, but programmers should also keep in mind this difference exists. A side-effect of libSBML's scheme is that certain methods on LocalParameter that are inherited from Parameter do not actually have relevance to LocalParameter objects. An example of this is the methods pertaining to Parameter's attribute 'constant' (i.e., isSetConstant(), setConstant(), and getConstant()).

See also:: isSetConstant(); setConstant()

def libsbml.SBase.getCVTerm	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getCVTerm(long n)    CVTerm

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters:

n

long the index of the CVTerm to retrieve

Returns:: the nth CVTerm in the list of CVTerms for this SBML object.

def libsbml.SBase.getCVTerms ( self ) [inherited]

Python method signature(s):

getCVTerms()    CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns:: the CVTermList for this SBase.

def libsbml.Parameter.getDerivedUnitDefinition	(	self,
		args
	)

Python method signature(s):

getDerivedUnitDefinition()    UnitDefinition
getDerivedUnitDefinition()    UnitDefinition

Constructs and returns a UnitDefinition that corresponds to the units of this Parameter's value.

Parameters in SBML have an attribute ('units') for declaring the units of measurement intended for the parameter's value. No defaults are defined by SBML in the absence of a definition for 'units'. This method returns a UnitDefinition object based on the units declared for this Parameter using its 'units' attribute, or it returns None if no units have been declared.

Note that unit declarations for Parameter objects are specified in terms of the identifier of a unit (e.g., using setUnits()), but this method returns a UnitDefinition object, not a unit identifier. It does this by constructing an appropriate UnitDefinition.For SBML Level 2 models, it will do this even when the value of the 'units' attribute is one of the special SBML Level 2 unit identifiers 'substance', 'volume', 'area', 'length' or 'time'. Callers may find this useful in conjunction with the helper methods provided by the UnitDefinition class for comparing different UnitDefinition objects.

Returns:: a UnitDefinition that expresses the units of this Parameter, or None if one cannot be constructed.

Note:: The libSBML system for unit analysis depends on the model as a whole. In cases where the Parameter object has not yet been added to a model, or the model itself is incomplete, unit analysis is not possible, and consequently this method will return None.

See also:: isSetUnits()

Reimplemented in libsbml.LocalParameter.

def libsbml.SBase.getElementByMetaId	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getElementByMetaId(string metaid)    SBase

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

Parameters:

metaid

string representing the 'metaid' attribute value of the object to find

Returns:: pointer to the first element found with the given meta-identifier.

Reimplemented in libsbml.ListOf, libsbml.Model, libsbml.SBMLDocument, libsbml.UnitDefinition, libsbml.Reaction, libsbml.KineticLaw, and libsbml.Event.

def libsbml.SBase.getElementBySId	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getElementBySId(string id)    SBase

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.

Parameters:

id

string representing the 'id' attribute value of the object to find

Returns:: pointer to the first element found with the given identifier.

Reimplemented in libsbml.ListOf, libsbml.Model, libsbml.SBMLDocument, libsbml.UnitDefinition, libsbml.ListOfUnitDefinitions, libsbml.ListOfLocalParameters, libsbml.Reaction, libsbml.KineticLaw, and libsbml.Event.

def libsbml.Parameter.getElementName ( self )

Python method signature(s):

getElementName()    string

Returns the XML element name of this object, which for Parameter, is always 'parameter'.

Returns:: the name of this element, i.e., 'parameter'.

Reimplemented from libsbml.SBase.

Reimplemented in libsbml.LocalParameter.

def libsbml.Parameter.getId ( self )

Python method signature(s):

getId()    string

Returns the value of the 'id' attribute of this Parameter.

Returns:: the id of this Parameter.

def libsbml.SBase.getLevel ( self ) [inherited]

Python method signature(s):

getLevel()    long

Returns the SBML Level of the SBMLDocument object containing this object.

Returns:: the SBML level of this SBML object.

See also:: getVersion(); getNamespaces(); getPackageVersion()

def libsbml.SBase.getLine ( self ) [inherited]

Python method signature(s):

getLine()    long

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns:: the line number of this SBML object.

Note:: The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also:: getColumn()

def libsbml.SBase.getListOfAllElements ( self ) [inherited]

Python method signature(s):

getListOfAllElements()    SBaseList

def libsbml.SBase.getListOfAllElementsFromPlugins ( self ) [inherited]

Python method signature(s):

getListOfAllElementsFromPlugins()    SBaseList

def libsbml.SBase.getMetaId ( self ) [inherited]

Python method signature(s):

getMetaId()    string

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns:: the metaid of this SBML object.

See also:: isSetMetaId(); setMetaId()

def libsbml.SBase.getModel ( self ) [inherited]

Python method signature(s):

getModel()    Model

Returns the Model object in which the current object is located.

Returns:: the parent Model of this SBML object.

See also:: getParentSBMLObject(); getSBMLDocument()

def libsbml.SBase.getModelHistory	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getModelHistory()    ModelHistory
getModelHistory()    ModelHistory

Returns the ModelHistory object, if any, attached to this object.

Returns:: the ModelHistory object attached to this object, or None if none exist.

Note:: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

def libsbml.Parameter.getName ( self )

Python method signature(s):

getName()    string

Returns the value of the 'name' attribute of this Parameter.

Returns:: the name of this Parameter.

def libsbml.SBase.getNamespaces ( self ) [inherited]

Python method signature(s):

getNamespaces()    XMLNamespaces

Returns a list of the XML Namespaces declared on this SBML document.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.

Returns:: the XML Namespaces associated with this SBML object

See also:: getLevel(); getVersion()

Reimplemented in libsbml.SBMLDocument.

def libsbml.SBase.getNotes ( self ) [inherited]

Python method signature(s):

getNotes()    XMLNode

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns:: the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.

See also:: getNotesString(); isSetNotes(); setNotes(); setNotes(); appendNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.getNotesString ( self ) [inherited]

Python method signature(s):

getNotesString()    string

Returns the content of the 'notes' subelement of this object as a string.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns:: the content of the 'notes' subelement of this SBML object as a string.

See also:: getNotes(); isSetNotes(); setNotes(); setNotes(); appendNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.getNumCVTerms ( self ) [inherited]

Python method signature(s):

getNumCVTerms()    long

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns:: the number of CVTerms for this SBML object.

def libsbml.SBase.getNumPlugins ( self ) [inherited]

Python method signature(s):

getNumPlugins()    long

Returns the number of plugin objects (extenstion interfaces) for SBML Level 3 package extensions known.

Returns:: the number of plugin objects (extension interfaces) of package extensions known by this instance of libSBML.

def libsbml.SBase.getPackageName ( self ) [inherited]

Python method signature(s):

getPackageName()    string

Returns the name of the SBML Level 3 package in which this element is defined.

Returns:: the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.

def libsbml.SBase.getPackageVersion ( self ) [inherited]

Python method signature(s):

getPackageVersion()    long

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns:: the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.

See also:: getLevel(); getVersion()

def libsbml.SBase.getParentSBMLObject	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getParentSBMLObject()    SBase
getParentSBMLObject()    SBase

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns:: the parent SBML object of this SBML object.

See also:: getSBMLDocument(); getModel()

def libsbml.SBase.getPlugin	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getPlugin(string package)    SBasePlugin
getPlugin(string package)    SBasePlugin
getPlugin(long n)    SBasePlugin
getPlugin(long n)    SBasePlugin

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getPlugin(long n)

Returns the nth plugin object (extension interface) for an SBML Level 3 package extension.

Parameters:

n

the index of the plugin to return

Returns:: the plugin object (the libSBML extension interface) of a package extension with the given package name or URI.

Method variant with the following signature:

getPlugin(string package)

Returns a plugin object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

Parameters:

package

the name or URI of the package

Returns:: the plugin object (the libSBML extension interface) of a package extension with the given package name or URI.

def libsbml.SBase.getResourceBiologicalQualifier	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getResourceBiologicalQualifier(string resource)    long

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using values whose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a value whose name begins with BQB_ from the interface class libsbml.

Parameters:

resource string representing the resource; e.g., 'http://www.geneontology.org/GO:0005892'.

Returns:: the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.

Note:: The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

def libsbml.SBase.getResourceModelQualifier	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getResourceModelQualifier(string resource)    long

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using values whose names begin with BQM_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a value whose name begins with BQM_ from the interface class libsbml.

Parameters:

resource string representing the resource; e.g., 'http://www.geneontology.org/GO:0005892'.

Returns:: the model qualifier typeassociated with the resource, or BQM_UNKNOWN if the resource does not exist.

Note:: The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

def libsbml.SBase.getSBMLDocument	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getSBMLDocument()    SBMLDocument
getSBMLDocument()    SBMLDocument

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 SBML object.

See also:: getParentSBMLObject(); getModel()

def libsbml.SBase.getSBOTerm ( self ) [inherited]

Python method signature(s):

getSBOTerm()    int

Returns the integer portion of the value of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns:: the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.

def libsbml.SBase.getSBOTermID ( self ) [inherited]

Python method signature(s):

getSBOTermID()    string

Returns the string representation of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns:: the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.

def libsbml.Parameter.getTypeCode ( self )

Python method signature(s):

getTypeCode()    int

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

Returns:: the SBML type code for this object, or SBML_UNKNOWN (default).

See also:: getElementName()

Reimplemented from libsbml.SBase.

Reimplemented in libsbml.LocalParameter.

def libsbml.Parameter.getUnits ( self )

Python method signature(s):

getUnits()    string

Gets the units defined for this Parameter.

The value of an SBML parameter's 'units' attribute establishes the unit of measurement associated with the parameter's value.

Returns:: the value of the 'units' attribute of this Parameter, as a string. An empty string indicates that no units have been assigned.

Note:: There is an important distinction to be made between no units assigned, and assuming a value without units has any specific unit such as dimensionless. In SBML, default units are never attributed to numbers, and numbers without units are not automatically assumed to have the unit dimensionless. Please consult the relevant SBML specification document for a more in-depth explanation of this topic and the SBML unit system.

See also:: isSetUnits(); setUnits(); getValue()

def libsbml.Parameter.getValue ( self )

Python method signature(s):

getValue()    float

Gets the numerical value of this Parameter.

Returns:: the value of the 'value' attribute of this Parameter, as a number of type float.

Note:: It is crucial that callers not blindly call Parameter.getValue() without first using Parameter.isSetValue() to determine whether a value has ever been set. Otherwise, the value return by Parameter.getValue() may not actually represent a value assigned to the parameter. The reason is simply that the data type float in a program always has some value. A separate test is needed to determine whether the value is a true model value, or uninitialized data in a computer's memory location.

See also:: isSetValue(); setValue(); getUnits()

def libsbml.SBase.getVersion ( self ) [inherited]

Python method signature(s):

getVersion()    long

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

Returns:: the SBML version of this SBML object.

See also:: getLevel(); getNamespaces()

def libsbml.Parameter.hasRequiredAttributes ( self )

Python method signature(s):

hasRequiredAttributes()    bool

Predicate returning true if all the required attributes for this Parameter object have been set.

Note:

The required attributes for a Parameter object are:

'id' (or 'name' in SBML Level 1)
'value' (required in Level 1, optional otherwise)

Returns:: a boolean value indicating whether all the required attributes for this object have been defined.

Reimplemented in libsbml.LocalParameter.

def libsbml.SBase.hasValidLevelVersionNamespaceCombination ( self ) [inherited]

Python method signature(s):

hasValidLevelVersionNamespaceCombination()    bool

def libsbml.Parameter.initDefaults ( self )

Python method signature(s):

initDefaults()

Initializes the fields of this Parameter object to 'typical' defaults values.

The SBML Parameter component has slightly different aspects and default attribute values in different SBML Levels and Versions. Many SBML object classes defined by libSBML have an initDefaults() method to set the values to certain common defaults, based mostly on what they are in SBML Level 2. In the case of Parameter, this method only sets the value of the 'constant' attribute to true.

See also:: getConstant(); isSetConstant(); setConstant()

def libsbml.SBase.isPackageEnabled	(	self,
		args
	)		`[inherited]`

Python method signature(s):

isPackageEnabled(string pkgName)    bool

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters:

pkgName

the name of the package

Returns:: true if the given package is enabled within this object, false otherwise.

See also:: isPackageURIEnabled()

def libsbml.SBase.isPackageURIEnabled	(	self,
		args
	)		`[inherited]`

Python method signature(s):

isPackageURIEnabled(string pkgURI)    bool

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters:

pkgURI

the URI of the package

Returns:: true if the given package is enabled within this object, false otherwise.

See also:: isPackageEnabled()

def libsbml.SBase.isPkgEnabled	(	self,
		args
	)		`[inherited]`

Python method signature(s):

isPkgEnabled(string pkgName)    bool

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters:

pkgName

the name of the package

Returns:: true if the given package is enabled within this object, false otherwise.

See also:: isPkgURIEnabled()

Deprecated:: Replaced in libSBML 5.2.0 by isPackageEnabled()

def libsbml.SBase.isPkgURIEnabled	(	self,
		args
	)		`[inherited]`

Python method signature(s):

isPkgURIEnabled(string pkgURI)    bool

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters:

pkgURI

the URI of the package

Returns:: true if the given package is enabled within this object, false otherwise.

See also:: isPkgEnabled()

Deprecated:: Replaced in libSBML 5.2.0 by isPackageURIEnabled()

def libsbml.SBase.isSetAnnotation ( self ) [inherited]

Python method signature(s):

isSetAnnotation()    bool

Predicate returning true if this object's 'annotation' subelement exists and has content.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns:: true if a 'annotation' subelement exists, false otherwise.

See also:: getAnnotation(); getAnnotationString(); setAnnotation(); setAnnotation(); appendAnnotation(); appendAnnotation(); unsetAnnotation()

def libsbml.Parameter.isSetConstant ( self )

Python method signature(s):

isSetConstant()    bool

Predicate returning true if the 'constant' attribute of this Parameter is set.

Returns:: true if the 'constant' attribute of this Parameter is set, false otherwise.

Note:: Readers who view the documentation for LocalParameter may be confused about the presence of this method. LibSBML derives LocalParameter from Parameter; however, this does not precisely match the object hierarchy defined by SBML Level 3, where LocalParameter is derived directly from SBase and not Parameter. We believe this arrangement makes it easier for libSBML users to program applications that work with both SBML Level 2 and SBML Level 3, but programmers should also keep in mind this difference exists. A side-effect of libSBML's scheme is that certain methods on LocalParameter that are inherited from Parameter do not actually have relevance to LocalParameter objects. An example of this is the methods pertaining to Parameter's attribute 'constant' (i.e., isSetConstant(), setConstant(), and getConstant()).

See also:: getConstant(); setConstant()

def libsbml.Parameter.isSetId ( self )

Python method signature(s):

isSetId()    bool

Predicate returning true if this Parameter's 'id' attribute is set.

Returns:: true if the 'id' attribute of this Parameter is set, false otherwise.

def libsbml.SBase.isSetMetaId ( self ) [inherited]

Python method signature(s):

isSetMetaId()    bool

Predicate returning true if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns:: true if the 'metaid' attribute of this SBML object is set, false otherwise.

See also:: getMetaId(); setMetaId()

def libsbml.SBase.isSetModelHistory ( self ) [inherited]

Python method signature(s):

isSetModelHistory()    bool

Predicate returning true if this object has a ModelHistory object attached to it.

Returns:: true if the ModelHistory of this object is set, false otherwise.

Note:: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

def libsbml.Parameter.isSetName ( self )

Python method signature(s):

isSetName()    bool

Predicate returning true if this Parameter's 'name' attribute is set.

Returns:: true if the 'name' attribute of this Parameter is set, false otherwise.

def libsbml.SBase.isSetNotes ( self ) [inherited]

Python method signature(s):

isSetNotes()    bool

Predicate returning true if this object's 'notes' subelement exists and has content.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Returns:: true if a 'notes' subelement exists, false otherwise.

See also:: getNotes(); getNotesString(); setNotes(); setNotes(); appendNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.isSetSBOTerm ( self ) [inherited]

Python method signature(s):

isSetSBOTerm()    bool

Predicate returning true if this object's 'sboTerm' attribute is set.

Returns:: true if the 'sboTerm' attribute of this SBML object is set, false otherwise.

def libsbml.Parameter.isSetUnits ( self )

Python method signature(s):

isSetUnits()    bool

Predicate returning true if the 'units' attribute of this Parameter is set.

Returns:: true if the 'units' attribute of this Parameter is set, false otherwise.

Note:: There is an important distinction to be made between no units assigned, and assuming a value without units has any specific unit such as dimensionless. In SBML, default units are never attributed to numbers, and numbers without units are not automatically assumed to have the unit dimensionless. Please consult the relevant SBML specification document for a more in-depth explanation of this topic and the SBML unit system.

def libsbml.Parameter.isSetValue ( self )

Python method signature(s):

isSetValue()    bool

Predicate returning true if the 'value' attribute of this Parameter is set.

In SBML definitions after SBML Level 1 Version 1, parameter values are optional and have no defaults. If a model read from a file does not contain a setting for the 'value' attribute of a parameter, its value is considered unset; it does not default to any particular value. Similarly, when a Parameter object is created in libSBML, it has no value until given a value. The Parameter.isSetValue() method allows calling applications to determine whether a given parameter's value has ever been set.

In SBML Level 1 Version 1, parameters are required to have values and therefore, the value of a Parameter should always be set. In Level 1 Version 2 and beyond, the value is optional and as such, the 'value' attribute may or may not be set.

Returns:: true if the value of this Parameter is set, false otherwise.

See also:: getValue(); setValue()

def libsbml.SBase.matchesSBMLNamespaces	(	self,
		args
	)		`[inherited]`

Python method signature(s):

matchesSBMLNamespaces(SBase sb)    bool

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

Parameters:

sb

an object to compare with respect to namespaces

Returns:: boolean, true if this object's collection of namespaces is the same as sb's, false otherwise.

def libsbml.SBase.removeFromParentAndDelete ( self ) [inherited]

Python method signature(s):

removeFromParentAndDelete()    int

Removes itself from its parent. If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

Reimplemented in libsbml.ListOf, libsbml.Model, libsbml.KineticLaw, libsbml.Trigger, libsbml.Delay, libsbml.Priority, and libsbml.StoichiometryMath.

def libsbml.SBase.renameMetaIdRefs	(	self,
		args
	)		`[inherited]`

Python method signature(s):

renameMetaIdRefs(string oldid, string newid)

Renames all the MetaIdRef attributes on this element.

This method works by looking at all meta-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

def libsbml.SBase.renameSIdRefs	(	self,
		args
	)		`[inherited]`

Python method signature(s):

renameSIdRefs(string oldid, string newid)

Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).

This method works by looking at all attributes and (if appropriate) math formulas, 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

Reimplemented in libsbml.Model, libsbml.Compartment, libsbml.Species, libsbml.InitialAssignment, libsbml.Rule, libsbml.AssignmentRule, libsbml.RateRule, libsbml.Constraint, libsbml.Reaction, libsbml.KineticLaw, libsbml.SimpleSpeciesReference, libsbml.EventAssignment, libsbml.Trigger, libsbml.Delay, libsbml.Priority, and libsbml.StoichiometryMath.

def libsbml.Parameter.renameUnitSIdRefs	(	self,
		args
	)

Python method signature(s):

renameUnitSIdRefs(string oldid, string newid)

Renames all the UnitSIdRef attributes on this element

Reimplemented from libsbml.SBase.

def libsbml.SBase.setAnnotation	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setAnnotation(XMLNode annotation)    int
setAnnotation(string annotation)    int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

setAnnotation(XMLNode annotation)

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().

Parameters:

annotation

an XML structure that is to be used as the new content of the 'annotation' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also:: getAnnotationString(); isSetAnnotation(); setAnnotation(); appendAnnotation(); appendAnnotation(); unsetAnnotation()

Method variant with the following signature:

setAnnotation(string annotation)

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().

Parameters:

annotation

an XML string that is to be used as the content of the 'annotation' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See also:: getAnnotationString(); isSetAnnotation(); setAnnotation(); appendAnnotation(); appendAnnotation(); unsetAnnotation()

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

def libsbml.Parameter.setConstant	(	self,
		args
	)

Python method signature(s):

setConstant(bool flag)    int

Sets the 'constant' attribute of this Parameter to the given boolean flag.

Parameters:

flag

a boolean, the value for the 'constant' attribute of this Parameter instance

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

Note:: Readers who view the documentation for LocalParameter may be confused about the presence of this method. LibSBML derives LocalParameter from Parameter; however, this does not precisely match the object hierarchy defined by SBML Level 3, where LocalParameter is derived directly from SBase and not Parameter. We believe this arrangement makes it easier for libSBML users to program applications that work with both SBML Level 2 and SBML Level 3, but programmers should also keep in mind this difference exists. A side-effect of libSBML's scheme is that certain methods on LocalParameter that are inherited from Parameter do not actually have relevance to LocalParameter objects. An example of this is the methods pertaining to Parameter's attribute 'constant' (i.e., isSetConstant(), setConstant(), and getConstant()).

See also:: getConstant(); isSetConstant()

def libsbml.Parameter.setId	(	self,
		args
	)

Python method signature(s):

setId(string sid)    int

Sets the value of the 'id' attribute of this Parameter.

The string sid is copied. Note that SBML has strict requirements for the syntax of identifiers. The following is a summary of the definition of the SBML identifier type SId, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation:

letter ::= 'a'..'z','A'..'Z'
digit ::= '0'..'9'
idChar ::= letter | digit | '_'
SId ::= ( letter | '_' ) idChar*

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact formulations.

Parameters:

sid

the string to use as the identifier of this Parameter

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.SBase.setMetaId	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setMetaId(string metaid)    int

Sets the value of the 'metaid' attribute of this object.

The string metaid is copied. The value of metaid must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement.

Parameters:

metaid

the identifier string to use as the value of the 'metaid' attribute

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See also:: getMetaId(); isSetMetaId()

def libsbml.SBase.setModelHistory	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setModelHistory(ModelHistory history)    int

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters:

history

ModelHistory of this object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

Note:: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

def libsbml.Parameter.setName	(	self,
		args
	)

Python method signature(s):

setName(string name)    int

Sets the value of the 'name' attribute of this Parameter.

The string in name is copied.

Parameters:

name

the new name for the Parameter

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.SBase.setNamespaces	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setNamespaces(XMLNamespaces xmlns)    int

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

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.

Parameters:

xmlns

the namespaces to set

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

def libsbml.SBase.setNotes	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setNotes(XMLNode notes)    int
setNotes(string notes)    int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

setNotes(string notes)

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.

Parameters:

notes

an XML string that is to be used as the content of the 'notes' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See also:: getNotesString(); isSetNotes(); setNotes(); appendNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:

setNotes(XMLNode notes)

Sets the value of the 'notes' subelement of this SBML object.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters:

notes

an XML structure that is to be used as the content of the 'notes' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See also:: getNotesString(); isSetNotes(); setNotes(); appendNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.setSBOTerm	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setSBOTerm(int value)    int
setSBOTerm(string sboid)    int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters:

value

the NNNNNNN integer portion of the SBO identifier

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See also:: setSBOTerm()

Method variant with the following signature:

setSBOTerm(string &sboid)

Sets the value of the 'sboTerm' attribute by string.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters:

sboid

the SBO identifier string of the form 'SBO:NNNNNNN'

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See also:: setSBOTerm()

def libsbml.Parameter.setUnits	(	self,
		args
	)

Python method signature(s):

setUnits(string units)    int

Sets the 'units' attribute of this Parameter to a copy of the given units identifier units.

Parameters:

units

a string, the identifier of the units to assign to this Parameter instance

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.Parameter.setValue	(	self,
		args
	)

Python method signature(s):

setValue (float value)    int

Sets the 'value' attribute of this Parameter to the given float value and marks the attribute as set.

Parameters:

value a float, the value to assign

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

def libsbml.SBase.toSBML ( self ) [inherited]

Python method signature(s):

toSBML()    string

Returns a string consisting of a partial SBML corresponding to just this object.

Returns:: the partial SBML that describes this SBML object.

Warning:: This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.

def libsbml.SBase.unsetAnnotation ( self ) [inherited]

Python method signature(s):

unsetAnnotation()    int

Unsets the value of the 'annotation' subelement of this SBML object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also:: getAnnotation(); getAnnotationString(); isSetAnnotation(); setAnnotation(); setAnnotation(); appendAnnotation(); appendAnnotation()

def libsbml.SBase.unsetCVTerms ( self ) [inherited]

Python method signature(s):

unsetCVTerms()    int

Clears the list of CVTerm objects attached to this SBML object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.SBase.unsetId ( self ) [inherited]

Python method signature(s):

unsetId()    int

Unsets the value of the 'id' attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always either Sid or UnitSId, depending on the object in question. Both data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The equality of SId and UnitSId type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId and UnitSId.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

Reimplemented in libsbml.Model, libsbml.SimpleSpeciesReference, and libsbml.Event.

def libsbml.SBase.unsetMetaId ( self ) [inherited]

Python method signature(s):

unsetMetaId()    int

Unsets the value of the 'metaid' attribute of this SBML object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.SBase.unsetModelHistory ( self ) [inherited]

Python method signature(s):

unsetModelHistory()    int

Unsets the ModelHistory object attached to this object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

Note:: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

def libsbml.Parameter.unsetName ( self )

Python method signature(s):

unsetName()    int

Unsets the value of the 'name' attribute of this Parameter.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

Reimplemented from libsbml.SBase.

def libsbml.SBase.unsetNotes ( self ) [inherited]

Python method signature(s):

unsetNotes()    int

Unsets the value of the 'notes' subelement of this SBML object.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also:: getNotesString(); isSetNotes(); setNotes(); setNotes(); appendNotes(); appendNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.unsetSBOTerm ( self ) [inherited]

Python method signature(s):

unsetSBOTerm()    int

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.Parameter.unsetUnits ( self )

Python method signature(s):

unsetUnits()    int

Unsets the 'units' attribute of this Parameter instance.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.Parameter.unsetValue ( self )

Python method signature(s):

unsetValue()    int

Unsets the 'value' attribute of this Parameter instance.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

In SBML Level 1 Version 1, parameters are required to have values and therefore, the value of a Parameter should always be set. In SBML Level 1 Version 2 and beyond, the value is optional and as such, the 'value' attribute may or may not be set.

libsbml.Parameter Class Reference

Detailed Description

Public Member Functions

Member Function Documentation