libsbml.Parameter Class Reference

Inheritance diagram for libsbml.Parameter:

Inheritance graph
[legend]

List of all members.

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 one required attribute, 'id', to give 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 specification (e.g., Section 3.3 in the Level 2 Version 4 specification).

The optional attribute 'value' determines the value (of type float) assigned to the identifier. 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 units associated with the value of the parameter are specified by the attribute named 'units'. 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. Please consult the SBML specification documents for more details about the meanings and implications of the various unit choices.

The Parameter structure has an optional boolean attribute named 'constant' that indicates whether the parameter's value can vary during a simulation. The attribute's default value is true. A value of false indicates the parameter's value can be changed by Rule constructs and that the 'value' attribute is actually intended to be the initial value of the parameter. Parameters 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; thus, 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.

See also:
ListOfParameters

KineticLaw

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.

Definition at line 14661 of file libsbml.py.


Public Member Functions

def __eq__
def __init__
def __init__
def __ne__
def addCVTerm
def appendAnnotation
def appendNotes
def clone
def getAncestorOfType
def getAnnotation
def getAnnotationString
def getColumn
def getConstant
def getCVTerm
def getCVTerms
def getDerivedUnitDefinition
def getElementName
def getId
def getLevel
def getLine
def getMetaId
def getModel
def getName
def getNamespaces
def getNotes
def getNotesString
def getNumCVTerms
def getParentSBMLObject
def getResourceBiologicalQualifier
def getResourceModelQualifier
def getSBMLDocument
def getSBOTerm
def getSBOTermID
def getTypeCode
def getUnits
def getValue
def getVersion
def hasRequiredAttributes
def hasRequiredElements
def hasValidLevelVersionNamespaceCombination
def initDefaults
def isSetAnnotation
def isSetId
def isSetMetaId
def isSetName
def isSetNotes
def isSetSBOTerm
def isSetUnits
def isSetValue
def setAnnotation
def setConstant
def setId
def setMetaId
def setName
def setNamespaces
def setNotes
def setSBOTerm
def setUnits
def setValue
def toSBML
def unsetAnnotation
def unsetCVTerms
def unsetMetaId
def unsetName
def unsetNotes
def unsetSBOTerm
def unsetUnits
def unsetValue

Public Attributes

 this

Member Function Documentation

def libsbml.SBase.__eq__ (   self,
  rhs 
) [inherited]

Definition at line 3296 of file libsbml.py.

def libsbml.SBase.__init__ (   self,
  args,
  kwargs 
) [inherited]

Reimplemented in libsbml.SimpleSpeciesReference.

Definition at line 1771 of file libsbml.py.

def libsbml.Parameter.__init__ (   self,
  args 
)

Python method signature(s): 

__init__(self, unsigned int level, unsigned int version)    Parameter
__init__(self, SBMLNamespaces sbmlns)    Parameter
__init__(self, Parameter orig)    Parameter

Predicate returning true or false depending on whether all the required attributes for this Parameter object have been set.

Note:
The required attributes for a Parameter object are: id (name in L1); value (L1V1 only)
Returns:
a boolean value indicating whether all the required attributes for this object have been defined.
Deprecated:
libSBML internal

Definition at line 14751 of file libsbml.py.

def libsbml.SBase.__ne__ (   self,
  rhs 
) [inherited]

Definition at line 3303 of file libsbml.py.

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

Python method signature(s): 

addCVTerm(self, CVTerm term)    int

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

Parameters:
term the CVTerm to assign
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
  • LIBSBML_INVALID_OBJECT
Note:
Since the CV Term uses the metaid of the object as a reference, if the object has no metaid set 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.

Definition at line 2974 of file libsbml.py.

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

Python method signature(s): 

appendAnnotation(self, XMLNode annotation)    int
appendAnnotation(self, string annotation)    int

Appends the annotation content given by annotation to any existing content in 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(const XMLNode* annotation) or SBase.setAnnotation(const std.string& annotation), this method allows other annotations to be preserved when an application adds its own data.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_OPERATION_FAILED
See also:
getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

unsetAnnotation()

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

Definition at line 2624 of file libsbml.py.

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

Python method signature(s): 

appendNotes(self, XMLNode notes)    int
appendNotes(self, string notes)    int

Appends notes content to the 'notes' element attached to this object.

The content in notes is copied.

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

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:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_OBJECT
  • LIBSBML_OPERATION_FAILED
See also:
getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

unsetNotes()

Definition at line 2726 of file libsbml.py.

def libsbml.Parameter.clone (   self  ) 

Python method signature(s): 

clone(self)    Parameter

Creates and returns a deep copy of this Parameter.

Returns:
a (deep) copy of this Parameter.

Reimplemented from libsbml.SBase.

Definition at line 14776 of file libsbml.py.

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

Python method signature(s): 

getAncestorOfType(self, SBMLTypeCode_t type)    SBase

Returns the ancestor SBML object that corresponds to the given SBMLTypeCode_t.

This function allows any object to determine its exact location/function within a model. For example a StoichiometryMath object has ancestors of type SpeciesReference, ListOfProducts/ListOfReactants/ListOfModifiers, Reaction, ListOfReactions and Model; any of which can be accessed via this function.

Parameters:
type the SBMLTypeCode_t of the ancestor to be returned.
Returns:
the ancestor SBML object of this SBML object, that corresponds to the given SBMLTypeCode_t, NULL if none exists.

Definition at line 2115 of file libsbml.py.

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

Python method signature(s): 

getAnnotation(self)    XMLNode

Returns the content of the 'annotation' subelement of this object as an XML node tree.

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.

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 an XMLNode
See also:
getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Definition at line 1971 of file libsbml.py.

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

Python method signature(s): 

getAnnotationString(self)    string

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

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.

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

Returns:
the annotation string of this SBML object.
See also:
getAnnotation()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Definition at line 2014 of file libsbml.py.

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

Python method signature(s): 

getColumn(self)    unsigned int

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.
See also:
getLine()

Definition at line 2217 of file libsbml.py.

def libsbml.Parameter.getConstant (   self  ) 

Python method signature(s): 

getConstant(self)    bool

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

Note that in SBML Level 2 and beyond, the default value of Parameter's 'constant' attribute is true. Since a boolean value can only be true or false, there is no 'isSetConstant()' method as is available for the other attributes on Parameter, because 'unset' is not an option.

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

Definition at line 14880 of file libsbml.py.

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

Python method signature(s): 

getCVTerm(self, unsigned int n)    CVTerm

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

Parameters:
n unsigned int the index of the CVTerm to retrieve
Returns:
the nth CVTerm in the list of CVTerms for this SBML object.

Definition at line 3042 of file libsbml.py.

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

Python method signature(s): 

getCVTerms(self)    CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns:
the CVTermList for this SBase.

Definition at line 3010 of file libsbml.py.

def libsbml.Parameter.getDerivedUnitDefinition (   self,
  args 
)

Python method signature(s): 

getDerivedUnitDefinition(self)    UnitDefinition
getDerivedUnitDefinition(self)    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'. The Parameter.getDerivedUnitDefinition() method returns a UnitDefinition object based on the units declared for this Parameter using its 'units' attribute, or it returns NULL if no units have been declared.

Note that the functionality that facilitates unit analysis depends on the model as a whole. Thus, in cases where the object has not been added to a model or the model itself is incomplete, unit analysis is not possible and this method will return NULL.

Note that unit declarations for Parameter are in terms of the identifier of a unit, but this method returns a UnitDefinition object, not a unit identifier. It does this by constructing an appropriate UnitDefinition even when the value of the 'units' attribute is one of the predefined SBML units 'substance', 'volume', 'area', 'length' or 'time'. Callers may find this particularly useful when used in conjunction with the helper methods on UnitDefinition for comparing different UnitDefinition objects.

Returns:
a UnitDefinition that expresses the units of this Parameter.

Definition at line 15210 of file libsbml.py.

def libsbml.Parameter.getElementName (   self  ) 

Python method signature(s): 

getElementName(self)    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.

Definition at line 15278 of file libsbml.py.

def libsbml.Parameter.getId (   self  ) 

Python method signature(s): 

getId(self)    string

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

Returns:
the id of this Parameter.

Reimplemented from libsbml.SBase.

Definition at line 14810 of file libsbml.py.

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

Python method signature(s): 

getLevel(self)    unsigned int

Returns the SBML Level of the overall SBML document.

Returns:
the SBML level of this SBML object.
See also:
getVersion()

Definition at line 3134 of file libsbml.py.

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

Python method signature(s): 

getLine(self)    unsigned int

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.
See also:
getColumn()

Definition at line 2199 of file libsbml.py.

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

Python method signature(s): 

getMetaId(self)    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(const std.string& metaid)

Definition at line 1790 of file libsbml.py.

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

Python method signature(s): 

getModel(self)    Model

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

Returns:
the parent Model of this SBML object.

Definition at line 3119 of file libsbml.py.

def libsbml.Parameter.getName (   self  ) 

Python method signature(s): 

getName(self)    string

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

Returns:
the name of this Parameter.

Reimplemented from libsbml.SBase.

Definition at line 14825 of file libsbml.py.

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

Python method signature(s): 

getNamespaces(self)    XMLNamespaces

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

Returns:
the XML Namespaces associated with this SBML object

Reimplemented in libsbml.SBMLDocument.

Definition at line 2053 of file libsbml.py.

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

Python method signature(s): 

getNotes(self)    XMLNode

Returns the content of the 'notes' subelement of this object as a tree of XML nodes.

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

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.

Returns:
the content of the 'notes' subelement of this SBML object.
See also:
getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 1891 of file libsbml.py.

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

Python method signature(s): 

getNotesString(self)    string

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

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

Returns:
the content of the 'notes' subelement of this SBML object.
See also:
getNotes()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 1934 of file libsbml.py.

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

Python method signature(s): 

getNumCVTerms(self)    unsigned int

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

Returns:
the number of CVTerms for this SBML object.

Definition at line 3026 of file libsbml.py.

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

Python method signature(s): 

getParentSBMLObject(self)    SBase

Returns the parent SBML object.

This method is convenient when holding an object nested inside other objects in an SBML model. It allows direct access to the <model> element containing it.

Returns:
the parent SBML object of this SBML object.

Definition at line 2096 of file libsbml.py.

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

Python method signature(s): 

getResourceBiologicalQualifier(self, string resource)    BiolQualifierType_t

Returns the BiologicalQualifier associated with this resource, or BQB_UNKNOWN if the resource does not exist.

Parameters:
resource string representing the resource; e.g., 'http://www.geneontology.org/GO:0005892'
Returns:
the BiolQualifierType_t value associated with the resource

Definition at line 3081 of file libsbml.py.

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

Python method signature(s): 

getResourceModelQualifier(self, string resource)    ModelQualifierType_t

Returns the ModelQualifier associated with this resource, or BQM_UNKNOWN if the resource does not exist.

Parameters:
resource string representing the resource; e.g., 'http://www.geneontology.org/GO:0005892'
Returns:
the ModelQualifierType_t value associated with the resource

Definition at line 3100 of file libsbml.py.

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

Python method signature(s): 

getSBMLDocument(self)    SBMLDocument
getSBMLDocument(self)    SBMLDocument

Returns the parent SBMLDocument object.

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 2 specification, 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 or Level 2.)

This method allows the SBMLDocument for the current object to be retrieved.

Returns:
the parent SBMLDocument object of this SBML object.

Definition at line 2068 of file libsbml.py.

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

Python method signature(s): 

getSBOTerm(self)    int

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

In SBML Level 2 Versions 2, 3 and 4, 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.

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

Definition at line 2141 of file libsbml.py.

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

Python method signature(s): 

getSBOTermID(self)    string

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

In SBML Level 2 Versions 2, 3 and 4, 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 function recreates the string representation from the stored value. 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 of the form SBO:NNNNNNN, or an empty string if the value is not set.

Definition at line 2169 of file libsbml.py.

def libsbml.Parameter.getTypeCode (   self  ) 

Python method signature(s): 

getTypeCode(self)    SBMLTypeCode_t

Returns the libSBML type code for this SBML object.

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

Reimplemented from libsbml.SBase.

Definition at line 15249 of file libsbml.py.

def libsbml.Parameter.getUnits (   self  ) 

Python method signature(s): 

getUnits(self)    string

Gets the units defined for this Parameter

Returns:
the value of the 'units' attribute of this Parameter, as a string.

Definition at line 14864 of file libsbml.py.

def libsbml.Parameter.getValue (   self  ) 

Python method signature(s): 

getValue(self)    float

Gets the numerical value of this Parameter.

Returns:
the value of the 'value' attribute of this Parameter, as a number of type float.
See also:
isSetValue()
Note:
It is crucial that callers not blindly call Parameter.getValue() without first checking with Parameter.isSetValue() to determine whether a value has been set. Otherwise, the value return by Parameter.getValue() may not actually represent a value assigned to the parameter.

Definition at line 14840 of file libsbml.py.

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

Python method signature(s): 

getVersion(self)    unsigned int

Returns the Version within the SBML Level of the overall SBML document.

Returns:
the SBML version of this SBML object.
See also:
getLevel()

Definition at line 3151 of file libsbml.py.

def libsbml.Parameter.hasRequiredAttributes (   self  ) 

Python method signature(s): 

hasRequiredAttributes(self)    bool

Predicate returning true or false depending on whether all the required attributes for this Parameter object have been set.

Note:
The required attributes for a Parameter object are: id (name in L1); value (L1V1 only)
Returns:
a boolean value indicating whether all the required attributes for this object have been defined.

Reimplemented from libsbml.SBase.

Definition at line 15294 of file libsbml.py.

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

Python method signature(s): 

hasRequiredElements(self)    bool

Subclasses should override this method to write out their contained SBML objects as XML elements. Be sure to call your parents implementation of this method as well. For example:

SBase.writeElements(stream); mReactans.write(stream); mProducts.write(stream); ...

Deprecated:
libSBML internal

Reimplemented in libsbml.Model, libsbml.FunctionDefinition, libsbml.UnitDefinition, libsbml.InitialAssignment, libsbml.Rule, libsbml.Constraint, libsbml.KineticLaw, libsbml.Event, libsbml.EventAssignment, libsbml.Trigger, libsbml.Delay, and libsbml.StoichiometryMath.

Definition at line 3275 of file libsbml.py.

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

Python method signature(s): 

hasValidLevelVersionNamespaceCombination(self)    bool

Predicate returning true or false depending on whether this object's level/version and namespace values correspond to a valid SBML specification.

The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:

  • Level 1 Version 2 'http://www.sbml.org/sbml/level1'
  • Level 2 Version 1 'http://www.sbml.org/sbml/level2'
  • Level 2 Version 2 'http://www.sbml.org/sbml/level2/version2'
  • Level 2 Version 3 'http://www.sbml.org/sbml/level2/version3'
  • Level 2 Version 4 'http://www.sbml.org/sbml/level2/version4'

Returns:
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.

Definition at line 3192 of file libsbml.py.

def libsbml.Parameter.initDefaults (   self  ) 

Python method signature(s): 

initDefaults(self)

Initializes the fields of this Parameter to the defaults defined in the specification of the relevant Level/Version of SBML.

The exact actions of this are as follows:

  • (SBML Level 2 only) set the 'constant' attribute to true.

Definition at line 14791 of file libsbml.py.

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

Python method signature(s): 

isSetAnnotation(self)    bool

Predicate returning true or false depending on whether 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.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:
true if a 'annotation' subelement exists, false otherwise.
See also:
getAnnotation()

getAnnotationString()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Definition at line 2387 of file libsbml.py.

def libsbml.Parameter.isSetId (   self  ) 

Python method signature(s): 

isSetId(self)    bool

Predicate returning true or false depending on whether this Parameter's 'id' attribute has been set.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

Reimplemented from libsbml.SBase.

Definition at line 14902 of file libsbml.py.

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

Python method signature(s): 

isSetMetaId(self)    bool

Predicate returning true or false depending on whether this object's 'metaid' attribute has been 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.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:
true if the 'metaid' attribute of this SBML object has been set, false otherwise.
See also:
getMetaId()

setMetaId(const std.string& metaid)

Definition at line 2235 of file libsbml.py.

def libsbml.Parameter.isSetName (   self  ) 

Python method signature(s): 

isSetName(self)    bool

Predicate returning true or false depending on whether this Parameter's 'name' attribute has been set.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

Reimplemented from libsbml.SBase.

Definition at line 14921 of file libsbml.py.

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

Python method signature(s): 

isSetNotes(self)    bool

Predicate returning true or false depending on whether this object's 'notes' subelement exists and has content.

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:
true if a 'notes' subelement exists, false otherwise.
See also:
getNotes()

getNotesString()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 2348 of file libsbml.py.

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

Python method signature(s): 

isSetSBOTerm(self)    bool

Predicate returning true or false depending on whether this object's 'sboTerm' attribute has been set.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

Definition at line 2427 of file libsbml.py.

def libsbml.Parameter.isSetUnits (   self  ) 

Python method signature(s): 

isSetUnits(self)    bool

Predicate returning true or false depending on whether the 'units' attribute of this Parameter has been set.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

Definition at line 14981 of file libsbml.py.

def libsbml.Parameter.isSetValue (   self  ) 

Python method signature(s): 

isSetValue(self)    bool

Predicate returning true or false depending on whether the 'value' attribute of this Parameter has been set.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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 has been set, false otherwise.
See also:
getValue()
Note:
It is crucial that callers not blindly call Parameter.getValue() without first checking with Parameter.isSetValue() to determine whether a value has been set. Otherwise, the value return by Parameter.getValue() may not actually represent a value assigned to the parameter.

Definition at line 14940 of file libsbml.py.

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

Python method signature(s): 

setAnnotation(self, XMLNode annotation)    int
setAnnotation(self, string annotation)    int

Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation given as a character string.

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(const XMLNode* annotation) or SBase.appendAnnotation(const std.string& annotation).

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_OPERATION_FAILED
See also:
getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

Definition at line 2568 of file libsbml.py.

def libsbml.Parameter.setConstant (   self,
  args 
)

Python method signature(s): 

setConstant(self, 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:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_UNEXPECTED_ATTRIBUTE

Definition at line 15116 of file libsbml.py.

def libsbml.Parameter.setId (   self,
  args 
)

Python method signature(s): 

setId(self, 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 summary of the definition of the SBML identifier type SId (here expressed in an extended form of BNF notation): 

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_ATTRIBUTE_VALUE

Reimplemented from libsbml.SBase.

Definition at line 15000 of file libsbml.py.

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

Python method signature(s): 

setMetaId(self, 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.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_ATTRIBUTE_VALUE
  • LIBSBML_UNEXPECTED_ATTRIBUTE
See also:
getMetaId()

isSetMetaId()

Definition at line 2446 of file libsbml.py.

def libsbml.Parameter.setName (   self,
  args 
)

Python method signature(s): 

setName(self, string name)    int

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

The string in name is copied.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_ATTRIBUTE_VALUE

Reimplemented from libsbml.SBase.

Definition at line 15040 of file libsbml.py.

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

Python method signature(s): 

setNamespaces(self, XMLNamespaces xmlns)    int

Sets the namespaces relevant of this SBML object.

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

Definition at line 2811 of file libsbml.py.

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

Python method signature(s): 

setNotes(self, XMLNode notes)    int
setNotes(self, string notes)    int

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

Any existing content of the 'notes' subelement is discarded.

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_OBJECT
  • LIBSBML_OPERATION_FAILED
See also:
getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 2676 of file libsbml.py.

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

Python method signature(s): 

setSBOTerm(self, int value)    int
setSBOTerm(self, string sboid)    int

Sets the value of the 'sboTerm' attribute.

In SBML Level 2 Versions 2, 3 and 4, the data type of the SBML 'sboTerm' 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.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_ATTRIBUTE_VALUE
  • LIBSBML_UNEXPECTED_ATTRIBUTE

Definition at line 2774 of file libsbml.py.

def libsbml.Parameter.setUnits (   self,
  args 
)

Python method signature(s): 

setUnits(self, string units)    int

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_ATTRIBUTE_VALUE

Definition at line 15090 of file libsbml.py.

def libsbml.Parameter.setValue (   self,
  args 
)

Python method signature(s): 

setValue(self, float value)    int

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

Definition at line 15066 of file libsbml.py.

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

Python method signature(s): 

toSBML(self)    char

Returns a string that consists of the partial SBML describing this object. This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.

Returns:
the partial SBML that describes this SBML object.

Definition at line 3237 of file libsbml.py.

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

Python method signature(s): 

unsetAnnotation(self)    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.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

Definition at line 2910 of file libsbml.py.

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

Python method signature(s): 

unsetCVTerms(self)    int

Clears the list of CVTerms of this SBML object.

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

Definition at line 3060 of file libsbml.py.

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

Python method signature(s): 

unsetMetaId(self)    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.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

Definition at line 2832 of file libsbml.py.

def libsbml.Parameter.unsetName (   self  ) 

Python method signature(s): 

unsetName(self)    int

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

Definition at line 15140 of file libsbml.py.

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

Python method signature(s): 

unsetNotes(self)    int

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

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

Definition at line 2869 of file libsbml.py.

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

Python method signature(s): 

unsetSBOTerm(self)    int

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

Definition at line 2952 of file libsbml.py.

def libsbml.Parameter.unsetUnits (   self  ) 

Python method signature(s): 

unsetUnits(self)    int

Unsets the 'units' attribute of this Parameter instance.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

Definition at line 15188 of file libsbml.py.

def libsbml.Parameter.unsetValue (   self  ) 

Python method signature(s): 

unsetValue(self)    int

Unsets the 'value' attribute of this Parameter instance.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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.

Definition at line 15162 of file libsbml.py.

Member Data Documentation

libsbml.Parameter.this

Reimplemented from libsbml.SBase.

Definition at line 14775 of file libsbml.py.


SBML Team
http://www.sbml.org/
sbml-team@caltech.edu

HTML documentation generated on Thu Jan 21 16:56:18 2010 using Doxygen 1.5.8.