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KineticLaw Class Reference
Inheritance diagram for KineticLaw:
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Detailed Description

Implementation of SBML's KineticLaw construct.

An object of class KineticLaw is used to describe the rate at which the process defined by a given Reaction takes place. KineticLaw has subelements called "math" (for MathML content) and "listOfParameters" (of class ListOfParameters), in addition to the attributes and subelements it inherits from SBase.

KineticLaw's "math" subelement for holding a MathML formula defines the rate of the reaction. The formula may refer to other entities in a model as well as local parameter definitions within the scope of the Reaction (see below). It is important to keep in mind, however, that the only Species identifiers that can be used in this formula are those declared in the lists of reactants, products and modifiers in the Reaction structure. (In other words, before a species can be referenced in the KineticLaw, it must be declared in one of those lists.)

KineticLaw provides a way to define local parameters whose identifiers can be used in the "math" formula of that KineticLaw instance. Prior to SBML Level 3, these parameter definitions are stored inside a "listOfParameters" subelement containing Parameter objects; in SBML Level 3, this is achieved using a specialized object class called LocalParameter and the containing subelement is called "listOfLocalParameters". In both cases, the parameters so defined are only visible within the KineticLaw; they cannot be accessed outside. A local parameter within one reaction is not visible from within another reaction, nor is it visible to any other construct outside of the KineticLaw in which it is defined. In addition, another important feature is that if such a Parameter (or in Level 3, LocalParameter) object has the same identifier as another object in the scope of the enclosing Model, the definition inside the KineticLaw takes precedence. In other words, within the KineticLaw's "math" formula, references to local parameter identifiers shadow any identical global identifiers.

The values of local parameters defined within KineticLaw objects cannot change. In SBML Level 3, this quality is built into the LocalParameter construct. In Level 2, where the same kind of Parameter object class is used as for global parameters, the Parameter objects' "constant" attribute must always have a value of true (either explicitly or left to its default value).

A warning about identifier shadowing

A common misconception is that different classes of objects (e.g., species, compartments, parameters) in SBML have different identifier scopes. They do not. The implication is that if a KineticLaw's local parameter definition uses an identifier identical to any other identifier defined in the model outside the KineticLaw, even if the other identifier does not belong to a parameter type of object, the local parameter's identifier takes precedence within that KineticLaw's "math" formula. It is not an error in SBML for identifiers to shadow each other this way, but can lead to confusing and subtle errors.

Version differences

In SBML Level 2 Version 1, the SBML specification included two additional attributes on KineticLaw called "substanceUnits" and "timeUnits". They were removed beginning with SBML Level 2 Version 2 because further research determined they introduced many problems. The most significant problem was that their use could easily lead to the creation of valid models whose reactions nevertheless could not be integrated into a system of equations without outside knowledge for converting the quantities used. Examination of real-life models revealed that a common reason for using "substanceUnits" on KineticLaw was to set the units of all reactions to the same set of substance units, something that is better achieved by using UnitDefinition to redefine "substance" for the whole Model.

As mentioned above, in SBML Level 2 Versions 2–4, local parameters are of class Parameter. In SBML Level 3, the class of object is LocalParameter.

Public Member Functions

virtual bool accept (SBMLVisitor &v) const
 Accepts the given SBMLVisitor for this instance of KineticLaw. More...
 
int addCVTerm (CVTerm *term, bool newBag=false)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
int addLocalParameter (const LocalParameter *p)
 Adds a copy of the given LocalParameter object to the list of local parameters in this KineticLaw. More...
 
int addParameter (const Parameter *p)
 Adds a copy of the given Parameter object to the list of local parameters in this KineticLaw. More...
 
virtual int appendAnnotation (const XMLNode *annotation)
 Appends the given annotation to the "annotation" subelement of this object. More...
 
virtual int appendAnnotation (const std::string &annotation)
 Appends the given annotation to the "annotation" subelement of this object. More...
 
int appendNotes (const XMLNode *notes)
 Appends the given notes to the "notes" subelement of this object. More...
 
int appendNotes (const std::string &notes)
 Appends the given notes to the "notes" subelement of this object. More...
 
virtual KineticLawclone () const
 Creates and returns a deep copy of this KineticLaw object. More...
 
bool containsUndeclaredUnits ()
 Predicate returning true if the math expression of this KineticLaw contains parameters/numbers with undeclared units. More...
 
bool containsUndeclaredUnits () const
 Predicate returning true if the math expression of this KineticLaw contains parameters/numbers with undeclared units. More...
 
LocalParametercreateLocalParameter ()
 Creates a new LocalParameter object, adds it to this KineticLaw's list of local parameters, and returns the LocalParameter object created. More...
 
ParametercreateParameter ()
 Creates a new Parameter object, adds it to this KineticLaw's list of local parameters, and returns the Parameter object created. More...
 
int disablePackage (const std::string &pkgURI, const std::string &pkgPrefix)
 Disables the given SBML Level 3 package. More...
 
int enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package. More...
 
virtual ListgetAllElements ()
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual ListgetAllElementsFromPlugins ()
 Returns a List of all child SBase objects contained in SBML package plug-ins. More...
 
SBasegetAncestorOfType (int type, const std::string pkgName="core")
 Returns the first ancestor object that has the given SBML type code. More...
 
const SBasegetAncestorOfType (int type, const std::string pkgName="core") const
 Returns the first ancestor object that has the given SBML type code. More...
 
XMLNodegetAnnotation ()
 Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More...
 
XMLNodegetAnnotation () const
 Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More...
 
std::string getAnnotationString ()
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
std::string getAnnotationString () const
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
unsigned int getColumn () const
 Returns the column number on which this object first appears in the XML representation of the SBML document. More...
 
CVTermgetCVTerm (unsigned int n)
 Returns the nth CVTerm in the list of CVTerms of this SBML object. More...
 
ListgetCVTerms ()
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
ListgetCVTerms () const
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
UnitDefinitiongetDerivedUnitDefinition ()
 Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math" expression of this KineticLaw. More...
 
const UnitDefinitiongetDerivedUnitDefinition () const
 Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math" expression of this KineticLaw. More...
 
virtual SBasegetElementByMetaId (std::string metaid)
 Returns the first child element it can find with the given metaid, or NULL if no such object is found. More...
 
virtual SBasegetElementBySId (std::string id)
 Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this object, which for Species, is always "kineticLaw". More...
 
const std::string & getFormula () const
 Returns the mathematical formula for this KineticLaw object and return it as as a text string. More...
 
unsigned int getLevel () const
 Returns the SBML Level of the SBMLDocument object containing this object. More...
 
unsigned int getLine () const
 Returns the line number on which this object first appears in the XML representation of the SBML document. More...
 
const ListOfLocalParametersgetListOfLocalParameters () const
 Returns the list of local parameters in this KineticLaw object. More...
 
ListOfLocalParametersgetListOfLocalParameters ()
 Returns the list of local parameters in this KineticLaw object. More...
 
const ListOfParametersgetListOfParameters () const
 Returns the list of local parameters in this KineticLaw object. More...
 
ListOfParametersgetListOfParameters ()
 Returns the list of local parameters in this KineticLaw object. More...
 
const LocalParametergetLocalParameter (unsigned int n) const
 Returns the nth LocalParameter object in the list of local parameters in this KineticLaw instance. More...
 
LocalParametergetLocalParameter (unsigned int n)
 Returns the nth LocalParameter object in the list of local parameters in this KineticLaw instance. More...
 
const LocalParametergetLocalParameter (const std::string &sid) const
 Returns a local parameter based on its identifier. More...
 
LocalParametergetLocalParameter (const std::string &sid)
 Returns a local parameter based on its identifier. More...
 
const ASTNodegetMath () const
 Returns the mathematical formula for this KineticLaw object and return it as as an AST. More...
 
const std::string & getMetaId () const
 Returns the value of the "metaid" attribute of this object. More...
 
std::string & getMetaId ()
 Returns the value of the "metaid" attribute of this object. More...
 
const ModelgetModel () const
 Returns the Model object in which the current object is located. More...
 
ModelHistorygetModelHistory () const
 Returns the ModelHistory object, if any, attached to this object. More...
 
ModelHistorygetModelHistory ()
 Returns the ModelHistory object, if any, attached to this object. More...
 
virtual XMLNamespacesgetNamespaces () const
 Returns a list of the XML Namespaces declared on this SBML document. More...
 
XMLNodegetNotes ()
 Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More...
 
XMLNodegetNotes () const
 Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More...
 
std::string getNotesString ()
 Returns the content of the "notes" subelement of this object as a string. More...
 
std::string getNotesString () const
 Returns the content of the "notes" subelement of this object as a string. More...
 
unsigned int getNumCVTerms ()
 Returns the number of CVTerm objects in the annotations of this SBML object. More...
 
unsigned int getNumLocalParameters () const
 Returns the number of local parameters in this KineticLaw instance. More...
 
unsigned int getNumParameters () const
 Returns the number of local parameters in this KineticLaw instance. More...
 
unsigned int getNumPlugins () const
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
const std::string & getPackageName () const
 Returns the name of the SBML Level 3 package in which this element is defined. More...
 
unsigned int getPackageVersion () const
 Returns the Version of the SBML Level 3 package to which this element belongs to. More...
 
const ParametergetParameter (unsigned int n) const
 Returns the nth Parameter object in the list of local parameters in this KineticLaw instance. More...
 
ParametergetParameter (unsigned int n)
 Returns the nth Parameter object in the list of local parameters in this KineticLaw instance. More...
 
const ParametergetParameter (const std::string &sid) const
 Returns a local parameter based on its identifier. More...
 
ParametergetParameter (const std::string &sid)
 Returns a local parameter based on its identifier. More...
 
SBasegetParentSBMLObject ()
 Returns the parent SBML object containing this object. More...
 
const SBasegetParentSBMLObject () const
 Returns the parent SBML object containing this object. More...
 
SBasePlugingetPlugin (const std::string &package)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
const SBasePlugingetPlugin (const std::string &package) const
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
SBasePlugingetPlugin (unsigned int n)
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasePlugingetPlugin (unsigned int n) const
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
BiolQualifierType_t getResourceBiologicalQualifier (std::string resource)
 Returns the MIRIAM biological qualifier associated with the given resource. More...
 
ModelQualifierType_t getResourceModelQualifier (std::string resource)
 Returns the MIRIAM model qualifier associated with the given resource. More...
 
const SBMLDocumentgetSBMLDocument () const
 Returns the SBMLDocument object containing this object instance. More...
 
SBMLDocumentgetSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
int getSBOTerm () const
 Returns the integer portion of the value of the "sboTerm" attribute of this object. More...
 
std::string getSBOTermAsURL () const
 Returns the identifiers.org URL representation of the "sboTerm" attribute of this object. More...
 
std::string getSBOTermID () const
 Returns the string representation of the "sboTerm" attribute of this object. More...
 
const std::string & getSubstanceUnits () const
 (SBML Level 2 Version 1 only) Returns the value of the "substanceUnits" attribute of this KineticLaw object. More...
 
const std::string & getTimeUnits () const
 (SBML Level 2 Version 1 only) Returns the value of the "timeUnits" attribute of this KineticLaw object. More...
 
virtual int getTypeCode () const
 Returns the libSBML type code for this SBML object. More...
 
void * getUserData () const
 Returns the user data that has been previously set via setUserData(). More...
 
unsigned int getVersion () const
 Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...
 
virtual bool hasRequiredAttributes () const
 Predicate returning true if all the required attributes for this KineticLaw object have been set. More...
 
virtual bool hasRequiredElements () const
 Predicate returning true if all the required elements for this KineticLaw object have been set. More...
 
bool hasValidLevelVersionNamespaceCombination ()
 Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More...
 
bool isPackageEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPackageURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPkgEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPkgURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isSetAnnotation () const
 Predicate returning true if this object's "annotation" subelement exists and has content. More...
 
bool isSetFormula () const
 Predicate returning true if this KineticLaw's "formula" attribute is set. More...
 
bool isSetMath () const
 Predicate returning true if this Kinetic's "math" subelement is set. More...
 
bool isSetMetaId () const
 Predicate returning true if this object's "metaid" attribute is set. More...
 
bool isSetModelHistory ()
 Predicate returning true if this object has a ModelHistory object attached to it. More...
 
bool isSetNotes () const
 Predicate returning true if this object's "notes" subelement exists and has content. More...
 
bool isSetSBOTerm () const
 Predicate returning true if this object's "sboTerm" attribute is set. More...
 
bool isSetSubstanceUnits () const
 (SBML Level 2 Version 1 only) Predicate returning true if this SpeciesReference's "substanceUnits" attribute is set. More...
 
bool isSetTimeUnits () const
 (SBML Level 2 Version 1 only) Predicate returning true if this SpeciesReference's "timeUnits" attribute is set. More...
 
 KineticLaw (unsigned int level, unsigned int version)
 Creates a new KineticLaw using the given SBML level and version values. More...
 
 KineticLaw (SBMLNamespaces *sbmlns)
 Creates a new KineticLaw using the given SBMLNamespaces object sbmlns. More...
 
 KineticLaw (const KineticLaw &orig)
 Copy constructor; creates a copy of this KineticLaw. More...
 
bool matchesRequiredSBMLNamespacesForAddition (const SBase *sb)
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (const SBase *sb)
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (const SBase *sb) const
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
KineticLawoperator= (const KineticLaw &rhs)
 Assignment operator for KineticLaw. More...
 
virtual int removeFromParentAndDelete ()
 Finds this KineticLaw's Reaction parent and calls unsetKineticLaw() on it, indirectly deleting itself. More...
 
LocalParameterremoveLocalParameter (unsigned int n)
 Removes the nth LocalParameter object in the list of local parameters in this KineticLaw instance and returns a pointer to it. More...
 
LocalParameterremoveLocalParameter (const std::string &sid)
 Removes a LocalParameter object with the given identifier in the list of local parameters in this KineticLaw instance and returns a pointer to it. More...
 
ParameterremoveParameter (unsigned int n)
 Removes the nth Parameter object in the list of local parameters in this KineticLaw instance and returns a pointer to it. More...
 
ParameterremoveParameter (const std::string &sid)
 Removes a Parameter object with the given identifier in the list of local parameters in this KineticLaw instance and returns a pointer to it. More...
 
int removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="")
 Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More...
 
virtual void renameMetaIdRefs (std::string oldid, std::string newid)
 Renames all the MetaIdRef attributes on this element. More...
 
virtual void renameSIdRefs (std::string oldid, std::string newid)
 Renames all the SIdRef attributes on this element, including any found in MathML. More...
 
virtual void renameUnitSIdRefs (std::string oldid, std::string newid)
 Renames all the UnitSIdRef attributes on this element. More...
 
int replaceTopLevelAnnotationElement (const XMLNode *annotation)
 Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More...
 
int replaceTopLevelAnnotationElement (const std::string &annotation)
 Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More...
 
virtual int setAnnotation (const XMLNode *annotation)
 Sets the value of the "annotation" subelement of this SBML object. More...
 
virtual int setAnnotation (const std::string &annotation)
 Sets the value of the "annotation" subelement of this SBML object. More...
 
int setFormula (const std::string &formula)
 Sets the mathematical expression of this KineticLaw instance to the given formula. More...
 
int setMath (const ASTNode *math)
 Sets the mathematical expression of this KineticLaw instance to a copy of the given ASTNode. More...
 
int setMetaId (const std::string &metaid)
 Sets the value of the "metaid" attribute of this object. More...
 
int setModelHistory (ModelHistory *history)
 Sets the ModelHistory of this object. More...
 
int setNamespaces (XMLNamespaces *xmlns)
 Sets the namespaces relevant of this SBML object. More...
 
int setNotes (const XMLNode *notes)
 Sets the value of the "notes" subelement of this SBML object. More...
 
int setNotes (const std::string &notes, bool addXHTMLMarkup=false)
 Sets the value of the "notes" subelement of this SBML object to a copy of the string notes. More...
 
virtual int setSBOTerm (int value)
 Sets the value of the "sboTerm" attribute. More...
 
virtual int setSBOTerm (const std::string &sboid)
 Sets the value of the "sboTerm" attribute by string. More...
 
int setSubstanceUnits (const std::string &sid)
 (SBML Level 2 Version 1 only) Sets the "substanceUnits" attribute of this KineticLaw object to a copy of the identifier given in sid. More...
 
int setTimeUnits (const std::string &sid)
 (SBML Level 2 Version 1 only) Sets the "timeUnits" attribute of this KineticLaw object to a copy of the identifier in sid. More...
 
int setUserData (void *userData)
 Sets the user data of this element. More...
 
char * toSBML ()
 Returns a string consisting of a partial SBML corresponding to just this object. More...
 
int unsetAnnotation ()
 Unsets the value of the "annotation" subelement of this SBML object. More...
 
int unsetCVTerms ()
 Clears the list of CVTerm objects attached to this SBML object. More...
 
virtual int unsetId ()
 Unsets the value of the "id" attribute of this SBML object. More...
 
int unsetMetaId ()
 Unsets the value of the "metaid" attribute of this SBML object. More...
 
int unsetModelHistory ()
 Unsets the ModelHistory object attached to this object. More...
 
virtual int unsetName ()
 Unsets the value of the "name" attribute of this SBML object. More...
 
int unsetNotes ()
 Unsets the value of the "notes" subelement of this SBML object. More...
 
int unsetSBOTerm ()
 Unsets the value of the "sboTerm" attribute of this SBML object. More...
 
int unsetSubstanceUnits ()
 (SBML Level 2 Version 1 only) Unsets the "substanceUnits" attribute of this KineticLaw object. More...
 
int unsetTimeUnits ()
 (SBML Level 2 Version 1 only) Unsets the "timeUnits" attribugte of this KineticLaw object. More...
 
virtual ~KineticLaw ()
 Destroys this KineticLaw. More...
 

Protected Member Functions

virtual void setElementText (const std::string &text)
 When overridden allows SBase elements to use the text included in between the elements tags. More...
 

Constructor & Destructor Documentation

KineticLaw::KineticLaw ( unsigned int  level,
unsigned int  version 
)

Creates a new KineticLaw using the given SBML level and version values.

Parameters
levelan unsigned int, the SBML Level to assign to this KineticLaw
versionan unsigned int, the SBML Version to assign to this KineticLaw
Exceptions
SBMLConstructorExceptionThrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object.
Note
Upon the addition of a KineticLaw object to an SBMLDocument (e.g., using Reaction::setKineticLaw()), the SBML Level, SBML Version and XML namespace of the document override the values used when creating the KineticLaw object via this constructor. This is necessary to ensure that an SBML document is a consistent structure. Nevertheless, the ability to supply the values at the time of creation of a KineticLaw is an important aid to producing valid SBML. Knowledge of the intented SBML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing SBMLDocument.
KineticLaw::KineticLaw ( SBMLNamespaces sbmlns)

Creates a new KineticLaw using the given SBMLNamespaces object sbmlns.

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. A common approach to using this class constructor is to create an SBMLNamespaces object somewhere in a program, once, then pass it to object constructors such as this one when needed.

Parameters
sbmlnsan SBMLNamespaces object.
Exceptions
SBMLConstructorExceptionThrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object.
Note
Upon the addition of a KineticLaw object to an SBMLDocument (e.g., using Reaction::setKineticLaw()), the SBML XML namespace of the document overrides the value used when creating the KineticLaw object via this constructor. This is necessary to ensure that an SBML document is a consistent structure. Nevertheless, the ability to supply the values at the time of creation of a KineticLaw is an important aid to producing valid SBML. Knowledge of the intented SBML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing SBMLDocument.
KineticLaw::~KineticLaw ( )
virtual

Destroys this KineticLaw.

KineticLaw::KineticLaw ( const KineticLaw orig)

Copy constructor; creates a copy of this KineticLaw.

Parameters
origthe object to copy.
Exceptions
SBMLConstructorExceptionThrown if the argument orig is NULL.

Member Function Documentation

bool KineticLaw::accept ( SBMLVisitor v) const
virtual

Accepts the given SBMLVisitor for this instance of KineticLaw.

Parameters
vthe SBMLVisitor instance to be used.
Returns
the result of calling v.visit().

Implements SBase.

int SBase::addCVTerm ( CVTerm term,
bool  newBag = false 
)
inherited

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

Parameters
termthe CVTerm to assign.
newBagif 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:
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.
int KineticLaw::addLocalParameter ( const LocalParameter p)

Adds a copy of the given LocalParameter object to the list of local parameters in this KineticLaw.

Parameters
pthe LocalParameter to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. 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 KineticLaw. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the KineticLaw. 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. Please see createParameter() for a method that does not lead to these issues.
See Also
createLocalParameter()
int KineticLaw::addParameter ( const Parameter p)

Adds a copy of the given Parameter object to the list of local parameters in this KineticLaw.

Parameters
pthe Parameter to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. 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 KineticLaw. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the KineticLaw. 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. Please see createParameter() for a method that does not lead to these issues.
See Also
createParameter()
int SBase::appendAnnotation ( const XMLNode annotation)
virtualinherited

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(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.

Parameters
annotationan 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(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int SBase::appendAnnotation ( const std::string &  annotation)
virtualinherited

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(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.

Parameters
annotationan 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(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int SBase::appendNotes ( const XMLNode notes)
inherited

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
notesan 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(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::appendNotes ( const std::string &  notes)
inherited

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
notesan 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(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
KineticLaw * KineticLaw::clone ( ) const
virtual

Creates and returns a deep copy of this KineticLaw object.

Returns
a (deep) copy of this KineticLaw.

Implements SBase.

bool KineticLaw::containsUndeclaredUnits ( )

Predicate returning true if the math expression of this KineticLaw contains parameters/numbers with undeclared units.

Returns
true if the math expression of this KineticLaw includes parameters/numbers with undeclared units, false otherwise.
Note
A return value of true indicates that the UnitDefinition returned by getDerivedUnitDefinition() may not accurately represent the units of the expression.
See Also
getDerivedUnitDefinition()
bool KineticLaw::containsUndeclaredUnits ( ) const

Predicate returning true if the math expression of this KineticLaw contains parameters/numbers with undeclared units.

Returns
true if the math expression of this KineticLaw includes parameters/numbers with undeclared units, false otherwise.
Note
A return value of true indicates that the UnitDefinition returned by getDerivedUnitDefinition() may not accurately represent the units of the expression.
See Also
getDerivedUnitDefinition()
LocalParameter * KineticLaw::createLocalParameter ( )

Creates a new LocalParameter object, adds it to this KineticLaw's list of local parameters, and returns the LocalParameter object created.

Returns
a new LocalParameter object instance
See Also
addLocalParameter(const LocalParameter* p)
Parameter * KineticLaw::createParameter ( )

Creates a new Parameter object, adds it to this KineticLaw's list of local parameters, and returns the Parameter object created.

Returns
a new Parameter object instance
See Also
addParameter(const Parameter* p)
int SBase::disablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix 
)
inherited

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
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int SBase::enablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix,
bool  flag 
)
inherited

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
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
flagwhether 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:
List * KineticLaw::getAllElements ( )
virtual

Returns a List of all child SBase objects, including those nested to an arbitrary depth.

Returns
a List of pointers to all children objects.

Reimplemented from SBase.

List * SBase::getAllElementsFromPlugins ( )
virtualinherited

Returns a List of all child SBase objects contained in SBML package plug-ins.

This method walks down the list of all packages used by the enclosing Model and returns all objects contained in them.

Returns
a pointer to a List of pointers to all children objects from plug-ins.
SBase * SBase::getAncestorOfType ( int  type,
const std::string  pkgName = "core" 
)
inherited

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

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
typethe 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 NULL 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.
const SBase * SBase::getAncestorOfType ( int  type,
const std::string  pkgName = "core" 
) const
inherited

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

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
typethe 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 NULL 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.
XMLNode * SBase::getAnnotation ( )
inherited

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(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
XMLNode * SBase::getAnnotation ( ) const
inherited

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(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
std::string SBase::getAnnotationString ( )
inherited

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(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
std::string SBase::getAnnotationString ( ) const
inherited

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(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
unsigned int SBase::getColumn ( ) const
inherited

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()
CVTerm * SBase::getCVTerm ( unsigned int  n)
inherited

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

Parameters
nunsigned int the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
List * SBase::getCVTerms ( )
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns
the list of CVTerms for this SBML object.
List * SBase::getCVTerms ( ) const
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns
the list of CVTerms for this SBML object.
UnitDefinition * KineticLaw::getDerivedUnitDefinition ( )

Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math" expression of this KineticLaw.

The units are calculated based on the mathematical expression in the KineticLaw and the model quantities referenced by <ci> elements used within that expression. The getDerivedUnitDefinition() method returns the calculated units.

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.

Warning
Note that it is possible the "math" expression in the KineticLaw contains pure numbers or parameters with undeclared units. In those cases, it is not possible to calculate the units of the overall expression without making assumptions. LibSBML does not make assumptions about the units, and getDerivedUnitDefinition() only returns the units as far as it is able to determine them. For example, in an expression X + Y, if X has unambiguously-defined units and Y does not, it will return the units of X. It is important that callers also invoke the method containsUndeclaredUnits() to determine whether this situation holds. Callers may wish to take suitable actions in those scenarios.
Returns
a UnitDefinition that expresses the units of the math expression of this KineticLaw, or NULL if one cannot be constructed.
See Also
containsUndeclaredUnits()
const UnitDefinition * KineticLaw::getDerivedUnitDefinition ( ) const

Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math" expression of this KineticLaw.

The units are calculated based on the mathematical expression in the KineticLaw and the model quantities referenced by <ci> elements used within that expression. The getDerivedUnitDefinition() method returns the calculated units.

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.

Warning
Note that it is possible the "math" expression in the KineticLaw contains pure numbers or parameters with undeclared units. In those cases, it is not possible to calculate the units of the overall expression without making assumptions. LibSBML does not make assumptions about the units, and getDerivedUnitDefinition() only returns the units as far as it is able to determine them. For example, in an expression X + Y, if X has unambiguously-defined units and Y does not, it will return the units of X. It is important that callers also invoke the method containsUndeclaredUnits() to determine whether this situation holds. Callers may wish to take suitable actions in those scenarios.
Returns
a UnitDefinition that expresses the units of the math expression of this KineticLaw, or NULL if one cannot be constructed.
See Also
containsUndeclaredUnits()
SBase * KineticLaw::getElementByMetaId ( std::string  metaid)
virtual

Returns the first child element it can find with the given metaid, or NULL if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.

Reimplemented from SBase.

SBase * KineticLaw::getElementBySId ( std::string  id)
virtual

Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.

Parameters
idstring representing the id of objects to find.
Returns
pointer to the first element found with the given id.

Reimplemented from SBase.

const string & KineticLaw::getElementName ( ) const
virtual

Returns the XML element name of this object, which for Species, is always "kineticLaw".

Returns
the name of this element, i.e., "kineticLaw".

Implements SBase.

const string & KineticLaw::getFormula ( ) const

Returns the mathematical formula for this KineticLaw object and return it as as a text string.

This is fundamentally equivalent to getMath(). This variant is provided principally for compatibility compatibility with SBML Level 1.

Returns
a string representing the formula of this KineticLaw.
Note
SBML Level 1 uses a text-string format for mathematical formulas. SBML Level 2 uses MathML, an XML format for representing mathematical expressions. LibSBML provides an Abstract Syntax Tree API for working with mathematical expressions; this API is more powerful than working with formulas directly in text form, and ASTs can be translated into either MathML or the text-string syntax. The libSBML methods that accept text-string formulas directly (such as this constructor) are provided for SBML Level 1 compatibility, but developers are encouraged to use the AST mechanisms.
See Also
getMath()
unsigned int SBase::getLevel ( ) const
inherited

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

Returns
the SBML level of this SBML object.
See Also
getVersion()
getNamespaces()
getPackageVersion()
unsigned int SBase::getLine ( ) const
inherited

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()
const ListOfLocalParameters * KineticLaw::getListOfLocalParameters ( ) const

Returns the list of local parameters in this KineticLaw object.

Returns
the list of LocalParameters for this KineticLaw.
ListOfLocalParameters * KineticLaw::getListOfLocalParameters ( )

Returns the list of local parameters in this KineticLaw object.

Returns
the list of LocalParameters for this KineticLaw.
const ListOfParameters * KineticLaw::getListOfParameters ( ) const

Returns the list of local parameters in this KineticLaw object.

Returns
the list of Parameters for this KineticLaw.
ListOfParameters * KineticLaw::getListOfParameters ( )

Returns the list of local parameters in this KineticLaw object.

Returns
the list of Parameters for this KineticLaw.
const LocalParameter * KineticLaw::getLocalParameter ( unsigned int  n) const

Returns the nth LocalParameter object in the list of local parameters in this KineticLaw instance.

Parameters
nthe index of the LocalParameter object sought
Returns
the nth LocalParameter of this KineticLaw.
LocalParameter * KineticLaw::getLocalParameter ( unsigned int  n)

Returns the nth LocalParameter object in the list of local parameters in this KineticLaw instance.

Parameters
nthe index of the LocalParameter object sought
Returns
the nth LocalParameter of this KineticLaw.
const LocalParameter * KineticLaw::getLocalParameter ( const std::string &  sid) const

Returns a local parameter based on its identifier.

Parameters
sidthe identifier of the LocalParameter being sought.
Returns
the LocalParameter object in this KineticLaw instace having the given "id", or NULL if no such LocalParameter exists.
LocalParameter * KineticLaw::getLocalParameter ( const std::string &  sid)

Returns a local parameter based on its identifier.

Parameters
sidthe identifier of the LocalParameter being sought.
Returns
the LocalParameter object in this KineticLaw instace having the given "id", or NULL if no such LocalParameter exists.
const ASTNode * KineticLaw::getMath ( ) const

Returns the mathematical formula for this KineticLaw object and return it as as an AST.

This is fundamentally equivalent to getFormula(). The latter is provided principally for compatibility compatibility with SBML Level 1, which represented mathematical formulas in text-string form.

Returns
the ASTNode representation of the mathematical formula.
See Also
getFormula()
const string & SBase::getMetaId ( ) const
inherited

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 meta-identifier of this SBML object.
See Also
isSetMetaId()
setMetaId(const std::string& metaid)
string & SBase::getMetaId ( )
inherited

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 meta-identifier of this SBML object, as a string.
See Also
isSetMetaId()
setMetaId(const std::string& metaid)
const Model * SBase::getModel ( ) const
inherited

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

Returns
the parent Model of this SBML object.
See Also
getParentSBMLObject()
getSBMLDocument()
ModelHistory * SBase::getModelHistory ( ) const
inherited

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

Returns
the ModelHistory object attached to this object, or NULL 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.
ModelHistory * SBase::getModelHistory ( )
inherited

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

Returns
the ModelHistory object attached to this object, or NULL 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.
XMLNamespaces * SBase::getNamespaces ( ) const
virtualinherited

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 SBMLDocument.

XMLNode * SBase::getNotes ( )
inherited

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(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
XMLNode * SBase::getNotes ( ) const
inherited

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(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
std::string SBase::getNotesString ( )
inherited

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(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
std::string SBase::getNotesString ( ) const
inherited

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(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
unsigned int SBase::getNumCVTerms ( )
inherited

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

Returns
the number of CVTerms for this SBML object.
unsigned int KineticLaw::getNumLocalParameters ( ) const

Returns the number of local parameters in this KineticLaw instance.

Returns
the number of LocalParameters in this KineticLaw.
unsigned int KineticLaw::getNumParameters ( ) const

Returns the number of local parameters in this KineticLaw instance.

Returns
the number of Parameters in this KineticLaw.
unsigned int SBase::getNumPlugins ( ) const
inherited

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

Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
const std::string & SBase::getPackageName ( ) const
inherited

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.
unsigned int SBase::getPackageVersion ( ) const
inherited

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()
const Parameter * KineticLaw::getParameter ( unsigned int  n) const

Returns the nth Parameter object in the list of local parameters in this KineticLaw instance.

Parameters
nthe index of the Parameter object sought
Returns
the nth Parameter of this KineticLaw.
Parameter * KineticLaw::getParameter ( unsigned int  n)

Returns the nth Parameter object in the list of local parameters in this KineticLaw instance.

Parameters
nthe index of the Parameter object sought
Returns
the nth Parameter of this KineticLaw.
const Parameter * KineticLaw::getParameter ( const std::string &  sid) const

Returns a local parameter based on its identifier.

Parameters
sidthe identifier of the Parameter being sought.
Returns
the Parameter object in this KineticLaw instace having the given "id", or NULL if no such Parameter exists.
Parameter * KineticLaw::getParameter ( const std::string &  sid)

Returns a local parameter based on its identifier.

Parameters
sidthe identifier of the Parameter being sought.
Returns
the Parameter object in this KineticLaw instace having the given "id", or NULL if no such Parameter exists.
SBase * SBase::getParentSBMLObject ( )
inherited

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()
const SBase * SBase::getParentSBMLObject ( ) const
inherited

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()
SBasePlugin * SBase::getPlugin ( const std::string &  package)
inherited

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

Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
const SBasePlugin * SBase::getPlugin ( const std::string &  package) const
inherited

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

Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
SBasePlugin * SBase::getPlugin ( unsigned int  n)
inherited

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
const SBasePlugin * SBase::getPlugin ( unsigned int  n) const
inherited

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
BiolQualifierType_t SBase::getResourceBiologicalQualifier ( std::string  resource)
inherited

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

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

Parameters
resourcestring 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.
ModelQualifierType_t SBase::getResourceModelQualifier ( std::string  resource)
inherited

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

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

Parameters
resourcestring representing the resource; e.g., "http://www.geneontology.org/#GO:0005892".
Returns
the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
const SBMLDocument * SBase::getSBMLDocument ( ) const
inherited

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()
SBMLDocument * SBase::getSBMLDocument ( )
inherited

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()
int SBase::getSBOTerm ( ) const
inherited

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.
std::string SBase::getSBOTermAsURL ( ) const
inherited

Returns the identifiers.org URL representation of the "sboTerm" attribute of this object.

This method returns the entire SBO identifier as a text string in the form "http://identifiers.org/biomodels.sbo/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 an identifiers.org URL (its value will be of the form "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN"), or an empty string if the value is not set.
std::string SBase::getSBOTermID ( ) const
inherited

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.
const string & KineticLaw::getSubstanceUnits ( ) const

(SBML Level 2 Version 1 only) Returns the value of the "substanceUnits" attribute of this KineticLaw object.

Returns
the "substanceUnits" attribute value.
Note
The attributes "timeUnits" and "substanceUnits" are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the "timeUnits" and "substanceUnits" attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
const string & KineticLaw::getTimeUnits ( ) const

(SBML Level 2 Version 1 only) Returns the value of the "timeUnits" attribute of this KineticLaw object.

Returns
the "timeUnits" attribute value.
Note
The attributes "timeUnits" and "substanceUnits" are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the "timeUnits" and "substanceUnits" attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
int KineticLaw::getTypeCode ( ) const
virtual

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 SBase.

void * SBase::getUserData ( ) const
inherited

Returns the user data that has been previously set via setUserData().

Returns
the user data of this node, or NULL if no user data has been set.
unsigned int SBase::getVersion ( ) const
inherited

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()
bool KineticLaw::hasRequiredAttributes ( ) const
virtual

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

Note
The required attributes for a KineticLaw object are:
  • "formula" (SBML Level 1 only)
Returns
a boolean value indicating whether all the required attributes for this object have been defined.
bool KineticLaw::hasRequiredElements ( ) const
virtual

Predicate returning true if all the required elements for this KineticLaw object have been set.

Note
The required elements for a KineticLaw object are:
  • "math"
Returns
a boolean value indicating whether all the required elements for this object have been defined.
bool SBase::hasValidLevelVersionNamespaceCombination ( )
inherited

Predicate returning true if 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"
  • Level 3 Version 1 Core: "http://www.sbml.org/sbml/level3/version1/core"
Returns
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
bool SBase::isPackageEnabled ( const std::string &  pkgName) const
inherited

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

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPackageURIEnabled()
bool SBase::isPackageURIEnabled ( const std::string &  pkgURI) const
inherited

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

Parameters
pkgURIthe URI of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPackageEnabled()
bool SBase::isPkgEnabled ( const std::string &  pkgName) const
inherited

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

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPkgURIEnabled()
bool SBase::isPkgURIEnabled ( const std::string &  pkgURI) const
inherited

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

Parameters
pkgURIthe URI of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPkgEnabled()
bool SBase::isSetAnnotation ( ) const
inherited

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(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
bool KineticLaw::isSetFormula ( ) const

Predicate returning true if this KineticLaw's "formula" attribute is set.

This is functionally identical to the method isSetMath(). It is provided in order to mirror the parallel between getFormula() and getMath().

Returns
true if the formula (meaning the math subelement) of this KineticLaw is set, false otherwise.
Note
SBML Level 1 uses a text-string format for mathematical formulas. SBML Level 2 uses MathML, an XML format for representing mathematical expressions. LibSBML provides an Abstract Syntax Tree API for working with mathematical expressions; this API is more powerful than working with formulas directly in text form, and ASTs can be translated into either MathML or the text-string syntax. The libSBML methods that accept text-string formulas directly (such as this constructor) are provided for SBML Level 1 compatibility, but developers are encouraged to use the AST mechanisms.
See Also
isSetMath()
bool KineticLaw::isSetMath ( ) const

Predicate returning true if this Kinetic's "math" subelement is set.

This is identical to the method isSetFormula(). It is provided in order to mirror the parallel between getFormula() and getMath().

Returns
true if the formula (meaning the math subelement) of this KineticLaw is set, false otherwise.
See Also
isSetFormula()
bool SBase::isSetMetaId ( ) const
inherited

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(const std::string& metaid)
bool SBase::isSetModelHistory ( )
inherited

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.
bool SBase::isSetNotes ( ) const
inherited

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(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
bool SBase::isSetSBOTerm ( ) const
inherited

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.
bool KineticLaw::isSetSubstanceUnits ( ) const

(SBML Level 2 Version 1 only) Predicate returning true if this SpeciesReference's "substanceUnits" attribute is set.

Returns
true if the "substanceUnits" attribute of this KineticLaw object is set, false otherwise.
Note
The attributes "timeUnits" and "substanceUnits" are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the "timeUnits" and "substanceUnits" attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
bool KineticLaw::isSetTimeUnits ( ) const

(SBML Level 2 Version 1 only) Predicate returning true if this SpeciesReference's "timeUnits" attribute is set.

Returns
true if the "timeUnits" attribute of this KineticLaw object is set, false otherwise.
Note
The attributes "timeUnits" and "substanceUnits" are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the "timeUnits" and "substanceUnits" attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase sb)
inherited

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

Parameters
sban object to compare with respect to namespaces
Returns
boolean, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase sb) const
inherited

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

Parameters
sban object to compare with respect to namespaces
Returns
boolean, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool SBase::matchesSBMLNamespaces ( const SBase sb)
inherited

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

Parameters
sban 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.
bool SBase::matchesSBMLNamespaces ( const SBase sb) const
inherited

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

Parameters
sban 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.
KineticLaw & KineticLaw::operator= ( const KineticLaw rhs)

Assignment operator for KineticLaw.

Parameters
rhsThe object whose values are used as the basis of the assignment.
Exceptions
SBMLConstructorExceptionThrown if the argument rhs is NULL.
int KineticLaw::removeFromParentAndDelete ( )
virtual

Finds this KineticLaw's Reaction parent and calls unsetKineticLaw() on it, indirectly deleting itself.

Overridden from the SBase function since the parent is not a ListOf.

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

Reimplemented from SBase.

LocalParameter * KineticLaw::removeLocalParameter ( unsigned int  n)

Removes the nth LocalParameter object in the list of local parameters in this KineticLaw instance and returns a pointer to it.

Removes the nth LocalParameter object in the list of local parameters in this KineticLaw instance.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the LocalParameter object to remove
Returns
the LocalParameter object removed. As mentioned above, the caller owns the returned item. NULL is returned if the given index is out of range.
LocalParameter * KineticLaw::removeLocalParameter ( const std::string &  sid)

Removes a LocalParameter object with the given identifier in the list of local parameters in this KineticLaw instance and returns a pointer to it.

Removes a LocalParameter object with the given identifier in the list of local parameters in this KineticLaw instance.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the LocalParameter to remove
Returns
the LocalParameter object removed. As mentioned above, the caller owns the returned object. NULL is returned if no LocalParameter object with the identifier exists in this KineticLaw instance.
Parameter * KineticLaw::removeParameter ( unsigned int  n)

Removes the nth Parameter object in the list of local parameters in this KineticLaw instance and returns a pointer to it.

Removes the nth Parameter object in the list of local parameters in this KineticLaw instance.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Parameter object to remove
Returns
the Parameter object removed. As mentioned above, the caller owns the returned item. NULL is returned if the given index is out of range.
Parameter * KineticLaw::removeParameter ( const std::string &  sid)

Removes a Parameter object with the given identifier in the list of local parameters in this KineticLaw instance and returns a pointer to it.

Removes a Parameter object with the given identifier in the list of local parameters in this KineticLaw instance.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the Parameter to remove
Returns
the Parameter object removed. As mentioned above, the caller owns the returned object. NULL is returned if no Parameter object with the identifier exists in this KineticLaw instance.
int SBase::removeTopLevelAnnotationElement ( const std::string  elementName,
const std::string  elementURI = "" 
)
inherited

Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI.

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.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
replaceTopLevelAnnotationElement(const XMLNode *)
replaceTopLevelAnnotationElement(const std::string&)
void SBase::renameMetaIdRefs ( std::string  oldid,
std::string  newid 
)
virtualinherited

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
oldidthe old identifier
newidthe new identifier

Reimplemented in Port.

void KineticLaw::renameSIdRefs ( std::string  oldid,
std::string  newid 
)
virtual

Renames all the SIdRef attributes on this element, including any found in MathML.

Reimplemented from SBase.

void KineticLaw::renameUnitSIdRefs ( std::string  oldid,
std::string  newid 
)
virtual

Renames all the UnitSIdRef attributes on this element.

Reimplemented from SBase.

int SBase::replaceTopLevelAnnotationElement ( const XMLNode annotation)
inherited

Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.

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.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters
annotationXMLNode representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI)
replaceTopLevelAnnotationElement(const std::string&)
int SBase::replaceTopLevelAnnotationElement ( const std::string &  annotation)
inherited

Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.

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.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters
annotationstring representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI)
replaceTopLevelAnnotationElement(const XMLNode*)
int SBase::setAnnotation ( const XMLNode annotation)
virtualinherited

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

Parameters
annotationan 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:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int SBase::setAnnotation ( const std::string &  annotation)
virtualinherited

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

Parameters
annotationan 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(const XMLNode* annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

void SBase::setElementText ( const std::string &  text)
protectedvirtualinherited

When overridden allows SBase elements to use the text included in between the elements tags.

The default implementation does nothing.

Parameters
textthe text string found between the element tags.
int KineticLaw::setFormula ( const std::string &  formula)

Sets the mathematical expression of this KineticLaw instance to the given formula.

The given formula string is copied. Internally, libSBML stores the mathematical expression as an ASTNode.

Parameters
formulathe mathematical expression to use, represented in text-string form.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
SBML Level 1 uses a text-string format for mathematical formulas. SBML Level 2 uses MathML, an XML format for representing mathematical expressions. LibSBML provides an Abstract Syntax Tree API for working with mathematical expressions; this API is more powerful than working with formulas directly in text form, and ASTs can be translated into either MathML or the text-string syntax. The libSBML methods that accept text-string formulas directly (such as this constructor) are provided for SBML Level 1 compatibility, but developers are encouraged to use the AST mechanisms.
See Also
setMath(const ASTNode* math)
int KineticLaw::setMath ( const ASTNode math)

Sets the mathematical expression of this KineticLaw instance to a copy of the given ASTNode.

This is fundamentally identical to getFormula(). The latter is provided principally for compatibility compatibility with SBML Level 1, which represented mathematical formulas in text-string form.

Parameters
mathan ASTNode representing a formula tree.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setFormula(const std::string& formula)
int SBase::setMetaId ( const std::string &  metaid)
inherited

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
metaidthe 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()
int SBase::setModelHistory ( ModelHistory history)
inherited

Sets the ModelHistory of this object.

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

Parameters
historyModelHistory 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.
int SBase::setNamespaces ( XMLNamespaces xmlns)
inherited

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
xmlnsthe namespaces to set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int SBase::setNotes ( const XMLNode notes)
inherited

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
notesan 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(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::setNotes ( const std::string &  notes,
bool  addXHTMLMarkup = false 
)
inherited

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
notesan XML string that is to be used as the content of the "notes" subelement of this object
addXHTMLMarkupa boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::setSBOTerm ( int  value)
virtualinherited

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
valuethe 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(const std::string &sboid)
int SBase::setSBOTerm ( const std::string &  sboid)
virtualinherited

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
sboidthe 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(int value)
int KineticLaw::setSubstanceUnits ( const std::string &  sid)

(SBML Level 2 Version 1 only) Sets the "substanceUnits" attribute of this KineticLaw object to a copy of the identifier given in sid.

Parameters
sidthe identifier of the units to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attributes "timeUnits" and "substanceUnits" are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the "timeUnits" and "substanceUnits" attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
int KineticLaw::setTimeUnits ( const std::string &  sid)

(SBML Level 2 Version 1 only) Sets the "timeUnits" attribute of this KineticLaw object to a copy of the identifier in sid.

Parameters
sidthe identifier of the units to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attributes "timeUnits" and "substanceUnits" are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the "timeUnits" and "substanceUnits" attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
int SBase::setUserData ( void *  userData)
inherited

Sets the user data of this element.

This can be used by the application developer to attach custom information to the node. In case of a deep copy this attribute will passed as it is. The attribute will be never interpreted by this class.

Parameters
userDataspecifies the new user data.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
char * SBase::toSBML ( )
inherited

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.
int SBase::unsetAnnotation ( )
inherited

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:
See Also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
int SBase::unsetCVTerms ( )
inherited

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:
int SBase::unsetId ( )
virtualinherited

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 Model, Event, SimpleSpeciesReference, Submodel, ExternalModelDefinition, Deletion, and Port.

int SBase::unsetMetaId ( )
inherited

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:
int SBase::unsetModelHistory ( )
inherited

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.
int SBase::unsetName ( )
virtualinherited

Unsets the value of the "name" attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: "id" and "name". In contrast to the "id" attribute, the "name" attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of "name" is the type string defined in XML Schema. SBML imposes no restrictions as to the content of "name" attributes beyond those restrictions defined by the string type in XML Schema.

The recommended practice for handling "name" is as follows. If a software tool has the capability for displaying the content of "name" attributes, it should display this content to the user as a component's label instead of the component's "id". If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the "name" attribute is missing on a given component, then the user interface should display the value of the "id" attribute instead. (Script language interpreters are especially likely to display "id" instead of "name".)

As a consequence of the above, authors of systems that automatically generate the values of "id" attributes should be aware some systems may display the "id"'s to the user. Authors therefore may wish to take some care to have their software create "id" values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the "id" attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of "id" values, there are no restrictions on the uniqueness of "name" values in a model. This allows software applications leeway in assigning component identifiers.

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

Reimplemented in Species, Compartment, Model, Event, Reaction, Parameter, UnitDefinition, FunctionDefinition, CompartmentType, SpeciesType, Submodel, SimpleSpeciesReference, ExternalModelDefinition, Deletion, and Port.

int SBase::unsetNotes ( )
inherited

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:
See Also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::unsetSBOTerm ( )
inherited

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:
int KineticLaw::unsetSubstanceUnits ( )

(SBML Level 2 Version 1 only) Unsets the "substanceUnits" attribute of this KineticLaw object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attributes "timeUnits" and "substanceUnits" are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the "timeUnits" and "substanceUnits" attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
int KineticLaw::unsetTimeUnits ( )

(SBML Level 2 Version 1 only) Unsets the "timeUnits" attribugte of this KineticLaw object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attributes "timeUnits" and "substanceUnits" are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the "timeUnits" and "substanceUnits" attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.