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InitialAssignment Class Reference
Inheritance diagram for InitialAssignment:
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Detailed Description

Implementation of SBML's InitialAssignment construct.

SBML Level 2 Versions 2–4 and SBML Level 3 provide two ways of assigning initial values to entities in a model. The simplest and most basic is to set the values of the appropriate attributes in the relevant components; for example, the initial value of a model parameter (whether it is a constant or a variable) can be assigned by setting its "value" attribute directly in the model definition. However, this approach is not suitable when the value must be calculated, because the initial value attributes on different components such as species, compartments, and parameters are single values and not mathematical expressions. In those situations, the InitialAssignment construct can be used; it permits the calculation of the value of a constant or the initial value of a variable from the values of other quantities in a model.

As explained below, the provision of InitialAssignment does not mean that models necessarily must use this construct when defining initial values of quantities in a model. If a value can be set directly using the relevant attribute of a component in a model, then that approach may be more efficient and more portable to other software tools. InitialAssignment should be used when the other mechanism is insufficient for the needs of a particular model.

The InitialAssignment construct has some similarities to AssignmentRule. The main differences are: (a) an InitialAssignment can set the value of a constant whereas an AssignmentRule cannot, and (b) unlike AssignmentRule, an InitialAssignment definition only applies up to and including the beginning of simulation time, i.e., t $\leq$ 0, while an AssignmentRule applies at all times.

InitialAssignment has a required attribute, "symbol", whose value must follow the guidelines for identifiers described in the SBML specification (e.g., Section 3.3 in the Level 2 Version 4 specification). The value of this attribute in an InitialAssignment object can be the identifier of a Compartment, Species or global Parameter elsewhere in the model. The InitialAssignment defines the initial value of the constant or variable referred to by the "symbol" attribute. (The attribute's name is "symbol" rather than "variable" because it may assign values to constants as well as variables in a model.) Note that an initial assignment cannot be made to reaction identifiers, that is, the "symbol" attribute value of an InitialAssignment cannot be an identifier that is the "id" attribute value of a Reaction object in the model. This is identical to a restriction placed on rules.

InitialAssignment also has a required "math" subelement that contains a MathML expression used to calculate the value of the constant or the initial value of the variable. The units of the value computed by the formula in the "math" subelement should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be identical to be the units associated with the identifier given in the "symbol" attribute. (That is, the units are the units of the species, compartment, or parameter, as appropriate for the kind of object identified by the value of "symbol".)

InitialAssignment was introduced in SBML Level 2 Version 2. It is not available in SBML Level 2 Version 1 nor in any version of Level 1.

Semantics of Initial Assignments

The value calculated by an InitialAssignment object overrides the value assigned to the given symbol by the object defining that symbol. For example, if a compartment's "size" attribute is set in its definition, and the model also contains an InitialAssignment having that compartment's identifier as its "symbol" attribute value, then the interpretation is that the "size" assigned in the Compartment object should be ignored and the value assigned based on the computation defined in the InitialAssignment. Initial assignments can take place for Compartment, Species and global Parameter objects regardless of the value of their "constant" attribute.

The actions of all InitialAssignment objects are in general terms the same, but differ in the precise details depending on the type of variable being set:

  • In the case of a species, an InitialAssignment sets the referenced species' initial quantity (concentration or amount of substance) to the value determined by the formula in the "math" subelement. The overall units of the formula should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be the same as the units specified for the species.

  • In the case of a compartment, an InitialAssignment sets the referenced compartment's initial size to the size determined by the formula in "math". The overall units of the formula should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be the same as the units specified for the size of the compartment.

  • In the case of a parameter, an InitialAssignment sets the referenced parameter's initial value to that determined by the formula in "math". The overall units of the formula should (in SBML Level 2 Version 4 and SBML Level 3) or must (in previous Versions) be the same as the units defined for the parameter.

In the context of a simulation, initial assignments establish values that are in effect prior to and including the start of simulation time, i.e., t $\leq$ 0. Section 3.4.8 in the SBML Level 2 Version 4 and SBML Level 3 Version 1 Core specifications provides information about the interpretation of assignments, rules, and entity values for simulation time up to and including the start time t = 0; this is important for establishing the initial conditions of a simulation if the model involves expressions containing the delay "csymbol".

There cannot be two initial assignments for the same symbol in a model; that is, a model must not contain two or more InitialAssignment objects that both have the same identifier as their "symbol" attribute value. A model must also not define initial assignments and assignment rules for the same entity. That is, there cannot be both an InitialAssignment and an AssignmentRule for the same symbol in a model, because both kinds of constructs apply prior to and at the start of simulated time—allowing both to exist for a given symbol would result in indeterminism).

The ordering of InitialAssignment objects is not significant. The combined set of InitialAssignment, AssignmentRule and KineticLaw objects form a set of assignment statements that must be considered as a whole. The combined set of assignment statements should not contain algebraic loops: a chain of dependency between these statements should terminate. (More formally, consider the directed graph of assignment statements where nodes are a model's assignment statements and directed arcs exist for each occurrence of a symbol in an assignment statement "math" attribute. The directed arcs in this graph start from the statement assigning the symbol and end at the statement that contains the symbol in their math elements. Such a graph must be acyclic.)

Finally, it is worth being explicit about the expected behavior in the following situation. Suppose (1) a given symbol has a value x assigned to it in its definition, and (2) there is an initial assignment having the identifier as its "symbol" value and reassigning the value to y, and (3) the identifier is also used in the mathematical formula of a second initial assignment. What value should the second initial assignment use? It is y, the value assigned to the symbol by the first initial assignment, not whatever value was given in the symbol's definition. This follows directly from the behavior described above: if an InitialAssignment object exists for a given symbol, then the symbol's value is overridden by that initial assignment.

Public Member Functions

virtual bool accept (SBMLVisitor &v) const
 Accepts the given SBMLVisitor for this instance of InitialAssignment. More...
 
int addCVTerm (CVTerm *term, bool newBag=false)
 Adds a copy of the given CVTerm object to this SBML object. 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 InitialAssignmentclone () const
 Creates and returns a deep copy of this InitialAssignment. More...
 
bool containsUndeclaredUnits ()
 Predicate returning true if the math expression of this InitialAssignment contains parameters/numbers with undeclared units. More...
 
bool containsUndeclaredUnits () const
 Predicate returning true if the math expression of this InitialAssignment contains parameters/numbers with undeclared units. 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 InitialAssignment. More...
 
const UnitDefinitiongetDerivedUnitDefinition () const
 Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math" expression of this InitialAssignment. More...
 
virtual SBasegetElementByMetaId (std::string metaid)
 Returns the first child element it can find with a specific "metaid" attribute value, 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 InitialAssignment, is always "initialAssignment". More...
 
virtual const std::string & getId () const
 
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 ASTNodegetMath () const
 Get the mathematical formula of this InitialAssignment. 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 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...
 
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 & getSymbol () const
 Get the value of the "symbol" attribute of this InitialAssignment. 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 InitialAssignment object have been set. More...
 
virtual bool hasRequiredElements () const
 Predicate returning true if all the required elements for this InitialAssignment 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...
 
 InitialAssignment (unsigned int level, unsigned int version)
 Creates a new InitialAssignment using the given SBML level and version values. More...
 
 InitialAssignment (SBMLNamespaces *sbmlns)
 Creates a new InitialAssignment using the given SBMLNamespaces object sbmlns. More...
 
 InitialAssignment (const InitialAssignment &orig)
 Copy constructor; creates a copy of this InitialAssignment. 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 isSetMath () const
 Predicate returning true if this InitialAssignment's "math" subelement contains a value. 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 isSetSymbol () const
 Predicate returning true if this InitialAssignment's "symbol" attribute is set. 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...
 
InitialAssignmentoperator= (const InitialAssignment &rhs)
 Assignment operator for InitialAssignment. More...
 
virtual int removeFromParentAndDelete ()
 Removes itself from its parent. 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 setMath (const ASTNode *math)
 Sets the "math" subelement of this InitialAssignment. 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 setSymbol (const std::string &sid)
 Sets the "symbol" attribute value of this InitialAssignment. 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...
 
virtual ~InitialAssignment ()
 Destroys this InitialAssignment. 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

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

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

Parameters
levelan unsigned int, the SBML Level to assign to this InitialAssignment
versionan unsigned int, the SBML Version to assign to this InitialAssignment
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 InitialAssignment object to an SBMLDocument (e.g., using Model::addInitialAssignment()), the SBML Level, SBML Version and XML namespace of the document override the values used when creating the InitialAssignment 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 InitialAssignment 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.
InitialAssignment::InitialAssignment ( SBMLNamespaces sbmlns)

Creates a new InitialAssignment 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 InitialAssignment object to an SBMLDocument (e.g., using Model::addInitialAssignment()), the SBML XML namespace of the document overrides the value used when creating the InitialAssignment 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 InitialAssignment 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.
InitialAssignment::~InitialAssignment ( )
virtual

Destroys this InitialAssignment.

InitialAssignment::InitialAssignment ( const InitialAssignment orig)

Copy constructor; creates a copy of this InitialAssignment.

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

Member Function Documentation

bool InitialAssignment::accept ( SBMLVisitor v) const
virtual

Accepts the given SBMLVisitor for this instance of InitialAssignment.

Parameters
vthe SBMLVisitor instance to be used.
Returns
the result of calling v.visit(), which indicates whether the Visitor would like to visit the next InitialAssignment in the list of compartment types.

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.
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()
InitialAssignment * InitialAssignment::clone ( ) const
virtual

Creates and returns a deep copy of this InitialAssignment.

Returns
a (deep) copy of this InitialAssignment.

Implements SBase.

bool InitialAssignment::containsUndeclaredUnits ( )

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

Returns
true if the math expression of this InitialAssignment 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 InitialAssignment::containsUndeclaredUnits ( ) const

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

Returns
true if the math expression of this InitialAssignment 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()
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 value is drawn from the enumeration OperationReturnValues_t. 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
List * SBase::getAllElements ( )
virtualinherited

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

Returns
a pointer to a List of pointers to all children objects.

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

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.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. The names of the type codes all begin with the characters SBML_.

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

Parameters
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 SBMLTypeCode_t value, or NULL if no ancestor exists.
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.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. The names of the type codes all begin with the characters SBML_.

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

Parameters
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 SBMLTypeCode_t value, or NULL if no ancestor exists.
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 * InitialAssignment::getDerivedUnitDefinition ( )

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

The units are calculated based on the mathematical expression in the InitialAssignment 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 InitialAssignment 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 InitialAssignment, or NULL if one cannot be constructed.
See Also
containsUndeclaredUnits()
const UnitDefinition * InitialAssignment::getDerivedUnitDefinition ( ) const

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

The units are calculated based on the mathematical expression in the InitialAssignment 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 InitialAssignment 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 InitialAssignment, or NULL if one cannot be constructed.
See Also
containsUndeclaredUnits()
SBase * SBase::getElementByMetaId ( std::string  metaid)
virtualinherited

Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found.

Parameters
metaidstring representing the "metaid" attribute value of the object to find.
Returns
pointer to the first element found with the given meta-identifier.

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

SBase * SBase::getElementBySId ( std::string  id)
virtualinherited

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" attribute value of the object to find.
Returns
pointer to the first element found with the given identifier.

Reimplemented in ListOfUnitDefinitions, ListOfRules, ListOfInitialAssignments, ListOfEventAssignments, ListOfLocalParameters, Model, SBMLDocument, UnitDefinition, Event, Reaction, ListOf, KineticLaw, ListOfPorts, Submodel, and SBaseRef.

const string & InitialAssignment::getElementName ( ) const
virtual

Returns the XML element name of this object, which for InitialAssignment, is always "initialAssignment".

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

Implements SBase.

const std::string & InitialAssignment::getId ( ) const
virtual
Returns
the string of symbol attribute of this object.
Note
this function is an alias for getSymbol()
See Also
getSymbol()
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 ASTNode * InitialAssignment::getMath ( ) const

Get the mathematical formula of this InitialAssignment.

Returns
an ASTNode, the value of the "math" subelement of this InitialAssignment
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 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()
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 from the enumeration type BiolQualifierType_t.

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 from the enumeration type BiolQualifierType_t.

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.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values in the enumeration BiolQualifierType_t are up to date with MIRIAM at the time of a given libSBML release. The set of values may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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 from the enumeration type ModelQualifierType_t.

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 from the enumeration type ModelQualifierType_t.

Parameters
resourcestring representing the resource; e.g., "http://www.geneontology.org/#GO:0005892".
Returns
the ModelQualifierType_t value associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values in the enumeration ModelQualifierType_t are up to date with MIRIAM at the time of a given libSBML release. The set of values may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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 & InitialAssignment::getSymbol ( ) const

Get the value of the "symbol" attribute of this InitialAssignment.

Returns
the identifier string stored as the "symbol" attribute value in this InitialAssignment.
int InitialAssignment::getTypeCode ( ) const
virtual

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. The names of the type codes all begin with the characters SBML_.

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

Reimplemented from 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.
See Also
ASTNode::setUserData(void *userData)
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 InitialAssignment::hasRequiredAttributes ( ) const
virtual

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

Note
The required attributes for an InitialAssignment object are:
  • "symbol"
Returns
a boolean value indicating whether all the required attributes for this object have been defined.
bool InitialAssignment::hasRequiredElements ( ) const
virtual

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

Note
The required elements for a InitialAssignment 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 InitialAssignment::isSetMath ( ) const

Predicate returning true if this InitialAssignment's "math" subelement contains a value.

Returns
true if the "math" for this InitialAssignment is set, false otherwise.
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 InitialAssignment::isSetSymbol ( ) const

Predicate returning true if this InitialAssignment's "symbol" attribute is set.

Returns
true if the "symbol" attribute of this InitialAssignment is set, false otherwise.
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.
InitialAssignment & InitialAssignment::operator= ( const InitialAssignment rhs)

Assignment operator for InitialAssignment.

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

Removes itself from its parent.

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

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented in Model, KineticLaw, SBaseRef, StoichiometryMath, Delay, Trigger, Priority, ListOf, ModelDefinition, and ReplacedBy.

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 InitialAssignment::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 InitialAssignment::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 InitialAssignment::setMath ( const ASTNode math)

Sets the "math" subelement of this InitialAssignment.

The AST passed in math is copied.

Parameters
mathan AST containing the mathematical expression to be used as the formula for this InitialAssignment.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
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.

SBMLDocument* s = new SBMLDocument(3, 1);
s->setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></body>");
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 InitialAssignment::setSymbol ( const std::string &  sid)

Sets the "symbol" attribute value of this InitialAssignment.

Parameters
sidthe identifier of a Species, Compartment or Parameter object defined elsewhere in this Model.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
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: