libSBML C++ API  libSBML 5.13.0 C++ API
UnitDefinition Class Reference
Inheritance diagram for UnitDefinition:
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Detailed Description

{core}

A definition of a unit used in an SBML model.

Units of measurement may be supplied in a number of contexts in an SBML model. The SBML unit definition facility uses two classes of objects, UnitDefinition and Unit. The approach to defining units in SBML is compositional; for example, meter second –2 is constructed by combining a Unit object representing meter with another Unit object representing second –2. The combination is wrapped inside a UnitDefinition, which provides for assigning an identifier and optional name to the combination. The identifier can then be referenced from elsewhere in a model. Thus, the UnitDefinition class is the container, and Unit instances are placed inside UnitDefinition instances.

Two points are worth discussing in the context of SBML units. First, unit declarations in SBML models are optional. The consequence of this is that a model must be numerically self-consistent independently of unit declarations, for the benefit of software tools that cannot interpret or manipulate units. Unit declarations in SBML are thus more akin to a type of annotation; they can indicate intentions, and can be used by model readers for checking the consistency of the model, labeling simulation output, etc., but any transformations of values implied by different units must be incorporated explicitly into a model.

Second, the vast majority of situations that require new SBML unit definitions involve simple multiplicative combinations of base units and factors. An example is moles per litre per second. What distinguishes these sorts of unit definitions from more complex ones is that they may be expressed without the use of an additive offset from a zero point. The use of offsets complicates all unit definition systems, yet in the domain of SBML, the real-life cases requiring offsets are few (and in fact, to the best of our knowledge, only involve temperature). Consequently, the SBML unit system has been consciously designed to simplify implementation of unit support for the most common cases in systems biology. The cost of this simplification is to require units with offsets to be handled explicitly by the modeler.

Summary of the UnitDefinition construct

UnitDefinition has two attributes and one subelement. The two attributes are "id" and "name", and the subelement is ListOfUnits.

The required attribute "id" and optional attribute "name" are both strings. The "id" attribute is used to give the defined unit a unique identifier by which other parts of an SBML model definition can refer to it. The "name" attribute is intended to be used for giving the unit definition an optional human-readable name. Please see the next section for information about the values permitted for "id".

A UnitDefinition must contain exactly one ListOfUnits, and this list must contain one or more Unit definitions; see the definitions of these other object classes for more information about them. The following example illustrates a complete unit definition (when written in XML) when they all the pieces are combined together. This defines "mmls" to be millimoles per litre per second.

<listOfUnitDefinitions>
    <unitDefinition id="mmls">
        <listOfUnits>
            <unit kind="mole"   scale="-3"/>
            <unit kind="litre"  exponent="-1"/>
            <unit kind="second" exponent="-1"/>
        </listOfUnits>
    </unitDefinition>
</listOfUnitDefinitions>

Special considerations for Unit object identifiers

The attribute "id" in UnitDefinition cannot be given simply any value, and the precise details of the values permitted differ slightly between Levels of SBML:

  • The "id" of a UnitDefinition must not contain a value from the list of SBML's predefined base unit names (i.e., the strings gram, litre, etc.). In SBML Level 3, this list consists of the following:

    amperefaradjouleluxradianvolt
    avogadrogramkatalmetresecondwatt
    becquerelgraykelvinmolesiemensweber
    candelahenrykilogramnewtonsievert
    coulombhertzlitreohmsteradian
    dimensionlessitemlumenpascaltesla

    This list of predefined base units is nearly identical in SBML Level 2 Version 4, the exception being that Level 2 does not define avogadro. SBML Level 2 Version 1 (and only this Level+Version combination) provides an additional predefined unit name, Celsius, not available in Level 3. Finally, SBML Level 1 Versions 2–3 provide two more additional predefined unit names, meter and liter. This is explained in somewhat greater detail in the description of the Unit class.

    • In SBML Level 2 (all Versions), there is an additional set of reserved identifiers: substance, volume, area, length, and time. Using one of these values for the attribute "id" of a UnitDefinition has the effect of redefining the model-wide default units for the corresponding quantities. The list of special unit names in SBML Level 2 is given in the table below:
    Identifier Possible scalable units Default units
    substancemole, item, gram, kilogram, dimensionlessmole
    volumelitre, cubic metre, dimensionlesslitre
    areasquare metre, dimensionlesssquare metre
    lengthmetre, dimensionlessmetre
    timesecond, dimensionlesssecond

    Also, SBML Level 2 imposes two limitations on redefining the predefined unit substance, volume, area, length, and time: (1) The UnitDefinition of a predefined SBML unit can only contain a single Unit object within it. (2) The value of the "kind" attribute in a Unit instance must be drawn from one of the values in the second column of the table above.

    The special unit names substance, volume, area, length, and time are not defined by SBML Level 3, which uses a different approach to setting model-wide inherited units.

Further comments about SBML's unit definition system

The vast majority of modeling situations requiring new SBML unit definitions involve simple multiplicative combinations of base units and factors. An example of this might be moles per litre per second. What distinguishes these sorts of simpler unit definitions from more complex ones is that they may be expressed without the use of an additive offset from a zero point. The use of offsets complicates all unit definition systems, yet in the domain of SBML the real-life cases requiring offsets are few (and in fact, to the best of our knowledge, only involve temperature). Consequently, the SBML unit system has been consciously designed in a way that attempts to simplify implementation of unit support for the most common cases in systems biology.

As of SBML Level 2 Version 2, Unit no longer has the attribute called "offset" introduced in SBML Level 2 Version 1. It turned out that the general case involving units with offsets was incorrectly defined, and few (if any) developers even attempted to support offset-based units in their software. In the development of Level 2 Version 2, a consensus among SBML developers emerged that a fully generalized unit scheme is so confusing and complicated that it actually impedes interoperability. SBML Level 2 Version 2, Version 3 and Version 4 acknowledge this reality by reducing and simplifying the unit system, specifically by removing the "offset" attribute on Unit and Celsius as a pre-defined unit.

The following guidelines suggest methods for handling units that do require the use of zero offsets for their definitions:

  • Handling Celsius. A model in which certain quantities are temperatures measured in degrees Celsius can be converted straightforwardly to a model in which those temperatures are in kelvin. A software tool could do this by performing a straightforward substitution using the following relationship: T kelvin = TCelsius + 273.15. In every mathematical formula of the model where a quantity (call it x) in degrees Celsius appears, replace x with xk+ 273.15, where xk is now in kelvin. An alternative approach would be to use a FunctionDefinition object to define a function encapsulating this relationship above and then using that in the rest of the model as needed. Since Celsius is a commonly-used unit, software tools could help users by providing users with the ability to express temperatures in Celsius in the tools' interfaces, and making substitutions automatically when writing out the SBML.

  • Other units requiring offsets. One approach to handling other kinds of units is to use a FunctionDefinition to define a function encapsulating the necessary mathematical relationship, then substituting a call to this function wherever the original quantity appeared in the model. For example, here is a possible definition for converting Fahrenheit to Celsius degrees:

    <functionDefinition id="Fahrenheit_to_kelvin">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <lambda>
                <bvar><ci> temp_in_fahrenheit </ci></bvar>
                <apply>
                    <divide/>
                    <apply>
                        <plus/>
                        <ci> temp_in_fahrenheit </ci>
                        <cn> 459.67 </cn>
                    </apply>
                    <cn> 1.8 </cn>
                </apply>
            </lambda>
        </math>
    </functionDefinition>
    

  • An alternative approach not requiring the use of function definitions is to use an AssignmentRule for each variable in Fahrenheit units. The AssignmentRule could compute the conversion from Fahrenheit to (say) kelvin, assign its value to a variable (in Kelvin units), and then that variable could be used elsewhere in the model.

  • Still another approach is to rewrite the mathematical formulas of a model to directly incorporate the conversion formula wherever the original quantity appeared.

Please consult the SBML specifications for more information about this and other issues involving units.

Examples:
createExampleSBML.cpp, printAnnotation.cpp, printNotes.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.

Public Member Functions

int addCVTerm (CVTerm *term, bool newBag=false)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
int addUnit (const Unit *u)
 Adds a copy of the given Unit to this UnitDefinition. 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 UnitDefinitionclone () const
 Creates and returns a deep copy of this UnitDefinition object. More...
 
UnitcreateUnit ()
 Creates a new and empty Unit, adds it to this UnitDefinition's list of units, and returns it. More...
 
void deleteDisabledPlugins (bool recursive=true)
 Deletes all information stored in disabled plugins. More...
 
int disablePackage (const std::string &pkgURI, const std::string &pkgPrefix)
 Disables the given SBML Level 3 package on this object. More...
 
int enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package on this object. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual ListgetAllElementsFromPlugins (ElementFilter *filter=NULL)
 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 from the given package. More...
 
const SBasegetAncestorOfType (int type, const std::string pkgName="core") const
 Returns the first ancestor object that has the given SBML type code from the given package. 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 where 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...
 
SBasePlugingetDisabledPlugin (unsigned int n)
 Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasePlugingetDisabledPlugin (unsigned int n) const
 Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasegetElementByMetaId (const std::string &metaid) const
 Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Returns the first child element it can find with the given metaid, or NULL if no such object is found. More...
 
const SBasegetElementBySId (const std::string &id) const
 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 SBasegetElementBySId (const 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 UnitDefinition, is always "unitDefinition". More...
 
virtual const std::string & getId () const
 Returns the value of the "id" attribute of this UnitDefinition. More...
 
unsigned int getLevel () const
 Returns the SBML Level of the SBMLDocument object containing this object. More...
 
unsigned int getLine () const
 Returns the line number where this object first appears in the XML representation of the SBML document. More...
 
const ListOfUnitsgetListOfUnits () const
 Returns the list of Units for this UnitDefinition instance. More...
 
ListOfUnitsgetListOfUnits ()
 Returns the list of Units for this UnitDefinition instance. 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 for the SBML Document 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 const std::string & getName () const
 Returns the value of the "name" attribute of this UnitDefinition. More...
 
virtual XMLNamespacesgetNamespaces () const
 Returns a list of the XML Namespaces declared on the SBML document owning this object. 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 getNumDisabledPlugins () const
 Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More...
 
unsigned int getNumPlugins () const
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
unsigned int getNumUnits () const
 Returns the number of Unit objects contained within this UnitDefinition. 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...
 
std::string getPrefix () const
 Returns the XML namespace prefix of this element. 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 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...
 
virtual int getTypeCode () const
 Returns the libSBML type code for this object instance. More...
 
UnitgetUnit (unsigned int n)
 Returns a specific Unit instance belonging to this UnitDefinition. More...
 
const UnitgetUnit (unsigned int n) const
 Returns a specific Unit instance belonging to this UnitDefinition. More...
 
std::string getURI () const
 Gets the namespace URI to which this element belongs to. 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 UnitDefinition object have been set. More...
 
virtual bool hasRequiredElements () const
 Predicate returning true if all the required elements for this UnitDefinition object have been set. More...
 
bool hasValidLevelVersionNamespaceCombination ()
 Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More...
 
bool isPackageEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPackageURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPkgEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPkgURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isSetAnnotation () const
 Predicate returning true if this object's "annotation" subelement exists and has content. More...
 
virtual bool isSetId () const
 Predicate returning true if this UnitDefinition's "id" attribute is set. More...
 
bool isSetMetaId () const
 Predicate returning true if this object's "metaid" attribute is set. More...
 
bool isSetModelHistory ()
 Predicate returning true if this object has a ModelHistory object attached to it. More...
 
virtual bool isSetName () const
 Predicate returning true if this UnitDefinition's "name" attribute is set. 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 isSetUserData () const
 Predicate returning true or false depending on whether the user data of this element has been set. More...
 
bool isVariantOfArea () const
 Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "area". More...
 
bool isVariantOfDimensionless () const
 Convenience function for testing if a given unit definition is a variant of the unit "dimensionless". More...
 
bool isVariantOfLength () const
 Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "length". More...
 
bool isVariantOfMass () const
 Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "mass". More...
 
bool isVariantOfSubstance () const
 Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "substance". More...
 
bool isVariantOfSubstancePerTime () const
 Convenience function for testing if a given unit definition is a variant of the predefined unit "substance" divided by the predefined unit "time". More...
 
bool isVariantOfTime () const
 Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "time". More...
 
bool isVariantOfVolume () const
 Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "volume". 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...
 
UnitDefinitionoperator= (const UnitDefinition &rhs)
 Assignment operator. More...
 
void read (XMLNode &node, XMLErrorSeverityOverride_t flag=LIBSBML_OVERRIDE_DISABLED)
 Reads (initializes) this SBML object by reading from the given XMLNode. More...
 
virtual int removeFromParentAndDelete ()
 Removes this object from its parent. More...
 
int removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="", bool removeEmpty=true)
 Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More...
 
UnitremoveUnit (unsigned int n)
 Removes the nth Unit object from this UnitDefinition object and returns a pointer to it. More...
 
virtual void renameMetaIdRefs (const std::string &oldid, const std::string &newid)
 
virtual void renameSIdRefs (const std::string &oldid, const std::string &newid)
 
virtual void renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
 
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...
 
virtual int setId (const std::string &sid)
 Sets the value of the "id" attribute of this UnitDefinition. More...
 
int setMetaId (const std::string &metaid)
 Sets the value of the meta-identifier attribute of this object. More...
 
int setModelHistory (ModelHistory *history)
 Sets the ModelHistory of this object. More...
 
virtual int setName (const std::string &name)
 Sets the value of the "name" attribute of this UnitDefinition. 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 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...
 
XMLNodetoXMLNode ()
 Returns this element as an XMLNode. More...
 
 UnitDefinition (unsigned int level, unsigned int version)
 Creates a new UnitDefinition using the given SBML level and version values. More...
 
 UnitDefinition (SBMLNamespaces *sbmlns)
 Creates a new UnitDefinition using the given SBMLNamespaces object sbmlns. More...
 
 UnitDefinition (const UnitDefinition &orig)
 Copy constructor; creates a copy of this UnitDefinition. 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 UnitDefinition. More...
 
int unsetNotes ()
 Unsets the value of the "notes" subelement of this SBML object. More...
 
int unsetSBOTerm ()
 Unsets the value of the "sboTerm" attribute of this SBML object. More...
 
int unsetUserData ()
 Unsets the user data of this element. More...
 
virtual ~UnitDefinition ()
 Destroys this UnitDefinition. More...
 

Static Public Member Functions

static bool areEquivalent (const UnitDefinition *ud1, const UnitDefinition *ud2)
 Predicate returning true if two UnitDefinition objects are equivalent. More...
 
static bool areIdentical (const UnitDefinition *ud1, const UnitDefinition *ud2)
 Predicate returning true if two UnitDefinition objects are identical. More...
 
static UnitDefinitioncombine (UnitDefinition *ud1, UnitDefinition *ud2)
 Combines two UnitDefinition objects into a single UnitDefinition. More...
 
static UnitDefinitionconvertToSI (const UnitDefinition *ud)
 Convert a given UnitDefinition into a new UnitDefinition object that uses SI units. More...
 
static UnitDefinitiondivide (UnitDefinition *ud1, UnitDefinition *ud2)
 Combines two UnitDefinition objects into a single UnitDefinition as a division. More...
 
static std::string printUnits (const UnitDefinition *ud, bool compact=false)
 Expresses the given definition in a plain-text form. More...
 
static void reorder (UnitDefinition *ud)
 Alphabetically orders the Unit objects within the ListOfUnits of a UnitDefinition. More...
 
static void simplify (UnitDefinition *ud)
 Simplifies the UnitDefinition such that any given kind of Unit object occurs only once in the ListOfUnits. 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

§ UnitDefinition() [1/3]

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

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

Parameters
levelan unsigned int, the SBML Level to assign to this UnitDefinition
versionan unsigned int, the SBML Version to assign to this UnitDefinition

§ UnitDefinition() [2/3]

UnitDefinition::UnitDefinition ( SBMLNamespaces sbmlns)

Creates a new UnitDefinition 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 libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sbmlnsan SBMLNamespaces object.

§ ~UnitDefinition()

UnitDefinition::~UnitDefinition ( )
virtual

Destroys this UnitDefinition.

§ UnitDefinition() [3/3]

UnitDefinition::UnitDefinition ( const UnitDefinition orig)

Copy constructor; creates a copy of this UnitDefinition.

Parameters
origthe object to copy.

Member Function Documentation

§ addCVTerm()

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.
Examples:
addCVTerms.cpp, addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.

§ addUnit()

int UnitDefinition::addUnit ( const Unit u)

Adds a copy of the given Unit to this UnitDefinition.

Parameters
uthe Unit instance to add to this UnitDefinition.

§ appendAnnotation() [1/2]

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

Reimplemented in Model, and SpeciesReference.

Examples:
addingEvidenceCodes_2.cpp, and appendAnnotation.cpp.

§ appendAnnotation() [2/2]

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

Reimplemented in Model, and SpeciesReference.

§ appendNotes() [1/2]

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

§ appendNotes() [2/2]

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

§ areEquivalent()

bool UnitDefinition::areEquivalent ( const UnitDefinition ud1,
const UnitDefinition ud2 
)
static

Predicate returning true if two UnitDefinition objects are equivalent.

For the purposes of performing this comparison, two UnitDefinition objects are considered equivalent when they contain equivalent list of Unit objects. Unit objects are in turn considered equivalent if they satisfy the predicate Unit::areEquivalent(). The predicate tests a subset of the objects's attributes.

Parameters
ud1the first UnitDefinition object to compare
ud2the second UnitDefinition object to compare
Returns
true if all the Unit objects in ud1 are equivalent to the Unit objects in ud2, false otherwise.
See also
UnitDefinition::areIdentical(const UnitDefinition * ud1, const UnitDefinition * ud2)
Unit::areEquivalent(Unit * unit1, Unit * unit2)

§ areIdentical()

bool UnitDefinition::areIdentical ( const UnitDefinition ud1,
const UnitDefinition ud2 
)
static

Predicate returning true if two UnitDefinition objects are identical.

* slightly less restrictive version that util_isEqual

For the purposes of performing this comparison, two UnitDefinition objects are considered identical when they contain identical lists of Unit objects. Pairs of Unit objects in the lists are in turn considered identical if they satisfy the predicate Unit::areIdentical(). The predicate compares every attribute of the Unit objects.

Parameters
ud1the first UnitDefinition object to compare
ud2the second UnitDefinition object to compare
Returns
true if all the Unit objects in ud1 are identical to the Unit objects of ud2, false otherwise.
See also
UnitDefinition::areEquivalent(const UnitDefinition * ud1, const UnitDefinition * ud2)
Unit::areIdentical(Unit * unit1, Unit * unit2)

§ clone()

UnitDefinition * UnitDefinition::clone ( ) const
virtual

Creates and returns a deep copy of this UnitDefinition object.

Returns
the (deep) copy of this UnitDefinition object.

Implements SBase.

§ combine()

UnitDefinition * UnitDefinition::combine ( UnitDefinition ud1,
UnitDefinition ud2 
)
static

Combines two UnitDefinition objects into a single UnitDefinition.

This takes UnitDefinition objects ud1 and ud2, and creates a UnitDefinition object that expresses the product of the units of ud1 and ud2.

Parameters
ud1the first UnitDefinition object
ud2the second UnitDefinition object
Returns
a UnitDefinition which represents the product of the units of the two argument UnitDefinitions.

§ convertToSI()

UnitDefinition * UnitDefinition::convertToSI ( const UnitDefinition ud)
static

Convert a given UnitDefinition into a new UnitDefinition object that uses SI units.

Parameters
udthe UnitDefinition object to convert to SI
Returns
a new UnitDefinition object representing the results of the conversion.

§ createUnit()

Unit * UnitDefinition::createUnit ( )

Creates a new and empty Unit, adds it to this UnitDefinition's list of units, and returns it.

Returns
a newly constructed (and empty) Unit instance.
Note
It is worth emphasizing that the attribute "kind" value of a Unit is a required attribute for a valid Unit definition. The createUnit() method does not assign a valid kind to the constructed unit (instead, it sets the "kind" to UNIT_KIND_INVALIDendif
Examples:
createExampleSBML.cpp.

§ deleteDisabledPlugins()

void SBase::deleteDisabledPlugins ( bool  recursive = true)
inherited

Deletes all information stored in disabled plugins.

If the plugin is re-enabled later, it will then not have any previously-stored information.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
recursiveif true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element.
See also
getNumDisabledPlugins()

§ disablePackage()

int SBase::disablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix 
)
inherited

Disables the given SBML Level 3 package on this object.

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

An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from another SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:

// We read in an SBML L3V1 model that uses the 'comp'
// package namespace.
doc = readSBML("sbml-file-with-comp-elements.xml");
// We extract one of the species from the model.
Species* s1 = doc->getModel()->getSpecies(0);
// We construct a new model. This model does not use the
// 'comp' package.
Model * newModel = new Model(3,1);
// The following will fail with an error, because addSpecies()
// will first check that the parent of the given object has
// namespaces declared, and will discover that s1 does but
// newModel does not.
// newModel->addSpecies(s1);
// However, if we disable the 'comp' package on s1, then
// the call to addSpecies will work.
s1->disablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1",
"comp");
newModel->addSpecies(s1);
Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package

§ divide()

UnitDefinition * UnitDefinition::divide ( UnitDefinition ud1,
UnitDefinition ud2 
)
static

Combines two UnitDefinition objects into a single UnitDefinition as a division.

This takes UnitDefinition objects ud1 and ud2, and creates a UnitDefinition object that expresses the division of the units of ud1 and ud2.

Parameters
ud1the first UnitDefinition object
ud2the second UnitDefinition object
Returns
a UnitDefinition which represents the division of the units of the two argument UnitDefinitions.

§ enablePackage()

int SBase::enablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix,
bool  flag 
)
inherited

Enables or disables the given SBML Level 3 package on this object.

This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase::disablePackage(const std::string& pkgURI, const std::string& pkgPrefix).

Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package
flagwhether to enable (true) or disable (false) the package
Examples:
addLayout.cpp.

§ getAllElements()

List * UnitDefinition::getAllElements ( ElementFilter filter = NULL)
virtual

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

Returns
a List of pointers to all children objects.

Reimplemented from SBase.

§ getAllElementsFromPlugins()

List * SBase::getAllElementsFromPlugins ( ElementFilter filter = NULL)
virtualinherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.

Returns
a pointer to a List of pointers to all children objects from plug-ins.

§ getAncestorOfType() [1/2]

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

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

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 from the given pkgName.

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.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the "core" namespace alone, not find any corresponding elements, and return NULL.

§ getAncestorOfType() [2/2]

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 from the given package.

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 from the given pkgName.

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.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the "core" namespace alone, not find any corresponding elements, and return NULL.

§ getAnnotation() [1/2]

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()

§ getAnnotation() [2/2]

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()

§ getAnnotationString() [1/2]

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. See the method getAnnotation() for a version that returns annotations in XML 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()
Examples:
printAnnotation.cpp.

§ getAnnotationString() [2/2]

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. See the method getAnnotation() for a version that returns annotations in XML 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()

§ getColumn()

unsigned int SBase::getColumn ( ) const
inherited

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

Returns
the column number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.
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()

§ getCVTerm()

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.

§ getCVTerms() [1/2]

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.

§ getCVTerms() [2/2]

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.

§ getDisabledPlugin() [1/2]

SBasePlugin * SBase::getDisabledPlugin ( unsigned int  n)
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
nthe index of the disabled plug-in to return
Returns
the nth disabled plug-in object (the libSBML extension interface) of a package extension.
See also
getNumDisabledPlugins()
getPlugin(const std::string& package)

§ getDisabledPlugin() [2/2]

const SBasePlugin * SBase::getDisabledPlugin ( unsigned int  n) const
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
nthe index of the disabled plug-in to return
Returns
the nth disabled plug-in object (the libSBML extension interface) of a package extension.
See also
getNumDisabledPlugins()
getPlugin(const std::string& package)

§ getElementByMetaId() [1/2]

const SBase * SBase::getElementByMetaId ( const std::string &  metaid) const
inherited

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

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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Parameters
metaidstring representing the "metaid" attribute value of the object to find.
Returns
pointer to the first element found with the given meta-identifier.

§ getElementByMetaId() [2/2]

SBase * UnitDefinition::getElementByMetaId ( const std::string &  metaid)
virtual

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

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

Reimplemented from SBase.

§ getElementBySId() [1/2]

const SBase * SBase::getElementBySId ( const std::string &  id) const
inherited

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.

§ getElementBySId() [2/2]

SBase * UnitDefinition::getElementBySId ( const std::string &  id)
virtual

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

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

Reimplemented from SBase.

§ getElementName()

const string & UnitDefinition::getElementName ( ) const
virtual

Returns the XML element name of this object, which for UnitDefinition, is always "unitDefinition".

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

Reimplemented from SBase.

§ getId()

const string & UnitDefinition::getId ( ) const
virtual

Returns the value of the "id" attribute of this UnitDefinition.

Returns
the id of this UnitDefinition.

§ getLevel()

unsigned int SBase::getLevel ( ) const
inherited

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

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 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.)
Returns
the SBML level of this SBML object.
See also
getVersion()
getNamespaces()
getPackageVersion()
Examples:
addLayout.cpp, convertSBML.cpp, and printSBML.cpp.

§ getLine()

unsigned int SBase::getLine ( ) const
inherited

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

Returns
the line number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.
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()

§ getListOfUnits() [1/2]

const ListOfUnits * UnitDefinition::getListOfUnits ( ) const

Returns the list of Units for this UnitDefinition instance.

Returns
the ListOfUnits value for this UnitDefinition.

§ getListOfUnits() [2/2]

ListOfUnits * UnitDefinition::getListOfUnits ( )

Returns the list of Units for this UnitDefinition instance.

Returns
the ListOfUnits value for this UnitDefinition.

§ getMetaId() [1/2]

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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object.
See also
isSetMetaId()
setMetaId(const std::string& metaid)
Examples:
addingEvidenceCodes_2.cpp.

§ getMetaId() [2/2]

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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object, as a string.
See also
isSetMetaId()
setMetaId(const std::string& metaid)

§ getModel()

const Model * SBase::getModel ( ) const
inherited

Returns the Model object for the SBML Document in which the current object is located.

Returns
the Model object for the SBML Document of this SBML object.
See also
getParentSBMLObject()
getSBMLDocument()

§ getModelHistory() [1/2]

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.

§ getModelHistory() [2/2]

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.

§ getName()

const string & UnitDefinition::getName ( ) const
virtual

Returns the value of the "name" attribute of this UnitDefinition.

Returns
the name of this UnitDefinition.

§ getNamespaces()

XMLNamespaces * SBase::getNamespaces ( ) const
virtualinherited

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

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.

Returns
the XML Namespaces associated with this SBML object, or NULL in certain very usual circumstances where a namespace is not set.
See also
getLevel()
getVersion()

Reimplemented in SBMLDocument.

§ getNotes() [1/2]

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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()

§ getNotes() [2/2]

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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()

§ getNotesString() [1/2]

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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
printNotes.cpp, and SBMLHttpResolverExample.cpp.

§ getNotesString() [2/2]

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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()

§ getNumCVTerms()

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.

§ getNumDisabledPlugins()

unsigned int SBase::getNumDisabledPlugins ( ) const
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Returns
the number of disabled plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.

§ getNumPlugins()

unsigned int SBase::getNumPlugins ( ) const
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
See also
getPlugin(unsigned int n)

§ getNumUnits()

unsigned int UnitDefinition::getNumUnits ( ) const

Returns the number of Unit objects contained within this UnitDefinition.

Returns
an integer representing the number of Units in this UnitDefinition.

§ getPackageName()

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.

§ getPackageVersion()

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()

§ getParentSBMLObject() [1/2]

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()

§ getParentSBMLObject() [2/2]

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()

§ getPlugin() [1/4]

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.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
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.
See also
getPlugin(unsigned int n)
Examples:
addLayout.cpp, convertLayout.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, groups_example1.cpp, groups_example2.cpp, qual_example1.cpp, SBMLHttpResolverExample.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.

§ getPlugin() [2/4]

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.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
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.
See also
getPlugin(unsigned int n)

§ getPlugin() [3/4]

SBasePlugin * SBase::getPlugin ( unsigned int  n)
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return
Returns
the nth plug-in object (the libSBML extension interface) of a package extension.
See also
getNumPlugins()
getPlugin(const std::string& package)

§ getPlugin() [4/4]

const SBasePlugin * SBase::getPlugin ( unsigned int  n) const
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return
Returns
the nth plug-in object (the libSBML extension interface) of a package extension.
See also
getNumPlugins()
getPlugin(const std::string& package)

§ getPrefix()

std::string SBase::getPrefix ( ) const
inherited

Returns the XML namespace prefix of this element.

This reports the XML namespace prefix chosen for this class of object in the current SBML document. This may be an empty string if the component has no explicit prefix (for instance, if it is a core SBML object placed in the default SBML namespace of the document). If it is not empty, then it corresponds to the XML namespace prefix used set the object, whatever that may be in a given SBML document.

Returns
a text string representing the XML namespace prefix

§ getResourceBiologicalQualifier()

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_UNKNOWNendif

§ getResourceModelQualifier()

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_UNKNOWNendif

§ getSBMLDocument() [1/2]

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()

§ getSBMLDocument() [2/2]

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()

§ getSBOTerm()

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.
Examples:
printSBML.cpp.

§ getSBOTermAsURL()

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

Returns the 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, or an empty string if the value is not set.

§ getSBOTermID()

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.

§ getTypeCode()

int UnitDefinition::getTypeCode ( ) const
virtual

Returns the libSBML type code for this object instance.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. The set of possible type codes for core elements is defined in the enumeration SBMLTypeCode_t, and in addition, libSBML plug-ins for SBML Level 3 packages define their own extra enumerations of type codes (e.g., SBMLLayoutTypeCode_t for the Level 3 Layout package). Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName() method on the object.
Returns
the SBML type code for this object: SBML_UNIT_DEFINITIONendif

Reimplemented from SBase.

§ getUnit() [1/2]

Unit * UnitDefinition::getUnit ( unsigned int  n)

Returns a specific Unit instance belonging to this UnitDefinition.

Parameters
nan integer, the index of the Unit to be returned.
Returns
the nth Unit of this UnitDefinition.
See also
getNumUnits()

§ getUnit() [2/2]

const Unit * UnitDefinition::getUnit ( unsigned int  n) const

Returns a specific Unit instance belonging to this UnitDefinition.

Parameters
nan integer, the index of the Unit to be returned.
Returns
the nth Unit of this UnitDefinition.

§ getURI()

std::string SBase::getURI ( ) const
inherited

Gets the namespace URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/layout/version1".

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.

Returns
the URI of this element, as a text string
See also
getSBMLDocument()
getPackageName()

§ getUserData()

void * SBase::getUserData ( ) const
inherited

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

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
the user data of this node, or NULL if no user data has been set.
See also
ASTNode::setUserData(void *userData)

§ getVersion()

unsigned int SBase::getVersion ( ) const
inherited

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

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 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.)
Returns
the SBML version of this SBML object.
See also
getLevel()
getNamespaces()
Examples:
addLayout.cpp, convertSBML.cpp, and printSBML.cpp.

§ hasRequiredAttributes()

bool UnitDefinition::hasRequiredAttributes ( ) const
virtual

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

The required attributes for a UnitDefinition object are:

  • "id"
Returns
true if the required attributes have been set, false otherwise.

§ hasRequiredElements()

bool UnitDefinition::hasRequiredElements ( ) const
virtual

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

Note
The required elements for a Constraint object are:
  • "listOfUnits" (required in SBML Level 2 only, optional in Level 3)
Returns
a boolean value indicating whether all the required elements for this object have been defined.

§ hasValidLevelVersionNamespaceCombination()

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 2 Version 5: "http://www.sbml.org/sbml/level2/version5"
  • 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.

§ isPackageEnabled()

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()

§ 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()

§ isPkgEnabled()

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()

§ 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()

§ isSetAnnotation()

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()
Examples:
printAnnotation.cpp.

§ isSetId()

bool UnitDefinition::isSetId ( ) const
virtual

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

Returns
true if the "id" attribute of this UnitDefinition is set, false otherwise.

§ isSetMetaId()

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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
true if the "metaid" attribute of this SBML object is set, false otherwise.
See also
getMetaId()
setMetaId(const std::string& metaid)
Examples:
addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.

§ isSetModelHistory()

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.

§ isSetName()

bool UnitDefinition::isSetName ( ) const
virtual

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

Returns
true if the "name" attribute of this UnitDefinition is set, false otherwise.

§ isSetNotes()

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, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
getAllElementsWithNotes.cpp, printNotes.cpp, and SBMLHttpResolverExample.cpp.

§ isSetSBOTerm()

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.
Examples:
printSBML.cpp.

§ isSetUserData()

bool SBase::isSetUserData ( ) const
inherited

Predicate returning true or false depending on whether the user data of this element has been set.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
boolean, true if this object's user data has been set, false otherwise.

§ isVariantOfArea()

bool UnitDefinition::isVariantOfArea ( ) const

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "area".

Returns
true if this UnitDefinition is a variant of the predefined unit area, meaning square metres with only abritrary variations in scale or multiplier values; false otherwise.

§ isVariantOfDimensionless()

bool UnitDefinition::isVariantOfDimensionless ( ) const

Convenience function for testing if a given unit definition is a variant of the unit "dimensionless".

Returns
true if this UnitDefinition is a variant of dimensionless, meaning dimensionless with only abritrary variations in scale or multiplier values; false otherwise.

§ isVariantOfLength()

bool UnitDefinition::isVariantOfLength ( ) const

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "length".

Returns
true if this UnitDefinition is a variant of the predefined unit length, meaning metres with only abritrary variations in scale or multiplier values; false otherwise.

§ isVariantOfMass()

bool UnitDefinition::isVariantOfMass ( ) const

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "mass".

Returns
true if this UnitDefinition is a variant of mass units, meaning gram or kilogram with only abritrary variations in scale or multiplier values; false otherwise.

§ isVariantOfSubstance()

bool UnitDefinition::isVariantOfSubstance ( ) const

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "substance".

Returns
true if this UnitDefinition is a variant of the predefined unit substance, meaning moles or items (and grams or kilograms from SBML Level 2 Version 2 onwards) with only abritrary variations in scale or multiplier values; false otherwise.

§ isVariantOfSubstancePerTime()

bool UnitDefinition::isVariantOfSubstancePerTime ( ) const

Convenience function for testing if a given unit definition is a variant of the predefined unit "substance" divided by the predefined unit "time".

Returns
true if this UnitDefinition is a variant of the predefined unit substance per predefined unit time, meaning it contains two units one of which is a variant of substance and the other is a variant of time which an exponent of -1; false otherwise.

§ isVariantOfTime()

bool UnitDefinition::isVariantOfTime ( ) const

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "time".

Returns
true if this UnitDefinition is a variant of the predefined unit time, meaning seconds with only abritrary variations in scale or multiplier values; false otherwise.

§ isVariantOfVolume()

bool UnitDefinition::isVariantOfVolume ( ) const

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier "volume".

Returns
true if this UnitDefinition is a variant of the predefined unit volume, meaning litre or cubic metre with only abritrary variations in scale or multiplier values; false otherwise.

§ matchesRequiredSBMLNamespacesForAddition() [1/2]

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.

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 libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
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.

§ matchesRequiredSBMLNamespacesForAddition() [2/2]

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.

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 libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
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.

§ matchesSBMLNamespaces() [1/2]

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.

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 libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
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.

§ matchesSBMLNamespaces() [2/2]

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.

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 libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
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.

§ operator=()

UnitDefinition & UnitDefinition::operator= ( const UnitDefinition rhs)

Assignment operator.

Parameters
rhsThe object whose values are used as the basis of the assignment.

§ printUnits()

std::string UnitDefinition::printUnits ( const UnitDefinition ud,
bool  compact = false 
)
static

Expresses the given definition in a plain-text form.

For example, UnitDefinition::printUnits() applied to

<unitDefinition>
 <listOfUnits>
   <unit kind="metre" exponent="1"/>
   <unit kind="second" exponent="-2"/>
 </listOfUnits>
<unitDefinition>

will return the string "metre (exponent = 1, multiplier = 1, scale = 0) second (exponent = -2, multiplier = 1, scale = 0)" or, if the optional parameter compact is given the value true, the string "(1 metre)^1 (1 second)^-2". This method may be useful for printing unit information to human users, or in debugging software, or other situations.

Parameters
udthe UnitDefinition object
compactboolean indicating whether the compact form should be used (defaults to false)
Returns
a string expressing the unit definition defined by the given UnitDefinition object ud.
Examples:
printUnits.cpp.

§ read()

void SBase::read ( XMLNode node,
XMLErrorSeverityOverride_t  flag = LIBSBML_OVERRIDE_DISABLED 
)
inherited

Reads (initializes) this SBML object by reading from the given XMLNode.

Parameters
nodeThe XMLNode to read from.
flagAn optional flag that determines how how errors are logged during the reading process.
Warning
This method is computationally expensive, because the given node has to be serialized to a string first. Attempting to serialize a large tree structure (e.g., a large Model) may consume significant computer memory and time.

§ removeFromParentAndDelete()

int SBase::removeFromParentAndDelete ( )
virtualinherited

Removes this object from its parent.

If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, 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.

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

§ removeTopLevelAnnotationElement()

int SBase::removeTopLevelAnnotationElement ( const std::string  elementName,
const std::string  elementURI = "",
bool  removeEmpty = true 
)
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
removeEmptyif after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).

§ removeUnit()

Unit * UnitDefinition::removeUnit ( unsigned int  n)

Removes the nth Unit object from this UnitDefinition object and returns a pointer to it.

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

Parameters
nthe index of the Unit object to remove
Returns
the Unit object removed, or NULL if the given index is out of range.

§ renameMetaIdRefs()

void SBase::renameMetaIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

Reimplemented in GraphicalObject.

§ renameSIdRefs()

§ renameUnitSIdRefs()

void SBase::renameUnitSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

§ reorder()

void UnitDefinition::reorder ( UnitDefinition ud)
static

Alphabetically orders the Unit objects within the ListOfUnits of a UnitDefinition.

Parameters
udthe UnitDefinition object whose units are to be reordered.

§ replaceTopLevelAnnotationElement() [1/2]

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) followed by calling 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

§ replaceTopLevelAnnotationElement() [2/2]

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) followed by calling 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

§ setAnnotation() [1/2]

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

Reimplemented in Model, and SpeciesReference.

§ setAnnotation() [2/2]

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

Reimplemented in Model, and SpeciesReference.

§ setElementText()

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.

§ setId()

int UnitDefinition::setId ( const std::string &  sid)
virtual

Sets the value of the "id" attribute of this UnitDefinition.

The string sid is copied.

SBML has strict requirements for the syntax of identifiers, that is, the values of the "id" attribute present on most types of SBML objects. The following is a summary of the definition of the SBML identifier type SId, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation:
   letter ::= 'a'..'z','A'..'Z'
   digit  ::= '0'..'9'
   idChar ::= letter | digit | '_'
   SId    ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact details of the uniqueness requirements.
Parameters
sidthe string to use as the identifier of this UnitDefinition
Examples:
createExampleSBML.cpp.

§ setMetaId()

int SBase::setMetaId ( const std::string &  metaid)
inherited

Sets the value of the meta-identifier 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

The string metaid is copied.

Parameters
metaidthe identifier string to use as the value of the "metaid" attribute
Examples:
addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.

§ setModelHistory()

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.
Examples:
addModelHistory.cpp.

§ setName()

int UnitDefinition::setName ( const std::string &  name)
virtual

Sets the value of the "name" attribute of this UnitDefinition.

The string in name is copied.

Parameters
namethe new name for the UnitDefinition

§ setNamespaces()

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

§ setNotes() [1/2]

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
Examples:
createExampleSBML.cpp.

§ setNotes() [2/2]

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.

§ setSBOTerm() [1/2]

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
Examples:
groups_example1.cpp, and qual_example1.cpp.

§ setSBOTerm() [2/2]

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"

§ setUserData()

int SBase::setUserData ( void *  userData)
inherited

Sets the user data of this element.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Parameters
userDataspecifies the new user data.

§ simplify()

void UnitDefinition::simplify ( UnitDefinition ud)
static

Simplifies the UnitDefinition such that any given kind of Unit object occurs only once in the ListOfUnits.

For example, the following definition,

<unitDefinition>
 <listOfUnits>
   <unit kind="metre" exponent="1"/>
   <unit kind="metre" exponent="2"/>
 </listOfUnits>
<unitDefinition>

will be simplified to

<unitDefinition>
  <listOfUnits>
    <unit kind="metre" exponent="3"/>
  </listOfUnits>
<unitDefinition>
Parameters
udthe UnitDefinition object to be simplified.

§ toSBML()

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.

§ toXMLNode()

XMLNode* SBase::toXMLNode ( )
inherited

Returns this element as an XMLNode.

Returns
this element as an XMLNode.
Warning
This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.

§ unsetAnnotation()

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.

Examples:
unsetAnnotation.cpp.

§ unsetCVTerms()

int SBase::unsetCVTerms ( )
inherited

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

§ unsetId()

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.

Reimplemented in Model, Layout, Event, Group, Member, Input, QualitativeSpecies, GeneProductAssociation, FluxObjective, Output, Objective, GeneProduct, GeneProductRef, ListOfMembers, SimpleSpeciesReference, Transition, GraphicalObject, Point, FluxBound, Dimensions, BoundingBox, and GeneAssociation.

§ unsetMetaId()

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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

§ unsetModelHistory()

int SBase::unsetModelHistory ( )
inherited

Unsets the ModelHistory object attached to this object.

§ unsetName()

int UnitDefinition::unsetName ( )
virtual

Unsets the value of the "name" attribute of this UnitDefinition.

Reimplemented from SBase.

§ unsetNotes()

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.

Examples:
unsetNotes.cpp.

§ unsetSBOTerm()

int SBase::unsetSBOTerm ( )
inherited

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

§ unsetUserData()

int SBase::unsetUserData ( )
inherited

Unsets the user data of this element.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.