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Compartment Class Reference
Inheritance diagram for Compartment:
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Detailed Description

Implementation of SBML's Compartment construct.

A compartment in SBML represents a bounded space in which species are located. Compartments do not necessarily have to correspond to actual structures inside or outside of a biological cell.

It is important to note that although compartments are optional in the overall definition of Model, every species in an SBML model must be located in a compartment. This in turn means that if a model defines any species, the model must also define at least one compartment. The reason is simply that species represent physical things, and therefore must exist somewhere. Compartments represent the somewhere.

Compartment has one required attribute, "id", to give the compartment a unique identifier by which other parts of an SBML model definition can refer to it. A compartment can also have an optional "name" attribute of type string. Identifiers and names must be used according to the guidelines described in the SBML specifications.

Compartment also has an optional attribute "spatialDimensions" that is used to indicate the number of spatial dimensions possessed by the compartment. Most modeling scenarios involve compartments with integer values of "spatialDimensions" of 3 (i.e., a three-dimensional compartment, which is to say, a volume), or 2 (a two-dimensional compartment, a surface), or 1 (a one-dimensional compartment, a line). In SBML Level 3, the type of this attribute is double, there are no restrictions on the permitted values of the "spatialDimensions" attribute, and there are no default values. In SBML Level 2, the value must be a positive integer, and the default value is 3; the permissible values in SBML Level 2 are 3, 2, 1, and 0 (for a point).

Another optional attribute on Compartment is "size", representing the initial total size of that compartment in the model. The "size" attribute must be a floating-point value and may represent a volume (if the compartment is a three-dimensional one), or an area (if the compartment is two-dimensional), or a length (if the compartment is one-dimensional). There is no default value of compartment size in SBML Level 2 or Level 3. In particular, a missing "size" value does not imply that the compartment size is 1. (This is unlike the definition of compartment "volume" in SBML Level 1.) When the compartment's "spatialDimensions" attribute does not have a value of 0, a missing value of "size" for a given compartment signifies that the value either is unknown, or to be obtained from an external source, or determined by an InitialAssignment, AssignmentRule, AlgebraicRule or RateRule elsewhere in the model. In SBML Level 2, there are additional special requirements on the values of "size"; we discuss them in a separate section below.

The units associated with a compartment's "size" attribute value may be set using the optional attribute "units". The rules for setting and using compartment size units differ between SBML Level 2 and Level 3, and are discussed separately below.

Finally, the optional Compartment attribute named "constant" is used to indicate whether the compartment's size stays constant after simulation begins. A value of true indicates the compartment's "size" cannot be changed by any other construct except InitialAssignment; a value of false indicates the compartment's "size" can be changed by other constructs in SBML. In SBML Level 2, there is an additional explicit restriction that if "spatialDimensions"="0", the value cannot be changed by InitialAssignment either. Further, in Level 2, "constant" has a default value of true. In SBML Level 3, there is no default value for the "constant" attribute.

Additional considerations in SBML Level 2

In SBML Level 2, the default units of compartment size, and the kinds of units allowed as values of the attribute "units", interact with the number of spatial dimensions of the compartment. The value of the "units" attribute of a Compartment object must be one of the base units (see Unit), or the predefined unit identifiers volume, area, length or dimensionless, or a new unit defined by a UnitDefinition object in the enclosing Model, subject to the restrictions detailed in the following table:

Restrictions on values permitted for compartment size and units attributes.
Value of
spatialDimensions
size
allowed?
units
allowed?
Allowable kinds of units Default value of attribute units
"3" yes yes units of volume, or dimensionless "volume"
"2" yes yes units of area, or dimensionless "area"
"1" yes yes units of length, or dimensionless "length"
"0" no no (no units allowed)

In SBML Level 2, the units of the compartment size, as defined by the "units" attribute or (if "units" is not set) the default value listed in the table above, are used in the following ways when the compartment has a "spatialDimensions" value greater than 0:

  • The value of the "units" attribute is used as the units of the compartment identifier when the identifier appears as a numerical quantity in a mathematical formula expressed in MathML.

  • The math element of an AssignmentRule or InitialAssignment referring to this compartment must have identical units.

  • In RateRule objects that set the rate of change of the compartment's size, the units of the rule's math element must be identical to the compartment's "units" attribute divided by the default time units. (In other words, the units for the rate of change of compartment size are compartment size/time units.

  • When a Species is to be treated in terms of concentrations or density, the units of the spatial size portion of the concentration value (i.e., the denominator in the units formula substance/size) are those indicated by the value of the "units" attribute on the compartment in which the species is located.

Compartments with "spatialDimensions"=0 require special treatment in this framework. As implied above, the "size" attribute must not have a value on an SBML Level 2 Compartment object if the "spatialDimensions" attribute has a value of 0. An additional related restriction is that the "constant" attribute must default to or be set to true if the value of the "spatialDimensions" attribute is 0, because a zero-dimensional compartment cannot ever have a size.

If a compartment has no size or dimensional units, how should such a compartment's identifier be interpreted when it appears in mathematical formulas? The answer is that such a compartment's identifier should not appear in mathematical formulas in the first place—it has no value, and its value cannot change. Note also that a zero-dimensional compartment is a point, and species located at points can only be described in terms of amounts, not spatially-dependent measures such as concentration. Since SBML KineticLaw formulas are already in terms of substance/time and not (say) concentration/time, volume or other factors in principle are not needed for species located in zero-dimensional compartments.

Finally, in SBML Level 2 Versions 2–4, each compartment in a model may optionally be designated as belonging to a particular compartment type. The optional attribute "compartmentType" is used identify the compartment type represented by the Compartment structure. The "compartmentType" attribute's value must be the identifier of a CompartmentType instance defined in the model. If the "compartmentType" attribute is not present on a particular compartment definition, a unique virtual compartment type is assumed for that compartment, and no other compartment can belong to that compartment type. The values of "compartmentType" attributes on compartments have no effect on the numerical interpretation of a model. Simulators and other numerical analysis software may ignore "compartmentType" attributes. The "compartmentType" attribute and the CompartmentType class of objects are not present in SBML Level 3 Core nor in SBML Level 1.

Additional considerations in SBML Level 3

One difference between SBML Level 3 and lower Levels of SBML is that there are no restrictions on the permissible values of the "spatialDimensions" attribute, and there is no default value defined for the attribute. The value of "spatialDimensions" does not have to be an integer, either; this is to allow for the possibility of representing structures with fractal dimensions.

The number of spatial dimensions possessed by a compartment cannot enter into mathematical formulas, and therefore cannot directly alter the numerical interpretation of a model. However, the value of "spatialDimensions" does affect the interpretation of the units associated with a compartment's size. Specifically, the value of "spatialDimensions" is used to select among the Model attributes "volumeUnits", "areaUnits" and "lengthUnits" when a Compartment object does not define a value for its "units" attribute.

The "units" attribute may be left unspecified for a given compartment in a model; in that case, the compartment inherits the unit of measurement specified by one of the attributes on the enclosing Model object instance. The applicable attribute on Model depends on the value of the compartment's "spatialDimensions" attribute; the relationship is shown in the table below. If the Model object does not define the relevant attribute ("volumeUnits", "areaUnits" or "lengthUnits") for a given "spatialDimensions" value, the unit associated with that Compartment object's size is undefined. If both "spatialDimensions" and "units" are left unset on a given Compartment object instance, then no unit can be chosen from among the Model's "volumeUnits", "areaUnits" or "lengthUnits" attributes (even if the Model instance provides values for those attributes), because there is no basis to select between them and there is no default value of "spatialDimensions". Leaving the units of compartments' sizes undefined in an SBML model does not render the model invalid; however, as a matter of best practice, we strongly recommend that all models specify the units of measurement for all compartment sizes.

Interpretation of the Compartment "units" attribute.
Value of attribute
"spatialDimensions"
Attribute of Model used
for inheriting the unit
Recommended candidate units
"3" "volumeUnits" units of volume, or dimensionless
"2" "areaUnits" units of area, or dimensionless
"1" "lengthUnits" units of length, or dimensionless
other no units inherited no specific recommendations

The unit of measurement associated with a compartment's size, as defined by the "units" attribute or (if "units" is not set) the inherited value from Model according to the table above, is used in the following ways:

  • When the identifier of the compartment appears as a numerical quantity in a mathematical formula expressed in MathML, it represents the size of the compartment, and the unit associated with the size is the value of the "units" attribute.

  • When a Species is to be treated in terms of concentrations or density, the unit associated with the spatial size portion of the concentration value (i.e., the denominator in the formula amount/size) is specified by the value of the "units" attribute on the compartment in which the species is located.

  • The "math" elements of AssignmentRule, InitialAssignment and EventAssignment objects setting the value of the compartment size should all have the same units as the unit associated with the compartment's size.

  • In a RateRule object that defines a rate of change for a compartment's size, the unit of the rule's "math" element should be identical to the compartment's "units" attribute divided by the model-wide unit of time. (In other words, {unit of compartment size}/{unit of time}.)

Other aspects of Compartment

In SBML Level 1 and Level 2, Compartment has an optional attribute named "outside", whose value can be the identifier of another Compartment object defined in the enclosing Model object. Doing so means that the other compartment contains it or is outside of it. This enables the representation of simple topological relationships between compartments, for those simulation systems that can make use of the information (e.g., for drawing simple diagrams of compartments). It is worth noting that in SBML, there is no relationship between compartment sizes when compartment positioning is expressed using the "outside" attribute. The size of a given compartment does not in any sense include the sizes of other compartments having it as the value of their "outside" attributes. In other words, if a compartment B has the identifier of compartment A as its "outside" attribute value, the size of A does not include the size of B. The compartment sizes are separate.

In Level 2, there are two restrictions on the "outside" attribute. First, because a compartment with "spatialDimensions" of 0 has no size, such a compartment cannot act as the container of any other compartment except compartments that also have "spatialDimensions" values of 0. Second, the directed graph formed by representing Compartment structures as vertexes and the "outside" attribute values as edges must be acyclic. The latter condition is imposed to prevent a compartment from being contained inside itself. In the absence of a value for "outside", compartment definitions in SBML Level 2 do not have any implied spatial relationships between each other.

Public Member Functions

virtual bool accept (SBMLVisitor &v) const
 Accepts the given SBMLVisitor for this instance of Compartment. More...
 
int addCVTerm (CVTerm *term, bool newBag=false)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
virtual int appendAnnotation (const XMLNode *annotation)
 Appends the given annotation to the "annotation" subelement of this object. More...
 
virtual int appendAnnotation (const std::string &annotation)
 Appends the given annotation to the "annotation" subelement of this object. More...
 
int appendNotes (const XMLNode *notes)
 Appends the given notes to the "notes" subelement of this object. More...
 
int appendNotes (const std::string &notes)
 Appends the given notes to the "notes" subelement of this object. More...
 
virtual Compartmentclone () const
 Creates and returns a deep copy of this Compartment object. More...
 
 Compartment (unsigned int level, unsigned int version)
 Creates a new Compartment using the given SBML level and version values. More...
 
 Compartment (SBMLNamespaces *sbmlns)
 Creates a new Compartment using the given SBMLNamespaces object sbmlns. More...
 
 Compartment (const Compartment &orig)
 Copy constructor; creates a copy of a Compartment. More...
 
int disablePackage (const std::string &pkgURI, const std::string &pkgPrefix)
 Disables the given SBML Level 3 package. More...
 
int enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package. More...
 
virtual ListgetAllElements ()
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual ListgetAllElementsFromPlugins ()
 Returns a List of all child SBase objects contained in SBML package plug-ins. More...
 
SBasegetAncestorOfType (int type, const std::string pkgName="core")
 Returns the first ancestor object that has the given SBML type code. More...
 
const SBasegetAncestorOfType (int type, const std::string pkgName="core") const
 Returns the first ancestor object that has the given SBML type code. More...
 
XMLNodegetAnnotation ()
 Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More...
 
XMLNodegetAnnotation () const
 Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More...
 
std::string getAnnotationString ()
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
std::string getAnnotationString () const
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
unsigned int getColumn () const
 Returns the column number on which this object first appears in the XML representation of the SBML document. More...
 
const std::string & getCompartmentType () const
 Get the value of the "compartmentType" attribute of this Compartment object. More...
 
bool getConstant () const
 Get the value of the "constant" attribute of this Compartment. More...
 
CVTermgetCVTerm (unsigned int n)
 Returns the nth CVTerm in the list of CVTerms of this SBML object. More...
 
ListgetCVTerms ()
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
ListgetCVTerms () const
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
UnitDefinitiongetDerivedUnitDefinition ()
 Constructs and returns a UnitDefinition that corresponds to the units of this Compartment's designated size. More...
 
const UnitDefinitiongetDerivedUnitDefinition () const
 Constructs and returns a UnitDefinition that corresponds to the units of this Compartment's designated size. More...
 
virtual SBasegetElementByMetaId (std::string metaid)
 Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found. More...
 
virtual SBasegetElementBySId (std::string id)
 Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this object, which for Compartment, is always "compartment". More...
 
virtual const std::string & getId () const
 Returns the value of the "id" attribute of this Compartment object. More...
 
unsigned int getLevel () const
 Returns the SBML Level of the SBMLDocument object containing this object. More...
 
unsigned int getLine () const
 Returns the line number on which this object first appears in the XML representation of the SBML document. More...
 
const std::string & getMetaId () const
 Returns the value of the "metaid" attribute of this object. More...
 
std::string & getMetaId ()
 Returns the value of the "metaid" attribute of this object. More...
 
const ModelgetModel () const
 Returns the Model object in which the current object is located. More...
 
ModelHistorygetModelHistory () const
 Returns the ModelHistory object, if any, attached to this object. More...
 
ModelHistorygetModelHistory ()
 Returns the ModelHistory object, if any, attached to this object. More...
 
virtual const std::string & getName () const
 Returns the value of the "name" attribute of this Compartment object. More...
 
virtual XMLNamespacesgetNamespaces () const
 Returns a list of the XML Namespaces declared on this SBML document. More...
 
XMLNodegetNotes ()
 Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More...
 
XMLNodegetNotes () const
 Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More...
 
std::string getNotesString ()
 Returns the content of the "notes" subelement of this object as a string. More...
 
std::string getNotesString () const
 Returns the content of the "notes" subelement of this object as a string. More...
 
unsigned int getNumCVTerms ()
 Returns the number of CVTerm objects in the annotations of this SBML object. More...
 
unsigned int getNumPlugins () const
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
const std::string & getOutside () const
 Get the identifier, if any, of the compartment that is designated as being outside of this one. More...
 
const std::string & getPackageName () const
 Returns the name of the SBML Level 3 package in which this element is defined. More...
 
unsigned int getPackageVersion () const
 Returns the Version of the SBML Level 3 package to which this element belongs to. More...
 
SBasegetParentSBMLObject ()
 Returns the parent SBML object containing this object. More...
 
const SBasegetParentSBMLObject () const
 Returns the parent SBML object containing this object. More...
 
SBasePlugingetPlugin (const std::string &package)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
const SBasePlugingetPlugin (const std::string &package) const
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
SBasePlugingetPlugin (unsigned int n)
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasePlugingetPlugin (unsigned int n) const
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
BiolQualifierType_t getResourceBiologicalQualifier (std::string resource)
 Returns the MIRIAM biological qualifier associated with the given resource. More...
 
ModelQualifierType_t getResourceModelQualifier (std::string resource)
 Returns the MIRIAM model qualifier associated with the given resource. More...
 
const SBMLDocumentgetSBMLDocument () const
 Returns the SBMLDocument object containing this object instance. More...
 
SBMLDocumentgetSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
int getSBOTerm () const
 Returns the integer portion of the value of the "sboTerm" attribute of this object. More...
 
std::string getSBOTermAsURL () const
 Returns the identifiers.org URL representation of the "sboTerm" attribute of this object. More...
 
std::string getSBOTermID () const
 Returns the string representation of the "sboTerm" attribute of this object. More...
 
double getSize () const
 Get the size of this Compartment. More...
 
unsigned int getSpatialDimensions () const
 Get the number of spatial dimensions of this Compartment object. More...
 
double getSpatialDimensionsAsDouble () const
 Get the number of spatial dimensions of this Compartment object as a double. More...
 
virtual int getTypeCode () const
 Returns the libSBML type code for this SBML object. More...
 
const std::string & getUnits () const
 Get the units of this compartment's size. 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...
 
double getVolume () const
 Get the volume of this Compartment. More...
 
virtual bool hasRequiredAttributes () const
 Predicate returning true if all the required attributes for this Compartment 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...
 
void initDefaults ()
 Initializes the fields of this Compartment object to "typical" default values. More...
 
bool isPackageEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPackageURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPkgEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPkgURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isSetAnnotation () const
 Predicate returning true if this object's "annotation" subelement exists and has content. More...
 
bool isSetCompartmentType () const
 Predicate returning true if this Compartment's "compartmentType" attribute is set. More...
 
bool isSetConstant () const
 Predicate returning true if this Compartment's "constant" attribute is set. More...
 
virtual bool isSetId () const
 Predicate returning true if this Compartment'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 Compartment's "name" attribute is set. More...
 
bool isSetNotes () const
 Predicate returning true if this object's "notes" subelement exists and has content. More...
 
bool isSetOutside () const
 Predicate returning true if this Compartment's "outside" attribute is set. More...
 
bool isSetSBOTerm () const
 Predicate returning true if this object's "sboTerm" attribute is set. More...
 
bool isSetSize () const
 Predicate returning true if this Compartment's "size" attribute is set. More...
 
bool isSetSpatialDimensions () const
 Predicate returning true if this Compartment's "spatialDimensions" attribute is set. More...
 
bool isSetUnits () const
 Predicate returning true if this Compartment's "units" attribute is set. More...
 
bool isSetVolume () const
 Predicate returning true if this Compartment's "volume" attribute is set. More...
 
bool matchesRequiredSBMLNamespacesForAddition (const SBase *sb)
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (const SBase *sb)
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (const SBase *sb) const
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
Compartmentoperator= (const Compartment &rhs)
 Assignment operator for Compartment. More...
 
virtual int removeFromParentAndDelete ()
 Removes itself from its parent. More...
 
int removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="")
 Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More...
 
virtual void renameMetaIdRefs (std::string oldid, std::string newid)
 Renames all the MetaIdRef attributes on this element. More...
 
virtual void renameSIdRefs (std::string oldid, std::string newid)
 Renames all the SIdRef attributes on this element, including any found in MathML. More...
 
virtual void renameUnitSIdRefs (std::string oldid, std::string newid)
 Renames all the UnitSIdRef attributes on this element. More...
 
int replaceTopLevelAnnotationElement (const XMLNode *annotation)
 Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More...
 
int replaceTopLevelAnnotationElement (const std::string &annotation)
 Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More...
 
virtual int setAnnotation (const XMLNode *annotation)
 Sets the value of the "annotation" subelement of this SBML object. More...
 
virtual int setAnnotation (const std::string &annotation)
 Sets the value of the "annotation" subelement of this SBML object. More...
 
int setCompartmentType (const std::string &sid)
 Sets the "compartmentType" attribute of this Compartment. More...
 
int setConstant (bool value)
 Sets the value of the "constant" attribute of this Compartment. More...
 
virtual int setId (const std::string &sid)
 Sets the value of the "id" attribute of this Compartment. More...
 
int setMetaId (const std::string &metaid)
 Sets the value of the "metaid" attribute of this object. More...
 
int setModelHistory (ModelHistory *history)
 Sets the ModelHistory of this object. More...
 
virtual int setName (const std::string &name)
 Sets the value of the "name" attribute of this Compartment. 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...
 
int setOutside (const std::string &sid)
 Sets the "outside" attribute of this Compartment. 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 setSize (double value)
 Sets the "size" attribute (or "volume" in SBML Level 1) of this Compartment. More...
 
int setSpatialDimensions (unsigned int value)
 Sets the "spatialDimensions" attribute of this Compartment. More...
 
int setSpatialDimensions (double value)
 Sets the "spatialDimensions" attribute of this Compartment as a double. More...
 
int setUnits (const std::string &sid)
 Sets the "units" attribute of this Compartment. More...
 
int setUserData (void *userData)
 Sets the user data of this element. More...
 
int setVolume (double value)
 Sets the "volume" attribute (or "size" in SBML Level 2) of this Compartment. More...
 
char * toSBML ()
 Returns a string consisting of a partial SBML corresponding to just this object. More...
 
int unsetAnnotation ()
 Unsets the value of the "annotation" subelement of this SBML object. More...
 
int unsetCompartmentType ()
 Unsets the value of the "compartmentType" attribute of this Compartment. 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 Compartment. More...
 
int unsetNotes ()
 Unsets the value of the "notes" subelement of this SBML object. More...
 
int unsetOutside ()
 Unsets the value of the "outside" attribute of this Compartment. More...
 
int unsetSBOTerm ()
 Unsets the value of the "sboTerm" attribute of this SBML object. More...
 
int unsetSize ()
 Unsets the value of the "size" attribute of this Compartment. More...
 
int unsetSpatialDimensions ()
 Unsets the value of the "spatialDimensions" attribute of this Compartment. More...
 
int unsetUnits ()
 Unsets the value of the "units" attribute of this Compartment. More...
 
int unsetVolume ()
 Unsets the value of the "volume" attribute of this Compartment. More...
 
virtual ~Compartment ()
 Destroys this Compartment. 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

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

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

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

Creates a new Compartment using the given SBMLNamespaces object sbmlns.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using this class constructor is to create an SBMLNamespaces object somewhere in a program, once, then pass it to object constructors such as this one when needed.

It is worth emphasizing that although this constructor does not take an identifier argument, in SBML Level 2 and beyond, the "id" (identifier) attribute of a Compartment is required to have a value. Thus, callers are cautioned to assign a value after calling this constructor. Setting the identifier can be accomplished using the method setId().

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

Destroys this Compartment.

Compartment::Compartment ( const Compartment orig)

Copy constructor; creates a copy of a Compartment.

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

Member Function Documentation

bool Compartment::accept ( SBMLVisitor v) const
virtual

Accepts the given SBMLVisitor for this instance of Compartment.

Parameters
vthe SBMLVisitor instance to be used.
Returns
the result of calling v.visit(), which indicates whether the Visitor would like to visit the next Compartment in the list of compartments within which this Compartment is embedded (i.e., the ListOfCompartments in the parent Model).

Implements SBase.

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

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

Parameters
termthe CVTerm to assign.
newBagif true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the "metaid" attribute of the object as a reference, if the object has no "metaid" attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
int SBase::appendAnnotation ( const XMLNode annotation)
virtualinherited

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

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

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

Unlike SBase::setAnnotation(const XMLNode* annotation) or SBase::setAnnotation(const std::string& annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the "annotation" subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

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

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

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

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

Unlike SBase::setAnnotation(const XMLNode* annotation) or SBase::setAnnotation(const std::string& annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the "annotation" subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int SBase::appendNotes ( const XMLNode notes)
inherited

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

The content of notes is copied.

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

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

Parameters
notesan XML node structure that is to appended to the content of the "notes" subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::appendNotes ( const std::string &  notes)
inherited

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

The content of the parameter notes is copied.

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

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

Parameters
notesan XML string that is to appended to the content of the "notes" subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Compartment * Compartment::clone ( ) const
virtual

Creates and returns a deep copy of this Compartment object.

Returns
a (deep) copy of this Compartment.

Implements SBase.

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

Disables the given SBML Level 3 package.

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

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

Enables or disables the given SBML Level 3 package.

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

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
flagwhether to enable (true) or disable (false) the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
List * SBase::getAllElements ( )
virtualinherited

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

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

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

List * SBase::getAllElementsFromPlugins ( )
virtualinherited

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

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

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

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

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

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or NULL if no ancestor exists.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
const SBase * SBase::getAncestorOfType ( int  type,
const std::string  pkgName = "core" 
) const
inherited

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

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

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or NULL if no ancestor exists.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
XMLNode * SBase::getAnnotation ( )
inherited

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

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

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

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

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
XMLNode * SBase::getAnnotation ( ) const
inherited

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

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

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

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

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
std::string SBase::getAnnotationString ( )
inherited

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

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

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

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

Returns
the annotation of this SBML object as a character string.
See Also
getAnnotation()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
std::string SBase::getAnnotationString ( ) const
inherited

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

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

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

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

Returns
the annotation of this SBML object as a character string.
See Also
getAnnotation()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
unsigned int SBase::getColumn ( ) const
inherited

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

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

Get the value of the "compartmentType" attribute of this Compartment object.

Returns
the value of the "compartmentType" attribute of this Compartment as a string.
Note
The "compartmentType" attribute is only available in SBML Level 2 Versions 2–4.
bool Compartment::getConstant ( ) const

Get the value of the "constant" attribute of this Compartment.

Returns
true if this Compartment's size is flagged as being constant, false otherwise.
CVTerm * SBase::getCVTerm ( unsigned int  n)
inherited

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

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

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

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

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

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

Constructs and returns a UnitDefinition that corresponds to the units of this Compartment's designated size.

Compartments in SBML have an attribute ("units") for declaring the units of measurement intended for the value of the compartment's size. In the absence of a value given for this attribute, the units are inherited from values either defined on the enclosing Model (in SBML Level 3) or in defaults (in SBML Level 2). This method returns a UnitDefinition object based on how this compartment's units are interpreted according to the relevant SBML guidelines, or it returns NULL if no units have been declared and no defaults are defined by the relevant SBML specification.

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

Returns
a UnitDefinition that expresses the units of this Compartment, or NULL if one cannot be constructed.
Note
The libSBML system for unit analysis depends on the model as a whole. In cases where the Compartment object has not yet been added to a model, or the model itself is incomplete, unit analysis is not possible, and consequently this method will return NULL.
See Also
isSetUnits()
getUnits()
const UnitDefinition * Compartment::getDerivedUnitDefinition ( ) const

Constructs and returns a UnitDefinition that corresponds to the units of this Compartment's designated size.

Compartments in SBML have an attribute ("units") for declaring the units of measurement intended for the value of the compartment's size. In the absence of a value given for this attribute, the units are inherited from values either defined on the enclosing Model (in SBML Level 3) or in defaults (in SBML Level 2). This method returns a UnitDefinition object based on how this compartment's units are interpreted according to the relevant SBML guidelines, or it returns NULL if no units have been declared and no defaults are defined by the relevant SBML specification.

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

Returns
a UnitDefinition that expresses the units of this Compartment, or NULL if one cannot be constructed.
Note
The libSBML system for unit analysis depends on the model as a whole. In cases where the Compartment object has not yet been added to a model, or the model itself is incomplete, unit analysis is not possible, and consequently this method will return NULL.
See Also
isSetUnits()
getUnits()
SBase * SBase::getElementByMetaId ( std::string  metaid)
virtualinherited

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

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

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

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

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

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

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

const string & Compartment::getElementName ( ) const
virtual

Returns the XML element name of this object, which for Compartment, is always "compartment".

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

Implements SBase.

const string & Compartment::getId ( ) const
virtual

Returns the value of the "id" attribute of this Compartment object.

Returns
the id of this Compartment.
unsigned int SBase::getLevel ( ) const
inherited

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

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

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

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

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

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

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

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

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

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

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

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

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

Returns
the ModelHistory object attached to this object, or NULL if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
ModelHistory * SBase::getModelHistory ( )
inherited

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

Returns
the ModelHistory object attached to this object, or NULL if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
const string & Compartment::getName ( ) const
virtual

Returns the value of the "name" attribute of this Compartment object.

Returns
the name of this Compartment.
XMLNamespaces * SBase::getNamespaces ( ) const
virtualinherited

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

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

Returns
the XML Namespaces associated with this SBML object
See Also
getLevel()
getVersion()

Reimplemented in SBMLDocument.

XMLNode * SBase::getNotes ( )
inherited

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

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

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

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

Returns
the content of the "notes" subelement of this SBML object as a tree structure composed of XMLNode objects.
See Also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
XMLNode * SBase::getNotes ( ) const
inherited

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

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

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

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

Returns
the content of the "notes" subelement of this SBML object as a tree structure composed of XMLNode objects.
See Also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
std::string SBase::getNotesString ( )
inherited

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

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

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

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

Returns
the content of the "notes" subelement of this SBML object as a string.
See Also
getNotes()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
std::string SBase::getNotesString ( ) const
inherited

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

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

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

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

Returns
the content of the "notes" subelement of this SBML object as a string.
See Also
getNotes()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
unsigned int SBase::getNumCVTerms ( )
inherited

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

Returns
the number of CVTerms for this SBML object.
unsigned int SBase::getNumPlugins ( ) const
inherited

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

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

Get the identifier, if any, of the compartment that is designated as being outside of this one.

Returns
the value of the "outside" attribute of this Compartment.
Note
The "outside" attribute is defined in SBML Level 1 and Level 2, but does not exist in SBML Level 3 Version 1 Core.
const std::string & SBase::getPackageName ( ) const
inherited

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

Returns
the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
unsigned int SBase::getPackageVersion ( ) const
inherited

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

Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See Also
getLevel()
getVersion()
SBase * SBase::getParentSBMLObject ( )
inherited

Returns the parent SBML object containing this object.

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

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

Returns the parent SBML object containing this object.

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

Returns
the parent SBML object of this SBML object.
See Also
getSBMLDocument()
getModel()
SBasePlugin * SBase::getPlugin ( const std::string &  package)
inherited

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

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

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

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

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

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

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

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

Returns the MIRIAM biological qualifier associated with the given resource.

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

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

Parameters
resourcestring representing the resource; e.g., "http://www.geneontology.org/#GO:0005892".
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
ModelQualifierType_t SBase::getResourceModelQualifier ( std::string  resource)
inherited

Returns the MIRIAM model qualifier associated with the given resource.

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

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

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

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See Also
getParentSBMLObject()
getModel()
SBMLDocument * SBase::getSBMLDocument ( )
inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See Also
getParentSBMLObject()
getModel()
int SBase::getSBOTerm ( ) const
inherited

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

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

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

Returns
the value of the "sboTerm" attribute as an integer, or -1 if the value is not set.
std::string SBase::getSBOTermAsURL ( ) const
inherited

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

This method returns the entire SBO identifier as a text string in the form "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN".

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

Returns
the value of the "sboTerm" attribute as an identifiers.org URL (its value will be of the form "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN"), or an empty string if the value is not set.
std::string SBase::getSBOTermID ( ) const
inherited

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

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

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

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

Get the size of this Compartment.

This method is identical to getVolume(). In SBML Level 1, compartments are always three-dimensional constructs and only have volumes, whereas in SBML Level 2, compartments may be other than three-dimensional and therefore the "volume" attribute is named "size" in Level 2. LibSBML provides both getSize() and getVolume() for easier compatibility between SBML Levels.

Returns
the value of the "size" attribute ("volume" in Level 1) of this Compartment as a float-point number.
See Also
isSetSize()
getVolume()
unsigned int Compartment::getSpatialDimensions ( ) const

Get the number of spatial dimensions of this Compartment object.

Note
In SBML Level 3, the data type of the "spatialDimensions" attribute is double, whereas in Level 2, it is integer. LibSBML provides a separate method for obtaining the value as a double, for models where it is relevant.
Returns
the value of the "spatialDimensions" attribute of this Compartment as an unsigned integer
See Also
getSpatialDimensionsAsDouble()
double Compartment::getSpatialDimensionsAsDouble ( ) const

Get the number of spatial dimensions of this Compartment object as a double.

Note
In SBML Level 3, the data type of the "spatialDimensions" attribute is double, whereas in Level 2, it is integer. To avoid backward compatibility issues, libSBML provides a separate method for obtaining the value as a double, for models where it is relevant.
Returns
the value of the "spatialDimensions" attribute of this Compartment as a double, or NaN if this model is not in SBML Level 3 format.
See Also
getSpatialDimensions()
int Compartment::getTypeCode ( ) const
virtual

Returns the libSBML type code for this SBML object.

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

Reimplemented from SBase.

const string & Compartment::getUnits ( ) const

Get the units of this compartment's size.

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

Returns
the value of the "units" attribute of this Compartment, as a string. An empty string indicates that no units have been assigned to the value of the size.
Note
There is an important distinction to be made between no units assigned, and assuming a value without units has any specific unit such as dimensionless. In SBML, default units are never attributed to numbers, and numbers without units are not automatically assumed to have the unit dimensionless. Please consult the relevant SBML specification document for a more in-depth explanation of this topic and the SBML unit system.
See Also
isSetUnits()
setUnits()
getSize()
void * SBase::getUserData ( ) const
inherited

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

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

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

Returns
the SBML version of this SBML object.
See Also
getLevel()
getNamespaces()
double Compartment::getVolume ( ) const

Get the volume of this Compartment.

This method is identical to getSize(). In SBML Level 1, compartments are always three-dimensional constructs and only have volumes, whereas in SBML Level 2, compartments may be other than three-dimensional and therefore the "volume" attribute is named "size" in Level 2. LibSBML provides both getSize() and getVolume() for easier compatibility between SBML Levels.

Returns
the value of the "volume" attribute ("size" in Level 2) of this Compartment, as a floating-point number.
Note
The attribute "volume" only exists by that name in SBML Level 1. In Level 2 and above, the equivalent attribute is named "size".
See Also
isSetVolume()
getSize()
bool Compartment::hasRequiredAttributes ( ) const
virtual

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

Note
The required attributes for a Compartment object are:
  • "id" (or "name" in SBML Level 1)
  • "constant" (in SBML Level 3 only)
Returns
a boolean value indicating whether all the required attributes for this object have been defined.
bool SBase::hasValidLevelVersionNamespaceCombination ( )
inherited

Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.

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

  • Level 1 Version 2: "http://www.sbml.org/sbml/level1"
  • Level 2 Version 1: "http://www.sbml.org/sbml/level2"
  • Level 2 Version 2: "http://www.sbml.org/sbml/level2/version2"
  • Level 2 Version 3: "http://www.sbml.org/sbml/level2/version3"
  • Level 2 Version 4: "http://www.sbml.org/sbml/level2/version4"
  • Level 3 Version 1 Core: "http://www.sbml.org/sbml/level3/version1/core"
Returns
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
void Compartment::initDefaults ( )

Initializes the fields of this Compartment object to "typical" default values.

The SBML Compartment component has slightly different aspects and default attribute values in different SBML Levels and Versions. This method sets the values to certain common defaults, based mostly on what they are in SBML Level 2. Specifically:

  • Sets attribute "spatialDimensions" to 3
  • Sets attribute "constant" to true
  • (Applies to Level 1 models only) Sets attribute "volume" to 1.0
  • (Applies to Level 3 models only) Sets attribute "units" to litre
bool SBase::isPackageEnabled ( const std::string &  pkgName) const
inherited

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

The search ignores the package version.

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

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

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

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

The search ignores the package version.

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

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

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

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

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

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

Returns
true if a "annotation" subelement exists, false otherwise.
See Also
getAnnotation()
getAnnotationString()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
bool Compartment::isSetCompartmentType ( ) const

Predicate returning true if this Compartment's "compartmentType" attribute is set.

Returns
true if the "compartmentType" attribute of this Compartment is set, false otherwise.
Note
The "compartmentType" attribute is only available in SBML Level 2 Versions 2–4.
bool Compartment::isSetConstant ( ) const

Predicate returning true if this Compartment's "constant" attribute is set.

Returns
true if the "constant" attribute of this Compartment is set, false otherwise.
bool Compartment::isSetId ( ) const
virtual

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

Returns
true if the "id" attribute of this Compartment is set, false otherwise.
bool SBase::isSetMetaId ( ) const
inherited

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

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

Returns
true if the "metaid" attribute of this SBML object is set, false otherwise.
See Also
getMetaId()
setMetaId(const std::string& metaid)
bool SBase::isSetModelHistory ( )
inherited

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

Returns
true if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
bool Compartment::isSetName ( ) const
virtual

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

Returns
true if the "name" attribute of this Compartment is set, false otherwise.
bool SBase::isSetNotes ( ) const
inherited

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

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

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

Returns
true if a "notes" subelement exists, false otherwise.
See Also
getNotes()
getNotesString()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
bool Compartment::isSetOutside ( ) const

Predicate returning true if this Compartment's "outside" attribute is set.

Returns
true if the "outside" attribute of this Compartment is set, false otherwise.
Note
The "outside" attribute is defined in SBML Level 1 and Level 2, but does not exist in SBML Level 3 Version 1 Core.
bool SBase::isSetSBOTerm ( ) const
inherited

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

Returns
true if the "sboTerm" attribute of this SBML object is set, false otherwise.
bool Compartment::isSetSize ( ) const

Predicate returning true if this Compartment's "size" attribute is set.

This method is similar but not identical to isSetVolume(). The latter should be used in the context of SBML Level 1 models instead of isSetSize() because isSetVolume() performs extra processing to take into account the difference in default values between SBML Levels 1 and 2.

Returns
true if the "size" attribute ("volume" in Level 2) of this Compartment is set, false otherwise.
See Also
isSetVolume()
setSize(double value)
bool Compartment::isSetSpatialDimensions ( ) const

Predicate returning true if this Compartment's "spatialDimensions" attribute is set.

Returns
true if the "spatialDimensions" attribute of this Compartment is set, false otherwise.
bool Compartment::isSetUnits ( ) const

Predicate returning true if this Compartment's "units" attribute is set.

Returns
true if the "units" attribute of this Compartment is set, false otherwise.
Note
There is an important distinction to be made between no units assigned, and assuming a value without units has any specific unit such as dimensionless. In SBML, default units are never attributed to numbers, and numbers without units are not automatically assumed to have the unit dimensionless. Please consult the relevant SBML specification document for a more in-depth explanation of this topic and the SBML unit system.
bool Compartment::isSetVolume ( ) const

Predicate returning true if this Compartment's "volume" attribute is set.

This method is similar but not identical to isSetSize(). The latter should not be used in the context of SBML Level 1 models because this method performs extra processing to take into account the difference in default values between SBML Levels 1 and 2.

Returns
true if the "volume" attribute ("size" in Level 2 and above) of this Compartment is set, false otherwise.
Note
The attribute "volume" only exists by that name in SBML Level 1. In Level 2 and above, the equivalent attribute is named "size". In SBML Level 1, a compartment's volume has a default value (1.0) and therefore this method will always return true. In Level 2, a compartment's size (the equivalent of SBML Level 1's "volume") is optional and has no default value, and therefore may or may not be set.
See Also
isSetSize()
setVolume()
bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase sb)
inherited

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

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

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

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

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

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

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

Parameters
sban object to compare with respect to namespaces
Returns
boolean, true if this object's collection of namespaces is the same as sb's, false otherwise.
Compartment & Compartment::operator= ( const Compartment rhs)

Assignment operator for Compartment.

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

Removes itself from its parent.

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

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

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

int SBase::removeTopLevelAnnotationElement ( const std::string  elementName,
const std::string  elementURI = "" 
)
inherited

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

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

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

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

Renames all the MetaIdRef attributes on this element.

This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier

Reimplemented in Port.

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

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

Reimplemented from SBase.

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

Renames all the UnitSIdRef attributes on this element.

Reimplemented from SBase.

int SBase::replaceTopLevelAnnotationElement ( const XMLNode annotation)
inherited

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

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

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

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

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

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

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

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

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

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

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

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

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

Parameters
annotationan XML structure that is to be used as the new content of the "annotation" subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

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

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

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

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

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

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

Parameters
annotationan XML string that is to be used as the content of the "annotation" subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int Compartment::setCompartmentType ( const std::string &  sid)

Sets the "compartmentType" attribute of this Compartment.

Parameters
sidthe identifier of a CompartmentType object defined elsewhere in this Model.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The "compartmentType" attribute is only available in SBML Level 2 Versions 2–4.
int Compartment::setConstant ( bool  value)

Sets the value of the "constant" attribute of this Compartment.

Parameters
valuea boolean indicating whether the size/volume of this compartment should be considered constant (true) or variable (false)
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
void SBase::setElementText ( const std::string &  text)
protectedvirtualinherited

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

The default implementation does nothing.

Parameters
textthe text string found between the element tags.
int Compartment::setId ( const std::string &  sid)
virtual

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

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

letter ::= 'a'..'z','A'..'Z'
digit  ::= '0'..'9'
idChar ::= letter | digit | '_'
SId    ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact formulations.

Parameters
sidthe string to use as the identifier of this Compartment
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int SBase::setMetaId ( const std::string &  metaid)
inherited

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

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

Parameters
metaidthe identifier string to use as the value of the "metaid" attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getMetaId()
isSetMetaId()
int SBase::setModelHistory ( ModelHistory history)
inherited

Sets the ModelHistory of this object.

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

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
int Compartment::setName ( const std::string &  name)
virtual

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

The string in name is copied.

Parameters
namethe new name for the Compartment
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int SBase::setNamespaces ( XMLNamespaces xmlns)
inherited

Sets the namespaces relevant of this SBML object.

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

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

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

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

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

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

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

Parameters
notesan XML structure that is to be used as the content of the "notes" subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::setNotes ( const std::string &  notes,
bool  addXHTMLMarkup = false 
)
inherited

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

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

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

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

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

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

Sets the "outside" attribute of this Compartment.

Parameters
sidthe identifier of a compartment that encloses this one.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The "outside" attribute is defined in SBML Level 1 and Level 2, but does not exist in SBML Level 3 Version 1 Core.
int SBase::setSBOTerm ( int  value)
virtualinherited

Sets the value of the "sboTerm" attribute.

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

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

Parameters
valuethe NNNNNNN integer portion of the SBO identifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm(const std::string &sboid)
int SBase::setSBOTerm ( const std::string &  sboid)
virtualinherited

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

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

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

Parameters
sboidthe SBO identifier string of the form "SBO:NNNNNNN"
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm(int value)
int Compartment::setSize ( double  value)

Sets the "size" attribute (or "volume" in SBML Level 1) of this Compartment.

This method is identical to setVolume() and is provided for compatibility between SBML Level 1 and Level 2.

Parameters
valuea double representing the size of this compartment instance in whatever units are in effect for the compartment.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attribute "volume" only exists by that name in SBML Level 1. In Level 2 and above, the equivalent attribute is named "size".
int Compartment::setSpatialDimensions ( unsigned int  value)

Sets the "spatialDimensions" attribute of this Compartment.

If value is not one of 0, 1, 2, or 3, this method will have no effect (i.e., the "spatialDimensions" attribute will not be set).

Parameters
valuean unsigned integer indicating the number of dimensions of this compartment.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int Compartment::setSpatialDimensions ( double  value)

Sets the "spatialDimensions" attribute of this Compartment as a double.

Parameters
valuea double indicating the number of dimensions of this compartment.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int Compartment::setUnits ( const std::string &  sid)

Sets the "units" attribute of this Compartment.

Parameters
sidthe identifier of the defined units to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int SBase::setUserData ( void *  userData)
inherited

Sets the user data of this element.

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

Parameters
userDataspecifies the new user data.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int Compartment::setVolume ( double  value)

Sets the "volume" attribute (or "size" in SBML Level 2) of this Compartment.

This method is identical to setVolume() and is provided for compatibility between SBML Level 1 and Level 2.

Parameters
valuea double representing the volume of this compartment instance in whatever units are in effect for the compartment.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attribute "volume" only exists by that name in SBML Level 1. In Level 2 and above, the equivalent attribute is named "size".
char * SBase::toSBML ( )
inherited

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

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
int SBase::unsetAnnotation ( )
inherited

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

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

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
int Compartment::unsetCompartmentType ( )

Unsets the value of the "compartmentType" attribute of this Compartment.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The "compartmentType" attribute is only available in SBML Level 2 Versions 2–4.
See Also
setCompartmentType(const std::string& sid)
isSetCompartmentType()
int SBase::unsetCVTerms ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int SBase::unsetId ( )
virtualinherited

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

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

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

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

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

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

int SBase::unsetMetaId ( )
inherited

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

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int SBase::unsetModelHistory ( )
inherited

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
int Compartment::unsetName ( )
virtual

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

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

Reimplemented from SBase.

int SBase::unsetNotes ( )
inherited

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

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

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
int Compartment::unsetOutside ( )

Unsets the value of the "outside" attribute of this Compartment.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The "outside" attribute is defined in SBML Level 1 and Level 2, but does not exist in SBML Level 3 Version 1 Core.
int SBase::unsetSBOTerm ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int Compartment::unsetSize ( )

Unsets the value of the "size" attribute of this Compartment.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attribute "volume" only exists by that name in SBML Level 1. In Level 2 and above, the equivalent attribute is named "size".
int Compartment::unsetSpatialDimensions ( )

Unsets the value of the "spatialDimensions" attribute of this Compartment.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This function is only valid for SBML Level 3.
int Compartment::unsetUnits ( )

Unsets the value of the "units" attribute of this Compartment.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int Compartment::unsetVolume ( )

Unsets the value of the "volume" attribute of this Compartment.

In SBML Level 1, a Compartment volume has a default value (1.0) and therefore should always be set. In Level 2, "size" is optional with no default value and as such may or may not be set.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attribute "volume" only exists by that name in SBML Level 1. In Level 2 and above, the equivalent attribute is named "size".