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libsbmlcs.Compartment Class Reference
Inheritance diagram for libsbmlcs.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

int addCVTerm (CVTerm term, bool newBag)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
int addCVTerm (CVTerm term)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
int appendAnnotation (XMLNode annotation)
 Appends the given annotation to the 'annotation' subelement of this object. More...
 
int appendAnnotation (string annotation)
 Appends the given annotation to the 'annotation' subelement of this object. More...
 
int appendNotes (XMLNode notes)
 Appends the given notes to the 'notes' subelement of this object. More...
 
int appendNotes (string notes)
 Appends the given notes to the 'notes' subelement of this object. More...
 
int checkCompatibility (SBase arg0)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
string checkMathMLNamespace (XMLToken elem)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
new Compartment clone ()
 Creates and returns a deep copy of this Compartment object. More...
 
 Compartment (long level, long 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 (Compartment orig)
 Copy constructor; creates a copy of a Compartment. More...
 
void connectToChild ()
 Sets this SBML object to child SBML objects (if any). More...
 
void connectToParent (SBase parent)
 Sets the parent SBML object of this SBML object. More...
 
int disablePackage (string pkgURI, string pkgPrefix)
 Disables the given SBML Level 3 package. More...
 
override void Dispose ()
 
void divideAssignmentsToSIdByFunction (string id, ASTNode function)
 If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More...
 
int enablePackage (string pkgURI, string pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package. More...
 
void enablePackageInternal (string pkgURI, string pkgPrefix, bool flag)
 Enables/Disables the given package with this element and child elements (if any). More...
 
override bool Equals (Object sb)
 
SBase getAncestorOfType (int type, string pkgName)
 Returns the first ancestor object that has the given SBML type code. More...
 
SBase getAncestorOfType (int type)
 Returns the first ancestor object that has the given SBML type code. More...
 
XMLNode getAnnotation ()
 Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More...
 
string getAnnotationString ()
 Returns the content of the 'annotation' subelement of this object as a character string. More...
 
long getColumn ()
 Returns the column number on which this object first appears in the XML representation of the SBML document. More...
 
string getCompartmentType ()
 Get the value of the 'compartmentType' attribute of this Compartment object. More...
 
bool getConstant ()
 Get the value of the 'constant' attribute of this Compartment. More...
 
CVTerm getCVTerm (long n)
 Returns the nth CVTerm in the list of CVTerms of this SBML object. More...
 
CVTermList getCVTerms ()
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
UnitDefinition getDerivedUnitDefinition ()
 Constructs and returns a UnitDefinition that corresponds to the units of this Compartment's designated size. More...
 
SBase getElementByMetaId (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...
 
SBase getElementBySId (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...
 
SBase getElementFromPluginsByMetaId (string metaid)
 Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found. More...
 
SBase getElementFromPluginsBySId (string id)
 Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found. More...
 
new string getElementName ()
 Returns the XML element name of this object, which for Compartment, is always 'compartment'. More...
 
override int GetHashCode ()
 
new string getId ()
 Returns the value of the 'id' attribute of this Compartment object. More...
 
long getLevel ()
 Returns the SBML Level of the SBMLDocument object containing this object. More...
 
long getLine ()
 Returns the line number on which this object first appears in the XML representation of the SBML document. More...
 
SBaseList getListOfAllElements ()
 
SBaseList getListOfAllElementsFromPlugins ()
 
string getMetaId ()
 Returns the value of the 'metaid' attribute of this object. More...
 
Model getModel ()
 Returns the Model object in which the current object is located. More...
 
ModelHistory getModelHistory ()
 Returns the ModelHistory object, if any, attached to this object. More...
 
new string getName ()
 Returns the value of the 'name' attribute of this Compartment object. More...
 
XMLNamespaces getNamespaces ()
 Returns a list of the XML Namespaces declared on this SBML document. More...
 
XMLNode getNotes ()
 Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More...
 
string getNotesString ()
 Returns the content of the 'notes' subelement of this object as a string. More...
 
long getNumCVTerms ()
 Returns the number of CVTerm objects in the annotations of this SBML object. More...
 
long getNumPlugins ()
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
string getOutside ()
 Get the identifier, if any, of the compartment that is designated as being outside of this one. More...
 
string getPackageName ()
 Returns the name of the SBML Level 3 package in which this element is defined. More...
 
long getPackageVersion ()
 Returns the Version of the SBML Level 3 package to which this element belongs to. More...
 
SBase getParentSBMLObject ()
 Returns the parent SBML object containing this object. More...
 
SBasePlugin getPlugin (string package)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
SBasePlugin getPlugin (long n)
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
int getResourceBiologicalQualifier (string resource)
 Returns the MIRIAM biological qualifier associated with the given resource. More...
 
int getResourceModelQualifier (string resource)
 Returns the MIRIAM model qualifier associated with the given resource. More...
 
SBMLDocument getSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
SBMLNamespaces getSBMLNamespaces ()
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
int getSBOTerm ()
 Returns the integer portion of the value of the 'sboTerm' attribute of this object. More...
 
string getSBOTermAsURL ()
 Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object. More...
 
string getSBOTermID ()
 Returns the string representation of the 'sboTerm' attribute of this object. More...
 
double getSize ()
 Get the size of this Compartment. More...
 
long getSpatialDimensions ()
 Get the number of spatial dimensions of this Compartment object. More...
 
double getSpatialDimensionsAsDouble ()
 Get the number of spatial dimensions of this Compartment object as a double. More...
 
new int getTypeCode ()
 Returns the libSBML type code for this SBML object. More...
 
string getUnits ()
 Get the units of this compartment's size. More...
 
long getVersion ()
 Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...
 
double getVolume ()
 Get the volume of this Compartment. More...
 
bool hasNonstandardIdentifierBeginningWith (string prefix)
 Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid'). More...
 
new bool hasRequiredAttributes ()
 Predicate returning true if all the required attributes for this Compartment object have been set. More...
 
bool hasRequiredElements ()
 Subclasses should override this method to write out their contained SBML objects as XML elements. 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 (string pkgName)
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPackageURIEnabled (string pkgURI)
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPkgEnabled (string pkgName)
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPkgURIEnabled (string pkgURI)
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isSetAnnotation ()
 Predicate returning true if this object's 'annotation' subelement exists and has content. More...
 
bool isSetCompartmentType ()
 Predicate returning true if this Compartment's 'compartmentType' attribute is set. More...
 
bool isSetConstant ()
 Predicate returning true if this Compartment's 'constant' attribute is set. More...
 
new bool isSetId ()
 Predicate returning true if this Compartment's 'id' attribute is set. More...
 
bool isSetMetaId ()
 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...
 
new bool isSetName ()
 Predicate returning true if this Compartment's 'name' attribute is set. More...
 
bool isSetNotes ()
 Predicate returning true if this object's 'notes' subelement exists and has content. More...
 
bool isSetOutside ()
 Predicate returning true if this Compartment's 'outside' attribute is set. More...
 
bool isSetSBOTerm ()
 Predicate returning true if this object's 'sboTerm' attribute is set. More...
 
bool isSetSize ()
 Predicate returning true if this Compartment's 'size' attribute is set. More...
 
bool isSetSpatialDimensions ()
 Predicate returning true if this Compartment's 'spatialDimensions' attribute is set. More...
 
bool isSetUnits ()
 Predicate returning true if this Compartment's 'units' attribute is set. More...
 
bool isSetVolume ()
 Predicate returning true if this Compartment's 'volume' attribute is set. More...
 
bool matchesRequiredSBMLNamespacesForAddition (SBase sb)
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (SBase sb)
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
void multiplyAssignmentsToSIdByFunction (string id, ASTNode function)
 If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More...
 
int prependStringToAllIdentifiers (string prefix)
 Add the given string to all identifiers in the object. More...
 
int removeFromParentAndDelete ()
 Removes itself from its parent. More...
 
int removeTopLevelAnnotationElement (string elementName, string elementURI)
 Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...
 
int removeTopLevelAnnotationElement (string elementName)
 Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...
 
void renameMetaIdRefs (string oldid, string newid)
 Renames all the MetaIdRef attributes on this element. More...
 
void renameSIdRefs (string oldid, string newid)
 Renames all the SIdRef attributes on this element, including any found in MathML. More...
 
void renameUnitSIdRefs (string oldid, string newid)
 Renames all the UnitSIdRef attributes on this element. More...
 
void replaceSIDWithFunction (string id, ASTNode function)
 If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More...
 
int replaceTopLevelAnnotationElement (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 (string annotation)
 Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More...
 
int setAnnotation (XMLNode annotation)
 Sets the value of the 'annotation' subelement of this SBML object. More...
 
int setAnnotation (string annotation)
 Sets the value of the 'annotation' subelement of this SBML object. More...
 
int setCompartmentType (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...
 
new int setId (string sid)
 Sets the value of the 'id' attribute of this Compartment. More...
 
int setMetaId (string metaid)
 Sets the value of the 'metaid' attribute of this object. More...
 
int setModelHistory (ModelHistory history)
 Sets the ModelHistory of this object. More...
 
new int setName (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 (XMLNode notes)
 Sets the value of the 'notes' subelement of this SBML object. More...
 
int setNotes (string notes, bool addXHTMLMarkup)
 Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes. More...
 
int setNotes (string notes)
 Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes. More...
 
int setOutside (string sid)
 Sets the 'outside' attribute of this Compartment. More...
 
void setSBMLNamespacesAndOwn (SBMLNamespaces sbmlns)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
int setSBOTerm (int value)
 Sets the value of the 'sboTerm' attribute. More...
 
int setSBOTerm (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 (long 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 (string sid)
 Sets the 'units' attribute of this Compartment. More...
 
int setVolume (double value)
 Sets the 'volume' attribute (or 'size' in SBML Level 2) of this Compartment. More...
 
string 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...
 
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...
 
new 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...
 
void writeExtensionElements (XMLOutputStream stream)
 Writes out contained SBML objects of package extensions (if any) as XML elements. More...
 

Static Public Member Functions

static bool operator!= (SBase lhs, SBase rhs)
 
static bool operator== (SBase lhs, SBase rhs)
 

Protected Attributes

bool swigCMemOwn
 

Constructor & Destructor Documentation

libsbmlcs.Compartment.Compartment ( long  level,
long  version 
)

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

Parameters
levela long integer, the SBML Level to assign to this Compartment
versiona long integer, 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.
libsbmlcs.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.
libsbmlcs.Compartment.Compartment ( 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

int libsbmlcs.SBase.addCVTerm ( CVTerm  term,
bool  newBag 
)
inherited

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

Parameters
termthe CVTerm to assign.
newBagif true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
int libsbmlcs.SBase.addCVTerm ( CVTerm  term)
inherited

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

Parameters
termthe CVTerm to assign.
newBagif true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
int libsbmlcs.SBase.appendAnnotation ( XMLNode  annotation)
inherited

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(XMLNode annotation) or SBase::setAnnotation(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(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.SBase.appendAnnotation ( string  annotation)
inherited

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(XMLNode annotation) or SBase::setAnnotation(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(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
unsetAnnotation()
int libsbmlcs.SBase.appendNotes ( 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(XMLNode notes)
setNotes(string notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.appendNotes ( 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(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.checkCompatibility ( SBase  arg0)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

string libsbmlcs.SBase.checkMathMLNamespace ( XMLToken  elem)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

new Compartment libsbmlcs.Compartment.clone ( )

Creates and returns a deep copy of this Compartment object.

Returns
a (deep) copy of this Compartment.
void libsbmlcs.SBase.connectToChild ( )
inherited

Sets this SBML object to child SBML objects (if any).

(Creates a child-parent relationship by the parent)

Subclasses must override this function if they define one ore more child elements. Basically, this function needs to be called in constructor, copy constructor, assignment operator.

void libsbmlcs.SBase.connectToParent ( SBase  parent)
inherited

Sets the parent SBML object of this SBML object.

(Creates a child-parent relationship by the child) This function is called when a child element is set/added/created by its parent element (e.g. by setXXX, addXXX, createXXX, and connectToChild functions of the parent element).

Parameters
parentthe SBML object to use
int libsbmlcs.SBase.disablePackage ( string  pkgURI,
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:
override void libsbmlcs.Compartment.Dispose ( )
virtual

Reimplemented from libsbmlcs.SBase.

void libsbmlcs.SBase.divideAssignmentsToSIdByFunction ( string  id,
ASTNode  function 
)
inherited

If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).

Note
This function does nothing itself—subclasses with ASTNode subelements must override this function.
int libsbmlcs.SBase.enablePackage ( string  pkgURI,
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:
void libsbmlcs.SBase.enablePackageInternal ( string  pkgURI,
string  pkgPrefix,
bool  flag 
)
inherited

Enables/Disables the given package with this element and child elements (if any).

(This is an internal implementation for enablePackage function)

Note
Subclasses in which one or more child elements are defined must override this function.
See Also
connectToChild()
override bool libsbmlcs.SBase.Equals ( Object  sb)
inherited
SBase libsbmlcs.SBase.getAncestorOfType ( int  type,
string  pkgName 
)
inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

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

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.
SBase libsbmlcs.SBase.getAncestorOfType ( int  type)
inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

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

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.
XMLNode libsbmlcs.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(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
string libsbmlcs.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(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
long libsbmlcs.SBase.getColumn ( )
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()
string libsbmlcs.Compartment.getCompartmentType ( )

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 libsbmlcs.Compartment.getConstant ( )

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 libsbmlcs.SBase.getCVTerm ( long  n)
inherited

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

Parameters
nlong the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
CVTermList libsbmlcs.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.
UnitDefinition libsbmlcs.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()
SBase libsbmlcs.SBase.getElementByMetaId ( string  metaid)
inherited

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.
SBase libsbmlcs.SBase.getElementBySId ( string  id)
inherited

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

Parameters
idstring representing the 'id' attribute value of the object to find.
Returns
pointer to the first element found with the given identifier.
SBase libsbmlcs.SBase.getElementFromPluginsByMetaId ( string  metaid)
inherited

Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
SBase libsbmlcs.SBase.getElementFromPluginsBySId ( string  id)
inherited

Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found.

Parameters
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.
new string libsbmlcs.Compartment.getElementName ( )

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

Returns
the name of this element, i.e., 'compartment'.
override int libsbmlcs.SBase.GetHashCode ( )
inherited
new string libsbmlcs.Compartment.getId ( )

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

Returns
the id of this Compartment.
long libsbmlcs.SBase.getLevel ( )
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()
long libsbmlcs.SBase.getLine ( )
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()
SBaseList libsbmlcs.SBase.getListOfAllElements ( )
inherited
SBaseList libsbmlcs.SBase.getListOfAllElementsFromPlugins ( )
inherited
string libsbmlcs.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.
See Also
isSetMetaId()
setMetaId(string metaid)
Model libsbmlcs.SBase.getModel ( )
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 libsbmlcs.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.
new string libsbmlcs.Compartment.getName ( )

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

Returns
the name of this Compartment.
XMLNamespaces libsbmlcs.SBase.getNamespaces ( )
inherited

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()
XMLNode libsbmlcs.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(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
string libsbmlcs.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(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
long libsbmlcs.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.
long libsbmlcs.SBase.getNumPlugins ( )
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.
string libsbmlcs.Compartment.getOutside ( )

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.
string libsbmlcs.SBase.getPackageName ( )
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.
long libsbmlcs.SBase.getPackageVersion ( )
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 libsbmlcs.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()
SBasePlugin libsbmlcs.SBase.getPlugin ( 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.
SBasePlugin libsbmlcs.SBase.getPlugin ( long  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.
int libsbmlcs.SBase.getResourceBiologicalQualifier ( 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 valueswhose names begin with BQB_ in the interface class libsbml.

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 valuewhose names begin with BQB_ in the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
int libsbmlcs.SBase.getResourceModelQualifier ( 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 valueswhose names begin with BQB_ in the interface class libsbml.

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 valuewhose names begin with BQB_ in the interface class libsbml.

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.
Note
The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
SBMLDocument libsbmlcs.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()
SBMLNamespaces libsbmlcs.SBase.getSBMLNamespaces ( )
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

int libsbmlcs.SBase.getSBOTerm ( )
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.
string libsbmlcs.SBase.getSBOTermAsURL ( )
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.
string libsbmlcs.SBase.getSBOTermID ( )
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 libsbmlcs.Compartment.getSize ( )

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()
long libsbmlcs.Compartment.getSpatialDimensions ( )

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 a long integereger
See Also
getSpatialDimensionsAsDouble()
double libsbmlcs.Compartment.getSpatialDimensionsAsDouble ( )

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()
new int libsbmlcs.Compartment.getTypeCode ( )

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml. The names of the type codes all begin with the characters SBML_.

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

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()
long libsbmlcs.SBase.getVersion ( )
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 libsbmlcs.Compartment.getVolume ( )

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 libsbmlcs.SBase.hasNonstandardIdentifierBeginningWith ( string  prefix)
inherited

Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid').

new bool libsbmlcs.Compartment.hasRequiredAttributes ( )

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 bool value indicating whether all the required attributes for this object have been defined.
bool libsbmlcs.SBase.hasRequiredElements ( )
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

bool libsbmlcs.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:

Returns
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
void libsbmlcs.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 libsbmlcs.SBase.isPackageEnabled ( string  pkgName)
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 libsbmlcs.SBase.isPackageURIEnabled ( string  pkgURI)
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 libsbmlcs.SBase.isPkgEnabled ( string  pkgName)
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 libsbmlcs.SBase.isPkgURIEnabled ( string  pkgURI)
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 libsbmlcs.SBase.isSetAnnotation ( )
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(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
bool libsbmlcs.Compartment.isSetCompartmentType ( )

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 libsbmlcs.Compartment.isSetConstant ( )

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

Returns
true if the 'constant' attribute of this Compartment is set, false otherwise.
new bool libsbmlcs.Compartment.isSetId ( )

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 libsbmlcs.SBase.isSetMetaId ( )
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(string metaid)
bool libsbmlcs.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.
new bool libsbmlcs.Compartment.isSetName ( )

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 libsbmlcs.SBase.isSetNotes ( )
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(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
bool libsbmlcs.Compartment.isSetOutside ( )

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 libsbmlcs.SBase.isSetSBOTerm ( )
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 libsbmlcs.Compartment.isSetSize ( )

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 libsbmlcs.Compartment.isSetSpatialDimensions ( )

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 libsbmlcs.Compartment.isSetUnits ( )

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 libsbmlcs.Compartment.isSetVolume ( )

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 libsbmlcs.SBase.matchesRequiredSBMLNamespacesForAddition ( 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
bool, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool libsbmlcs.SBase.matchesSBMLNamespaces ( 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
bool, true if this object's collection of namespaces is the same as sb's, false otherwise.
void libsbmlcs.SBase.multiplyAssignmentsToSIdByFunction ( string  id,
ASTNode  function 
)
inherited

If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).

static bool libsbmlcs.SBase.operator!= ( SBase  lhs,
SBase  rhs 
)
staticinherited
static bool libsbmlcs.SBase.operator== ( SBase  lhs,
SBase  rhs 
)
staticinherited
int libsbmlcs.SBase.prependStringToAllIdentifiers ( string  prefix)
inherited

Add the given string to all identifiers in the object.

If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.

int libsbmlcs.SBase.removeFromParentAndDelete ( )
inherited

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:
int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string  elementName,
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(XMLNode )
replaceTopLevelAnnotationElement(string)
int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string  elementName)
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(XMLNode )
replaceTopLevelAnnotationElement(string)
void libsbmlcs.SBase.renameMetaIdRefs ( string  oldid,
string  newid 
)
inherited

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
void libsbmlcs.Compartment.renameSIdRefs ( string  oldid,
string  newid 
)

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

void libsbmlcs.Compartment.renameUnitSIdRefs ( string  oldid,
string  newid 
)

Renames all the UnitSIdRef attributes on this element.

void libsbmlcs.SBase.replaceSIDWithFunction ( string  id,
ASTNode  function 
)
inherited

If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.

Note
This function does nothing itself—subclasses with ASTNode subelements must override this function.
int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( 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(string elementName, string elementURI)
replaceTopLevelAnnotationElement(string)
int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( 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(string elementName, string elementURI)
replaceTopLevelAnnotationElement(XMLNode)
int libsbmlcs.SBase.setAnnotation ( XMLNode  annotation)
inherited

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(XMLNode annotation) or SBase::appendAnnotation(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(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.SBase.setAnnotation ( string  annotation)
inherited

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(XMLNode annotation) or SBase::appendAnnotation(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(XMLNode annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.Compartment.setCompartmentType ( 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 libsbmlcs.Compartment.setConstant ( bool  value)

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

Parameters
valuea bool 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:
new int libsbmlcs.Compartment.setId ( string  sid)

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 libsbmlcs.SBase.setMetaId ( 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 libsbmlcs.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.
new int libsbmlcs.Compartment.setName ( string  name)

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 libsbmlcs.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 libsbmlcs.SBase.setNotes ( 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(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.setNotes ( string  notes,
bool  addXHTMLMarkup 
)
inherited

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

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

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

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

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa bool 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(XMLNode notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.setNotes ( string  notes)
inherited

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

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

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

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

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa bool 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(XMLNode notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.Compartment.setOutside ( 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.
void libsbmlcs.SBase.setSBMLNamespacesAndOwn ( SBMLNamespaces  sbmlns)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

int libsbmlcs.SBase.setSBOTerm ( int  value)
inherited

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(string sboid)
int libsbmlcs.SBase.setSBOTerm ( string  sboid)
inherited

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 libsbmlcs.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 libsbmlcs.Compartment.setSpatialDimensions ( long  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
valuea long integereger 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 libsbmlcs.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 libsbmlcs.Compartment.setUnits ( 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 libsbmlcs.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'.
string libsbmlcs.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 libsbmlcs.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(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
int libsbmlcs.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(string sid)
isSetCompartmentType()
int libsbmlcs.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 libsbmlcs.SBase.unsetId ( )
inherited

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:
int libsbmlcs.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 libsbmlcs.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.
new int libsbmlcs.Compartment.unsetName ( )

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:
int libsbmlcs.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(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.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 libsbmlcs.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 libsbmlcs.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 libsbmlcs.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 libsbmlcs.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 libsbmlcs.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'.
void libsbmlcs.SBase.writeExtensionElements ( XMLOutputStream  stream)
inherited

Writes out contained SBML objects of package extensions (if any) as XML elements.

Member Data Documentation

bool libsbmlcs.SBase.swigCMemOwn
protectedinherited