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libSBML C# API
5.18.0
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libSBML C# API
5.18.0
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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 objectelsewhere 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 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' is optional, and has a default value of true. In SBML Level 3, there is no default value for the 'constant' attribute, and it is required.
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 objectmust 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 objectin the enclosing Model, subject to the restrictions detailed in the following table:
Value ofspatialDimensions | sizeallowed? | unitsallowed? | 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 (in Level 2 Versions 1-3) or should (in Level 2 Version 4) 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 (in Level 2 Versions 1–3) or should (in Level 2 Version 4) be identical to the compartment's units (whether defined by the 'units' attribute or by taking the default value from the Model) divided by the default time units. (In other words, the units for the rate of change of compartment size are compartment size/time units.
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 objectif 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 objectsare not present in SBML Level 3 Core nor in SBML Level 1.
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 structuredoes 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 objectinstance. 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 objectdoes 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 a given Compartment's 'units' are left unset and the 'spatialDimensions' either has a value other than 1, 2, or 3 or is left unset itself (as it has no default value), 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. 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.
| 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 objectssetting the value of the compartment size should all have the same units as the unit associated with the compartment's size.
In a RateRule objectthat 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}.)
In SBML Level 1 and Level 2, Compartment has an optional attribute named 'outside', whose value can be the identifier of another Compartment objectdefined 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... | |
| new int | appendAnnotation (XMLNode annotation) |
Appends the given annotation to the 'annotation' subelement of this object. More... | |
| new 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) |
| string | checkMathMLNamespace (XMLToken elem) |
| new Compartment | clone () |
| Creates and returns a deep copy of this Compartment object. More... | |
| Compartment (long level, long version) | |
Creates a new Compartment object using the given SBML level and version values. More... | |
| Compartment (SBMLNamespaces sbmlns) | |
Creates a new Compartment object using the given SBMLNamespaces object sbmlns. More... | |
| Compartment (Compartment orig) | |
| Copy constructor. More... | |
| virtual void | connectToChild () |
| void | deleteDisabledPlugins (bool recursive) |
| Deletes all information stored in disabled plugins. More... | |
| void | deleteDisabledPlugins () |
| Deletes all information stored in disabled plugins. More... | |
| int | disablePackage (string pkgURI, string pkgPrefix) |
| Disables the given SBML Level 3 package on this object. More... | |
| override void | Dispose () |
| int | enablePackage (string pkgURI, string pkgPrefix, bool flag) |
| Enables or disables the given SBML Level 3 package on this object. More... | |
| override bool | Equals (Object sb) |
| SBase | getAncestorOfType (int type, string pkgName) |
| Returns the first ancestor object that has the given SBML type code from the given package. More... | |
| SBase | getAncestorOfType (int type) |
| Returns the first ancestor object that has the given SBML type code from the given package. 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 where 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 object. 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 object's designated size. More... | |
| SBasePlugin | getDisabledPlugin (long n) |
| Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| new 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... | |
| new 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... | |
| new string | getElementName () |
| Returns the XML element name of this object. More... | |
| override int | GetHashCode () |
| new string | getId () |
| Returns the value of the 'id' attribute of this Compartment. More... | |
| string | getIdAttribute () |
| Returns the value of the 'id' attribute of this SBML object. More... | |
| long | getLevel () |
| Returns the SBML Level of the SBMLDocument object containing this object. More... | |
| long | getLine () |
| Returns the line number where this object first appears in the XML representation of the SBML document. More... | |
| SBaseList | getListOfAllElements (ElementFilter filter) |
| SBaseList | getListOfAllElements () |
| SBaseList | getListOfAllElementsFromPlugins (ElementFilter filter) |
| SBaseList | getListOfAllElementsFromPlugins () |
| string | getMetaId () |
| Returns the value of the 'metaid' attribute of this SBML object. More... | |
| Model | getModel () |
| Returns the Model object for the SBML Document 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... | |
| new XMLNamespaces | getNamespaces () |
| Returns a list of the XML Namespaces declared on the SBML document owning this object. 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 | getNumDisabledPlugins () |
| Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. 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 object that is designated as being outside of this one. More... | |
| long | getPackageCoreVersion () |
| Returns the SBML Core Version within the SBML Level of the actual object. 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... | |
| string | getPrefix () |
| Returns the XML namespace prefix of this element. 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... | |
| int | getSBOTerm () |
| Returns the integer portion of the value of the 'sboTerm' attribute of this object. More... | |
| string | getSBOTermAsURL () |
| Returns the 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 object. 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 object's size. More... | |
| string | getURI () |
| Gets the namespace URI to which this element belongs to. 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 object. More... | |
| new bool | hasRequiredAttributes () |
Predicate returning true if all the required attributes for this Compartment object have been set. More... | |
| bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
| void | initDefaults () |
| Initializes the fields of this Compartment object to 'typical' default values. More... | |
| bool | isPackageEnabled (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 object's 'compartmentType' attribute is set. More... | |
| bool | isSetConstant () |
Predicate returning true if this Compartment object's 'constant' attribute is set. More... | |
| new bool | isSetId () |
Predicate returning true if this Compartment object's 'id' attribute is set. More... | |
| bool | isSetIdAttribute () |
Predicate returning true if this object'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 object'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 object'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 object's 'size' attribute is set. More... | |
| bool | isSetSpatialDimensions () |
Predicate returning true if this Compartment object's 'spatialDimensions' attribute is set. More... | |
| bool | isSetUnits () |
Predicate returning true if this Compartment object's 'units' attribute is set. More... | |
| bool | isSetUserData () |
| Predicate returning true or false depending on whether the user data of this element has been set. More... | |
| bool | isSetVolume () |
Predicate returning true if this Compartment object'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... | |
| new int | removeFromParentAndDelete () |
| Removes this object from its parent. More... | |
| int | removeTopLevelAnnotationElement (string elementName, string elementURI, bool removeEmpty) |
| 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, 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... | |
| new void | renameMetaIdRefs (string oldid, string newid) |
| Replaces all uses of a given meta identifier attribute value with another value. More... | |
| new void | renameSIdRefs (string oldid, string newid) |
Replaces all uses of a given SIdRef type attribute value with another value. More... | |
| new void | renameUnitSIdRefs (string oldid, string newid) |
Replaces all uses of a given UnitSIdRef type attribute value with another value. 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... | |
| new int | setAnnotation (XMLNode annotation) |
| Sets the value of the 'annotation' subelement of this SBML object. More... | |
| new 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 object. More... | |
| int | setConstant (bool value) |
| Sets the value of the 'constant' attribute of this Compartment object. More... | |
| new int | setId (string sid) |
| Sets the value of the 'id' attribute of this Compartment object. More... | |
| new int | setIdAttribute (string sid) |
| Sets the value of the 'id' attribute of this SBML object. More... | |
| int | setMetaId (string metaid) |
| Sets the value of the meta-identifier attribute of this SBML 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 object. 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 object. More... | |
| void | setSBMLNamespacesAndOwn (SBMLNamespaces disownedNs) |
| new int | setSBOTerm (int value) |
| Sets the value of the 'sboTerm' attribute. More... | |
| new 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 object. More... | |
| int | setSpatialDimensions (long value) |
| Sets the 'spatialDimensions' attribute of this Compartment object. More... | |
| int | setSpatialDimensions (double value) |
| Sets the 'spatialDimensions' attribute of this Compartment object as a double. More... | |
| int | setUnits (string sid) |
| Sets the 'units' attribute of this Compartment object. More... | |
| int | setVolume (double value) |
| Sets the 'volume' attribute (or 'size' in SBML Level 2) of this Compartment object. More... | |
| string | toSBML () |
| Returns a string consisting of a partial SBML corresponding to just this object. More... | |
| XMLNode | toXMLNode () |
| Returns this element as an XMLNode. 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 object. More... | |
| int | unsetConstant () |
| Unsets the value of the 'constant' attribute of this Compartment object. More... | |
| int | unsetCVTerms () |
| Clears the list of CVTerm objects attached to this SBML object. More... | |
| new int | unsetId () |
| Unsets the value of the 'id' attribute of this SBML object. More... | |
| int | unsetIdAttribute () |
| 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 object. 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 object. 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 object. More... | |
| int | unsetSpatialDimensions () |
| Unsets the value of the 'spatialDimensions' attribute of this Compartment object. More... | |
| int | unsetUnits () |
| Unsets the value of the 'units' attribute of this Compartment object. More... | |
| int | unsetUserData () |
| Unsets the user data of this element. More... | |
| int | unsetVolume () |
| Unsets the value of the 'volume' attribute of this Compartment object. More... | |
Static Public Member Functions | |
| static bool | operator!= (SBase lhs, SBase rhs) |
| static bool | operator== (SBase lhs, SBase rhs) |
Protected Attributes | |
| bool | swigCMemOwn |
| libsbmlcs.Compartment.Compartment | ( | long | level, |
| long | version | ||
| ) |
Creates a new Compartment object using the given SBML level and version values.
| level | a long integer, the SBML Level to assign to this Compartment. |
| version | a long integer, the SBML Version to assign to this Compartment. |
| SBMLConstructorException | Thrown if the given level and version combination are invalid or if this object is incompatible with the given level and version. |
| libsbmlcs.Compartment.Compartment | ( | SBMLNamespaces | sbmlns | ) |
Creates a new Compartment object using the given SBMLNamespaces object sbmlns.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
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 object 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().
| sbmlns | an SBMLNamespaces object. |
| SBMLConstructorException | Thrown if the given sbmlns is inconsistent or incompatible with this object. |
| libsbmlcs.Compartment.Compartment | ( | Compartment | orig | ) |
Copy constructor.
This creates a copy of a Compartment object.
| orig | the Compartment instance to copy. |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
| term | the CVTerm to assign. |
| newBag | if 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. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
| term | the CVTerm to assign. |
| newBag | if 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. |
create) for alternatives that do not lead to these issues.
|
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.
| annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object. |
|
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.
| annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object. |
|
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.
| notes | an XML node structure that is to appended to the content of the 'notes' subelement of this object. |
|
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.
| notes | an XML string that is to appended to the content of the 'notes' subelement of this object. |
|
inherited |
|
inherited |
| new Compartment libsbmlcs.Compartment.clone | ( | ) |
Creates and returns a deep copy of this Compartment object.
|
virtualinherited |
Reimplemented in libsbmlcs.Model, libsbmlcs.Reaction, libsbmlcs.Event, libsbmlcs.Layout, libsbmlcs.Submodel, libsbmlcs.UnitDefinition, libsbmlcs.KineticLaw, libsbmlcs.BoundingBox, libsbmlcs.SBaseRef, libsbmlcs.GraphicalObject, libsbmlcs.GeneralGlyph, libsbmlcs.ReactionGlyph, libsbmlcs.ListOf, libsbmlcs.SpeciesReferenceGlyph, libsbmlcs.ReferenceGlyph, libsbmlcs.CubicBezier, libsbmlcs.LineSegment, and libsbmlcs.Curve.
|
inherited |
Deletes all information stored in disabled plugins.
If the plugin is re-enabled later, it will then not have any previously-stored information.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
| recursive | if true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element. |
|
inherited |
Deletes all information stored in disabled plugins.
If the plugin is re-enabled later, it will then not have any previously-stored information.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
| recursive | if true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element. |
|
inherited |
Disables the given SBML Level 3 package on this object.
This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from an other SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
|
virtual |
Reimplemented from libsbmlcs.SBase.
|
inherited |
Enables or disables the given SBML Level 3 package on this object.
This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase::disablePackage(string pkgURI, string pkgPrefix).
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
| flag | whether to enable (true) or disable (false) the package. |
|
inherited |
|
inherited |
Returns the first ancestor object that has the given SBML type code from the given package.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. 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 from the given pkgName.
| type | the 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. |
null if no ancestor exists.pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return null.
|
inherited |
Returns the first ancestor object that has the given SBML type code from the given package.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. 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 from the given pkgName.
| type | the 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. |
null if no ancestor exists.pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return null.
|
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.
|
inherited |
Returns the content of the 'annotation' subelement of this object as a character string.
Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.
|
inherited |
Returns the column number where this object first appears in the XML representation of the SBML document.
0.| string libsbmlcs.Compartment.getCompartmentType | ( | ) |
Get the value of the 'compartmentType' attribute of this Compartment object.
| bool libsbmlcs.Compartment.getConstant | ( | ) |
Get the value of the 'constant' attribute of this Compartment object.
true if this Compartment object's size is flagged as being constant, false otherwise.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
| UnitDefinition libsbmlcs.Compartment.getDerivedUnitDefinition | ( | ) |
Constructs and returns a UnitDefinition that corresponds to the units of this Compartment object'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 objectbased 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, but this method returns an object , not a unit identifier. It does this by constructing an appropriate UnitDefinition object. 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 classfor comparing different UnitDefinition objects.
null if one cannot be constructed.null.
|
inherited |
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.
If no such plugin exists, null is returned.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
| n | the index of the disabled plug-in to return. |
n is invalid, null is returned.
|
inherited |
Returns the first child element it can find with a specific 'metaid' attribute value, or null if no such object is found.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
| metaid | string representing the 'metaid' attribute value of the object to find. |
|
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.
| id | string representing the 'id' attribute value of the object to find. |
| new string libsbmlcs.Compartment.getElementName | ( | ) |
Returns the XML element name of this object.
For Compartment, the XML element name is always 'compartment'.
|
inherited |
| new string libsbmlcs.Compartment.getId | ( | ) |
Returns the value of the 'id' attribute of this Compartment.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
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. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
|
inherited |
Returns the value of the 'id' attribute of this SBML object.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
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. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
|
inherited |
Returns the line number where this object first appears in the XML representation of the SBML document.
0.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Returns the value of the 'metaid' attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
null if none exist.| new string libsbmlcs.Compartment.getName | ( | ) |
Returns the value of the 'name' attribute of this Compartment object.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
|
inherited |
Returns a list of the XML Namespaces declared on the SBML document owning this object.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
null in certain very usual circumstances where a namespace is not set.
|
inherited |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
|
inherited |
Returns the content of the 'notes' subelement of this object as a string.
The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
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Returns the number of CVTerm objects in the annotations of this SBML object.
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Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
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Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
| string libsbmlcs.Compartment.getOutside | ( | ) |
Get the identifier, if any, of the Compartment object that is designated as being outside of this one.
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Returns the SBML Core Version within the SBML Level of the actual object.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
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Returns the name of the SBML Level 3 package in which this element is defined.
"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.
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Returns the Version of the SBML Level 3 package to which this element belongs to.
0 will be returned if this element belongs to the SBML Level 3 Core package.
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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.
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Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin('fbc') will return an FbcModelPlugin; calling Parameter::getPlugin('comp') will return CompSBasePlugin, etc.
If no such plugin exists, null is returned.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
| package | the name or URI of the package. |
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Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin('fbc') will return an FbcModelPlugin; calling Parameter::getPlugin('comp') will return CompSBasePlugin, etc.
If no such plugin exists, null is returned.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
| n | the index of the plug-in to return. |
n is invalid, null is returned.
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Returns the XML namespace prefix of this element.
This reports the XML namespace prefix chosen for this class of object in the current SBML document. This may be an empty string if the component has no explicit prefix (for instance, if it is a core SBML object placed in the default SBML namespace of the document). If it is not empty, then it corresponds to the XML namespace prefix used set the object, whatever that may be in a given SBML document.
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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.
| resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'. |
BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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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.
| resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'. |
BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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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.
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Returns the integer portion of the value of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 2, 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'. More details can be found in SBML specifications for Level 2 Version 2 and above.
-1 if the value is not set.
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Returns the URL representation of the 'sboTerm' attribute of this object.
This method returns the entire SBO identifier as a text string in the form http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.
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Returns the string representation of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 2, 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'. More details can be found in SBML specifications for Level 2 Version 2 and above.
| double libsbmlcs.Compartment.getSize | ( | ) |
Get the size of this Compartment object.
In SBML Level 1, compartments are always three-dimensional constructs and only have volumes, whereas in SBML Level 2 and higher, compartments may be other than three-dimensional, and therefore the 'volume' attribute is named 'size' in Level 2 and above. LibSBML provides both getSize() and getVolume()for easier support of different SBML Levels.
| long libsbmlcs.Compartment.getSpatialDimensions | ( | ) |
Get the number of spatial dimensions of this Compartment object.
double, whereas in Level 2, it is integer. To avoid backward compatibility issues, libSBML provides two separate methods for obtaining the value as either an integer or a type double, for models where it is relevant.| double libsbmlcs.Compartment.getSpatialDimensionsAsDouble | ( | ) |
Get the number of spatial dimensions of this Compartment object, as a double.
NaN if this model is not in SBML Level 3 format.double, whereas in Level 2, it is integer. To avoid backward compatibility issues, libSBML provides two separate methods for obtaining the value as either an integer or a type double, for models where it is relevant.| 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 integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml.Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the SBase::getPackageName() method on the object.
The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.
| string libsbmlcs.Compartment.getUnits | ( | ) |
Get the units of this Compartment object's size.
The value of an SBML compartment's 'units' attribute establishes the unit of measurement associated with the compartment's size.
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.
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Gets the namespace URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1'.
This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.
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inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
| double libsbmlcs.Compartment.getVolume | ( | ) |
Get the volume of this Compartment object.
In SBML Level 1, compartments are always three-dimensional constructs and only have volumes, whereas in SBML Level 2 and higher, compartments may be other than three-dimensional, and therefore the 'volume' attribute is named 'size' in Level 2 and above. LibSBML provides both getSize() and getVolume()for easier support of different SBML Levels.
1.0) and therefore methods such as isSetVolume()will always return true for a Level 1 model. 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.| new bool libsbmlcs.Compartment.hasRequiredAttributes | ( | ) |
Predicate returning true if all the required attributes for this Compartment object have been set.
The required attributes for a Compartment object are:
true if the required attributes have been set, false otherwise.
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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:
http://www.sbml.org/sbml/level1" http://www.sbml.org/sbml/level2" http://www.sbml.org/sbml/level2/version2" http://www.sbml.org/sbml/level2/version3" http://www.sbml.org/sbml/level2/version4" http://www.sbml.org/sbml/level2/version5" http://www.sbml.org/sbml/level3/version1/core" http://www.sbml.org/sbml/level3/version2/core" 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:
3 true 1.0 litre
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inherited |
Predicate returning true if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
| pkgName | the name of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.
| pkgURI | the URI of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
| pkgName | the name of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.
| pkgURI | the URI of the package. |
true if the given package is enabled within this object, false otherwise.
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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.
true if a 'annotation' subelement exists, false otherwise.| bool libsbmlcs.Compartment.isSetCompartmentType | ( | ) |
Predicate returning true if this Compartment object's 'compartmentType' attribute is set.
true if the 'compartmentType' attribute of this Compartment is set, false otherwise.| bool libsbmlcs.Compartment.isSetConstant | ( | ) |
Predicate returning true if this Compartment object's 'constant' attribute is set.
true if the 'constant' attribute of this Compartment object is set, false otherwise.| new bool libsbmlcs.Compartment.isSetId | ( | ) |
Predicate returning true if this Compartment object's 'id' attribute is set.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
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. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
true if the 'id' attribute of this SBML object is set, false otherwise.
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inherited |
Predicate returning true if this object's 'id' attribute is set.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
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. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
true if the 'id' attribute of this SBML object is set, false otherwise.
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inherited |
Predicate returning true if this object's 'metaid' attribute is set.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
true if the 'metaid' attribute of this SBML object is set, false otherwise.
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inherited |
Predicate returning true if this object has a ModelHistory object attached to it.
true if the ModelHistory of this object is set, false otherwise.| new bool libsbmlcs.Compartment.isSetName | ( | ) |
Predicate returning true if this Compartment object's 'name' attribute is set.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
true if the 'name' attribute of this SBML object is set, false otherwise.
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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.
true if a 'notes' subelement exists, false otherwise.| bool libsbmlcs.Compartment.isSetOutside | ( | ) |
Predicate returning true if this Compartment object's 'outside' attribute is set.
true if the 'outside' attribute of this Compartment object is set, false otherwise.
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inherited |
Predicate returning true if this object's 'sboTerm' attribute is set.
true if the 'sboTerm' attribute of this SBML object is set, false otherwise. | bool libsbmlcs.Compartment.isSetSize | ( | ) |
Predicate returning true if this Compartment object'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.
true if the 'size' attribute ('volume' in Level 2) of this Compartment object is set, false otherwise.| bool libsbmlcs.Compartment.isSetSpatialDimensions | ( | ) |
Predicate returning true if this Compartment object's 'spatialDimensions' attribute is set.
true if the 'spatialDimensions' attribute of this Compartment object is set, false otherwise.| bool libsbmlcs.Compartment.isSetUnits | ( | ) |
Predicate returning true if this Compartment object's 'units' attribute is set.
true if the 'units' attribute of this Compartment object is set, false otherwise.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.
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inherited |
Predicate returning true or false depending on whether the user data of this element has been set.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
true if this object's user data has been set, false otherwise. | bool libsbmlcs.Compartment.isSetVolume | ( | ) |
Predicate returning true if this Compartment object'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 the present method performs extra processing to take into account the difference in default values between SBML Levels 1 and 2.
true if the 'volume' attribute ('size' in Level 2 and above) of this Compartment object is set, false otherwise.1.0) and therefore methods such as isSetVolume()will always return true for a Level 1 model. 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.
|
inherited |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
| sb | an object to compare with respect to namespaces. |
true if this object's collection of namespaces is a subset of sb's, false otherwise.
|
inherited |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
| sb | an object to compare with respect to namespaces. |
true if this object's collection of namespaces is the same as sb's, false otherwise.
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inherited |
Removes this object from its parent.
If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
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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.
| elementName | a string representing the name of the top level annotation element that is to be removed. |
| elementURI | an optional string that is used to check both the name and URI of the top level element to be removed. |
| removeEmpty | if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default). |
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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.
| elementName | a string representing the name of the top level annotation element that is to be removed. |
| elementURI | an optional string that is used to check both the name and URI of the top level element to be removed. |
| removeEmpty | if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default). |
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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.
| elementName | a string representing the name of the top level annotation element that is to be removed. |
| elementURI | an optional string that is used to check both the name and URI of the top level element to be removed. |
| removeEmpty | if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default). |
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inherited |
Replaces all uses of a given meta identifier attribute value with another value.
In SBML, object 'meta' identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef.
This method works by looking at all meta-identifier 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.
| oldid | the old identifier. |
| newid | the new identifier. |
| new void libsbmlcs.Compartment.renameSIdRefs | ( | string | oldid, |
| string | newid | ||
| ) |
Replaces all uses of a given SIdRef type attribute value with another value.
In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier. |
| newid | the new identifier. |
| new void libsbmlcs.Compartment.renameUnitSIdRefs | ( | string | oldid, |
| string | newid | ||
| ) |
Replaces all uses of a given UnitSIdRef type attribute value with another value.
In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier. |
| newid | the new identifier. |
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inherited |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.
| annotation | XMLNode representing the replacement top level annotation. |
|
inherited |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.
| annotation | string representing the replacement top level 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).
| annotation | an XML structure that is to be used as the new content of the 'annotation' subelement of this object. |
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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).
| annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object. |
| int libsbmlcs.Compartment.setCompartmentType | ( | string | sid | ) |
Sets the 'compartmentType' attribute of this Compartment object.
| sid | the identifier of a CompartmentType object defined elsewhere in this Model. If the string is null, this method will return LIBSBML_INVALID_ATTRIBUTE_VALUE. |
| int libsbmlcs.Compartment.setConstant | ( | bool | value | ) |
Sets the value of the 'constant' attribute of this Compartment object.
| value | a boolean indicating whether the size/volume of this compartment should be considered constant (true) or variable (false). |
| new int libsbmlcs.Compartment.setId | ( | string | sid | ) |
Sets the value of the 'id' attribute of this Compartment object.
The string sid is copied.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
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. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
| sid | the string to use as the identifier of this Compartment object. If the string is null, this method will return LIBSBML_INVALID_ATTRIBUTE_VALUE. |
|
inherited |
Sets the value of the 'id' attribute of this SBML object.
The string sid is copied.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
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. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
| sid | the string to use as the identifier of this object. |
|
inherited |
Sets the value of the meta-identifier attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
The string metaid is copied.
| metaid | the identifier string to use as the value of the 'metaid' attribute. |
|
inherited |
Sets the ModelHistory of this object.
The content of history is copied, and this object's existing model history content is deleted.
| history | ModelHistory of this object. |
| new int libsbmlcs.Compartment.setName | ( | string | name | ) |
Sets the value of the 'name' attribute of this Compartment object.
The string in name is copied.
| name | the new name for the SBML object. |
|
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.
| xmlns | the namespaces to set. |
|
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.
| notes | an XML structure that is to be used as the content of the 'notes' subelement of this object. |
|
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.
| notes | an XML string that is to be used as the content of the 'notes' subelement of this object. |
| addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
|
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.
| notes | an XML string that is to be used as the content of the 'notes' subelement of this object. |
| addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
| int libsbmlcs.Compartment.setOutside | ( | string | sid | ) |
Sets the 'outside' attribute of this Compartment object.
| sid | the identifier of a compartment that encloses this one. If sid is null, then this method will return LIBSBML_INVALID_ATTRIBUTE_VALUE. |
|
inherited |
|
inherited |
Sets the value of the 'sboTerm' attribute.
Beginning with SBML Level 2 Version 2, 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'. More details can be found in SBML specifications for Level 2 Version 2 and above.
| value | the NNNNNNN integer portion of the SBO identifier. |
|
inherited |
Sets the value of the 'sboTerm' attribute by string.
Beginning with SBML Level 2 Version 2, 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'. More details can be found in SBML specifications for Level 2 Version 2 and above.
| int libsbmlcs.Compartment.setSize | ( | double | value | ) |
Sets the 'size' attribute (or 'volume' in SBML Level 1) of this Compartment object.
| value | a double representing the size of this compartment instance in whatever units are in effect for the compartment. |
| int libsbmlcs.Compartment.setSpatialDimensions | ( | long | value | ) |
Sets the 'spatialDimensions' attribute of this Compartment object.
| value | a long integereger indicating the number of dimensions of this compartment. |
| int libsbmlcs.Compartment.setSpatialDimensions | ( | double | value | ) |
Sets the 'spatialDimensions' attribute of this Compartment object as a double.
| value | a double indicating the number of dimensions of this compartment. |
| int libsbmlcs.Compartment.setUnits | ( | string | sid | ) |
Sets the 'units' attribute of this Compartment object.
| sid | the identifier of the defined units to use. If sid is null, then this method will return LIBSBML_INVALID_ATTRIBUTE_VALUE. |
| int libsbmlcs.Compartment.setVolume | ( | double | value | ) |
Sets the 'volume' attribute (or 'size' in SBML Level 2) of this Compartment object.
This method is identical to setSize() and is provided for compatibility between SBML Level 1 and higher Levels of SBML.
| value | a double representing the volume of this compartment instance in whatever units are in effect for the compartment. |
1.0) and therefore methods such as isSetVolume()will always return true for a Level 1 model. 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.
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
|
inherited |
|
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.
| int libsbmlcs.Compartment.unsetCompartmentType | ( | ) |
Unsets the value of the 'compartmentType' attribute of this Compartment object.
| int libsbmlcs.Compartment.unsetConstant | ( | ) |
Unsets the value of the 'constant' attribute of this Compartment object.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
|
inherited |
Unsets the value of the 'id' attribute of this SBML object.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
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. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
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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.
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Unsets the value of the 'metaid' attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
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Unsets the ModelHistory object attached to this object.
| new int libsbmlcs.Compartment.unsetName | ( | ) |
Unsets the value of the 'name' attribute of this Compartment object.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
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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.
| int libsbmlcs.Compartment.unsetOutside | ( | ) |
Unsets the value of the 'outside' attribute of this Compartment object.
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Unsets the value of the 'sboTerm' attribute of this SBML object.
| int libsbmlcs.Compartment.unsetSize | ( | ) |
Unsets the value of the 'size' attribute of this Compartment object.
In SBML Level 1, a compartment's volume has a default value (1.0) and therefore should always be set. Calling this method on a Level 1 model resets the value to 1.0 rather than actually unsetting it. In Level 2, a compartment's 'size' is optional with no default value, and unsetting it will result in the compartment having no defined size.
| int libsbmlcs.Compartment.unsetSpatialDimensions | ( | ) |
Unsets the value of the 'spatialDimensions' attribute of this Compartment object.
In SBML Levels prior to Level 3, compartments must always have a value for the number of dimensions. Consequently, calling this method on a model of SBML Level 1–2 will result in a return value of LIBSBML_UNEXPECTED_ATTRIBUTE
| int libsbmlcs.Compartment.unsetUnits | ( | ) |
Unsets the value of the 'units' attribute of this Compartment object.
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inherited |
Unsets the user data of this element.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
| int libsbmlcs.Compartment.unsetVolume | ( | ) |
Unsets the value of the 'volume' attribute of this Compartment object.
This method is identical to unsetSize(). Please refer to that method's documentation for more information about its behavior.
1.0) and therefore methods such as isSetVolume()will always return true for a Level 1 model. 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.
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protectedinherited |