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libSBML C# API
5.18.0
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libSBML C# API
5.18.0
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The SBaseRef class was introduced by the SBML Level 3 Hierarchical Model Composition (“comp”) package as the principle way by which submodel elements may be referenced. The SBaseRef class is usually found as the base class of a Port, Deletion, ReplacedElement, or ReplacedBy class, but may appear as an child of one of the above classes if the parent object references a Submodel.
An SBaseRef object must reference an element using exactly one of the optional attributes of the class. Subclasses of SBaseRef may define additional optional attributes that are legal ways to reference an element.
SBaseRef objects may reference elements that do not live in the Model parent of the SBaseRef object. However, the SBaseRef class itself does not provide a method of determining which Model or Submodel is being referenced. The subclasses of SBaseRef provide methods for this instead.
Once the Model to which the SBaseRef object is referencing has been established, there are four optional attributes defined in the SBaseRef class that are each methods of referencing an element:
PortSIdRef): As its name implies, this attribute is used to refer to a port identifier, in the case when the reference being constructed with the SBaseRef is intended to refer to a port on a submodel. The namespace of the PortSIdRef value is the set of identifiers of type PortSId defined in the submodel, not the parent model. SIdRef): As its name implies, this attribute is used to refer to a regular identifier (i.e., the value of an 'id' attribute on some other object), in the case when the reference being constructed with the SBaseRef is intended to refer to an object that does not have a port identifier. The namespace of the SIdRef value is the set of identifiers of type SId defined in the submodel, not the parent model. UnitSIdRef): This attribute is used to refer to the identifier of a UnitDefinition object. The namespace of the UnitSIdRef value is the set of unit identifiers defined in the submodel, not the parent model. (Note that even though this attribute is of type UnitSIdRef, the reserved unit identifiers that are defined by SBML Level 3 (see Section 3.1.10 of the core specification) are *not* permitted as values of 'unitRef'. Reserved unit identifiers may not be replaced or deleted.) IDREF): This attribute is used to refer to a 'metaid' attribute value on some other object, in the case when the reference being constructed with the SBaseRef is intended to refer to an object that does not have a port identifier. The namespace of the 'metaIdRef' value is the entire document in which the referenced model resides, but must refer to a subelement of the referenced model. Since meta identifiers are optional attributes of SBase, all SBML objects have the potential to have a meta identifier value.An SBaseRef object may have up to one subcomponent named 'sBaseRef', of type SBaseRef. This permits recursive structures to be constructed so that objects inside submodels can be referenced.
The form of such recursive references must be as follows. The highest-level SBaseRef object of such a chain (which will necessarily be an object of class Port, Deletion, ReplacedElement or ReplacedBy, because they are the only classes derived from the class SBaseRef) must refer to a Submodel object in the containing model. All child SBaseRef objects in the chain must refer to components inside the Model instance to which the Submodel refers.
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 void | clearReferencedElement () |
| Removes the saved referenced element, if it had been saved earlier. More... | |
| new SBase | clone () |
| Creates and returns a deep copy of this SBaseRef object. More... | |
| override void | connectToChild () |
| SBaseRef | createSBaseRef () |
| Creates a new, empty SBaseRef, adds it to this SBaseRef and returns the created SBaseRef. More... | |
| 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... | |
| 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... | |
| 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 the given metaid, or itself if it has the given metaid, 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 SBML object. More... | |
| override int | GetHashCode () |
| new string | getId () |
| Returns the value of the 'id' attribute of this SBML object, if it has one, or the 'variable' attribute of a Rule, or the 'symbol' attribute of an InitialAssignment. More... | |
| string | getIdAttribute () |
| Returns the value of the 'id' attribute of this SBML object. More... | |
| new string | getIdRef () |
| Returns the value of the 'idRef' attribute of this SBaseRef. 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... | |
| new string | getMetaIdRef () |
| Returns the value of the 'metaIdRef' attribute of this SBaseRef. 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 SBML 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... | |
| new int | getNumReferents () |
| Returns how many elements are being referred to by this SBaseRef. More... | |
| long | getPackageCoreVersion () |
| Returns the SBML Core Version within the SBML Level of the actual object. More... | |
| string | getPackageName () |
| Returns the package name of this plugin object. More... | |
| string | getPackageURI () |
| Returns the XML namespace (URI) of the package extension of this object. More... | |
| long | getPackageVersion () |
| Returns the package version of the package extension of this plugin object. 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... | |
| new string | getPortRef () |
| Returns the value of the 'portRef' attribute of this SBaseRef. More... | |
| string | getPrefix () |
| Returns the XML namespace prefix of this element. More... | |
| new SBase | getReferencedElement () |
| Returns the object pointed to by this element. More... | |
| new SBase | getReferencedElementFrom (Model model) |
| Examines the referenced Model for the referenced object, and returns it, if found. 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... | |
| SBaseRef | getSBaseRef () |
| Get the child sBaseRef of this sBaseRef. 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... | |
| new int | getTypeCode () |
| Returns the libSBML type code of this object instance. More... | |
| new string | getUnitRef () |
| Returns the value of the 'unitRef' attribute of this SBaseRef. 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... | |
| new bool | hasRequiredAttributes () |
Returns true if getNumReferents() is exactly 1. More... | |
| bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. 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... | |
| new bool | isSetId () |
Predicate returning true if a call to getId() returns a non-empty string. More... | |
| bool | isSetIdAttribute () |
Predicate returning true if this object's 'id' attribute is set. More... | |
| new bool | isSetIdRef () |
Predicate returning true or false depending on whether this SBaseRef's 'idRef' attribute has been set. More... | |
| bool | isSetMetaId () |
Predicate returning true if this object's 'metaid' attribute is set. More... | |
| new bool | isSetMetaIdRef () |
Predicate returning true or false depending on whether this SBaseRef's 'metaIdRef' attribute has been 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 object's 'name' attribute is set. More... | |
| bool | isSetNotes () |
Predicate returning true if this object's 'notes' subelement exists and has content. More... | |
| new bool | isSetPortRef () |
Predicate returning true or false depending on whether this SBaseRef's 'portRef' attribute has been set. More... | |
| bool | isSetSBaseRef () |
| Predicate for testing whether the sBaseRef for this SBaseRef is set. More... | |
| bool | isSetSBOTerm () |
Predicate returning true if this object's 'sboTerm' attribute is set. More... | |
| new bool | isSetUnitRef () |
Predicate returning true or false depending on whether this SBaseRef's 'unitRef' attribute has been set. More... | |
| bool | isSetUserData () |
| Predicate returning true or false depending on whether the user data of this element has been 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 | performDeletion () |
| DEPRECATED FUNCTION: DO NOT USE. More... | |
| new int | removeFromParentAndDelete () |
| Finds this SBaseRef's parent, which can either be a List or can be another SBaseRef, and tells it to remove this. 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 | saveReferencedElement () |
| Finds and stores the referenced object by finding the Model it needs to point to, calling 'saveReferencedElement' on its parent (which will also be a SBaseRef or one of its subclasses), and the storing the result. More... | |
| SBaseRef (long level, long version, long pkgVersion) | |
| Creates a new SBaseRef with the given level, version, and package version. More... | |
| SBaseRef (long level, long version) | |
| Creates a new SBaseRef with the given level, version, and package version. More... | |
| SBaseRef (long level) | |
| Creates a new SBaseRef with the given level, version, and package version. More... | |
| SBaseRef () | |
| Creates a new SBaseRef with the given level, version, and package version. More... | |
| SBaseRef (CompPkgNamespaces compns) | |
| Creates a new SBaseRef with the given CompPkgNamespaces object. More... | |
| SBaseRef (SBaseRef source) | |
| Copy constructor. 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... | |
| new int | setId (string sid) |
| Sets the value of the 'id' attribute of this SBML object. More... | |
| new int | setIdAttribute (string sid) |
| Sets the value of the 'id' attribute of this SBML object. More... | |
| new int | setIdRef (string id) |
| Sets the value of the 'idRef' attribute of this SBaseRef. More... | |
| int | setMetaId (string metaid) |
| Sets the value of the meta-identifier attribute of this SBML object. More... | |
| new int | setMetaIdRef (string id) |
| Sets the value of the 'metaIdRef' attribute of this SBaseRef. 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 SBML 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... | |
| new int | setPortRef (string id) |
| Sets the value of the 'portRef' attribute of this SBaseRef. More... | |
| int | setSBaseRef (SBaseRef sBaseRef) |
| Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance. 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... | |
| new int | setUnitRef (string id) |
| Sets the value of the 'unitRef' attribute of this SBaseRef. 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 | 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... | |
| new int | unsetIdRef () |
| Unsets the value of the 'idRef' attribute of this SBaseRef. More... | |
| int | unsetMetaId () |
| Unsets the value of the 'metaid' attribute of this SBML object. More... | |
| new int | unsetMetaIdRef () |
| Unsets the value of the 'metaIdRef' attribute of this SBaseRef. More... | |
| int | unsetModelHistory () |
| Unsets the ModelHistory object attached to this object. More... | |
| new int | unsetName () |
| Unsets the value of the 'name' attribute of this SBML object. More... | |
| int | unsetNotes () |
| Unsets the value of the 'notes' subelement of this SBML object. More... | |
| new int | unsetPortRef () |
| Unsets the value of the 'portRef' attribute of this SBaseRef. More... | |
| new int | unsetSBaseRef () |
| Unsets the child SBaseRef of this SBaseRef. More... | |
| int | unsetSBOTerm () |
| Unsets the value of the 'sboTerm' attribute of this SBML object. More... | |
| new int | unsetUnitRef () |
| Unsets the value of the 'unitRef' attribute of this SBaseRef. More... | |
| int | unsetUserData () |
| Unsets the user data of this element. More... | |
Static Public Member Functions | |
| static Model | getParentModel (SBase child) |
| Returns the Model object to which the referenced child object belongs. More... | |
| static bool | operator!= (SBase lhs, SBase rhs) |
| static bool | operator== (SBase lhs, SBase rhs) |
Protected Attributes | |
| bool | swigCMemOwn |
| libsbmlcs.SBaseRef.SBaseRef | ( | long | level, |
| long | version, | ||
| long | pkgVersion | ||
| ) |
Creates a new SBaseRef with the given level, version, and package version.
| level | the SBML Level. |
| version | the Version within the SBML Level. |
| pkgVersion | the version of the package. |
| libsbmlcs.SBaseRef.SBaseRef | ( | long | level, |
| long | version | ||
| ) |
Creates a new SBaseRef with the given level, version, and package version.
| level | the SBML Level. |
| version | the Version within the SBML Level. |
| pkgVersion | the version of the package. |
| libsbmlcs.SBaseRef.SBaseRef | ( | long | level | ) |
Creates a new SBaseRef with the given level, version, and package version.
| level | the SBML Level. |
| version | the Version within the SBML Level. |
| pkgVersion | the version of the package. |
| libsbmlcs.SBaseRef.SBaseRef | ( | ) |
Creates a new SBaseRef with the given level, version, and package version.
| level | the SBML Level. |
| version | the Version within the SBML Level. |
| pkgVersion | the version of the package. |
| libsbmlcs.SBaseRef.SBaseRef | ( | CompPkgNamespaces | compns | ) |
Creates a new SBaseRef with the given CompPkgNamespaces object.
The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.
| compns | the CompPkgNamespaces object. |
| libsbmlcs.SBaseRef.SBaseRef | ( | SBaseRef | source | ) |
Copy constructor.
| source | the 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 void libsbmlcs.SBaseRef.clearReferencedElement | ( | ) |
Removes the saved referenced element, if it had been saved earlier.
| new SBase libsbmlcs.SBaseRef.clone | ( | ) |
|
virtual |
Reimplemented from libsbmlcs.SBase.
| SBaseRef libsbmlcs.SBaseRef.createSBaseRef | ( | ) |
|
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.CompBase.
|
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.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
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.| new SBase libsbmlcs.SBaseRef.getElementByMetaId | ( | string | metaid | ) |
Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
| metaid | string representing the metaid of the object to find. |
metaid. | new SBase libsbmlcs.SBaseRef.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.
| id | string representing the id of the object to find. |
id. | new string libsbmlcs.SBaseRef.getElementName | ( | ) |
Returns the XML element name of this SBML object.
|
inherited |
|
inherited |
Returns the value of the 'id' attribute of this SBML object, if it has one, or the 'variable' attribute of a Rule, or the 'symbol' attribute of an InitialAssignment.
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.
| new string libsbmlcs.SBaseRef.getIdRef | ( | ) |
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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.
| new string libsbmlcs.SBaseRef.getMetaIdRef | ( | ) |
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
null if none exist.
|
inherited |
Returns the value of the 'name' attribute of this SBML 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.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
| new int libsbmlcs.SBaseRef.getNumReferents | ( | ) |
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inherited |
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.)
|
inherited |
Returns the package name of this plugin object.
|
inherited |
Returns the XML namespace (URI) of the package extension of this object.
|
inherited |
Returns the package version of the package extension of this plugin object.
Returns the Model object to which the referenced child object belongs.
|
inherited |
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
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. |
|
inherited |
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.| new string libsbmlcs.SBaseRef.getPortRef | ( | ) |
|
inherited |
Returns the XML namespace prefix of this element.
This reports the XML namespace prefix chosen for this class of object in the current SBML document. This may be an empty string if the component has no explicit prefix (for instance, if it is a core SBML object placed in the default SBML namespace of the document). If it is not empty, then it corresponds to the XML namespace prefix used set the object, whatever that may be in a given SBML document.
| new SBase libsbmlcs.SBaseRef.getReferencedElement | ( | ) |
Returns the object pointed to by this element.
If that element was previously found and set with 'saveReferencedElement', that element is returned; otherwise, 'saveReferencedElement' is called first, and the found element is returned.
Examines the referenced Model for the referenced object, and returns it, if found.
|
inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml. This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.
| 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.
|
inherited |
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml. This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.
| 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. | SBaseRef libsbmlcs.SBaseRef.getSBaseRef | ( | ) |
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inherited |
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
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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inherited |
Returns the URL representation of the 'sboTerm' attribute of this object.
This method returns the entire SBO identifier as a text string in the form http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.
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inherited |
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.
| new int libsbmlcs.SBaseRef.getTypeCode | ( | ) |
Returns the libSBML type code of this object instance.
LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. 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.
| new string libsbmlcs.SBaseRef.getUnitRef | ( | ) |
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inherited |
Gets the namespace URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1'.
This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.
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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.)
| new bool libsbmlcs.SBaseRef.hasRequiredAttributes | ( | ) |
Returns true if getNumReferents() is exactly 1.
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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.
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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.
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inherited |
Predicate returning true if a call to getId() returns a non-empty string.
For most objects, this function will return true if its 'id' attribute is set, and false if it is not, or if the object has no 'id' attribute at all. However, for an EventAssignment or a Rule, isSetId() checks whether the 'variable' attribute is set, and for an InitialAssignment, it checks whether the 'symbol' attribute is set. Because those elements will also have an 'id' attribute in SBML Level 3 Version 2 which isSetId() will not check, the function itself is deprecated, and it is recommended to use isSetIdAttribute() in all cases where one needs to know whether the 'id' attribute is set, and to use EventAssignment::isSetVariable(), Rule::isSetVariable() and InitialAssignment::isSetSymbol() when the status of the 'variable' or 'symbol' attributes need to be checked.
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.| new bool libsbmlcs.SBaseRef.isSetIdRef | ( | ) |
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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.| new bool libsbmlcs.SBaseRef.isSetMetaIdRef | ( | ) |
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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.
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inherited |
Predicate returning true if this 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.| new bool libsbmlcs.SBaseRef.isSetPortRef | ( | ) |
| bool libsbmlcs.SBaseRef.isSetSBaseRef | ( | ) |
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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. | new bool libsbmlcs.SBaseRef.isSetUnitRef | ( | ) |
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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.
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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.
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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. | new int libsbmlcs.SBaseRef.performDeletion | ( | ) |
DEPRECATED FUNCTION: DO NOT USE.
Deletes the referenced object, plus any other elements that element points to through ReplacedElement or ReplacedBy children. Instead of calling this function directly, use 'CompModelPlugin::instantiateSubmodels' instead, which deals with all the intricacies of replacements and deletions, and gives you access to the non-flattened hierarchical form of the model.
| new int libsbmlcs.SBaseRef.removeFromParentAndDelete | ( | ) |
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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.SBaseRef.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. |
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inherited |
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. |
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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 | string representing the replacement top level annotation. |
| new int libsbmlcs.SBaseRef.saveReferencedElement | ( | ) |
Finds and stores the referenced object by finding the Model it needs to point to, calling 'saveReferencedElement' on its parent (which will also be a SBaseRef or one of its subclasses), and the storing the result.
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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 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. |
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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. |
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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. |
| new int libsbmlcs.SBaseRef.setIdRef | ( | string | id | ) |
Sets the value of the 'idRef' attribute of this SBaseRef.
This method fails if the id is not a valid syntax for an SIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). A sBaseRef must use exactly one method to point to a submodel element.
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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. |
| new int libsbmlcs.SBaseRef.setMetaIdRef | ( | string | id | ) |
Sets the value of the 'metaIdRef' attribute of this SBaseRef.
This method fails if the id is not a valid syntax for an IDREF (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). An sBaseRef must use exactly one method to point to a submodel element.
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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. |
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inherited |
Sets the value of the 'name' attribute of this SBML object.
The string in name is copied.
| name | the new name for the SBML object. |
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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. |
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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. |
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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. |
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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. |
| new int libsbmlcs.SBaseRef.setPortRef | ( | string | id | ) |
Sets the value of the 'portRef' attribute of this SBaseRef.
Fails if the id is not a valid syntax for a PortSIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). An SBaseRef must use exactly one method to point to a submodel element.
| int libsbmlcs.SBaseRef.setSBaseRef | ( | SBaseRef | sBaseRef | ) |
Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance.
This method fails if the added sBaseRef does not match the level/version/package of the parent object or if the added sBaseRef cannot be copied.
| sBaseRef | the SBaseRef object instance to use. |
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inherited |
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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. |
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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.
| new int libsbmlcs.SBaseRef.setUnitRef | ( | string | id | ) |
Sets the value of the 'unitRef' attribute of this SBaseRef.
This method fails if the id is not a valid syntax for a UnitSIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). A sBaseRef must use exactly one method to point to a submodel element.
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inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
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inherited |
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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.
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inherited |
Clears the list of CVTerm objects attached to this SBML object.
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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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inherited |
Unsets the value of the 'id' attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier.
| new int libsbmlcs.SBaseRef.unsetIdRef | ( | ) |
Unsets the value of the 'idRef' attribute of this SBaseRef.
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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inherited |
Unsets the value of the 'metaid' attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
| new int libsbmlcs.SBaseRef.unsetMetaIdRef | ( | ) |
Unsets the value of the 'metaIdRef' attribute of this SBaseRef.
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inherited |
Unsets the ModelHistory object attached to this object.
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inherited |
Unsets the value of the 'name' attribute of this SBML 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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inherited |
Unsets the value of the 'notes' subelement of this SBML object.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
| new int libsbmlcs.SBaseRef.unsetPortRef | ( | ) |
Unsets the value of the 'portRef' attribute of this SBaseRef.
| new int libsbmlcs.SBaseRef.unsetSBaseRef | ( | ) |
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inherited |
Unsets the value of the 'sboTerm' attribute of this SBML object.
| new int libsbmlcs.SBaseRef.unsetUnitRef | ( | ) |
Unsets the value of the 'unitRef' attribute of this SBaseRef.
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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.
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protectedinherited |