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libSBML C++ API
5.20.4
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The ReplacedElement class was introduced by the SBML Level 3 Hierarchical Model Composition (“comp”) package to allow submodel elements to be replaced, but still allow references to those elements to be valid. A ReplacedElement object is essentially a pointer to a submodel object that should be considered 'replaced'. The object holding the ReplacedElement instance is the one doing the replacing; the object pointed to by the ReplacedElement object is the object being replaced.
A replacement implies that dependencies involving the replaced object must be updated: all references to the replaced object elsewhere in the model are taken to refer to the replacement object instead. For example, if one species replaces another, then any reference to the original species in mathematical formulas, or lists of reactants or products or modifiers in reactions, or initial assignments, or any other SBML construct, are taken to refer to the replacement species, with its value possibly modified by either this object's "conversionFactor" attribute or the relevant submodel's conversion factors. Moreover, any annotations that refer to the replaced species' "metaid" value must be made to refer to the replacement species' "metaid" value instead; and anything else that referred either to an object identifier (i.e., attributes such as the "id" attribute whose types inherit from the SId primitive data type) or the meta identifier (i.e., the "metaid" attribute or any other attribute that inherits from the ID primitive data type) must be made to refer to the replacement species object instead.
It is worth noting that local parameters (inside Reaction objects) pose an interesting edge case for these rules. In order to determine which element is pointed to by a <cn> element within the <math> element of a KineticLaw object, it is necessary to examine the local parameters of that kinetic law's parent Reaction object. Whether the <cn> element is considered to point to something new, then, depends on whether it pointed to the local parameter and whether that local parameter was replaced, even if the text of the element matched the SId value of another element in the model. Note that local parameters may only effectively be replaced by global parameters, since references to its SId are only valid from within the Reaction element to which it belongs.
When referencing an element within the Submodel pointed to by the "submodelRef" attribute (defined in libSBML in the Replacing class), any of the four attributes inherited from SBaseRef for the purpose may be used (portRef, idRef, unitRef, or metaIdRef), or a new optional attribute "deletion" may be used. This attribute must be the identifier of a Deletion object in the parent Model of the ReplacedElement (i.e., the value of some Deletion object's "id" attribute). When "deletion" is set, it means the ReplacedElement object is actually an annotation to indicate that the replacement object replaces something deleted from a submodel. The use of the "deletion" attribute overrides the use of the attributes inherited from SBaseRef: instead of using, e.g., "portRef" or "idRef", the ReplacedElement instance sets "deletion" to the identifier of the Deletion object. In addition, the referenced Deletion must be a child of the Submodel referenced by the "submodelRef" attribute.
The use of ReplacedElement objects to refer to deletions has no effect on the composition of models or the mathematical properties of the result. It serves instead to help record the decision-making process that lead to a given model. It can be particularly useful for visualization purposes, as well as to serve as scaffolding where other types of annotations can be added using the normal Annotation subcomponents available on all SBase objects in SBML.
As with the Submodel class, it may be that the units of the replaced element may not match the units of the replacement element. In this case, the optional "conversionFactor" attribute may be used. This attribute, if present, defines how to transform or rescale the replaced object's value so that it is appropriate for the new contexts in which the object appears. This attribute takes a value of type SIdRef, and the value must refer to a Parameter object instance defined in the model. This parameter then acts as a conversion factor.
The value of the conversion factor should be defined such that a single unit of the replaced element multiplied by the conversion factor should equal a single unit of the replacement element, and the units of the conversion factor should be commensurate with that transformation. The referenced Parameter may be non-constant, particularly if a Species is replaced by a Species with a different "hasOnlySubstanceUnits" attribute value, thus changing amount to concentration, or visa versa.
Public Member Functions | |
| int | addCVTerm (CVTerm *term, bool newBag=false) |
| Adds a copy of the given CVTerm object to this SBML object. More... | |
| int | addModifiedDate (Date *date) |
| Adds a modified date to the ModelHistory of this object. More... | |
| virtual int | appendAnnotation (const std::string &annotation) |
Appends the given annotation to the "annotation" subelement of this object. More... | |
| virtual int | appendAnnotation (const XMLNode *annotation) |
Appends the given annotation to the "annotation" subelement of this object. More... | |
| int | appendNotes (const std::string ¬es) |
Appends the given notes to the "notes" subelement of this object. More... | |
| int | appendNotes (const XMLNode *notes) |
Appends the given notes to the "notes" subelement of this object. More... | |
| virtual void | clearReferencedElement () |
| Removes the saved referenced element, if it had been saved earlier. More... | |
| virtual ReplacedElement * | clone () const |
| Creates and returns a deep copy of this ReplacedElement object. More... | |
| SBaseRef * | createSBaseRef () |
| Creates a new, empty SBaseRef, adds it to this SBaseRef and returns the created SBaseRef. More... | |
| void | deleteDisabledPlugins (bool recursive=true) |
| Deletes all information stored in disabled plugins. More... | |
| int | disablePackage (const std::string &pkgURI, const std::string &pkgPrefix) |
| Disables the given SBML Level 3 package on this object. More... | |
| int | enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag) |
| Enables or disables the given SBML Level 3 package on this object. More... | |
| virtual List * | getAllElements (ElementFilter *filter=NULL) |
| Returns a List of all child SBase* objects, including those nested to an arbitrary depth. More... | |
| virtual List * | getAllElementsFromPlugins (ElementFilter *filter=NULL) |
| Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
| SBase * | getAncestorOfType (int type, const std::string &pkgName="core") |
| Returns the first ancestor object that has the given SBML type code from the given package. More... | |
| const SBase * | getAncestorOfType (int type, const std::string pkgName="core") const |
| Returns the first ancestor object that has the given SBML type code from the given package. More... | |
| XMLNode * | getAnnotation () |
| Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
| XMLNode * | getAnnotation () const |
| Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
| std::string | getAnnotationString () |
| Returns the content of the "annotation" subelement of this object as a character string. More... | |
| std::string | getAnnotationString () const |
| Returns the content of the "annotation" subelement of this object as a character string. More... | |
| unsigned int | getColumn () const |
| Returns the column number where this object first appears in the XML representation of the SBML document. More... | |
| virtual const std::string & | getConversionFactor () const |
| Returns the value of the "conversionFactor" attribute of this ReplacedElement. More... | |
| Date * | getCreatedDate () |
| Returns the "creation date" portion of the ModelHistory of this object. More... | |
| Date * | getCreatedDate () const |
| Returns the "creation date" portion of the ModelHistory of this object. More... | |
| CVTerm * | getCVTerm (unsigned int n) |
| Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
| List * | getCVTerms () |
| Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
| List * | getCVTerms () const |
| Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
| virtual const std::string & | getDeletion () const |
| Returns the value of the "deletion" attribute of this ReplacedElement. More... | |
| SBasePlugin * | getDisabledPlugin (unsigned int n) |
| Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| const SBasePlugin * | getDisabledPlugin (unsigned int n) const |
| Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| virtual SBase * | getElementByMetaId (const std::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... | |
| const SBase * | getElementByMetaId (const std::string &metaid) const |
Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found. More... | |
| virtual SBase * | getElementBySId (const std::string &id) |
Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More... | |
| virtual const SBase * | getElementBySId (const std::string &id) const |
Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More... | |
| virtual const std::string & | getElementName () const |
| Returns the XML element name of this SBML object. More... | |
| virtual const std::string & | getId () const |
| 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... | |
| const std::string & | getIdAttribute () const |
| Returns the value of the "id" attribute of this SBML object. More... | |
| virtual const std::string & | getIdRef () const |
| Returns the value of the "idRef" attribute of this SBaseRef. More... | |
| unsigned int | getLevel () const |
| Returns the SBML Level of the SBMLDocument object containing this object. More... | |
| unsigned int | getLine () const |
| Returns the line number where this object first appears in the XML representation of the SBML document. More... | |
| std::string & | getMetaId () |
| Returns the value of the "metaid" attribute of this SBML object. More... | |
| const std::string & | getMetaId () const |
| Returns the value of the "metaid" attribute of this SBML object. More... | |
| virtual const std::string & | getMetaIdRef () const |
| Returns the value of the "metaIdRef" attribute of this SBaseRef. More... | |
| const Model * | getModel () const |
| 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... | |
| ModelHistory * | getModelHistory () const |
| Returns the ModelHistory object, if any, attached to this object. More... | |
| Date * | getModifiedDate (unsigned int n) |
| Get the nth Date object in the list of "modified date" values stored in the ModelHistory of this object. More... | |
| virtual const std::string & | getName () const |
| Returns the value of the "name" attribute of this SBML object. More... | |
| virtual XMLNamespaces * | getNamespaces () const |
| 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... | |
| XMLNode * | getNotes () const |
| Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More... | |
| std::string | getNotesString () |
| Returns the content of the "notes" subelement of this object as a string. More... | |
| std::string | getNotesString () const |
| Returns the content of the "notes" subelement of this object as a string. More... | |
| unsigned int | getNumCVTerms () const |
| Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
| unsigned int | getNumDisabledPlugins () const |
| Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More... | |
| unsigned int | getNumModifiedDates () |
| Get the number of Date objects in the ModelHistory of this Iobject's list of "modified dates". More... | |
| unsigned int | getNumPlugins () const |
| Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
| virtual int | getNumReferents () const |
| Returns how many elements are being referred to by this ReplacedElement. More... | |
| unsigned int | getPackageCoreVersion () const |
| Returns the SBML Core Version within the SBML Level of the actual object. More... | |
| const std::string & | getPackageName () const |
| Returns the package name of this plugin object. More... | |
| const std::string & | getPackageURI () const |
| Returns the XML namespace (URI) of the package extension of this object. More... | |
| unsigned int | getPackageVersion () const |
| Returns the package version of the package extension of this plugin object. More... | |
| SBase * | getParentSBMLObject () |
| Returns the parent SBML object containing this object. More... | |
| const SBase * | getParentSBMLObject () const |
| Returns the parent SBML object containing this object. More... | |
| SBasePlugin * | getPlugin (const std::string &package) |
| Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
| const SBasePlugin * | getPlugin (const std::string &package) const |
| Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
| SBasePlugin * | getPlugin (unsigned int n) |
| Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| const SBasePlugin * | getPlugin (unsigned int n) const |
| Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| virtual const std::string & | getPortRef () const |
| Returns the value of the "portRef" attribute of this SBaseRef. More... | |
| std::string | getPrefix () const |
| Returns the XML namespace prefix of this element. More... | |
| virtual SBase * | getReferencedElement () |
| Returns the object pointed to by this element. More... | |
| virtual SBase * | getReferencedElementFrom (Model *model) |
| Finds the SBase object this ReplacedElement object points to, if any. More... | |
| BiolQualifierType_t | getResourceBiologicalQualifier (std::string resource) const |
| Returns the MIRIAM biological qualifier associated with the given resource. More... | |
| ModelQualifierType_t | getResourceModelQualifier (std::string resource) const |
| Returns the MIRIAM model qualifier associated with the given resource. More... | |
| SBaseRef * | getSBaseRef () |
| Get the child sBaseRef of this SBaseRef. More... | |
| const SBaseRef * | getSBaseRef () const |
| Get the child sBaseRef of this sBaseRef. More... | |
| SBMLDocument * | getSBMLDocument () |
| Returns the SBMLDocument object containing this object instance. More... | |
| const SBMLDocument * | getSBMLDocument () const |
| Returns the SBMLDocument object containing this object instance. More... | |
| int | getSBOTerm () const |
| Returns the integer portion of the value of the "sboTerm" attribute of this object. More... | |
| std::string | getSBOTermAsURL () const |
| Returns the URL representation of the "sboTerm" attribute of this object. More... | |
| std::string | getSBOTermID () const |
| Returns the string representation of the "sboTerm" attribute of this object. More... | |
| virtual const std::string & | getSubmodelRef () const |
| Returns the value of the "submodelRef" attribute of this SBaseRef. More... | |
| virtual int | getTypeCode () const |
| Returns the libSBML type code of this object instance. More... | |
| virtual const std::string & | getUnitRef () const |
| Returns the value of the "unitRef" attribute of this SBaseRef. More... | |
| std::string | getURI () const |
| Returns the namespace URI to which this element belongs to. More... | |
| void * | getUserData () const |
| Returns the user data that has been previously set via setUserData(). More... | |
| unsigned int | getVersion () const |
| Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
| virtual bool | hasRequiredAttributes () const |
Returns true if getNumReferents() is exactly 1 and if the submodelRef is set. More... | |
| bool | isPackageEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
| bool | isPackageURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| bool | isPkgEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
| bool | isPkgURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| bool | isSetAnnotation () const |
Predicate returning true if this object's "annotation" subelement exists and has content. More... | |
| virtual bool | isSetConversionFactor () const |
Predicate returning true or false depending on whether this ReplacedElement's "conversionFactor" attribute has been set. More... | |
| bool | isSetCreatedDate () const |
Predicate returning true if this object has a ModelHistory object attached to it and the created date is set. More... | |
| virtual bool | isSetDeletion () const |
Predicate returning true or false depending on whether this SBaseRef's "deletion" attribute has been set. More... | |
| virtual bool | isSetId () const |
Predicate returning true if a call to getId() returns a non-empty string. More... | |
| bool | isSetIdAttribute () const |
Predicate returning true if this object's "id" attribute is set. More... | |
| virtual bool | isSetIdRef () const |
Predicate returning true or false depending on whether this SBaseRef's "idRef" attribute has been set. More... | |
| bool | isSetMetaId () const |
Predicate returning true if this object's "metaid" attribute is set. More... | |
| virtual bool | isSetMetaIdRef () const |
Predicate returning true or false depending on whether this SBaseRef's "metaIdRef" attribute has been set. More... | |
| bool | isSetModelHistory () const |
Predicate returning true if this object has a ModelHistory object attached to it. More... | |
| bool | isSetModifiedDate () const |
Predicate returning true or false depending on whether the ModelHistory's "modified date" of this object is set. More... | |
| virtual bool | isSetName () const |
Predicate returning true if this object's "name" attribute is set. More... | |
| bool | isSetNotes () const |
Predicate returning true if this object's "notes" subelement exists and has content. More... | |
| virtual bool | isSetPortRef () const |
Predicate returning true or false depending on whether this SBaseRef's "portRef" attribute has been set. More... | |
| bool | isSetSBaseRef () const |
| Predicate for testing whether the sBaseRef for this SBaseRef is set. More... | |
| bool | isSetSBOTerm () const |
Predicate returning true if this object's "sboTerm" attribute is set. More... | |
| virtual bool | isSetSubmodelRef () const |
Predicate returning true or false depending on whether this SBaseRef's "submodelRef" attribute has been set. More... | |
| virtual bool | isSetUnitRef () const |
Predicate returning true or false depending on whether this SBaseRef's "unitRef" attribute has been set. More... | |
| bool | isSetUserData () const |
| Predicate returning true or false depending on whether the user data of this element has been set. More... | |
| bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
| bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
| bool | matchesSBMLNamespaces (const SBase *sb) |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
| bool | matchesSBMLNamespaces (const SBase *sb) const |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
| ReplacedElement & | operator= (const ReplacedElement &source) |
| Assignment operator. More... | |
| virtual int | performDeletion () |
| DEPRECATED FUNCTION: DO NOT USE. More... | |
| virtual int | performReplacement () |
| DEPRECATED FUNCTION: DO NOT USE. More... | |
| void | read (const XMLNode &node, XMLErrorSeverityOverride_t flag=LIBSBML_OVERRIDE_DISABLED) |
| Reads (initializes) this SBML object by reading from the given XMLNode. More... | |
| virtual 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 (const std::string &elementName, const std::string elementURI="", bool removeEmpty=true) |
| Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More... | |
| virtual void | renameMetaIdRefs (const std::string &oldid, const std::string &newid) |
| virtual void | renameSIdRefs (const std::string &oldid, const std::string &newid) |
| virtual void | renameUnitSIdRefs (const std::string &oldid, const std::string &newid) |
| ReplacedElement (CompPkgNamespaces *compns) | |
| Creates a new ReplacedElement with the given CompPkgNamespaces object. More... | |
| ReplacedElement (const ReplacedElement &source) | |
| Copy constructor. More... | |
| ReplacedElement (unsigned int level=CompExtension::getDefaultLevel(), unsigned int version=CompExtension::getDefaultVersion(), unsigned int pkgVersion=CompExtension::getDefaultPackageVersion()) | |
| Creates a new ReplacedElement with the given level, version, and package version. More... | |
| int | replaceTopLevelAnnotationElement (const std::string &annotation) |
| Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
| int | replaceTopLevelAnnotationElement (const XMLNode *annotation) |
| Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
| virtual int | saveReferencedElement () |
| Finds and stores the referenced object. More... | |
| virtual int | setAnnotation (const std::string &annotation) |
| Sets the value of the "annotation" subelement of this SBML object. More... | |
| virtual int | setAnnotation (const XMLNode *annotation) |
| Sets the value of the "annotation" subelement of this SBML object. More... | |
| virtual int | setConversionFactor (const std::string &id) |
| Sets the value of the "conversionFactor" attribute of this ReplacedElement. More... | |
| int | setCreatedDate (Date *date) |
| Sets the creation date of the ModelHistory of this object. More... | |
| virtual int | setDeletion (const std::string &id) |
| Sets the value of the "deletion" attribute of this ReplacedElement. More... | |
| virtual int | setId (const std::string &sid) |
| Sets the value of the "id" attribute of this SBML object. More... | |
| virtual int | setIdAttribute (const std::string &sid) |
| Sets the value of the "id" attribute of this SBML object. More... | |
| virtual int | setIdRef (const std::string &id) |
| Sets the value of the "idRef" attribute of this SBaseRef. More... | |
| int | setMetaId (const std::string &metaid) |
| Sets the value of the meta-identifier attribute of this SBML object. More... | |
| virtual int | setMetaIdRef (const std::string &id) |
| Sets the value of the "metaIdRef" attribute of this SBaseRef. More... | |
| int | setModelHistory (ModelHistory *history) |
| Sets the ModelHistory of this object. More... | |
| virtual int | setName (const std::string &name) |
| Sets the value of the "name" attribute of this SBML object. More... | |
| int | setNamespaces (XMLNamespaces *xmlns) |
| Sets the namespaces relevant of this SBML object. More... | |
| int | setNotes (const std::string ¬es, bool addXHTMLMarkup=false) |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes. More... | |
| int | setNotes (const XMLNode *notes) |
| Sets the value of the "notes" subelement of this SBML object. More... | |
| virtual int | setPortRef (const std::string &id) |
| Sets the value of the "portRef" attribute of this SBaseRef. More... | |
| int | setSBaseRef (const SBaseRef *sBaseRef) |
| Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance. More... | |
| virtual int | setSBOTerm (const std::string &sboid) |
| Sets the value of the "sboTerm" attribute by string. More... | |
| virtual int | setSBOTerm (int value) |
| Sets the value of the "sboTerm" attribute. More... | |
| virtual int | setSubmodelRef (const std::string &id) |
| Sets the value of the "submodelRef" attribute of this SBaseRef. More... | |
| virtual int | setUnitRef (const std::string &id) |
| Sets the value of the "unitRef" attribute of this SBaseRef. More... | |
| int | setUserData (void *userData) |
| Sets the user data of this element. More... | |
| char * | toSBML () |
| Returns a string consisting of a partial SBML corresponding to just this object. More... | |
| XMLNode * | toXMLNode () |
| Returns this element as an XMLNode. More... | |
| int | unsetAnnotation () |
| Unsets the value of the "annotation" subelement of this SBML object. More... | |
| virtual int | unsetConversionFactor () |
| Unsets the value of the "conversionFactor" attribute of this ReplacedElement. More... | |
| int | unsetCreatedDate () |
| Unsets the created date of the ModelHistory object attached to this object. More... | |
| int | unsetCVTerms () |
| Clears the list of CVTerm objects attached to this SBML object. More... | |
| virtual int | unsetDeletion () |
| Unsets the value of the "deletion" attribute of this ReplacedElement. More... | |
| virtual 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... | |
| virtual 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... | |
| virtual int | unsetMetaIdRef () |
| Unsets the value of the "metaIdRef" attribute of this SBaseRef. More... | |
| int | unsetModelHistory () |
| Unsets the ModelHistory object attached to this object. More... | |
| int | unsetModifiedDates () |
| Unsets the modified dates of the ModelHistory object attached to this object. More... | |
| virtual 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... | |
| virtual int | unsetPortRef () |
| Unsets the value of the "portRef" attribute of this SBaseRef. More... | |
| virtual int | unsetSBaseRef () |
| Unsets the child SBaseRef of this SBaseRef. More... | |
| int | unsetSBOTerm () |
| Unsets the value of the "sboTerm" attribute of this SBML object. More... | |
| virtual int | unsetSubmodelRef () |
| Unsets the value of the "SubmodelRef" attribute of this SBaseRef. More... | |
| virtual int | unsetUnitRef () |
| Unsets the value of the "unitRef" attribute of this SBaseRef. More... | |
| int | unsetUserData () |
| Unsets the user data of this element. More... | |
| virtual | ~ReplacedElement () |
| Destructor. More... | |
Static Public Member Functions | |
| static Model * | getParentModel (SBase *child) |
| Returns the Model object to which the referenced child object belongs. More... | |
Protected Member Functions | |
| bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
| virtual void | logEmptyString (const std::string &attribute, const std::string &element) |
| Helper to log a common type of error. More... | |
| virtual void | logInvalidId (const std::string &attribute, const std::string &wrongattribute, const std::string object="") |
| Helper to log a common type of error. More... | |
| virtual void | logMissingAttribute (const std::string &attribute, const std::string &element) |
| Helper to log a common type of error. More... | |
| virtual void | logUnknownAttribute (const std::string &attribute, const std::string &element) |
| Helper to log a common type of error. More... | |
| virtual void | logUnknownElement (const std::string &element) |
| Helper to log a common type of error for elements. More... | |
| virtual int | performReplacementAndCollect (std::set< SBase * > *removed, std::set< SBase * > *toremove) |
| Updates all IDs and references to those IDs, as well as performing all necessary conversions based on the conversion factors. More... | |
| virtual void | readAttributes (const XMLAttributes &attributes, const ExpectedAttributes &expectedAttributes, bool hasCompIdName, bool idRequired, CompSBMLErrorCode_t errcode) |
| Subclasses should override this method to read values from the given XMLAttributes set into their specific fields. More... | |
| virtual void | setElementText (const std::string &text) |
| When overridden allows SBase elements to use the text included in between the elements tags. More... | |
| virtual void | writeAttributes (XMLOutputStream &stream) const |
| Subclasses should override this method to write their XML attributes to the XMLOutputStream. More... | |
Static Protected Member Functions | |
| static int | removeFromParentAndPorts (SBase *todelete, std::set< SBase * > *removed) |
| Remove the given SBase object, and any Ports that point to it. More... | |
Private Member Functions | |
| virtual int | collectDeletions (std::set< SBase * > *removed, std::set< SBase * > *toremove) |
| Collects (in 'toremove') the referenced object, plus any other elements that element points to through ReplacedElement or ReplacedBy children. More... | |
Friends | |
| class | CompModelPlugin |
| ReplacedElement::ReplacedElement | ( | unsigned int | level = CompExtension::getDefaultLevel(), |
| unsigned int | version = CompExtension::getDefaultVersion(), |
||
| unsigned int | pkgVersion = CompExtension::getDefaultPackageVersion() |
||
| ) |
Creates a new ReplacedElement 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. |
| ReplacedElement::ReplacedElement | ( | CompPkgNamespaces * | compns | ) |
Creates a new ReplacedElement with the given CompPkgNamespaces object.
| compns | the CompPkgNamespaces object. |
| ReplacedElement::ReplacedElement | ( | const ReplacedElement & | source | ) |
Copy constructor.
| source | the instance to copy. |
|
virtual |
Destructor.
|
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 modified date to the ModelHistory of this object.
| date | a Date object representing the date to which the "modified date" portion of this ModelHistory should be set. |
|
virtualinherited |
Appends the given annotation to the "annotation" subelement of this object.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase::setAnnotation(const XMLNode* annotation) or SBase::setAnnotation(const std::string& annotation), this method allows other annotations to be preserved when an application adds its own data.
| annotation | an XML string that is to be copied and appended to the content of the "annotation" subelement of this object. |
Reimplemented in SpeciesReference, and Model.
|
virtualinherited |
Appends the given annotation to the "annotation" subelement of this object.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase::setAnnotation(const XMLNode* annotation) or SBase::setAnnotation(const std::string& annotation), this method allows other annotations to be preserved when an application adds its own data.
| annotation | an XML structure that is to be copied and appended to the content of the "annotation" subelement of this object. |
Reimplemented in SpeciesReference, and Model.
|
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 |
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. |
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virtualinherited |
Removes the saved referenced element, if it had been saved earlier.
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virtual |
Creates and returns a deep copy of this ReplacedElement object.
Reimplemented from SBaseRef.
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privatevirtualinherited |
Collects (in 'toremove') the referenced object, plus any other elements that element points to through ReplacedElement or ReplacedBy children.
Does not delete the object directly; this should be done carefully to avoid double-deletions or misinterpretation of nested replacements/deletions. Any element already in 'removed' will not be added to 'toremove', nor will its children be checked.
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inherited |
|
inherited |
Deletes all information stored in disabled plugins.
If the plugin is re-enabled later, it will then not have any previously-stored information.
| 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. |
|
inherited |
Enables or disables the given SBML Level 3 package on this object.
This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase::disablePackage(const std::string& pkgURI, const std::string& pkgPrefix).
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
| flag | whether to enable (true) or disable (false) the package. |
|
virtualinherited |
Returns a List of all child SBase* objects, including those nested to an arbitrary depth.
| filter | a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects. |
Reimplemented from SBase.
|
virtualinherited |
Returns a List of all child SBase objects contained in SBML package plug-ins.
This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.
| filter | a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects. |
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inherited |
Returns the first ancestor object that has the given SBML type code from the given package.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. The names of the type codes all begin with the characters SBML_.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.
| 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.
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inherited |
Returns the first ancestor object that has the given SBML type code from the given package.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. The names of the type codes all begin with the characters SBML_.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.
| 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.
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inherited |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.
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 tree of XMLNode objects.
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.
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.
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inherited |
Returns the content of the "annotation" subelement of this object as a character string.
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.
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inherited |
Returns the column number where this object first appears in the XML representation of the SBML document.
0.
|
virtual |
Returns the value of the "conversionFactor" attribute of this ReplacedElement.
|
inherited |
Returns the "creation date" portion of the ModelHistory of this object.
|
inherited |
Returns the "creation date" portion of the ModelHistory of this object.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
virtual |
Returns the value of the "deletion" attribute of this ReplacedElement.
|
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.
| n | the index of the disabled plug-in to return. |
n is invalid, NULL is returned.
|
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.
| n | the index of the disabled plug-in to return. |
n is invalid, NULL is returned.
|
virtualinherited |
|
inherited |
Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found.
ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.| metaid | string representing the "metaid" attribute value of the object to find. |
|
virtualinherited |
|
virtualinherited |
Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.
| id | string representing the "id" attribute value of the object to find. |
|
virtual |
Returns the XML element name of this SBML object.
Reimplemented from SBaseRef.
|
virtualinherited |
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.
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.
Reimplemented in UnitDefinition, SpeciesType, Species, SimpleSpeciesReference, Rule, Reaction, Parameter, SpatialPoints, SampledVolume, SampledField, ParametricObject, GeometryDefinition, Geometry, DomainType, Domain, CSGObject, CSGNode, CoordinateComponent, CompartmentMapping, Boundary, AnalyticVolume, AdjacentDomains, Style, RenderInformationBase, LineEnding, Image, GraphicalPrimitive1D, GradientBase, ColorDefinition, Transition, QualitativeSpecies, Output, Input, SubListOfSpeciesFeatures, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, SpeciesFeatureType, SpeciesFeature, PossibleSpeciesFeatureValue, OutwardBindingSite, MultiSpeciesType, InSpeciesTypeBond, CompartmentReference, Point, Layout, GraphicalObject, Dimensions, BoundingBox, Member, ListOfMembers, Group, UserDefinedConstraintComponent, UserDefinedConstraint, Objective, KeyValuePair, GeneProductRef, GeneProductAssociation, GeneProduct, GeneAssociation, FluxObjective, FluxBound, DistribBase, Submodel, Port, ExternalModelDefinition, Deletion, Model, InitialAssignment, FunctionDefinition, EventAssignment, Event, CompartmentType, and Compartment.
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inherited |
Returns the value of the "id" attribute of this SBML object.
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.
|
virtualinherited |
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Returns the line number where this object first appears in the XML representation of the SBML document.
0.
|
inherited |
Returns the value of the "metaid" attribute of this SBML object.
ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
Returns the value of the "metaid" attribute of this SBML object.
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.
|
virtualinherited |
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL if none exist.
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL if none exist.
|
inherited |
Get the nth Date object in the list of "modified date" values stored in the ModelHistory of this object.
In the MIRIAM format for annotations, there can be multiple modification dates. The libSBML ModelHistory class supports this by storing a list of "modified date" values.
NULL if no such object exists.
|
virtualinherited |
Returns the value of the "name" attribute of this SBML object.
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.
Reimplemented in UnitDefinition, SpeciesType, Species, SimpleSpeciesReference, Reaction, Parameter, SpatialPoints, SampledVolume, SampledField, ParametricObject, GeometryDefinition, DomainType, Domain, CSGObject, CSGNode, CoordinateComponent, CompartmentMapping, Boundary, AnalyticVolume, AdjacentDomains, Transformation, Style, RenderInformationBase, GradientBase, ColorDefinition, Transition, QualitativeSpecies, Output, Input, SubListOfSpeciesFeatures, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, SpeciesFeatureType, SpeciesFeature, PossibleSpeciesFeatureValue, OutwardBindingSite, MultiSpeciesType, InSpeciesTypeBond, CompartmentReference, Layout, Member, ListOfMembers, Group, UserDefinedConstraintComponent, UserDefinedConstraint, Objective, KeyValuePair, GeneProductRef, GeneProductAssociation, GeneProduct, FluxObjective, FluxBound, DistribBase, Submodel, Port, ExternalModelDefinition, Deletion, Model, FunctionDefinition, Event, CompartmentType, and Compartment.
|
virtualinherited |
Returns a list of the XML Namespaces declared on the SBML document owning this object.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
NULL in certain very usual circumstances where a namespace is not set.Reimplemented in SBMLDocument.
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inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
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 tree of XMLNode objects.
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 format of "notes" elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
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inherited |
Returns the content of the "notes" subelement of this object as a string.
The format of "notes" elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
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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.
|
inherited |
Get the number of Date objects in the ModelHistory of this Iobject's list of "modified dates".
In the MIRIAM format for annotations, there can be multiple modification dates. The libSBML ModelHistory class supports this by storing a list of "modified date" values.
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
|
virtual |
Returns how many elements are being referred to by this ReplacedElement.
A valid ReplacedElement will have exactly one. Possible referents are deletion, port, idRef, unitRef, and metaIdRef.
Reimplemented from SBaseRef.
|
inherited |
Returns the SBML Core Version within the SBML Level of the actual object.
|
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 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.
| package | the name or URI of the package. |
|
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.
| package | the name or URI of the package. |
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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.
| n | the index of the plug-in to return. |
n is invalid, NULL is returned.
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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.
| n | the index of the plug-in to return. |
n is invalid, NULL is returned.
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virtualinherited |
|
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.
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virtualinherited |
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.
Finds the SBase object this ReplacedElement object points to, if any.
Reimplemented from SBaseRef.
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inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include "is" and "has part", but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using values from the enumeration type BiolQualifierType_t.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a value from the enumeration type BiolQualifierType_t.
| resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892". |
|
inherited |
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is "isDerivedFrom", to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using values from the enumeration type ModelQualifierType_t.
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a value from the enumeration type ModelQualifierType_t.
| resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892". |
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inherited |
|
inherited |
|
inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the integer portion of the value of the "sboTerm" attribute of this object.
int, and SBO identifiers are stored simply as integers. -1 if the value is not set.
|
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".
|
inherited |
Returns the string representation of the "sboTerm" attribute of this object.
int, and SBO identifiers are stored simply as integers.
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virtualinherited |
|
virtual |
Returns the libSBML type code of this object instance.
SBML_. The set of possible type codes for core elements is defined in the enumeration SBMLTypeCode_t, and in addition, libSBML plug-ins for SBML Level 3 packages define their own extra enumerations of type codes (e.g., SBMLLayoutTypeCode_t for the Level 3 Layout package). Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the 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.
Reimplemented from SBaseRef.
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virtualinherited |
|
inherited |
Returns 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 user data that has been previously set via setUserData().
NULL if no user data has been set.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
|
virtualinherited |
Returns true if getNumReferents() is exactly 1 and if the submodelRef is set.
Reimplemented from SBaseRef.
|
protectedinherited |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.
The valid combination of SBML Level and Version, “comp” package version, and Namespace as of this release of libSBML is the following:
"http://www.sbml.org/sbml/level3/version1/comp/version1" 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.
|
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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virtual |
Predicate returning true or false depending on whether this ReplacedElement's "conversionFactor" attribute has been set.
true if this ReplacedElement's "conversionFactor" attribute has been set, otherwise false is returned.
|
inherited |
Predicate returning true if this object has a ModelHistory object attached to it and the created date is set.
true if the CreatedDate of the ModelHistory of this object is set, false otherwise.
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virtual |
Predicate returning true or false depending on whether this SBaseRef's "deletion" attribute has been set.
true if this ReplacedElement's "deletion" attribute has been set, otherwise false is returned.
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virtualinherited |
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.
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.Reimplemented in UnitDefinition, SpeciesType, Species, SimpleSpeciesReference, Reaction, Parameter, SpatialPoints, SampledVolume, SampledField, ParametricObject, GeometryDefinition, Geometry, DomainType, Domain, CSGObject, CSGNode, CoordinateComponent, CompartmentMapping, Boundary, AnalyticVolume, AdjacentDomains, Style, RenderInformationBase, LineEnding, Image, GraphicalPrimitive1D, GradientBase, ColorDefinition, Transition, QualitativeSpecies, Output, Input, SubListOfSpeciesFeatures, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, SpeciesFeatureType, SpeciesFeature, PossibleSpeciesFeatureValue, OutwardBindingSite, MultiSpeciesType, InSpeciesTypeBond, CompartmentReference, Point, Layout, GraphicalObject, Dimensions, BoundingBox, Member, ListOfMembers, Group, UserDefinedConstraintComponent, UserDefinedConstraint, Objective, KeyValuePair, GeneProductRef, GeneProductAssociation, GeneProduct, GeneAssociation, FluxObjective, FluxBound, DistribBase, Submodel, Port, ExternalModelDefinition, Deletion, Model, FunctionDefinition, Event, CompartmentType, and Compartment.
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inherited |
Predicate returning true if this object's "id" attribute is set.
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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virtualinherited |
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inherited |
Predicate returning true if this object's "metaid" attribute is set.
ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.true if the "metaid" attribute of this SBML object is set, false otherwise.
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virtualinherited |
|
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.
|
inherited |
Predicate returning true or false depending on whether the ModelHistory's "modified date" of this object is set.
true if the modification date value of this ModelHistory object is set, false otherwise.
|
virtualinherited |
Predicate returning true if this object's "name" attribute is set.
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.Reimplemented in UnitDefinition, SpeciesType, Species, SimpleSpeciesReference, Reaction, Parameter, SpatialPoints, SampledVolume, SampledField, ParametricObject, GeometryDefinition, DomainType, Domain, CSGObject, CSGNode, CoordinateComponent, CompartmentMapping, Boundary, AnalyticVolume, AdjacentDomains, Transformation, Style, RenderInformationBase, GradientBase, ColorDefinition, Transition, QualitativeSpecies, Output, Input, SubListOfSpeciesFeatures, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, SpeciesFeatureType, SpeciesFeature, PossibleSpeciesFeatureValue, OutwardBindingSite, MultiSpeciesType, InSpeciesTypeBond, CompartmentReference, Layout, Member, ListOfMembers, Group, UserDefinedConstraintComponent, UserDefinedConstraint, Objective, KeyValuePair, GeneProductRef, GeneProductAssociation, GeneProduct, FluxObjective, FluxBound, DistribBase, Submodel, Port, ExternalModelDefinition, Deletion, Model, FunctionDefinition, Event, CompartmentType, and Compartment.
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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.
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virtualinherited |
|
inherited |
|
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.
|
virtualinherited |
|
virtualinherited |
|
inherited |
Predicate returning true or false depending on whether the user data of this element has been set.
true if this object's user data has been set, false otherwise.
|
protectedvirtualinherited |
Helper to log a common type of error.
|
protectedvirtualinherited |
Helper to log a common type of error.
|
protectedvirtualinherited |
Helper to log a common type of error.
|
protectedvirtualinherited |
Helper to log a common type of error.
|
protectedvirtualinherited |
Helper to log a common type of error for elements.
|
inherited |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.
| sb | an object to compare with respect to namespaces. |
true if this object's collection of namespaces is a subset of sb's, false otherwise.
|
inherited |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.
| sb | an object to compare with respect to namespaces. |
true if this object's collection of namespaces is a subset of sb's, false otherwise.
|
inherited |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.
| 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.
|
inherited |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.
| 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. | ReplacedElement & ReplacedElement::operator= | ( | const ReplacedElement & | source | ) |
Assignment operator.
| source | the object whose values are used as the basis of the assignment. |
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virtualinherited |
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.
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virtualinherited |
DEPRECATED FUNCTION: DO NOT USE.
To retain old functionality, this function calls performReplacementAndCollect, and then actually removes the now-redundant element. However, this can lead to doubly-deleted elements, as well as the incorrect interpretation of some models. The replacement function performReplacementAndCollect has been marked protected, in the hopes that people will instead simply use CompModelPlugin::instantiateSubmodels, which hides all the complexity while still allowing access to a non-flattened version of a hierarchical model.
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protectedvirtual |
Updates all IDs and references to those IDs, as well as performing all necessary conversions based on the conversion factors.
Does not actually remove the now-redundant element! The elements to be removed is instead added to 'toremove', allowing one to remove the element carefully to prevent double-deletion of elements, and to allow the correct interpretation of 'nested' replacements and deletions.
The 'removed' argument is present to ensure that the replaced element was not already removed, which would make it impossible to check it for its old IDs. In normal comp flattening, 'removed' will only contain comp elements, which should usually not be replaced, only deleted.
Implements Replacing.
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inherited |
Reads (initializes) this SBML object by reading from the given XMLNode.
| node | the XMLNode to read from. |
| flag | an optional flag that determines how how errors are logged during the reading process. |
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protectedvirtualinherited |
Subclasses should override this method to read values from the given XMLAttributes set into their specific fields.
Be sure to call your parent's implementation of this method as well.
|
virtualinherited |
Finds this SBaseRef's parent, which can either be a List or can be another SBaseRef, and tells it to remove this.
Reimplemented from SBase.
Reimplemented in ReplacedBy.
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staticprotectedinherited |
Remove the given SBase object, and any Ports that point to it.
A static function for removing elements–it is illegal to reference an element from a port that has been deleted or replaced, but if it happens, we need to not actually crash. This function finds and deletes all such invalid ports before deleting the object.
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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). |
|
virtualinherited |
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. |
Reimplemented in GraphicalObject, and Port.
|
virtual |
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. |
Reimplemented from Replacing.
|
virtualinherited |
UnitSIdRef type attribute value with another value.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. |
Reimplemented in Trigger, StoichiometryMath, Species, Rule, Priority, Parameter, UncertParameter, Port, Model, KineticLaw, InitialAssignment, FunctionDefinition, EventAssignment, Delay, Constraint, and Compartment.
|
inherited |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.
| annotation | string representing the replacement top level annotation. |
|
inherited |
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. |
|
virtualinherited |
Finds and stores the referenced object.
Finds the Submodel to which it refers, getting the instantiated Model inside that Submodel, calling 'getReferencedElementFrom' on that model, and storing the result.
Reimplemented from SBaseRef.
|
virtualinherited |
Sets the value of the "annotation" subelement of this SBML object.
The content of annotation is copied, and any previous content of this object's "annotation" subelement is deleted.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the "annotation" subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(const XMLNode* annotation) or SBase::appendAnnotation(const std::string& annotation).
| annotation | an XML string that is to be used as the content of the "annotation" subelement of this object. |
Reimplemented in SpeciesReference, and Model.
|
virtualinherited |
Sets the value of the "annotation" subelement of this SBML object.
The content of annotation is copied, and any previous content of this object's "annotation" subelement is deleted.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the "annotation" subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(const XMLNode* annotation) or SBase::appendAnnotation(const std::string& annotation).
| annotation | an XML structure that is to be used as the new content of the "annotation" subelement of this object. |
Reimplemented in SpeciesReference, and Model.
|
virtual |
Sets the value of the "conversionFactor" attribute of this ReplacedElement.
|
inherited |
Sets the creation date of the ModelHistory of this object.
| date | a Date object representing the date to which the "created date" portion of this ModelHistory should be set. |
|
virtual |
Sets the value of the "deletion" attribute of this ReplacedElement.
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 ReplacedElement must use exactly one method to point to a submodel element: deletion, port, idRef, unitRef, or metaIdRef.
|
protectedvirtualinherited |
When overridden allows SBase elements to use the text included in between the elements tags.
The default implementation does nothing.
| text | the text string found between the element tags. |
|
virtualinherited |
Sets the value of the "id" attribute of this SBML object.
sid is copied.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. |
Reimplemented in UnitDefinition, SpeciesType, Species, SimpleSpeciesReference, Reaction, Parameter, Transition, QualitativeSpecies, Output, Input, Point, Layout, GraphicalObject, Dimensions, BoundingBox, Objective, GeneProductRef, GeneProductAssociation, GeneProduct, GeneAssociation, FluxObjective, FluxBound, Submodel, Port, ExternalModelDefinition, Deletion, Model, FunctionDefinition, Event, CompartmentType, Compartment, SpatialPoints, SampledVolume, SampledField, ParametricObject, GeometryDefinition, Geometry, DomainType, Domain, CSGObject, CSGNode, CoordinateComponent, CompartmentMapping, Boundary, AnalyticVolume, AdjacentDomains, Style, RenderInformationBase, LineEnding, Image, GraphicalPrimitive1D, GradientBase, ColorDefinition, SubListOfSpeciesFeatures, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, SpeciesFeatureType, SpeciesFeature, PossibleSpeciesFeatureValue, OutwardBindingSite, MultiSpeciesType, InSpeciesTypeBond, CompartmentReference, Member, ListOfMembers, Group, UserDefinedConstraintComponent, UserDefinedConstraint, KeyValuePair, and DistribBase.
|
virtualinherited |
Sets the value of the "id" attribute of this SBML object.
sid is copied.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. |
|
virtualinherited |
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.
|
inherited |
Sets the value of the meta-identifier attribute of this SBML object.
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. |
|
virtualinherited |
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.
|
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. |
|
virtualinherited |
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. |
Reimplemented in UnitDefinition, SpeciesType, Species, SimpleSpeciesReference, Reaction, Parameter, SpatialPoints, SampledVolume, SampledField, ParametricObject, GeometryDefinition, DomainType, Domain, CSGObject, CSGNode, CoordinateComponent, CompartmentMapping, Boundary, AnalyticVolume, AdjacentDomains, Transformation, Style, RenderInformationBase, GradientBase, ColorDefinition, Transition, QualitativeSpecies, Output, Input, SubListOfSpeciesFeatures, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, SpeciesFeatureType, SpeciesFeature, PossibleSpeciesFeatureValue, OutwardBindingSite, MultiSpeciesType, InSpeciesTypeBond, CompartmentReference, Layout, Member, ListOfMembers, Group, UserDefinedConstraintComponent, UserDefinedConstraint, Objective, KeyValuePair, GeneProductRef, GeneProductAssociation, GeneProduct, FluxObjective, FluxBound, DistribBase, Submodel, Port, ExternalModelDefinition, Deletion, Model, FunctionDefinition, Event, CompartmentType, and Compartment.
|
inherited |
Sets the namespaces relevant of this SBML object.
The content of xmlns is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
| xmlns | the namespaces to set. |
|
inherited |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes.
The content of notes is copied, and any existing content of this object's "notes" subelement is deleted.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.
| notes | an XML string that is to be used as the content of the "notes" subelement of this object. |
| addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
|
inherited |
Sets the value of the "notes" subelement of this SBML object.
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. |
|
virtualinherited |
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.
Reimplemented in Port.
|
inherited |
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. |
|
virtualinherited |
Sets the value of the "sboTerm" attribute by string.
int, and SBO identifiers are stored simply as integers. | sboid | the SBO identifier string of the form "SBO:NNNNNNN". |
|
virtualinherited |
Sets the value of the "sboTerm" attribute.
int, and SBO identifiers are stored simply as integers. | value | the NNNNNNN integer portion of the SBO identifier. |
|
virtualinherited |
Sets the value of the "submodelRef" attribute of this SBaseRef.
Fails if the id is not a valid syntax for an SIdRef.
|
virtualinherited |
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.
|
inherited |
Sets the user data of this element.
| userData | specifies the new user data. |
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
|
inherited |
|
inherited |
Unsets the value of the "annotation" subelement of this SBML object.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
|
virtual |
Unsets the value of the "conversionFactor" attribute of this ReplacedElement.
|
inherited |
Unsets the created date of the ModelHistory object attached to this object.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
|
virtual |
Unsets the value of the "deletion" attribute of this ReplacedElement.
|
virtualinherited |
Unsets the value of the "id" attribute of this SBML object.
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.
Reimplemented in SimpleSpeciesReference, SpatialPoints, SampledVolume, SampledField, ParametricObject, GeometryDefinition, Geometry, DomainType, Domain, CSGObject, CSGNode, CoordinateComponent, CompartmentMapping, Boundary, AnalyticVolume, AdjacentDomains, Style, RenderInformationBase, LineEnding, Image, GraphicalPrimitive1D, GradientBase, ColorDefinition, Transition, QualitativeSpecies, Output, Input, SubListOfSpeciesFeatures, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, SpeciesFeatureType, SpeciesFeature, PossibleSpeciesFeatureValue, OutwardBindingSite, MultiSpeciesType, InSpeciesTypeBond, CompartmentReference, Point, Layout, GraphicalObject, Dimensions, BoundingBox, Member, ListOfMembers, Group, UserDefinedConstraintComponent, UserDefinedConstraint, Objective, KeyValuePair, GeneProductRef, GeneProductAssociation, GeneProduct, GeneAssociation, FluxObjective, FluxBound, DistribBase, Submodel, Port, ExternalModelDefinition, Deletion, Model, and Event.
|
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.
|
virtualinherited |
Unsets the value of the "idRef" attribute of this SBaseRef.
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 |
Unsets the value of the "metaid" attribute of this SBML object.
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.
|
virtualinherited |
Unsets the value of the "metaIdRef" attribute of this SBaseRef.
|
inherited |
Unsets the ModelHistory object attached to this object.
|
inherited |
Unsets the modified dates of the ModelHistory object attached to this object.
|
virtualinherited |
Unsets the value of the "name" attribute of this SBML object.
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.
Reimplemented in UnitDefinition, SpeciesType, Species, SimpleSpeciesReference, Reaction, Parameter, SpatialPoints, SampledVolume, SampledField, ParametricObject, GeometryDefinition, DomainType, Domain, CSGObject, CSGNode, CoordinateComponent, CompartmentMapping, Boundary, AnalyticVolume, AdjacentDomains, Transformation, Style, RenderInformationBase, GradientBase, ColorDefinition, Transition, QualitativeSpecies, Output, Input, SubListOfSpeciesFeatures, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, SpeciesFeatureType, SpeciesFeature, PossibleSpeciesFeatureValue, OutwardBindingSite, MultiSpeciesType, InSpeciesTypeBond, CompartmentReference, Layout, Member, ListOfMembers, Group, UserDefinedConstraintComponent, UserDefinedConstraint, Objective, KeyValuePair, GeneProductRef, GeneProductAssociation, GeneProduct, FluxObjective, FluxBound, DistribBase, Submodel, Port, ExternalModelDefinition, Deletion, Model, FunctionDefinition, Event, CompartmentType, and Compartment.
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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.
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virtualinherited |
Unsets the value of the "portRef" attribute of this SBaseRef.
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virtualinherited |
Unsets the child SBaseRef of this SBaseRef.
Deletes the former SBaseRef child, if one existed.
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inherited |
Unsets the value of the "sboTerm" attribute of this SBML object.
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virtualinherited |
Unsets the value of the "SubmodelRef" attribute of this SBaseRef.
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virtualinherited |
Unsets the value of the "unitRef" attribute of this SBaseRef.
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inherited |
Unsets the user data of this element.
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protectedvirtualinherited |
Subclasses should override this method to write their XML attributes to the XMLOutputStream.
Be sure to call your parent's implementation of this method as well. For example:
SBase::writeAttributes(stream); stream.writeAttribute( "submodel" , mSubmodel ); ...
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friend |