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libSBML Perl API
libSBML 5.8.0 Perl API
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libSBML Perl API
libSBML 5.8.0 Perl API
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The CompBase class derives from SBase, and defines a few common functions and features common to all SBase-derived classes in the SBML Level 3 Hierarchical Model Composition package ('comp').
Public Member Functions | |
| virtual bool | accept (SBMLVisitor &v) const =0 |
| Accepts the given SBMLVisitor for this SBase object. More... | |
| int | addCVTerm (CVTerm *term, bool newBag=false) |
| Adds a copy of the given CVTerm object to this SBML object. More... | |
| virtual int | appendAnnotation (const XMLNode *annotation) |
Appends the given annotation to the "annotation" subelement of this object. More... | |
| virtual int | appendAnnotation (const std::string &annotation) |
Appends the given annotation to the "annotation" subelement of this object. More... | |
| int | appendNotes (const XMLNode *notes) |
Appends the given notes to the "notes" subelement of this object. More... | |
| int | appendNotes (const std::string ¬es) |
Appends the given notes to the "notes" subelement of this object. More... | |
| virtual SBase * | clone () const =0 |
| Creates and returns a deep copy of this SBase object. More... | |
| CompBase (unsigned int level=CompExtension::getDefaultLevel(), unsigned int version=CompExtension::getDefaultVersion(), unsigned int pkgVersion=CompExtension::getDefaultPackageVersion()) | |
| Creates a new CompBase with the given level, version, and package version. More... | |
| CompBase (CompPkgNamespaces *compns) | |
| Creates a new CompBase with the given SBMLExtensionNamespaces object. More... | |
| CompBase (const CompBase &source) | |
| Copy constructor. More... | |
| int | disablePackage (const std::string &pkgURI, const std::string &pkgPrefix) |
| Disables the given SBML Level 3 package. More... | |
| int | enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag) |
| Enables or disables the given SBML Level 3 package. More... | |
| virtual List * | getAllElements () |
| Returns a List of all child SBase objects, including those nested to an arbitrary depth. More... | |
| virtual List * | getAllElementsFromPlugins () |
| 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. More... | |
| const SBase * | getAncestorOfType (int type, const std::string pkgName="core") const |
| Returns the first ancestor object that has the given SBML type code. More... | |
| XMLNode * | getAnnotation () |
| Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
| 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 on which this object first appears in the XML representation of the SBML document. 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 SBase * | getElementByMetaId (std::string metaid) |
Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found. More... | |
| virtual SBase * | getElementBySId (std::string id) |
Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More... | |
| virtual const std::string & | getElementName () const =0 |
| Returns the XML element name of this object. More... | |
| unsigned int | getLevel () const |
| Returns the SBML Level of the SBMLDocument object containing this object. More... | |
| unsigned int | getLine () const |
| Returns the line number on which this object first appears in the XML representation of the SBML document. More... | |
| const std::string & | getMetaId () const |
| Returns the value of the "metaid" attribute of this object. More... | |
| std::string & | getMetaId () |
| Returns the value of the "metaid" attribute of this object. More... | |
| const Model * | getModel () const |
| Returns the Model object in which the current object is located. More... | |
| ModelHistory * | getModelHistory () const |
| Returns the ModelHistory object, if any, attached to this object. More... | |
| ModelHistory * | getModelHistory () |
| Returns the ModelHistory object, if any, attached to this object. More... | |
| virtual XMLNamespaces * | getNamespaces () const |
| Returns a list of the XML Namespaces declared on this SBML document. More... | |
| XMLNode * | getNotes () |
| Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More... | |
| 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 () |
| Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
| unsigned int | getNumPlugins () const |
| Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
| const std::string & | 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... | |
| const std::string & | getPrefix () const |
| Returns the prefix of the package extension of this plugin object. More... | |
| BiolQualifierType_t | getResourceBiologicalQualifier (std::string resource) |
| Returns the MIRIAM biological qualifier associated with the given resource. More... | |
| ModelQualifierType_t | getResourceModelQualifier (std::string resource) |
| Returns the MIRIAM model qualifier associated with the given resource. More... | |
| const SBMLDocument * | getSBMLDocument () const |
| Returns the SBMLDocument object containing this object instance. More... | |
| SBMLDocument * | getSBMLDocument () |
| Returns the SBMLDocument object containing this object instance. More... | |
| int | getSBOTerm () const |
| Returns the integer portion of the value of the "sboTerm" attribute of this object. More... | |
| std::string | getSBOTermAsURL () const |
| Returns the identifiers.org URL representation of the "sboTerm" attribute of this object. More... | |
| std::string | getSBOTermID () const |
| Returns the string representation of the "sboTerm" attribute of this object. More... | |
| virtual int | getTypeCode () const |
| Returns the libSBML type code for this object. 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... | |
| bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
| bool | isPackageEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
| bool | isPackageURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| bool | isPkgEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
| bool | isPkgURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| bool | isSetAnnotation () const |
Predicate returning true if this object's "annotation" subelement exists and has content. More... | |
| bool | isSetMetaId () const |
Predicate returning true if this object's "metaid" attribute is set. More... | |
| bool | isSetModelHistory () |
Predicate returning true if this object has a ModelHistory object attached to it. More... | |
| bool | isSetNotes () const |
Predicate returning true if this object's "notes" subelement exists and has content. More... | |
| bool | isSetSBOTerm () const |
Predicate returning true if this object's "sboTerm" attribute is set. More... | |
| bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
| bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
| bool | matchesSBMLNamespaces (const SBase *sb) |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
| bool | matchesSBMLNamespaces (const SBase *sb) const |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
| CompBase & | operator= (const CompBase &source) |
| Assignment operator. More... | |
| virtual int | removeFromParentAndDelete () |
| Removes itself from its parent. More... | |
| int | removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="") |
| Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More... | |
| virtual void | renameMetaIdRefs (std::string oldid, std::string newid) |
Renames all the MetaIdRef attributes on this element. More... | |
| virtual void | renameSIdRefs (std::string oldid, std::string newid) |
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists). More... | |
| virtual void | renameUnitSIdRefs (std::string oldid, std::string newid) |
Renames all the UnitSIdRef attributes on this element. More... | |
| int | replaceTopLevelAnnotationElement (const XMLNode *annotation) |
| Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
| int | replaceTopLevelAnnotationElement (const std::string &annotation) |
| Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
| virtual int | setAnnotation (const XMLNode *annotation) |
| Sets the value of the "annotation" subelement of this SBML object. More... | |
| virtual int | setAnnotation (const std::string &annotation) |
| Sets the value of the "annotation" subelement of this SBML object. More... | |
| int | setMetaId (const std::string &metaid) |
| Sets the value of the "metaid" attribute of this object. More... | |
| int | setModelHistory (ModelHistory *history) |
| Sets the ModelHistory of this object. More... | |
| int | setNamespaces (XMLNamespaces *xmlns) |
| Sets the namespaces relevant of this SBML object. More... | |
| int | setNotes (const XMLNode *notes) |
| Sets the value of the "notes" subelement of this SBML object. More... | |
| int | setNotes (const std::string ¬es, bool addXHTMLMarkup=false) |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes. More... | |
| virtual int | setSBOTerm (int value) |
| Sets the value of the "sboTerm" attribute. More... | |
| virtual int | setSBOTerm (const std::string &sboid) |
| Sets the value of the "sboTerm" attribute by string. More... | |
| int | 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... | |
| int | unsetAnnotation () |
| Unsets the value of the "annotation" subelement of this SBML object. More... | |
| int | unsetCVTerms () |
| Clears the list of CVTerm objects attached to this SBML object. More... | |
| virtual int | unsetId () |
| Unsets the value of the "id" attribute of this SBML object. More... | |
| int | unsetMetaId () |
| Unsets the value of the "metaid" attribute of this SBML object. More... | |
| int | unsetModelHistory () |
| Unsets the ModelHistory object attached to this object. More... | |
| virtual int | unsetName () |
| Unsets the value of the "name" attribute of this SBML object. More... | |
| int | unsetNotes () |
| Unsets the value of the "notes" subelement of this SBML object. More... | |
| int | unsetSBOTerm () |
| Unsets the value of the "sboTerm" attribute of this SBML object. More... | |
| virtual | ~CompBase () |
| 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 | |
| virtual void | setElementText (const std::string &text) |
| When overridden allows SBase elements to use the text included in between the elements tags. More... | |
Static Protected Member Functions | |
| static int | removeFromParentAndPorts (SBase *todelete) |
| 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. More... | |
| CompBase::CompBase | ( | unsigned int | level = CompExtension::getDefaultLevel(), |
| unsigned int | version = CompExtension::getDefaultVersion(), |
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| unsigned int | pkgVersion = CompExtension::getDefaultPackageVersion() |
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| ) |
Creates a new CompBase 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 |
| CompBase::CompBase | ( | CompPkgNamespaces * | compns | ) |
Creates a new CompBase with the given SBMLExtensionNamespaces object.
| compns | the namespace object. |
| CompBase::CompBase | ( | const CompBase & | source | ) |
Copy constructor.
| source | the object to copy. |
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virtual |
Destructor.
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pure virtualinherited |
Accepts the given SBMLVisitor for this SBase object.
| v | the SBMLVisitor instance to be used |
v.visit(). Implemented in Submodel, SBaseRef, Model, Species, ExternalModelDefinition, SBMLDocument, Compartment, UnitDefinition, Event, SpeciesReference, InitialAssignment, Reaction, EventAssignment, Unit, StoichiometryMath, Parameter, Priority, LocalParameter, Constraint, Delay, FunctionDefinition, AssignmentRule, CompartmentType, SpeciesType, KineticLaw, Trigger, RateRule, Replacing, AlgebraicRule, Rule, ListOf, SimpleSpeciesReference, and ModifierSpeciesReference.
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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. |
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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 Model, and SpeciesReference.
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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 Model, and SpeciesReference.
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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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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 |
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pure virtualinherited |
Creates and returns a deep copy of this SBase object.
Implemented in ListOfSpecies, ListOfReactions, ListOfCompartments, ListOfUnits, ListOfEvents, ListOfUnitDefinitions, ListOfSpeciesReferences, ListOfRules, ListOfParameters, ListOfInitialAssignments, ListOfEventAssignments, ListOfFunctionDefinitions, ListOfConstraints, Model, Species, ListOfLocalParameters, ListOfSpeciesTypes, ListOfCompartmentTypes, SBMLDocument, Compartment, UnitDefinition, Event, SpeciesReference, InitialAssignment, Reaction, EventAssignment, Unit, StoichiometryMath, Parameter, Priority, LocalParameter, Constraint, Delay, FunctionDefinition, CompartmentType, SpeciesType, AssignmentRule, KineticLaw, Trigger, RateRule, Rule, AlgebraicRule, ReplacedElement, ListOf, Submodel, ExternalModelDefinition, SBaseRef, ModifierSpeciesReference, Deletion, Port, ModelDefinition, ReplacedBy, ListOfExternalModelDefinitions, ListOfModelDefinitions, ListOfReplacedElements, ListOfDeletions, ListOfSubmodels, and ListOfPorts.
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inherited |
Disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
| pkgURI | the URI of the package |
| pkgPrefix | the XML prefix of the package |
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inherited |
Enables or disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
| pkgURI | the URI of the package |
| pkgPrefix | the XML prefix of the package |
| flag | whether to enable (true) or disable (false) the package |
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virtualinherited |
Returns a List of all child SBase objects, including those nested to an arbitrary depth.
Reimplemented in Model, SBMLDocument, UnitDefinition, Event, Reaction, ListOf, KineticLaw, Submodel, and SBaseRef.
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virtualinherited |
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inherited |
Returns the first ancestor object that has the given SBML type code.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.
| 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.
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inherited |
Returns the first ancestor object that has the given SBML type code.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.
| 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.
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inherited |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.
Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
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inherited |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.
Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
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inherited |
Returns the content of the "annotation" subelement of this object as a character string.
Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form.
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inherited |
Returns the content of the "annotation" subelement of this object as a character string.
Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form.
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inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
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inherited |
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inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
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inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
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virtualinherited |
Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found.
| metaid | string representing the "metaid" attribute value of the object to find. |
Reimplemented in Model, SBMLDocument, UnitDefinition, Event, Reaction, ListOf, KineticLaw, Submodel, and SBaseRef.
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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. |
Reimplemented in ListOfUnitDefinitions, ListOfRules, ListOfInitialAssignments, ListOfEventAssignments, ListOfLocalParameters, Model, SBMLDocument, UnitDefinition, Event, Reaction, ListOf, KineticLaw, ListOfPorts, Submodel, and SBaseRef.
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pure virtualinherited |
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the SBML component. For example, Model defines it as returning "model", CompartmentType defines it as returning "compartmentType", and so on.
Implemented in Model, ListOfSpecies, ListOfReactions, Species, ListOfCompartments, ListOfUnits, ListOfEvents, Reaction, SBMLDocument, ListOfUnitDefinitions, Compartment, Event, ListOfSpeciesReferences, ListOfRules, KineticLaw, ListOfParameters, Unit, SpeciesReference, ListOfInitialAssignments, ListOfEventAssignments, UnitDefinition, Rule, Parameter, ListOfFunctionDefinitions, ListOfConstraints, Submodel, ListOfLocalParameters, ListOfSpeciesTypes, ListOfCompartmentTypes, InitialAssignment, EventAssignment, StoichiometryMath, SBaseRef, Delay, FunctionDefinition, ListOf, ExternalModelDefinition, Constraint, Trigger, LocalParameter, CompartmentType, SpeciesType, Priority, ReplacedElement, Port, Deletion, ListOfExternalModelDefinitions, ListOfModelDefinitions, ListOfSubmodels, ListOfDeletions, ListOfPorts, ModifierSpeciesReference, ListOfReplacedElements, ModelDefinition, and ReplacedBy.
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inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
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inherited |
Returns the line number on which this object first appears in the XML representation of the SBML document.
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inherited |
Returns the value of the "metaid" attribute of this object.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
|
inherited |
Returns the value of the "metaid" attribute of this object.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
|
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.
|
virtualinherited |
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.
Reimplemented in SBMLDocument.
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
The "notes" element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
The "notes" element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
|
inherited |
Returns the content of the "notes" subelement of this object as a string.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
|
inherited |
Returns the content of the "notes" subelement of this object as a string.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
| const std::string & CompBase::getPackageName | ( | ) | const |
Returns the package name of this plugin object.
| const std::string & CompBase::getPackageURI | ( | ) | const |
Returns the XML namespace (URI) of the package extension of this object.
| unsigned int CompBase::getPackageVersion | ( | ) | const |
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.
| 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.
| package | the name or URI of the package |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
| n | the index of the plug-in to return |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
| n | the index of the plug-in to return |
| const std::string & CompBase::getPrefix | ( | ) | const |
Returns the prefix of the package extension of this plugin object.
|
inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include "is" and "has part", but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using values
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a value
| 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
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
| resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892". |
|
inherited |
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the integer portion of the value of the "sboTerm" attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
-1 if the value is not set.
|
inherited |
Returns the identifiers.org URL representation of the "sboTerm" attribute of this object.
This method returns the entire SBO identifier as a text string in the form "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN".
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
|
inherited |
Returns the string representation of the "sboTerm" attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form "SBO:NNNNNNN".
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
|
virtualinherited |
Returns the libSBML type code for this object.
This method may return the type code of this SBML object, or it may return SBML_UNKNOWN. This is because subclasses of SBase are not required to implement this method to return a type code. This method is meant primarily for the LibSBML C interface, in which class and subclass information is not readily available.
Reimplemented in Model, ListOfSpecies, ListOfReactions, Species, ListOfCompartments, ListOfUnits, ListOfEvents, Reaction, SBMLDocument, Compartment, ListOfUnitDefinitions, Event, ListOfSpeciesReferences, ListOfRules, KineticLaw, ListOfParameters, Unit, SpeciesReference, ListOfInitialAssignments, ListOfEventAssignments, UnitDefinition, Parameter, Rule, ListOfFunctionDefinitions, Submodel, ListOfConstraints, InitialAssignment, EventAssignment, ListOfLocalParameters, SBaseRef, ListOfSpeciesTypes, ListOfCompartmentTypes, StoichiometryMath, Delay, FunctionDefinition, ExternalModelDefinition, ListOf, Constraint, Trigger, LocalParameter, CompartmentType, SpeciesType, Priority, ReplacedElement, Port, Deletion, ModifierSpeciesReference, ReplacedBy, and ModelDefinition.
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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.
|
inherited |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.
The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
"http://www.sbml.org/sbml/level1" "http://www.sbml.org/sbml/level2" "http://www.sbml.org/sbml/level2/version2" "http://www.sbml.org/sbml/level2/version3" "http://www.sbml.org/sbml/level2/version4" "http://www.sbml.org/sbml/level3/version1/core" true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
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inherited |
Predicate returning true if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
| pkgName | the name of the package |
true if the given package is enabled within this object, false otherwise.
|
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.
|
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 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.
|
inherited |
Predicate returning true if this object's "metaid" attribute is set.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
true if the "metaid" attribute of this SBML object is set, false otherwise.
|
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 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.
|
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.
|
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.
|
virtualinherited |
Removes itself from its parent.
If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
Reimplemented in Model, KineticLaw, SBaseRef, StoichiometryMath, Delay, Trigger, Priority, ListOf, ModelDefinition, and ReplacedBy.
|
staticprotected |
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.
|
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 |
|
virtualinherited |
Renames all the MetaIdRef attributes on this element.
This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier |
| newid | the new identifier |
Reimplemented in Port.
|
virtualinherited |
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate) mathematical formulas, 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 Model, Species, KineticLaw, Compartment, Rule, Submodel, InitialAssignment, EventAssignment, StoichiometryMath, Delay, SBaseRef, Trigger, Priority, Constraint, Reaction, ReplacedElement, Port, SimpleSpeciesReference, AssignmentRule, RateRule, and Replacing.
|
virtualinherited |
Renames all the UnitSIdRef attributes on this element.
This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit 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 Model, Species, KineticLaw, Compartment, Rule, Parameter, InitialAssignment, EventAssignment, StoichiometryMath, Delay, FunctionDefinition, Trigger, Priority, Constraint, and Port.
|
inherited |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.
| annotation | XMLNode representing the replacement top level annotation |
|
inherited |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); 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 |
|
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 Model, and SpeciesReference.
|
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 Model, and SpeciesReference.
|
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. |
|
inherited |
Sets the value of the "metaid" attribute of this object.
The string metaid is copied. The value of metaid must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the "metaid" attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement.
| metaid | the identifier string to use as the value of the "metaid" attribute |
|
inherited |
Sets the ModelHistory of this object.
The content of history is copied, and this object's existing model history content is deleted.
| history | ModelHistory of this object. |
|
inherited |
Sets the namespaces relevant of this SBML object.
The content of xmlns is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
| xmlns | the namespaces to set |
|
inherited |
Sets the value of the "notes" subelement of this SBML object.
The content of notes is copied, and any existing content of this object's "notes" subelement is deleted.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
| notes | an XML structure that is to be used as the content of the "notes" subelement of this object |
|
inherited |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes.
The content of notes is copied, and any existing content of this object's "notes" subelement is deleted.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.
| notes | an XML string that is to be used as the content of the "notes" subelement of this object |
| addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
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virtualinherited |
Sets the value of the "sboTerm" attribute.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
| value | the NNNNNNN integer portion of the SBO identifier |
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virtualinherited |
Sets the value of the "sboTerm" attribute by string.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of "sboTerm" as a complete string of the form "SBO:NNNNNNN", whereas setSBOTerm(int value) allows you to set it using the integer form.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
| sboid | the SBO identifier string of the form "SBO:NNNNNNN" |
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inherited |
Sets the user data of this element.
This can be used by the application developer to attach custom information to the node. In case of a deep copy this attribute will passed as it is. The attribute will be never interpreted by this class.
| userData | specifies the new user data. |
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inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
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inherited |
Unsets the value of the "annotation" subelement of this SBML object.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
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inherited |
Clears the list of CVTerm objects attached to this SBML object.
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virtualinherited |
Unsets the value of the "id" attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: "id" and "name". The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always either Sid or UnitSId, depending on the object in question. Both data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The equality of SId and UnitSId type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId and UnitSId.
Reimplemented in Model, Event, SimpleSpeciesReference, Submodel, ExternalModelDefinition, Deletion, and Port.
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inherited |
Unsets the value of the "metaid" attribute of this SBML object.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
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inherited |
Unsets the ModelHistory object attached to this object.
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virtualinherited |
Unsets the value of the "name" attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: "id" and "name". In contrast to the "id" attribute, 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.
Reimplemented in Species, Compartment, Model, Event, Reaction, Parameter, UnitDefinition, FunctionDefinition, CompartmentType, SpeciesType, Submodel, SimpleSpeciesReference, ExternalModelDefinition, Deletion, and Port.
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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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inherited |
Unsets the value of the "sboTerm" attribute of this SBML object.