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libSBML C++ API
5.18.0
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libSBML C++ API
5.18.0
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A reaction represents any transformation, transport or binding process, typically a chemical reaction, that can change the quantity of one or more species. In SBML, a reaction is defined primarily in terms of the participating reactants and products (and their corresponding stoichiometries), along with optional modifier species, an optional rate at which the reaction takes place, and optional parameters.
As with other major objects in SBML, Reaction has a mandatory attribute, "id", used to give the reaction an identifier. The identifier must be a text string conforming to the identifer syntax permitted in SBML. In SBML Level 2 and Level 3, the reaction "id" identifier can be used in mathematical formulas elsewhere in an SBML model to represent the rate of that reaction; this usage is explained below. Reaction also has an optional "name" attribute, of type string. The "id" and "name" must be used according to the guidelines described in the SBML specification.
The species participating as reactants, products, and/or modifiers in a reaction are declared using lists of SpeciesReference and/or ModifierSpeciesReference instances stored in subelements "listOfReactants", "listOfProducts" and "listOfModifiers". Certain restrictions are placed on the appearance of species in reaction definitions:
The ability of a species to appear as a reactant or product of any reaction in a model is governed by certain flags in that species' definition; see the definition of Species for more information.
Any species appearing in the mathematical formula of the subelement "kineticLaw" (described below) of a Reaction must be declared in at least one of that Reaction's lists of reactants, products, and/or modifiers. Put another way, it is an error for a reaction's kinetic law formula to refer to species that have not been declared for that reaction.
A reaction can contain up to one KineticLaw object in a subelement named "kineticLaw". It defines the speed at which the process defined by the reaction takes place. The description of KineticLaw provides more details about its use. Note that although the inclusion of a KineticLaw object in an instance of a Reaction component is optional, there is no useful default that can be substituted in place of a missing rate expression in a reaction. Moreover, a reaction's rate cannot be defined in any other way in SBML—InitialAssignment, AssignmentRule, RateRule, AlgebraicRule, Event, and other constructs in SBML cannot be used to set the reaction rate separately. Nevertheless, for some modeling applications, reactions without any defined rate can be perfectly acceptable.
Reaction also has a boolean attribute named "reversible" for indicating whether the reaction is reversible. This attribute is optional in SBML Level 2, with a default of true; it is mandatory in SBML Level 3 (with no default value). To say that a reaction is reversible is to say it can proceed in either the forward or the reverse direction. Although the reversibility of a reaction can sometimes be deduced by inspecting its rate expression, this is not always the case, especially for complicated expressions. Moreover, the need in SBML to allow rate expressions (i.e., KineticLaw) to be optional leads to the need for a separate flag indicating reversibility. Note that labeling a reaction as irreversible is an assertion that the reaction always proceeds in the given forward direction. (Why else would it be flagged as irreversible?) This implies the rate expression in the KineticLaw always has a non-negative value during simulations. Software tools could provide a means of optionally testing that this condition holds. The presence of reversibility information in two places (i.e., the rate expression and the "reversible" attribute on Reaction) leaves open the possibility that a model could contain contradictory information, but the creation of such a model would be an error on the part of the software generating it.
The Reaction object class has another boolean attribute called "fast". This attribute is optional in SBML Level 2, with a default of false; it is mandatory in SBML Level 3 (with no default value). In SBML Level 3 Version 2, a value of true for the "fast" attribute is deprecated in favor of all reactions having a "fast" value of false. It is used to indicate that a reaction occurs on a vastly faster time scale than others in a system. Readers are directed to the SBML Level 2 Version 4 specification, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense. SBML Level 1 and Level 2 Version 1 incorrectly claimed that software tools could ignore this attribute if they did not implement support for the corresponding concept; however, further research in SBML has revealed that this is not true, and "fast" cannot be ignored if it is set to true. SBML Level 2 Versions 2–4 therefore stipulate that if a model has any reactions with "fast" set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Analysis software cannot ignore the value of the "fast" attribute because doing so may lead to different results as compared to a software system that does make use of "fast".
false. Users should be aware that even for previous levels/versions of the specification, "fast" attribute values of true never achieved widespread support, and many software packages may ignore it. To achieve the same or similar effects as setting the fast attribute to true for a given reaction, the KineticLaw attribute should be constructed to produce a value in the desired time scale, or else the reaction could be replaced with an AssignmentRule or AlgebraicRule.In SBML Level 3, the Reaction object has an additional optional attribute named "compartment", whose value must be the identifier of a compartment defined in the enclosing Model object. The "compartment" attribute can be used to indicate the compartment in which the reaction is assumed to take place. If the attribute is present, its value must be the identifier of a Compartment object defined in the enclosing Model object. Similar to the "reversible" attribute, the value of the "compartment" attribute has no direct impact on the construction of mathematical equations for the SBML model. When a kinetic law is given for a reaction, the compartment location may already be implicit in the kinetic law (although this cannot always be guaranteed). Nevertheless, software tools may find the "compartment" attribute value useful for such purposes as analyzing the structure of the model, guiding the modeler in constructing correct rate formulas, and visualization purposes.
Readers are urged to read the SBML specification for more details about the proper use of Reaction.
Public Member Functions | |
| int | addCVTerm (CVTerm *term, bool newBag=false) |
| Adds a copy of the given CVTerm object to this SBML object. More... | |
| int | addModifier (const ModifierSpeciesReference *msr) |
| Adds a given ModifierSpeciesReference object as a product in this Reaction. More... | |
| int | addModifier (const Species *species, const std::string id="") |
| Adds the given species as a modifier to this reaction. More... | |
| int | addProduct (const SpeciesReference *sr) |
| Adds a given SpeciesReference object as a product in this Reaction. More... | |
| int | addProduct (const Species *species, double stoichiometry=1.0, const std::string id="", bool constant=true) |
| Adds the given species as a product with the given stoichiometry. More... | |
| int | addReactant (const SpeciesReference *sr) |
| Adds a given SpeciesReference object as a reactant in this Reaction. More... | |
| int | addReactant (const Species *species, double stoichiometry=1.0, const std::string id="", bool constant=true) |
| Adds the given species as a reactant with the given stoichiometry. 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 Reaction * | clone () const |
| Creates and returns a deep copy of this Reaction object. More... | |
| KineticLaw * | createKineticLaw () |
| Creates a new KineticLaw object, installs it as this Reaction's "kineticLaw" subelement, and returns it. More... | |
| ModifierSpeciesReference * | createModifier () |
| Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it. More... | |
| SpeciesReference * | createProduct () |
| Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it. More... | |
| SpeciesReference * | createReactant () |
| Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it. 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... | |
| const std::string & | getCompartment () const |
| (SBML Level 3 only) Returns the value of the "compartment" attribute on the Reaction. 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... | |
| 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... | |
| 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 * | getElementByMetaId (const std::string &metaid) |
Returns the first child element it can find with the given metaid, or NULL if no such object is found. More... | |
| 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 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 std::string & | getElementName () const |
Returns the XML element name of this object, which for Reaction, is always "reaction". More... | |
| bool | getFast () const |
| Returns the value of the "fast" attribute of this Reaction. More... | |
| virtual const std::string & | getId () const |
| Returns the value of the "id" attribute of this Reaction. More... | |
| const std::string & | getIdAttribute () const |
| Returns the value of the "id" attribute of this SBML object. More... | |
| const KineticLaw * | getKineticLaw () const |
| Returns the KineticLaw object contained in this Reaction. More... | |
| KineticLaw * | getKineticLaw () |
| Returns the KineticLaw object contained in this Reaction. 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... | |
| const ListOfSpeciesReferences * | getListOfModifiers () const |
| Returns the list of modifiers in this Reaction object. More... | |
| ListOfSpeciesReferences * | getListOfModifiers () |
| Returns the list of modifiers in this Reaction object. More... | |
| const ListOfSpeciesReferences * | getListOfProducts () const |
| Returns the list of products in this Reaction object. More... | |
| ListOfSpeciesReferences * | getListOfProducts () |
| Returns the list of products in this Reaction object. More... | |
| const ListOfSpeciesReferences * | getListOfReactants () const |
| Returns the list of reactants in this Reaction object. More... | |
| ListOfSpeciesReferences * | getListOfReactants () |
| Returns the list of reactants in this Reaction object. More... | |
| const std::string & | getMetaId () const |
| Returns the value of the "metaid" attribute of this SBML object. More... | |
| std::string & | getMetaId () |
| Returns the value of the "metaid" attribute of this SBML object. More... | |
| const Model * | getModel () const |
| Returns the Model object for the SBML Document 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... | |
| const ModifierSpeciesReference * | getModifier (unsigned int n) const |
| Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of this Reaction. More... | |
| ModifierSpeciesReference * | getModifier (unsigned int n) |
| Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of this Reaction. More... | |
| const ModifierSpeciesReference * | getModifier (const std::string &species) const |
| Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction. More... | |
| ModifierSpeciesReference * | getModifier (const std::string &species) |
| Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction. More... | |
| virtual const std::string & | getName () const |
| Returns the value of the "name" attribute of this Reaction 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 () |
| 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 | getNumModifiers () const |
| Returns the number of modifier species in this Reaction. More... | |
| unsigned int | getNumPlugins () const |
| Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
| unsigned int | getNumProducts () const |
| Returns the number of product species in this Reaction. More... | |
| unsigned int | getNumReactants () const |
| Returns the number of reactant species in this Reaction. 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 name of the SBML Level 3 package in which this element is defined. More... | |
| unsigned int | getPackageVersion () const |
| Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
| SBase * | getParentSBMLObject () |
| Returns the parent SBML object containing this object. More... | |
| 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... | |
| std::string | getPrefix () const |
| Returns the XML namespace prefix of this element. More... | |
| const SpeciesReference * | getProduct (unsigned int n) const |
| Returns the nth product species (as a SpeciesReference object) in the list of products in this Reaction. More... | |
| SpeciesReference * | getProduct (unsigned int n) |
| Returns the nth product species (as a SpeciesReference object) in the list of products in this Reaction. More... | |
| const SpeciesReference * | getProduct (const std::string &species) const |
| Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction. More... | |
| SpeciesReference * | getProduct (const std::string &species) |
| Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction. More... | |
| const SpeciesReference * | getReactant (unsigned int n) const |
| Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reaction. More... | |
| SpeciesReference * | getReactant (unsigned int n) |
| Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reaction. More... | |
| const SpeciesReference * | getReactant (const std::string &species) const |
| Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction. More... | |
| SpeciesReference * | getReactant (const std::string &species) |
| Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction. 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... | |
| bool | getReversible () const |
| Returns the value of the "reversible" attribute on the Reaction as a boolean value. 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 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 SBML object. More... | |
| std::string | getURI () const |
| Gets 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 |
Predicate returning true if all the required attributes for this Reaction object have been set. More... | |
| bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
| void | initDefaults () |
| Initializes the fields of this Reaction object to "typical" default values. 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 | isSetCompartment () const |
Predicate returning true if this Reaction's "compartment" attribute is set. More... | |
| bool | isSetFast () const |
Predicate returning true if the value of the "fast" attribute on this Reaction is set. More... | |
| virtual bool | isSetId () const |
Predicate returning true if this Reaction's "id" attribute is set. More... | |
| bool | isSetIdAttribute () const |
Predicate returning true if this object's "id" attribute is set. More... | |
| bool | isSetKineticLaw () const |
Predicate returning true if this Reaction contains a kinetic law object. 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... | |
| virtual bool | isSetName () const |
Predicate returning true if this Reaction's "name" attribute is set. More... | |
| bool | isSetNotes () const |
Predicate returning true if this object's "notes" subelement exists and has content. More... | |
| bool | isSetReversible () const |
Predicate returning true if this Reaction's "reversible" attribute is set. More... | |
| bool | isSetSBOTerm () const |
Predicate returning true if this object's "sboTerm" attribute is 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... | |
| Reaction & | operator= (const Reaction &rhs) |
| Assignment operator for Reaction. More... | |
| Reaction (unsigned int level, unsigned int version) | |
Creates a new Reaction using the given SBML level and version values. More... | |
| Reaction (SBMLNamespaces *sbmlns) | |
Creates a new Reaction using the given SBMLNamespaces object sbmlns. More... | |
| Reaction (const Reaction &orig) | |
| Copy constructor; creates a copy of this Reaction. More... | |
| void | read (XMLNode &node, XMLErrorSeverityOverride_t flag=LIBSBML_OVERRIDE_DISABLED) |
| Reads (initializes) this SBML object by reading from the given XMLNode. More... | |
| virtual int | removeFromParentAndDelete () |
| Removes this object from its parent. More... | |
| ModifierSpeciesReference * | removeModifier (unsigned int n) |
| Removes the nth modifier species (ModifierSpeciesReference object) in the list of modifiers in this Reaction and returns a pointer to it. More... | |
| ModifierSpeciesReference * | removeModifier (const std::string &species) |
| Removes the modifier species (ModifierSpeciesReference object) having the given "species" attribute in this Reaction and returns a pointer to it. More... | |
| SpeciesReference * | removeProduct (unsigned int n) |
| Removes the nth product species (SpeciesReference object) in the list of products in this Reaction and returns a pointer to it. More... | |
| SpeciesReference * | removeProduct (const std::string &species) |
| Removes the product species (SpeciesReference object) having the given "species" attribute in this Reaction and returns a pointer to it. More... | |
| SpeciesReference * | removeReactant (unsigned int n) |
| Removes the nth reactant species (SpeciesReference object) in the list of reactants in this Reaction and returns a pointer to it. More... | |
| SpeciesReference * | removeReactant (const std::string &species) |
| Removes the reactant species (SpeciesReference object) having the given "species" attribute in this Reaction and returns a pointer to it. 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) |
| Replaces all uses of a given meta identifier attribute value with another value. More... | |
| virtual void | renameSIdRefs (const std::string &oldid, const std::string &newid) |
Replaces all uses of a given SIdRef type attribute value with another value. More... | |
| virtual void | renameUnitSIdRefs (const std::string &oldid, const std::string &newid) |
Replaces all uses of a given UnitSIdRef type attribute value with another value. 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 | setCompartment (const std::string &sid) |
| Sets the value of the "compartment" attribute of this Reaction. More... | |
| int | setFast (bool value) |
| Sets the value of the "fast" attribute of this Reaction. More... | |
| virtual int | setId (const std::string &sid) |
| Sets the value of the "id" attribute of this Reaction. More... | |
| virtual int | setIdAttribute (const std::string &sid) |
| Sets the value of the "id" attribute of this SBML object. More... | |
| int | setKineticLaw (const KineticLaw *kl) |
| Sets the "kineticLaw" subelement of this Reaction to a copy of the given KineticLaw object. More... | |
| int | setMetaId (const std::string &metaid) |
| Sets the value of the meta-identifier attribute of this SBML object. More... | |
| int | setModelHistory (ModelHistory *history) |
| Sets the ModelHistory of this object. More... | |
| virtual int | setName (const std::string &name) |
| Sets the value of the "name" attribute of this Reaction. 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... | |
| int | setReversible (bool value) |
| Sets the value of the "reversible" attribute of this Reaction. 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... | |
| XMLNode * | toXMLNode () |
| Returns this element as an XMLNode. More... | |
| int | unsetAnnotation () |
| Unsets the value of the "annotation" subelement of this SBML object. More... | |
| int | unsetCompartment () |
| Unsets the value of the "compartment" attribute of this Reaction. More... | |
| int | unsetCVTerms () |
| Clears the list of CVTerm objects attached to this SBML object. More... | |
| int | unsetFast () |
| Unsets the value of the "fast" attribute of this Reaction. 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... | |
| int | unsetKineticLaw () |
| Unsets the "kineticLaw" subelement of this Reaction. 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 Reaction. More... | |
| int | unsetNotes () |
| Unsets the value of the "notes" subelement of this SBML object. More... | |
| int | unsetReversible () |
| Unsets the value of the "reversible" attribute of this Reaction. More... | |
| int | unsetSBOTerm () |
| Unsets the value of the "sboTerm" attribute of this SBML object. More... | |
| int | unsetUserData () |
| Unsets the user data of this element. More... | |
| virtual | ~Reaction () |
| Destroys this Reaction. 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... | |
| Reaction::Reaction | ( | unsigned int | level, |
| unsigned int | version | ||
| ) |
Creates a new Reaction using the given SBML level and version values.
| level | an unsigned int, the SBML Level to assign to this Reaction. |
| version | an unsigned int, the SBML Version to assign to this Reaction. |
| SBMLConstructorException | Thrown if the given level and version combination are invalid or if this object is incompatible with the given level and version. |
| Reaction::Reaction | ( | SBMLNamespaces * | sbmlns | ) |
Creates a new Reaction using the given SBMLNamespaces object sbmlns.
| sbmlns | an SBMLNamespaces object. |
| SBMLConstructorException | Thrown if the given sbmlns is inconsistent or incompatible with this object. |
|
virtual |
Destroys this Reaction.
| Reaction::Reaction | ( | const Reaction & | orig | ) |
Copy constructor; creates a copy of this Reaction.
| orig | the object to copy. |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
| term | the CVTerm to assign. |
| newBag | if true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
create) for alternatives that do not lead to these issues. | int Reaction::addModifier | ( | const ModifierSpeciesReference * | msr | ) |
Adds a given ModifierSpeciesReference object as a product in this Reaction.
The ModifierSpeciesReference instance in msr is copied.
| msr | a ModifierSpeciesReference object referring to a Species in the enclosing Model. |
create) for alternatives that do not lead to these issues.| int Reaction::addModifier | ( | const Species * | species, |
| const std::string | id = "" |
||
| ) |
Adds the given species as a modifier to this reaction.
| species | the species to be added as modifier. |
| id | an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set). |
create) for alternatives that do not lead to these issues.| int Reaction::addProduct | ( | const SpeciesReference * | sr | ) |
Adds a given SpeciesReference object as a product in this Reaction.
The SpeciesReference instance in sr is copied.
| sr | a SpeciesReference object referring to a Species in the enclosing Model. |
create) for alternatives that do not lead to these issues.| int Reaction::addProduct | ( | const Species * | species, |
| double | stoichiometry = 1.0, |
||
| const std::string | id = "", |
||
| bool | constant = true |
||
| ) |
Adds the given species as a product with the given stoichiometry.
| species | the species to be added as product. |
| stoichiometry | an optional parameter specifying the stoichiometry of the added product (defaulting to 1). |
| id | an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set). |
| constant | an attribute specifying whether the species reference is constant or not (defaulting to true). |
create) for alternatives that do not lead to these issues.| int Reaction::addReactant | ( | const SpeciesReference * | sr | ) |
Adds a given SpeciesReference object as a reactant in this Reaction.
The SpeciesReference instance in sr is copied.
| sr | a SpeciesReference object referring to a Species in the enclosing Model. |
create) for alternatives that do not lead to these issues.| int Reaction::addReactant | ( | const Species * | species, |
| double | stoichiometry = 1.0, |
||
| const std::string | id = "", |
||
| bool | constant = true |
||
| ) |
Adds the given species as a reactant with the given stoichiometry.
| species | the species to be added as reactant. |
| stoichiometry | an optional parameter specifying the stoichiometry of the added reactant (defaulting to 1). |
| id | an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set). |
| constant | an attribute specifying whether the species reference is constant or not (defaulting to true). |
create) for alternatives that do not lead to these issues.
|
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.
|
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.
|
inherited |
Appends the given notes to the "notes" subelement of this object.
The content of notes is copied.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
| notes | an XML node structure that is to appended to the content of the "notes" subelement of this object. |
|
inherited |
Appends the given notes to the "notes" subelement of this object.
The content of the parameter notes is copied.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
| notes | an XML string that is to appended to the content of the "notes" subelement of this object. |
|
virtual |
Creates and returns a deep copy of this Reaction object.
Implements SBase.
Reimplemented in IntraSpeciesReaction.
| KineticLaw * Reaction::createKineticLaw | ( | ) |
Creates a new KineticLaw object, installs it as this Reaction's "kineticLaw" subelement, and returns it.
If this Reaction had a previous KineticLaw, it will be destroyed.
| ModifierSpeciesReference * Reaction::createModifier | ( | ) |
Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it.
| SpeciesReference * Reaction::createProduct | ( | ) |
Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it.
| SpeciesReference * Reaction::createReactant | ( | ) |
Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it.
|
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. |
|
virtual |
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. |
|
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.
|
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.
|
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.
|
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.
|
inherited |
Returns the column number where this object first appears in the XML representation of the SBML document.
0.| const string & Reaction::getCompartment | ( | ) | const |
|
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.
|
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.
|
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. |
|
virtual |
Returns the first child element it can find with the given metaid, or NULL if no such object is found.
| metaid | string representing the metaid of the object to find. |
metaid. Reimplemented from SBase.
|
inherited |
Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.
| id | string representing the "id" attribute value of the object to find. |
|
virtual |
Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.
| id | string representing the id of the object to find. |
id. Reimplemented from SBase.
|
virtual |
Returns the XML element name of this object, which for Reaction, is always "reaction".
"reaction". Reimplemented from SBase.
Reimplemented in IntraSpeciesReaction.
| bool Reaction::getFast | ( | ) | const |
Returns the value of the "fast" attribute of this Reaction.
false. Users should be aware that even for previous levels/versions of the specification, "fast" attribute values of true never achieved widespread support, and many software packages may ignore it. To achieve the same or similar effects as setting the fast attribute to true for a given reaction, the KineticLaw attribute should be constructed to produce a value in the desired time scale, or else the reaction could be replaced with an AssignmentRule or AlgebraicRule.true. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with "fast" set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.
|
virtual |
Returns the value of the "id" attribute of this Reaction.
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 from SBase.
|
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.
| const KineticLaw * Reaction::getKineticLaw | ( | ) | const |
Returns the KineticLaw object contained in this Reaction.
| KineticLaw * Reaction::getKineticLaw | ( | ) |
Returns the KineticLaw object contained in this Reaction.
|
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.| const ListOfSpeciesReferences * Reaction::getListOfModifiers | ( | ) | const |
Returns the list of modifiers in this Reaction object.
| ListOfSpeciesReferences * Reaction::getListOfModifiers | ( | ) |
Returns the list of modifiers in this Reaction object.
| const ListOfSpeciesReferences * Reaction::getListOfProducts | ( | ) | const |
Returns the list of products in this Reaction object.
| ListOfSpeciesReferences * Reaction::getListOfProducts | ( | ) |
Returns the list of products in this Reaction object.
| const ListOfSpeciesReferences * Reaction::getListOfReactants | ( | ) | const |
Returns the list of reactants in this Reaction object.
| ListOfSpeciesReferences * Reaction::getListOfReactants | ( | ) |
Returns the list of reactants in this Reaction object.
|
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.
|
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.| const ModifierSpeciesReference * Reaction::getModifier | ( | unsigned int | n | ) | const |
Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of this Reaction.
Callers should first call getNumModifiers() to find out how many modifiers there are, to avoid using an invalid index number.
| n | the index of the modifier species sought. |
n is invalid, NULL is returned. | ModifierSpeciesReference * Reaction::getModifier | ( | unsigned int | n | ) |
Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of this Reaction.
Callers should first call getNumModifiers() to find out how many modifiers there are, to avoid using an invalid index number.
| n | the index of the modifier species sought. |
n is invalid, NULL is returned. | const ModifierSpeciesReference * Reaction::getModifier | ( | const std::string & | species | ) | const |
Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction.
| species | the identifier of the modifier Species ("species" attribute of the ModifierSpeciesReference object). |
NULL if no species with the given identifier species appears as a modifier in this Reaction. | ModifierSpeciesReference * Reaction::getModifier | ( | const std::string & | species | ) |
Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction.
| species | the identifier of the modifier Species ("species" attribute of the ModifierSpeciesReference object). |
NULL if no species with the given identifier species appears as a modifier in this Reaction.
|
virtual |
Returns the value of the "name" attribute of this Reaction 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 from SBase.
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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().
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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().
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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 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.
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inherited |
Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.
| unsigned int Reaction::getNumModifiers | ( | ) | const |
Returns the number of modifier species in this Reaction.
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inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
| unsigned int Reaction::getNumProducts | ( | ) | const |
Returns the number of product species in this Reaction.
| unsigned int Reaction::getNumReactants | ( | ) | const |
Returns the number of reactant species in this Reaction.
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inherited |
Returns the SBML Core Version within the SBML Level of the actual object.
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inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
"core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
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inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
0 will be returned if this element belongs to the SBML Level 3 Core package.
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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.
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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.
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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 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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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.
| const SpeciesReference * Reaction::getProduct | ( | unsigned int | n | ) | const |
Returns the nth product species (as a SpeciesReference object) in the list of products in this Reaction.
Callers should first call getNumProducts() to find out how many products there are, to avoid using an invalid index number.
| n | the index of the product sought. |
n is invalid, NULL is returned. | SpeciesReference * Reaction::getProduct | ( | unsigned int | n | ) |
Returns the nth product species (as a SpeciesReference object) in the list of products in this Reaction.
Callers should first call getNumProducts() to find out how many products there are, to avoid using an invalid index number.
| n | the index of the product sought. |
n is invalid, NULL is returned. | const SpeciesReference * Reaction::getProduct | ( | const std::string & | species | ) | const |
Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction.
| species | the identifier of the product Species ("species" attribute of the product SpeciesReference object). |
NULL if no species with the given identifier species appears as a product in this Reaction. | SpeciesReference * Reaction::getProduct | ( | const std::string & | species | ) |
Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction.
| species | the identifier of the product Species ("species" attribute of the product SpeciesReference object). |
NULL if no species with the given identifier species appears as a product in this Reaction. | const SpeciesReference * Reaction::getReactant | ( | unsigned int | n | ) | const |
Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reaction.
Callers should first call getNumReactants() to find out how many reactants there are, to avoid using an invalid index number.
| n | the index of the reactant sought. |
n is invalid, NULL is returned. | SpeciesReference * Reaction::getReactant | ( | unsigned int | n | ) |
Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reaction.
Callers should first call getNumReactants() to find out how many reactants there are, to avoid using an invalid index number.
| n | the index of the reactant sought. |
n is invalid, NULL is returned. | const SpeciesReference * Reaction::getReactant | ( | const std::string & | species | ) | const |
Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction.
| species | the identifier of the reactant Species ("species" attribute of the reactant SpeciesReference object). |
NULL if no species with the given identifier species appears as a reactant in this Reaction. | SpeciesReference * Reaction::getReactant | ( | const std::string & | species | ) |
Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction.
| species | the identifier of the reactant Species ("species" attribute of the reactant SpeciesReference object). |
NULL if no species with the given identifier species appears as a reactant in this Reaction.
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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". |
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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". |
| bool Reaction::getReversible | ( | ) | const |
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inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
Returns the integer portion of the value of the "sboTerm" attribute of this object.
int, and SBO identifiers are stored simply as integers. -1 if the value is not set.
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inherited |
Returns the URL representation of the "sboTerm" attribute of this object.
This method returns the entire SBO identifier as a text string in the form http://identifiers.org/biomodels.sbo/SBO:NNNNNNN".
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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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virtual |
Returns the libSBML type code for this SBML object.
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 SBase.
Reimplemented in IntraSpeciesReaction.
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inherited |
Gets the namespace URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/layout/version1".
This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.
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inherited |
Returns the user data that has been previously set via setUserData().
NULL if no user data has been set.
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inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
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virtual |
Predicate returning true if all the required attributes for this Reaction object have been set.
The required attributes for a Reaction object are:
true if the required attributes have been set, false otherwise. Reimplemented in IntraSpeciesReaction.
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inherited |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.
The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
http://www.sbml.org/sbml/level1" http://www.sbml.org/sbml/level2" http://www.sbml.org/sbml/level2/version2" http://www.sbml.org/sbml/level2/version3" http://www.sbml.org/sbml/level2/version4" http://www.sbml.org/sbml/level2/version5" http://www.sbml.org/sbml/level3/version1/core" http://www.sbml.org/sbml/level3/version2/core" true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise. | void Reaction::initDefaults | ( | ) |
Initializes the fields of this Reaction object to "typical" default values.
The SBML Reaction component has slightly different aspects and default attribute values in different SBML Levels and Versions. This method sets the values to certain common defaults, based mostly on what they are in SBML Level 2. Specifically:
true false true. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with "fast" set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.
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inherited |
Predicate returning true if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
| pkgName | the name of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.
| pkgURI | the URI of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
| pkgName | the name of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.
| pkgURI | the URI of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if this object's "annotation" subelement exists and has content.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
true if a "annotation" subelement exists, false otherwise.| bool Reaction::isSetCompartment | ( | ) | const |
| bool Reaction::isSetFast | ( | ) | const |
Predicate returning true if the value of the "fast" attribute on this Reaction is set.
false. Users should be aware that even for previous levels/versions of the specification, "fast" attribute values of true never achieved widespread support, and many software packages may ignore it. To achieve the same or similar effects as setting the fast attribute to true for a given reaction, the KineticLaw attribute should be constructed to produce a value in the desired time scale, or else the reaction could be replaced with an AssignmentRule or AlgebraicRule.true if the "fast" attribute is set, false otherwise.true. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with "fast" set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.
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virtual |
Predicate returning true if this Reaction'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.Reimplemented from SBase.
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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.| bool Reaction::isSetKineticLaw | ( | ) | const |
Predicate returning true if this Reaction contains a kinetic law object.
true if a KineticLaw is present in this Reaction,, false otherwise.
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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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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.
|
virtual |
Predicate returning true if this Reaction'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 from SBase.
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inherited |
Predicate returning true if this object's "notes" subelement exists and has content.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
true if a "notes" subelement exists, false otherwise.| bool Reaction::isSetReversible | ( | ) | const |
|
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 |
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.
|
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. Assignment operator for Reaction.
| rhs | the object whose values are used as the basis of the assignment. |
|
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. |
|
virtualinherited |
Removes this object from its parent.
If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
Reimplemented in Model, KineticLaw, SBaseRef, StoichiometryMath, Trigger, Delay, ListOf, Priority, ModelDefinition, and ReplacedBy.
| ModifierSpeciesReference * Reaction::removeModifier | ( | unsigned int | n | ) |
Removes the nth modifier species (ModifierSpeciesReference object) in the list of modifiers in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. The caller should first call getNumModifiers() to find out how many modifiers there are, to avoid using an invalid index number.
| n | the index of the ModifierSpeciesReference object to remove. |
NULL if the given index is out of range. | ModifierSpeciesReference * Reaction::removeModifier | ( | const std::string & | species | ) |
Removes the modifier species (ModifierSpeciesReference object) having the given "species" attribute in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
| species | the "species" attribute of the ModifierSpeciesReference object. |
NULL if no ModifierSpeciesReference object with the given "species" attribute species exists in this Reaction. | SpeciesReference * Reaction::removeProduct | ( | unsigned int | n | ) |
Removes the nth product species (SpeciesReference object) in the list of products in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. The caller should first call getNumProducts() to find out how many products there are, to avoid using an invalid index number.
| n | the index of the product SpeciesReference object to remove. |
NULL if the given index is out of range. | SpeciesReference * Reaction::removeProduct | ( | const std::string & | species | ) |
Removes the product species (SpeciesReference object) having the given "species" attribute in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
| species | the "species" attribute of the product SpeciesReference object. |
NULL if no product SpeciesReference object with the given "species" attribute species exists in this Reaction. | SpeciesReference * Reaction::removeReactant | ( | unsigned int | n | ) |
Removes the nth reactant species (SpeciesReference object) in the list of reactants in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. The caller should first call getNumReactants() to find out how many reactants there are, to avoid using an invalid index number.
| n | the index of the reactant SpeciesReference object to remove. |
NULL if the given index is out of range. | SpeciesReference * Reaction::removeReactant | ( | const std::string & | species | ) |
Removes the reactant species (SpeciesReference object) having the given "species" attribute in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
| species | the "species" attribute of the reactant SpeciesReference object. |
NULL if no reactant SpeciesReference object with the given "species" attribute species exists in this Reaction.
|
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 |
Replaces all uses of a given meta identifier attribute value with another value.
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 Port, and GraphicalObject.
|
virtual |
Replaces all uses of a given SIdRef type attribute value with another value.
In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to an identifier", but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier. |
| newid | the new identifier. |
Reimplemented from SBase.
|
virtualinherited |
Replaces all uses of a given 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 Model, Species, Compartment, KineticLaw, Rule, Parameter, EventAssignment, InitialAssignment, 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) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.
| annotation | XMLNode representing the replacement top level annotation. |
|
inherited |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.
| annotation | string representing the replacement top level annotation. |
|
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.
| int Reaction::setCompartment | ( | const std::string & | sid | ) |
Sets the value of the "compartment" attribute of this Reaction.
The string sid is copied.
| sid | the string to use as the compartment of this Reaction. |
|
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. |
| int Reaction::setFast | ( | bool | value | ) |
Sets the value of the "fast" attribute of this Reaction.
false. Users should be aware that even for previous levels/versions of the specification, "fast" attribute values of true never achieved widespread support, and many software packages may ignore it. To achieve the same or similar effects as setting the fast attribute to true for a given reaction, the KineticLaw attribute should be constructed to produce a value in the desired time scale, or else the reaction could be replaced with an AssignmentRule or AlgebraicRule.Calling this function with an argument of true for an SBML Level 3 Version 2 Reaction will not set the value, as the attribute does not exist for that level/version.
| value | the value of the "fast" attribute. |
true. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with "fast" set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.
|
virtual |
Sets the value of the "id" attribute of this Reaction.
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 from SBase.
|
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. |
| int Reaction::setKineticLaw | ( | const KineticLaw * | kl | ) |
Sets the "kineticLaw" subelement of this Reaction to a copy of the given KineticLaw object.
| kl | the KineticLaw object to use. |
|
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. |
|
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. |
|
virtual |
Sets the value of the "name" attribute of this Reaction.
The string in name is copied.
| name | the new name for the SBML object. |
Reimplemented from SBase.
|
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. |
| int Reaction::setReversible | ( | bool | value | ) |
Sets the value of the "reversible" attribute of this Reaction.
| value | the value of the "reversible" attribute. |
|
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 "sboTerm" attribute by string.
int, and SBO identifiers are stored simply as integers. | sboid | the SBO identifier string of the form "SBO:NNNNNNN". |
|
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.
| int Reaction::unsetCompartment | ( | ) |
Unsets the value of the "compartment" attribute of this Reaction.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
| int Reaction::unsetFast | ( | ) |
Unsets the value of the "fast" attribute of this Reaction.
false. Users should be aware that even for previous levels/versions of the specification, "fast" attribute values of true never achieved widespread support, and many software packages may ignore it. To achieve the same or similar effects as setting the fast attribute to true for a given reaction, the KineticLaw attribute should be constructed to produce a value in the desired time scale, or else the reaction could be replaced with an AssignmentRule or AlgebraicRule.true. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with "fast" set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.
|
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 Model, Layout, Event, RenderInformationBase, ColorDefinition, GraphicalPrimitive1D, GradientBase, Group, Input, QualitativeSpecies, Objective, GeneProductAssociation, Output, FluxObjective, GeneProduct, Submodel, Image, Member, LineEnding, Dimensions, GeneProductRef, Style, GraphicalObject, Transition, ListOfMembers, SimpleSpeciesReference, OutwardBindingSite, Point, FluxBound, ExternalModelDefinition, SubListOfSpeciesFeatures, Deletion, BoundingBox, MultiSpeciesType, SpeciesFeature, Port, SpeciesFeatureType, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, InSpeciesTypeBond, PossibleSpeciesFeatureValue, GeneAssociation, and CompartmentReference.
|
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.
| int Reaction::unsetKineticLaw | ( | ) |
Unsets the "kineticLaw" subelement of this Reaction.
|
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.
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inherited |
Unsets the ModelHistory object attached to this object.
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virtual |
Unsets the value of the "name" attribute of this Reaction.
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 from SBase.
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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.
| int Reaction::unsetReversible | ( | ) |
Unsets the value of the "reversible" attribute of this Reaction.
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inherited |
Unsets the value of the "sboTerm" attribute of this SBML object.
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inherited |
Unsets the user data of this element.