libSBML C# API  libSBML 5.8.0 C# API
 All Classes Namespaces Files Functions Variables Properties Pages
libsbmlcs.Reaction Class Reference
Inheritance diagram for libsbmlcs.Reaction:
[legend]

Detailed Description

Implementation of SBML's Reaction construct.

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 object in SBML, Reaction has a mandatory attribute, 'id', used to give the compartment type 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 definition can contain an empty list of reactants or an empty list of products, but it must have at least one reactant or product; in other words, a reaction without any reactant or product species is not permitted. (This restriction does not apply to modifier species, which remain optional in all cases.)

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 bool 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 bool 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). 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. The attribute's default value is false. 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'.

In SBML Level 3 Version 1, 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)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
int addCVTerm (CVTerm term)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
int addModifier (ModifierSpeciesReference msr)
 Adds a given ModifierSpeciesReference object as a product in this Reaction. More...
 
int addProduct (SpeciesReference sr)
 Adds a given SpeciesReference object as a product in this Reaction. More...
 
int addReactant (SpeciesReference sr)
 Adds a given SpeciesReference object as a reactant in this Reaction. More...
 
int appendAnnotation (XMLNode annotation)
 Appends the given annotation to the 'annotation' subelement of this object. More...
 
int appendAnnotation (string annotation)
 Appends the given annotation to the 'annotation' subelement of this object. More...
 
int appendNotes (XMLNode notes)
 Appends the given notes to the 'notes' subelement of this object. More...
 
int appendNotes (string notes)
 Appends the given notes to the 'notes' subelement of this object. More...
 
int checkCompatibility (SBase arg0)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
string checkMathMLNamespace (XMLToken elem)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
new Reaction clone ()
 Creates and returns a deep copy of this Reaction. More...
 
void connectToParent (SBase parent)
 Sets the parent SBML object of this SBML 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...
 
int disablePackage (string pkgURI, string pkgPrefix)
 Disables the given SBML Level 3 package. More...
 
override void Dispose ()
 
void divideAssignmentsToSIdByFunction (string id, ASTNode function)
 If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More...
 
int enablePackage (string pkgURI, string pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package. More...
 
override bool Equals (Object sb)
 
SBase getAncestorOfType (int type, string pkgName)
 Returns the first ancestor object that has the given SBML type code. More...
 
SBase getAncestorOfType (int type)
 Returns the first ancestor object that has the given SBML type code. More...
 
XMLNode getAnnotation ()
 Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More...
 
string getAnnotationString ()
 Returns the content of the 'annotation' subelement of this object as a character string. More...
 
long getColumn ()
 Returns the column number on which this object first appears in the XML representation of the SBML document. More...
 
string getCompartment ()
 (SBML Level 3 only) Returns the value of the 'compartment' attribute on the Reaction. More...
 
CVTerm getCVTerm (long n)
 Returns the nth CVTerm in the list of CVTerms of this SBML object. More...
 
CVTermList getCVTerms ()
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
SBase getElementByMetaId (string metaid)
 Returns the first child element it can find with the given metaid, or null if no such object is found. More...
 
SBase getElementBySId (string id)
 Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found. More...
 
SBase getElementFromPluginsByMetaId (string metaid)
 Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found. More...
 
SBase getElementFromPluginsBySId (string id)
 Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found. More...
 
new string getElementName ()
 Returns the XML element name of this object, which for Reaction, is always 'reaction'. More...
 
bool getFast ()
 Returns the value of the 'fast' attribute of this Reaction. More...
 
override int GetHashCode ()
 
new string getId ()
 Returns the value of the 'id' attribute of this Reaction. More...
 
KineticLaw getKineticLaw ()
 Returns the KineticLaw object contained in this Reaction. More...
 
long getLevel ()
 Returns the SBML Level of the SBMLDocument object containing this object. More...
 
long getLine ()
 Returns the line number on which this object first appears in the XML representation of the SBML document. More...
 
SBaseList getListOfAllElements ()
 
SBaseList getListOfAllElementsFromPlugins ()
 
ListOfSpeciesReferences getListOfModifiers ()
 Returns the list of modifiers in this Reaction object. More...
 
ListOfSpeciesReferences getListOfProducts ()
 Returns the list of products in this Reaction object. More...
 
ListOfSpeciesReferences getListOfReactants ()
 Returns the list of reactants in this Reaction object. More...
 
string getMetaId ()
 Returns the value of the 'metaid' attribute of this object. More...
 
Model getModel ()
 Returns the Model object in which the current object is located. More...
 
ModelHistory getModelHistory ()
 Returns the ModelHistory object, if any, attached to this object. More...
 
ModifierSpeciesReference getModifier (long n)
 Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of this Reaction. More...
 
ModifierSpeciesReference getModifier (string species)
 Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction. More...
 
new string getName ()
 Returns the value of the 'name' attribute of this Reaction. More...
 
XMLNamespaces getNamespaces ()
 Returns a list of the XML Namespaces declared on this SBML document. More...
 
XMLNode getNotes ()
 Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More...
 
string getNotesString ()
 Returns the content of the 'notes' subelement of this object as a string. More...
 
long getNumCVTerms ()
 Returns the number of CVTerm objects in the annotations of this SBML object. More...
 
long getNumModifiers ()
 Returns the number of modifier species in this Reaction. More...
 
long getNumPlugins ()
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
long getNumProducts ()
 Returns the number of product species in this Reaction. More...
 
long getNumReactants ()
 Returns the number of reactant species in this Reaction. More...
 
string getPackageName ()
 Returns the name of the SBML Level 3 package in which this element is defined. More...
 
long getPackageVersion ()
 Returns the Version of the SBML Level 3 package to which this element belongs to. More...
 
SBase getParentSBMLObject ()
 Returns the parent SBML object containing this object. More...
 
SBasePlugin getPlugin (string package)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
SBasePlugin getPlugin (long n)
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
SpeciesReference getProduct (long n)
 Returns the nth product species (as a SpeciesReference object) in the list of products in this Reaction. More...
 
SpeciesReference getProduct (string species)
 Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction. More...
 
SpeciesReference getReactant (long n)
 Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reaction. More...
 
SpeciesReference getReactant (string species)
 Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction. More...
 
int getResourceBiologicalQualifier (string resource)
 Returns the MIRIAM biological qualifier associated with the given resource. More...
 
int getResourceModelQualifier (string resource)
 Returns the MIRIAM model qualifier associated with the given resource. More...
 
bool getReversible ()
 Returns the value of the 'reversible' attribute on the Reaction as a bool value. More...
 
SBMLDocument getSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
SBMLNamespaces getSBMLNamespaces ()
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
int getSBOTerm ()
 Returns the integer portion of the value of the 'sboTerm' attribute of this object. More...
 
string getSBOTermAsURL ()
 Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object. More...
 
string getSBOTermID ()
 Returns the string representation of the 'sboTerm' attribute of this object. More...
 
new int getTypeCode ()
 Returns the libSBML type code for this SBML object. More...
 
long getVersion ()
 Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...
 
bool hasNonstandardIdentifierBeginningWith (string prefix)
 Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid'). More...
 
new bool hasRequiredAttributes ()
 Predicate returning true if all the required attributes for this Reaction object have been set. More...
 
bool hasRequiredElements ()
 Subclasses should override this method to write out their contained SBML objects as XML elements. 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 (string pkgName)
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPackageURIEnabled (string pkgURI)
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPkgEnabled (string pkgName)
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPkgURIEnabled (string pkgURI)
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isSetAnnotation ()
 Predicate returning true if this object's 'annotation' subelement exists and has content. More...
 
bool isSetCompartment ()
 Predicate returning true if this Reaction's 'compartment' attribute is set. More...
 
bool isSetFast ()
 Predicate returning true if the value of the 'fast' attribute on this Reaction. More...
 
new bool isSetId ()
 Predicate returning true if this Reaction's 'id' attribute is set. More...
 
bool isSetKineticLaw ()
 Predicate returning true if this Reaction contains a kinetic law object. More...
 
bool isSetMetaId ()
 Predicate returning true if this object's 'metaid' attribute is set. More...
 
bool isSetModelHistory ()
 Predicate returning true if this object has a ModelHistory object attached to it. More...
 
new bool isSetName ()
 Predicate returning true if this Reaction's 'name' attribute is set. More...
 
bool isSetNotes ()
 Predicate returning true if this object's 'notes' subelement exists and has content. More...
 
bool isSetReversible ()
 Predicate returning true if this Reaction's 'reversible' attribute is set. More...
 
bool isSetSBOTerm ()
 Predicate returning true if this object's 'sboTerm' attribute is set. More...
 
bool matchesRequiredSBMLNamespacesForAddition (SBase sb)
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (SBase sb)
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
void multiplyAssignmentsToSIdByFunction (string id, ASTNode function)
 If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More...
 
int prependStringToAllIdentifiers (string prefix)
 Add the given string to all identifiers in the object. More...
 
 Reaction (long level, long 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 (Reaction orig)
 Copy constructor; creates a copy of this Reaction. More...
 
int removeFromParentAndDelete ()
 Removes itself from its parent. More...
 
ModifierSpeciesReference removeModifier (long 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 (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 (long 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 (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 (long 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 (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 (string elementName, string elementURI)
 Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...
 
int removeTopLevelAnnotationElement (string elementName)
 Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...
 
void renameMetaIdRefs (string oldid, string newid)
 Renames all the MetaIdRef attributes on this element. More...
 
void renameSIdRefs (string oldid, string newid)
 Renames all the SIdRef attributes on this element, including any found in MathML. More...
 
void renameUnitSIdRefs (string oldid, string newid)
 Renames all the UnitSIdRef attributes on this element. More...
 
void replaceSIDWithFunction (string id, ASTNode function)
 If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More...
 
int replaceTopLevelAnnotationElement (XMLNode annotation)
 Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More...
 
int replaceTopLevelAnnotationElement (string annotation)
 Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More...
 
int setAnnotation (XMLNode annotation)
 Sets the value of the 'annotation' subelement of this SBML object. More...
 
int setAnnotation (string annotation)
 Sets the value of the 'annotation' subelement of this SBML object. More...
 
int setCompartment (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...
 
new int setId (string sid)
 Sets the value of the 'id' attribute of this Reaction. More...
 
int setKineticLaw (KineticLaw kl)
 Sets the 'kineticLaw' subelement of this Reaction to a copy of the given KineticLaw object. More...
 
int setMetaId (string metaid)
 Sets the value of the 'metaid' attribute of this object. More...
 
int setModelHistory (ModelHistory history)
 Sets the ModelHistory of this object. More...
 
new int setName (string name)
 Sets the value of the 'name' attribute of this Reaction. More...
 
int setNamespaces (XMLNamespaces xmlns)
 Sets the namespaces relevant of this SBML object. More...
 
int setNotes (XMLNode notes)
 Sets the value of the 'notes' subelement of this SBML object. More...
 
int setNotes (string notes, bool addXHTMLMarkup)
 Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes. More...
 
int setNotes (string notes)
 Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes. More...
 
int setReversible (bool value)
 Sets the value of the 'reversible' attribute of this Reaction. More...
 
void setSBMLNamespacesAndOwn (SBMLNamespaces sbmlns)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
int setSBOTerm (int value)
 Sets the value of the 'sboTerm' attribute. More...
 
int setSBOTerm (string sboid)
 Sets the value of the 'sboTerm' attribute by string. More...
 
string toSBML ()
 Returns a string consisting of a partial SBML corresponding to just this object. More...
 
int unsetAnnotation ()
 Unsets the value of the 'annotation' subelement of this SBML object. More...
 
int 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...
 
int unsetId ()
 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...
 
new 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 unsetSBOTerm ()
 Unsets the value of the 'sboTerm' attribute of this SBML object. More...
 
void writeExtensionElements (XMLOutputStream stream)
 Writes out contained SBML objects of package extensions (if any) as XML elements. More...
 

Static Public Member Functions

static bool operator!= (SBase lhs, SBase rhs)
 
static bool operator== (SBase lhs, SBase rhs)
 

Protected Attributes

bool swigCMemOwn
 

Constructor & Destructor Documentation

libsbmlcs.Reaction.Reaction ( long  level,
long  version 
)

Creates a new Reaction using the given SBML level and version values.

Parameters
levela long integer, the SBML Level to assign to this Reaction
versiona long integer, the SBML Version to assign to this Reaction
Exceptions
SBMLConstructorExceptionThrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object.
Note
Upon the addition of a Reaction object to an SBMLDocument (e.g., using Model::addReaction()), the SBML Level, SBML Version and XML namespace of the document override the values used when creating the Reaction object via this constructor. This is necessary to ensure that an SBML document is a consistent structure. Nevertheless, the ability to supply the values at the time of creation of a Reaction is an important aid to producing valid SBML. Knowledge of the intented SBML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing SBMLDocument.
libsbmlcs.Reaction.Reaction ( SBMLNamespaces  sbmlns)

Creates a new Reaction using the given SBMLNamespaces object sbmlns.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using this class constructor is to create an SBMLNamespaces object somewhere in a program, once, then pass it to object constructors such as this one when needed.

Parameters
sbmlnsan SBMLNamespaces object.
Exceptions
SBMLConstructorExceptionThrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object.
Note
Upon the addition of a Reaction object to an SBMLDocument (e.g., using Model::addReaction()), the SBML XML namespace of the document overrides the value used when creating the Reaction object via this constructor. This is necessary to ensure that an SBML document is a consistent structure. Nevertheless, the ability to supply the values at the time of creation of a Reaction is an important aid to producing valid SBML. Knowledge of the intented SBML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing SBMLDocument.
libsbmlcs.Reaction.Reaction ( Reaction  orig)

Copy constructor; creates a copy of this Reaction.

Parameters
origthe object to copy.
Exceptions
SBMLConstructorExceptionThrown if the argument orig is null.

Member Function Documentation

int libsbmlcs.SBase.addCVTerm ( CVTerm  term,
bool  newBag 
)
inherited

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif 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.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
int libsbmlcs.SBase.addCVTerm ( CVTerm  term)
inherited

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif 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.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
int libsbmlcs.Reaction.addModifier ( ModifierSpeciesReference  msr)

Adds a given ModifierSpeciesReference object as a product in this Reaction.

The ModifierSpeciesReference instance in msr is copied.

Parameters
msra ModifierSpeciesReference object referring to a Species in the enclosing Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Reaction. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Reaction. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Reaction::createModifier() for a method that does not lead to these issues.
See Also
createModifier()
int libsbmlcs.Reaction.addProduct ( SpeciesReference  sr)

Adds a given SpeciesReference object as a product in this Reaction.

The SpeciesReference instance in sr is copied.

Parameters
sra SpeciesReference object referring to a Species in the enclosing Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Reaction. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Reaction. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Reaction::createProduct() for a method that does not lead to these issues.
See Also
createProduct()
int libsbmlcs.Reaction.addReactant ( SpeciesReference  sr)

Adds a given SpeciesReference object as a reactant in this Reaction.

The SpeciesReference instance in sr is copied.

Parameters
sra SpeciesReference object referring to a Species in the enclosing Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Reaction. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Reaction. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Reaction::createReactant() for a method that does not lead to these issues.
See Also
createReactant()
int libsbmlcs.SBase.appendAnnotation ( XMLNode  annotation)
inherited

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.SBase.appendAnnotation ( string  annotation)
inherited

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
unsetAnnotation()
int libsbmlcs.SBase.appendNotes ( XMLNode  notes)
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.

Parameters
notesan XML node structure that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.appendNotes ( string  notes)
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.

Parameters
notesan XML string that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.checkCompatibility ( SBase  arg0)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

string libsbmlcs.SBase.checkMathMLNamespace ( XMLToken  elem)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

new Reaction libsbmlcs.Reaction.clone ( )

Creates and returns a deep copy of this Reaction.

Returns
a (deep) copy of this Reaction.
void libsbmlcs.SBase.connectToParent ( SBase  parent)
inherited

Sets the parent SBML object of this SBML object.

(Creates a child-parent relationship by the child) This function is called when a child element is set/added/created by its parent element (e.g. by setXXX, addXXX, createXXX, and connectToChild functions of the parent element).

Parameters
parentthe SBML object to use
KineticLaw libsbmlcs.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.

Returns
the new KineticLaw object
ModifierSpeciesReference libsbmlcs.Reaction.createModifier ( )

Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it.

Returns
a new ModifierSpeciesReference object.
SpeciesReference libsbmlcs.Reaction.createProduct ( )

Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it.

Returns
a new SpeciesReference object.
SpeciesReference libsbmlcs.Reaction.createReactant ( )

Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it.

Returns
a new SpeciesReference object.
int libsbmlcs.SBase.disablePackage ( string  pkgURI,
string  pkgPrefix 
)
inherited

Disables the given SBML Level 3 package.

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
override void libsbmlcs.Reaction.Dispose ( )
virtual

Reimplemented from libsbmlcs.SBase.

void libsbmlcs.SBase.divideAssignmentsToSIdByFunction ( string  id,
ASTNode  function 
)
inherited

If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).

Note
This function does nothing itself—subclasses with ASTNode subelements must override this function.
int libsbmlcs.SBase.enablePackage ( string  pkgURI,
string  pkgPrefix,
bool  flag 
)
inherited

Enables or disables the given SBML Level 3 package.

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
flagwhether to enable (true) or disable (false) the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
override bool libsbmlcs.SBase.Equals ( Object  sb)
inherited
SBase libsbmlcs.SBase.getAncestorOfType ( int  type,
string  pkgName 
)
inherited

Returns the first ancestor object that has the given SBML type code.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters
typethe 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
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.
SBase libsbmlcs.SBase.getAncestorOfType ( int  type)
inherited

Returns the first ancestor object that has the given SBML type code.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters
typethe 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
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.
XMLNode libsbmlcs.SBase.getAnnotation ( )
inherited

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
string libsbmlcs.SBase.getAnnotationString ( )
inherited

Returns the content of the 'annotation' subelement of this object as a character string.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form.

Returns
the annotation of this SBML object as a character string.
See Also
getAnnotation()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
long libsbmlcs.SBase.getColumn ( )
inherited

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns
the column number of this SBML object.
Note
The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See Also
getLine()
string libsbmlcs.Reaction.getCompartment ( )

(SBML Level 3 only) Returns the value of the 'compartment' attribute on the Reaction.

Returns
the compartment of this Reaction.
Note
The 'compartment' attribute is available in SBML Level 3 Version 1 Core, but is not present on Reaction in lower Levels of SBML.
CVTerm libsbmlcs.SBase.getCVTerm ( long  n)
inherited

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters
nlong the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
CVTermList libsbmlcs.SBase.getCVTerms ( )
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns
the list of CVTerms for this SBML object.
SBase libsbmlcs.Reaction.getElementByMetaId ( string  metaid)

Returns the first child element it can find with the given metaid, or null if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
SBase libsbmlcs.Reaction.getElementBySId ( string  id)

Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.

Parameters
idstring representing the id of objects to find.
Returns
pointer to the first element found with the given id.
SBase libsbmlcs.SBase.getElementFromPluginsByMetaId ( string  metaid)
inherited

Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
SBase libsbmlcs.SBase.getElementFromPluginsBySId ( string  id)
inherited

Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found.

Parameters
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.
new string libsbmlcs.Reaction.getElementName ( )

Returns the XML element name of this object, which for Reaction, is always 'reaction'.

Returns
the name of this element, i.e., 'reaction'.
bool libsbmlcs.Reaction.getFast ( )

Returns the value of the 'fast' attribute of this Reaction.

Returns
the 'fast' status of this Reaction.
Warning
SBML definitions before SBML Level 2 Version 2 incorrectly indicated 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, 3 and 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. 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.
override int libsbmlcs.SBase.GetHashCode ( )
inherited
new string libsbmlcs.Reaction.getId ( )

Returns the value of the 'id' attribute of this Reaction.

Returns
the id of this Reaction.
KineticLaw libsbmlcs.Reaction.getKineticLaw ( )

Returns the KineticLaw object contained in this Reaction.

Returns
the KineticLaw instance.
long libsbmlcs.SBase.getLevel ( )
inherited

Returns the SBML Level of the SBMLDocument object containing this object.

Returns
the SBML level of this SBML object.
See Also
getVersion()
getNamespaces()
getPackageVersion()
long libsbmlcs.SBase.getLine ( )
inherited

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns
the line number of this SBML object.
Note
The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See Also
getColumn()
SBaseList libsbmlcs.SBase.getListOfAllElements ( )
inherited
SBaseList libsbmlcs.SBase.getListOfAllElementsFromPlugins ( )
inherited
ListOfSpeciesReferences libsbmlcs.Reaction.getListOfModifiers ( )

Returns the list of modifiers in this Reaction object.

Returns
the ListOfSpeciesReferences containing the references to the species acting as modifiers in this reaction
ListOfSpeciesReferences libsbmlcs.Reaction.getListOfProducts ( )

Returns the list of products in this Reaction object.

Returns
the ListOfSpeciesReferences containing the references to the species acting as products in this reaction
ListOfSpeciesReferences libsbmlcs.Reaction.getListOfReactants ( )

Returns the list of reactants in this Reaction object.

Returns
the ListOfSpeciesReferences containing the references to the species acting as reactants in this reaction
string libsbmlcs.SBase.getMetaId ( )
inherited

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
the meta-identifier of this SBML object.
See Also
isSetMetaId()
setMetaId(string metaid)
Model libsbmlcs.SBase.getModel ( )
inherited

Returns the Model object in which the current object is located.

Returns
the parent Model of this SBML object.
See Also
getParentSBMLObject()
getSBMLDocument()
ModelHistory libsbmlcs.SBase.getModelHistory ( )
inherited

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or null if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
ModifierSpeciesReference libsbmlcs.Reaction.getModifier ( long  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.

Parameters
nthe index of the modifier species sought
Returns
the nth modifier (as a ModifierSpeciesReference object) of this Reaction.
ModifierSpeciesReference libsbmlcs.Reaction.getModifier ( string  species)

Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction.

Parameters
speciesthe identifier of the modifier Species ('species' attribute of the ModifierSpeciesReference object)
Returns
a ModifierSpeciesReference object, or null if no species with the given identifier species appears as a modifier in this Reaction.
new string libsbmlcs.Reaction.getName ( )

Returns the value of the 'name' attribute of this Reaction.

Returns
the name of this Reaction.
XMLNamespaces libsbmlcs.SBase.getNamespaces ( )
inherited

Returns a list of the XML Namespaces declared on this SBML document.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.

Returns
the XML Namespaces associated with this SBML object
See Also
getLevel()
getVersion()
XMLNode libsbmlcs.SBase.getNotes ( )
inherited

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns
the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
string libsbmlcs.SBase.getNotesString ( )
inherited

Returns the content of the 'notes' subelement of this object as a string.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns
the content of the 'notes' subelement of this SBML object as a string.
See Also
getNotes()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
long libsbmlcs.SBase.getNumCVTerms ( )
inherited

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns
the number of CVTerms for this SBML object.
long libsbmlcs.Reaction.getNumModifiers ( )

Returns the number of modifier species in this Reaction.

Returns
the number of modifiers in this Reaction.
long libsbmlcs.SBase.getNumPlugins ( )
inherited

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
long libsbmlcs.Reaction.getNumProducts ( )

Returns the number of product species in this Reaction.

Returns
the number of products in this Reaction.
long libsbmlcs.Reaction.getNumReactants ( )

Returns the number of reactant species in this Reaction.

Returns
the number of reactants in this Reaction.
string libsbmlcs.SBase.getPackageName ( )
inherited

Returns the name of the SBML Level 3 package in which this element is defined.

Returns
the name of the SBML package in which this element is defined. The string "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.
long libsbmlcs.SBase.getPackageVersion ( )
inherited

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See Also
getLevel()
getVersion()
SBase libsbmlcs.SBase.getParentSBMLObject ( )
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.

Returns
the parent SBML object of this SBML object.
See Also
getSBMLDocument()
getModel()
SBasePlugin libsbmlcs.SBase.getPlugin ( string  package)
inherited

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
SBasePlugin libsbmlcs.SBase.getPlugin ( long  n)
inherited

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
SpeciesReference libsbmlcs.Reaction.getProduct ( long  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.

Parameters
nthe index of the product sought.
Returns
the nth product (as a SpeciesReference object) of this Reaction.
SpeciesReference libsbmlcs.Reaction.getProduct ( string  species)

Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction.

Parameters
speciesthe identifier of the product Species ('species' attribute of the product SpeciesReference object)
Returns
a SpeciesReference object, or null if no species with the given identifier species appears as a product in this Reaction.
SpeciesReference libsbmlcs.Reaction.getReactant ( long  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.

Parameters
nthe index of the reactant sought.
Returns
the nth reactant (as a SpeciesReference object) of this Reaction.
SpeciesReference libsbmlcs.Reaction.getReactant ( string  species)

Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction.

Parameters
speciesthe identifier of the reactant Species ('species' attribute of the reactant SpeciesReference object)
Returns
a SpeciesReference object, or null if no species with the given identifier species appears as a reactant in this Reaction.
int libsbmlcs.SBase.getResourceBiologicalQualifier ( string  resource)
inherited

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
int libsbmlcs.SBase.getResourceModelQualifier ( string  resource)
inherited

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
bool libsbmlcs.Reaction.getReversible ( )

Returns the value of the 'reversible' attribute on the Reaction as a bool value.

Returns
the reversibility status of this Reaction.
SBMLDocument libsbmlcs.SBase.getSBMLDocument ( )
inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See Also
getParentSBMLObject()
getModel()
SBMLNamespaces libsbmlcs.SBase.getSBMLNamespaces ( )
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

int libsbmlcs.SBase.getSBOTerm ( )
inherited

Returns the integer portion of the value of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.
string libsbmlcs.SBase.getSBOTermAsURL ( )
inherited

Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.

This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.
string libsbmlcs.SBase.getSBOTermID ( )
inherited

Returns the string representation of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.
new int libsbmlcs.Reaction.getTypeCode ( )

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml. The names of the type codes all begin with the characters SBML_.

Returns
the SBML type code for this object, or SBML_UNKNOWN (default).
See Also
getElementName()
long libsbmlcs.SBase.getVersion ( )
inherited

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

Returns
the SBML version of this SBML object.
See Also
getLevel()
getNamespaces()
bool libsbmlcs.SBase.hasNonstandardIdentifierBeginningWith ( string  prefix)
inherited

Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid').

new bool libsbmlcs.Reaction.hasRequiredAttributes ( )

Predicate returning true if all the required attributes for this Reaction object have been set.

Note
The required attributes for a Reaction object are:
  • 'id' (or 'name' in SBML Level 1)
  • 'fast' (in Level 3 only, where it is defined as a required attribute)
  • 'reversible' (in Level 3 only, where it is defined as a required attribute)
Returns
a bool value indicating whether all the required attributes for this object have been defined.
bool libsbmlcs.SBase.hasRequiredElements ( )
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

bool libsbmlcs.SBase.hasValidLevelVersionNamespaceCombination ( )
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:

Returns
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
void libsbmlcs.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:

  • Sets the 'reversible' attribute to true
  • Sets the 'fast' attribute to false
  • Marks the 'fast' attribute as not having been set
Warning
The 'fast' attribute must be used with care. SBML definitions before SBML Level 2 Version 2 incorrectly indicated 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. 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.
bool libsbmlcs.SBase.isPackageEnabled ( string  pkgName)
inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPackageURIEnabled()
bool libsbmlcs.SBase.isPackageURIEnabled ( string  pkgURI)
inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPackageEnabled()
bool libsbmlcs.SBase.isPkgEnabled ( string  pkgName)
inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPkgURIEnabled()
bool libsbmlcs.SBase.isPkgURIEnabled ( string  pkgURI)
inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPkgEnabled()
bool libsbmlcs.SBase.isSetAnnotation ( )
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.

Returns
true if a 'annotation' subelement exists, false otherwise.
See Also
getAnnotation()
getAnnotationString()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
bool libsbmlcs.Reaction.isSetCompartment ( )

Predicate returning true if this Reaction's 'compartment' attribute is set.

Returns
true if the 'compartment' attribute of this Reaction is set, false otherwise.
Note
The 'compartment' attribute is available in SBML Level 3 Version 1 Core, but is not present on Reaction in lower Levels of SBML.
bool libsbmlcs.Reaction.isSetFast ( )

Predicate returning true if the value of the 'fast' attribute on this Reaction.

Returns
true if the 'fast' attribute is true, false otherwise.
Warning
SBML definitions before SBML Level 2 Version 2 incorrectly indicated 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, 3 and 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. 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. Note also that in SBML Level 1, 'fast' is defined as optional with a default of false, which means it is effectively always set.
new bool libsbmlcs.Reaction.isSetId ( )

Predicate returning true if this Reaction's 'id' attribute is set.

Returns
true if the 'id' attribute of this Reaction is set, false otherwise.
bool libsbmlcs.Reaction.isSetKineticLaw ( )

Predicate returning true if this Reaction contains a kinetic law object.

Returns
true if a KineticLaw is present in this Reaction,, false otherwise.
bool libsbmlcs.SBase.isSetMetaId ( )
inherited

Predicate returning true if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
true if the 'metaid' attribute of this SBML object is set, false otherwise.
See Also
getMetaId()
setMetaId(string metaid)
bool libsbmlcs.SBase.isSetModelHistory ( )
inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns
true if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new bool libsbmlcs.Reaction.isSetName ( )

Predicate returning true if this Reaction's 'name' attribute is set.

Returns
true if the 'name' attribute of this Reaction is set, false otherwise.
bool libsbmlcs.SBase.isSetNotes ( )
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.

Returns
true if a 'notes' subelement exists, false otherwise.
See Also
getNotes()
getNotesString()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
bool libsbmlcs.Reaction.isSetReversible ( )

Predicate returning true if this Reaction's 'reversible' attribute is set.

Returns
true if the 'reversible' attribute of this Reaction is set, false otherwise.
bool libsbmlcs.SBase.isSetSBOTerm ( )
inherited

Predicate returning true if this object's 'sboTerm' attribute is set.

Returns
true if the 'sboTerm' attribute of this SBML object is set, false otherwise.
bool libsbmlcs.SBase.matchesRequiredSBMLNamespacesForAddition ( SBase  sb)
inherited

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

Parameters
sban object to compare with respect to namespaces
Returns
bool, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool libsbmlcs.SBase.matchesSBMLNamespaces ( SBase  sb)
inherited

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

Parameters
sban object to compare with respect to namespaces
Returns
bool, true if this object's collection of namespaces is the same as sb's, false otherwise.
void libsbmlcs.SBase.multiplyAssignmentsToSIdByFunction ( string  id,
ASTNode  function 
)
inherited

If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).

static bool libsbmlcs.SBase.operator!= ( SBase  lhs,
SBase  rhs 
)
staticinherited
static bool libsbmlcs.SBase.operator== ( SBase  lhs,
SBase  rhs 
)
staticinherited
int libsbmlcs.SBase.prependStringToAllIdentifiers ( string  prefix)
inherited

Add the given string to all identifiers in the object.

If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.

int libsbmlcs.SBase.removeFromParentAndDelete ( )
inherited

Removes itself from its parent.

If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
ModifierSpeciesReference libsbmlcs.Reaction.removeModifier ( long  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.

Parameters
nthe index of the ModifierSpeciesReference object to remove
Returns
the removed ModifierSpeciesReference object, or null if the given index is out of range.
ModifierSpeciesReference libsbmlcs.Reaction.removeModifier ( 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.

Parameters
speciesthe 'species' attribute of the ModifierSpeciesReference object
Returns
the removed ModifierSpeciesReference object, or null if no ModifierSpeciesReference object with the given 'species' attribute species exists in this Reaction.
SpeciesReference libsbmlcs.Reaction.removeProduct ( long  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.

Parameters
nthe index of the product SpeciesReference object to remove
Returns
the removed product SpeciesReference object, or null if the given index is out of range.
SpeciesReference libsbmlcs.Reaction.removeProduct ( 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.

Parameters
speciesthe 'species' attribute of the product SpeciesReference object
Returns
the removed product SpeciesReference object, or null if no product SpeciesReference object with the given 'species' attribute species exists in this Reaction.
SpeciesReference libsbmlcs.Reaction.removeReactant ( long  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.

Parameters
nthe index of the reactant SpeciesReference object to remove
Returns
the removed reactant SpeciesReference object, or null if the given index is out of range.
SpeciesReference libsbmlcs.Reaction.removeReactant ( 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.

Parameters
speciesthe 'species' attribute of the reactant SpeciesReference object
Returns
the removed reactant SpeciesReference object, or null if no reactant SpeciesReference object with the given 'species' attribute species exists in this Reaction.
int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string  elementName,
string  elementURI 
)
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.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
replaceTopLevelAnnotationElement(XMLNode )
replaceTopLevelAnnotationElement(string)
int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string  elementName)
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.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
replaceTopLevelAnnotationElement(XMLNode )
replaceTopLevelAnnotationElement(string)
void libsbmlcs.SBase.renameMetaIdRefs ( string  oldid,
string  newid 
)
inherited

Renames all the MetaIdRef attributes on this element.

This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
void libsbmlcs.Reaction.renameSIdRefs ( string  oldid,
string  newid 
)

Renames all the SIdRef attributes on this element, including any found in MathML.

void libsbmlcs.SBase.renameUnitSIdRefs ( string  oldid,
string  newid 
)
inherited

Renames all the UnitSIdRef attributes on this element.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
void libsbmlcs.SBase.replaceSIDWithFunction ( string  id,
ASTNode  function 
)
inherited

If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.

Note
This function does nothing itself—subclasses with ASTNode subelements must override this function.
int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( XMLNode  annotation)
inherited

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters
annotationXMLNode representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(string elementName, string elementURI)
replaceTopLevelAnnotationElement(string)
int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( string  annotation)
inherited

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters
annotationstring representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(string elementName, string elementURI)
replaceTopLevelAnnotationElement(XMLNode)
int libsbmlcs.SBase.setAnnotation ( XMLNode  annotation)
inherited

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).

Parameters
annotationan XML structure that is to be used as the new content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.SBase.setAnnotation ( string  annotation)
inherited

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).

Parameters
annotationan XML string that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.Reaction.setCompartment ( string  sid)

Sets the value of the 'compartment' attribute of this Reaction.

The string sid is copied.

Parameters
sidthe string to use as the compartment of this Reaction
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'compartment' attribute is available in SBML Level 3 Version 1 Core, but is not present on Reaction in lower Levels of SBML.
int libsbmlcs.Reaction.setFast ( bool  value)

Sets the value of the 'fast' attribute of this Reaction.

Parameters
valuethe value of the 'fast' attribute.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
SBML definitions before SBML Level 2 Version 2 incorrectly indicated 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, 3 and 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. 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.
new int libsbmlcs.Reaction.setId ( string  sid)

Sets the value of the 'id' attribute of this Reaction.

The string sid is copied. Note that SBML has strict requirements for the syntax of identifiers. The following is a summary of the definition of the SBML identifier type SId, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation:

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. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact formulations.

Parameters
sidthe string to use as the identifier of this Reaction
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.Reaction.setKineticLaw ( KineticLaw  kl)

Sets the 'kineticLaw' subelement of this Reaction to a copy of the given KineticLaw object.

Parameters
klthe KineticLaw object to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.setMetaId ( string  metaid)
inherited

Sets the value of the 'metaid' attribute of this object.

The string metaid is copied. The value of metaid must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement.

Parameters
metaidthe identifier string to use as the value of the 'metaid' attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getMetaId()
isSetMetaId()
int libsbmlcs.SBase.setModelHistory ( ModelHistory  history)
inherited

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new int libsbmlcs.Reaction.setName ( string  name)

Sets the value of the 'name' attribute of this Reaction.

The string in name is copied.

Parameters
namethe new name for the Reaction
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.setNamespaces ( XMLNamespaces  xmlns)
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.

Parameters
xmlnsthe namespaces to set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.setNotes ( XMLNode  notes)
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.

Parameters
notesan XML structure that is to be used as the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.setNotes ( string  notes,
bool  addXHTMLMarkup 
)
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. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa bool 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.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.setNotes ( string  notes)
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. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa bool 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.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.Reaction.setReversible ( bool  value)

Sets the value of the 'reversible' attribute of this Reaction.

Parameters
valuethe value of the 'reversible' attribute.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
void libsbmlcs.SBase.setSBMLNamespacesAndOwn ( SBMLNamespaces  sbmlns)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

int libsbmlcs.SBase.setSBOTerm ( int  value)
inherited

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
valuethe NNNNNNN integer portion of the SBO identifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm(string sboid)
int libsbmlcs.SBase.setSBOTerm ( string  sboid)
inherited

Sets the value of the 'sboTerm' attribute by string.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
sboidthe SBO identifier string of the form 'SBO:NNNNNNN'
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm(int value)
string libsbmlcs.SBase.toSBML ( )
inherited

Returns a string consisting of a partial SBML corresponding to just this object.

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
int libsbmlcs.SBase.unsetAnnotation ( )
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.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
int libsbmlcs.Reaction.unsetCompartment ( )

Unsets the value of the 'compartment' attribute of this Reaction.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'compartment' attribute is available in SBML Level 3 Version 1 Core, but is not present on Reaction in lower Levels of SBML.
int libsbmlcs.SBase.unsetCVTerms ( )
inherited

Clears the list of CVTerm objects attached to this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.Reaction.unsetFast ( )

Unsets the value of the 'fast' attribute of this Reaction.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
In SBML Level 1, 'fast' is optional with a default of false, which means it is effectively always set (and reset to false if this method is called). Further, SBML definitions before SBML Level 2 Version 2 incorrectly indicated 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, 3 and 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. 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.
int libsbmlcs.SBase.unsetId ( )
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. The data type of 'id' is always either Sid or UnitSId, depending on the object in question. Both data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The equality of SId and UnitSId type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId and UnitSId.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.Reaction.unsetKineticLaw ( )

Unsets the 'kineticLaw' subelement of this Reaction.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetMetaId ( )
inherited

Unsets the value of the 'metaid' attribute of this SBML object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetModelHistory ( )
inherited

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new int libsbmlcs.Reaction.unsetName ( )

Unsets the value of the 'name' attribute of this Reaction.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetNotes ( )
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.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.unsetSBOTerm ( )
inherited

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
void libsbmlcs.SBase.writeExtensionElements ( XMLOutputStream  stream)
inherited

Writes out contained SBML objects of package extensions (if any) as XML elements.

Member Data Documentation

bool libsbmlcs.SBase.swigCMemOwn
protectedinherited