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* @file Reaction.h
* @brief Definitions of Reaction and ListOfReactions.
* @author Ben Bornstein
*
* <!--------------------------------------------------------------------------
* This file is part of libSBML. Please visit http://sbml.org for more
* information about SBML, and the latest version of libSBML.
*
* Copyright (C) 2013-2014 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
* 3. University of Heidelberg, Heidelberg, Germany
*
* Copyright (C) 2009-2013 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
*
* Copyright (C) 2006-2008 by the California Institute of Technology,
* Pasadena, CA, USA
*
* Copyright (C) 2002-2005 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. Japan Science and Technology Agency, Japan
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online as http://sbml.org/software/libsbml/license.html
* ------------------------------------------------------------------------ -->
*
* @class Reaction
* @sbmlbrief{core} Implementation of SBML's %Reaction construct.
*
* A @em reaction represents any transformation, transport or binding
* process, typically a chemical reaction, that can change the quantity of
* one or more species. In SBML, a reaction is defined primarily in terms
* of the participating reactants and products (and their corresponding
* stoichiometries), along with optional modifier species, an optional rate
* at which the reaction takes place, and optional parameters.
*
* As with other major objects in SBML, Reaction has a mandatory attribute,
* "id", used to give the 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 @c
* 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:
* <ul>
* <li> 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.
*
* <li> 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.
*
* <li> A reaction definition can contain an empty list of reactants
* <em>or</em> 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.)
* </ul>
*
* A reaction can contain up to one KineticLaw object in a subelement named
* "kineticLaw". It defines the speed at which the process defined by the
* reaction takes place. The description of KineticLaw provides more
* details about its use. Note that although the inclusion of a KineticLaw
* object in an instance of a Reaction component is optional, there is no
* useful default that can be substituted in place of a missing rate
* expression in a reaction. Moreover, a reaction's rate cannot be defined
* in any other way in SBML—InitialAssignment, AssignmentRule,
* RateRule, AlgebraicRule, Event, and other constructs in SBML cannot be
* used to set the reaction rate separately. Nevertheless, for some
* modeling applications, reactions without any defined rate can be
* perfectly acceptable.
*
* Reaction also has a boolean attribute named "reversible" for indicating
* whether the reaction is reversible. This attribute is optional in SBML
* Level 2, with a default of @c true; it is mandatory in SBML
* Level 3 (with no default value). To say that a reaction is @em
* reversible is to say it can proceed in either the forward or the reverse
* direction. Although the reversibility of a reaction can sometimes be
* deduced by inspecting its rate expression, this is not always the case,
* especially for complicated expressions. Moreover, the need in SBML to
* allow rate expressions (i.e., KineticLaw) to be optional leads to the
* need for a separate flag indicating reversibility. Note that labeling a
* reaction as irreversible is an assertion that the reaction always
* proceeds in the given forward direction. (Why else would it be flagged
* as irreversible?) This implies the rate expression in the KineticLaw
* always has a non-negative value during simulations. Software tools
* could provide a means of optionally testing that this condition holds.
* The presence of reversibility information in two places (i.e., the rate
* expression and the "reversible" attribute on Reaction) leaves open the
* possibility that a model could contain contradictory information, but
* the creation of such a model would be an error on the part of the
* software generating it.
*
* The Reaction object class has another boolean attribute called "fast".
* This attribute is optional in SBML Level 2, with a default of @c
* 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
* thanothers 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 @c 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" <em>cannot be ignored</em> if it is
* set to @c true. SBML Level 2 Versions 2–4 therefore
* stipulate that if a model has any reactions with "fast" set to @c 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
* <em>does</em> 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.
*
*
* <!-- ------------------------------------------------------------------- -->
* @class ListOfReactions
* @sbmlbrief{core} Implementation of SBML's %ListOfReactions construct.
*
* @copydetails doc_what_is_listof
*/
/**
* <!-- ~ ~ ~ ~ ~ Start of common documentation strings ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
* The following text is used as common documentation blocks copied multiple
* times elsewhere in this file. The use of @class is a hack needed because
* Doxygen's @copydetails command has limited functionality. Symbols
* beginning with "doc_" are marked as ignored in our Doxygen configuration.
* ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ -->
*
* @class doc_note_reaction_setting_lv
*
* @note Upon the addition of a Reaction object to an SBMLDocument (e.g.,
* using Model::addReaction(@if java Reaction r@endif)), the SBML Level, SBML Version and
* XML namespace of the document @em 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.
*
* @class doc_warning_reaction_cant_ignore_fast
*
* @warning <span class="warning">SBML definitions before SBML Level 2
* Version 2 incorrectly indicated that software tools could ignore the
* "fast" 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" <em>cannot be ignored</em> if it is set to @c true.
* Beginning with SBML Level 2 Versions 2, the SBML specifications
* therefore stipulate that if a model has any reactions with "fast" set to
* @c 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.</span>
*
*/
#ifndef Reaction_h
#define Reaction_h
#include <sbml/common/sbmlfwd.h>
#ifdef __cplusplus
#include <string>
#include <sbml/SBase.h>
#include <sbml/ListOf.h>
#include <sbml/SpeciesReference.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class KineticLaw;
class SBMLVisitor;
class LIBSBML_EXTERN Reaction : public SBase
{
public:
/**
* Creates a new Reaction using the given SBML @p level and @p version
* values.
*
* @param level an unsigned int, the SBML Level to assign to this Reaction
*
* @param version an unsigned int, the SBML Version to assign to this
* Reaction
*
* @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
*
* @copydetails doc_note_reaction_setting_lv
*/
Reaction (unsigned int level, unsigned int version);
/**
* Creates a new Reaction using the given SBMLNamespaces object
* @p sbmlns.
*
* @copydetails doc_what_are_sbmlnamespaces
*
* @param sbmlns an SBMLNamespaces object.
*
* @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
*
* @copydetails doc_note_reaction_setting_lv
*/
Reaction (SBMLNamespaces* sbmlns);
/**
* Destroys this Reaction.
*/
virtual ~Reaction ();
/**
* Copy constructor; creates a copy of this Reaction.
*
* @param orig the object to copy.
*
* @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the argument @p orig is @c NULL.
*/
Reaction (const Reaction& orig);
/**
* Assignment operator for Reaction.
*
* @param rhs The object whose values are used as the basis of the
* assignment.
*
* @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the argument @p rhs is @c NULL.
*/
Reaction& operator=(const Reaction& rhs);
/**
* Accepts the given SBMLVisitor for this instance of Reaction.
*
* @param v the SBMLVisitor instance to be used.
*
* @return the result of calling <code>v.visit()</code>.
*/
virtual bool accept (SBMLVisitor& v) const;
/**
* Creates and returns a deep copy of this Reaction.
*
* @return a (deep) copy of this Reaction.
*/
virtual Reaction* clone () const;
/**
* Returns the first child element found that has the given @p id in the
* model-wide SId namespace, or @c NULL if no such object is found.
*
* @param id string representing the id of objects to find.
*
* @return pointer to the first element found with the given @p id.
*/
virtual SBase* getElementBySId(const std::string& id);
/**
* Returns the first child element it can find with the given @p metaid, or
* @c NULL if no such object is found.
*
* @param metaid string representing the metaid of objects to find
*
* @return pointer to the first element found with the given @p metaid.
*/
virtual SBase* getElementByMetaId(const std::string& metaid);
/**
* Returns a List of all child SBase objects, including those nested to an
* arbitrary depth
*
* @return a List of pointers to all children objects.
*/
virtual List* getAllElements(ElementFilter* filter=NULL);
/**
* Renames all the @c SIdRef attributes on this element, including any
* found in MathML.
*
* @copydetails doc_what_is_sidref
*
* This method works by looking at all attributes and (if appropriate)
* mathematical formulas, comparing the identifiers to the value of @p
* oldid. If any matches are found, the matching identifiers are replaced
* with @p newid. The method does @em not descend into child elements.
*
* @param oldid the old identifier
* @param newid the new identifier
*/
virtual void renameSIdRefs(const std::string& oldid, const std::string& newid);
/**
* 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:
*
* @li Sets the "reversible" attribute to @c true
* @li Sets the "fast" attribute to @c false
* @li Marks the "fast" attribute as @em not having been set
*
* @copydetails doc_warning_reaction_cant_ignore_fast
*/
void initDefaults ();
/**
* Returns the value of the "id" attribute of this Reaction.
*
* @return the id of this Reaction.
*/
virtual const std::string& getId () const;
/**
* Returns the value of the "name" attribute of this Reaction.
*
* @return the name of this Reaction.
*/
virtual const std::string& getName () const;
/**
* Returns the KineticLaw object contained in this Reaction.
*
* @return the KineticLaw instance.
*/
const KineticLaw* getKineticLaw () const;
/**
* Returns the KineticLaw object contained in this Reaction.
*
* @return the KineticLaw instance.
*/
KineticLaw* getKineticLaw ();
/**
* Returns the value of the "reversible" attribute on the Reaction as a
* boolean value.
*
* @return the reversibility status of this Reaction.
*/
bool getReversible () const;
/**
* Returns the value of the "fast" attribute of this Reaction.
*
* @return the "fast" status of this Reaction.
*
* @copydetails doc_warning_reaction_cant_ignore_fast
*/
bool getFast () const;
/**
* (SBML Level 3 only) Returns the value of the "compartment"
* attribute on the Reaction.
*
* @return 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.
*/
const std::string& getCompartment () const;
/**
* Predicate returning @c true if this
* Reaction's "id" attribute is set.
*
* @return @c true if the "id" attribute of this Reaction is
* set, @c false otherwise.
*/
virtual bool isSetId () const;
/**
* Predicate returning @c true if this
* Reaction's "name" attribute is set.
*
* @return @c true if the "name" attribute of this Reaction is
* set, @c false otherwise.
*/
virtual bool isSetName () const;
/**
* Predicate returning @c true if this
* Reaction contains a kinetic law object.
*
* @return @c true if a KineticLaw is present in this Reaction,, @c false
* otherwise.
*/
bool isSetKineticLaw () const;
/**
* Predicate returning @c true if the value of
* the "fast" attribute on this Reaction.
*
* @return @c true if the "fast" attribute is true, @c false otherwise.
*
* @copydetails doc_warning_reaction_cant_ignore_fast
*/
bool isSetFast () const;
/**
* Predicate returning @c true if this
* Reaction's "compartment" attribute is set.
*
* @return @c true if the "compartment" attribute of this Reaction is
* set, @c 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 isSetCompartment () const;
/**
* Predicate returning @c true if this
* Reaction's "reversible" attribute is set.
*
* @return @c true if the "reversible" attribute of this Reaction is
* set, @c false otherwise.
*/
bool isSetReversible () const;
/**
* Sets the value of the "id" attribute of this Reaction.
*
* The string @p sid is copied.
*
* @copydetails doc_id_syntax
*
* @param sid the string to use as the identifier of this Reaction
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*/
virtual int setId (const std::string& sid);
/**
* Sets the value of the "name" attribute of this Reaction.
*
* The string in @p name is copied.
*
* @param name the new name for the Reaction
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*/
virtual int setName (const std::string& name);
/**
* Sets the "kineticLaw" subelement of this Reaction to a copy of the
* given KineticLaw object.
*
* @param kl the KineticLaw object to use.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
*/
int setKineticLaw (const KineticLaw* kl);
/**
* Sets the value of the "reversible" attribute of this Reaction.
*
* @param value the value of the "reversible" attribute.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*/
int setReversible (bool value);
/**
* Sets the value of the "fast" attribute of this Reaction.
*
* @param value the value of the "fast" attribute.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*
* @copydetails doc_warning_reaction_cant_ignore_fast
*/
int setFast (bool value);
/**
* Sets the value of the "compartment" attribute of this Reaction.
*
* The string @p sid is copied.
*
* @param sid the string to use as the compartment of this Reaction
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*
* @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 setCompartment (const std::string& sid);
/**
* Unsets the value of the "name" attribute of this Reaction.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*/
virtual int unsetName ();
/**
* Unsets the "kineticLaw" subelement of this Reaction.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*/
int unsetKineticLaw ();
/**
* Unsets the value of the "fast" attribute of this Reaction.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @copydetails doc_warning_reaction_cant_ignore_fast
*/
int unsetFast ();
/**
* Unsets the value of the "compartment" attribute of this Reaction.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @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 unsetCompartment ();
/**
* Adds a given SpeciesReference object as a reactant in this Reaction.
*
* The SpeciesReference instance in @p sr is copied.
*
* @param sr a SpeciesReference object referring to a Species in the
* enclosing Model
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @copydetails doc_note_object_is_copied
*
* @see createReactant()
*/
int addReactant (const SpeciesReference* sr);
/**
* Adds a given SpeciesReference object as a product in this Reaction.
*
* The SpeciesReference instance in @p sr is copied.
*
* @param sr a SpeciesReference object referring to a Species in the
* enclosing Model
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @copydetails doc_note_object_is_copied
*
* @see createProduct()
*/
int addProduct (const SpeciesReference* sr);
/**
* Adds a given ModifierSpeciesReference object as a product in this
* Reaction.
*
* The ModifierSpeciesReference instance in @p msr is copied.
*
* @param msr a ModifierSpeciesReference object referring to a Species in
* the enclosing Model
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
* @li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
* @li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @copydetails doc_note_object_is_copied
*
* @see createModifier()
*/
int addModifier (const ModifierSpeciesReference* msr);
/**
* Creates a new SpeciesReference, adds it to this Reaction's list of
* reactants, and returns it.
*
* @return a new SpeciesReference object.
*/
SpeciesReference* createReactant ();
/**
* Creates a new SpeciesReference, adds it to this Reaction's list of
* products, and returns it.
*
* @return a new SpeciesReference object.
*/
SpeciesReference* createProduct ();
/**
* Creates a new ModifierSpeciesReference, adds it to this Reaction's
* list of modifiers and returns it.
*
* @return a new ModifierSpeciesReference object.
*/
ModifierSpeciesReference* createModifier ();
/**
* 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.
*
* @return the new KineticLaw object
*/
KineticLaw* createKineticLaw ();
/**
* Returns the list of reactants in this Reaction object.
*
* @return the ListOfSpeciesReferences containing the references to the
* species acting as reactants in this reaction
*/
const ListOfSpeciesReferences* getListOfReactants () const;
/**
* Returns the list of reactants in this Reaction object.
*
* @return the ListOfSpeciesReferences containing the references to the
* species acting as reactants in this reaction
*/
ListOfSpeciesReferences* getListOfReactants ();
/**
* Returns the list of products in this Reaction object.
*
* @return the ListOfSpeciesReferences containing the references to the
* species acting as products in this reaction
*/
const ListOfSpeciesReferences* getListOfProducts () const;
/**
* Returns the list of products in this Reaction object.
*
* @return the ListOfSpeciesReferences containing the references to the
* species acting as products in this reaction
*/
ListOfSpeciesReferences* getListOfProducts ();
/**
* Returns the list of modifiers in this Reaction object.
*
* @return the ListOfSpeciesReferences containing the references to the
* species acting as modifiers in this reaction
*/
const ListOfSpeciesReferences* getListOfModifiers () const;
/**
* Returns the list of modifiers in this Reaction object.
*
* @return the ListOfSpeciesReferences containing the references to the
* species acting as modifiers in this reaction
*/
ListOfSpeciesReferences* getListOfModifiers ();
/**
* 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.
*
* @param n the index of the reactant sought.
*
* @return the nth reactant (as a SpeciesReference object) of this
* Reaction.
*/
const SpeciesReference* getReactant (unsigned int n) const;
/**
* Returns the nth reactant species (as a SpeciesReference object)
* in the list of reactants in this Reaction.
*
* Callers should first call getNumReactants() to find out how many
* reactants there are, to avoid using an invalid index number.
*
* @param n the index of the reactant sought.
*
* @return the nth reactant (as a SpeciesReference object) of this
* Reaction.
*/
SpeciesReference* getReactant (unsigned int n);
/**
* Returns the reactant species (as a SpeciesReference object) having
* a specific identifier in this Reaction.
*
* @param species the identifier of the reactant Species ("species"
* attribute of the reactant SpeciesReference object)
*
* @return a SpeciesReference object, or @c NULL if no species with the
* given identifier @p species appears as a reactant in this Reaction.
*/
const SpeciesReference* getReactant (const std::string& species) const;
/**
* Returns the reactant species (as a SpeciesReference object) having
* a specific identifier in this Reaction.
*
* @param species the identifier of the reactant Species ("species"
* attribute of the reactant SpeciesReference object)
*
* @return a SpeciesReference object, or @c NULL if no species with the
* given identifier @p species appears as a reactant in this Reaction.
*/
SpeciesReference* getReactant (const std::string& species);
/**
* 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.
*
* @param n the index of the product sought.
*
* @return the nth product (as a SpeciesReference object) of this
* Reaction.
*/
const SpeciesReference* getProduct (unsigned int n) const;
/**
* Returns the nth product species (as a SpeciesReference object)
* in the list of products in this Reaction.
*
* Callers should first call getNumProducts() to find out how many
* products there are, to avoid using an invalid index number.
*
* @param n the index of the product sought.
*
* @return the nth product (as a SpeciesReference object) of this
* Reaction.
*/
SpeciesReference* getProduct (unsigned int n);
/**
* Returns the product species (as a SpeciesReference object) having
* a specific identifier in this Reaction.
*
* @param species the identifier of the product Species ("species"
* attribute of the product SpeciesReference object)
*
* @return a SpeciesReference object, or @c NULL if no species with the
* given identifier @p species appears as a product in this Reaction.
*/
const SpeciesReference* getProduct (const std::string& species) const;
/**
* Returns the product species (as a SpeciesReference object) having
* a specific identifier in this Reaction.
*
* @param species the identifier of the product Species ("species"
* attribute of the product SpeciesReference object)
*
* @return a SpeciesReference object, or @c NULL if no species with the
* given identifier @p species appears as a product in this Reaction.
*/
SpeciesReference* getProduct (const std::string& species);
/**
* 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.
*
* @param n the index of the modifier species sought
*
* @return the nth modifier (as a ModifierSpeciesReference object) of
* this Reaction.
*/
const ModifierSpeciesReference* getModifier (unsigned int n) const;
/**
* Returns the nth modifier species (as a ModifierSpeciesReference object)
* in the list of modifiers of this Reaction.
*
* Callers should first call getNumModifiers() to find out how many
* modifiers there are, to avoid using an invalid index number.
*
* @param n the index of the modifier species sought
*
* @return the nth modifier (as a ModifierSpeciesReference object) of
* this Reaction.
*/
ModifierSpeciesReference* getModifier (unsigned int n);
/**
* Returns the modifier species (as a ModifierSpeciesReference object)
* having a specific identifier in this Reaction.
*
* @param species the identifier of the modifier Species ("species"
* attribute of the ModifierSpeciesReference object)
*
* @return a ModifierSpeciesReference object, or @c NULL if no species with
* the given identifier @p species appears as a modifier in this
* Reaction.
*/
const ModifierSpeciesReference*
getModifier (const std::string& species) const;
/**
* Returns the modifier species (as a ModifierSpeciesReference object)
* having a specific identifier in this Reaction.
*
* @param species the identifier of the modifier Species ("species"
* attribute of the ModifierSpeciesReference object)
*
* @return a ModifierSpeciesReference object, or @c NULL if no species with
* the given identifier @p species appears as a modifier in this
* Reaction.
*/
ModifierSpeciesReference* getModifier (const std::string& species);
/**
* Returns the number of reactant species in this Reaction.
*
* @return the number of reactants in this Reaction.
*/
unsigned int getNumReactants () const;
/**
* Returns the number of product species in this Reaction.
*
* @return the number of products in this Reaction.
*/
unsigned int getNumProducts () const;
/**
* Returns the number of modifier species in this Reaction.
*
* @return the number of modifiers in this Reaction.
*/
unsigned int getNumModifiers () const;
/**
* 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.
*
* @param n the index of the reactant SpeciesReference object to remove
*
* @return the removed reactant SpeciesReference object, or @c NULL if the
* given index is out of range.
*/
SpeciesReference* removeReactant (unsigned int n);
/**
* 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.
*
* @param species the "species" attribute of the reactant SpeciesReference
* object
*
* @return the removed reactant SpeciesReference object, or @c NULL if no
* reactant SpeciesReference object with the given "species" attribute
* @p species exists in this Reaction.
*/
SpeciesReference* removeReactant (const std::string& species);
/**
* 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.
*
* @param n the index of the product SpeciesReference object to remove
*
* @return the removed product SpeciesReference object, or @c NULL if the
* given index is out of range.
*/
SpeciesReference* removeProduct (unsigned int n);
/**
* 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.
*
* @param species the "species" attribute of the product SpeciesReference
* object
*
* @return the removed product SpeciesReference object, or @c NULL if no
* product SpeciesReference object with the given "species" attribute
* @p species exists in this Reaction.
*/
SpeciesReference* removeProduct (const std::string& species);
/**
* 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.
*
* @param n the index of the ModifierSpeciesReference object to remove
*
* @return the removed ModifierSpeciesReference object, or @c NULL if the
* given index is out of range.
*/
ModifierSpeciesReference* removeModifier (unsigned int n);
/**
* 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.
*
* @param species the "species" attribute of the ModifierSpeciesReference
* object
*
* @return the removed ModifierSpeciesReference object, or @c NULL if no
* ModifierSpeciesReference object with the given "species" attribute @p
* species exists in this Reaction.
*/
ModifierSpeciesReference* removeModifier (const std::string& species);
/** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument of this SBML object.
*/
virtual void setSBMLDocument (SBMLDocument* d);
/**
* Sets this SBML object to child SBML objects (if any).
* (Creates a child-parent relationship by the parent)
*
* Subclasses must override this function if they define
* one ore more child elements.
* Basically, this function needs to be called in
* constructor, copy constructor and assignment operator.
*
* @see setSBMLDocument
* @see enablePackageInternal
*/
virtual void connectToChild ();
/**
* Enables/Disables the given package with this element and child
* elements (if any).
* (This is an internal implementation for enablePackage function)
*
* @note Subclasses of the SBML Core package in which one or more child
* elements are defined must override this function.
*/
virtual void enablePackageInternal(const std::string& pkgURI,
const std::string& pkgPrefix, bool flag);
/** @endcond */
/**
* Returns the libSBML type code for this SBML object.
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for this object:
* @link SBMLTypeCode_t#SBML_REACTION SBML_REACTION@endlink (default).
*
* @copydetails doc_warning_typecodes_not_unique
*
* @see getElementName()
* @see getPackageName()
*/
virtual int getTypeCode () const;
/**
* Returns the XML element name of this object, which for Reaction, is
* always @c "reaction".
*
* @return the name of this element, i.e., @c "reaction".
*/
virtual const std::string& getElementName () const;
/** @cond doxygenLibsbmlInternal */
/**
* 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.
*/
virtual void writeElements (XMLOutputStream& stream) const;
/** @endcond */
/**
* Predicate returning @c true if all the required attributes for this
* Reaction object have been set.
*
* @note The required attributes for a Reaction object are:
* @li "id" (or "name" in SBML Level 1)
* @li "fast" (in Level 3 only, where it is defined as a required attribute)
* @li "reversible" (in Level 3 only, where it is defined as a required attribute)
*
* @return a boolean value indicating whether all the required
* attributes for this object have been defined.
*/
virtual bool hasRequiredAttributes() const ;
protected:
/** @cond doxygenLibsbmlInternal */
/**
* Create and return an SBML object of this class, if present.
*
* @return the SBML object corresponding to next XMLToken in the
* XMLInputStream or @c NULL if the token was not recognized.
*/
virtual SBase* createObject (XMLInputStream& stream);
/**
* Subclasses should override this method to get the list of
* expected attributes.
* This function is invoked from corresponding readAttributes()
* function.
*/
virtual void addExpectedAttributes(ExpectedAttributes& attributes);
/**
* Subclasses should override this method to read values from the given
* XMLAttributes set into their specific fields. Be sure to call your
* parents implementation of this method as well.
*/
virtual void readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes);
void readL1Attributes (const XMLAttributes& attributes);
void readL2Attributes (const XMLAttributes& attributes);
void readL3Attributes (const XMLAttributes& attributes);
/**
* Subclasses should override this method to write their XML attributes
* to the XMLOutputStream. Be sure to call your parents implementation
* of this method as well.
*/
virtual void writeAttributes (XMLOutputStream& stream) const;
bool isExplicitlySetReversible() const { return mExplicitlySetReversible; };
bool isExplicitlySetFast() const { return mExplicitlySetFast; };
std::string mId;
std::string mName;
ListOfSpeciesReferences mReactants;
ListOfSpeciesReferences mProducts;
ListOfSpeciesReferences mModifiers;
KineticLaw* mKineticLaw;
bool mReversible;
bool mFast;
bool mIsSetFast;
std::string mCompartment;
bool mIsSetReversible;
bool mExplicitlySetReversible;
bool mExplicitlySetFast;
/* the validator classes need to be friends to access the
* protected constructor that takes no arguments
*/
friend class Validator;
friend class ConsistencyValidator;
friend class IdentifierConsistencyValidator;
friend class InternalConsistencyValidator;
friend class L1CompatibilityValidator;
friend class L2v1CompatibilityValidator;
friend class L2v2CompatibilityValidator;
friend class L2v3CompatibilityValidator;
friend class L2v4CompatibilityValidator;
friend class MathMLConsistencyValidator;
friend class ModelingPracticeValidator;
friend class OverdeterminedValidator;
friend class SBOConsistencyValidator;
friend class UnitConsistencyValidator;
/** @endcond */
};
class LIBSBML_EXTERN ListOfReactions : public ListOf
{
public:
/**
* Creates a new ListOfReactions object.
*
* The object is constructed such that it is valid for the given SBML
* Level and Version combination.
*
* @param level the SBML Level
*
* @param version the Version within the SBML Level
*/
ListOfReactions (unsigned int level, unsigned int version);
/**
* Creates a new ListOfReactions object.
*
* The object is constructed such that it is valid for the SBML Level and
* Version combination determined by the SBMLNamespaces object in @p
* sbmlns.
*
* @param sbmlns an SBMLNamespaces object that is used to determine the
* characteristics of the ListOfReactions object to be created.
*/
ListOfReactions (SBMLNamespaces* sbmlns);
/**
* Creates and returns a deep copy of this ListOfReactions instance.
*
* @return a (deep) copy of this ListOfReactions.
*/
virtual ListOfReactions* clone () const;
/**
* Returns the libSBML type code for the objects contained in this ListOf
* (i.e., Reaction objects, if the list is non-empty).
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for objects contained in this list:
* @link SBMLTypeCode_t#SBML_REACTION SBML_REACTION@endlink (default).
*
* @see getElementName()
* @see getPackageName()
*/
virtual int getItemTypeCode () const;
/**
* Returns the XML element name of this object
*
* For ListOfReactions, the XML element name is @c "listOfReactions".
*
* @return the name of this element, i.e., @c "listOfReactions".
*/
virtual const std::string& getElementName () const;
/**
* Get a Reaction from the ListOfReactions.
*
* @param n the index number of the Reaction to get.
*
* @return the nth Reaction in this ListOfReactions.
*
* @see size()
*/
virtual Reaction * get(unsigned int n);
/**
* Get a Reaction from the ListOfReactions.
*
* @param n the index number of the Reaction to get.
*
* @return the nth Reaction in this ListOfReactions.
*
* @see size()
*/
virtual const Reaction * get(unsigned int n) const;
/**
* Get a Reaction from the ListOfReactions based on its identifier.
*
* @param sid a string representing the identifier of the Reaction to get.
*
* @return Reaction in this ListOfReactions with the given @p sid or @c
* NULL if no such Reaction exists.
*
* @see get(unsigned int n)
* @see size()
*/
virtual Reaction* get (const std::string& sid);
/**
* Get a Reaction from the ListOfReactions based on its identifier.
*
* @param sid a string representing the identifier of the Reaction to get.
*
* @return Reaction in this ListOfReactions with the given @p sid or @c
* NULL if no such Reaction exists.
*
* @see get(unsigned int n)
* @see size()
*/
virtual const Reaction* get (const std::string& sid) const;
/**
* Removes the nth item from this ListOfReactions items and returns a
* pointer to it.
*
* The caller owns the returned item and is responsible for deleting it.
*
* @param n the index of the item to remove
*
* @see size()
*/
virtual Reaction* remove (unsigned int n);
/**
* Removes item in this ListOfReactions items with the given identifier.
*
* The caller owns the returned item and is responsible for deleting it.
* If none of the items in this list have the identifier @p sid, then
* NULL is returned.
*
* @param sid the identifier of the item to remove
*
* @return the item removed. As mentioned above, the caller owns the
* returned item.
*/
virtual Reaction* remove (const std::string& sid);
/** @cond doxygenLibsbmlInternal */
/**
* Return the position of this element.
*
* @return the ordinal position of the element with respect to its
* siblings or -1 (default) to indicate the position is not significant.
*/
virtual int getElementPosition () const;
/** @endcond */
protected:
/** @cond doxygenLibsbmlInternal */
/**
* Create and return an SBML object of this class, if present.
*
* @return the SBML object corresponding to next XMLToken in the
* XMLInputStream or @c NULL if the token was not recognized.
*/
virtual SBase* createObject (XMLInputStream& stream);
/** @endcond */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#ifndef SWIG
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
/**
* Creates a new Reaction_t structure using the given SBML @p level
* and @p version values.
*
* @param level an unsigned int, the SBML Level to assign to this
* Reaction_t
*
* @param version an unsigned int, the SBML Version to assign to this
* Reaction_t
*
* @return a pointer to the newly created Reaction_t structure.
*
* @note Once a Reaction_t has been added to an SBMLDocument_t, the @p
* level and @p version for the document @em override those used to create
* the Reaction_t. Despite this, the ability to supply the values at
* creation time is an important aid to creating valid SBML. Knowledge of
* the intended SBML Level and Version determine whether it is valid to
* assign a particular value to an attribute, or whether it is valid to add
* a structure to an existing SBMLDocument_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
Reaction_t *
Reaction_create (unsigned int level, unsigned int version);
/**
* Creates a new Reaction_t structure using the given
* SBMLNamespaces_t structure.
*
* @param sbmlns SBMLNamespaces_t, a pointer to an SBMLNamespaces_t structure
* to assign to this Reaction_t
*
* @return a pointer to the newly created Reaction_t structure.
*
* @note Once a Reaction_t has been added to an SBMLDocument_t, the
* @p sbmlns namespaces for the document @em override those used to create
* the Reaction_t. Despite this, the ability to supply the values at creation
* time is an important aid to creating valid SBML. Knowledge of the intended
* SBML Level and Version determine whether it is valid to assign a particular
* value to an attribute, or whether it is valid to add a structure to an
* existing SBMLDocument_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
Reaction_t *
Reaction_createWithNS (SBMLNamespaces_t *sbmlns);
/**
* Frees the given Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
void
Reaction_free (Reaction_t *r);
/**
* @return a (deep) copy of this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
Reaction_t *
Reaction_clone (const Reaction_t *r);
/**
* Initializes the fields of this Reaction_t to their defaults:
*
* - reversible = 1 (true)
* - fast = 0 (false) (L1 only)
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
void
Reaction_initDefaults (Reaction_t *r);
/**
* Returns a list of XMLNamespaces_t associated with this Reaction_t
* structure.
*
* @param r the Reaction_t structure
*
* @return pointer to the XMLNamespaces_t structure associated with
* this structure
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
const XMLNamespaces_t *
Reaction_getNamespaces(Reaction_t *r);
/**
* @return the id of this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
const char *
Reaction_getId (const Reaction_t *r);
/**
* @return the name of this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
const char *
Reaction_getName (const Reaction_t *r);
/**
* @return the KineticLaw_t of this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
KineticLaw_t *
Reaction_getKineticLaw (Reaction_t *r);
/**
* @return the reversible status of this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_getReversible (const Reaction_t *r);
/**
* @return the fast status of this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_getFast (const Reaction_t *r);
/**
* @return the compartment of this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
const char *
Reaction_getCompartment (const Reaction_t *r);
/**
* @return true (non-zero) if the id of this Reaction_t is set, false
* (0) otherwise.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_isSetId (const Reaction_t *r);
/**
* @return true (non-zero) if the name of this Reaction_t is set, false
* (0) otherwise.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_isSetName (const Reaction_t *r);
/**
* @return true (non-zero) if the KineticLaw_t of this Reaction_t is set,
* false (0) otherwise.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_isSetKineticLaw (const Reaction_t *r);
/**
* @return true (non-zero) if the fast status of this Reaction_t is set,
* false (0) otherwise.
*
* In L1, fast is optional with a default of false, which means it is
* effectively always set. In L2, however, fast is optional with no
* default value, so it may or may not be set to a specific value.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_isSetFast (const Reaction_t *r);
/**
* @return true (non-zero) if the KineticLaw_t of this Reaction_t is set,
* false (0) otherwise.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_isSetCompartment (const Reaction_t *r);
/**
* @return true (non-zero) if the reversible attribute of this Reaction_t is set,
* false (0) otherwise.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_isSetReversible (const Reaction_t *r);
/**
* Sets the id of this Reaction_t to a copy of sid.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*
* @note Using this function with an id of NULL is equivalent to
* unsetting the "id" attribute.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_setId (Reaction_t *r, const char *sid);
/**
* Sets the name of this Reaction_t to a copy of name.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*
* @note Using this function with the name set to NULL is equivalent to
* unsetting the "name" attribute.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_setName (Reaction_t *r, const char *name);
/**
* Sets the KineticLaw_t of this Reaction_t to a copy of the given KineticLaw_t.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_setKineticLaw (Reaction_t *r, const KineticLaw_t *kl);
/**
* Sets the reversible status of this Reaction_t to value (boolean).
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_setReversible (Reaction_t *r, int value);
/**
* Sets the fast status of this Reaction_t to value (boolean).
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_setFast (Reaction_t *r, int value);
/**
* Sets the compartment of this Reaction_t to a copy of compartment.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*
* @note Using this function with the compartment set to NULL is equivalent to
* unsetting the "compartment" attribute.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_setCompartment (Reaction_t *r, const char *compartment);
/**
* Unsets the name of this Reaction_t.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_unsetName (Reaction_t *r);
/**
* Unsets the compartment of this Reaction_t.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_unsetCompartment (Reaction_t *r);
/**
* Unsets the KineticLaw_t of this Reaction_t.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_unsetKineticLaw (Reaction_t *r);
/**
* Unsets the fast status of this Reation_t.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* In L1, fast is optional with a default of false, which means it is
* effectively always set. In L2, however, fast is optional with no
* default value, so it may or may not be set to a specific value.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_unsetFast (Reaction_t *r);
/**
* Predicate returning @c true or @c false depending on whether
* all the required attributes for this Reaction_t structure
* have been set.
*
* @param r the Reaction_t structure to check.
*
* @note The required attributes for a Reaction_t structure are:
* @li id (name in L1)
* @li fast (in L3 only)
* @li reversible (in L3 only)
*
* @return a true if all the required
* attributes for this structure have been defined, false otherwise.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_hasRequiredAttributes (Reaction_t *r);
/**
* Adds a copy of the given reactant (SpeciesReference_t) to this Reaction_t.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_addReactant (Reaction_t *r, const SpeciesReference_t *sr);
/**
* Adds a copy of the given product (SpeciesReference_t) to this Reaction_t.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_addProduct (Reaction_t *r, const SpeciesReference_t *sr);
/**
* Adds a copy of the given modifier (modifier SpeciesReference_t) to this
* Reaction_t.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
* @li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
int
Reaction_addModifier (Reaction_t *r, const SpeciesReference_t *msr);
/**
* Creates a new SpeciesReference, adds it to this Reaction_t's list of
* reactants and returns it.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_createReactant (Reaction_t *r);
/**
* Creates a new SpeciesReference, adds it to this Reaction_t's list of
* products and returns it.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_createProduct (Reaction_t *r);
/**
* Creates a new SpeciesReference, adds it to this Reaction_t's list of
* modifiers and returns it.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_createModifier (Reaction_t *r);
/**
* Creates a new KineticLaw_t for this Reaction_t and returns it. If this
* Reaction_t had a previous KineticLaw_t, it will be destroyed.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
KineticLaw_t *
Reaction_createKineticLaw (Reaction_t *r);
/**
* @return the list of Reactants for this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
ListOf_t *
Reaction_getListOfReactants (Reaction_t *r);
/**
* @return the list of Products for this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
ListOf_t *
Reaction_getListOfProducts (Reaction_t *r);
/**
* @return the list of Modifiers for this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
ListOf_t *
Reaction_getListOfModifiers (Reaction_t *r);
/**
* @return the nth reactant (SpeciesReference_t) of this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_getReactant (Reaction_t *r, unsigned int n);
/**
* @return the reactant (SpeciesReference_t) in this Reaction_t with the given
* species or @c NULL if no such reactant exists.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_getReactantBySpecies (Reaction_t *r, const char *species);
/**
* @return the nth product (SpeciesReference_t) of this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_getProduct (Reaction_t *r, unsigned int n);
/**
* @return the product (SpeciesReference_t) in this Reaction_t with the given
* species or @c NULL if no such product exists.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_getProductBySpecies (Reaction_t *r, const char *species);
/**
* @return the nth modifier (modifier SpeciesReference_t) of this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_getModifier (Reaction_t *r, unsigned int n);
/**
* @return the modifier (modifier SpeciesReference_t) in this Reaction_t with
* the given species or @c NULL if no such modifier exists.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_getModifierBySpecies (Reaction_t *r, const char *species);
/**
* @return the number of reactants (SpeciesReference_t's) in this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
unsigned int
Reaction_getNumReactants (const Reaction_t *r);
/**
* @return the number of products (SpeciesReference_t's) in this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
unsigned int
Reaction_getNumProducts (const Reaction_t *r);
/**
* @return the number of modifiers (modifier SpeciesReference_t's) in this
* Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
unsigned int
Reaction_getNumModifiers (const Reaction_t *r);
/**
* Removes the nth reactant SpeciesReference_t structure from this
* Reaction_t structure and returns a pointer to it.
*
* The caller owns the returned structure and is responsible for deleting it.
*
* @param r the Reaction_t structure
* @param n the integer index of the reactant SpeciesReference_t to remove
*
* @return the reactant SpeciesReference_t structure removed. As mentioned
* above, the caller owns the returned structure. @c NULL is returned if the
* given index is out of range.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_removeReactant (Reaction_t *r, unsigned int n);
/**
* Removes the reactant SpeciesReference_t structure with the given
* "species" attribute from this Reaction_t structure and returns a pointer
* to it.
*
* The caller owns the returned structure and is responsible for deleting it.
*
* @param r the Reaction_t structure
* @param species the "species" attribute of the reactant SpeciesReference_t
* to remove
*
* @return the reactant SpeciesReference_t structure removed. As mentioned
* above, the caller owns the returned structure. @c NULL is returned if no
* reactant SpeciesReference_t structure with the "species" attribute exists
* in this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_removeReactantBySpecies (Reaction_t *r, const char *species);
/**
* Removes the nth product SpeciesReference_t structure from this
* Reaction_t structure and returns a pointer to it.
*
* The caller owns the returned structure and is responsible for deleting it.
*
* @param r the Reaction_t structure
* @param n the integer index of the product SpeciesReference_t to remove
*
* @return the product SpeciesReference_t structure removed. As mentioned
* above, the caller owns the returned structure. @c NULL is returned if the
* given index is out of range.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_removeProduct (Reaction_t *r, unsigned int n);
/**
* Removes the product SpeciesReference_t structure with the given
* "species" attribute from this Reaction_t structure and returns a pointer
* to it.
*
* The caller owns the returned structure and is responsible for deleting it.
*
* @param r the Reaction_t structure
* @param species the "species" attribute of the product SpeciesReference_t
* to remove
*
* @return the product SpeciesReference_t structure removed. As mentioned
* above, the caller owns the returned structure. @c NULL is returned if no
* product SpeciesReference_t structure with the "species" attribute exists
* in this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_removeProductBySpecies (Reaction_t *r, const char *species);
/**
* Removes the nth modifier SpeciesReference_t structure from this
* Reaction_t structure and returns a pointer to it.
*
* The caller owns the returned structure and is responsible for deleting it.
*
* @param r the Reaction_t structure
* @param n the integer index of the modifier SpeciesReference_t to remove
*
* @return the modifier SpeciesReference_t structure removed. As mentioned
* above, the caller owns the returned structure. @c NULL is returned if the
* given index is out of range.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_removeModifier (Reaction_t *r, unsigned int n);
/**
* Removes the modifier SpeciesReference_t structure with the given
* "species" attribute from this Reaction_t structure and returns a pointer
* to it.
*
* The caller owns the returned structure and is responsible for deleting it.
*
* @param r the Reaction_t structure
* @param species the "species" attribute of the modifier SpeciesReference_t
* to remove
*
* @return the modifier SpeciesReference_t structure removed. As mentioned
* above, the caller owns the returned structure. @c NULL is returned if no
* modifier SpeciesReference_t structure with the "species" attribute exists
* in this Reaction_t.
*
* @memberof Reaction_t
*/
LIBSBML_EXTERN
SpeciesReference_t *
Reaction_removeModifierBySpecies (Reaction_t *r, const char *species);
/**
* Returns the Reaction_t structure having a given identifier.
*
* @param lo the ListOfReactions_t structure to search.
* @param sid the "id" attribute value being sought.
*
* @return item in the @p lo ListOfReactions with the given @p sid or a
* null pointer if no such item exists.
*
* @see ListOf_t
*
* @memberof ListOfReactions_t
*/
LIBSBML_EXTERN
Reaction_t *
ListOfReactions_getById (ListOf_t *lo, const char *sid);
/**
* Removes a Reaction_t structure based on its identifier.
*
* The caller owns the returned item and is responsible for deleting it.
*
* @param lo the list of Reaction_t structures to search.
* @param sid the "id" attribute value of the structure to remove
*
* @return The Reaction_t structure removed, or a null pointer if no such
* item exists in @p lo.
*
* @see ListOf_t
*
* @memberof ListOfReactions_t
*/
LIBSBML_EXTERN
Reaction_t *
ListOfReactions_removeById (ListOf_t *lo, const char *sid);
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* Reaction_h */
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