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* @file ModifierSpeciesReference.h
* @brief Definitions of ModifierSpeciesReference.
* @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) 2013-2017 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 ModifierSpeciesReference
* @sbmlbrief{core} A reference to an SBML <em>modifier species</em>.
*
* Sometimes a species appears in the kinetic rate formula of a reaction
* but is itself neither created nor destroyed in that reaction (for
* example, because it acts as a catalyst or inhibitor). In SBML, all such
* species are simply called @em modifiers without regard to the detailed
* role of those species in the model. The Reaction structure provides a
* way to express which species act as modifiers in a given reaction. This
* is the purpose of the list of modifiers available in Reaction. The list
* contains instances of ModifierSpeciesReference structures.
*
* The ModifierSpeciesReference structure inherits the mandatory attribute
* "species" and optional attributes "id" and "name" from the parent class
* SimpleSpeciesReference. See the description of SimpleSpeciesReference
* for more information about these.
*
* The value of the "species" attribute must be the identifier of a species
* defined in the enclosing Model; this species is designated as a modifier
* for the current reaction. A reaction may have any number of modifiers.
* It is permissible for a modifier species to appear simultaneously in the
* list of reactants and products of the same reaction where it is
* designated as a modifier, as well as to appear in the list of reactants,
* products and modifiers of other reactions in the model.
*
*/
#ifndef ModifierSpeciesReference_h
#define ModifierSpeciesReference_h
#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>
#ifdef __cplusplus
#include <string>
#include <sbml/SimpleSpeciesReference.h>
#include <sbml/SBMLVisitor.h>
#include <sbml/ListOf.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class SBMLNamespaces;
class LIBSBML_EXTERN ModifierSpeciesReference : public SimpleSpeciesReference
{
public:
/**
* Creates a new ModifierSpeciesReference using the given SBML @p level and
* @p version values.
*
* @param level an unsigned int, the SBML Level to assign to this
* ModifierSpeciesReference.
*
* @param version an unsigned int, the SBML Version to assign to this
* ModifierSpeciesReference.
*
* @copydetails doc_throw_exception_lv
*
* @copydetails doc_note_setting_lv
*/
ModifierSpeciesReference (unsigned int level, unsigned int version);
/**
* Creates a new ModifierSpeciesReference using the given SBMLNamespaces
* object @p sbmlns.
*
* @param sbmlns an SBMLNamespaces object.
*
* @copydetails doc_throw_exception_namespace
*
* @copydetails doc_note_setting_lv
*/
ModifierSpeciesReference (SBMLNamespaces* sbmlns);
/**
* Destroys this ModifierSpeciesReference.
*/
virtual ~ModifierSpeciesReference();
/** @cond doxygenLibsbmlInternal */
/**
* Accepts the given SBMLVisitor.
*
* @param v the SBMLVisitor instance to be used.
*
* @return the result of calling <code>v.visit()</code>.
*/
virtual bool accept (SBMLVisitor& v) const;
/** @endcond */
/**
* Creates and returns a deep copy of this ModifierSpeciesReference object.
*
* @return the (deep) copy of this ModifierSpeciesReference object.
*/
virtual ModifierSpeciesReference* clone () const;
/**
* Returns the libSBML type code for this %SBML object.
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for this object:
* @sbmlconstant{SBML_MODIFIER_SPECIES_REFERENCE, SBMLTypeCode_t} (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 Species, is
* always @c "modifierSpeciesReference".
*
* @return the name of this element, i.e., @c "modifierSpeciesReference".
*/
virtual const std::string& getElementName () const;
/**
* Predicate returning @c true if
* all the required attributes for this ModifierSpeciesReference object
* have been set.
*
* The required attributes for a ModifierSpeciesReference object are:
* species
*
* @return @c true if the required attributes have been set, @c false
* otherwise.
*/
virtual bool hasRequiredAttributes() const ;
#ifndef SWIG
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName, bool& value)
const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName, int& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
double& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
unsigned int& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
std::string& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
const char* value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Predicate returning @c true if this ModifierSpeciesReference's attribute
* "attributeName" is set.
*
* @param attributeName, the name of the attribute to query.
*
* @return @c true if this ModifierSpeciesReference's attribute
* "attributeName" has been set, otherwise @c false is returned.
*/
virtual bool isSetAttribute(const std::string& attributeName) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, bool value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, int value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, double value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName,
unsigned int value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName,
const std::string& value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, const char*
value);
/** @endcond */
/**
* Unsets the value of the "attributeName" attribute of this
* ModifierSpeciesReference.
*
* @param attributeName, the name of the attribute to query.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetAttribute(const std::string& attributeName);
/** @endcond */
#endif /* !SWIG */
protected:
/** @cond doxygenLibsbmlInternal */
/* 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 */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#ifndef SWIG
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
/**
* Creates a new ModifierSpeciesReference_t structure using the given SBML @p level and
* @p version values.
*
* @param level an unsigned int, the SBML level to assign to this
* ModifierSpeciesReference_t structure.
*
* @param version an unsigned int, the SBML version to assign to this
* ModifierSpeciesReference_t structure.
*
* @returns the newly-created ModifierSpeciesReference_t structure, or a null pointer if
* an error occurred during construction.
*
* @copydetails doc_note_setting_lv
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
ModifierSpeciesReference_t *
ModifierSpeciesReference_create(unsigned int level, unsigned int version);
/**
* Creates a new ModifierSpeciesReference_t structure using the given SBMLNamespaces_t
* structure, @p sbmlns.
*
* @copydetails doc_what_are_sbmlnamespaces
*
* @param sbmlns an SBMLNamespaces_t structure.
*
* @returns the newly-created ModifierSpeciesReference_t structure, or a null pointer if
* an error occurred during construction.
*
* @copydetails doc_note_setting_lv
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
ModifierSpeciesReference_t *
ModifierSpeciesReference_createWithNS(SBMLNamespaces_t* sbmlns);
/**
* Frees the given ModifierSpeciesReference_t structure.
*
* @param msr the ModifierSpeciesReference_t structure to be freed.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
void
ModifierSpeciesReference_free(ModifierSpeciesReference_t * msr);
/**
* Creates a deep copy of the given ModifierSpeciesReference_t structure.
*
* @param msr the ModifierSpeciesReference_t structure to be copied.
*
* @returns a (deep) copy of the given ModifierSpeciesReference_t structure, or a null
* pointer if a failure occurred.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
ModifierSpeciesReference_t *
ModifierSpeciesReference_clone(ModifierSpeciesReference_t * msr);
/**
* Returns the value of the "id" attribute of the given ModifierSpeciesReference_t
* structure.
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @return the id of this structure.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
const char *
ModifierSpeciesReference_getId(const ModifierSpeciesReference_t * msr);
/**
* Returns the value of the "name" attribute of the given ModifierSpeciesReference_t
* structure.
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @return the name of this structure.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
const char *
ModifierSpeciesReference_getName(const ModifierSpeciesReference_t * msr);
/**
* Returns the value of the "species" attribute of the given ModifierSpeciesReference_t
* structure.
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @return the species of this structure.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
const char *
ModifierSpeciesReference_getSpecies(const ModifierSpeciesReference_t * msr);
/**
* Predicate returning @c 1 (true) if the given ModifierSpeciesReference_t structure's "id"
* is set.
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @return @c 1 (true) if the "id" of this ModifierSpeciesReference_t structure is
* set, @c 0 (false) otherwise.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
int
ModifierSpeciesReference_isSetId(const ModifierSpeciesReference_t * msr);
/**
* Predicate returning @c 1 (true) if the given ModifierSpeciesReference_t structure's "name"
* is set.
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @return @c 1 (true) if the "name" of this ModifierSpeciesReference_t structure is
* set, @c 0 (false) otherwise.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
int
ModifierSpeciesReference_isSetName(const ModifierSpeciesReference_t * msr);
/**
* Predicate returning @c 1 (true) if the given ModifierSpeciesReference_t structure's "species"
* is set.
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @return @c 1 (true) if the "species" of this ModifierSpeciesReference_t structure is
* set, @c 0 (false) otherwise.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
int
ModifierSpeciesReference_isSetSpecies(const ModifierSpeciesReference_t * msr);
/**
* Sets the "id" attribute of the given ModifierSpeciesReference_t structure.
*
* This function copies the string given in @p id. If the string is
* a null pointer, this function is equivalent to calling ModifierSpeciesReference_unsetId().
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @param id the string to which the structures "id" attribute should be
* set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @note Using this function with a null pointer for @p id is equivalent to
* unsetting the value of the "id" attribute.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
int
ModifierSpeciesReference_setId(ModifierSpeciesReference_t * msr, const char * id);
/**
* Sets the "name" attribute of the given ModifierSpeciesReference_t structure.
*
* This function copies the string given in @p name. If the string is
* a null pointer, this function is equivalent to calling ModifierSpeciesReference_unsetName().
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @param name the string to which the structures "name" attribute should be
* set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @note Using this function with a null pointer for @p name is equivalent to
* unsetting the value of the "name" attribute.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
int
ModifierSpeciesReference_setName(ModifierSpeciesReference_t * msr, const char * name);
/**
* Sets the "species" attribute of the given ModifierSpeciesReference_t structure.
*
* This function copies the string given in @p species. If the string is
* a null pointer, this function is equivalent to calling ModifierSpeciesReference_unsetSpecies().
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @param species the string to which the structures "species" attribute should be
* set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @note Using this function with a null pointer for @p species is equivalent to
* unsetting the value of the "species" attribute.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
int
ModifierSpeciesReference_setSpecies(ModifierSpeciesReference_t * msr, const char * species);
/**
* Unsets the value of the "id" attribute of the given
*ModifierSpeciesReference_t structure.
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
int
ModifierSpeciesReference_unsetId(ModifierSpeciesReference_t * msr);
/**
* Unsets the value of the "name" attribute of the given
*ModifierSpeciesReference_t structure.
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
int
ModifierSpeciesReference_unsetName(ModifierSpeciesReference_t * msr);
/**
* Unsets the value of the "species" attribute of the given
*ModifierSpeciesReference_t structure.
*
* @param msr the ModifierSpeciesReference_t structure.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
int
ModifierSpeciesReference_unsetSpecies(ModifierSpeciesReference_t * msr);
/**
* Predicate returning @c 1 (true) or @c 0 (false) depending on whether all the required
* attributes of the given ModifierSpeciesReference_t structure have been set.
*
* @param msr the ModifierSpeciesReference_t structure to check.
*
* @return @c 1 (true) if all the required attributes for this
* structure have been defined, @c 0 (false) otherwise.
*
* @memberof ModifierSpeciesReference_t
*/
LIBSBML_EXTERN
int
ModifierSpeciesReference_hasRequiredAttributes(const ModifierSpeciesReference_t * msr);
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* ModifierSpeciesReference_h */
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