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* @file SimpleSpeciesReference.h
* @brief Definitions of SimpleSpeciesReference.
* @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 SimpleSpeciesReference
* @sbmlbrief{core} Abstract class for references to species in reactions.
*
* As mentioned in the description of Reaction, every species that enters
* into a given reaction must appear in that reaction's lists of reactants,
* products and/or modifiers. In an SBML model, all species that may
* participate in any reaction are listed in the "listOfSpecies" element of
* the top-level Model object. Lists of products, reactants and modifiers
* in Reaction objects do not introduce new species, but rather, they refer
* back to those listed in the model's top-level "listOfSpecies". For
* reactants and products, the connection is made using SpeciesReference
* objects; for modifiers, it is made using ModifierSpeciesReference
* objects. SimpleSpeciesReference is an abstract type that serves as the
* parent class of both SpeciesReference and ModifierSpeciesReference. It
* is used simply to hold the attributes and elements that are common to
* the latter two structures.
*
* The SimpleSpeciesReference structure has a mandatory attribute,
* "species", which must be a text string conforming to the identifer
* syntax permitted in %SBML. This attribute is inherited by the
* SpeciesReference and ModifierSpeciesReference subclasses derived from
* SimpleSpeciesReference. The value of the "species" attribute must be
* the identifier of a species defined in the enclosing Model. The species
* is thereby declared as participating in the reaction being defined. The
* precise role of that species as a reactant, product, or modifier in the
* reaction is determined by the subclass of SimpleSpeciesReference (i.e.,
* either SpeciesReference or ModifierSpeciesReference) in which the
* identifier appears.
*
* SimpleSpeciesReference also contains an optional attribute, "id",
* allowing instances to be referenced from other structures. No SBML
* structures currently do this; however, such structures are anticipated
* in future SBML Levels.
*
*/
#ifndef SimpleSpeciesReference_h
#define SimpleSpeciesReference_h
#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>
#ifdef __cplusplus
#include <string>
#include <sbml/ExpectedAttributes.h>
#include <sbml/SBase.h>
#include <sbml/SBMLVisitor.h>
#include <sbml/xml/XMLAttributes.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class SBMLNamespaces;
class LIBSBML_EXTERN SimpleSpeciesReference : public SBase
{
public:
/**
* Creates a new SimpleSpeciesReference using the given SBML @p level and @p version
* values.
*
* @param level an unsigned int, the SBML Level to assign to this SimpleSpeciesReference.
*
* @param version an unsigned int, the SBML Version to assign to this
* SimpleSpeciesReference.
*
* @copydetails doc_throw_exception_lv
*
* @copydetails doc_note_setting_lv
*/
SimpleSpeciesReference (unsigned int level, unsigned int version);
/**
* Destroys this SimpleSpeciesReference.
*/
virtual ~SimpleSpeciesReference ();
/**
* Copy constructor; creates a copy of this SimpleSpeciesReference.
*
* @param orig the object to copy.
*/
SimpleSpeciesReference(const SimpleSpeciesReference& orig);
/**
* Assignment operator.
*
* @param rhs the object whose values are used as the basis of the
* assignment.
*/
SimpleSpeciesReference& operator=(const SimpleSpeciesReference& rhs);
/** @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 */
/**
* Returns the value of the "id" attribute of this SimpleSpeciesReference.
*
* @note Because of the inconsistent behavior of this function with
* respect to assignments and rules, it is now recommended to
* use the getIdAttribute() function instead.
*
* @copydetails doc_id_attribute
*
* @return the id of this SimpleSpeciesReference.
*
* @see getIdAttribute()
* @see setIdAttribute(const std::string& sid)
* @see isSetIdAttribute()
* @see unsetIdAttribute()
*/
virtual const std::string& getId () const;
/**
* Returns the value of the "name" attribute of this SimpleSpeciesReference object.
*
* @copydetails doc_get_name
*/
virtual const std::string& getName () const;
/**
* Get the value of the "species" attribute.
*
* @return the value of the attribute "species" for this
* SimpleSpeciesReference.
*/
const std::string& getSpecies () const;
/**
* Predicate returning @c true if this
* SimpleSpeciesReference's "id" attribute is set.
*
* @copydetails doc_isset_id
*/
virtual bool isSetId () const;
/**
* Predicate returning @c true if this
* SimpleSpeciesReference's "name" attribute is set.
*
* @copydetails doc_isset_name
*/
virtual bool isSetName () const;
/**
* Predicate returning @c true if this
* SimpleSpeciesReference's "species" attribute is set.
*
* @return @c true if the "species" attribute of this
* SimpleSpeciesReference is set, @c false otherwise.
*/
bool isSetSpecies () const;
/**
* Sets the "species" attribute of this SimpleSpeciesReference.
*
* The identifier string passed in @p sid is copied.
*
* @param sid the identifier of a species defined in the enclosing
* Model's ListOfSpecies.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
int setSpecies (const std::string& sid);
/**
* Sets the value of the "id" attribute of this SimpleSpeciesReference.
*
* @copydetails doc_set_id
*/
virtual int setId(const std::string& sid);
/**
* Sets the value of the "name" attribute of this SimpleSpeciesReference.
*
* @copydetails doc_set_name
*/
virtual int setName (const std::string& name);
/**
* Unsets the value of the "id" attribute of this SimpleSpeciesReference.
*
* @copydetails doc_unset_id
*/
virtual int unsetId ();
/**
* Unsets the value of the "name" attribute of this SimpleSpeciesReference.
*
* @copydetails doc_unset_name
*/
virtual int unsetName ();
/**
* Unsets the value of the "species" attribute of this SimpleSpeciesReference.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetSpecies ();
/**
* Predicate returning @c true if this
* is a ModifierSpeciesReference.
*
* @return @c true if this SimpleSpeciesReference's subclass is
* ModiferSpeciesReference, @c false if it is a plain SpeciesReference.
*/
bool isModifier () const;
/**
* @copydoc doc_renamesidref_common
*/
virtual void renameSIdRefs(const std::string& oldid, const std::string& newid);
#ifndef SWIG
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this SimpleSpeciesReference.
*
* @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
* SimpleSpeciesReference.
*
* @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
* SimpleSpeciesReference.
*
* @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
* SimpleSpeciesReference.
*
* @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
* SimpleSpeciesReference.
*
* @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
* SimpleSpeciesReference.
*
* @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 SimpleSpeciesReference's attribute
* "attributeName" is set.
*
* @param attributeName, the name of the attribute to query.
*
* @return @c true if this SimpleSpeciesReference'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
* SimpleSpeciesReference.
*
* @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
* SimpleSpeciesReference.
*
* @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
* SimpleSpeciesReference.
*
* @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
* SimpleSpeciesReference.
*
* @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
* SimpleSpeciesReference.
*
* @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
* SimpleSpeciesReference.
*
* @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 */
/** @cond doxygenLibsbmlInternal */
/**
* Unsets the value of the "attributeName" attribute of this
* SimpleSpeciesReference.
*
* @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 */
virtual bool hasRequiredAttributes() const ;
/**
* Creates a new SimpleSpeciesReference using the given SBMLNamespaces object
* @p sbmlns.
*
* @copydetails doc_what_are_sbmlnamespaces
*
* @param sbmlns an SBMLNamespaces object.
*
* @note Upon the addition of a SimpleSpeciesReference object to an
* SBMLDocument (e.g., using Model::addSimpleSpeciesReference()), the
* SBML XML namespace of the document @em overrides the value used when
* creating the SimpleSpeciesReference 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 SimpleSpeciesReference 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.
*/
SimpleSpeciesReference (SBMLNamespaces* sbmlns);
/**
* 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
* parent's 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 parent's implementation
* of this method as well.
*/
virtual void writeAttributes (XMLOutputStream& stream) const;
//std::string mId;
//std::string mName;
std::string mSpecies;
/** @endcond */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#ifndef SWIG
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* SimpleSpeciesReference_h */
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