/usr/include/sbml/packages/fbc/extension/FbcSpeciesPlugin.h is in libsbml5-dev 5.10.0+dfsg-1.
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* @file FbcSpeciesPlugin.h
* @brief Definition of FbcSpeciesPlugin, the plugin class of
* the fbc package for the Species element.
* @author Frank T. Bergmann
*
*<!---------------------------------------------------------------------------
* 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
*
* 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 FbcSpeciesPlugin
* @sbmlbrief{fbc} Implementation of the 'fbc' package extention to the
* %Species construct.
*
* The Flux Balance Constraints package extends the SBML Level 3 Version 1 Core Species class with the addition of two attributes: 'charge' and 'chemicalFormula'.
*/
#ifndef FbcSpeciesPlugin_h
#define FbcSpeciesPlugin_h
#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>
#include <sbml/packages/fbc/common/fbcfwd.h>
#ifdef __cplusplus
#include <sbml/SBMLErrorLog.h>
#include <sbml/Model.h>
#include <sbml/xml/XMLInputStream.h>
#include <sbml/xml/XMLOutputStream.h>
#include <sbml/extension/SBasePlugin.h>
#include <sbml/packages/fbc/sbml/FluxBound.h>
#include <sbml/packages/fbc/sbml/Objective.h>
#include <sbml/packages/fbc/sbml/GeneAssociation.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class LIBSBML_EXTERN FbcSpeciesPlugin : public SBasePlugin
{
public:
/**
* Constructor
*/
FbcSpeciesPlugin (const std::string &uri, const std::string &prefix,
FbcPkgNamespaces *fbcns);
/**
* Copy constructor. Creates a copy of this FbcSpeciesPlugin object.
*/
FbcSpeciesPlugin (const FbcSpeciesPlugin & orig);
/**
* Destroy this object.
*/
virtual ~FbcSpeciesPlugin ();
/**
* Assignment operator for FbcSpeciesPlugin .
*/
FbcSpeciesPlugin & operator=(const FbcSpeciesPlugin & orig);
/**
* Creates and returns a deep copy of this FbcSpeciesPlugin object.
*
* @return a (deep) copy of this FbcSpeciesPlugin object
*/
virtual FbcSpeciesPlugin * clone () const;
/**
* Predicate returning @c true or @c false depending on whether this
* FbcSpeciesPlugin "charge" attribute has been set.
*
* @return @c true if this FbcSpeciesPlugin "charge" attribute has been set,
* otherwise @c false is returned.
*/
virtual bool isSetCharge() const;
/**
* Sets the value of the "charge" attribute of this FbcSpeciesPlugin.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif The only possible value
* returned by this function is:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*/
virtual int setCharge(int charge);
/**
* Returns the value of the "charge" attribute of this FbcSpeciesPlugin.
*
* @return the value of the "charge" attribute of this FbcSpeciesPlugin.
*/
virtual int getCharge() const;
/**
* Unsets the value of the "charge" attribute of this FbcSpeciesPlugin.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif The only possible value
* returned by this function is:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*/
virtual int unsetCharge();
/**
* Predicate returning @c true or @c false depending on whether this
* FbcSpeciesPlugin "chemicalFormula" attribute has been set.
*
* @return @c true if this FbcSpeciesPlugin "chemicalFormula" attribute has been set,
* otherwise @c false is returned.
*/
virtual bool isSetChemicalFormula() const;
/**
* Sets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
* The format of chemicalFormula must consist only of atomic names (as in the Periodic Table) or user defined compounds either of which take the form of a single capital letter followed by zero or more lowercase letters. Where there is more than a single atom present, this is indicated with an integer. With regards to order (and enhance inter-operability) it is recommended to use the Hill system order. (However, no error-checking is performed by this routine.)
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif The only possible value
* returned by this function is:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*/
virtual int setChemicalFormula(const std::string& chemicalFormula);
/**
* Returns the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
*
* @return the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
*/
virtual const std::string& getChemicalFormula() const;
/**
* Unsets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif The only possible value
* returned by this function is:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*/
virtual int unsetChemicalFormula();
// ---------------------------------------------------------
//
// virtual functions (internal implementation) which should
// be overridden by subclasses.
//
// ---------------------------------------------------------
/** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument of this plugin object.
*
* Subclasses which contain one or more SBase derived elements must
* override this function.
*
* @param d the SBMLDocument object to use
*
* @see connectToParent
* @see enablePackageInternal
*/
virtual void setSBMLDocument (SBMLDocument* d);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBML object of this plugin object to
* this object and child elements (if any).
* (Creates a child-parent relationship by this plugin object)
*
* This function is called when this object is created by
* the parent element.
* Subclasses must override this this function if they have one
* or more child elements.Also, SBasePlugin::connectToParent()
* must be called in the overridden function.
*
* @param sbase the SBase object to use
*
* @see setSBMLDocument
* @see enablePackageInternal
*/
virtual void connectToParent (SBase *sbase);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Enables/Disables the given package with child elements in this plugin
* object (if any).
* (This is an internal implementation invoked from
* SBase::enablePakcageInternal() function)
*
* @note Subclasses in which one or more SBase derived elements are
* defined must override this function.
*
* @see setSBMLDocument
* @see connectToParent
*/
virtual void enablePackageInternal(const std::string& pkgURI,
const std::string& pkgPrefix, bool flag);
/** @endcond */
protected:
// --------------------------------------------------------
//
// overridden virtual functions for reading/writing/checking
// elements
//
// --------------------------------------------------------
/** @cond doxygenLibsbmlInternal */
/**
* 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);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Reads the attributes of corresponding package in SBMLDocument element.
*/
virtual void readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Writes the attributes of corresponding package in SBMLDocument element.
*/
virtual void writeAttributes (XMLOutputStream& stream) const;
/** @endcond */
/*-- data members --*/
/** @cond doxygenLibsbmlInternal */
int mCharge;
bool mIsSetCharge;
std::string mChemicalFormula;
/** @endcond */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#ifndef SWIG
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
/**
* Takes a FbcSpeciesPlugin_t structure and returns its charge.
*
* @param fbc the FbcSpeciesPlugin_t whose charge is sought.
*
* @return the charge attribute of the given FbcSpeciesPlugin_t, as an @c int.
*
* @memberof FbcSpeciesPlugin_t
*/
LIBSBML_EXTERN
int
FbcSpeciesPlugin_getCharge(SBasePlugin_t * fbc);
/**
* Predicate returning @c true or @c false depending on whether the given
* FbcSpeciesPlugin_t structure's charge is set.
*
* @param fbc the FbcSpeciesPlugin_t structure to query
*
* @return @c non-zero (true) if the "charge" attribute of the given
* FbcSpeciesPlugin_t structure is set, zero (false) otherwise.
*
* @memberof FbcSpeciesPlugin_t
*/
LIBSBML_EXTERN
int
FbcSpeciesPlugin_isSetCharge(SBasePlugin_t * fbc);
/**
* Sets the "charge" attribute of the given FbcSpeciesPlugin_t
* structure.
*
* @param fbc the FbcSpeciesPlugin_t structure
*
* @param charge the value of charge to assign to the "charge" 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
* @li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
*
* @memberof FbcSpeciesPlugin_t
*/
LIBSBML_EXTERN
int
FbcSpeciesPlugin_setCharge(SBasePlugin_t * fbc, int charge);
/**
* Unsets the "charge" attribute of the given FbcSpeciesPlugin_t structure.
*
* @param fbc the FbcSpeciesPlugin_t structure to unset
*
* @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 FbcSpeciesPlugin_t
*/
LIBSBML_EXTERN
int
FbcSpeciesPlugin_unsetCharge(SBasePlugin_t * fbc);
/**
* Takes a FbcSpeciesPlugin_t structure and returns its chemicalFormula.
*
* @param fbc the FbcSpeciesPlugin_t whose chemicalFormula is sought.
*
* @return the chemicalFormula of the given FbcSpeciesPlugin_t, as a pointer to a string.
*
* @memberof FbcSpeciesPlugin_t
*/
LIBSBML_EXTERN
char *
FbcSpeciesPlugin_getChemicalFormula(SBasePlugin_t * fbc);
/**
* Predicate returning @c true or @c false depending on whether the given
* FbcSpeciesPlugin_t structure's chemicalFormula is set.
*
* @param fbc the FbcSpeciesPlugin_t structure to query
*
* @return @c non-zero (true) if the "chemicalFormula" attribute of the given
* FbcSpeciesPlugin_t structure is set, zero (false) otherwise.
*
* @memberof FbcSpeciesPlugin_t
*/
LIBSBML_EXTERN
int
FbcSpeciesPlugin_isSetChemicalFormula(SBasePlugin_t * fbc);
/**
* Sets the chemicalFormula of the given FbcSpeciesPlugin_t to a copy of @p chemicalFormula.
*
* @param fbc the FbcSpeciesPlugin_t structure to set
* @param chemicalFormula the chemicalFormula to assign to the given FbcSpeciesPlugin_t's "chemicalFormula" 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
* @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 "chemicalFormula" attribute.
*
* @memberof FbcSpeciesPlugin_t
*/
LIBSBML_EXTERN
int
FbcSpeciesPlugin_setChemicalFormula(SBasePlugin_t * fbc, const char * chemicalFormula);
/**
* Unsets the "chemicalFormula" attribute of the given FbcSpeciesPlugin_t structure.
*
* @param fbc the FbcSpeciesPlugin_t structure to unset
*
* @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 FbcSpeciesPlugin_t
*/
LIBSBML_EXTERN
int
FbcSpeciesPlugin_unsetChemicalFormula(SBasePlugin_t * fbc);
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* FbcSpeciesPlugin_h */
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