/usr/include/sbml/packages/qual/extension/QualModelPlugin.h is in libsbml5-dev 5.13.0+dfsg-1.
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* @file QualModelPlugin.h
* @brief Definition of QualModelPlugin, the plugin class of
* qual package for the Model element.
* @author Akiya Jouraku
*
* <!--------------------------------------------------------------------------
* This file is part of libSBML. Please visit http://sbml.org for more
* information about SBML, and the latest version of libSBML.
*
* Copyright (C) 2013-2016 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) 2009-2011 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 QualModelPlugin
* @sbmlbrief{qual} Extension of Model.
*
* The extension of SBML Level 3 Core's Model class is relatively
* straightforward: the Qualitative Models Package adds two lists, one for
* holding qualitativeSpecies (ListOfQualitativeSpecies), and the other for
* holding transitions (ListOfTransitions). The Model element may contain at
* most one ListOfQualitativeSpecies, which must contain at least one
* QualitativeSpecies. It may also contain at most one ListOfTransitions
* which must contain at least one Transition.
*/
#ifndef QualModelPlugin_h
#define QualModelPlugin_h
#include <sbml/common/extern.h>
#ifdef __cplusplus
#include <sbml/extension/SBasePlugin.h>
#include <sbml/packages/qual/sbml/QualitativeSpecies.h>
#include <sbml/packages/qual/sbml/Transition.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class LIBSBML_EXTERN QualModelPlugin : public SBasePlugin
{
public:
/**
* Constructor
*/
QualModelPlugin (const std::string &uri, const std::string &prefix,
QualPkgNamespaces *qualns);
/**
* Copy constructor. Creates a copy of this SBase object.
*/
QualModelPlugin(const QualModelPlugin& orig);
/**
* Destroy this object.
*/
virtual ~QualModelPlugin ();
/**
* Assignment operator for QualModelPlugin.
*/
QualModelPlugin& operator=(const QualModelPlugin& orig);
/**
* Creates and returns a deep copy of this QualModelPlugin object.
*
* @return a (deep) copy of this SBase object
*/
virtual QualModelPlugin* clone () const;
// --------------------------------------------------------
//
// overridden virtual functions for reading/writing/checking
// elements
//
// --------------------------------------------------------
/** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
* return an SBML object corresponding to the next XMLToken in the
* XMLInputStream if they have their specific elements.
*
* @return the SBML object corresponding to next XMLToken in the
* XMLInputStream or NULL if the token was not recognized.
*/
virtual SBase* createObject (XMLInputStream& stream);
/**
* Subclasses must override this method to write out their contained
* SBML objects as XML elements if they have their specific elements.
*/
virtual void writeElements (XMLOutputStream& stream) const;
/** ------------------------------------------------------------------
*
* Additional public functions
*
* ------------------------------------------------------------------
*/
/** @cond doxygenLibsbmlInternal */
int appendFrom(const Model* model);
/** @endcond */
/**
* Returns a List of all child SBase objects, including those nested to an
* arbitary depth.
*
* @return a List* of pointers to all child objects.
*/
virtual List* getAllElements(ElementFilter * filter = NULL);
/**
* Returns the ListOfQualitativeSpecies in this plugin object.
*
* @return ListOfQualitativeSpecies object in this plugin object.
*/
const ListOfQualitativeSpecies* getListOfQualitativeSpecies () const;
/**
* Returns the ListOfQualitativeSpecies in this plugin object.
*
* @return ListOfQualitativeSpecies object in this plugin object.
*/
ListOfQualitativeSpecies* getListOfQualitativeSpecies ();
/**
* Returns the QualitativeSpecies object that belongs to the given index. If the
* index is invalid, NULL is returned.
*
* @param n the index number of the QualitativeSpecies to get.
*
* @return the nth QualitativeSpecies in the ListOfQualitativeSpecies.
*/
const QualitativeSpecies* getQualitativeSpecies (unsigned int n) const;
/**
* Returns the QualitativeSpecies object that belongs to the given index. If the
* index is invalid, NULL is returned.
*
* @param n the index number of the QualitativeSpecies to get.
*
* @return the nth QualitativeSpecies in the ListOfQualitativeSpecies.
*/
QualitativeSpecies* getQualitativeSpecies (unsigned int n);
/**
* Returns the qualitativeSpecies object based on its identifier.
*
* @param sid a string representing the identifier
* of the QualitativeSpecies to get.
*
* @return QualitativeSpecies in the ListOfQualitativeSpecies with the given id
* or NULL if no such QualitativeSpecies exists.
*
* @see getQualitativeSpecies(unsigned int n)
* @see getListOfQualitativeSpecies()
*/
QualitativeSpecies* getQualitativeSpecies (const std::string& sid);
/**
* Returns the qualitativeSpecies object based on its identifier.
*
* @param sid a string representing the identifier
* of the QualitativeSpecies to get.
*
* @return QualitativeSpecies in the ListOfQualitativeSpecies with the given id
* or NULL if no such QualitativeSpecies exists.
*
* @see getQualitativeSpecies(unsigned int n)
* @see getListOfQualitativeSpecies()
*/
const QualitativeSpecies* getQualitativeSpecies (const std::string& sid) const;
/**
* Adds a copy of the given QualitativeSpecies object to the list of qual.
*
* @param qualitativeSpecies the QualitativeSpecies object to be added to the list of qual.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
*/
int addQualitativeSpecies (const QualitativeSpecies* qualitativeSpecies);
/**
* Creates a new qual object and adds it to the list of qual objects
* and returns it.
*
* @return a newly created QualitativeSpecies object
*/
QualitativeSpecies* createQualitativeSpecies();
/**
* Removes the nth QualitativeSpecies object from this plugin object and
* returns a pointer to it.
*
* The caller owns the returned object and is responsible for
* deleting it.
*
* @param n the index of the QualitativeSpecies object to remove
*
* @return the QualitativeSpecies object removed. As mentioned above, the
* caller owns the returned object. NULL is returned if the
* given index is out of range.
*/
QualitativeSpecies* removeQualitativeSpecies (unsigned int n);
/**
* Removes the QualitativeSpecies object with the given id attribute from
* this plugin object and returns a pointer to it.
*
* The caller owns the returned object and is responsible for
* deleting it.
*
* @param sid the id attribute of the QualitativeSpecies object to remove
*
* @return the QualitativeSpecies object removed. As mentioned above, the
* caller owns the returned object. NULL is returned if the
* given index is out of range.
*/
QualitativeSpecies* removeQualitativeSpecies (const std::string& sid);
/**
* Returns the number of QualitativeSpecies object in this plugin object.
*
* @return the number of QualitativeSpecies object in this plugin object.
*/
unsigned int getNumQualitativeSpecies() const;
/**
* Returns the ListOfTransitions in this plugin object.
*
* @return ListOfTransitions object in this plugin object.
*/
const ListOfTransitions* getListOfTransitions () const;
/**
* Returns the ListOfTransitions in this plugin object.
*
* @return ListOfTransitions object in this plugin object.
*/
ListOfTransitions* getListOfTransitions ();
/**
* Returns the Transition object that belongs to the given index. If the
* index is invalid, NULL is returned.
*
* @param n the index number of the Transition to get.
*
* @return the nth Transition in the ListOfTransitions.
*/
const Transition* getTransition (unsigned int n) const;
/**
* Returns the Transition object that belongs to the given index. If the
* index is invalid, NULL is returned.
*
* @param n the index number of the Transition to get.
*
* @return the nth Transition in the ListOfTransitions.
*/
Transition* getTransition (unsigned int n);
/**
* Returns the qualitativeSpecies object based on its identifier.
*
* @param sid a string representing the identifier
* of the Transition to get.
*
* @return Transition in the ListOfTransitions with the given id
* or NULL if no such Transition exists.
*
* @see getTransition(unsigned int n)
* @see getListOfTransitions()
*/
Transition* getTransition (const std::string& sid);
/**
* Returns the qualitativeSpecies object based on its identifier.
*
* @param sid a string representing the identifier
* of the Transition to get.
*
* @return Transition in the ListOfTransitions with the given id
* or NULL if no such Transition exists.
*
* @see getTransition(unsigned int n)
* @see getListOfTransitions()
*/
const Transition* getTransition (const std::string& sid) const;
/**
* Adds a copy of the given Transition object to the list of qual.
*
* @param transition the Transition object to be added to the list of qual.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
*/
int addTransition (const Transition* transition);
/**
* Creates a new qual object and adds it to the list of qual objects
* and returns it.
*
* @return a newly created Transition object
*/
Transition* createTransition();
/**
* Removes the nth Transition object from this plugin object and
* returns a pointer to it.
*
* The caller owns the returned object and is responsible for
* deleting it.
*
* @param n the index of the Transition object to remove
*
* @return the Transition object removed. As mentioned above, the
* caller owns the returned object. NULL is returned if the
* given index is out of range.
*/
Transition* removeTransition (unsigned int n);
/**
* Removes the Transition object with the given id attribute from
* this plugin object and returns a pointer to it.
*
* The caller owns the returned object and is responsible for
* deleting it.
*
* @param sid the id attribute of the Transition object to remove
*
* @return the Transition object removed. As mentioned above, the
* caller owns the returned object. NULL is returned if the
* given index is out of range.
*/
Transition* removeTransition (const std::string& sid);
/**
* Returns the number of Transition object in this plugin object.
*
* @return the number of Transition object in this plugin object.
*/
unsigned int getNumTransitions() const;
// ---------------------------------------------------------
//
// 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* of this SBML object to child SBML objects (if any).
* (Creates a child-parent relationship by the parent)
*
* @see setSBMLDocument
* @see enablePackageInternal
*/
virtual void connectToChild ();
/** @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::enablePackageInternal() 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 */
/** @cond doxygenLibsbmlInternal */
/**
* Accepts the given SBMLVisitor.
*/
virtual bool accept (SBMLVisitor& v) const;
/** @endcond */
protected:
/** @cond doxygenLibsbmlInternal */
/*-- data members --*/
ListOfQualitativeSpecies mQualitativeSpecies;
ListOfTransitions mTransitions;
/** @endcond */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#endif /* QualModelPlugin_h */
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