libsbml5-dev 5.13.0+dfsg-1 / usr / include / sbml / packages / groups / extension / GroupsModelPlugin.h

/**
 * @file GroupsModelPlugin.h
 * @brief Definition of the GroupsModelPlugin class.
 * @author SBMLTeam
 *
 * <!--------------------------------------------------------------------------
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 * 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) 2009-2013 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 GroupsModelPlugin
 * @sbmlbrief{groups} Extension of Model.
 *
 * The GroupsModelPlugin class inherits from the SBMLSBasePlugin class, and
 * codifies the extensions to the Model class defined in the SBML
 * Level&nbsp;3 @ref groups (&ldquo;groups&rdquo;) package.  This extension
 * allows a Model to contain an optional ListOfGroups object inside a new
 * element called <code>&lt;listOfGroups&gt;</code>.  This list holds the
 * definition of optional groups defined in the model.
 *
 * A "group" in SBML Level&nbsp;3 provides a mechanism for
 * indicating that components of an SBML model are related in some way.
 * Groups may contain either the same or different types of SBML objects, and
 * groups may be nested if desired. There are no predefined behavioral
 * semantics associated with groups.  All groups in a given model have to be
 * defined as Group objects and included in the ListOfGroups object attached
 * to the Model object containing them.
 */


#ifndef GroupsModelPlugin_H__
#define GroupsModelPlugin_H__


#include <sbml/common/extern.h>


#ifdef __cplusplus


#include <sbml/extension/SBasePlugin.h>
#include <sbml/packages/groups/sbml/ListOfGroups.h>
#include <sbml/packages/groups/sbml/Group.h>


LIBSBML_CPP_NAMESPACE_BEGIN


class LIBSBML_EXTERN GroupsModelPlugin : public SBasePlugin
{
protected:

  /** @cond doxygenLibsbmlInternal */

  ListOfGroups mGroups;

  /** @endcond */

public:

  /**
   * Creates a new GroupsModelPlugin using the given URI, prefix and package
   * namespace.
   *
   * @param uri a string, representing the URI of the package.
   *
   * @param prefix a string, the prefix to be used.
   *
   * @param groupsns a pointer to the GroupsPkgNamespaces object to be used.
   */
  GroupsModelPlugin(const std::string& uri,
                    const std::string& prefix,
                    GroupsPkgNamespaces* groupsns);


  /**
   * Copy constructor for GroupsModelPlugin.
   *
   * @param orig the GroupsModelPlugin instance to copy.
   */
  GroupsModelPlugin(const GroupsModelPlugin& orig);


  /**
   * Assignment operator for GroupsModelPlugin.
   *
   * @param rhs the GroupsModelPlugin object whose values are to be used as
   * the basis of the assignment.
   */
  GroupsModelPlugin& operator=(const GroupsModelPlugin& rhs);


  /**
   * Creates and returns a deep copy of this GroupsModelPlugin object.
   *
   * @return a (deep) copy of this GroupsModelPlugin object.
   */
  virtual GroupsModelPlugin* clone() const;


  /**
   * Destructor for GroupsModelPlugin.
   */
  virtual ~GroupsModelPlugin();


  /**
   * Returns the ListOfGroups from this GroupsModelPlugin.
   *
   * @return the ListOfGroups from this GroupsModelPlugin.
   *
   * @see addGroup(const Group* g)
   * @see createGroup()
   * @see getGroup(const std::string& sid)
   * @see getGroup(unsigned int n)
   * @see getNumGroups()
   * @see removeGroup(unsigned int n)
   * @see removeGroup(const std::string& sid)
   */
  const ListOfGroups* getListOfGroups() const;


  /**
   * Returns the ListOfGroups from this GroupsModelPlugin.
   *
   * @return the ListOfGroups from this GroupsModelPlugin.
   *
   * @see addGroup(const Group* g)
   * @see createGroup()
   * @see getGroup(const std::string& sid)
   * @see getGroup(unsigned int n)
   * @see getNumGroups()
   * @see removeGroup(unsigned int n)
   * @see removeGroup(const std::string& sid)
   */
  ListOfGroups* getListOfGroups();


  /**
   * Returns the nth Group.
   *
   * @param n an unsigned int representing the index of the Group to retrieve.
   *
   * @return the nth Group in the ListOfGroups within this GroupsModelPlugin.
   *
   * @see addGroup(const Group* g)
   * @see createGroup()
   * @see getGroup(const std::string& sid)
   * @see getGroup(unsigned int n)
   * @see getNumGroups()
   * @see removeGroup(unsigned int n)
   * @see removeGroup(const std::string& sid)
   */
  Group* getGroup(unsigned int n);


  /**
   * Get a Group from the GroupsModelPlugin.
   *
   * @param n an unsigned int representing the index of the Group to retrieve.
   *
   * @return the nth Group in the ListOfGroups within this GroupsModelPlugin
   * object.
   *
   * @see addGroup(const Group* g)
   * @see createGroup()
   * @see getGroup(const std::string& sid)
   * @see getGroup(unsigned int n)
   * @see getNumGroups()
   * @see removeGroup(unsigned int n)
   * @see removeGroup(const std::string& sid)
   */
  const Group* getGroup(unsigned int n) const;


  /**
   * Get a Group from the GroupsModelPlugin based on its identifier.
   *
   * @param sid a string representing the identifier of the Group to retrieve.
   *
   * @return the Group in the ListOfGroups within this GroupsModelPlugin with
   * the given identifier @p sid, or @c NULL if no such Group exists.
   *
   * @see addGroup(const Group* g)
   * @see createGroup()
   * @see getGroup(const std::string& sid)
   * @see getGroup(unsigned int n)
   * @see getNumGroups()
   * @see removeGroup(unsigned int n)
   * @see removeGroup(const std::string& sid)
   */
  Group* getGroup(const std::string& sid);


  /**
   * Get a Group from the GroupsModelPlugin based on its identifier.
   *
   * @param sid a string representing the identifier of the Group to retrieve.
   *
   * @return the Group in the ListOfGroups within this GroupsModelPlugin with
   * the given identifier @p sid, or @c NULL if no such Group exists.
   *
   * @see addGroup(const Group* g)
   * @see createGroup()
   * @see getGroup(unsigned int n)
   * @see getNumGroups()
   * @see removeGroup(unsigned int n)
   * @see removeGroup(const std::string& sid)
   */
  const Group* getGroup(const std::string& sid) const;


  /**
   * Adds a copy of the given Group to this GroupsModelPlugin.
   *
   * @param g the Group object to add.
   *
   * @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}
   * @li @sbmlconstant{LIBSBML_LEVEL_MISMATCH, OperationReturnValues_t}
   * @li @sbmlconstant{LIBSBML_VERSION_MISMATCH, OperationReturnValues_t}
   * @li @sbmlconstant{LIBSBML_PKG_VERSION_MISMATCH, OperationReturnValues_t}
   * @li @sbmlconstant{LIBSBML_DUPLICATE_OBJECT_ID, OperationReturnValues_t}
   *
   * @copydetails doc_note_object_is_copied
   *
   * @see createGroup()
   * @see getGroup(const std::string& sid)
   * @see getGroup(unsigned int n)
   * @see getNumGroups()
   * @see removeGroup(unsigned int n)
   * @see removeGroup(const std::string& sid)
   */
  int addGroup(const Group* g);


  /**
   * Get the number of Group objects in this GroupsModelPlugin.
   *
   * @return the number of Group objects in this GroupsModelPlugin.
   *
   * @see createGroup()
   * @see getGroup(const std::string& sid)
   * @see getGroup(unsigned int n)
   * @see removeGroup(unsigned int n)
   * @see removeGroup(const std::string& sid)
   */
  unsigned int getNumGroups() const;


  /**
   * Creates a new Group object
   *
   * This method creates a new Group object, adds it to this
   * GroupsModelPlugin object, and returns the Group object created.
   *
   * @return a new Group object instance.
   *
   * @see addGroup(const Group* g)
   * @see getGroup(const std::string& sid)
   * @see getGroup(unsigned int n)
   * @see removeGroup(unsigned int n)
   * @see removeGroup(const std::string& sid)
   */
  Group* createGroup();


  /**
   * Removes the nth Group.
   *
   * This removes the nth Group from this GroupsModelPlugin object and
   * returns a pointer to it.
   *
   * @param n an unsigned int representing the index of the Group to remove.
   *
   * @return a pointer to the nth Group in this GroupsModelPlugin.
   *
   * @note The caller owns the returned object and is responsible for deleting
   * it.
   *
   * @see addGroup(const Group* g)
   * @see createGroup()
   * @see getGroup(const std::string& sid)
   * @see getGroup(unsigned int n)
   * @see getNumGroups()
   * @see removeGroup(const std::string& sid)
   */
  Group* removeGroup(unsigned int n);


  /**
   * Removes the Group from this GroupsModelPlugin based on its identifier.
   *
   * This method removes the Group from this GroupsModelPlugin based on its
   * identifier, and returns a pointer to it.
   *
   * @param sid a string representing the identifier of the Group to remove.
   *
   * @return the Group in this GroupsModelPlugin based on the identifier, or
   * @c @c NULL if no such Group exists.
   *
   * @note The caller owns the returned object and is responsible for deleting
   * it.
   *
   * @see addGroup(const Group* g)
   * @see createGroup()
   * @see getGroup(const std::string& sid)
   * @see getGroup(unsigned int n)
   * @see getNumGroups()
   */
  Group* removeGroup(const std::string& sid);


  /** @cond doxygenLibsbmlInternal */

  /**
   * Write any contained elements
   */
  virtual void writeElements(XMLOutputStream& stream) const;

  /** @endcond */



  /** @cond doxygenLibsbmlInternal */

  /**
   * Accepts the given SBMLVisitor
   */
  virtual bool accept(SBMLVisitor& v) const;

  /** @endcond */



  /** @cond doxygenLibsbmlInternal */

  /**
   * Sets the parent SBMLDocument
   */
  virtual void setSBMLDocument(SBMLDocument* d);

  /** @endcond */



  /** @cond doxygenLibsbmlInternal */

  /**
   * Connects to child elements
   */
  virtual void connectToChild();

  /** @endcond */



  /** @cond doxygenLibsbmlInternal */

  /**
   * Connects to parent element
   */
  virtual void connectToParent(SBase* base);

  /** @endcond */



  /** @cond doxygenLibsbmlInternal */

  /**
   * Enables/disables the given package with this element
   */
  virtual void enablePackageInternal(const std::string& pkgURI,
                                     const std::string& pkgPrefix,
                                     bool flag);

  /** @endcond */


  /**
   * Returns the first child element that has the given @p id
   *
   * This method searches the model-wide SId namespace for the @p id.
   *
   * @param id a string representing the id attribute of the object to
   * retrieve.
   *
   * @return a pointer to the SBase element with the given @p id.  If no such
   * object is found, this method returns @c NULL.
   */
  virtual SBase* getElementBySId(const std::string& id);


  /**
   * Returns the first child element that has the given @p metaid.
   *
   * @param metaid a string representing the metaid attribute of the object to
   * retrieve.
   *
   * @return a pointer to the SBase element with the given @p metaid.  If
   * no such object is found, this method returns @c NULL.
   */
  virtual SBase* getElementByMetaId(const std::string& metaid);


  /**
   * Returns a List of all child SBase objects, including those nested to an
   * arbitrary depth.
   *
   * @param filter an ElementFilter that may impose restrictions on the
   * objects to be retrieved.
   *
   * @return a List pointer of pointers to all SBase child objects with any
   * restriction imposed.
   */
  virtual List* getAllElements(ElementFilter * filter = NULL);



  /** @cond doxygenLibsbmlInternal */

  /**
   * Append items from model (used in comp flattening)
   *
   * @param model a pointer to a model object.
   *
   */
  int appendFrom(const Model* model);

  /** @endcond */


protected:


  /** @cond doxygenLibsbmlInternal */

  /**
   * Creates a new object from the next XMLToken on the XMLInputStream
   */
  virtual SBase* createObject(XMLInputStream& stream);

  /** @endcond */


public:

  /**
   * For nested groups (Member objects that reference a ListOfMembers 
   * object), SBO terms, Notes, and Annotation from the
   * parent ListOfMembers applies to the child.  This function
   * copies any information from any of those three things to all 
   * child ListOfMembers, and if that information is not already 
   * set.  After calling
   * this function, it is sufficient to check any ListOfMembers
   * to see if its SBO term, Notes, or Annotation is set, without
   * further checking to see if that element was nested in another
   * Group.
   */
  virtual void copyInformationToNestedLists();


};



LIBSBML_CPP_NAMESPACE_END




#endif /* __cplusplus */




#endif /* !GroupsModelPlugin_H__ */