/usr/include/sbml/packages/layout/extension/LayoutModelPlugin.h is in libsbml5-dev 5.13.0+dfsg-1.
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* @file LayoutModelPlugin.h
* @brief Definition of LayoutModelPlugin, the plugin class of
* layout package for 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) 2009-2013 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 LayoutModelPlugin
* @sbmlbrief{layout} Extension of Model.
*/
#ifndef LayoutModelPlugin_h
#define LayoutModelPlugin_h
#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>
#include <sbml/packages/layout/common/layoutfwd.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/layout/sbml/Layout.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class LIBSBML_EXTERN LayoutModelPlugin : public SBasePlugin
{
public:
/**
* Constructor
*/
LayoutModelPlugin (const std::string &uri, const std::string &prefix,
LayoutPkgNamespaces* layoutns);
/**
* Copy constructor. Creates a copy of this SBase object.
*/
LayoutModelPlugin(const LayoutModelPlugin& orig);
/**
* Destroy this object.
*/
virtual ~LayoutModelPlugin ();
/**
* Assignment operator for LayoutModelPlugin.
*/
LayoutModelPlugin& operator=(const LayoutModelPlugin& orig);
/**
* Creates and returns a deep copy of this LayoutModelPlugin object.
*
* @return a (deep) copy of this LayoutModelPlugin object
*/
virtual LayoutModelPlugin* clone () const;
#ifndef SWIG
// --------------------------------------------------------
//
// 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);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Parses Layout Extension of SBML Level 2
*/
virtual bool readOtherXML (SBase* parentObject, XMLInputStream& stream);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* 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;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* This function is a bit tricky.
* This function is used only for setting annotation element of layout
* extension for SBML Level2 because annotation element needs to be
* set before invoking the above writeElements function.
* Thus, no attribute is written by this function.
*/
virtual void writeAttributes (XMLOutputStream& stream) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/* function returns true if component has all the required
* elements
* needs to be overloaded for each component
*/
virtual bool hasRequiredElements() const ;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Parse L2 annotation if supported
*
*/
virtual void parseAnnotation(SBase *parentObject, XMLNode *annotation);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Synchronizes the annotation of this SBML object.
*
* Annotation element (XMLNode* mAnnotation) is synchronized with the
* current CVTerm objects (List* mCVTerm), ModelHistory object
* (ModelHistory* mHistory) and ListOfLayouts object (ListOfLayouts mLayouts).
* Currently, this method is called in getAnnotation, isSetAnnotation,
* and writeElements methods.
*/
virtual void syncAnnotation(SBase* parentObject, XMLNode *annotation);
/** @endcond */
#endif
/** ------------------------------------------------------------------
*
* Additional public functions
*
* ------------------------------------------------------------------
*/
/**
* Returns a List of all child SBase objects, including those nested to an
* arbitrary depth
*
* @return a List* of pointers to all children objects.
*/
virtual List* getAllElements(ElementFilter* filter=NULL);
/**
* Returns the ListOfLayouts object for this Model.
*
* @return the ListOfLayouts object for this Model.
*/
const ListOfLayouts* getListOfLayouts () const;
/**
* Returns the ListOfLayouts object for this Model.
*
* @return the ListOfLayouts object for this Model.
*/
ListOfLayouts* getListOfLayouts ();
/**
* Returns the layout object that belongs to the given index. If the
* index is invalid, @c NULL is returned.
*
* @param index the index of list of layout objects.
*
* @return the Layout object that belongs to the given index. NULL
* is returned if the index is invalid.
*/
Layout* getLayout (unsigned int index);
/**
* Returns the layout object that belongs to the given index. If the
* index is invalid, @c NULL is returned.
*
* @param index the index of list of layout objects.
*
* @return the Layout object that belongs to the given index. NULL
* is returned if the index is invalid.
*/
const Layout* getLayout (unsigned int index) const;
/**
* Returns the layout object with the given @p sid attribute. If the
* id is invalid, @c NULL is returned.
*
* @param sid the id attribute of the layout object.
*
* @return the Layout object with the given @p sid attribute. NULL
* is returned if the given @p sid is invalid.
*/
Layout* getLayout (const std::string& sid);
/**
* Returns the layout object with the given @p sid attribute. If the
* id is invalid, @c NULL is returned.
*
* @param sid the id attribute of the layout object.
*
* @return the Layout object with the given @p sid attribute. NULL
* is returned if the given @p sid is invalid.
*/
const Layout* getLayout (const std::string& sid) const;
/**
* Adds a copy of the layout object to the list of layouts.
*
* @param layout the layout object to be added.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
*/
int addLayout (const Layout* layout);
/**
* Creates a new layout object and adds it to the list of layout objects
* and returns it.
*
* @return a new layout object.
*/
Layout* createLayout();
/**
* Removes the nth Layout object from this Model 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 Layout object to remove
*
* @return the Layout object removed. As mentioned above, the caller owns the
* returned object. @c NULL is returned if the given index is out of range.
*/
Layout* removeLayout (unsigned int n);
/**
* Returns the number of layout objects.
*
* @return the number of layout objects.
*/
int getNumLayouts() const;
// ---------------------------------------------------------
//
// virtual functions (internal implementation) which should
// be overridden by subclasses.
//
// ---------------------------------------------------------
/** @cond doxygenLibsbmlInternal */
int appendFrom(const Model* model);
/** @endcond */
/** @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
*
* @if cpp
* @see setSBMLDocument
* @see enablePackageInternal
* @endif
*/
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.
*
* @if cpp
* @see setSBMLDocument
* @see connectToParent
* @endif
*/
virtual void enablePackageInternal(const std::string& pkgURI,
const std::string& pkgPrefix, bool flag);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
virtual bool accept (SBMLVisitor& v) const;
/** @endcond */
protected:
/** @cond doxygenLibsbmlInternal */
/*-- data members --*/
ListOfLayouts mLayouts;
/** @endcond */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#endif /* LayoutModelPlugin_h */
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