/usr/include/sbml/conversion/SBMLRuleConverter.h is in libsbml5-dev 5.10.0+dfsg-1.
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* @file SBMLRuleConverter.h
* @brief Definition of SBMLRuleConverter, a converter sorting rules
* @author Frank 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
*
* 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 SBMLRuleConverter
* @sbmlbrief{core} SBML converter for reordering rules and assignments in a
* model.
*
* @htmlinclude libsbml-facility-only-warning.html
*
* This converter reorders assignments in a model. Specifically, it sorts
* the list of assignment rules (i.e., the AssignmentRule objects contained
* in the ListOfAssignmentRules within the Model object) and the initial
* assignments (i.e., the InitialAssignment objects contained in the
* ListOfInitialAssignments) such that, within each set, assignments that
* depend on prior values are placed after the values are set. For
* example, if there is an assignment rule stating <i>a = b + 1</i>, and
* another rule stating <i>b = 3</i>, the list of rules is sorted and the
* rules are arranged so that the rule for <i>b = 3</i> appears @em before
* the rule for <i>a = b + 1</i>. Similarly, if dependencies of this
* sort exist in the list of initial assignments in the model, the initial
* assignments are sorted as well.
*
* Beginning with SBML Level 2, assignment rules have no ordering
* required—the order in which the rules appear in an SBML file has
* no significance. Software tools, however, may need to reorder
* assignments for purposes of evaluating them. For example, for
* simulators that use time integration methods, it would be a good idea to
* reorder assignment rules such as the following,
*
* <i>b = a + 10 seconds</i><br>
* <i>a = time</i>
*
* so that the evaluation of the rules is independent of integrator
* step sizes. (This is due to the fact that, in this case, the order in
* which the rules are evaluated changes the result.) This converter
* can be used to reorder the SBML objects regardless of whether the
* input file contained them in the desired order. Here is a code
* fragment to illustrate how to do that:
* @verbatim
ConversionProperties props;
props.addOption("sortRules", true, "sort rules");
SBMLConverter converter;
converter.setProperties(&props);
converter.setDocument(&doc);
converter.convert();
@endverbatim
*
* @note The two sets of assignments (list of assignment rules on the one
* hand, and list of initial assignments on the other hand) are handled @em
* independently. In an SBML model, these entities are treated differently
* and no amount of sorting can deal with inter-dependencies between
* assignments of the two kinds.
*
* @see SBMLFunctionDefinitionConverter
* @see SBMLInitialAssignmentConverter
* @see SBMLLevelVersionConverter
* @see SBMLStripPackageConverter
* @see SBMLUnitsConverter
*/
#ifndef SBMLRuleConverter_h
#define SBMLRuleConverter_h
#include <sbml/SBMLNamespaces.h>
#include <sbml/conversion/SBMLConverter.h>
#include <sbml/conversion/SBMLConverterRegister.h>
#ifdef __cplusplus
LIBSBML_CPP_NAMESPACE_BEGIN
class LIBSBML_EXTERN SBMLRuleConverter : public SBMLConverter
{
public:
/** @cond doxygenLibsbmlInternal */
/* register with the ConversionRegistry */
static void init();
/** @endcond */
/**
* Creates a new SBMLLevelVersionConverter object.
*/
SBMLRuleConverter();
/**
* Copy constructor; creates a copy of an SBMLLevelVersionConverter
* object.
*
* @param obj the SBMLLevelVersionConverter object to copy.
*/
SBMLRuleConverter(const SBMLRuleConverter& obj);
/**
* Creates and returns a deep copy of this SBMLLevelVersionConverter
* object.
*
* @return a (deep) copy of this converter.
*/
virtual SBMLConverter* clone() const;
/**
* Destroy this SBMLRuleConverter object.
*/
virtual ~SBMLRuleConverter ();
/**
* Returns @c true if this converter object's properties match the given
* properties.
*
* A typical use of this method involves creating a ConversionProperties
* object, setting the options desired, and then calling this method on
* an SBMLLevelVersionConverter object to find out if the object's
* property values match the given ones. This method is also used by
* SBMLConverterRegistry::getConverterFor(@if java const ConversionProperties& props@endif)
* to search across all registered converters for one matching particular
* properties.
*
* @param props the properties to match.
*
* @return @c true if this converter's properties match, @c false
* otherwise.
*/
virtual bool matchesProperties(const ConversionProperties &props) const;
/**
* Perform the conversion.
*
* This method causes the converter to do the actual conversion work,
* that is, to convert the SBMLDocument object set by
* SBMLConverter::setDocument(@if java const SBMLDocument* doc@endif) and
* with the configuration options set by
* SBMLConverter::setProperties(@if java const ConversionProperties *props@endif).
*
* @return integer value indicating the success/failure of the operation.
* @if clike The value is drawn from the enumeration
* #OperationReturnValues_t. @endif@~ The possible values are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
* @li @link OperationReturnValues_t#LIBSBML_CONV_INVALID_SRC_DOCUMENT LIBSBML_CONV_INVALID_SRC_DOCUMENT @endlink
*/
virtual int convert();
/**
* Returns the default properties of this converter.
*
* A given converter exposes one or more properties that can be adjusted
* in order to influence the behavior of the converter. This method
* returns the @em default property settings for this converter. It is
* meant to be called in order to discover all the settings for the
* converter object.
*
* @return the ConversionProperties object describing the default properties
* for this converter.
*/
virtual ConversionProperties getDefaultProperties() const;
private:
/** @cond doxygenLibsbmlInternal */
/** @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 /* SBMLRuleConverter_h */
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