/usr/include/sbml/conversion/SBMLReactionConverter.h is in libsbml5-dev 5.13.0+dfsg-1.
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* @file SBMLReactionConverter.h
* @brief Definition of SBMLReactionConverter, a converter changing reactions into rate rules
* @author Sarah Keating
*
* <!--------------------------------------------------------------------------
* 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 SBMLReactionConverter
* @sbmlbrief{core} Converter to replace reactions with SBML <em>rate rules</em>.
*
* @htmlinclude libsbml-facility-only-warning.html
*
* This converter will take an SBML model and replace the definitions of
* reactions in the model with definitions of SBML rate rules. Equivalent
* RateRule objects are only created for species mentioned in reactions that
* have KineticLaw subobjects, since those are the only reactions that have
* an effect on the rates of change of species in the model; however, the
* converter removes all Reaction objects in the model after it is done.
*
* @section SBMLReactionConverter-usage Configuration and use of SBMLReactionConverter
*
* SBMLReactionConverter is enabled by creating a ConversionProperties object
* with the option @c "replaceReactions", and passing this properties object
* to SBMLDocument::convert(@if java ConversionProperties@endif). This
* converter does not offer any additional configuration options.
*
* @copydetails doc_section_using_sbml_converters
*/
#ifndef SBMLReactionConverter_h
#define SBMLReactionConverter_h
#include <sbml/SBMLNamespaces.h>
#include <sbml/conversion/SBMLConverter.h>
#include <sbml/conversion/SBMLConverterRegister.h>
#include <sbml/util/IdList.h>
#ifdef __cplusplus
#include <map>
#include <string>
LIBSBML_CPP_NAMESPACE_BEGIN
class SpeciesReference;
typedef std::vector< std::pair<std::string, ASTNode *> > RuleMap;
typedef std::vector< std::pair<std::string, ASTNode *> >::iterator RuleMapIter;
class LIBSBML_EXTERN SBMLReactionConverter : public SBMLConverter
{
public:
/** @cond doxygenLibsbmlInternal */
/**
* Register with the ConversionRegistry.
*/
static void init();
/** @endcond */
/**
* Creates a new SBMLReactionConverter object.
*/
SBMLReactionConverter();
/**
* Copy constructor; creates a copy of an SBMLReactionConverter
* object.
*
* @param obj the SBMLReactionConverter object to copy.
*/
SBMLReactionConverter(const SBMLReactionConverter& obj);
/**
* Creates and returns a deep copy of this SBMLReactionConverter
* object.
*
* @return a (deep) copy of this converter.
*/
virtual SBMLReactionConverter* clone() const;
/**
* Destroy this SBMLReactionConverter object.
*/
virtual ~SBMLReactionConverter ();
/**
* 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 SBMLReactionConverter object to find out if the object's
* property values match the given ones. This method is also used by
* SBMLConverterRegistry::getConverterFor(@if java ConversionProperties@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 SBMLDocument@endif) and
* with the configuration options set by
* SBMLConverter::setProperties(@if java ConversionProperties@endif).
*
* @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_CONV_INVALID_SRC_DOCUMENT, OperationReturnValues_t}
*/
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;
/**
* Sets the current SBML document to the given SBMLDocument object.
*
* @param doc the document to use for this conversion.
*
* @warning Even though the @p doc is 'const', it is immediately cast
* to a non-const version, which is then usually changed by the
* converter upon a successful conversion. This function is here
* solely to preserve backwards compatibility.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
*/
virtual int setDocument(const SBMLDocument* doc);
/**
* Sets the current SBML document to the given SBMLDocument object.
*
* @param doc the document to use for this conversion.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
*/
virtual int setDocument(SBMLDocument* doc);
private:
ASTNode * createRateRuleMathForSpecies(const std::string& spId,
Reaction * rn, bool isReactant);
ASTNode* determineStoichiometryNode(SpeciesReference * sr,
bool isReactant);
int createRateRule(const std::string& spId, ASTNode * math);
bool replaceReactions();
bool isDocumentValid();
// member variables
IdList mReactionsToRemove;
RuleMap mRateRulesMap;
Model * mOriginalModel;
};
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 /* SBMLReactionConverter_h */
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