libsbml5-dev 5.10.0+dfsg-1 / usr / include / sbml / conversion / SBMLUnitsConverter.h

/**
 * @file    SBMLUnitsConverter.h
 * @brief   Definition of SBMLUnitsConverter, for converting units to SI.
 * @author  Sarah Keating
 * 
 * <!--------------------------------------------------------------------------
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 * 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 SBMLUnitsConverter
 * @sbmlbrief{core} SBML converter to convert a model's units to SI units.
 * 
 * @htmlinclude libsbml-facility-only-warning.html
 *
 * This SBML converter converts the units in a model to base SI units,
 * namely metre, kilogram, second, Ampere, Kelvin, mole and candela.
 *
 * Unit conversion will only be performed on models that are fully unit
 * consistent; that is, all objects have associated units, and there are no
 * literal numbers with no units specified.  In the case of an SBML
 * Level&nbsp;3 model involving math expressions, this means that the @c
 * timeUnits attribute on the Model object must be set, and if there are
 * any reactions in the model, the @c extentUnits attribute on the Model
 * object must also be set.
 *
 * This converter has the additional Boolean property "removeUnusedUnits"
 * that can be used to tell the converter whether to remove any
 * UnitDefinition objects that are not referred to, after conversion is
 * complete.  You can set this value by adding the property using
 * @verbatim
prop.addOption("removeUnusedUnits", false);
@endverbatim
 * The converter's default behavior is to remove the unused
 * UnitDefinition objects in the model.
 *
 * @see SBMLFunctionDefinitionConverter
 * @see SBMLLevelVersionConverter
 * @see SBMLRuleConverter
 * @see SBMLStripPackageConverter
 * @see SBMLUnitsConverter
 */

#ifndef SBMLUnitsConverter_h
#define SBMLUnitsConverter_h

#include <sbml/SBMLNamespaces.h>
#include <sbml/conversion/SBMLConverter.h>
#include <sbml/conversion/SBMLConverterRegister.h>

#ifdef __cplusplus


LIBSBML_CPP_NAMESPACE_BEGIN


class LIBSBML_EXTERN SBMLUnitsConverter : public SBMLConverter
{
public:

  /** @cond doxygenLibsbmlInternal */
  
  /* register with the ConversionRegistry */
  static void init();  
#ifndef SWIG
  typedef std::map<const std::string, const std::string> GlobalUnits;
  typedef GlobalUnits::iterator                  GlobalUnitsIter;
#endif

  /** @endcond */


  /**
   * Creates a new SBMLUnitsConverter object.
   */
  SBMLUnitsConverter ();


  /**
   * Copy constructor; creates a copy of an SBMLUnitsConverter
   * object.
   *
   * @param obj the SBMLUnitsConverter object to copy.
   */
  SBMLUnitsConverter(const SBMLUnitsConverter& obj);

  
  /**
   * Destroy this object.
   */
  virtual ~SBMLUnitsConverter ();


  /**
   * Assignment operator for SBMLUnitsConverter.
   *
   * @param rhs The object whose values are used as the basis of the
   * assignment.
   *
   * @throws @if python ValueError @else SBMLConstructorException @endif@~
   * Thrown if the argument @p rhs is @c NULL.
   */
  SBMLUnitsConverter& operator=(const SBMLUnitsConverter& rhs);


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


  /**
   * 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 SBMLUnitsConverter 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;

  
  /**
   * Convers the units in the model to base SI units; namely metre,
   * kilogram, second, Ampere, Kelvin, mole and candela.
   * 
   * @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_CONVERSION_NOT_AVAILABLE LIBSBML_CONV_CONVERSION_NOT_AVAILABLE @endlink
   * @li @link OperationReturnValues_t#LIBSBML_CONV_INVALID_SRC_DOCUMENT LIBSBML_CONV_INVALID_SRC_DOCUMENT @endlink
   * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @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;



#ifndef SWIG

#endif // SWIG


private:
  /** @cond doxygenLibsbmlInternal */

  bool convertUnits(SBase& sb, Model& m);

  bool convertUnits(SBase& sb, Model& m, std::string &modelUnitAttribute, ASTNode *ast = 0);

  int applyNewUnitDefinition(SBase& sb, Model& m, UnitDefinition *newUD,
    std::string &modelUnitAttribute, ASTNode * ast);

  std::string existsAlready(Model& m, UnitDefinition *newUD);

  bool getRemoveUnusedUnitsFlag();

  void removeUnusedUnitDefinitions(Model& m);
  
  
  bool convertGlobalUnits(Model& m);

 
  bool convertCnUnits(Model& m);


  bool isUsed(Model& m, std::string unitSId);


  bool unacceptable_errors(unsigned int errors);

  bool hasCnUnits(Model& m);

  bool mathHasCnUnits(const ASTNode *ast);

  bool matchesCnUnits(Model& m, std::string& units);

  bool mathMatchesCnUnits(const ASTNode *ast, std::string& units);
  bool convertAST(ASTNode *ast, Model &m);

  unsigned int newIdCount;

  GlobalUnits mGlobalUnits;

  /** @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  /* SBMLUnitsConverter_h */