/usr/include/sbml/units/UnitFormulaFormatter.h is in libsbml5-dev 5.13.0+dfsg-1.
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*@cond doxygenLibsbmlInternal
**
* @file UnitFormulaFormatter.h
* @brief Formats an AST formula tree as a unit definition
* @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 UnitFormulaFormatter
* @sbmlbrief{core} Object for deriving the units associated with objects and
* math expressions.
*
* @htmlinclude not-sbml-warning.html
*
* A UnitFormulaFormatter object is created using a Model object
* and uses the information from that Model to derive the units
* of either an ASTNode respresenting a math expression or
* an appropriate SBML object. The derived units are formulated into
* a UnitDefinition object.
*/
#ifndef UnitFormulaFormatter_h
#define UnitFormulaFormatter_h
#include <math.h>
#include <sbml/common/extern.h>
#include <sbml/util/StringBuffer.h>
#include <sbml/UnitDefinition.h>
#include <sbml/Unit.h>
#include <sbml/Model.h>
#include <sbml/FunctionDefinition.h>
#include <sbml/Compartment.h>
#include <sbml/Species.h>
#include <sbml/Parameter.h>
#include <sbml/Reaction.h>
#include <sbml/KineticLaw.h>
#include <sbml/Event.h>
#include <sbml/math/ASTNode.h>
#ifdef __cplusplus
#include <cstring>
LIBSBML_CPP_NAMESPACE_BEGIN
class FormulaUnitsData;
class LIBSBML_EXTERN UnitFormulaFormatter
{
public:
/**
* Creates a new UnitFormulaFormatter.
*
* @param m pointer to the Model object for which the units
* are to be derived.
*
* @note The UnitFormulaFormatter creates a deep copy of the
* Model object.
*/
UnitFormulaFormatter(const Model * m);
/**
* Destroys this UnitFormulaFormatter.
*/
~UnitFormulaFormatter();
/**
* Visits the ASTNode and returns the unitDefinition of the formula.
* This function is really a dispatcher to the other
* getUnitDefinition() methods.
*
* @param node the ASTNode for which the unitDefinition is to be
* constructed.
*
* @param inKL boolean indicating whether the ASTNode represents the
* math element of a KineticLaw (default = false).
*
* @param reactNo integer indicating which Reaction within the Model
* contains the KineticLaw under consideration (default = -1).
*
* @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html @endif@~
*/
UnitDefinition * getUnitDefinition(const ASTNode * node,
bool inKL = false, int reactNo = -1);
/**
* Visits the Compartment and returns the unitDefinition constructed
* from the units of this Compartment.
*
* @param compartment the Compartment object for which the unitDefinition
* is to be constructed.
*
* @return the unitDefinition constructed to represent the units
* of the Compartment.
*/
UnitDefinition * getUnitDefinitionFromCompartment
(const Compartment * compartment);
/**
* Visits the Species and returns the unitDefinition constructed
* from the units of this Species.
*
* @param species the Species object for which the unitDefinition
* is to be constructed.
*
* @return the unitDefinition constructed to represent the units
* of the Species.
*/
UnitDefinition * getUnitDefinitionFromSpecies(const Species * species);
/**
* Visits the Parameter and returns the unitDefinition constructed
* from the units of this Parameter.
*
* @param parameter the Parameter object for which the unitDefinition
* is to be constructed.
*
* @return the unitDefinition constructed to represent the units
* of the Parameter.
*/
UnitDefinition * getUnitDefinitionFromParameter(const Parameter * parameter);
/**
* Visits the Event and returns the unitDefinition constructed
* from the time units of this Event.
*
* @param event the Event object for which the unitDefinition
* is to be constructed.
*
* @return the unitDefinition constructed to represent the time units
* of the Event.
*/
UnitDefinition * getUnitDefinitionFromEventTime(const Event * event);
/**
* Returns the unitDefinition constructed
* from the extent units of this Model.
*
* @return the unitDefinition constructed to represent the extent units
* of the Model.
*/
UnitDefinition * getExtentUnitDefinition();
/**
* Returns the unitDefinition constructed
* from the substance units of this Species.
*/
UnitDefinition * getSpeciesSubstanceUnitDefinition(const Species * species);
/**
* Returns the unitDefinition constructed
* from the substance units of this Species.
*/
UnitDefinition * getSpeciesExtentUnitDefinition(const Species * species);
/**
* Predicate returning @c true or @c false depending on whether
* undeclared units can be ignored.
*
* On occasion it is possible to "ignore" undeclared units when
* determining the overall units of an expression.
* For example, if p has known units and k does not then the units
* resulting from the expression 'p + k' must have the units of p and
* thus it is possible to "ignore" the fact that the units of k are
* unknown. However, it is not possible to "ignore" the unknown units
* in the expression 'p * k' as the units of k will impact on the
* units resulting from the expression.
*
* @return @c true if the math last processed by the UnitFormulaFormatter
* includes parameters/numbers
* with undeclared units which will not impact the overall units
* of the expression, @c false otherwise.
*
* @note Each time the getUnitDefinition function is called by the
* UnitFormulaFormatter the value of the "containsUndeclaredUnits"
* flag and the "canIgnoreUndeclaredUnits" may change. These flags
* are specific to the ASTNode for which units are being derived.
*
* @see resetFlags()
*/
bool canIgnoreUndeclaredUnits();
/**
* Get the current value of the "containsUndeclaredUnits" flag for this
* UnitFormulaFormatter.
*
* @return @c true if the math last processed by the UnitFormulaFormatter
* includes parameters/numbers
* with undeclared units, @c false otherwise.
*
* @note Each time the getUnitDefinition function is called by the
* UnitFormulaFormatter the value of the "containsUndeclaredUnits"
* flag and the "canIgnoreUndeclaredUnits" may change. These flags
* are specific to the ASTNode for which units are being derived.
*
* @see resetFlags()
*/
bool getContainsUndeclaredUnits();
/**
* Resets the "containsUndeclaredUnits" and "canIgnoreUndeclaredUnits" flags
* to their initial values.
*
* @note Each time the getUnitDefinition function is called by the
* UnitFormulaFormatter the value of the "containsUndeclaredUnits"
* flag and the "canIgnoreUndeclaredUnits" may change. These flags
* are specific to the ASTNode for which units are being derived.
*/
void resetFlags();
/* @cond doxygenLibsbmlInternal */
/**
* returns the unitDefinition for the ASTNode from a function
*/
UnitDefinition * getUnitDefinitionFromFunction(const ASTNode *node,
bool inKL, int reactNo);
/**
* returns the unitDefinition for the ASTNode from a times function
*/
UnitDefinition * getUnitDefinitionFromTimes(const ASTNode *node,
bool inKL, int reactNo);
/**
* returns the unitDefinition for the ASTNode from a divide function
*/
UnitDefinition * getUnitDefinitionFromDivide(const ASTNode *node,
bool inKL, int reactNo);
/**
* returns the unitDefinition for the ASTNode from a power function
*/
UnitDefinition * getUnitDefinitionFromPower(const ASTNode *node,
bool inKL, int reactNo);
/**
* returns the unitDefinition for the ASTNode from
* a piecewise function
*/
UnitDefinition * getUnitDefinitionFromPiecewise(const ASTNode *node,
bool inKL, int reactNo);
/**
* returns the unitDefinition for the ASTNode from a root function
*/
UnitDefinition * getUnitDefinitionFromRoot(const ASTNode *node,
bool inKL, int reactNo);
/**
* returns the unitDefinition for the ASTNode from
* a function returning dimensionless value
*/
UnitDefinition * getUnitDefinitionFromDimensionlessReturnFunction(const ASTNode *node,
bool inKL, int reactNo);
/**
* returns the unitDefinition for the ASTNode from
* a function returning value with same units as argument(s)
*/
UnitDefinition * getUnitDefinitionFromArgUnitsReturnFunction(const ASTNode *node,
bool inKL, int reactNo);
/**
* returns the unitDefinition for the ASTNode from
* a delay function
*/
UnitDefinition * getUnitDefinitionFromDelay(const ASTNode * node,
bool inKL, int reactNo);
/**
* returns the unitDefinition for the ASTNode from anything else
*/
UnitDefinition * getUnitDefinitionFromOther(const ASTNode * node,
bool inKL, int reactNo);
/** @endcond */
/* @cond doxygenLibsbmlInternal */
UnitDefinition * inferUnitDefinition(UnitDefinition* expectedUD,
const ASTNode * LHS, std::string id, bool inKL = false, int reactNo = -1);
/** @endcond */
/* @cond doxygenLibsbmlInternal */
bool variableCanBeDeterminedFromMath(const ASTNode * node, std::string id);
/** @endcond */
/* @cond doxygenLibsbmlInternal */
bool possibleToUseUnitsData(FormulaUnitsData * fud);
/** @endcond */
private:
/* @cond doxygenLibsbmlInternal */
const Model * model;
bool mContainsUndeclaredUnits;
unsigned int mCanIgnoreUndeclaredUnits;
/* a depth of recursive call of getUnitDefinition()*/
int depthRecursiveCall;
std::map<const ASTNode*, UnitDefinition*> unitDefinitionMap;
std::map<const ASTNode*, bool> undeclaredUnitsMap;
std::map<const ASTNode*, unsigned int> canIgnoreUndeclaredUnitsMap;
UnitDefinition * inverseFunctionOnUnits(UnitDefinition* expectedUD,
const ASTNode * math, ASTNodeType_t functionType, bool inKL, int reactNo,
bool unknownInLeftChild = false);
/** @endcond */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* !cplusplus */
/* NOT YET NECESSARY
#ifndef SWIG
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
LIBSBML_EXTERN
UnitFormulaFormatter_t*
UnitFormulaFormatter_create(Model_t * model);
LIBSBML_EXTERN
UnitDefinition_t *
UnitFormulaFormatter_getUnitDefinition(UnitFormulaFormatter_t * uff,
const ASTNode_t * node,
unsigned int inKL, int reactNo);
LIBSBML_EXTERN
UnitDefinition_t *
UnitFormulaFormatter_getUnitDefinitionFromCompartment
(UnitFormulaFormatter_t * uff,
const Compartment_t * compartment);
LIBSBML_EXTERN
UnitDefinition_t *
UnitFormulaFormatter_getUnitDefinitionFromSpecies
(UnitFormulaFormatter_t * uff,
const Species_t * species);
LIBSBML_EXTERN
UnitDefinition_t *
UnitFormulaFormatter_getUnitDefinitionFromParameter
(UnitFormulaFormatter_t * uff,
const Parameter * parameter);
LIBSBML_EXTERN
UnitDefinition_t *
UnitFormulaFormatter_getUnitDefinitionFromEventTime
(UnitFormulaFormatter_t * uff,
const Event * event);
LIBSBML_EXTERN
int
UnitFormulaFormatter_canIgnoreUndeclaredUnits(UnitFormulaFormatter_t * uff);
LIBSBML_EXTERN
int
UnitFormulaFormatter_getContainsUndeclaredUnits(UnitFormulaFormatter_t * uff);
LIBSBML_EXTERN
void
UnitFormulaFormatter_resetFlags(UnitFormulaFormatter_t * uff);
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif !SWIG */
#endif /* UnitFormulaFormatter_h */
/** @endcond */
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