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* @file Parameter.h
* @brief Definitions of Parameter and ListOfParameters.
* @author Ben Bornstein
*
* <!--------------------------------------------------------------------------
* 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 Parameter.
* @sbmlbrief{core} Implementation of SBML's %Parameter construct.
*
* A Parameter is used in SBML to define a symbol associated with a value;
* this symbol can then be used in mathematical formulas in a model. By
* default, parameters have constant value for the duration of a
* simulation, and for this reason are called @em parameters instead of @em
* variables in SBML, although it is crucial to understand that <em>SBML
* parameters represent both concepts</em>. Whether a given SBML
* parameter is intended to be constant or variable is indicated by the
* value of its "constant" attribute.
*
* SBML's Parameter has a required attribute, "id", that gives the
* parameter a unique identifier by which other parts of an SBML model
* definition can refer to it. A parameter can also have an optional
* "name" attribute of type @c string. Identifiers and names must be used
* according to the guidelines described in the SBML specifications.
*
* The optional attribute "value" determines the value (of type @c double)
* assigned to the parameter. A missing value for "value" implies that
* the value either is unknown, or to be obtained from an external source,
* or determined by an initial assignment. The unit of measurement
* associated with the value of the parameter can be specified using the
* optional attribute "units". Here we only mention briefly some notable
* points about the possible unit choices, but readers are urged to consult
* the SBML specification documents for more information:
* <ul>
*
* <li> In SBML Level 3, there are no constraints on the units that
* can be assigned to parameters in a model; there are also no units to
* inherit from the enclosing Model object (unlike the case for, e.g.,
* Species and Compartment).
*
* <li> In SBML Level 2, the value assigned to the parameter's "units"
* attribute must be chosen from one of the following possibilities: one of
* the base unit identifiers defined in SBML; one of the built-in unit
* identifiers @c "substance", @c "time", @c "volume", @c "area" or @c
* "length"; or the identifier of a new unit defined in the list of unit
* definitions in the enclosing Model structure. There are no constraints
* on the units that can be chosen from these sets. There are no default
* units for parameters.
* </ul>
*
* The Parameter structure has another boolean attribute named "constant"
* that is used to indicate whether the parameter's value can vary during a
* simulation. (In SBML Level 3, the attribute is mandatory and must
* be given a value; in SBML Levels below Level 3, the attribute is
* optional.) A value of @c true indicates the parameter's value cannot be
* changed by any construct except InitialAssignment. Conversely, if the
* value of "constant" is @c false, other constructs in SBML, such as rules
* and events, can change the value of the parameter.
*
* SBML Level 3 uses a separate object class, LocalParameter, for
* parameters that are local to a Reaction's KineticLaw. In Levels prior
* to SBML Level 3, the Parameter class is used both for definitions
* of global parameters, as well as reaction-local parameters stored in a
* list within KineticLaw objects. Parameter objects that are local to a
* reaction (that is, those defined within the KineticLaw structure of a
* Reaction) cannot be changed by rules and therefore are <em>implicitly
* always constant</em>; consequently, in SBML Level 2, parameter
* definitions within Reaction structures should @em not have their
* "constant" attribute set to @c false.
*
* What if a global parameter has its "constant" attribute set to @c false,
* but the model does not contain any rules, events or other constructs
* that ever change its value over time? Although the model may be
* suspect, this situation is not strictly an error. A value of @c false
* for "constant" only indicates that a parameter @em can change value, not
* that it @em must.
*
* As with all other major SBML components, Parameter is derived from
* SBase, and the methods defined on SBase are available on Parameter.
*
* @note The use of the term @em parameter in SBML sometimes leads to
* confusion among readers who have a particular notion of what something
* called "parameter" should be. It has been the source of heated debate,
* but despite this, no one has yet found an adequate replacement term that
* does not have different connotations to different people and hence leads
* to confusion among @em some subset of users. Perhaps it would have been
* better to have two constructs, one called @em constants and the other
* called @em variables. The current approach in SBML is simply more
* parsimonious, using a single Parameter construct with the boolean flag
* "constant" indicating which flavor it is. In any case, readers are
* implored to look past their particular definition of a @em parameter and
* simply view SBML's Parameter as a single mechanism for defining both
* constants and (additional) variables in a model. (We write @em
* additional because the species in a model are usually considered to be
* the central variables.) After all, software tools are not required to
* expose to users the actual names of particular SBML constructs, and
* thus tools can present to their users whatever terms their designers
* feel best matches their target audience.
*
* @see ListOfParameters
*
*
* <!-- ------------------------------------------------------------------- -->
* @class ListOfParameters
* @sbmlbrief{core} Implementation of SBML's %ListOfParameters construct.
*
* @copydetails doc_what_is_listof
*/
/**
* <!-- ~ ~ ~ ~ ~ Start of common documentation strings ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
* The following text is used as common documentation blocks copied multiple
* times elsewhere in this file. The use of @class is a hack needed because
* Doxygen's @copydetails command has limited functionality. Symbols
* beginning with "doc_" are marked as ignored in our Doxygen configuration.
* ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ -->
*
* @class doc_note_parameter_setting_lv
*
* @note Upon the addition of a Parameter object to an SBMLDocument
* (e.g., using Model::addParameter(@if java Parameter p@endif)), the SBML Level, SBML Version
* and XML namespace of the document @em override the values used
* when creating the Parameter object via this constructor. This is
* necessary to ensure that an SBML document is a consistent structure.
* Nevertheless, the ability to supply the values at the time of creation
* of a Parameter is an important aid to producing valid SBML. Knowledge
* of the intented SBML Level and Version determine whether it is valid
* to assign a particular value to an attribute, or whether it is valid
* to add an object to an existing SBMLDocument.
*
* @class doc_note_parameter_about_constant
*
* @note Readers who view the documentation for LocalParameter may be
* confused about the presence of this method. LibSBML derives
* LocalParameter from Parameter; however, this does not precisely match
* the object hierarchy defined by SBML Level 3, where
* LocalParameter is derived directly from SBase and not Parameter. We
* believe this arrangement makes it easier for libSBML users to program
* applications that work with both SBML Level 2 and SBML
* Level 3, but programmers should also keep in mind this difference
* exists. A side-effect of libSBML's scheme is that certain methods on
* LocalParameter that are inherited from Parameter do not actually have
* relevance to LocalParameter objects. An example of this is the
* methods pertaining to Parameter's attribute "constant" (i.e.,
* isSetConstant(), setConstant(), and getConstant()).
*
*/
#ifndef Parameter_h
#define Parameter_h
#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>
#include <sbml/SBase.h>
#include <sbml/ListOf.h>
#ifdef __cplusplus
#include <string>
LIBSBML_CPP_NAMESPACE_BEGIN
class SBMLVisitor;
class UnitFormulaFormatter;
class LIBSBML_EXTERN Parameter : public SBase
{
public:
/**
* Creates a new Parameter using the given SBML @p level and @p version
* values.
*
* @param level an unsigned int, the SBML Level to assign to this Parameter
*
* @param version an unsigned int, the SBML Version to assign to this
* Parameter
*
* @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
*
* @copydetails doc_note_parameter_setting_lv
*/
Parameter (unsigned int level, unsigned int version);
/**
* Creates a new Parameter using the given SBMLNamespaces object
* @p sbmlns.
*
* @copydetails doc_what_are_sbmlnamespaces
*
* It is worth emphasizing that although this constructor does not take
* an identifier argument, in SBML Level 2 and beyond, the "id"
* (identifier) attribute of a Parameter is required to have a value.
* Thus, callers are cautioned to assign a value after calling this
* constructor if no identifier is provided as an argument. Setting the
* identifier can be accomplished using the method
* @if java setId(String id)@else setId()@endif.
*
* @param sbmlns an SBMLNamespaces object.
*
* @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
*
* @copydetails doc_note_parameter_setting_lv
*/
Parameter (SBMLNamespaces* sbmlns);
/**
* Destroys this Parameter.
*/
virtual ~Parameter ();
/**
* Copy constructor; creates a copy of a Parameter.
*
* @param orig the Parameter instance to copy.
*
* @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the argument @p orig is @c NULL.
*/
Parameter(const Parameter& orig);
/**
* Assignment operator for Parameter.
*
* @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.
*/
Parameter& operator=(const Parameter& rhs);
/**
* Accepts the given SBMLVisitor for this instance of Parameter.
*
* @param v the SBMLVisitor instance to be used.
*
* @return the result of calling <code>v.visit()</code>, indicating
* whether the Visitor would like to visit the next Parameter object in
* the list of parameters within which @em the present object is
* embedded.
*/
virtual bool accept (SBMLVisitor& v) const;
/**
* Creates and returns a deep copy of this Parameter.
*
* @return a (deep) copy of this Parameter.
*/
virtual Parameter* clone () const;
/**
* Initializes the fields of this Parameter object to "typical" defaults
* values.
*
* The SBML Parameter component has slightly different aspects and
* default attribute values in different SBML Levels and Versions. Many
* SBML object classes defined by libSBML have an initDefaults() method
* to set the values to certain common defaults, based mostly on what
* they are in SBML Level 2. In the case of Parameter, this method
* only sets the value of the "constant" attribute to @c true.
*
* @see getConstant()
* @see isSetConstant()
* @see setConstant(@if java boolean flag@endif)
*/
void initDefaults ();
/**
* Returns the value of the "id" attribute of this Parameter.
*
* @return the id of this Parameter.
*/
virtual const std::string& getId () const;
/**
* Returns the value of the "name" attribute of this Parameter.
*
* @return the name of this Parameter.
*/
virtual const std::string& getName () const;
/**
* Gets the numerical value of this Parameter.
*
* @return the value of the "value" attribute of this Parameter, as a
* number of type @c double.
*
* @note <b>It is crucial</b> that callers not blindly call
* Parameter::getValue() without first using Parameter::isSetValue() to
* determine whether a value has ever been set. Otherwise, the value
* return by Parameter::getValue() may not actually represent a value
* assigned to the parameter. The reason is simply that the data type
* @c double in a program always has @em some value. A separate test is
* needed to determine whether the value is a true model value, or
* uninitialized data in a computer's memory location.
*
* @see isSetValue()
* @see setValue(double value)
* @see getUnits()
*/
double getValue () const;
/**
* Gets the units defined for this Parameter.
*
* The value of an SBML parameter's "units" attribute establishes the
* unit of measurement associated with the parameter's value.
*
* @return the value of the "units" attribute of this Parameter, as a
* string. An empty string indicates that no units have been assigned.
*
* @copydetails doc_note_unassigned_unit_are_not_a_default
*
* @see isSetUnits()
* @see setUnits(@if java String units@endif)
* @see getValue()
*/
const std::string& getUnits () const;
/**
* Gets the value of the "constant" attribute of this Parameter instance.
*
* @return @c true if this Parameter is declared as being constant,
* @c false otherwise.
*
* @copydetails doc_note_parameter_about_constant
*
* @see isSetConstant()
* @see setConstant(@if java boolean flag@endif)
*/
virtual bool getConstant () const;
/**
* Predicate returning @c true if this
* Parameter's "id" attribute is set.
*
* @return @c true if the "id" attribute of this Parameter is
* set, @c false otherwise.
*/
virtual bool isSetId () const;
/**
* Predicate returning @c true if this
* Parameter's "name" attribute is set.
*
* @return @c true if the "name" attribute of this Parameter is
* set, @c false otherwise.
*/
virtual bool isSetName () const;
/**
* Predicate returning @c true if the
* "value" attribute of this Parameter is set.
*
* In SBML definitions after SBML Level 1 Version 1,
* parameter values are optional and have no defaults. If a model read
* from a file does not contain a setting for the "value" attribute of a
* parameter, its value is considered unset; it does not default to any
* particular value. Similarly, when a Parameter object is created in
* libSBML, it has no value until given a value. The
* Parameter::isSetValue() method allows calling applications to
* determine whether a given parameter's value has ever been set.
*
* In SBML Level 1 Version 1, parameters are required to have
* values and therefore, the value of a Parameter <b>should always be
* set</b>. In Level 1 Version 2 and beyond, the value is
* optional and as such, the "value" attribute may or may not be set.
*
* @return @c true if the value of this Parameter is set,
* @c false otherwise.
*
* @see getValue()
* @see setValue(double value)
*/
bool isSetValue () const;
/**
* Predicate returning @c true if the
* "units" attribute of this Parameter is set.
*
* @return @c true if the "units" attribute of this Parameter is
* set, @c false otherwise.
*
* @copydetails doc_note_unassigned_unit_are_not_a_default
*/
bool isSetUnits () const;
/**
* Predicate returning @c true if the
* "constant" attribute of this Parameter is set.
*
* @return @c true if the "constant" attribute of this Parameter is
* set, @c false otherwise.
*
* @copydetails doc_note_parameter_about_constant
*
* @see getConstant()
* @see setConstant(@if java boolean flag@endif)
*/
virtual bool isSetConstant () const;
/**
* Sets the value of the "id" attribute of this Parameter.
*
* The string @p sid is copied.
*
* @copydetails doc_id_syntax
*
* @param sid the string to use as the identifier of this Parameter
*
* @return integer value indicating success/failure of the
* function. The possible values returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*/
virtual int setId (const std::string& sid);
/**
* Sets the value of the "name" attribute of this Parameter.
*
* The string in @p name is copied.
*
* @param name the new name for the Parameter
*
* @return integer value indicating success/failure of the
* function. The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*/
int setName (const std::string& name);
/**
* Sets the "value" attribute of this Parameter to the given @c double
* value and marks the attribute as set.
*
* @param value a @c double, the value to assign
*
* @return integer value indicating success/failure of the
* function. The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*/
int setValue (double value);
/**
* Sets the "units" attribute of this Parameter to a copy of the given
* units identifier @p units.
*
* @param units a string, the identifier of the units to assign to this
* Parameter instance
*
* @return integer value indicating success/failure of the
* function. The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*/
int setUnits (const std::string& units);
/**
* Sets the "constant" attribute of this Parameter to the given boolean
* @p flag.
*
* @param flag a boolean, the value for the "constant" attribute of this
* Parameter instance
*
* @return integer value indicating success/failure of the
* function. The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
*
* @copydetails doc_note_parameter_about_constant
*
* @see getConstant()
* @see isSetConstant()
*/
virtual int setConstant (bool flag);
/**
* Unsets the value of the "name" attribute of this Parameter.
*
* @return integer value indicating success/failure of the
* function. The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*/
virtual int unsetName ();
/**
* Unsets the "value" attribute of this Parameter instance.
*
* @return integer value indicating success/failure of the
* function. The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*
* In SBML Level 1 Version 1, parameters are required to have
* values and therefore, the value of a Parameter <b>should always be
* set</b>. In SBML Level 1 Version 2 and beyond, the value
* is optional and as such, the "value" attribute may or may not be set.
*/
int unsetValue ();
/**
* Unsets the "units" attribute of this Parameter instance.
*
* @return integer value indicating success/failure of the
* function. The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*/
int unsetUnits ();
/**
* Constructs and returns a UnitDefinition that corresponds to the units
* of this Parameter's value.
*
* Parameters in SBML have an attribute ("units") for declaring the units
* of measurement intended for the parameter's value. <b>No defaults are
* defined</b> by SBML in the absence of a definition for "units". This
* method returns a UnitDefinition object based on the units declared for
* this Parameter using its "units" attribute, or it returns @c NULL if
* no units have been declared.
*
* Note that unit declarations for Parameter objects are specified in
* terms of the @em identifier of a unit (e.g., using setUnits()), but
* @em this method returns a UnitDefinition object, not a unit
* identifier. It does this by constructing an appropriate
* UnitDefinition.For SBML Level 2 models, it will do this even when
* the value of the "units" attribute is one of the special SBML
* Level 2 unit identifiers @c "substance", @c "volume", @c "area",
* @c "length" or @c "time". Callers may find this useful in conjunction
* with the helper methods provided by the UnitDefinition class for
* comparing different UnitDefinition objects.
*
* @return a UnitDefinition that expresses the units of this
* Parameter, or @c NULL if one cannot be constructed.
*
* @note The libSBML system for unit analysis depends on the model as a
* whole. In cases where the Parameter object has not yet been added to
* a model, or the model itself is incomplete, unit analysis is not
* possible, and consequently this method will return @c NULL.
*
* @see isSetUnits()
*/
UnitDefinition * getDerivedUnitDefinition();
/**
* Constructs and returns a UnitDefinition that corresponds to the units
* of this Parameter's value.
*
* Parameters in SBML have an attribute ("units") for declaring the units
* of measurement intended for the parameter's value. <b>No defaults are
* defined</b> by SBML in the absence of a definition for "units". This
* method returns a UnitDefinition object based on the units declared for
* this Parameter using its "units" attribute, or it returns @c NULL if
* no units have been declared.
*
* Note that unit declarations for Parameter objects are specified in
* terms of the @em identifier of a unit (e.g., using setUnits()), but
* @em this method returns a UnitDefinition object, not a unit
* identifier. It does this by constructing an appropriate
* UnitDefinition. For SBML Level 2 models, it will do this even
* when the value of the "units" attribute is one of the predefined SBML
* units @c "substance", @c "volume", @c "area", @c "length" or @c
* "time". Callers may find this useful in conjunction with the helper
* methods provided by the UnitDefinition class for comparing different
* UnitDefinition objects.
*
* @return a UnitDefinition that expresses the units of this
* Parameter, or @c NULL if one cannot be constructed.
*
* @note The libSBML system for unit analysis depends on the model as a
* whole. In cases where the Parameter object has not yet been added to
* a model, or the model itself is incomplete, unit analysis is not
* possible, and consequently this method will return @c NULL.
*
* @see isSetUnits()
*/
const UnitDefinition * getDerivedUnitDefinition() const;
/**
* Returns the libSBML type code for this SBML object.
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for this object:
* @link SBMLTypeCode_t#SBML_PARAMETER SBML_PARAMETER@endlink (default).
*
* @copydetails doc_warning_typecodes_not_unique
*
* @see getElementName()
* @see getPackageName()
*/
virtual int getTypeCode () const;
/**
* Returns the XML element name of this object, which for Parameter, is
* always @c "parameter".
*
* @return the name of this element, i.e., @c "parameter".
*/
virtual const std::string& getElementName () const;
/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to write out their contained
* SBML objects as XML elements. Be sure to call your parents
* implementation of this method as well.
*/
virtual void writeElements (XMLOutputStream& stream) const;
/** @endcond */
/**
* Predicate returning @c true if
* all the required attributes for this Parameter object
* have been set.
*
* @note The required attributes for a Parameter object are:
* @li "id" (or "name" in SBML Level 1)
* @li "value" (required in Level 1, optional otherwise)
*
* @return a boolean value indicating whether all the required
* attributes for this object have been defined.
*/
virtual bool hasRequiredAttributes() const ;
/**
* Renames all the @c UnitSIdRef attributes on this element.
*
* @copydetails doc_what_is_unitsidref
*
* This method works by looking at all unit identifier attribute values
* (including, if appropriate, inside mathematical formulas), comparing the
* unit identifiers to the value of @p oldid. If any matches are found,
* the matching identifiers are replaced with @p newid. The method does
* @em not descend into child elements.
*
* @param oldid the old identifier
* @param newid the new identifier
*/
virtual void renameUnitSIdRefs(const std::string& oldid, const std::string& newid);
/** @cond doxygenLibsbmlInternal */
/* set a flag to indicate that a parameter should
* calculate its units from math */
virtual void setCalculatingUnits(bool calculatingUnits);
/** @endcond */
protected:
/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to get the list of
* expected attributes.
* This function is invoked from corresponding readAttributes()
* function.
*/
virtual void addExpectedAttributes(ExpectedAttributes& attributes);
/**
* Subclasses should override this method to read values from the given
* XMLAttributes set into their specific fields. Be sure to call your
* parents implementation of this method as well.
*/
virtual void readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes);
void readL1Attributes (const XMLAttributes& attributes);
void readL2Attributes (const XMLAttributes& attributes);
void readL3Attributes (const XMLAttributes& attributes);
/**
* Subclasses should override this method to write their XML attributes
* to the XMLOutputStream. Be sure to call your parents implementation
* of this method as well.
*/
virtual void writeAttributes (XMLOutputStream& stream) const;
bool isExplicitlySetConstant() const
{ return mExplicitlySetConstant; } ;
std::string mId;
std::string mName;
double mValue;
std::string mUnits;
bool mConstant;
bool mIsSetValue;
bool mIsSetConstant;
bool mExplicitlySetConstant;
/* the validator classes need to be friends to access the
* protected constructor that takes no arguments
*/
friend class Validator;
friend class ConsistencyValidator;
friend class IdentifierConsistencyValidator;
friend class InternalConsistencyValidator;
friend class L1CompatibilityValidator;
friend class L2v1CompatibilityValidator;
friend class L2v2CompatibilityValidator;
friend class L2v3CompatibilityValidator;
friend class L2v4CompatibilityValidator;
friend class MathMLConsistencyValidator;
friend class ModelingPracticeValidator;
friend class OverdeterminedValidator;
friend class SBOConsistencyValidator;
friend class UnitConsistencyValidator;
/** @endcond */
private:
/** @cond doxygenLibsbmlInternal */
UnitDefinition * inferUnits(Model* m, bool globalParameter);
UnitDefinition * inferUnitsFromAssignments(UnitFormulaFormatter *uff,
Model *m);
UnitDefinition * inferUnitsFromRules(UnitFormulaFormatter *uff,
Model *m);
UnitDefinition * inferUnitsFromReactions(UnitFormulaFormatter *uff,
Model *m);
UnitDefinition * inferUnitsFromEvents(UnitFormulaFormatter *uff,
Model *m);
UnitDefinition * inferUnitsFromEvent(Event * e, UnitFormulaFormatter *uff,
Model *m);
UnitDefinition * inferUnitsFromKineticLaw(KineticLaw* kl,
UnitFormulaFormatter *uff, Model *m);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/* flag to indicate that a parameter should calculate its units from math */
bool getCalculatingUnits() const;
bool mCalculatingUnits;
/** @endcond */
};
class LIBSBML_EXTERN ListOfParameters : public ListOf
{
public:
/**
* Creates a new ListOfParameters object.
*
* The object is constructed such that it is valid for the given SBML
* Level and Version combination.
*
* @param level the SBML Level
*
* @param version the Version within the SBML Level
*/
ListOfParameters (unsigned int level, unsigned int version);
/**
* Creates a new ListOfParameters object.
*
* The object is constructed such that it is valid for the SBML Level and
* Version combination determined by the SBMLNamespaces object in @p
* sbmlns.
*
* @param sbmlns an SBMLNamespaces object that is used to determine the
* characteristics of the ListOfParameters object to be created.
*/
ListOfParameters (SBMLNamespaces* sbmlns);
/**
* Creates and returns a deep copy of this ListOfParameters instance.
*
* @return a (deep) copy of this ListOfParameters.
*/
virtual ListOfParameters* clone () const;
/**
* Returns the libSBML type code for the objects contained in this ListOf
* (i.e., Parameter objects, if the list is non-empty).
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for this objects contained in this list:
* @link SBMLTypeCode_t#SBML_PARAMETER SBML_PARAMETER@endlink (default).
*
* @see getElementName()
* @see getPackageName()
*/
virtual int getItemTypeCode () const;
/**
* Returns the XML element name of this object.
*
* For ListOfParameters, the XML element name is @c "listOfParameters".
*
* @return the name of this element, i.e., @c "listOfParameters".
*/
virtual const std::string& getElementName () const;
/**
* Returns the Parameter object located at position @p n within this
* ListOfParameters instance.
*
* @param n the index number of the Parameter to get.
*
* @return the nth Parameter in this ListOfParameters. If the index @p n
* is out of bounds for the length of the list, then @c NULL is returned.
*
* @see size()
* @see get(const std::string& sid)
*/
virtual Parameter * get(unsigned int n);
/**
* Returns the Parameter object located at position @p n within this
* ListOfParameters instance.
*
* @param n the index number of the Parameter to get.
*
* @return the nth Parameter in this ListOfParameters. If the index @p n
* is out of bounds for the length of the list, then @c NULL is returned.
*
* @see size()
* @see get(const std::string& sid)
*/
virtual const Parameter * get(unsigned int n) const;
/**
* Returns the first Parameter object matching the given identifier.
*
* @param sid a string, the identifier of the Parameter to get.
*
* @return the Parameter object found. The caller owns the returned
* object and is responsible for deleting it. If none of the items have
* an identifier matching @p sid, then @c NULL is returned.
*
* @see get(unsigned int n)
* @see size()
*/
virtual Parameter* get (const std::string& sid);
/**
* Returns the first Parameter object matching the given identifier.
*
* @param sid a string representing the identifier of the Parameter to
* get.
*
* @return the Parameter object found. The caller owns the returned
* object and is responsible for deleting it. If none of the items have
* an identifier matching @p sid, then @c NULL is returned.
*
* @see get(unsigned int n)
* @see size()
*/
virtual const Parameter* get (const std::string& sid) const;
/**
* Removes the nth item from this ListOfParameters, and returns a pointer
* to it.
*
* @param n the index of the item to remove
*
* @return the item removed. The caller owns the returned object and is
* responsible for deleting it. If the index number @p n is out of
* bounds for the length of the list, then @c NULL is returned.
*
* @see size()
*/
virtual Parameter* remove (unsigned int n);
/**
* Removes the first Parameter object in this ListOfParameters
* matching the given identifier, and returns a pointer to it.
*
* @param sid the identifier of the item to remove.
*
* @return the item removed. The caller owns the returned object and is
* responsible for deleting it. If none of the items have an identifier
* matching @p sid, then @c NULL is returned.
*/
virtual Parameter* remove (const std::string& sid);
/** @cond doxygenLibsbmlInternal */
/**
* Gets the ordinal position of this element in the containing object
* (which in this case is the Model object).
*
* The ordering of elements in the XML form of SBML is generally fixed
* for most components in SBML. So, for example, the ListOfParameters
* in a model is (in SBML Level 2 Version 4) the seventh
* ListOf___. (However, it differs for different Levels and Versions of
* SBML.)
*
* @return the ordinal position of the element with respect to its
* siblings, or @c -1 (default) to indicate the position is not significant.
*/
virtual int getElementPosition () const;
/** @endcond */
protected:
/** @cond doxygenLibsbmlInternal */
/**
* Create a ListOfParameters object corresponding to the next token in
* the XML input stream.
*
* @return the SBML object corresponding to next XMLToken in the
* XMLInputStream, or @c NULL if the token was not recognized.
*/
virtual SBase* createObject (XMLInputStream& stream);
/** @endcond */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#ifndef SWIG
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
/**
* Creates a new Parameter_t structure using the given SBML @p level
* and @p version values.
*
* @param level an unsigned int, the SBML Level to assign to this
* Parameter_t
*
* @param version an unsigned int, the SBML Version to assign to this
* Parameter_t
*
* @return a pointer to the newly created Parameter_t structure.
*
* @note Once a Parameter_t has been added to an SBMLDocument_t, the @p
* level and @p version for the document @em override those used to create
* the Parameter_t. Despite this, the ability to supply the values at
* creation time is an important aid to creating valid SBML. Knowledge of
* the intended SBML Level and Version determine whether it is valid to
* assign a particular value to an attribute, or whether it is valid to add
* a structure to an existing SBMLDocument_t.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
Parameter_t *
Parameter_create (unsigned int level, unsigned int version);
/**
* Creates a new Parameter_t structure using the given
* SBMLNamespaces_t structure.
*
* @param sbmlns SBMLNamespaces_t, a pointer to an SBMLNamespaces_t structure
* to assign to this Parameter_t
*
* @return a pointer to the newly created Parameter_t structure.
*
* @note Once a Parameter_t has been added to an SBMLDocument_t, the
* @p sbmlns namespaces for the document @em override those used to create
* the Parameter_t. Despite this, the ability to supply the values at creation time
* is an important aid to creating valid SBML. Knowledge of the intended SBML
* Level and Version determine whether it is valid to assign a particular value
* to an attribute, or whether it is valid to add a structure to an existing
* SBMLDocument_t.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
Parameter_t *
Parameter_createWithNS (SBMLNamespaces_t *sbmlns);
/**
* Frees the given Parameter_t structure.
*
* @param p the Parameter_t structure to be freed.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
void
Parameter_free (Parameter_t *p);
/**
* Creates a deep copy of the given Parameter_t structure
*
* @param p the Parameter_t structure to be copied
*
* @return a (deep) copy of the given Parameter_t structure.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
Parameter_t *
Parameter_clone (const Parameter_t *p);
/**
* Initializes the attributes of this Parameter_t structure to their defaults.
*
* The exact results depends on the %SBML Level and Version in use. The
* cases are currently the following:
*
* @li (%SBML Level 2 only) constant = 1 (true)
*
* @param p the Parameter_t structure to initialize
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
void
Parameter_initDefaults (Parameter_t *p);
/**
* Returns a list of XMLNamespaces_t associated with this Parameter_t
* structure.
*
* @param p the Parameter_t structure
*
* @return pointer to the XMLNamespaces_t structure associated with
* this structure
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
const XMLNamespaces_t *
Parameter_getNamespaces(Parameter_t *p);
/**
* Takes a Parameter_t structure and returns its identifier.
*
* @param p the Parameter_t structure whose identifier is sought
*
* @return the identifier of this Parameter_t, as a pointer to a string.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
const char *
Parameter_getId (const Parameter_t *p);
/**
* Takes a Parameter_t structure and returns its name.
*
* @param p the Parameter_t whose name is sought.
*
* @return the name of this Parameter_t, as a pointer to a string.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
const char *
Parameter_getName (const Parameter_t *p);
/**
* Takes a Parameter_t structure and returns its value.
*
* @param p the Parameter_t whose value is sought.
*
* @return the value assigned to this Parameter_t structure, as a @c double.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
double
Parameter_getValue (const Parameter_t *p);
/**
* Takes a Parameter_t structure and returns its units.
*
* @param p the Parameter_t whose units are sought.
*
* @return the units assigned to this Parameter_t structure, as a pointer
* to a string.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
const char *
Parameter_getUnits (const Parameter_t *p);
/**
* Takes a Parameter_t structure and returns zero or nonzero, depending
* on the value of the parameter's "constant" attribute.
*
* @param p the Parameter_t whose constant value is sought.
*
* @return the value of the "constant" attribute, with nonzero meaning
* true and zero meaning false.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_getConstant (const Parameter_t *p);
/**
* Predicate returning @c true or @c false depending on whether the given
* Parameter_t structure's identifier is set.
*
* @param p the Parameter_t structure to query
*
* @return @c non-zero (true) if the "id" attribute of the given
* Parameter_t structure is set, zero (false) otherwise.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_isSetId (const Parameter_t *p);
/**
* Predicate returning @c true or @c false depending on whether the given
* Parameter_t structure's name is set.
*
* @param p the Parameter_t structure to query
*
* @return @c non-zero (true) if the "name" attribute of the given
* Parameter_t structure is set, zero (false) otherwise.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_isSetName (const Parameter_t *p);
/**
* Predicate returning @c true or @c false depending on whether the given
* Parameter_t structure's value is set.
*
* @param p the Parameter_t structure to query
*
* @return @c non-zero (true) if the "value" attribute of the given
* Parameter_t structure is set, zero (false) otherwise.
*
* @note In SBML Level 1 Version 1, a Parameter_t value is required and
* therefore <em>should always be set</em>. In Level 1 Version 2 and
* later, the value is optional, and as such, may or may not be set.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_isSetValue (const Parameter_t *p);
/**
* Predicate returning @c true or @c false depending on whether the given
* Parameter_t structure's units have been set.
*
* @param p the Parameter_t structure to query
*
* @return @c non-zero (true) if the "units" attribute of the given
* Parameter_t structure is set, zero (false) otherwise.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_isSetUnits (const Parameter_t *p);
/**
* Predicate returning @c true or @c false depending on whether the given
* Parameter_t structure's constant attribute have been set.
*
* @param p the Parameter_t structure to query
*
* @return @c non-zero (true) if the "constant" attribute of the given
* Parameter_t structure is set, zero (false) otherwise.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_isSetConstant (const Parameter_t *p);
/**
* Assigns the identifier of a Parameter_t structure.
*
* This makes a copy of the string passed in the param @p sid.
*
* @param p the Parameter_t structure to set.
* @param sid the string to use as the identifier.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*
* @note Using this function with an id of NULL is equivalent to
* unsetting the "id" attribute.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_setId (Parameter_t *p, const char *sid);
/**
* Assign the name of a Parameter_t structure.
*
* This makes a copy of the string passed in as the argument @p name.
*
* @param p the Parameter_t structure to set.
* @param name the string to use as the name.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*
* @note Using this function with the name set to NULL is equivalent to
* unsetting the "name" attribute.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_setName (Parameter_t *p, const char *name);
/**
* Assign the value of a Parameter_t structure.
*
* @param p the Parameter_t structure to set.
* @param value the @c double value to use.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_setValue (Parameter_t *p, double value);
/**
* Assign the units of a Parameter_t structure.
*
* This makes a copy of the string passed in as the argument @p units.
*
* @param p the Parameter_t structure to set.
* @param units the string to use as the identifier of the units to assign.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*
* @note Using this function with units set to NULL is equivalent to
* unsetting the "units" attribute.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_setUnits (Parameter_t *p, const char *units);
/**
* Assign the "constant" attribute of a Parameter_t structure.
*
* @param p the Parameter_t structure to set.
* @param value the value to assign as the "constant" attribute
* of the parameter, either zero for false or nonzero for true.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_setConstant (Parameter_t *p, int value);
/**
* Unsets the name of this Parameter_t structure.
*
* @param p the Parameter_t structure whose name is to be unset.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_unsetName (Parameter_t *p);
/**
* Unsets the value of this Parameter_t structure.
*
* In SBML Level 1 Version 1, a parameter is required to have a value and
* therefore this attribute <em>should always be set</em>. In Level 1
* Version 2 and beyond, a value is optional, and as such, may or may not be
* set.
*
* @param p the Parameter_t structure whose value is to be unset.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_unsetValue (Parameter_t *p);
/**
* Unsets the units of this Parameter_t structure.
*
* @param p the Parameter_t structure whose units are to be unset.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_unsetUnits (Parameter_t *p);
/**
* Constructs and returns a UnitDefinition_t structure that expresses
* the units of this Parameter_t structure.
*
* @param p the Parameter_t structure whose units are to be returned.
*
* @return a UnitDefinition_t structure that expresses the units
* of this Parameter_t strucuture.
*
* @note This function returns the units of the Parameter_t expressed
* as a UnitDefinition_t. The units may be those explicitly declared.
* In the case where no units have been declared, @c NULL is returned.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
UnitDefinition_t *
Parameter_getDerivedUnitDefinition(Parameter_t *p);
/**
* Predicate returning @c true or @c false depending on whether
* all the required attributes for this Parameter_t structure
* have been set.
*
* @param p the Parameter_t structure to check.
*
* @note The required attributes for a Parameter_t structure are:
* @li id (name in L1)
* @li constant (in L3 only)
*
* @return a true if all the required
* attributes for this structure have been defined, false otherwise.
*
* @memberof Parameter_t
*/
LIBSBML_EXTERN
int
Parameter_hasRequiredAttributes (Parameter_t *p);
/**
* Returns the Parameter_t structure having a given identifier.
*
* @param lo the ListOfParameters_t structure to search.
* @param sid the "id" attribute value being sought.
*
* @return item in the @p lo ListOfParameters with the given @p sid or a
* null pointer if no such item exists.
*
* @see ListOf_t
*
* @memberof ListOfParameters_t
*/
LIBSBML_EXTERN
Parameter_t *
ListOfParameters_getById (ListOf_t *lo, const char *sid);
/**
* Removes a Parameter_t structure based on its identifier.
*
* The caller owns the returned item and is responsible for deleting it.
*
* @param lo the list of Parameter_t structures to search.
* @param sid the "id" attribute value of the structure to remove
*
* @return The Parameter_t structure removed, or a null pointer if no such
* item exists in @p lo.
*
* @see ListOf_t
*
* @memberof ListOfParameters_t
*/
LIBSBML_EXTERN
Parameter_t *
ListOfParameters_removeById (ListOf_t *lo, const char *sid);
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* Parameter_h */
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