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* @file Compartment.h
* @brief Definitions of Compartment and ListOfCompartments
* @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) 2013-2017 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 Compartment
* @sbmlbrief{core} An SBML compartment, where species are located.
*
* A compartment in SBML represents a bounded space in which species are
* located. Compartments do not necessarily have to correspond to actual
* structures inside or outside of a biological cell.
*
* It is important to note that although compartments are optional in the
* overall definition of Model, every species in an SBML model must be
* located in a compartment. This in turn means that if a model defines
* any species, the model must also define at least one compartment. The
* reason is simply that species represent physical things, and therefore
* must exist @em somewhere. Compartments represent the @em somewhere.
*
* Compartment has one required attribute, "id", to give the compartment a
* unique identifier by which other parts of an SBML model definition can
* refer to it. A compartment 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.
*
* Compartment also has an optional attribute "spatialDimensions" that is
* used to indicate the number of spatial dimensions possessed by the
* compartment. Most modeling scenarios involve compartments with integer
* values of "spatialDimensions" of @c 3 (i.e., a three-dimensional
* compartment, which is to say, a volume), or 2 (a two-dimensional
* compartment, a surface), or @c 1 (a one-dimensional compartment, a
* line). In SBML Level 3, the type of this attribute is @c double,
* there are no restrictions on the permitted values of the
* "spatialDimensions" attribute, and there are no default values. In SBML
* Level 2, the value must be a positive @c integer, and the default
* value is @c 3; the permissible values in SBML Level 2 are @c 3,
* @c 2, @c 1, and @c 0 (for a point).
*
* Another optional attribute on Compartment is "size", representing the @em
* initial total size of that compartment in the model. The "size" attribute
* must be a floating-point value and may represent a volume (if the
* compartment is a three-dimensional one), or an area (if the compartment is
* two-dimensional), or a length (if the compartment is one-dimensional).
* There is no default value of compartment size in SBML Level 2 or
* Level 3. In particular, a missing "size" value <em>does not imply
* that the compartment size is 1</em>. (This is unlike the definition of
* compartment "volume" in SBML Level 1.) When the compartment's
* "spatialDimensions" attribute does not have a value of @c 0, a missing
* value of "size" for a given compartment signifies that the value either is
* unknown, or to be obtained from an external source, or determined by an
* InitialAssignment, AssignmentRule, AlgebraicRule or RateRule
* @if conly structure @else object@endif@~ elsewhere in the model. In SBML
* Level 2, there are additional special requirements on the values of
* "size"; we discuss them in a <a href="#comp-l2">separate section
* below</a>.
*
* The units associated with a compartment's "size" attribute value may be
* set using the optional attribute "units". The rules for setting and
* using compartment size units differ between SBML Level 2 and
* Level 3, and are discussed separately below.
*
* Finally, the Compartment attribute named "constant" is used to
* indicate whether the compartment's size stays constant after simulation
* begins. A value of @c true indicates the compartment's "size" cannot be
* changed by any other construct except InitialAssignment; a value of
* @c false indicates the compartment's "size" can be changed by other
* constructs in SBML. In SBML Level 2, there is an additional
* explicit restriction that if "spatialDimensions"=@c "0", the value
* cannot be changed by InitialAssignment either. Further, in
* Level 2, "constant" is optional, and has a default value of @c true. In SBML
* Level 3, there is no default value for the "constant" attribute,
* and it is required.
*
*
* @section comp-l2 Additional considerations in SBML Level 2
*
* In SBML Level 2, the default units of compartment size, and the kinds
* of units allowed as values of the attribute "units", interact with the
* number of spatial dimensions of the compartment. The value of the "units"
* attribute of a Compartment @if conly structure @else object@endif@~ must
* be one of the base units (see Unit), or the predefined unit identifiers
* @c volume, @c area, @c length or @c dimensionless, or a new unit defined by a
* UnitDefinition @if conly structure @else object@endif@~ in the enclosing
* Model, subject to the restrictions detailed in the following table:
*
* <table border="0" class="centered text-table width80 normal-font alt-row-colors"
* style="padding-bottom: 0.5em">
* <caption class="top-caption">Restrictions on values permitted for
* compartment <code>size</code> and <code>units</code> attributes.</caption>
* <tr>
* <th align="left" valign="bottom">
* Value of<br><code>spatialDimensions</code>
* </th>
* <th align="left" valign="bottom">
* <code>size</code><br>allowed?
* </th>
* <th align="left" valign="bottom">
* <code>units</code><br>allowed?
* </th>
* <th align="left" valign="bottom">
* Allowable kinds of units
* </th>
* <th align="left" valign="bottom">
* Default value of attribute <code>units</code>
* </th>
* </tr>
* <tr>
* <td><code>3</code></td>
* <td>yes</td>
* <td>yes</td>
* <td>units of volume, or <code>dimensionless</code></td>
* <td><code>volume</code></td>
* </tr>
* <tr>
* <td><code>2</code></td>
* <td>yes</td>
* <td>yes</td>
* <td>units of area, or <code>dimensionless</code></td>
* <td><code>area</code></td>
* </tr>
* <tr>
* <td><code>1</code></td>
* <td>yes</td>
* <td>yes</td>
* <td>units of length, or <code>dimensionless</code></td>
* <td><code>length</code></td>
* </tr>
* <tr>
* <td><code>0</code></td>
* <td>no</td>
* <td>no</td>
* <td>(no units allowed)</td>
* <td></td>
* </tr>
* </tr>
* </table>
*
* In SBML Level 2, the units of the compartment size, as defined by the
* "units" attribute or (if "units" is not set) the default value listed in
* the table above, are used in the following ways when the compartment has
* a "spatialDimensions" value greater than @c 0:
* <ul>
* <li> The value of the "units" attribute is used as the units of the
* compartment identifier when the identifier appears as a numerical
* quantity in a mathematical formula expressed in MathML.
*
* <li> The @c math element of an AssignmentRule or InitialAssignment
* referring to this compartment @em must (in Level 2 Versions 1-3)
* or @em should (in Level 2 Version 4) have identical units.
*
* <li> In RateRule objects that set the rate of change of the compartment's
* size, the units of the rule's @c math element @em must (in Level 2
* Versions 1–3) or @em should (in Level 2 Version 4) be identical to the
* compartment's units (whether defined by the "units" attribute or by taking the
* default value from the Model) divided by the default @em time units.
* (In other words, the units for the rate of change of compartment size
* are <em>compartment size</em>/<em>time</em> units.
*
* <li> When a Species is to be treated in terms of concentrations or
* density, the units of the spatial size portion of the concentration
* value (i.e., the denominator in the units formula @em substance/@em
* size) are those indicated by the value of the "units" attribute on the
* compartment in which the species is located.
* </ul>
*
* Compartments with "spatialDimensions"=@c 0 require special treatment in
* this framework. As implied above, the "size" attribute must not have a
* value on an SBML Level 2 Compartment
* @if conly structure @else object@endif@~ if the "spatialDimensions"
* attribute has a value of @c 0. An additional related restriction is that
* the "constant" attribute must default to or be set to @c true if the value
* of the "spatialDimensions" attribute is @c 0, because a zero-dimensional
* compartment cannot ever have a size.
*
* If a compartment has no size or dimensional units, how should such a
* compartment's identifier be interpreted when it appears in mathematical
* formulas? The answer is that such a compartment's identifier should not
* appear in mathematical formulas in the first place---it has no
* value, and its value cannot change. Note also that a zero-dimensional
* compartment is a point, and species located at points can only be
* described in terms of amounts, not spatially-dependent measures such as
* concentration. Since SBML KineticLaw formulas are already in terms of
* @em substance/@em time and not (say) @em concentration/@em time, volume
* or other factors in principle are not needed for species located in
* zero-dimensional compartments.
*
* Finally, in SBML Level 2 Versions 2–4, each compartment in a
* model may optionally be designated as belonging to a particular
* compartment @em type. The optional attribute "compartmentType" is used
* identify the compartment type represented by the Compartment structure.
* The "compartmentType" attribute's value must be the identifier of a
* CompartmentType instance defined in the model. If the "compartmentType"
* attribute is not present on a particular compartment definition, a
* unique virtual compartment type is assumed for that compartment, and no
* other compartment can belong to that compartment type. The values of
* "compartmentType" attributes on compartments have no effect on the
* numerical interpretation of a model. Simulators and other numerical
* analysis software may ignore "compartmentType" attributes. The
* "compartmentType" attribute and the CompartmentType
* @if conly structures @else class of objects@endif@~ are
* not present in SBML Level 3 Core nor in SBML Level 1.
*
*
* @section comp-l3 Additional considerations in SBML Level 3
*
* One difference between SBML Level 3 and lower Levels of SBML is
* that there are no restrictions on the permissible values of the
* "spatialDimensions" attribute, and there is no default value defined for
* the attribute. The value of "spatialDimensions" does not have to be an
* integer, either; this is to allow for the possibility of representing
* structures with fractal dimensions.
*
* The number of spatial dimensions possessed by a compartment cannot enter
* into mathematical formulas, and therefore cannot directly alter the
* numerical interpretation of a model. However, the value of
* "spatialDimensions" @em does affect the interpretation of the units
* associated with a compartment's size. Specifically, the value of
* "spatialDimensions" is used to select among the Model attributes
* "volumeUnits", "areaUnits" and "lengthUnits" when a Compartment
* @if conly object @else structure@endif@~ does not define a value for its
* "units" attribute.
*
* The "units" attribute may be left unspecified for a given compartment in a
* model; in that case, the compartment inherits the unit of measurement
* specified by one of the attributes on the enclosing Model
* @if conly structure @else object@endif@~ instance. The applicable
* attribute on Model depends on the value of the compartment's
* "spatialDimensions" attribute; the relationship is shown in the table
* below. If the Model @if conly structure @else object@endif@~ does not
* define the relevant attribute ("volumeUnits", "areaUnits" or
* "lengthUnits") for a given "spatialDimensions" value, the unit associated
* with that Compartment @if conly structure @else object@endif's size is
* undefined. If a given Compartment's "units" are left unset and
* the "spatialDimensions" either has a value other than @c 1, @c 2, or
* @c 3 or is left unset itself (as it has no default value),
* then no unit can be chosen from among the Model's "volumeUnits",
* "areaUnits" or "lengthUnits" attributes (even if the Model instance
* provides values for those attributes), because there is no basis to select
* between them.
* Leaving the units of compartments' sizes undefined in an SBML model does
* not render the model invalid; however, as a matter of best practice, we
* strongly recommend that all models specify the units of measurement for
* all compartment sizes.
*
* <table border="0" class="centered text-table width80 normal-font alt-row-colors"
* style="padding-bottom: 0.5em">
* <caption class="top-caption">Interpretation of the Compartment "units" attribute.</caption>
* <tr>
* <th align="left" valign="bottom">
* Value of attribute<br>"spatialDimensions"
* </th>
* <th align="left" valign="bottom">
* Attribute of Model used<br>for inheriting the unit
* </th>
* <th align="left" valign="bottom">
* Recommended candidate units
* </th>
* </tr>
* <tr>
* <td><code>3</code></td>
* <td>"volumeUnits"</td>
* <td>units of volume, or <code>dimensionless</code></td>
* </tr>
* <tr>
* <td><code>2</code></td>
* <td>"areaUnits"</td>
* <td>units of area, or <code>dimensionless</code></td>
* </tr>
* <tr>
* <td><code>1</code></td>
* <td>"lengthUnits"</td>
* <td>units of length, or <code>dimensionless</code></td>
* </tr>
* <tr>
* <td><em>other</em></td>
* <td><em>no units inherited</em></td>
* <td><em>no specific recommendations</em></td>
* </tr>
* </tr>
* </table>
*
* The unit of measurement associated with a compartment's size, as defined
* by the "units" attribute or (if "units" is not set) the inherited value
* from Model according to the table above, is used in the following ways:
*
* <ul>
*
* <li> When the identifier of the compartment appears as a numerical
* quantity in a mathematical formula expressed in MathML, it represents
* the size of the compartment, and the unit associated with the size is
* the value of the "units" attribute.
*
* <li> When a Species is to be treated in terms of concentrations or
* density, the unit associated with the spatial size portion of the
* concentration value (i.e., the denominator in the formula
* <em>amount</em>/<em>size</em>) is specified by the value of the "units"
* attribute on the compartment in which the species is located.
*
* <li> The "math" elements of AssignmentRule, InitialAssignment and
* EventAssignment @if conly structures @else objects@endif@~ setting the
* value of the compartment size should all have the same units as the unit
* associated with the compartment's size.
*
* <li> In a RateRule @if conly structure @else object@endif@~ that defines a
* rate of change for a compartment's size, the unit of the rule's "math"
* element should be identical to the compartment's "units" attribute divided
* by the model-wide unit of <em>time</em>. (In other words, {<em>unit of
* compartment size</em>}/{<em>unit of time</em>}.)
*
* </ul>
*
*
* @section comp-other Other aspects of Compartment
*
* In SBML Level 1 and Level 2, Compartment has an optional
* attribute named "outside", whose value can be the identifier of another
* Compartment @if conly structure @else object@endif@~ defined in the
* enclosing Model @if conly structure @else object@endif@~. Doing so means
* that the other compartment contains it or is outside of it. This enables
* the representation of simple topological relationships between
* compartments, for those simulation systems that can make use of the
* information (e.g., for drawing simple diagrams of compartments). It is
* worth noting that in SBML, there is no relationship between compartment
* sizes when compartment positioning is expressed using the "outside"
* attribute. The size of a given compartment does not in any sense include
* the sizes of other compartments having it as the value of their "outside"
* attributes. In other words, if a compartment @em B has the identifier of
* compartment @em A as its "outside" attribute value, the size of @em A does
* not include the size of @em B. The compartment sizes are separate.
*
* In Level 2, there are two restrictions on the "outside" attribute.
* First, because a compartment with "spatialDimensions" of @c 0 has no
* size, such a compartment cannot act as the container of any other
* compartment @em except compartments that @em also have
* "spatialDimensions" values of @c 0. Second, the directed graph formed
* by representing Compartment structures as vertexes and the "outside"
* attribute values as edges must be acyclic. The latter condition is
* imposed to prevent a compartment from being contained inside itself. In
* the absence of a value for "outside", compartment definitions in SBML
* Level 2 do not have any implied spatial relationships between each
* other.
*
*
* <!-- ------------------------------------------------------------------- -->
* @class ListOfCompartments
* @sbmlbrief{core} A list of Compartment objects.
*
* @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_compartment_units
*
* @par
* Compartments in SBML have an attribute ("units") for declaring the
* units of measurement intended for the value of the compartment's size. In
* the absence of a value given for this attribute, the units are inherited
* from values either defined on the enclosing Model (in SBML Level 3)
* or in defaults (in SBML Level 2). This method returns a
* @if conly UnitDefinition_t structure @else UnitDefinition object@endif@~
* based on how this compartment's units are interpreted according to the
* relevant SBML guidelines, or it returns @c NULL if no units have been
* declared and no defaults are defined by the relevant SBML specification.
*
* Note that unit declarations for
* @if conly Compartment_t structures @else Compartment objects @endif@~
* are specified in terms of the @em identifier of a unit,
* but @em this method returns @if conly a structure @else an object @endif,
* not a unit identifier. It does this by constructing an appropriate
* @if conly UnitDefinition_t structure @else UnitDefinition object@endif. 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 @if conly UnitDefinition_t structure @else UnitDefinition
* class@endif@~ for comparing different UnitDefinition objects.
*
* <!-- ------------------------------------------------------------------- -->
* @class doc_compartment_both_size_and_volume
*
* @par
* In SBML Level 1, compartments are always three-dimensional
* constructs and only have volumes, whereas in SBML Level 2 and higher,
* compartments may be other than three-dimensional, and therefore the
* "volume" attribute is named "size" in Level 2 and above. LibSBML
* provides both @if conly Compartment_getSize() and Compartment_getVolume()
* @else getSize() and getVolume()@endif@~
* for easier support of different SBML Levels.
*
* <!-- ------------------------------------------------------------------- -->
* @class doc_note_compartment_volume
*
* @note The attribute "volume" only exists by that name in SBML
* Level 1. In Level 2 and above, the equivalent attribute is
* named "size". In SBML Level 1, a compartment's volume has a default
* value (@c 1.0) and therefore methods such as
* @if conly Compartment_isSetVolume() @else isSetVolume()@endif@~
* will always return @c true for a Level 1 model. In Level 2, a
* compartment's size (the equivalent of SBML Level 1's "volume") is
* optional and has no default value, and therefore may or may not be set.
*
* <!-- ------------------------------------------------------------------- -->
* @class doc_note_spatial_dimensions_as_double
*
* @note In SBML Level 3, the data type of the "spatialDimensions"
* attribute is @c double, whereas in Level 2, it is @c integer. To
* avoid backward compatibility issues, libSBML provides two separate methods
* for obtaining the value as either an integer or a type @c double, for
* models where it is relevant.
*
* <!-- ------------------------------------------------------------------- -->
* @class doc_note_unit_analysis_depends_on_model
*
* @note The libSBML system for unit analysis depends on the model as a
* whole. In cases where the
* @if conly Compartment_t structure @else Compartment object@endif@~ 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.
*/
#ifndef Compartment_h
#define Compartment_h
#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>
#ifndef LIBSBML_USE_STRICT_INCLUDES
#include <sbml/annotation/RDFAnnotation.h>
#endif
#include <sbml/common/operationReturnValues.h>
#ifdef __cplusplus
#include <string>
#include <sbml/SBase.h>
#include <sbml/ListOf.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class SBMLVisitor;
class LIBSBML_EXTERN Compartment : public SBase
{
public:
/**
* Creates a new Compartment object using the given SBML @p level and @p
* version values.
*
* @param level an unsigned int, the SBML Level to assign to this Compartment.
*
* @param version an unsigned int, the SBML Version to assign to this
* Compartment.
*
* @copydetails doc_throw_exception_lv
*
* @copydetails doc_note_setting_lv
*/
Compartment (unsigned int level, unsigned int version);
/**
* Creates a new Compartment object 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 Compartment object is required to have a
* value. Thus, callers are cautioned to assign a value after calling this
* constructor. Setting the identifier can be accomplished using the
* method @if java Compartment::setId(String id)@else setId()@endif.
*
* @param sbmlns an SBMLNamespaces object.
*
* @copydetails doc_throw_exception_namespace
*
* @copydetails doc_note_setting_lv
*/
Compartment (SBMLNamespaces* sbmlns);
/**
* Destroys this Compartment object.
*/
virtual ~Compartment ();
/**
* Copy constructor.
*
* This creates a copy of a Compartment object.
*
* @param orig the Compartment instance to copy.
*/
Compartment(const Compartment& orig);
/**
* Assignment operator for Compartment.
*
* @param rhs the object whose values are used as the basis of the
* assignment.
*/
Compartment& operator=(const Compartment& rhs);
/** @cond doxygenLibsbmlInternal */
/**
* Accepts the given SBMLVisitor for this instance of Compartment.
*
* @param v the SBMLVisitor instance to be used.
*
* @return the result of calling <code>v.visit()</code>, which indicates
* whether the Visitor would like to visit the next Compartment object in the
* list of compartments within which this Compartment object is embedded (i.e.,
* the ListOfCompartments in the parent Model).
*/
virtual bool accept (SBMLVisitor& v) const;
/** @endcond */
/**
* Creates and returns a deep copy of this Compartment object.
*
* @return the (deep) copy of this Compartment object.
*/
virtual Compartment* clone () const;
/**
* Initializes the fields of this Compartment object to "typical" default
* values.
*
* The SBML Compartment component has slightly different aspects and
* default attribute values in different SBML Levels and Versions.
* This method sets the values to certain common defaults, based
* mostly on what they are in SBML Level 2. Specifically:
*
* @li Sets attribute "spatialDimensions" to @c 3
* @li Sets attribute "constant" to @c true
* @li (Applies to Level 1 models only) Sets attribute "volume" to @c 1.0
* @li (Applies to Level 3 models only) Sets attribute "units" to @c litre
*/
void initDefaults ();
/**
* Returns the value of the "id" attribute of this Compartment.
*
* @note Because of the inconsistent behavior of this function with
* respect to assignments and rules, it is now recommended to
* use the getIdAttribute() function instead.
*
* @copydetails doc_id_attribute
*
* @return the id of this Compartment.
*
* @see getIdAttribute()
* @see setIdAttribute(const std::string& sid)
* @see isSetIdAttribute()
* @see unsetIdAttribute()
*/
virtual const std::string& getId () const;
/**
* Returns the value of the "name" attribute of this Compartment object.
*
* @copydetails doc_get_name
*/
virtual const std::string& getName () const;
/**
* Get the value of the "compartmentType" attribute of this Compartment
* object.
*
* @return the value of the "compartmentType" attribute of this
* Compartment object as a string.
*
* @note The "compartmentType" attribute is only available in SBML
* Level 2 Versions 2–4.
*
* @see isSetCompartmentType()
* @see setCompartmentType(@if java String@endif)
* @see unsetCompartmentType()
*/
const std::string& getCompartmentType () const;
/**
* Get the number of spatial dimensions of this Compartment object.
*
* @return the value of the "spatialDimensions" attribute of this
* Compartment object as an unsigned integer.
*
* @copydetails doc_note_spatial_dimensions_as_double
*
* @see getSpatialDimensionsAsDouble()
* @see setSpatialDimensions(@if java unsigned int@endif)
* @see isSetSpatialDimensions()
* @see unsetSpatialDimensions()
*/
unsigned int getSpatialDimensions () const;
/**
* Get the number of spatial dimensions of this Compartment object,
* as a double.
*
* @return the value of the "spatialDimensions" attribute of this
* Compartment object as a double, or @c NaN if this model is not in SBML
* Level 3 format.
*
* @copydetails doc_note_spatial_dimensions_as_double
*
* @see getSpatialDimensions()
* @see setSpatialDimensions(@if java unsigned int@endif)
* @see isSetSpatialDimensions()
* @see unsetSpatialDimensions()
*/
double getSpatialDimensionsAsDouble () const;
/**
* Get the size of this Compartment object.
*
* @copydetails doc_compartment_both_size_and_volume
*
* @return the value of the "size" attribute ("volume" in Level 1) of
* this Compartment object as a floating-point number.
*
* @note This method is identical to
* @if java Compartment::getVolume()@else getVolume()@endif.
*
* @see getVolume()
* @see isSetSize()
* @see setSize(@if java double@endif)
* @see unsetSize()
*/
double getSize () const;
/**
* Get the volume of this Compartment object.
*
* @copydetails doc_compartment_both_size_and_volume
*
* @return the value of the "volume" attribute ("size" in Level 2) of
* this Compartment object, as a floating-point number.
*
* @copydetails doc_note_compartment_volume
*
* @note This method is identical to
* @if java Compartment::getSize()@else getSize()@endif.
*
* @see getSize()
* @see isSetVolume()
* @see setVolume(@if java double@endif)
* @see unsetVolume()
*/
double getVolume () const;
/**
* Get the units of this Compartment object's size.
*
* The value of an SBML compartment's "units" attribute establishes the
* unit of measurement associated with the compartment's size.
*
* @return the value of the "units" attribute of this Compartment object,
* as a string. An empty string indicates that no units have been assigned
* to the value of the size.
*
* @copydetails doc_note_unassigned_unit_are_not_a_default
*
* @see isSetUnits()
* @see setUnits(@if java String@endif)
* @see unsetUnits()
*/
const std::string& getUnits () const;
/**
* Get the identifier, if any, of the Compartment object that is designated
* as being outside of @em this one.
*
* @return the value of the "outside" attribute of this Compartment object.
*
* @note The "outside" attribute is defined in SBML Level 1 and
* Level 2, but does not exist in SBML Level 3.
*
* @see isSetOutside()
* @see setOutside(@if java String@endif)
* @see unsetOutside()
*/
const std::string& getOutside () const;
/**
* Get the value of the "constant" attribute of this Compartment object.
*
* @return @c true if this Compartment object's size is flagged as being
* constant, @c false otherwise.
*
* @see isSetConstant()
* @see setConstant(@if java bool@endif)
*/
bool getConstant () const;
/**
* Predicate returning @c true if this Compartment object's "id" attribute
* is set.
*
* @copydetails doc_isset_id
*/
virtual bool isSetId () const;
/**
* Predicate returning @c true if this Compartment object's "name"
* attribute is set.
*
* @copydetails doc_isset_name
*/
virtual bool isSetName () const;
/**
* Predicate returning @c true if this Compartment object's
* "compartmentType" attribute is set.
*
* @return @c true if the "compartmentType" attribute of this Compartment
* is set, @c false otherwise.
*
* @note The "compartmentType" attribute is only available in SBML
* Level 2 Versions 2–4.
*
* @see setCompartmentType(@if java String@endif)
* @see getCompartmentType()
* @see unsetCompartmentType()
*/
bool isSetCompartmentType () const;
/**
* Predicate returning @c true if this Compartment object's "size"
* attribute is set.
*
* This method is similar but not identical to
* @if java Compartment::isSetVolume()@else isSetVolume()@endif. The latter
* should be used in the context of SBML Level 1 models instead of
* @if java Compartment::isSetSize()@else isSetSize()@endif@~
* because @if java Compartment::isSetVolume()@else isSetVolume()@endif@~
* performs extra processing to take into account the difference in
* default values between SBML Levels 1 and 2.
*
* @return @c true if the "size" attribute ("volume" in Level 2) of
* this Compartment object is set, @c false otherwise.
*
* @see isSetVolume()
* @see setSize(@if java double@endif)
* @see getSize()
* @see unsetSize()
*/
bool isSetSize () const;
/**
* Predicate returning @c true if this Compartment object's "volume"
* attribute is set.
*
* This method is similar but not identical to
* @if java Compartment::isSetSize()@else isSetSize()@endif. The latter
* should not be used in the context of SBML Level 1 models because the
* present method performs extra processing to take into account
* the difference in default values between SBML Levels 1 and 2.
*
* @return @c true if the "volume" attribute ("size" in Level 2 and
* above) of this Compartment object is set, @c false otherwise.
*
* @copydetails doc_note_compartment_volume
*
* @see isSetSize()
* @see getVolume()
* @see setVolume(@if java double@endif)
* @see unsetVolume()
*/
bool isSetVolume () const;
/**
* Predicate returning @c true if this Compartment object's "units"
* attribute is set.
*
* @return @c true if the "units" attribute of this Compartment object is
* set, @c false otherwise.
*
* @copydetails doc_note_unassigned_unit_are_not_a_default
*
* @see setUnits(@if java String@endif)
* @see getUnits()
* @see unsetUnits()
*/
bool isSetUnits () const;
/**
* Predicate returning @c true if this Compartment object's "outside"
* attribute is set.
*
* @return @c true if the "outside" attribute of this Compartment object is
* set, @c false otherwise.
*
* @note The "outside" attribute is defined in SBML Level 1 and
* Level 2, but does not exist in SBML Level 3.
*
* @see getOutside()
* @see setOutside(@if java String@endif)
* @see unsetOutside()
*/
bool isSetOutside () const;
/**
* Predicate returning @c true if this Compartment object's
* "spatialDimensions" attribute is set.
*
* @return @c true if the "spatialDimensions" attribute of this
* Compartment object is set, @c false otherwise.
*
* @see getSpatialDimensions()
* @see setSpatialDimensions(@if java unsigned int@endif)
* @see unsetSpatialDimensions()
*/
bool isSetSpatialDimensions () const;
/**
* Predicate returning @c true if this Compartment object's "constant"
* attribute is set.
*
* @return @c true if the "constant" attribute of this Compartment object is
* set, @c false otherwise.
*
* @see getConstant()
* @see setConstant(@if java bool@endif)
*/
bool isSetConstant () const;
/**
* Sets the value of the "id" attribute of this Compartment object.
*
* The string @p sid is copied.
*
* @copydetails doc_id_attribute
*
* @param sid the string to use as the identifier of this Compartment object. If
* the string is @c NULL, this method will return
* @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*
* @see getId()
* @see unsetId()
* @see isSetId()
*/
virtual int setId(const std::string& sid);
/**
* Sets the value of the "name" attribute of this Compartment object.
*
* @copydetails doc_set_name
*/
virtual int setName (const std::string& name);
/**
* Sets the "compartmentType" attribute of this Compartment object.
*
* @param sid the identifier of a CompartmentType object defined elsewhere
* in this Model. If the string is @c NULL, this method will return
* @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @note The "compartmentType" attribute is only available in SBML
* Level 2 Versions 2–4.
*
* @see isSetCompartmentType()
* @see getCompartmentType()
* @see unsetCompartmentType()
*/
int setCompartmentType (const std::string& sid);
/**
* Sets the "spatialDimensions" attribute of this Compartment object.
*
* @param value an unsigned integer indicating the number of dimensions
* of this compartment.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @see getSpatialDimensions()
* @see isSetSpatialDimensions()
* @see unsetSpatialDimensions()
*/
int setSpatialDimensions (unsigned int value);
/**
* Sets the "spatialDimensions" attribute of this Compartment object as a double.
*
* @param value a double indicating the number of dimensions
* of this compartment.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @see getSpatialDimensions()
* @see isSetSpatialDimensions()
* @see unsetSpatialDimensions()
*/
int setSpatialDimensions (double value);
/**
* Sets the "size" attribute (or "volume" in SBML Level 1) of this
* Compartment object.
*
* @param value a @c double representing the size of this compartment
* instance in whatever units are in effect for the compartment.
*
* @copydetails doc_returns_one_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
*
* @note This method is identical to
* @if java Compartment::setVolume(double value)@else setVolume()@endif.
*
* @see setVolume(@if java double@endif)
* @see getSize()
* @see isSetSize()
* @see unsetSize()
*/
int setSize (double value);
/**
* Sets the "volume" attribute (or "size" in SBML Level 2) of this
* Compartment object.
*
* This method is identical to
* @if java Compartment::setSize(double value)@else setSize()@endif@~
* and is provided for compatibility between SBML Level 1 and
* higher Levels of SBML.
*
* @param value a @c double representing the volume of this compartment
* instance in whatever units are in effect for the compartment.
*
* @copydetails doc_returns_one_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
*
* @copydetails doc_note_compartment_volume
*
* @see setSize(@if java double@endif)
* @see getVolume()
* @see isSetVolume()
* @see unsetVolume()
*/
int setVolume (double value);
/**
* Sets the "units" attribute of this Compartment object.
*
* @param sid the identifier of the defined units to use. If @p sid is
* @c NULL, then this method will return
* @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*
* @see isSetUnits()
* @see getUnits()
* @see unsetUnits()
*/
int setUnits (const std::string& sid);
/**
* Sets the "outside" attribute of this Compartment object.
*
* @param sid the identifier of a compartment that encloses this one. If @p
* sid is @c NULL, then this method will return
* @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*
* @note The "outside" attribute is defined in SBML Level 1 and
* Level 2, but does not exist in SBML Level 3.
*
* @see isSetOutside()
* @see getOutside()
* @see unsetOutside()
*/
int setOutside (const std::string& sid);
/**
* Sets the value of the "constant" attribute of this Compartment object.
*
* @param value a boolean indicating whether the size/volume of this
* compartment should be considered constant (@c true) or variable
* (@c false).
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @see isSetConstant()
* @see getConstant()
*/
int setConstant (bool value);
/**
* @copydoc doc_renamesidref_common
*/
virtual void renameSIdRefs(const std::string& oldid, const std::string& newid);
/**
* @copydoc doc_renameunitsidref_common
*/
virtual void renameUnitSIdRefs(const std::string& oldid, const std::string& newid);
/**
* Unsets the value of the "name" attribute of this Compartment object.
*
* @copydetails doc_unset_name
*/
virtual int unsetName ();
/**
* Unsets the value of the "compartmentType" attribute of this Compartment object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @note The "compartmentType" attribute is only available in SBML
* Level 2 Versions 2–4.
*
* @see setCompartmentType(@if java String@endif)
* @see isSetCompartmentType()
* @see getCompartmentType()
*/
int unsetCompartmentType ();
/**
* Unsets the value of the "constant" attribute of this Compartment object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @see isSetConstant()
* @see setConstant(@if java bool@endif)
* @see getConstant()
*/
int unsetConstant ();
/**
* Unsets the value of the "size" attribute of this Compartment object.
*
* In SBML Level 1, a compartment's volume has a default value
* (@c 1.0) and therefore <em>should always be set</em>. Calling this method
* on a Level 1 model resets the value to @c 1.0 rather than actually
* unsetting it. In Level 2, a compartment's "size" is optional with
* no default value, and unsetting it will result in the compartment having
* no defined size.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @note This method is identical to
* @if java Compartment::unsetVolume()@else unsetVolume()@endif.
*
* @see unsetVolume()
* @see getSize()
* @see isSetSize()
* @see setSize(@if java double@endif)
*/
int unsetSize ();
/**
* Unsets the value of the "volume" attribute of this Compartment object.
*
* This method is identical to
* @if java Compartment::unsetSize()@else unsetSize()@endif. Please refer
* to that method's documentation for more information about its behavior.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @copydetails doc_note_compartment_volume
*
* @see unsetSize()
* @see getVolume()
* @see setVolume(@if java double@endif)
* @see isSetVolume()
*/
int unsetVolume ();
/**
* Unsets the value of the "units" attribute of this Compartment object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @see isSetUnits()
* @see setUnits(@if java String@endif)
* @see getUnits()
*/
int unsetUnits ();
/**
* Unsets the value of the "outside" attribute of this Compartment object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @note The "outside" attribute is defined in SBML Level 1 and
* Level 2, but does not exist in SBML Level 3.
*
* @see isSetOutside()
* @see getOutside()
* @see setOutside(@if java String@endif)
*/
int unsetOutside ();
/**
* Unsets the value of the "spatialDimensions" attribute of this
* Compartment object.
*
* In SBML Levels prior to Level 3, compartments must always have a
* value for the number of dimensions. Consequently, calling this method
* on a model of SBML Level 1–2 will result in a return value of
* @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @note This function is only valid for SBML Level 3.
*
* @see getSpatialDimensions()
* @see isSetSpatialDimensions()
* @see setSpatialDimensions(@if java unsigned int@endif)
*/
int unsetSpatialDimensions ();
/**
* Constructs and returns a UnitDefinition that corresponds to the units
* of this Compartment object's designated size.
*
* @copydetails doc_compartment_units
*
* @return a UnitDefinition that expresses the units of this
* Compartment object, or @c NULL if one cannot be constructed.
*
* @copydetails doc_note_unit_analysis_depends_on_model
*
* @see isSetUnits()
* @see getUnits()
*/
UnitDefinition * getDerivedUnitDefinition();
/**
* Constructs and returns a UnitDefinition that corresponds to the units
* of this Compartment object's designated size.
*
* @copydetails doc_compartment_units
*
* @return a UnitDefinition that expresses the units of this
* Compartment object, or @c NULL if one cannot be constructed.
*
* @copydetails doc_note_unit_analysis_depends_on_model
*
* @see isSetUnits()
* @see getUnits()
*/
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:
* @sbmlconstant{SBML_COMPARTMENT, SBMLTypeCode_t} (default).
*
* @copydetails doc_warning_typecodes_not_unique
*
* @see getElementName()
* @see getPackageName()
*/
virtual int getTypeCode () const;
/**
* Returns the XML element name of this object
*
* For Compartment, the XML element name is always @c "compartment".
*
* @return the name of this element.
*/
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 parent's
* implementation of this method as well.
*/
virtual void writeElements (XMLOutputStream& stream) const;
/** @endcond */
/**
* Predicate returning @c true if all the required attributes for this
* Compartment object have been set.
*
* The required attributes for a Compartment object are:
* @li "id" (or "name" in SBML Level 1)
* @li "constant" (in SBML Level 3 only)
*
* @return @c true if the required attributes have been set, @c false
* otherwise.
*/
virtual bool hasRequiredAttributes() const;
#ifndef SWIG
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName, bool& value)
const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName, int& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
double& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
unsigned int& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
std::string& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
const char* value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Predicate returning @c true if this Compartment's attribute
* "attributeName" is set.
*
* @param attributeName, the name of the attribute to query.
*
* @return @c true if this Compartment's attribute "attributeName" has been
* set, otherwise @c false is returned.
*/
virtual bool isSetAttribute(const std::string& attributeName) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, bool value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, int value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, double value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName,
unsigned int value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName,
const std::string& value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, const char*
value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Unsets the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to query.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetAttribute(const std::string& attributeName);
/** @endcond */
#endif /* !SWIG */
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
* parent's 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 parent's implementation
* of this method as well.
*/
virtual void writeAttributes (XMLOutputStream& stream) const;
bool isExplicitlySetSpatialDimensions() const {
return mExplicitlySetSpatialDimensions; };
bool isExplicitlySetConstant() const { return mExplicitlySetConstant; } ;
//std::string mId;
//std::string mName;
std::string mCompartmentType;
unsigned int mSpatialDimensions;
double mSpatialDimensionsDouble;
double mSize;
std::string mUnits;
std::string mOutside;
bool mConstant;
bool mIsSetSize;
bool mIsSetSpatialDimensions;
bool mIsSetConstant;
bool mExplicitlySetSpatialDimensions;
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 L3v1CompatibilityValidator;
friend class MathMLConsistencyValidator;
friend class ModelingPracticeValidator;
friend class OverdeterminedValidator;
friend class SBOConsistencyValidator;
friend class UnitConsistencyValidator;
/** @endcond */
};
class LIBSBML_EXTERN ListOfCompartments : public ListOf
{
public:
/**
* Creates a new ListOfCompartments 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.
*
* @copydetails doc_throw_exception_lv
*
* @copydetails doc_note_setting_lv
*/
ListOfCompartments (unsigned int level, unsigned int version);
/**
* Creates a new ListOfCompartments 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 ListOfCompartments object to be created.
*
* @copydetails doc_throw_exception_namespace
*
* @copydetails doc_note_setting_lv
*/
ListOfCompartments (SBMLNamespaces* sbmlns);
/**
* Creates and returns a deep copy of this ListOfCompartments object.
*
* @return the (deep) copy of this ListOfCompartments object.
*/
virtual ListOfCompartments* clone () const;
/**
* Returns the libSBML type code for the objects contained in this ListOf
* (i.e., Compartment objects, if the list is non-empty).
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for the objects contained in this ListOf
* instance: @sbmlconstant{SBML_COMPARTMENT, SBMLTypeCode_t} (default).
*
* @see getElementName()
* @see getPackageName()
*/
virtual int getItemTypeCode () const;
/**
* Returns the XML element name of this object.
*
* For ListOfCompartments, the XML element name is always
* @c "listOfCompartments".
*
* @return the name of this element.
*/
virtual const std::string& getElementName () const;
/**
* Get a Compartment object from the ListOfCompartments.
*
* @param n the index number of the Compartment object to get.
*
* @return the nth Compartment object in this ListOfCompartments.
*
* @see size()
*/
virtual Compartment * get(unsigned int n);
/**
* Get a Compartment object from the ListOfCompartments.
*
* @param n the index number of the Compartment object to get.
*
* @return the nth Compartment object in this ListOfCompartments.
*
* @see size()
*/
virtual const Compartment * get(unsigned int n) const;
/**
* Get a Compartment object from the ListOfCompartments
* based on its identifier.
*
* @param sid a string representing the identifier
* of the Compartment object to get.
*
* @return Compartment object in this ListOfCompartments
* with the given @p sid or @c NULL if no such
* Compartment object exists.
*
* @see get(unsigned int n)
* @see size()
*/
virtual Compartment* get (const std::string& sid);
/**
* Get a Compartment object from the ListOfCompartments
* based on its identifier.
*
* @param sid a string representing the identifier
* of the Compartment object to get.
*
* @return Compartment object in this ListOfCompartments
* with the given @p sid or @c NULL if no such
* Compartment object exists.
*
* @see get(unsigned int n)
* @see size()
*/
virtual const Compartment* get (const std::string& sid) const;
/**
* Removes the nth item from this ListOfCompartments items and returns a pointer to
* it.
*
* The caller owns the returned item and is responsible for deleting it.
*
* @param n the index of the item to remove.
*
* @see size()
*/
virtual Compartment* remove (unsigned int n);
/**
* Removes item in this ListOfCompartments items with the given identifier.
*
* The caller owns the returned item and is responsible for deleting it.
* If none of the items in this list have the identifier @p sid, then
* @c NULL is returned.
*
* @param sid the identifier of the item to remove.
*
* @return the item removed. As mentioned above, the caller owns the
* returned item.
*/
virtual Compartment* remove (const std::string& sid);
/** @cond doxygenLibsbmlInternal */
/**
* Get 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 ListOfCompartments
* in a model is (in SBML Level 2 Version 4) the fifth
* 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 and return an SBML object of this class, if present.
*
* @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
/* ----------------------------------------------------------------------------
* See the .cpp file for the documentation of the following functions.
* --------------------------------------------------------------------------*/
/*
LIBSBML_EXTERN
Compartment_t *
Compartment_createWithLevelVersionAndNamespaces (unsigned int level,
unsigned int version, XMLNamespaces_t *xmlns);
*/
/**
* Creates a new Compartment_t structure using the given SBML @p level and @p
* version values.
*
* @param level an unsigned int, the SBML Level to assign to this
* Compartment_t structure.
*
* @param version an unsigned int, the SBML Version to assign to this
* Compartment_t structure.
*
* @returns the newly-created Compartment_t structure, or a null pointer if
* an error occurred during constructions.
*
* @copydetails doc_note_setting_lv
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
Compartment_t *
Compartment_create (unsigned int level, unsigned int version);
/**
* Creates a new Compartment_t structure using the given SBMLNamespaces_t
* structure, @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 Compartment_t instance is required to have a
* value. Thus, callers are cautioned to assign a value after calling this
* constructor. Setting the identifier can be accomplished using the method
* Compartment_setId().
*
* @param sbmlns an SBMLNamespaces_t structure.
*
* @returns the newly-created Compartment_t structure, or a null pointer if
* an error occurred during constructions
*
* @copydetails doc_note_setting_lv
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
Compartment_t *
Compartment_createWithNS (SBMLNamespaces_t *sbmlns);
/**
* Frees the given Compartment_t structure.
*
* @param c the Compartment_t structure to be freed.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
void
Compartment_free (Compartment_t *c);
/**
* Creates a deep copy of the given Compartment_t structure.
*
* @param c the Compartment_t structure to be copied.
*
* @return a (deep) copy of the given Compartment_t structure, or a null
* pointer if a failure occurred.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
Compartment_t *
Compartment_clone (const Compartment_t* c);
/**
* Initializes the fields of the given Compartment_t structure to "typical"
* default values.
*
* The SBML Compartment component has slightly different aspects and
* default attribute values in different SBML Levels and Versions.
* This method sets the values to certain common defaults, based
* mostly on what they are in SBML Level 2. Specifically:
*
* @li Sets attribute "spatialDimensions" to @c 3
* @li Sets attribute "constant" to @c 1 (true)
* @li (Applies to Level 1 models only) Sets attribute "volume" to @c 1.0
* @li (Applies to Level 3 models only) Sets attribute "units" to @c litre
*
* @param c the Compartment_t structure.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
void
Compartment_initDefaults (Compartment_t *c);
/**
* Returns a list of XMLNamespaces_t structures associated with the given
* Compartment_t structure.
*
* @param c the Compartment_t structure.
*
* @return pointer to the XMLNamespaces_t structure associated with this SBML
* structure
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
const XMLNamespaces_t *
Compartment_getNamespaces(Compartment_t *c);
/**
* Returns the value of the "id" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
*
* @return the id of this structure.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
const char *
Compartment_getId (const Compartment_t *c);
/**
* Returns the value of the "name" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
*
* @return the name of the Compartment_t structure @p c, as a pointer to a
* string.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
const char *
Compartment_getName (const Compartment_t *c);
/**
* Get the value of the "compartmentType" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
*
* @return the value of the "compartmentType" attribute of the
* Compartment_t structure @p c as a string.
*
* @note The "compartmentType" attribute is only available in SBML
* Level 2 Versions 2–4.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
const char *
Compartment_getCompartmentType (const Compartment_t *c);
/**
* Get the number of spatial dimensions of the given Compartment_t structure.
*
* @param c the Compartment_t structure.
*
* @return the value of the "spatialDimensions" attribute of the
* Compartment_t structure @p c as an unsigned integer
*
* @copydetails doc_note_spatial_dimensions_as_double
*
* @see Compartment_getSpatialDimensionsAsDouble()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
unsigned int
Compartment_getSpatialDimensions (const Compartment_t *c);
/**
* Get the number of spatial dimensions of the given Compartment_t structure,
* as a double.
*
* @param c the Compartment_t structure.
*
* @return the value of the "spatialDimensions" attribute of the
* Compartment_t structure @p c as a double.
*
* @copydetails doc_note_spatial_dimensions_as_double
*
* @see Compartment_getSpatialDimensions()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
double
Compartment_getSpatialDimensionsAsDouble (const Compartment_t *c);
/**
* Get the size of the given Compartment_t structure.
*
* @copydetails doc_compartment_both_size_and_volume
*
* @param c the Compartment_t structure.
*
* @return the value of the "size" attribute ("volume" in Level 1) of
* the Compartment_t structure @p c as a floating point number.
*
* @note This method is identical to Compartment_getVolume().
*
* @see Compartment_isSetSize()
* @see Compartment_getVolume()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
double
Compartment_getSize (const Compartment_t *c);
/**
* Get the volume of the given Compartment_t structure.
*
* @copydetails doc_compartment_both_size_and_volume
*
* @param c the Compartment_t structure.
*
* @return the value of the "volume" attribute ("size" in Level 2) of
* @p c, as a floating-point number.
*
* @copydetails doc_note_compartment_volume
*
* @note This method is identical to Compartment_getSize().
*
* @see Compartment_isSetVolume()
* @see Compartment_getSize()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
double
Compartment_getVolume (const Compartment_t *c);
/**
* Get the units of the given Compartment_t structure's size.
*
* The value of an SBML compartment's "units" attribute establishes the
* unit of measurement associated with the compartment's size.
*
* @param c the Compartment_t structure.
*
* @return the value of the "units" attribute of the Compartment_t structure,
* as a string. An empty string indicates that no units have been assigned
* to the value of the size.
*
* @copydetails doc_note_unassigned_unit_are_not_a_default
*
* @see Compartment_isSetUnits()
* @see Compartment_setUnits()
* @see Compartment_getSize()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
const char *
Compartment_getUnits (const Compartment_t *c);
/**
* Get the identifier, if any, of the compartment that is designated
* as being outside of the given Compartment_t structure.
*
* @param c the Compartment_t structure.
*
* @return the value of the "outside" attribute of this Compartment_t
* structure.
*
* @note The "outside" attribute is defined in SBML Level 1 and
* Level 2, but does not exist in SBML Level 3.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
const char *
Compartment_getOutside (const Compartment_t *c);
/**
* Get the value of the "constant" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
*
* @return @c 1 (true) if this compartment's size is flagged as being
* constant, @c 0 (false) otherwise.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_getConstant (const Compartment_t *c);
/**
* Predicate returning @c 1 (true) if the given Compartment_t structure's "id"
* attribute is set.
*
* @param c the Compartment_t structure.
*
* @return @c 1 (true) if the "id" attribute of this Compartment_t structure is
* set, @c 0 (false) otherwise.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_isSetId (const Compartment_t *c);
/**
* Predicate returning @c 1 (true) if the given Compartment_t structure's "name"
* attribute is set.
*
* @param c the Compartment_t structure.
*
* @return @c 1 (true) if the "name" attribute of this Compartment_t structure is
* set, @c 0 (false) otherwise.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_isSetName (const Compartment_t *c);
/**
* Predicate returning @c 1 (true) if the given Compartment_t structure's
* "compartmentType" attribute is set.
*
* @param c the Compartment_t structure.
*
* @return @c 1 (true) if the "compartmentType" attribute of this Compartment_t
* structure is set, @c 0 (false) otherwise.
*
* @note The "compartmentType" attribute is only available in SBML
* Level 2 Versions 2–4.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_isSetCompartmentType (const Compartment_t *c);
/**
* Predicate returning @c 1 (true) if the given Compartment_t structure's "size"
* attribute is set.
*
* This method is similar but not identical to Compartment_isSetVolume().
* The latter should be used in the context of SBML Level 1 models
* instead of Compartment_isSetSize() because Compartment_isSetVolume()
* performs extra processing to take into account the difference in default
* values between SBML Levels 1 and 2.
*
* @param c the Compartment_t structure.
*
* @return @c 1 (true) if the "size" attribute ("volume" in Level 2) of
* this Compartment_t structure is set, @c 0 (false) otherwise.
*
* @see Compartment_isSetVolume()
* @see Compartment_setSize()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_isSetSize (const Compartment_t *c);
/**
* Predicate returning @c 1 (true) if the given Compartment_t structures's "volume"
* attribute is set.
*
* This method is similar but not identical to Compartment_isSetSize(). The
* latter should not be used in the context of SBML Level 1 models
* because the present method performs extra processing to take into account
* the difference in default values between SBML Levels 1 and 2.
*
* @param c the Compartment_t structure.
*
* @return @c 1 (true) if the "volume" attribute ("size" in Level 2 and
* above) of this Compartment_t structure is set, @c 0 (false) otherwise.
*
* @copydetails doc_note_compartment_volume
*
* @see Compartment_isSetSize()
* @see Compartment_setVolume()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_isSetVolume (const Compartment_t *c);
/**
* Predicate returning @c 1 (true) if the given Compartment_t structure's "units"
* attribute is set.
*
* @param c the Compartment_t structure.
*
* @return @c 1 (true) if the "units" attribute of this Compartment_t structure
* is set, @c 0 (false) otherwise.
*
* @copydetails doc_note_unassigned_unit_are_not_a_default
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_isSetUnits (const Compartment_t *c);
/**
* Predicate returning @c 1 (true) if the given Compartment_t structure's "outside"
* attribute is set.
*
* @param c the Compartment_t structure.
*
* @return @c 1 (true) if the "outside" attribute of this Compartment_t structure
* is set, @c 0 (false) otherwise.
*
* @note The "outside" attribute is defined in SBML Level 1 and
* Level 2, but does not exist in SBML Level 3.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_isSetOutside (const Compartment_t *c);
/**
* Predicate returning @c 1 (true) if the given Compartment_t structure's
* "spatialDimensions" attribute is set.
*
* @param c the Compartment_t structure.
*
* @return @c 1 (true) if the "spatialDimensions" attribute of this Compartment_t
* structure is set, @c 0 (false) otherwise.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_isSetSpatialDimensions (const Compartment_t *c);
/**
* Predicate returning @c 1 (true) if the given Compartment_t structure's "constant"
* attribute is set.
*
* @return @c 1 (true) if the "constant" attribute of this Compartment_t
* structure is set, @c 0 (false) otherwise.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_isSetConstant (const Compartment_t *c);
/**
* Sets the value of the "id" attribute of the given Compartment_t structure.
*
* The string @p sid is copied.
*
* @copydetails doc_id_attribute
*
* @param c the Compartment_t structure.
*
* @param sid the identifier to which the structures "id" attribute should
* be set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @note Using this function with a null pointer for @p sid is equivalent to
* unsetting the "id" attribute.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_setId (Compartment_t *c, const char *sid);
/**
* Sets the "name" attribute of the given Compartment_t structure.
*
* This function copies the string given in @p name. If the string is
* a null pointer, this function is equivalent to calling Compartment_unsetName().
*
* @param c the Compartment_t structure.
*
* @param name the string to which the structures "name" attribute should be
* set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @note Using this function with a null pointer for @p name is equivalent to
* unsetting the value of the "name" attribute.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_setName (Compartment_t *c, const char *name);
/**
* Sets the "compartmentType" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
* @param sid the identifier of a CompartmentType_t structure defined
* elsewhere in the enclosing Model_t structure.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @note Using this function with a null pointer for @p sid is equivalent to
* unsetting the value of the "compartmentType" attribute.
*
* @note The "compartmentType" attribute is only available in SBML
* Level 2 Versions 2–4.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_setCompartmentType (Compartment_t *c, const char *sid);
/**
* Sets the "spatialDimensions" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
* @param value an unsigned integer indicating the number of dimensions
* of the given compartment.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_setSpatialDimensions (Compartment_t *c, unsigned int value);
/**
* Sets the "spatialDimensions" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
* @param value a double indicating the number of dimensions
* of the given compartment.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_setSpatialDimensionsAsDouble (Compartment_t *c, double value);
/**
* Sets the "size" attribute (or "volume" in SBML Level 1) of the given
* Compartment_t structure.
*
* @param c the Compartment_t structure.
* @param value a @c double representing the size of the given
* Compartment_t structure in whatever units are in effect.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @see Compartment_isSetSize()
* @see Compartment_setVolume()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_setSize (Compartment_t *c, double value);
/**
* Sets the "volume" attribute (or "size" in SBML Level 2) of the given
* Compartment_t structure.
*
* This method is identical to Compartment_setSize() and is provided for
* compatibility between SBML Level 1 and higher Levels of SBML.
*
* @param c the Compartment_t structure.
*
* @param value a @c double representing the volume of the given
* Compartment_t structure in whatever units are in effect.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @copydetails doc_note_compartment_volume
*
* @see Compartment_isSetVolume()
* @see Compartment_setSize()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_setVolume (Compartment_t *c, double value);
/**
* Sets the "units" attribute of the given Compartment_t structure.
*
* @param c the Compartment_t structure.
*
* @param sid the identifier of the defined units to use. The string will
* be copied.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @note Using this function with a null pointer for @p sid is equivalent to
* unsetting the value of the "units" attribute.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_setUnits (Compartment_t *c, const char *sid);
/**
* Sets the "outside" attribute of the given Compartment_t structure.
*
* @param c the Compartment_t structure.
*
* @param sid the identifier of a compartment that encloses this one. The
* string will be copied.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @note Using this function with a null pointer for @p sid is equivalent to
* unsetting the value of the "outside" attribute.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_setOutside (Compartment_t *c, const char *sid);
/**
* Sets the value of the "constant" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
*
* @param value an integer indicating whether the size/volume of the
* compartment @p c should be considered constant (indicated by a nonzero @p
* value) or variable (@p value is zero).
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_setConstant (Compartment_t *c, int value);
/**
* Unsets the "name" attribute of the given Compartment_t structure.
*
* @param c the Compartment_t structure.
*
* @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}
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_unsetName (Compartment_t *c);
/**
* Unsets the value of the "compartmentType" attribute of the given
* Compartment_t structure.
*
* @param c the Compartment_t structure.
*
* @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}
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_unsetCompartmentType (Compartment_t *c);
/**
* Unsets the value of the "constant" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
*
* @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}
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_unsetConstant (Compartment_t *c);
/**
* Unsets the value of the "size" attribute of the given Compartment_t
* structure.
*
* In SBML Level 1, a compartment's volume has a default value
* (@c 1.0) and therefore <em>should always be set</em>. Calling this method
* on a Level 1 model resets the value to @c 1.0 rather than actually
* unsetting it. In Level 2, a compartment's "size" is optional with
* no default value, and unsetting it will result in the compartment having
* no defined size.
*
* @param c the Compartment_t structure.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_unsetSize (Compartment_t *c);
/**
* (For SBML Level 1) Unsets the value of the "volume" attribute of the
* given Compartment_t structure.
*
* This method is identical to Compartment_unsetSize(). Please refer to that
* method's documentation for more information about its behavior.
*
* @param c the Compartment_t structure.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @copydetails doc_note_compartment_volume
*
* @see Compartment_unsetSize()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_unsetVolume (Compartment_t *c);
/**
* Unsets the value of the "units" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
*
* @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}
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_unsetUnits (Compartment_t *c);
/**
* Unsets the value of the "outside" attribute of the given Compartment_t
* structure.
*
* @param c the Compartment_t structure.
*
* @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}
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_unsetOutside (Compartment_t *c);
/**
* Unsets the value of the "spatialDimensions" attribute of the given
* Compartment_t structure.
*
* In SBML Levels prior to Level 3, compartments must always have a
* value for the number of dimensions. Consequently, calling this method
* on a model of SBML Level 1–2 will result in a return value of
* @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @param c the Compartment_t structure.
*
* @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}
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_unsetSpatialDimensions (Compartment_t *c);
/**
* Constructs and returns a UnitDefinition that corresponds to the units
* of the given Compartment_t structure's designated size.
*
* @copydetails doc_compartment_units
*
* @param c the Compartment_t structure whose units are to be returned.
*
* @return a UnitDefinition_t structure that expresses the units
* of the given Compartment_t structure.
*
* @copydetails doc_note_unit_analysis_depends_on_model
*
* @see Compartment_isSetUnits()
* @see Compartment_getUnits()
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
UnitDefinition_t *
Compartment_getDerivedUnitDefinition(Compartment_t *c);
/**
* Predicate returning @c 1 (true) or @c 0 (false) depending on whether all the required
* attributes for the given Compartment_t structure have been set.
*
* The required attributes for a Compartment_t structure are:
* @li id (name in SBML Level 1 only)
* @li constant (in SBML Level 3 only)
*
* @param c the Compartment_t structure to check.
*
* @return @c 1 (true) if all the required attributes for this
* structure have been defined, @c 0 (false) otherwise.
*
* @memberof Compartment_t
*/
LIBSBML_EXTERN
int
Compartment_hasRequiredAttributes (Compartment_t *c);
/**
* Returns the Compartment_t structure having a given identifier.
*
* @param lo the list of Compartments_t structures to search.
* @param sid the "id" attribute value being sought.
*
* @return item in the @p lo ListOfCompartments with the given @p sid or a
* null pointer if no such item exists.
*
* @see ListOf_t
*
* @memberof ListOfCompartments_t
*/
LIBSBML_EXTERN
Compartment_t *
ListOfCompartments_getById (ListOf_t *lo, const char *sid);
/**
* Removes a Compartment_t structure based on its identifier.
*
* The caller owns the returned item and is responsible for deleting it.
*
* @param lo the list of Compartment_t structures to search.
* @param sid the "id" attribute value of the structure to remove.
*
* @return The Compartment_t structure removed, or a null pointer if no such
* item exists in @p lo.
*
* @see ListOf_t
*
* @memberof ListOfCompartments_t
*/
LIBSBML_EXTERN
Compartment_t *
ListOfCompartments_removeById (ListOf_t *lo, const char *sid);
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* Compartment_h */
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