libSBML Perl API
libSBML 5.8.0 Perl API
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Implementation of SBML's Compartment construct.
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 somewhere. Compartments represent the 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 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 3
(i.e., a three-dimensional compartment, which is to say, a volume), or 2 (a two-dimensional compartment, a surface), or 1
(a one-dimensional compartment, a line). In SBML Level 3, the type of this attribute is 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 integer
, and the default value is 3
; the permissible values in SBML Level 2 are 3
, 2
, 1
, and 0
(for a point).
Another optional attribute on Compartment is "size", representing the 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 does not imply that the compartment size is 1. (This is unlike the definition of compartment "volume" in SBML Level 1.) When the compartment's "spatialDimensions" attribute does not have a value of 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 elsewhere in the model. In SBML Level 2, there are additional special requirements on the values of "size"; we discuss them in a separate section below.
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 optional Compartment attribute named "constant" is used to indicate whether the compartment's size stays constant after simulation begins. A value of true
indicates the compartment's "size" cannot be changed by any other construct except InitialAssignment; a value of 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"="0"
, the value cannot be changed by InitialAssignment either. Further, in Level 2, "constant" has a default value of true
. In SBML Level 3, there is no default value for the "constant" attribute.
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 object must be one of the base units (see Unit), or the predefined unit identifiers volume
, area
, length
or dimensionless
, or a new unit defined by a UnitDefinition object in the enclosing Model, subject to the restrictions detailed in the following table:
Value ofspatialDimensions
|
size allowed? |
units allowed? |
Allowable kinds of units |
Default value of attribute units
|
---|---|---|---|---|
"3 " |
yes | yes | units of volume, or dimensionless |
"volume " |
"2 " |
yes | yes | units of area, or dimensionless |
"area " |
"1 " |
yes | yes | units of length, or dimensionless |
"length " |
"0 " |
no | no | (no units allowed) |
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 0
:
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.
The math
element of an AssignmentRule or InitialAssignment referring to this compartment must have identical units.
In RateRule objects that set the rate of change of the compartment's size, the units of the rule's math
element must be identical to the compartment's "units" attribute divided by the default time units. (In other words, the units for the rate of change of compartment size are compartment size/time units.
Compartments with "spatialDimensions"=0
require special treatment in this framework. As implied above, the "size" attribute must not have a value on an SBML Level 2 Compartment object if the "spatialDimensions" attribute has a value of 0
. An additional related restriction is that the "constant" attribute must default to or be set to true
if the value of the "spatialDimensions" attribute is 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 substance/time and not (say) concentration/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 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 class of objects are not present in SBML Level 3 Core nor in SBML Level 1.
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" 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 object 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 object 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 object does not define the relevant attribute ("volumeUnits", "areaUnits" or "lengthUnits") for a given "spatialDimensions" value, the unit associated with that Compartment object's size is undefined. If both "spatialDimensions" and "units" are left unset on a given Compartment object instance, 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 and there is no default value of "spatialDimensions". 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.
Value of attribute "spatialDimensions" |
Attribute of Model used for inheriting the unit |
Recommended candidate units |
---|---|---|
"3 " |
"volumeUnits" | units of volume, or dimensionless |
"2 " |
"areaUnits" | units of area, or dimensionless |
"1 " |
"lengthUnits" | units of length, or dimensionless |
other | no units inherited | no specific recommendations |
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:
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.
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 amount/size) is specified by the value of the "units" attribute on the compartment in which the species is located.
The "math" elements of AssignmentRule, InitialAssignment and EventAssignment objects setting the value of the compartment size should all have the same units as the unit associated with the compartment's size.
In a RateRule object 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 time. (In other words, {unit of compartment size}/{unit of time}.)
In SBML Level 1 and Level 2, Compartment has an optional attribute named "outside", whose value can be the identifier of another Compartment object defined in the enclosing Model object. 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 B has the identifier of compartment A as its "outside" attribute value, the size of A does not include the size of B. The compartment sizes are separate.
In Level 2, there are two restrictions on the "outside" attribute. First, because a compartment with "spatialDimensions" of 0
has no size, such a compartment cannot act as the container of any other compartment except compartments that also have "spatialDimensions" values of 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.
Public Member Functions | |
virtual bool | accept (SBMLVisitor &v) const |
Accepts the given SBMLVisitor for this instance of Compartment. More... | |
int | addCVTerm (CVTerm *term, bool newBag=false) |
Adds a copy of the given CVTerm object to this SBML object. More... | |
virtual int | appendAnnotation (const XMLNode *annotation) |
Appends the given annotation to the "annotation" subelement of this object. More... | |
virtual int | appendAnnotation (const std::string &annotation) |
Appends the given annotation to the "annotation" subelement of this object. More... | |
int | appendNotes (const XMLNode *notes) |
Appends the given notes to the "notes" subelement of this object. More... | |
int | appendNotes (const std::string ¬es) |
Appends the given notes to the "notes" subelement of this object. More... | |
virtual Compartment * | clone () const |
Creates and returns a deep copy of this Compartment object. More... | |
Compartment (unsigned int level, unsigned int version) | |
Creates a new Compartment using the given SBML level and version values. More... | |
Compartment (SBMLNamespaces *sbmlns) | |
Creates a new Compartment using the given SBMLNamespaces object sbmlns . More... | |
Compartment (const Compartment &orig) | |
Copy constructor; creates a copy of a Compartment. More... | |
int | disablePackage (const std::string &pkgURI, const std::string &pkgPrefix) |
Disables the given SBML Level 3 package. More... | |
int | enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag) |
Enables or disables the given SBML Level 3 package. More... | |
virtual List * | getAllElements () |
Returns a List of all child SBase objects, including those nested to an arbitrary depth. More... | |
virtual List * | getAllElementsFromPlugins () |
Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
SBase * | getAncestorOfType (int type, const std::string pkgName="core") |
Returns the first ancestor object that has the given SBML type code. More... | |
const SBase * | getAncestorOfType (int type, const std::string pkgName="core") const |
Returns the first ancestor object that has the given SBML type code. More... | |
XMLNode * | getAnnotation () |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
XMLNode * | getAnnotation () const |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
std::string | getAnnotationString () |
Returns the content of the "annotation" subelement of this object as a character string. More... | |
std::string | getAnnotationString () const |
Returns the content of the "annotation" subelement of this object as a character string. More... | |
unsigned int | getColumn () const |
Returns the column number on which this object first appears in the XML representation of the SBML document. More... | |
const std::string & | getCompartmentType () const |
Get the value of the "compartmentType" attribute of this Compartment object. More... | |
bool | getConstant () const |
Get the value of the "constant" attribute of this Compartment. More... | |
CVTerm * | getCVTerm (unsigned int n) |
Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
List * | getCVTerms () |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
List * | getCVTerms () const |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
UnitDefinition * | getDerivedUnitDefinition () |
Constructs and returns a UnitDefinition that corresponds to the units of this Compartment's designated size. More... | |
const UnitDefinition * | getDerivedUnitDefinition () const |
Constructs and returns a UnitDefinition that corresponds to the units of this Compartment's designated size. More... | |
virtual SBase * | getElementByMetaId (std::string metaid) |
Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found. More... | |
virtual SBase * | getElementBySId (std::string id) |
Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More... | |
virtual const std::string & | getElementName () const |
Returns the XML element name of this object, which for Compartment, is always "compartment" . More... | |
virtual const std::string & | getId () const |
Returns the value of the "id" attribute of this Compartment object. More... | |
unsigned int | getLevel () const |
Returns the SBML Level of the SBMLDocument object containing this object. More... | |
unsigned int | getLine () const |
Returns the line number on which this object first appears in the XML representation of the SBML document. More... | |
const std::string & | getMetaId () const |
Returns the value of the "metaid" attribute of this object. More... | |
std::string & | getMetaId () |
Returns the value of the "metaid" attribute of this object. More... | |
const Model * | getModel () const |
Returns the Model object in which the current object is located. More... | |
ModelHistory * | getModelHistory () const |
Returns the ModelHistory object, if any, attached to this object. More... | |
ModelHistory * | getModelHistory () |
Returns the ModelHistory object, if any, attached to this object. More... | |
virtual const std::string & | getName () const |
Returns the value of the "name" attribute of this Compartment object. More... | |
virtual XMLNamespaces * | getNamespaces () const |
Returns a list of the XML Namespaces declared on this SBML document. More... | |
XMLNode * | getNotes () |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More... | |
XMLNode * | getNotes () const |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More... | |
std::string | getNotesString () |
Returns the content of the "notes" subelement of this object as a string. More... | |
std::string | getNotesString () const |
Returns the content of the "notes" subelement of this object as a string. More... | |
unsigned int | getNumCVTerms () |
Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
unsigned int | getNumPlugins () const |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
const std::string & | getOutside () const |
Get the identifier, if any, of the compartment that is designated as being outside of this one. More... | |
const std::string & | getPackageName () const |
Returns the name of the SBML Level 3 package in which this element is defined. More... | |
unsigned int | getPackageVersion () const |
Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
SBase * | getParentSBMLObject () |
Returns the parent SBML object containing this object. More... | |
const SBase * | getParentSBMLObject () const |
Returns the parent SBML object containing this object. More... | |
SBasePlugin * | getPlugin (const std::string &package) |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
const SBasePlugin * | getPlugin (const std::string &package) const |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
SBasePlugin * | getPlugin (unsigned int n) |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
const SBasePlugin * | getPlugin (unsigned int n) const |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
BiolQualifierType_t | getResourceBiologicalQualifier (std::string resource) |
Returns the MIRIAM biological qualifier associated with the given resource. More... | |
ModelQualifierType_t | getResourceModelQualifier (std::string resource) |
Returns the MIRIAM model qualifier associated with the given resource. More... | |
const SBMLDocument * | getSBMLDocument () const |
Returns the SBMLDocument object containing this object instance. More... | |
SBMLDocument * | getSBMLDocument () |
Returns the SBMLDocument object containing this object instance. More... | |
int | getSBOTerm () const |
Returns the integer portion of the value of the "sboTerm" attribute of this object. More... | |
std::string | getSBOTermAsURL () const |
Returns the identifiers.org URL representation of the "sboTerm" attribute of this object. More... | |
std::string | getSBOTermID () const |
Returns the string representation of the "sboTerm" attribute of this object. More... | |
double | getSize () const |
Get the size of this Compartment. More... | |
unsigned int | getSpatialDimensions () const |
Get the number of spatial dimensions of this Compartment object. More... | |
double | getSpatialDimensionsAsDouble () const |
Get the number of spatial dimensions of this Compartment object as a double. More... | |
virtual int | getTypeCode () const |
Returns the libSBML type code for this SBML object. More... | |
const std::string & | getUnits () const |
Get the units of this compartment's size. More... | |
void * | getUserData () const |
Returns the user data that has been previously set via setUserData(). More... | |
unsigned int | getVersion () const |
Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
double | getVolume () const |
Get the volume of this Compartment. More... | |
virtual bool | hasRequiredAttributes () const |
Predicate returning true if all the required attributes for this Compartment object have been set. More... | |
bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
void | initDefaults () |
Initializes the fields of this Compartment object to "typical" default values. More... | |
bool | isPackageEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPackageURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isPkgEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPkgURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isSetAnnotation () const |
Predicate returning true if this object's "annotation" subelement exists and has content. More... | |
bool | isSetCompartmentType () const |
Predicate returning true if this Compartment's "compartmentType" attribute is set. More... | |
bool | isSetConstant () const |
Predicate returning true if this Compartment's "constant" attribute is set. More... | |
virtual bool | isSetId () const |
Predicate returning true if this Compartment's "id" attribute is set. More... | |
bool | isSetMetaId () const |
Predicate returning true if this object's "metaid" attribute is set. More... | |
bool | isSetModelHistory () |
Predicate returning true if this object has a ModelHistory object attached to it. More... | |
virtual bool | isSetName () const |
Predicate returning true if this Compartment's "name" attribute is set. More... | |
bool | isSetNotes () const |
Predicate returning true if this object's "notes" subelement exists and has content. More... | |
bool | isSetOutside () const |
Predicate returning true if this Compartment's "outside" attribute is set. More... | |
bool | isSetSBOTerm () const |
Predicate returning true if this object's "sboTerm" attribute is set. More... | |
bool | isSetSize () const |
Predicate returning true if this Compartment's "size" attribute is set. More... | |
bool | isSetSpatialDimensions () const |
Predicate returning true if this Compartment's "spatialDimensions" attribute is set. More... | |
bool | isSetUnits () const |
Predicate returning true if this Compartment's "units" attribute is set. More... | |
bool | isSetVolume () const |
Predicate returning true if this Compartment's "volume" attribute is set. More... | |
bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
bool | matchesSBMLNamespaces (const SBase *sb) |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
bool | matchesSBMLNamespaces (const SBase *sb) const |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
Compartment & | operator= (const Compartment &rhs) |
Assignment operator for Compartment. More... | |
virtual int | removeFromParentAndDelete () |
Removes itself from its parent. More... | |
int | removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="") |
Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More... | |
virtual void | renameMetaIdRefs (std::string oldid, std::string newid) |
Renames all the MetaIdRef attributes on this element. More... | |
virtual void | renameSIdRefs (std::string oldid, std::string newid) |
Renames all the SIdRef attributes on this element, including any found in MathML. More... | |
virtual void | renameUnitSIdRefs (std::string oldid, std::string newid) |
Renames all the UnitSIdRef attributes on this element. More... | |
int | replaceTopLevelAnnotationElement (const XMLNode *annotation) |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
int | replaceTopLevelAnnotationElement (const std::string &annotation) |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
virtual int | setAnnotation (const XMLNode *annotation) |
Sets the value of the "annotation" subelement of this SBML object. More... | |
virtual int | setAnnotation (const std::string &annotation) |
Sets the value of the "annotation" subelement of this SBML object. More... | |
int | setCompartmentType (const std::string &sid) |
Sets the "compartmentType" attribute of this Compartment. More... | |
int | setConstant (bool value) |
Sets the value of the "constant" attribute of this Compartment. More... | |
virtual int | setId (const std::string &sid) |
Sets the value of the "id" attribute of this Compartment. More... | |
int | setMetaId (const std::string &metaid) |
Sets the value of the "metaid" attribute of this object. More... | |
int | setModelHistory (ModelHistory *history) |
Sets the ModelHistory of this object. More... | |
virtual int | setName (const std::string &name) |
Sets the value of the "name" attribute of this Compartment. More... | |
int | setNamespaces (XMLNamespaces *xmlns) |
Sets the namespaces relevant of this SBML object. More... | |
int | setNotes (const XMLNode *notes) |
Sets the value of the "notes" subelement of this SBML object. More... | |
int | setNotes (const std::string ¬es, bool addXHTMLMarkup=false) |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes . More... | |
int | setOutside (const std::string &sid) |
Sets the "outside" attribute of this Compartment. More... | |
virtual int | setSBOTerm (int value) |
Sets the value of the "sboTerm" attribute. More... | |
virtual int | setSBOTerm (const std::string &sboid) |
Sets the value of the "sboTerm" attribute by string. More... | |
int | setSize (double value) |
Sets the "size" attribute (or "volume" in SBML Level 1) of this Compartment. More... | |
int | setSpatialDimensions (unsigned int value) |
Sets the "spatialDimensions" attribute of this Compartment. More... | |
int | setSpatialDimensions (double value) |
Sets the "spatialDimensions" attribute of this Compartment as a double. More... | |
int | setUnits (const std::string &sid) |
Sets the "units" attribute of this Compartment. More... | |
int | setUserData (void *userData) |
Sets the user data of this element. More... | |
int | setVolume (double value) |
Sets the "volume" attribute (or "size" in SBML Level 2) of this Compartment. More... | |
char * | toSBML () |
Returns a string consisting of a partial SBML corresponding to just this object. More... | |
int | unsetAnnotation () |
Unsets the value of the "annotation" subelement of this SBML object. More... | |
int | unsetCompartmentType () |
Unsets the value of the "compartmentType" attribute of this Compartment. More... | |
int | unsetCVTerms () |
Clears the list of CVTerm objects attached to this SBML object. More... | |
virtual int | unsetId () |
Unsets the value of the "id" attribute of this SBML object. More... | |
int | unsetMetaId () |
Unsets the value of the "metaid" attribute of this SBML object. More... | |
int | unsetModelHistory () |
Unsets the ModelHistory object attached to this object. More... | |
virtual int | unsetName () |
Unsets the value of the "name" attribute of this Compartment. More... | |
int | unsetNotes () |
Unsets the value of the "notes" subelement of this SBML object. More... | |
int | unsetOutside () |
Unsets the value of the "outside" attribute of this Compartment. More... | |
int | unsetSBOTerm () |
Unsets the value of the "sboTerm" attribute of this SBML object. More... | |
int | unsetSize () |
Unsets the value of the "size" attribute of this Compartment. More... | |
int | unsetSpatialDimensions () |
Unsets the value of the "spatialDimensions" attribute of this Compartment. More... | |
int | unsetUnits () |
Unsets the value of the "units" attribute of this Compartment. More... | |
int | unsetVolume () |
Unsets the value of the "volume" attribute of this Compartment. More... | |
virtual | ~Compartment () |
Destroys this Compartment. More... | |
Protected Member Functions | |
virtual void | setElementText (const std::string &text) |
When overridden allows SBase elements to use the text included in between the elements tags. More... | |
Compartment::Compartment | ( | unsigned int | level, |
unsigned int | version | ||
) |
Creates a new Compartment using the given SBML level
and version
values.
level | an unsigned int, the SBML Level to assign to this Compartment |
version | an unsigned int, the SBML Version to assign to this Compartment |
SBMLConstructorException | Thrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object. |
Compartment::Compartment | ( | SBMLNamespaces * | sbmlns | ) |
Creates a new Compartment using the given SBMLNamespaces object sbmlns
.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using this class constructor is to create an SBMLNamespaces object somewhere in a program, once, then pass it to object constructors such as this one when needed.
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 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 setId().
sbmlns | an SBMLNamespaces object. |
SBMLConstructorException | Thrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object. |
|
virtual |
Destroys this Compartment.
Compartment::Compartment | ( | const Compartment & | orig | ) |
Copy constructor; creates a copy of a Compartment.
orig | the Compartment instance to copy. |
SBMLConstructorException | Thrown if the argument orig is NULL . |
|
virtual |
Accepts the given SBMLVisitor for this instance of Compartment.
v | the SBMLVisitor instance to be used. |
v.visit()
, which indicates whether the Visitor would like to visit the next Compartment in the list of compartments within which this Compartment is embedded (i.e., the ListOfCompartments in the parent Model). Implements SBase.
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if true , creates a new RDF bag with the same identifier as a previous bag, and if false , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
|
virtualinherited |
Appends the given annotation
to the "annotation" subelement of this object.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase::setAnnotation(const XMLNode* annotation) or SBase::setAnnotation(const std::string& annotation), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML structure that is to be copied and appended to the content of the "annotation" subelement of this object |
Reimplemented in Model, and SpeciesReference.
|
virtualinherited |
Appends the given annotation
to the "annotation" subelement of this object.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase::setAnnotation(const XMLNode* annotation) or SBase::setAnnotation(const std::string& annotation), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML string that is to be copied and appended to the content of the "annotation" subelement of this object |
Reimplemented in Model, and SpeciesReference.
|
inherited |
Appends the given notes
to the "notes" subelement of this object.
The content of notes
is copied.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
notes | an XML node structure that is to appended to the content of the "notes" subelement of this object |
|
inherited |
Appends the given notes
to the "notes" subelement of this object.
The content of the parameter notes
is copied.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
notes | an XML string that is to appended to the content of the "notes" subelement of this object |
|
virtual |
Creates and returns a deep copy of this Compartment object.
Implements SBase.
|
inherited |
Disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
|
inherited |
Enables or disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (true ) or disable (false ) the package |
|
virtualinherited |
Returns a List of all child SBase objects, including those nested to an arbitrary depth.
Reimplemented in Model, SBMLDocument, UnitDefinition, Event, Reaction, ListOf, KineticLaw, Submodel, and SBaseRef.
|
virtualinherited |
|
inherited |
Returns the first ancestor object that has the given SBML type code.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
NULL
if no ancestor exists.
|
inherited |
Returns the first ancestor object that has the given SBML type code.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
NULL
if no ancestor exists.
|
inherited |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.
Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
|
inherited |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.
Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
|
inherited |
Returns the content of the "annotation" subelement of this object as a character string.
Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form.
|
inherited |
Returns the content of the "annotation" subelement of this object as a character string.
Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form.
|
inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
const string & Compartment::getCompartmentType | ( | ) | const |
Get the value of the "compartmentType" attribute of this Compartment object.
bool Compartment::getConstant | ( | ) | const |
Get the value of the "constant" attribute of this Compartment.
true
if this Compartment's size is flagged as being constant, false
otherwise.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
UnitDefinition * Compartment::getDerivedUnitDefinition | ( | ) |
Constructs and returns a UnitDefinition that corresponds to the units of this Compartment's designated size.
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 UnitDefinition object based on how this compartment's units are interpreted according to the relevant SBML guidelines, or it returns NULL
if no units have been declared and no defaults are defined by the relevant SBML specification.
Note that unit declarations for Compartment objects are specified in terms of the identifier of a unit (e.g., using setUnits()), but 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 "substance"
, "volume"
, "area"
, "length"
or "time"
. Callers may find this useful in conjunction with the helper methods provided by the UnitDefinition class for comparing different UnitDefinition objects.
NULL
if one cannot be constructed.NULL
.const UnitDefinition * Compartment::getDerivedUnitDefinition | ( | ) | const |
Constructs and returns a UnitDefinition that corresponds to the units of this Compartment's designated size.
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 UnitDefinition object based on how this compartment's units are interpreted according to the relevant SBML guidelines, or it returns NULL
if no units have been declared and no defaults are defined by the relevant SBML specification.
Note that unit declarations for Compartment objects are specified in terms of the identifier of a unit (e.g., using setUnits()), but 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 "substance"
, "volume"
, "area"
, "length"
or "time"
. Callers may find this useful in conjunction with the helper methods provided by the UnitDefinition class for comparing different UnitDefinition objects.
NULL
if one cannot be constructed.NULL
.
|
virtualinherited |
Returns the first child element it can find with a specific "metaid" attribute value, or NULL
if no such object is found.
metaid | string representing the "metaid" attribute value of the object to find. |
Reimplemented in Model, SBMLDocument, UnitDefinition, Event, Reaction, ListOf, KineticLaw, Submodel, and SBaseRef.
|
virtualinherited |
Returns the first child element found that has the given id
in the model-wide SId
namespace, or NULL
if no such object is found.
id | string representing the "id" attribute value of the object to find. |
Reimplemented in ListOfUnitDefinitions, ListOfRules, ListOfInitialAssignments, ListOfEventAssignments, ListOfLocalParameters, Model, SBMLDocument, UnitDefinition, Event, Reaction, ListOf, KineticLaw, ListOfPorts, Submodel, and SBaseRef.
|
virtual |
Returns the XML element name of this object, which for Compartment, is always "compartment"
.
"compartment"
. Implements SBase.
|
virtual |
Returns the value of the "id" attribute of this Compartment object.
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Returns the line number on which this object first appears in the XML representation of the SBML document.
|
inherited |
Returns the value of the "metaid" attribute of this object.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
|
inherited |
Returns the value of the "metaid" attribute of this object.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL
if none exist.
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL
if none exist.
|
virtual |
Returns the value of the "name" attribute of this Compartment object.
|
virtualinherited |
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.
Reimplemented in SBMLDocument.
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
The "notes" element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
The "notes" element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
|
inherited |
Returns the content of the "notes" subelement of this object as a string.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
|
inherited |
Returns the content of the "notes" subelement of this object as a string.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
const string & Compartment::getOutside | ( | ) | const |
Get the identifier, if any, of the compartment that is designated as being outside of this one.
|
inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
"core"
will be returned if this element is defined in SBML Level 3 Core. The string "unknown"
will be returned if this element is not defined in any SBML package.
|
inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
0
will be returned if this element belongs to the SBML Level 3 Core package.
|
inherited |
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
|
inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
|
inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include "is" and "has part", but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using values
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a value
resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892" . |
|
inherited |
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is "isDerivedFrom", to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using values
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a value
resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892" . |
|
inherited |
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the integer portion of the value of the "sboTerm" attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
-1
if the value is not set.
|
inherited |
Returns the identifiers.org URL representation of the "sboTerm" attribute of this object.
This method returns the entire SBO identifier as a text string in the form "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN".
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
|
inherited |
Returns the string representation of the "sboTerm" attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form "SBO:NNNNNNN".
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
double Compartment::getSize | ( | ) | const |
Get the size of this Compartment.
This method is identical to getVolume(). In SBML Level 1, compartments are always three-dimensional constructs and only have volumes, whereas in SBML Level 2, compartments may be other than three-dimensional and therefore the "volume" attribute is named "size" in Level 2. LibSBML provides both getSize() and getVolume() for easier compatibility between SBML Levels.
unsigned int Compartment::getSpatialDimensions | ( | ) | const |
Get the number of spatial dimensions of this Compartment object.
double
, whereas in Level 2, it is integer
. LibSBML provides a separate method for obtaining the value as a double, for models where it is relevant.double Compartment::getSpatialDimensionsAsDouble | ( | ) | const |
Get the number of spatial dimensions of this Compartment object as a double.
double
, whereas in Level 2, it is integer
. To avoid backward compatibility issues, libSBML provides a separate method for obtaining the value as a double, for models where it is relevant.NaN
if this model is not in SBML Level 3 format.
|
virtual |
Returns the libSBML type code for this SBML object.
Reimplemented from SBase.
const string & Compartment::getUnits | ( | ) | const |
Get the units of this compartment's size.
The value of an SBML compartment's "units" attribute establishes the unit of measurement associated with the compartment's size.
dimensionless
. In SBML, default units are never
attributed to numbers, and numbers without units are not automatically
assumed to have the unit dimensionless
. Please consult the
relevant SBML specification document for a more in-depth explanation of
this topic and the SBML unit system.
|
inherited |
Returns the user data that has been previously set via setUserData().
NULL
if no user data has been set.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
double Compartment::getVolume | ( | ) | const |
Get the volume of this Compartment.
This method is identical to getSize(). In SBML Level 1, compartments are always three-dimensional constructs and only have volumes, whereas in SBML Level 2, compartments may be other than three-dimensional and therefore the "volume" attribute is named "size" in Level 2. LibSBML provides both getSize() and getVolume() for easier compatibility between SBML Levels.
|
virtual |
Predicate returning true
if all the required attributes for this Compartment object have been set.
|
inherited |
Predicate returning true
if this object's level/version and namespace values correspond to a valid SBML specification.
The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
"http://www.sbml.org/sbml/level1"
"http://www.sbml.org/sbml/level2"
"http://www.sbml.org/sbml/level2/version2"
"http://www.sbml.org/sbml/level2/version3"
"http://www.sbml.org/sbml/level2/version4"
"http://www.sbml.org/sbml/level3/version1/core"
true
if the level, version and namespace values of this SBML object correspond to a valid set of values, false
otherwise. void Compartment::initDefaults | ( | ) |
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:
3
true
1.0
litre
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if this object's "annotation" subelement exists and has content.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
true
if a "annotation" subelement exists, false
otherwise.bool Compartment::isSetCompartmentType | ( | ) | const |
Predicate returning true
if this Compartment's "compartmentType" attribute is set.
true
if the "compartmentType" attribute of this Compartment is set, false
otherwise.bool Compartment::isSetConstant | ( | ) | const |
Predicate returning true
if this Compartment's "constant" attribute is set.
true
if the "constant" attribute of this Compartment is set, false
otherwise.
|
virtual |
Predicate returning true
if this Compartment's "id" attribute is set.
true
if the "id" attribute of this Compartment is set, false
otherwise.
|
inherited |
Predicate returning true
if this object's "metaid" attribute is set.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
true
if the "metaid" attribute of this SBML object is set, false
otherwise.
|
inherited |
Predicate returning true
if this object has a ModelHistory object attached to it.
true
if the ModelHistory of this object is set, false
otherwise.
|
virtual |
Predicate returning true
if this Compartment's "name" attribute is set.
true
if the "name" attribute of this Compartment is set, false
otherwise.
|
inherited |
Predicate returning true
if this object's "notes" subelement exists and has content.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
true
if a "notes" subelement exists, false
otherwise.bool Compartment::isSetOutside | ( | ) | const |
Predicate returning true
if this Compartment's "outside" attribute is set.
true
if the "outside" attribute of this Compartment is set, false
otherwise.
|
inherited |
Predicate returning true
if this object's "sboTerm" attribute is set.
true
if the "sboTerm" attribute of this SBML object is set, false
otherwise. bool Compartment::isSetSize | ( | ) | const |
Predicate returning true
if this Compartment's "size" attribute is set.
This method is similar but not identical to isSetVolume(). The latter should be used in the context of SBML Level 1 models instead of isSetSize() because isSetVolume() performs extra processing to take into account the difference in default values between SBML Levels 1 and 2.
true
if the "size" attribute ("volume" in Level 2) of this Compartment is set, false
otherwise.bool Compartment::isSetSpatialDimensions | ( | ) | const |
Predicate returning true
if this Compartment's "spatialDimensions" attribute is set.
true
if the "spatialDimensions" attribute of this Compartment is set, false
otherwise. bool Compartment::isSetUnits | ( | ) | const |
Predicate returning true
if this Compartment's "units" attribute is set.
true
if the "units" attribute of this Compartment is set, false
otherwise.dimensionless
. In SBML, default units are never
attributed to numbers, and numbers without units are not automatically
assumed to have the unit dimensionless
. Please consult the
relevant SBML specification document for a more in-depth explanation of
this topic and the SBML unit system.
bool Compartment::isSetVolume | ( | ) | const |
Predicate returning true
if this Compartment's "volume" attribute is set.
This method is similar but not identical to isSetSize(). The latter should not be used in the context of SBML Level 1 models because this method performs extra processing to take into account the difference in default values between SBML Levels 1 and 2.
true
if the "volume" attribute ("size" in Level 2 and above) of this Compartment is set, false
otherwise.1.0
) and therefore this method will always return true
. 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.
|
inherited |
Returns true
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is a subset of sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is a subset of sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are the same as the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is the same as sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are the same as the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is the same as sb's
, false
otherwise. Compartment & Compartment::operator= | ( | const Compartment & | rhs | ) |
Assignment operator for Compartment.
rhs | The object whose values are used as the basis of the assignment. |
SBMLConstructorException | Thrown if the argument rhs is NULL . |
|
virtualinherited |
Removes itself from its parent.
If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
Reimplemented in Model, KineticLaw, SBaseRef, StoichiometryMath, Delay, Trigger, Priority, ListOf, ModelDefinition, and ReplacedBy.
|
inherited |
Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
|
virtualinherited |
Renames all the MetaIdRef
attributes on this element.
This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid
. If any matches are found, the matching identifiers are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier |
newid | the new identifier |
Reimplemented in Port.
|
virtual |
Renames all the SIdRef attributes on this element, including any found in MathML.
Reimplemented from SBase.
|
virtual |
Renames all the UnitSIdRef attributes on this element.
Reimplemented from SBase.
|
inherited |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name);
with the exception that the placement of the annotation element remains the same.
annotation | XMLNode representing the replacement top level annotation |
|
inherited |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name);
with the exception that the placement of the annotation element remains the same.
annotation | string representing the replacement top level annotation |
|
virtualinherited |
Sets the value of the "annotation" subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's "annotation" subelement is deleted.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the "annotation" subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(const XMLNode* annotation) or SBase::appendAnnotation(const std::string& annotation).
annotation | an XML structure that is to be used as the new content of the "annotation" subelement of this object |
Reimplemented in Model, and SpeciesReference.
|
virtualinherited |
Sets the value of the "annotation" subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's "annotation" subelement is deleted.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the "annotation" subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(const XMLNode* annotation) or SBase::appendAnnotation(const std::string& annotation).
annotation | an XML string that is to be used as the content of the "annotation" subelement of this object |
Reimplemented in Model, and SpeciesReference.
int Compartment::setCompartmentType | ( | const std::string & | sid | ) |
Sets the "compartmentType" attribute of this Compartment.
sid | the identifier of a CompartmentType object defined elsewhere in this Model. |
int Compartment::setConstant | ( | bool | value | ) |
Sets the value of the "constant" attribute of this Compartment.
value | a boolean indicating whether the size/volume of this compartment should be considered constant (true ) or variable (false ) |
|
protectedvirtualinherited |
When overridden allows SBase elements to use the text included in between the elements tags.
The default implementation does nothing.
text | the text string found between the element tags. |
|
virtual |
Sets the value of the "id" attribute of this Compartment.
The string sid
is copied. Note that SBML has strict requirements for the syntax of identifiers. The following is a summary of the definition of the SBML identifier type
SId
, which defines the permitted syntax of identifiers. We
express the syntax using an extended form of BNF notation:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*The characters
(
and )
are used for grouping, the
character *
"zero or more times", and the character
|
indicates logical "or". The equality of SBML identifiers is
determined by an exact character sequence match; i.e., comparisons must be
performed in a case-sensitive manner. In addition, there are a few
conditions for the uniqueness of identifiers in an SBML model. Please
consult the SBML specifications for the exact formulations.
sid | the string to use as the identifier of this Compartment |
|
inherited |
Sets the value of the "metaid" attribute of this object.
The string metaid
is copied. The value of metaid
must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the "metaid" attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement.
metaid | the identifier string to use as the value of the "metaid" attribute |
|
inherited |
Sets the ModelHistory of this object.
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
|
virtual |
Sets the value of the "name" attribute of this Compartment.
The string in name
is copied.
name | the new name for the Compartment |
|
inherited |
Sets the namespaces relevant of this SBML object.
The content of xmlns
is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
xmlns | the namespaces to set |
|
inherited |
Sets the value of the "notes" subelement of this SBML object.
The content of notes
is copied, and any existing content of this object's "notes" subelement is deleted.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
notes | an XML structure that is to be used as the content of the "notes" subelement of this object |
|
inherited |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's "notes" subelement is deleted.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.
notes | an XML string that is to be used as the content of the "notes" subelement of this object |
addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
int Compartment::setOutside | ( | const std::string & | sid | ) |
Sets the "outside" attribute of this Compartment.
sid | the identifier of a compartment that encloses this one. |
|
virtualinherited |
Sets the value of the "sboTerm" attribute.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int
, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
value | the NNNNNNN integer portion of the SBO identifier |
|
virtualinherited |
Sets the value of the "sboTerm" attribute by string.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method lets you set the value of "sboTerm" as a complete string of the form "SBO:NNNNNNN", whereas setSBOTerm(int value) allows you to set it using the integer form.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
sboid | the SBO identifier string of the form "SBO:NNNNNNN" |
int Compartment::setSize | ( | double | value | ) |
Sets the "size" attribute (or "volume" in SBML Level 1) of this Compartment.
This method is identical to setVolume() and is provided for compatibility between SBML Level 1 and Level 2.
value | a double representing the size of this compartment instance in whatever units are in effect for the compartment. |
int Compartment::setSpatialDimensions | ( | unsigned int | value | ) |
Sets the "spatialDimensions" attribute of this Compartment.
If value
is not one of 0
, 1
, 2
, or 3
, this method will have no effect (i.e., the "spatialDimensions" attribute will not be set).
value | an unsigned integer indicating the number of dimensions of this compartment. |
int Compartment::setSpatialDimensions | ( | double | value | ) |
Sets the "spatialDimensions" attribute of this Compartment as a double.
value | a double indicating the number of dimensions of this compartment. |
int Compartment::setUnits | ( | const std::string & | sid | ) |
Sets the "units" attribute of this Compartment.
sid | the identifier of the defined units to use. |
|
inherited |
Sets the user data of this element.
This can be used by the application developer to attach custom information to the node. In case of a deep copy this attribute will passed as it is. The attribute will be never interpreted by this class.
userData | specifies the new user data. |
int Compartment::setVolume | ( | double | value | ) |
Sets the "volume" attribute (or "size" in SBML Level 2) of this Compartment.
This method is identical to setVolume() and is provided for compatibility between SBML Level 1 and Level 2.
value | a double representing the volume of this compartment instance in whatever units are in effect for the compartment. |
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
|
inherited |
Unsets the value of the "annotation" subelement of this SBML object.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
int Compartment::unsetCompartmentType | ( | ) |
Unsets the value of the "compartmentType" attribute of this Compartment.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
|
virtualinherited |
Unsets the value of the "id" attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: "id" and "name". The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always either Sid
or UnitSId
, depending on the object in question. Both data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The equality of SId
and UnitSId
type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId
and UnitSId
.
Reimplemented in Model, Event, SimpleSpeciesReference, Submodel, ExternalModelDefinition, Deletion, and Port.
|
inherited |
Unsets the value of the "metaid" attribute of this SBML object.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
|
inherited |
Unsets the ModelHistory object attached to this object.
|
virtual |
Unsets the value of the "name" attribute of this Compartment.
Reimplemented from SBase.
|
inherited |
Unsets the value of the "notes" subelement of this SBML object.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
int Compartment::unsetOutside | ( | ) |
Unsets the value of the "outside" attribute of this Compartment.
|
inherited |
Unsets the value of the "sboTerm" attribute of this SBML object.
int Compartment::unsetSize | ( | ) |
Unsets the value of the "size" attribute of this Compartment.
int Compartment::unsetSpatialDimensions | ( | ) |
Unsets the value of the "spatialDimensions" attribute of this Compartment.
int Compartment::unsetUnits | ( | ) |
Unsets the value of the "units" attribute of this Compartment.
int Compartment::unsetVolume | ( | ) |
Unsets the value of the "volume" attribute of this Compartment.
In SBML Level 1, a Compartment volume has a default value (1.0
) and therefore should always be set. In Level 2, "size" is optional with no default value and as such may or may not be set.