libSBML C++ API
5.20.2
|
The QualSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin class, and codifies the extensions to the SBMLDocument class defined in the SBML Level 3 Qualitative Models (“qual”) package.
The QualSBMLDocumentPlugin defines a required flag named required
, which indicates whether the 'qual' constructs can be used to change the core mathematics of the <model>
child of the <sbml>
element. Because they can not, this attribute must be set false
.
Public Member Functions | |
virtual QualSBMLDocumentPlugin * | clone () const |
Creates and returns a deep copy of this QualSBMLDocumentPlugin object. More... | |
virtual List * | getAllElements (ElementFilter *filter=NULL) |
Returns all child objects of this object. More... | |
virtual SBase * | getElementByMetaId (const std::string &metaid) |
Return the first child object found with a given meta identifier. More... | |
virtual SBase * | getElementBySId (const std::string &id) |
Return the first child object found with a given identifier. More... | |
const std::string & | getElementNamespace () const |
Returns the namespace URI of the package to which this plugin object belongs. More... | |
unsigned int | getLevel () const |
Returns the SBML Level of the package extension of this plugin object. More... | |
const std::string & | getPackageName () const |
Returns the short-form name of the package to which this plugin object belongs. More... | |
unsigned int | getPackageVersion () const |
Returns the package version of the package extension of this plugin object. More... | |
SBase * | getParentSBMLObject () |
Returns the parent object to which this plugin object is connected. More... | |
const SBase * | getParentSBMLObject () const |
Returns the parent object to which this plugin object is connected. More... | |
const std::string & | getPrefix () const |
Returns the XML namespace prefix of the package to which this plugin object belongs. More... | |
virtual bool | getRequired () const |
Returns the value of the "required" attribute. More... | |
SBMLDocument * | getSBMLDocument () |
Returns the SBMLDocument object containing this object instance. More... | |
const SBMLDocument * | getSBMLDocument () const |
Returns the SBMLDocument object containing this object instance. More... | |
std::string | getURI () const |
Returns the XML namespace URI for the package to which this object belongs. More... | |
unsigned int | getVersion () const |
Returns the Version within the SBML Level of the package extension of this plugin object. More... | |
virtual bool | isSetRequired () const |
Returns the value of the "required" attribute. More... | |
virtual bool | isValidTypeForList (SBase *item) const |
QualSBMLDocumentPlugin & | operator= (const QualSBMLDocumentPlugin &rhs) |
Assignment operator for QualSBMLDocumentPlugin. More... | |
QualSBMLDocumentPlugin (const QualSBMLDocumentPlugin &orig) | |
Copy constructor for QualSBMLDocumentPlugin. More... | |
QualSBMLDocumentPlugin (const std::string &uri, const std::string &prefix, QualPkgNamespaces *qualns) | |
Creates a new QualSBMLDocumentPlugin object using the given parameters. More... | |
virtual void | renameMetaIdRefs (const std::string &oldid, const std::string &newid) |
virtual void | renameSIdRefs (const std::string &oldid, const std::string &newid) |
virtual void | renameUnitSIdRefs (const std::string &oldid, const std::string &newid) |
int | setElementNamespace (const std::string &uri) |
Sets the XML namespace to which this object belongs. More... | |
virtual int | setRequired (bool value) |
Sets the SBML "required" attribute value. More... | |
virtual int | unsetRequired () |
Unsets the value of the "required" attribute of this SBMLDocumentPlugin. More... | |
virtual | ~QualSBMLDocumentPlugin () |
Destructor for QualSBMLDocumentPlugin. More... | |
QualSBMLDocumentPlugin::QualSBMLDocumentPlugin | ( | const std::string & | uri, |
const std::string & | prefix, | ||
QualPkgNamespaces * | qualns | ||
) |
Creates a new QualSBMLDocumentPlugin object using the given parameters.
"http://www.sbml.org/sbml/level3/version1/core"
. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/"
.uri | the URI of the SBML Level 3 package implemented by this libSBML package extension. |
prefix | the XML namespace prefix being used for the package. |
qualns | the namespaces object for the package. |
QualSBMLDocumentPlugin::QualSBMLDocumentPlugin | ( | const QualSBMLDocumentPlugin & | orig | ) |
Copy constructor for QualSBMLDocumentPlugin.
orig | the QualSBMLDocumentPlugin instance to copy. |
|
virtual |
Destructor for QualSBMLDocumentPlugin.
|
virtual |
Creates and returns a deep copy of this QualSBMLDocumentPlugin object.
Reimplemented from SBMLDocumentPlugin.
|
virtualinherited |
Returns all child objects of this object.
This returns a List object containing all child SBase objects of this one, at any nesting depth. Optionally, callers can supply a filter that will establish the search criteria for matching objects.
filter | a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects. |
Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, RenderListOfLayoutsPlugin, RenderLayoutPlugin, QualModelPlugin, MultiSpeciesReferencePlugin, MultiSpeciesPlugin, MultiSimpleSpeciesReferencePlugin, MultiModelPlugin, MultiCompartmentPlugin, LayoutModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcReactionPlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.
|
virtualinherited |
Return the first child object found with a given meta identifier.
This method searches all the subobjects under this one, compares their meta identifiers to metaid
, and returns the first one that machines.
metaid | string, the metaid of the object to find. |
metaid
. Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, QualModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.
|
virtualinherited |
Return the first child object found with a given identifier.
This method searches all the subobjects under this one, compares their identifiers to id
, and returns the first one that machines. It uses SBasePlugin::getAllElements(ElementFilter* filter) to get the list of identifiers, so the order in which identifiers are searched is the order in which they appear in the results returned by that method.
Normally, SId
type identifier values are unique across a model in SBML. However, in some circumstances they may not be, such as if a model is invalid because of multiple objects having the same identifier.
id | string representing the identifier of the object to find. |
id
. Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, QualModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.
|
inherited |
Returns the namespace URI of the package to which this plugin object belongs.
|
inherited |
Returns the SBML Level of the package extension of this plugin object.
|
inherited |
Returns the short-form name of the package to which this plugin object belongs.
|
inherited |
Returns the package version of the package extension of this plugin object.
|
inherited |
Returns the parent object to which this plugin object is connected.
|
inherited |
Returns the parent object to which this plugin object is connected.
|
inherited |
Returns the XML namespace prefix of the package to which this plugin object belongs.
|
virtualinherited |
Returns the value of the "required" attribute.
<sbml>
element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true
indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true
in any SBML document that uses the package.The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.
|
inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the XML namespace URI for the package to which this object belongs.
"http://www.sbml.org/sbml/level3/version1/core"
. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/"
.This method first looks into the SBMLNamespaces object possessed by the parent SBMLDocument object of the current object. If this cannot be found, this method returns the result of getElementNamespace().
|
inherited |
Returns the Version within the SBML Level of the package extension of this plugin object.
|
virtualinherited |
Returns the value of the "required" attribute.
<sbml>
element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true
indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true
in any SBML document that uses the package.The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.
true
if the "required" attribute of this SBMLDocument has been set to true
, false
otherwise.
|
virtualinherited |
QualSBMLDocumentPlugin & QualSBMLDocumentPlugin::operator= | ( | const QualSBMLDocumentPlugin & | rhs | ) |
Assignment operator for QualSBMLDocumentPlugin.
rhs | the object whose values are used as the basis of the assignment |
|
virtualinherited |
ID
; the SBML object attribute itself is typically named metaid
. All attributes that hold values referring to values of type ID
are of the XML data type IDREF
. They are also sometimes informally referred to as "metaid refs", in analogy to the SBML-defined type SIdRef
.This method works by looking at all meta-identifier 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. |
|
virtualinherited |
SIdRef
type attribute value with another value.In SBML, object identifiers are of a data type called SId
. In SBML Level 3, an explicit data type called SIdRef
was introduced for attribute values that refer to SId
values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to an identifier", but the effective data type was the same as SIdRef
in Level 3. These and other methods of libSBML refer to the type SIdRef
for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid
. If any matches are found, the matching values are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier. |
newid | the new identifier. |
Reimplemented in FbcReactionPlugin.
|
virtualinherited |
UnitSIdRef
type attribute value with another value.UnitSId
. In SBML Level 3, an explicit data type called UnitSIdRef
was introduced for attribute values that refer to UnitSId
values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to a unit identifier", but the effective data type was the same as UnitSIdRef
in Level 3. These and other methods of libSBML refer to the type UnitSIdRef
for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid
. If any matches are found, the matching values are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier. |
newid | the new identifier. |
|
inherited |
Sets the XML namespace to which this object belongs.
"http://www.sbml.org/sbml/level3/version1/core"
. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/"
.uri | the URI to assign to this object. |
|
virtualinherited |
Sets the SBML "required" attribute value.
<sbml>
element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true
indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true
in any SBML document that uses the package.The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.
value | the value to be assigned to the "required" attribute. The "required" attribute takes a Boolean value, either true or false . |
Reimplemented in CompSBMLDocumentPlugin.
|
virtualinherited |
Unsets the value of the "required" attribute of this SBMLDocumentPlugin.