libSBML C++ API
5.18.0
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The MultiSpeciesPlugin class extends the Species class to have a new attribute "speciesType", and two extra optional ListOfOutwardBindingSites and ListOfSpeciesFeatures children. A species may have a ListOfOutwardBindingSites child and/or a ListOfSpeciesFeatures child only when its speciesType attribute has been defined. The relationship among the elements of a ListOfOutwardBindingSites or a ListOfSpeciesFeatures is "and".
Public Member Functions | |
int | addOutwardBindingSite (const OutwardBindingSite *outwardBindingSite) |
Adds a copy of the given OutwardBindingSite to the ListOfOutwardBindingSites. More... | |
int | addSpeciesFeature (const SpeciesFeature *speciesFeature) |
Adds a copy of the given SpeciesFeature to the ListOfSpeciesFeatures of this "multi" Species. More... | |
int | addSubListOfSpeciesFeatures (SubListOfSpeciesFeatures *subListOfSpeciesFeatures) |
Adds a copy of the given SubListOfSpeciesFeatures to the ListOfSpeciesFeatures. More... | |
virtual MultiSpeciesPlugin * | clone () const |
Creates and returns a deep copy of this MultiSpeciesPlugin object. More... | |
OutwardBindingSite * | createOutwardBindingSite () |
Creates a new OutwardBindingSite object and adds it to the ListOfOutwardBindingSites. More... | |
SpeciesFeature * | createSpeciesFeature () |
Creates a new SpeciesFeature object and adds it to the ListOfSpeciesFeatures of this "multi" Species. More... | |
SubListOfSpeciesFeatures * | createSubListOfSpeciesFeatures () |
Creates a new SubListOfSpeciesFeatures object and adds it to the SubListOfSpeciesFeatures. More... | |
virtual List * | getAllElements (ElementFilter *filter=NULL) |
Returns a List of all child SBase objects, including those nested to an arbitary depth. 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 ListOfOutwardBindingSites * | getListOfOutwardBindingSites () const |
Returns the ListOfOutwardBindingSites of this "multi" Species. More... | |
ListOfOutwardBindingSites * | getListOfOutwardBindingSites () |
Returns the ListOfOutwardBindingSites of this "multi" Species. More... | |
const ListOfSpeciesFeatures * | getListOfSpeciesFeatures () const |
Returns the ListOfSpeciesFeatures of this "multi" Species. More... | |
ListOfSpeciesFeatures * | getListOfSpeciesFeatures () |
Returns the ListOfSpeciesFeatures of this "multi" Species. More... | |
unsigned int | getNumOutwardBindingSites () const |
Returns the number of OutwardBindingSite objects of this "multi" Species. More... | |
unsigned int | getNumSpeciesFeatures () const |
Returns the number of SpeciesFeature objects of this "multi" Species. More... | |
unsigned int | getNumSubListOfSpeciesFeatures () const |
Returns the number of SubListOfSpeciesFeatures objects of this "multi" Species. More... | |
const OutwardBindingSite * | getOutwardBindingSite (unsigned int n) const |
Returns the nth OutwardBindingSite object. More... | |
OutwardBindingSite * | getOutwardBindingSite (unsigned int n) |
Returns the nth OutwardBindingSite object. More... | |
const OutwardBindingSite * | getOutwardBindingSite (const std::string &sid) const |
Returns the OutwardBindingSite object with the given identifier sid . More... | |
OutwardBindingSite * | getOutwardBindingSite (const std::string &sid) |
Returns the OutwardBindingSite object with the given identifier sid . 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... | |
SBMLDocument * | getSBMLDocument () |
Returns the SBMLDocument object containing this object instance. More... | |
const SBMLDocument * | getSBMLDocument () const |
Returns the SBMLDocument object containing this object instance. More... | |
const SpeciesFeature * | getSpeciesFeature (unsigned int n) const |
Returns the nth SpeciesFeature object. More... | |
SpeciesFeature * | getSpeciesFeature (unsigned int n) |
Returns the nth SpeciesFeature object. More... | |
const SpeciesFeature * | getSpeciesFeature (const std::string &sid) const |
Returns the SpeciesFeature object with the given identifier sid . More... | |
SpeciesFeature * | getSpeciesFeature (const std::string &sid) |
Returns the SpeciesFeature object with the given identifier sid . More... | |
virtual const std::string & | getSpeciesType () const |
Returns the value of the "speciesType" attribute of this "multi" Species. More... | |
const SubListOfSpeciesFeatures * | getSubListOfSpeciesFeatures (unsigned int n) const |
Returns the nth SubListOfSpeciesFeatures object. More... | |
SubListOfSpeciesFeatures * | getSubListOfSpeciesFeatures (unsigned int n) |
Returns the nth SubListOfSpeciesFeatures object. More... | |
const SubListOfSpeciesFeatures * | getSubListOfSpeciesFeatures (const std::string &sid) const |
Returns the SubListOfSpeciesFeatures object with the given identifier sid . More... | |
SubListOfSpeciesFeatures * | getSubListOfSpeciesFeatures (const std::string &sid) |
Returns the SubListOfSpeciesFeatures object with the given identifier sid . 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 | hasRequiredElements () const |
Returns true if this object has all the required elements. More... | |
virtual bool | isSetSpeciesType () const |
Returns true if the "speciesType" attribute of this "multi" Species has been set. More... | |
virtual bool | isValidTypeForList (SBase *item) const |
MultiSpeciesPlugin (const std::string &uri, const std::string &prefix, MultiPkgNamespaces *multins) | |
Creates a new MultiSpeciesPlugin object. More... | |
MultiSpeciesPlugin (const MultiSpeciesPlugin &orig) | |
Copy constructor for MultiSpeciesPlugin. More... | |
MultiSpeciesPlugin & | operator= (const MultiSpeciesPlugin &rhs) |
Assignment operator for MultiSpeciesPlugin. More... | |
OutwardBindingSite * | removeOutwardBindingSite (unsigned int n) |
Removes the nth OutwardBindingSite object and returns a pointer to it. More... | |
OutwardBindingSite * | removeOutwardBindingSite (const std::string &sid) |
Removes the OutwardBindingSite object with the given id sid and returns a pointer to it. More... | |
SpeciesFeature * | removeSpeciesFeature (unsigned int n) |
Removes the nth SpeciesFeature object and returns a pointer to it. More... | |
SpeciesFeature * | removeSpeciesFeature (const std::string &sid) |
Removes the SpeciesFeature object with the given identifier sid . More... | |
virtual void | renameMetaIdRefs (const std::string &oldid, const std::string &newid) |
Replaces all uses of a given meta identifier attribute value with another value. More... | |
virtual void | renameSIdRefs (const std::string &oldid, const std::string &newid) |
Replaces all uses of a given SIdRef type attribute value with another value. More... | |
virtual void | renameUnitSIdRefs (const std::string &oldid, const std::string &newid) |
Replaces all uses of a given UnitSIdRef type attribute value with another value. More... | |
int | setElementNamespace (const std::string &uri) |
Sets the XML namespace to which this object belongs. More... | |
virtual int | setSpeciesType (const std::string &speciesType) |
Sets the value of the "speciesType" attribute on this "multi" Species. More... | |
virtual int | unsetSpeciesType () |
Unsets the value of the "speciesType" attribute on this "multi" Species. More... | |
virtual | ~MultiSpeciesPlugin () |
Destructor for MultiSpeciesPlugin. More... | |
MultiSpeciesPlugin::MultiSpeciesPlugin | ( | const std::string & | uri, |
const std::string & | prefix, | ||
MultiPkgNamespaces * | multins | ||
) |
Creates a new MultiSpeciesPlugin object.
"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. |
multins | the namespaces object for the package. |
MultiSpeciesPlugin::MultiSpeciesPlugin | ( | const MultiSpeciesPlugin & | orig | ) |
Copy constructor for MultiSpeciesPlugin.
orig | the MultiSpeciesPlugin instance to copy. |
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virtual |
Destructor for MultiSpeciesPlugin.
int MultiSpeciesPlugin::addOutwardBindingSite | ( | const OutwardBindingSite * | outwardBindingSite | ) |
Adds a copy of the given OutwardBindingSite to the ListOfOutwardBindingSites.
outwardBindingSite | the outwardBindingSite to be added. |
int MultiSpeciesPlugin::addSpeciesFeature | ( | const SpeciesFeature * | speciesFeature | ) |
Adds a copy of the given SpeciesFeature to the ListOfSpeciesFeatures of this "multi" Species.
speciesFeature | the SpeciesFeature to be added. |
int MultiSpeciesPlugin::addSubListOfSpeciesFeatures | ( | SubListOfSpeciesFeatures * | subListOfSpeciesFeatures | ) |
Adds a copy of the given SubListOfSpeciesFeatures to the ListOfSpeciesFeatures.
subListOfSpeciesFeatures | the SubListOfSpeciesFeatures to be added. |
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virtual |
Creates and returns a deep copy of this MultiSpeciesPlugin object.
Reimplemented from SBasePlugin.
OutwardBindingSite * MultiSpeciesPlugin::createOutwardBindingSite | ( | ) |
Creates a new OutwardBindingSite object and adds it to the ListOfOutwardBindingSites.
SpeciesFeature * MultiSpeciesPlugin::createSpeciesFeature | ( | ) |
Creates a new SpeciesFeature object and adds it to the ListOfSpeciesFeatures of this "multi" Species.
SubListOfSpeciesFeatures * MultiSpeciesPlugin::createSubListOfSpeciesFeatures | ( | ) |
Creates a new SubListOfSpeciesFeatures object and adds it to the SubListOfSpeciesFeatures.
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virtual |
Returns a List of all child SBase objects, including those nested to an arbitary depth.
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 from SBasePlugin.
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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 QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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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 QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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inherited |
Returns the namespace URI of the package to which this plugin object belongs.
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inherited |
Returns the SBML Level of the package extension of this plugin object.
const ListOfOutwardBindingSites * MultiSpeciesPlugin::getListOfOutwardBindingSites | ( | ) | const |
Returns the ListOfOutwardBindingSites of this "multi" Species.
ListOfOutwardBindingSites * MultiSpeciesPlugin::getListOfOutwardBindingSites | ( | ) |
Returns the ListOfOutwardBindingSites of this "multi" Species.
const ListOfSpeciesFeatures * MultiSpeciesPlugin::getListOfSpeciesFeatures | ( | ) | const |
Returns the ListOfSpeciesFeatures of this "multi" Species.
ListOfSpeciesFeatures * MultiSpeciesPlugin::getListOfSpeciesFeatures | ( | ) |
Returns the ListOfSpeciesFeatures of this "multi" Species.
unsigned int MultiSpeciesPlugin::getNumOutwardBindingSites | ( | ) | const |
Returns the number of OutwardBindingSite objects of this "multi" Species.
unsigned int MultiSpeciesPlugin::getNumSpeciesFeatures | ( | ) | const |
Returns the number of SpeciesFeature objects of this "multi" Species.
unsigned int MultiSpeciesPlugin::getNumSubListOfSpeciesFeatures | ( | ) | const |
Returns the number of SubListOfSpeciesFeatures objects of this "multi" Species.
const OutwardBindingSite * MultiSpeciesPlugin::getOutwardBindingSite | ( | unsigned int | n | ) | const |
Returns the nth OutwardBindingSite object.
n | the index number of the OutwardBindingSite to get |
OutwardBindingSite * MultiSpeciesPlugin::getOutwardBindingSite | ( | unsigned int | n | ) |
Returns the nth OutwardBindingSite object.
n | the index number of the OutwardBindingSite to get |
const OutwardBindingSite * MultiSpeciesPlugin::getOutwardBindingSite | ( | const std::string & | sid | ) | const |
Returns the OutwardBindingSite object with the given identifier sid
.
sid | a string representing the id of the OutwardBindingSite to get. |
NULL
if no such OutwardBindingSite exists. OutwardBindingSite * MultiSpeciesPlugin::getOutwardBindingSite | ( | const std::string & | sid | ) |
Returns the OutwardBindingSite object with the given identifier sid
.
sid | a string representing the id of the OutwardBindingSite to get. |
NULL
if no such OutwardBindingSite exists.
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inherited |
Returns the short-form name of the package to which this plugin object belongs.
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inherited |
Returns the package version of the package extension of this plugin object.
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inherited |
Returns the parent object to which this plugin object is connected.
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inherited |
Returns the parent object to which this plugin object is connected.
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inherited |
Returns the XML namespace prefix of the package to which this plugin object belongs.
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inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
const SpeciesFeature * MultiSpeciesPlugin::getSpeciesFeature | ( | unsigned int | n | ) | const |
Returns the nth SpeciesFeature object.
n | the index number of the SpeciesFeature to get. |
SpeciesFeature * MultiSpeciesPlugin::getSpeciesFeature | ( | unsigned int | n | ) |
Returns the nth SpeciesFeature object.
n | the index number of the SpeciesFeature to get. |
const SpeciesFeature * MultiSpeciesPlugin::getSpeciesFeature | ( | const std::string & | sid | ) | const |
Returns the SpeciesFeature object with the given identifier sid
.
sid | a string representing the id of the SpeciesFeature to get |
sid
, or NULL
if no such SpeciesFeature exists. SpeciesFeature * MultiSpeciesPlugin::getSpeciesFeature | ( | const std::string & | sid | ) |
Returns the SpeciesFeature object with the given identifier sid
.
sid | a string representing the id of the SpeciesFeature to get |
sid
, or NULL
if no such SpeciesFeature exists.
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virtual |
Returns the value of the "speciesType" attribute of this "multi" Species.
const SubListOfSpeciesFeatures * MultiSpeciesPlugin::getSubListOfSpeciesFeatures | ( | unsigned int | n | ) | const |
Returns the nth SubListOfSpeciesFeatures object.
n | the index number of the SubListOfSpeciesFeatures to get |
SubListOfSpeciesFeatures * MultiSpeciesPlugin::getSubListOfSpeciesFeatures | ( | unsigned int | n | ) |
Returns the nth SubListOfSpeciesFeatures object.
n | the index number of the SubListOfSpeciesFeatures to get |
const SubListOfSpeciesFeatures * MultiSpeciesPlugin::getSubListOfSpeciesFeatures | ( | const std::string & | sid | ) | const |
Returns the SubListOfSpeciesFeatures object with the given identifier sid
.
sid | the id of the SubListOfSpeciesFeatures to get. |
sid
, or NULL
if no such SubListOfSpeciesFeatures exists. SubListOfSpeciesFeatures * MultiSpeciesPlugin::getSubListOfSpeciesFeatures | ( | const std::string & | sid | ) |
Returns the SubListOfSpeciesFeatures object with the given identifier sid
.
sid | the id of the SubListOfSpeciesFeatures to get. |
sid
, or NULL
if no such SubListOfSpeciesFeatures exists.
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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().
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inherited |
Returns the Version within the SBML Level of the package extension of this plugin object.
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virtual |
Returns true
if this object has all the required elements.
true
if this object has all the elements required by the package specification; otherwise, false
will be returned.
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virtual |
Returns true
if the "speciesType" attribute of this "multi" Species has been set.
true
if this SpeciesPlugin's "speciesType" attribute has been set, otherwise false
is returned.
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virtualinherited |
MultiSpeciesPlugin & MultiSpeciesPlugin::operator= | ( | const MultiSpeciesPlugin & | rhs | ) |
Assignment operator for MultiSpeciesPlugin.
rhs | the object whose values are used as the basis of the assignment |
OutwardBindingSite * MultiSpeciesPlugin::removeOutwardBindingSite | ( | unsigned int | n | ) |
Removes the nth OutwardBindingSite object and returns a pointer to it.
n | the index of the OutwardBindingSite to remove. |
NULL
index was out of range. Note that the caller owns the returned object and is responsible for deleting it. OutwardBindingSite * MultiSpeciesPlugin::removeOutwardBindingSite | ( | const std::string & | sid | ) |
Removes the OutwardBindingSite object with the given id sid
and returns a pointer to it.
sid | a string representing the id of the OutwardBindingSite to remove. |
NULL
index was out of range. Note that the caller owns the returned object and is responsible for deleting it. SpeciesFeature * MultiSpeciesPlugin::removeSpeciesFeature | ( | unsigned int | n | ) |
Removes the nth SpeciesFeature object and returns a pointer to it.
n | the index of the SpeciesFeature to remove. |
NULL
index was out of range. Note that the caller owns the returned object and is responsible for deleting it. SpeciesFeature * MultiSpeciesPlugin::removeSpeciesFeature | ( | const std::string & | sid | ) |
Removes the SpeciesFeature object with the given identifier sid
.
sid | a string representing the id of the SpeciesFeature to get. |
NULL
index was out of range. Note that the caller owns the returned object and is responsible for deleting it.
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virtualinherited |
Replaces all uses of a given meta identifier attribute value with another value.
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. |
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virtualinherited |
Replaces all uses of a given 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.
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virtualinherited |
Replaces all uses of a given 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. |
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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. |
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virtual |
Sets the value of the "speciesType" attribute on this "multi" Species.
speciesType | the new value for the attribute. |
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virtual |
Unsets the value of the "speciesType" attribute on this "multi" Species.