libSBML Perl API
libSBML 5.17.2 Perl API
|
{multi}
multi Extension of Species for the "multi" package.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) |
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 | 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. |
|
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. |
|
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.
|
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.
|
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.
|
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.
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.
|
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.
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.
|
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.
|
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.
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
virtualinherited |
|
virtualinherited |
Reimplemented in FbcReactionPlugin.
|
virtualinherited |
|
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. |
|
virtual |
Sets the value of the "speciesType" attribute on this "multi" Species.
speciesType | the new value for the attribute. |
|
virtual |
Unsets the value of the "speciesType" attribute on this "multi" Species.