libSBML C++ API
5.11.0
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The extension of SBML Level 3 Core's Model class is relatively straightforward: the Qualitative Models Package adds two lists, one for holding qualitativeSpecies (ListOfQualitativeSpecies), and the other for holding transitions (ListOfTransitions). The Model element may contain at most one ListOfQualitativeSpecies, which must contain at least one QualitativeSpecies. It may also contain at most one ListOfTransitions which must contain at least one Transition.
Public Member Functions | |
int | addQualitativeSpecies (const QualitativeSpecies *qualitativeSpecies) |
Adds a copy of the given QualitativeSpecies object to the list of qual. More... | |
int | addTransition (const Transition *transition) |
Adds a copy of the given Transition object to the list of qual. More... | |
virtual QualModelPlugin * | clone () const |
Creates and returns a deep copy of this QualModelPlugin object. More... | |
QualitativeSpecies * | createQualitativeSpecies () |
Creates a new qual object and adds it to the list of qual objects and returns it. More... | |
Transition * | createTransition () |
Creates a new qual object and adds it to the list of qual objects and returns it. 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 ListOfQualitativeSpecies * | getListOfQualitativeSpecies () const |
Returns the ListOfQualitativeSpecies in this plugin object. More... | |
ListOfQualitativeSpecies * | getListOfQualitativeSpecies () |
Returns the ListOfQualitativeSpecies in this plugin object. More... | |
const ListOfTransitions * | getListOfTransitions () const |
Returns the ListOfTransitions in this plugin object. More... | |
ListOfTransitions * | getListOfTransitions () |
Returns the ListOfTransitions in this plugin object. More... | |
unsigned int | getNumQualitativeSpecies () const |
Returns the number of QualitativeSpecies object in this plugin object. More... | |
unsigned int | getNumTransitions () const |
Returns the number of Transition object in 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... | |
const QualitativeSpecies * | getQualitativeSpecies (unsigned int n) const |
Returns the QualitativeSpecies object that belongs to the given index. More... | |
QualitativeSpecies * | getQualitativeSpecies (unsigned int n) |
Returns the QualitativeSpecies object that belongs to the given index. More... | |
QualitativeSpecies * | getQualitativeSpecies (const std::string &sid) |
Returns the qualitativeSpecies object based on its identifier. More... | |
const QualitativeSpecies * | getQualitativeSpecies (const std::string &sid) const |
Returns the qualitativeSpecies object based on its identifier. 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 Transition * | getTransition (unsigned int n) const |
Returns the Transition object that belongs to the given index. More... | |
Transition * | getTransition (unsigned int n) |
Returns the Transition object that belongs to the given index. More... | |
Transition * | getTransition (const std::string &sid) |
Returns the qualitativeSpecies object based on its identifier. More... | |
const Transition * | getTransition (const std::string &sid) const |
Returns the qualitativeSpecies object based on its identifier. 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... | |
QualModelPlugin & | operator= (const QualModelPlugin &orig) |
Assignment operator for QualModelPlugin. More... | |
QualModelPlugin (const std::string &uri, const std::string &prefix, QualPkgNamespaces *qualns) | |
Constructor. More... | |
QualModelPlugin (const QualModelPlugin &orig) | |
Copy constructor. More... | |
QualitativeSpecies * | removeQualitativeSpecies (unsigned int n) |
Removes the nth QualitativeSpecies object from this plugin object and returns a pointer to it. More... | |
QualitativeSpecies * | removeQualitativeSpecies (const std::string &sid) |
Removes the QualitativeSpecies object with the given id attribute from this plugin object and returns a pointer to it. More... | |
Transition * | removeTransition (unsigned int n) |
Removes the nth Transition object from this plugin object and returns a pointer to it. More... | |
Transition * | removeTransition (const std::string &sid) |
Removes the Transition object with the given id attribute from this plugin object and returns a pointer to it. More... | |
int | setElementNamespace (const std::string &uri) |
Sets the XML namespace to which this object belongs. More... | |
virtual | ~QualModelPlugin () |
Destroy this object. More... | |
QualModelPlugin::QualModelPlugin | ( | const std::string & | uri, |
const std::string & | prefix, | ||
QualPkgNamespaces * | qualns | ||
) |
Constructor.
QualModelPlugin::QualModelPlugin | ( | const QualModelPlugin & | orig | ) |
Copy constructor.
Creates a copy of this SBase object.
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virtual |
Destroy this object.
int QualModelPlugin::addQualitativeSpecies | ( | const QualitativeSpecies * | qualitativeSpecies | ) |
Adds a copy of the given QualitativeSpecies object to the list of qual.
qualitativeSpecies | the QualitativeSpecies object to be added to the list of qual. |
int QualModelPlugin::addTransition | ( | const Transition * | transition | ) |
Adds a copy of the given Transition object to the list of qual.
transition | the Transition object to be added to the list of qual. |
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virtual |
Creates and returns a deep copy of this QualModelPlugin object.
Implements SBasePlugin.
QualitativeSpecies* QualModelPlugin::createQualitativeSpecies | ( | ) |
Creates a new qual object and adds it to the list of qual objects and returns it.
Transition* QualModelPlugin::createTransition | ( | ) |
Creates a new qual object and adds it to the list of qual objects and returns it.
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virtual |
Returns a List of all child SBase objects, including those nested to an arbitary depth.
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 FbcModelPlugin, 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 FbcModelPlugin, 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 ListOfQualitativeSpecies* QualModelPlugin::getListOfQualitativeSpecies | ( | ) | const |
Returns the ListOfQualitativeSpecies in this plugin object.
ListOfQualitativeSpecies* QualModelPlugin::getListOfQualitativeSpecies | ( | ) |
Returns the ListOfQualitativeSpecies in this plugin object.
const ListOfTransitions* QualModelPlugin::getListOfTransitions | ( | ) | const |
Returns the ListOfTransitions in this plugin object.
ListOfTransitions* QualModelPlugin::getListOfTransitions | ( | ) |
Returns the ListOfTransitions in this plugin object.
unsigned int QualModelPlugin::getNumQualitativeSpecies | ( | ) | const |
Returns the number of QualitativeSpecies object in this plugin object.
unsigned int QualModelPlugin::getNumTransitions | ( | ) | const |
Returns the number of Transition object in this plugin object.
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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.
const QualitativeSpecies* QualModelPlugin::getQualitativeSpecies | ( | unsigned int | n | ) | const |
Returns the QualitativeSpecies object that belongs to the given index.
If the index is invalid, NULL is returned.
n | the index number of the QualitativeSpecies to get. |
QualitativeSpecies* QualModelPlugin::getQualitativeSpecies | ( | unsigned int | n | ) |
Returns the QualitativeSpecies object that belongs to the given index.
If the index is invalid, NULL is returned.
n | the index number of the QualitativeSpecies to get. |
QualitativeSpecies* QualModelPlugin::getQualitativeSpecies | ( | const std::string & | sid | ) |
Returns the qualitativeSpecies object based on its identifier.
sid | a string representing the identifier of the QualitativeSpecies to get. |
const QualitativeSpecies* QualModelPlugin::getQualitativeSpecies | ( | const std::string & | sid | ) | const |
Returns the qualitativeSpecies object based on its identifier.
sid | a string representing the identifier of the QualitativeSpecies to get. |
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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 Transition* QualModelPlugin::getTransition | ( | unsigned int | n | ) | const |
Returns the Transition object that belongs to the given index.
If the index is invalid, NULL is returned.
n | the index number of the Transition to get. |
Transition* QualModelPlugin::getTransition | ( | unsigned int | n | ) |
Returns the Transition object that belongs to the given index.
If the index is invalid, NULL is returned.
n | the index number of the Transition to get. |
Transition* QualModelPlugin::getTransition | ( | const std::string & | sid | ) |
Returns the qualitativeSpecies object based on its identifier.
sid | a string representing the identifier of the Transition to get. |
const Transition* QualModelPlugin::getTransition | ( | const std::string & | sid | ) | const |
Returns the qualitativeSpecies object based on its identifier.
sid | a string representing the identifier of the Transition to get. |
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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.
QualModelPlugin & QualModelPlugin::operator= | ( | const QualModelPlugin & | orig | ) |
Assignment operator for QualModelPlugin.
QualitativeSpecies* QualModelPlugin::removeQualitativeSpecies | ( | unsigned int | n | ) |
Removes the nth QualitativeSpecies object from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the QualitativeSpecies object to remove |
QualitativeSpecies* QualModelPlugin::removeQualitativeSpecies | ( | const std::string & | sid | ) |
Removes the QualitativeSpecies object with the given id attribute from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
sid | the id attribute of the QualitativeSpecies object to remove |
Transition* QualModelPlugin::removeTransition | ( | unsigned int | n | ) |
Removes the nth Transition object from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Transition object to remove |
Transition* QualModelPlugin::removeTransition | ( | const std::string & | sid | ) |
Removes the Transition object with the given id attribute from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
sid | the id attribute of the Transition object to remove |
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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. |