libSBML Perl API
libSBML 5.10.0 Perl API
|
{qual} Implementation of the 'qual' package extention to the Model construct.
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) |
Returns the first child element it can find with the given metaid , or NULL if no such object is found. More... | |
virtual SBase * | getElementBySId (const 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... | |
const std::string & | getElementNamespace () const |
Returns the XML namespace (URI) of the package extension of this plugin object. 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 package name of this plugin object. More... | |
unsigned int | getPackageVersion () const |
Returns the package version of the package extension of this plugin object. More... | |
SBase * | getParentSBMLObject () |
Returns the parent SBase object to which this plugin object connected. More... | |
const SBase * | getParentSBMLObject () const |
Returns the parent SBase object to which this plugin object connected. More... | |
const std::string & | getPrefix () const |
Returns the prefix of the package extension of this plugin object. 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 parent SBMLDocument of this plugin object. More... | |
const SBMLDocument * | getSBMLDocument () const |
Returns the parent SBMLDocument of this plugin object. 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 |
Gets the URI to which this element belongs to. More... | |
unsigned int | getVersion () const |
Returns the SBML version 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 element belongs to. 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.
|
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. |
|
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.
|
virtual |
Returns a List of all child SBase objects, including those nested to an arbitary depth.
Reimplemented from SBasePlugin.
|
virtualinherited |
Returns the first child element it can find with the given metaid
, or NULL
if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
. Reimplemented in FbcModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
|
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 of objects to find |
id
. Reimplemented in FbcModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
|
inherited |
Returns the XML namespace (URI) of the package extension of this plugin object.
|
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.
|
inherited |
Returns the package name of this plugin object.
|
inherited |
Returns the package version of the package extension of this plugin object.
|
inherited |
|
inherited |
|
inherited |
Returns the prefix of the package extension of this plugin object.
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. |
|
inherited |
Returns the parent SBMLDocument of this plugin object.
|
inherited |
Returns the parent SBMLDocument of this plugin 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. |
|
inherited |
Gets the URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/layout/version1/"
Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace
|
inherited |
Returns the SBML version 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 |
|
inherited |
Sets the XML namespace to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to "http://www.sbml.org/sbml/level3/version1/layout/version1/"