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QualModelPlugin Class Reference
Inheritance diagram for QualModelPlugin:
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Detailed Description

{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 QualModelPluginclone () const
 Creates and returns a deep copy of this QualModelPlugin object. More...
 
QualitativeSpeciescreateQualitativeSpecies ()
 Creates a new qual object and adds it to the list of qual objects and returns it. More...
 
TransitioncreateTransition ()
 Creates a new qual object and adds it to the list of qual objects and returns it. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects, including those nested to an arbitary depth. More...
 
virtual SBasegetElementByMetaId (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 SBasegetElementBySId (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 ListOfQualitativeSpeciesgetListOfQualitativeSpecies () const
 Returns the ListOfQualitativeSpecies in this plugin object. More...
 
ListOfQualitativeSpeciesgetListOfQualitativeSpecies ()
 Returns the ListOfQualitativeSpecies in this plugin object. More...
 
const ListOfTransitionsgetListOfTransitions () const
 Returns the ListOfTransitions in this plugin object. More...
 
ListOfTransitionsgetListOfTransitions ()
 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...
 
SBasegetParentSBMLObject ()
 Returns the parent SBase object to which this plugin object connected. More...
 
const SBasegetParentSBMLObject () 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 QualitativeSpeciesgetQualitativeSpecies (unsigned int n) const
 Returns the QualitativeSpecies object that belongs to the given index. More...
 
QualitativeSpeciesgetQualitativeSpecies (unsigned int n)
 Returns the QualitativeSpecies object that belongs to the given index. More...
 
QualitativeSpeciesgetQualitativeSpecies (const std::string &sid)
 Returns the qualitativeSpecies object based on its identifier. More...
 
const QualitativeSpeciesgetQualitativeSpecies (const std::string &sid) const
 Returns the qualitativeSpecies object based on its identifier. More...
 
SBMLDocumentgetSBMLDocument ()
 Returns the parent SBMLDocument of this plugin object. More...
 
const SBMLDocumentgetSBMLDocument () const
 Returns the parent SBMLDocument of this plugin object. More...
 
const TransitiongetTransition (unsigned int n) const
 Returns the Transition object that belongs to the given index. More...
 
TransitiongetTransition (unsigned int n)
 Returns the Transition object that belongs to the given index. More...
 
TransitiongetTransition (const std::string &sid)
 Returns the qualitativeSpecies object based on its identifier. More...
 
const TransitiongetTransition (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...
 
QualModelPluginoperator= (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...
 
QualitativeSpeciesremoveQualitativeSpecies (unsigned int n)
 Removes the nth QualitativeSpecies object from this plugin object and returns a pointer to it. More...
 
QualitativeSpeciesremoveQualitativeSpecies (const std::string &sid)
 Removes the QualitativeSpecies object with the given id attribute from this plugin object and returns a pointer to it. More...
 
TransitionremoveTransition (unsigned int n)
 Removes the nth Transition object from this plugin object and returns a pointer to it. More...
 
TransitionremoveTransition (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...
 

Constructor & Destructor Documentation

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.

QualModelPlugin::~QualModelPlugin ( )
virtual

Destroy this object.

Member Function Documentation

int QualModelPlugin::addQualitativeSpecies ( const QualitativeSpecies qualitativeSpecies)

Adds a copy of the given QualitativeSpecies object to the list of qual.

Parameters
qualitativeSpeciesthe QualitativeSpecies object to be added to the list of qual.
Returns
integer value indicating success/failure of the operation. The possible return values are:
int QualModelPlugin::addTransition ( const Transition transition)

Adds a copy of the given Transition object to the list of qual.

Parameters
transitionthe Transition object to be added to the list of qual.
Returns
integer value indicating success/failure of the operation. The possible return values are:
QualModelPlugin * QualModelPlugin::clone ( ) const
virtual

Creates and returns a deep copy of this QualModelPlugin object.

Returns
a (deep) copy of this SBase object

Implements SBasePlugin.

QualitativeSpecies* QualModelPlugin::createQualitativeSpecies ( )

Creates a new qual object and adds it to the list of qual objects and returns it.

Returns
a newly created QualitativeSpecies object
Transition* QualModelPlugin::createTransition ( )

Creates a new qual object and adds it to the list of qual objects and returns it.

Returns
a newly created Transition object
List * QualModelPlugin::getAllElements ( ElementFilter *  filter = NULL)
virtual

Returns a List of all child SBase objects, including those nested to an arbitary depth.

Returns
a List* of pointers to all child objects.

Reimplemented from SBasePlugin.

SBase * SBasePlugin::getElementByMetaId ( const std::string &  metaid)
virtualinherited

Returns the first child element it can find with the given metaid, or NULL if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.

Reimplemented in FbcModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

SBase * SBasePlugin::getElementBySId ( const std::string &  id)
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.

Parameters
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.

Reimplemented in FbcModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

const std::string & SBasePlugin::getElementNamespace ( ) const
inherited

Returns the XML namespace (URI) of the package extension of this plugin object.

Returns
the URI of the package extension of this plugin object.
unsigned int SBasePlugin::getLevel ( ) const
inherited

Returns the SBML level of the package extension of this plugin object.

Returns
the SBML level of the package extension of this plugin object.
const ListOfQualitativeSpecies* QualModelPlugin::getListOfQualitativeSpecies ( ) const

Returns the ListOfQualitativeSpecies in this plugin object.

Returns
ListOfQualitativeSpecies object in this plugin object.
ListOfQualitativeSpecies* QualModelPlugin::getListOfQualitativeSpecies ( )

Returns the ListOfQualitativeSpecies in this plugin object.

Returns
ListOfQualitativeSpecies object in this plugin object.
const ListOfTransitions* QualModelPlugin::getListOfTransitions ( ) const

Returns the ListOfTransitions in this plugin object.

Returns
ListOfTransitions object in this plugin object.
ListOfTransitions* QualModelPlugin::getListOfTransitions ( )

Returns the ListOfTransitions in this plugin object.

Returns
ListOfTransitions object in this plugin object.
unsigned int QualModelPlugin::getNumQualitativeSpecies ( ) const

Returns the number of QualitativeSpecies object in this plugin object.

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.

Returns
the number of Transition object in this plugin object.
const std::string & SBasePlugin::getPackageName ( ) const
inherited

Returns the package name of this plugin object.

Returns
the package name of this plugin object.
unsigned int SBasePlugin::getPackageVersion ( ) const
inherited

Returns the package version of the package extension of this plugin object.

Returns
the package version of the package extension of this plugin object.
SBase * SBasePlugin::getParentSBMLObject ( )
inherited

Returns the parent SBase object to which this plugin object connected.

Returns
the parent SBase object to which this plugin object connected.
const SBase * SBasePlugin::getParentSBMLObject ( ) const
inherited

Returns the parent SBase object to which this plugin object connected.

Returns
the parent SBase object to which this plugin object connected.
const std::string & SBasePlugin::getPrefix ( ) const
inherited

Returns the prefix of the package extension of this plugin object.

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.

Parameters
nthe index number of the QualitativeSpecies to get.
Returns
the nth QualitativeSpecies in the ListOfQualitativeSpecies.
QualitativeSpecies* QualModelPlugin::getQualitativeSpecies ( unsigned int  n)

Returns the QualitativeSpecies object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters
nthe index number of the QualitativeSpecies to get.
Returns
the nth QualitativeSpecies in the ListOfQualitativeSpecies.
QualitativeSpecies* QualModelPlugin::getQualitativeSpecies ( const std::string &  sid)

Returns the qualitativeSpecies object based on its identifier.

Parameters
sida string representing the identifier of the QualitativeSpecies to get.
Returns
QualitativeSpecies in the ListOfQualitativeSpecies with the given id or NULL if no such QualitativeSpecies exists.
See also
getQualitativeSpecies(unsigned int n)
getListOfQualitativeSpecies()
const QualitativeSpecies* QualModelPlugin::getQualitativeSpecies ( const std::string &  sid) const

Returns the qualitativeSpecies object based on its identifier.

Parameters
sida string representing the identifier of the QualitativeSpecies to get.
Returns
QualitativeSpecies in the ListOfQualitativeSpecies with the given id or NULL if no such QualitativeSpecies exists.
See also
getQualitativeSpecies(unsigned int n)
getListOfQualitativeSpecies()
SBMLDocument * SBasePlugin::getSBMLDocument ( )
inherited

Returns the parent SBMLDocument of this plugin object.

Returns
the parent SBMLDocument object of this plugin object.
const SBMLDocument * SBasePlugin::getSBMLDocument ( ) const
inherited

Returns the parent SBMLDocument of this plugin object.

Returns
the parent SBMLDocument object 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.

Parameters
nthe index number of the Transition to get.
Returns
the nth Transition in the ListOfTransitions.
Transition* QualModelPlugin::getTransition ( unsigned int  n)

Returns the Transition object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters
nthe index number of the Transition to get.
Returns
the nth Transition in the ListOfTransitions.
Transition* QualModelPlugin::getTransition ( const std::string &  sid)

Returns the qualitativeSpecies object based on its identifier.

Parameters
sida string representing the identifier of the Transition to get.
Returns
Transition in the ListOfTransitions with the given id or NULL if no such Transition exists.
See also
getTransition(unsigned int n)
getListOfTransitions()
const Transition* QualModelPlugin::getTransition ( const std::string &  sid) const

Returns the qualitativeSpecies object based on its identifier.

Parameters
sida string representing the identifier of the Transition to get.
Returns
Transition in the ListOfTransitions with the given id or NULL if no such Transition exists.
See also
getTransition(unsigned int n)
getListOfTransitions()
std::string SBasePlugin::getURI ( ) const
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

Returns
the URI this elements
See also
getPackageName()
getElementNamespace()
SBMLDocument::getSBMLNamespaces()
getSBMLDocument()
unsigned int SBasePlugin::getVersion ( ) const
inherited

Returns the SBML version of the package extension of this plugin object.

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.

Parameters
nthe index of the QualitativeSpecies object to remove
Returns
the QualitativeSpecies object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.
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.

Parameters
sidthe id attribute of the QualitativeSpecies object to remove
Returns
the QualitativeSpecies object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.
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.

Parameters
nthe index of the Transition object to remove
Returns
the Transition object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.
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.

Parameters
sidthe id attribute of the Transition object to remove
Returns
the Transition object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.
int SBasePlugin::setElementNamespace ( const std::string &  uri)
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/"

Returns
integer value indicating success/failure of the function. The possible values returned by this function are: