libSBML Perl API
libSBML 5.17.2 Perl API
|
{qual}
qual Extension of Model.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 that has the given metaid , or NULL if no such object is found. More... | |
virtual SBase * | getElementBySId (const std::string &id) |
Returns the first child element 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 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... | |
virtual bool | isValidTypeForList (SBase *item) const |
QualModelPlugin & | operator= (const QualModelPlugin &orig) |
Assignment operator for QualModelPlugin. More... | |
QualModelPlugin (const std::string &uri, const std::string &prefix, QualPkgNamespaces *qualns) | |
Creates a new QualModelPlugin object using the given parameters. 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... | |
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 | ~QualModelPlugin () |
Destroy this object. More... | |
QualModelPlugin::QualModelPlugin | ( | const std::string & | uri, |
const std::string & | prefix, | ||
QualPkgNamespaces * | qualns | ||
) |
Creates a new QualModelPlugin object using the given parameters.
"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. |
qualns | the namespaces object for the package. |
QualModelPlugin::QualModelPlugin | ( | const QualModelPlugin & | orig | ) |
Copy constructor.
Creates a copy of this object.
orig | the instance to copy. |
|
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.
Reimplemented from 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.
|
virtual |
Returns the first child element that has the given metaid
, or NULL
if no such object is found.
metaid | a string representing the metaid attribute of the object to retrieve. |
metaid
. Reimplemented from SBasePlugin.
|
virtual |
Returns the first child element that has the given id
in the model-wide SId namespace, or NULL
if no such object is found.
id | a string representing the id attribute of the object to retrieve. |
id
. Reimplemented from SBasePlugin.
|
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 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 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.
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. |
n
is invalid, NULL
is returned. 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. |
n
is invalid, NULL
is returned. 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. |
NULL
if no such QualitativeSpecies exists.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. |
NULL
if no such QualitativeSpecies exists.
|
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 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. |
n
is invalid, NULL
is returned. 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. |
n
is invalid, NULL
is returned. 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. |
NULL
if no such Transition exists.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. |
NULL
if no such Transition 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.
|
virtualinherited |
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. |
|
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. |