QualModelPlugin (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBasePlugin
- - org.sbml.libsbml.QualModelPlugin

```
public class QualModelPlugin
extends SBasePlugin
```
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.

Constructor Summary

Constructors
Constructor and Description
`QualModelPlugin(QualModelPlugin orig)` Copy constructor.
`QualModelPlugin(java.lang.String uri, java.lang.String prefix, QualPkgNamespaces qualns)` Constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addQualitativeSpecies(QualitativeSpecies qualitativeSpecies)` Adds a copy of the given `QualitativeSpecies` object to the list of qual.
`int`	`addTransition(Transition transition)` Adds a copy of the given `Transition` object to the list of qual.
`SBasePlugin`	`cloneObject()` Creates and returns a deep copy of this `QualModelPlugin` object.
`QualitativeSpecies`	`createQualitativeSpecies()` Creates a new qual object and adds it to the list of qual objects and returns it.
`Transition`	`createTransition()` Creates a new qual object and adds it to the list of qual objects and returns it.
`void`	`delete()` Explicitly deletes the underlying native object.
`ListOfQualitativeSpecies`	`getListOfQualitativeSpecies()` Returns the `ListOfQualitativeSpecies` in this plugin object.
`ListOfTransitions`	`getListOfTransitions()` Returns the `ListOfTransitions` in this plugin object.
`long`	`getNumQualitativeSpecies()` Returns the number of `QualitativeSpecies` object in this plugin object.
`long`	`getNumTransitions()` Returns the number of `Transition` object in this plugin object.
`QualitativeSpecies`	`getQualitativeSpecies(long n)` Returns the `QualitativeSpecies` object that belongs to the given index.
`QualitativeSpecies`	`getQualitativeSpecies(java.lang.String sid)` Returns the qualitativeSpecies object based on its identifier.
`Transition`	`getTransition(long n)` Returns the `Transition` object that belongs to the given index.
`Transition`	`getTransition(java.lang.String sid)` Returns the qualitativeSpecies object based on its identifier.
`QualitativeSpecies`	`removeQualitativeSpecies(long n)` Removes the nth `QualitativeSpecies` object from this plugin object and returns a pointer to it.
`QualitativeSpecies`	`removeQualitativeSpecies(java.lang.String sid)` Removes the `QualitativeSpecies` object with the given id attribute from this plugin object and returns a pointer to it.
`Transition`	`removeTransition(long n)` Removes the nth `Transition` object from this plugin object and returns a pointer to it.
`Transition`	`removeTransition(java.lang.String sid)` Removes the `Transition` object with the given id attribute from this plugin object and returns a pointer to it.

Methods inherited from class org.sbml.libsbml.SBasePlugin
getElementByMetaId, getElementBySId, getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, isValidTypeForList, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, setElementNamespace

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - QualModelPlugin
```
public QualModelPlugin(java.lang.String uri,
                       java.lang.String prefix,
                       QualPkgNamespaces qualns)
```
    Constructor
  - QualModelPlugin
```
public QualModelPlugin(QualModelPlugin orig)
```
    Copy constructor. Creates a copy of this SBase object.
- Method Detail
  - delete
```
public void delete()
```
    Explicitly deletes the underlying native object.
    In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize() methods for the objects. The finalize() methods in turn call the QualModelPlugin.delete() method on the libSBML object.
    This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke QualModelPlugin.delete() themselves.
    
    Overrides:
    
    delete in class SBasePlugin
  - cloneObject
```
public SBasePlugin cloneObject()
```
    Creates and returns a deep copy of this QualModelPlugin object.
    
    Overrides:
    
    cloneObject in class SBasePlugin
    
    Returns:
    
    a (deep) copy of this SBase object
  - getListOfQualitativeSpecies
```
public ListOfQualitativeSpecies getListOfQualitativeSpecies()
```
    Returns the ListOfQualitativeSpecies in this plugin object.
    
    Returns:
    
    ListOfQualitativeSpecies object in this plugin object.
  - getQualitativeSpecies
```
public QualitativeSpecies getQualitativeSpecies(long n)
```
    Returns the QualitativeSpecies object that belongs to the given index. If the index is invalid, null is returned.
    
    Parameters:
    
    n - the index number of the QualitativeSpecies to get.
    
    Returns:
    
    the nth QualitativeSpecies in the ListOfQualitativeSpecies.
  - getQualitativeSpecies
```
public QualitativeSpecies getQualitativeSpecies(java.lang.String sid)
```
    Returns the qualitativeSpecies object based on its identifier.
    
    Parameters:
    
    sid - a 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:
    
    QualModelPlugin.getQualitativeSpecies(long n), QualModelPlugin.getListOfQualitativeSpecies()
  - addQualitativeSpecies
```
public int addQualitativeSpecies(QualitativeSpecies qualitativeSpecies)
```
    Adds a copy of the given QualitativeSpecies object to the list of qual.
    Parameters:
    
    qualitativeSpecies - the QualitativeSpecies object to be added to the list of qual.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
  - createQualitativeSpecies
```
public QualitativeSpecies createQualitativeSpecies()
```
    Creates a new qual object and adds it to the list of qual objects and returns it.
    
    Returns:
    
    a newly created QualitativeSpecies object
  - removeQualitativeSpecies
```
public QualitativeSpecies removeQualitativeSpecies(long 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:
    
    n - the 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.
  - removeQualitativeSpecies
```
public QualitativeSpecies removeQualitativeSpecies(java.lang.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:
    
    sid - the 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.
  - getNumQualitativeSpecies
```
public long getNumQualitativeSpecies()
```
    Returns the number of QualitativeSpecies object in this plugin object.
    
    Returns:
    
    the number of QualitativeSpecies object in this plugin object.
  - getListOfTransitions
```
public ListOfTransitions getListOfTransitions()
```
    Returns the ListOfTransitions in this plugin object.
    
    Returns:
    
    ListOfTransitions object in this plugin object.
  - getTransition
```
public Transition getTransition(long n)
```
    Returns the Transition object that belongs to the given index. If the index is invalid, null is returned.
    
    Parameters:
    
    n - the index number of the Transition to get.
    
    Returns:
    
    the nth Transition in the ListOfTransitions.
  - getTransition
```
public Transition getTransition(java.lang.String sid)
```
    Returns the qualitativeSpecies object based on its identifier.
    
    Parameters:
    
    sid - a 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:
    
    QualModelPlugin.getTransition(long n), QualModelPlugin.getListOfTransitions()
  - addTransition
```
public int addTransition(Transition transition)
```
    Adds a copy of the given Transition object to the list of qual.
    Parameters:
    
    transition - the Transition object to be added to the list of qual.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
  - createTransition
```
public Transition createTransition()
```
    Creates a new qual object and adds it to the list of qual objects and returns it.
    
    Returns:
    
    a newly created Transition object
  - removeTransition
```
public Transition removeTransition(long 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:
    
    n - the 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.
  - removeTransition
```
public Transition removeTransition(java.lang.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:
    
    sid - the 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.
  - getNumTransitions
```
public long getNumTransitions()
```
    Returns the number of Transition object in this plugin object.
    
    Returns:
    
    the number of Transition object in this plugin object.

Class QualModelPlugin

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBasePlugin

Methods inherited from class java.lang.Object

Constructor Detail

QualModelPlugin

QualModelPlugin

Method Detail

delete

cloneObject

getListOfQualitativeSpecies

getQualitativeSpecies

getQualitativeSpecies

addQualitativeSpecies

createQualitativeSpecies

removeQualitativeSpecies

removeQualitativeSpecies

getNumQualitativeSpecies

getListOfTransitions

getTransition

getTransition

addTransition

createTransition

removeTransition

removeTransition

getNumTransitions