GroupsModelPlugin (LibSBML Java API)

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

public class GroupsModelPlugin
extends SBasePlugin

groups Extension of Model.

Constructor Summary

Constructors
Constructor and Description
`GroupsModelPlugin(GroupsModelPlugin orig)` Copy constructor for `GroupsModelPlugin`.
`GroupsModelPlugin(java.lang.String uri, java.lang.String prefix, GroupsPkgNamespaces groupsns)` Creates a new `GroupsModelPlugin` using the given URI, prefix and package namespace.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addGroup(Group g)` Adds a copy of the given `Group` to this `GroupsModelPlugin`.
`SBasePlugin`	`cloneObject()` Creates and returns a deep copy of this `GroupsModelPlugin` object.
`void`	`copyInformationToNestedLists()` For nested groups (Member objects that reference a `ListOfMembers` object), `SBO` terms, Notes, and Annotation from the parent `ListOfMembers` applies to the child.
`Group`	`createGroup()` Creates a new `Group` object, adds it to this `GroupsModelPlugin` object and returns the `Group` object created.
`void`	`delete()` Explicitly deletes the underlying native object.
`SBase`	`getElementByMetaId(java.lang.String metaid)` Returns the first child element that has the given `metaid`, or `null` if no such object is found.
`SBase`	`getElementBySId(java.lang.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.
`Group`	`getGroup(long n)` Get a `Group` from the `GroupsModelPlugin`.
`Group`	`getGroup(java.lang.String sid)` Get a `Group` from the `GroupsModelPlugin` based on its identifier.
`ListOfGroups`	`getListOfGroups()` Returns the `ListOfGroups` from this `GroupsModelPlugin`.
`long`	`getNumGroups()` Get the number of `Group` objects in this `GroupsModelPlugin`.
`Group`	`removeGroup(long n)` Removes the nth `Group` from this `GroupsModelPlugin` and returns a pointer to it.
`Group`	`removeGroup(java.lang.String sid)` Removes the `Group` from this `GroupsModelPlugin` based on its identifier and returns a pointer to it.

Methods inherited from class org.sbml.libsbml.SBasePlugin
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
  - GroupsModelPlugin
```
public GroupsModelPlugin(java.lang.String uri,
                         java.lang.String prefix,
                         GroupsPkgNamespaces groupsns)
```
    Creates a new GroupsModelPlugin using the given URI, prefix and package namespace.
    
    Parameters:
    
    uri - a string, representing the URI of the SBML Level 3 package implemented by this libSBML package extension.
    
    prefix - a string, the XML namespace prefix being used for this package.
    
    groupsns - a pointer to the namesspaces object (GroupsPkgNamespaces) for this package.
    
    In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI '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/'.
    
    The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
  - GroupsModelPlugin
```
public GroupsModelPlugin(GroupsModelPlugin orig)
```
    Copy constructor for GroupsModelPlugin.
    
    Parameters:
    
    orig - the GroupsModelPlugin instance to copy.
- 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 GroupsModelPlugin.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 GroupsModelPlugin.delete() themselves.
    
    Overrides:
    
    delete in class SBasePlugin
  - cloneObject
```
public SBasePlugin cloneObject()
```
    Creates and returns a deep copy of this GroupsModelPlugin object.
    
    Overrides:
    
    cloneObject in class SBasePlugin
    
    Returns:
    
    a (deep) copy of this GroupsModelPlugin object.
  - getListOfGroups
```
public ListOfGroups getListOfGroups()
```
    Returns the ListOfGroups from this GroupsModelPlugin.
    
    Returns:
    
    the ListOfGroups from this GroupsModelPlugin.
    
    The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
    
    See Also:
    
    GroupsModelPlugin.addGroup(Group object), GroupsModelPlugin.createGroup(), GroupsModelPlugin.getGroup(String sid), GroupsModelPlugin.getGroup(long n), GroupsModelPlugin.getNumGroups(), GroupsModelPlugin.removeGroup(String sid), GroupsModelPlugin.removeGroup(long n)
  - getGroup
```
public Group getGroup(long n)
```
    Get a Group from the GroupsModelPlugin.
    
    Parameters:
    
    n - a long integer representing the index of the Group to retrieve.
    
    Returns:
    
    the nth Group in the ListOfGroups within this GroupsModelPlugin.
    
    The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
    
    See Also:
    
    GroupsModelPlugin.addGroup(Group object), GroupsModelPlugin.createGroup(), GroupsModelPlugin.getGroup(String sid), GroupsModelPlugin.getNumGroups(), GroupsModelPlugin.removeGroup(String sid), GroupsModelPlugin.removeGroup(long n)
  - getGroup
```
public Group getGroup(java.lang.String sid)
```
    Get a Group from the GroupsModelPlugin based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the Group to retrieve.
    
    Returns:
    
    the Group in the ListOfGroups within this GroupsModelPlugin with the given sid or null if no such Group exists.
    
    The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
    
    See Also:
    
    GroupsModelPlugin.addGroup(Group object), GroupsModelPlugin.createGroup(), GroupsModelPlugin.getGroup(long n), GroupsModelPlugin.getNumGroups(), GroupsModelPlugin.removeGroup(String sid), GroupsModelPlugin.removeGroup(long n)
  - addGroup
```
public int addGroup(Group g)
```
    Adds a copy of the given Group to this GroupsModelPlugin.
    Parameters:
    
    g - the Group object to add.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    LIBSBML_INVALID_OBJECT
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
    LIBSBML_DUPLICATE_OBJECT_ID
    See Also:
    
    GroupsModelPlugin.createGroup(), GroupsModelPlugin.getGroup(String sid), GroupsModelPlugin.getGroup(long n), GroupsModelPlugin.getNumGroups(), GroupsModelPlugin.removeGroup(String sid), GroupsModelPlugin.removeGroup(long n)
    
    "Note:"
    
    This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
  - getNumGroups
```
public long getNumGroups()
```
    Get the number of Group objects in this GroupsModelPlugin.
    
    Returns:
    
    the number of Group objects in this GroupsModelPlugin.
    
    See Also:
    
    GroupsModelPlugin.addGroup(Group object), GroupsModelPlugin.createGroup(), GroupsModelPlugin.getGroup(String sid), GroupsModelPlugin.getGroup(long n), GroupsModelPlugin.removeGroup(String sid), GroupsModelPlugin.removeGroup(long n)
  - createGroup
```
public Group createGroup()
```
    Creates a new Group object, adds it to this GroupsModelPlugin object and returns the Group object created.
    
    Returns:
    
    a new Group object instance.
    
    The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
    
    See Also:
    
    GroupsModelPlugin.addGroup(Group object), GroupsModelPlugin.getGroup(String sid), GroupsModelPlugin.getGroup(long n), GroupsModelPlugin.getNumGroups(), GroupsModelPlugin.removeGroup(String sid), GroupsModelPlugin.removeGroup(long n)
  - removeGroup
```
public Group removeGroup(long n)
```
    Removes the nth Group from this GroupsModelPlugin and returns a pointer to it.
    
    Parameters:
    
    n - a long integer representing the index of the Group to remove.
    
    Returns:
    
    a pointer to the nth Group in this GroupsModelPlugin.
    
    The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the 'disownedItem' in the * ListOf#appendAndOwn() or ListOf#insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.
    
    See Also:
    
    GroupsModelPlugin.addGroup(Group object), GroupsModelPlugin.createGroup(), GroupsModelPlugin.getGroup(String sid), GroupsModelPlugin.getGroup(long n), GroupsModelPlugin.getNumGroups(), GroupsModelPlugin.removeGroup(String sid)
  - removeGroup
```
public Group removeGroup(java.lang.String sid)
```
    Removes the Group from this GroupsModelPlugin based on its identifier and returns a pointer to it.
    
    Parameters:
    
    sid - a string representing the identifier of the Group to remove.
    
    Returns:
    
    the Group in this GroupsModelPlugin based on the identifier or null if no such Group exists.
    
    The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the 'disownedItem' in the * ListOf#appendAndOwn() or ListOf#insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.
    
    See Also:
    
    GroupsModelPlugin.addGroup(Group object), GroupsModelPlugin.createGroup(), GroupsModelPlugin.getGroup(String sid), GroupsModelPlugin.getGroup(long n), GroupsModelPlugin.getNumGroups(), GroupsModelPlugin.removeGroup(long n)
  - getElementBySId
```
public SBase getElementBySId(java.lang.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.
    
    Overrides:
    
    getElementBySId in class SBasePlugin
    
    Parameters:
    
    id - a string representing the id attribute of the object to retrieve.
    
    Returns:
    
    a pointer to the SBase element with the given id. If no such object is found, this method returns null.
  - getElementByMetaId
```
public SBase getElementByMetaId(java.lang.String metaid)
```
    Returns the first child element that has the given metaid, or null if no such object is found.
    
    Overrides:
    
    getElementByMetaId in class SBasePlugin
    
    Parameters:
    
    metaid - a string representing the metaid attribute of the object to retrieve.
    
    Returns:
    
    a pointer to the SBase element with the given metaid. If no such object is found this method returns null.
  - copyInformationToNestedLists
```
public void copyInformationToNestedLists()
```
    For nested groups (Member objects that reference a ListOfMembers object), SBO terms, Notes, and Annotation from the parent ListOfMembers applies to the child. This function copies any information from any of those three things to all child ListOfMembers, and if that information is not already set. After calling this function, it is sufficient to check any ListOfMembers to see if its SBO term, Notes, or Annotation is set, without further checking to see if that element was nested in another Group.

Class GroupsModelPlugin

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBasePlugin

Methods inherited from class java.lang.Object

Constructor Detail

GroupsModelPlugin

GroupsModelPlugin

Method Detail

delete

cloneObject

getListOfGroups

getGroup

getGroup

addGroup

getNumGroups

createGroup

removeGroup

removeGroup

getElementBySId

getElementByMetaId

copyInformationToNestedLists