org.sbml.jsbml.ext.groups

Class Group

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.groups.Group

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

public class Group
extends AbstractNamedSBase
implements UniqueNamedSBase

Since:

1.0

Author:

Nicolas Rodriguez, Clemens Wrzodek

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Group.Kind This is a collection of possible values for the kind attribute within a Group.

Field Summary

Fields

Modifier and Type	Field and Description
protected ListOfMembers	listOfMembers

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
Group() Creates a new Group instance.
Group(Group group) Creates a new Group instance from the given Group.
Group(int level, int version) Creates a new Group instance.

Method Summary

Modifier and Type	Method and Description
boolean	addMember(Member member) Adds a new Member to the listOfMembers.
Group	clone()
Member	createMember() Creates a new Member element and adds it to the listOfMembers list.
Member	createMember(String id) Creates a new Member element and adds it to the listOfMembers list.
Member	createMember(String id, SBase sbase)
Member	createMemberWithIdRef(String idRef) Creates a new instance of Member and add it to this Group.
Member	createMemberWithIdRef(String id, String idRef) Creates a new instance of Member and add it to this Group.
Member	createMemberWithMetaIdRef(String metaIdRef) Creates a new instance of Member and add it to this Group.
Member	createMemberWithMetaIdRef(String id, String metaIdRef) Creates a new instance of Member and add it to this Group.
Member	creteMember(SBase sbase)
boolean	equals(Object obj)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
Group.Kind	getKind()
ListOfMembers	getListOfMembers() Returns the listOfMembers.
Member	getMember(int i) Gets an element from the listOfMembers at the given index.
Member	getMember(String id) Gets an element from the listOfMembers, with the given id.
int	getMemberCount() Returns the number of Members of this Group.
int	getNumMembers() Returns the number of Members of this Group.
int	hashCode()
boolean	isIdMandatory()
boolean	isSetKind()
boolean	isSetListOfMembers() Returns true if listOfMembers is not null.
boolean	readAttribute(String attributeName, String prefix, String value)
Member	removeMember(int i) Removes an element from the listOfMembers at the given index.
boolean	removeMember(Member member) Removes an element from the listOfMembers.
Member	removeMember(String id) Removes an element from the listOfMembers.
void	setKind(Group.Kind kind)
void	setListOfMembers(ListOfMembers listOfMembers) Sets the given ListOf<Member>.
boolean	unsetListOfMembers() Returns true if listOfMembers contains at least one element, otherwise false.
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

Field Detail

listOfMembers

protected ListOfMembers listOfMembers

Constructor Detail

Group

public Group()

Creates a new Group instance.

Group

public Group(Group group)

Creates a new Group instance from the given Group.

Parameters:

group - the Group to clone

Group

public Group(int level,
             int version)

Creates a new Group instance.

Parameters:

level - the SBML level

version - the SBML version

Method Detail

clone

public Group clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

createMemberWithIdRef

public Member createMemberWithIdRef(String idRef)

Creates a new instance of Member and add it to this Group.

Parameters:

idRef - the identifier of an object elsewhere in the Model. An example value of idRef might be the identifier of a species in the model, or the identifier of another group.

Returns:

the new Member instance.

createMemberWithMetaIdRef

public Member createMemberWithMetaIdRef(String metaIdRef)

Creates a new instance of Member and add it to this Group.

Parameters:

metaIdRef -

Returns:

the new Member instance.

createMemberWithIdRef

public Member createMemberWithIdRef(String id,
                                    String idRef)

Creates a new instance of Member and add it to this Group.

Parameters:

id - the id to be set to the new Member.

idRef - the identifier of an object elsewhere in the Model. An example value of idRef might be the identifier of a species in the model, or the identifier of another group.

Returns:

the new Member instance.

createMemberWithMetaIdRef

public Member createMemberWithMetaIdRef(String id,
                                        String metaIdRef)

Creates a new instance of Member and add it to this Group.

Parameters:

id - the id to be set to the new Member.

metaIdRef -

Returns:

the new Member instance.

creteMember

public Member creteMember(SBase sbase)

Parameters:

sbase - the element that should be referenced as a new member of this Group.

Returns:

the newly created Member or null if the given SBase neither has a metaId nor an id.

See Also:

createMember(String, SBase)

createMember

public Member createMember(String id,
                           SBase sbase)

Parameters:

id - the identifier to be set for the new Member, can be null.

sbase - the element that should be referenced as a new member of this Group.

Returns:

the newly created Member or null if the given SBase neither has a metaId nor an id.

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSBase

getKind

public Group.Kind getKind()

Returns:

getListOfMembers

public ListOfMembers getListOfMembers()

Returns the listOfMembers. Creates it if it does not already exist.

Returns:

the listOfMembers.

isSetListOfMembers

public boolean isSetListOfMembers()

Returns true if listOfMembers is not null.

Returns:

true if listOfMembers is not null.

setListOfMembers

public void setListOfMembers(ListOfMembers listOfMembers)

Sets the given ListOf<Member>. If listOfMembers was defined before and contains some elements, they are all unset.

Parameters:

listOfMembers -

unsetListOfMembers

public boolean unsetListOfMembers()

Returns true if listOfMembers contains at least one element, otherwise false.

Returns:

true if listOfMembers contains at least one element, otherwise false.

addMember

public boolean addMember(Member member)

Adds a new Member to the listOfMembers.

The listOfMembers is initialized if necessary.

Parameters:

member - the element to add to the list

Returns:

true (as specified by Collection.add(E))

See Also:

Collection.add(Object)

removeMember

public boolean removeMember(Member member)

Removes an element from the listOfMembers.

Parameters:

member - the element to be removed from the list.

Returns:

true if the list contained the specified element and it was removed.

See Also:

List.remove(Object)

removeMember

public Member removeMember(String id)

Removes an element from the listOfMembers.

Parameters:

id - the id of the element to be removed from the list.

Returns:

the removed element, if it was successfully found and removed or null.

removeMember

public Member removeMember(int i)

Removes an element from the listOfMembers at the given index.

Parameters:

i - the index where to remove the Member.

Returns:

the specified element if it was successfully found and removed.

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound ((i < 0) || (i > listOfMembers)).

createMember

public Member createMember()

Creates a new Member element and adds it to the listOfMembers list.

Returns:

the newly created element, i.e., the last item in the listOfMembers

createMember

public Member createMember(String id)

Creates a new Member element and adds it to the listOfMembers list.

Parameters:

id - the identifier that is to be applied to the new element.

Returns:

the newly created Member element, which is the last element in the listOfMembers.

getMember

public Member getMember(int i)

Gets an element from the listOfMembers at the given index.

Parameters:

i - the index of the Member element to get.

Returns:

an element from the listOfMembers at the given index.

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).

getMember

public Member getMember(String id)

Gets an element from the listOfMembers, with the given id.

Parameters:

id - the id of the Member element to get.

Returns:

an element from the listOfMembers with the given id or null.

getMemberCount

public int getMemberCount()

Returns the number of Members of this Group.

Returns:

the number of Members of this Group.

getNumMembers

public int getNumMembers()

Returns the number of Members of this Group.

Returns:

the number of Members of this Group.

Note: this method is kept here as it exist in libSBML.

same as getMemberCount()

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

isSetKind

public boolean isSetKind()

Returns:

readAttribute

public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

setKind

public void setKind(Group.Kind kind)

Parameters:

kind -

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase