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, TreeNodeWithChangeSupport

public class Group
extends AbstractNamedSBase
implements UniqueNamedSBase

Since:

1.0

Version:

$Rev$

Author:

Nicolas Rodriguez, Clemens Wrzodek

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ListOf<Member>	listOfMembers

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
Group()
Group(Group group)
Group(int level, int version)

Method Summary

Modifier and Type	Method and Description
boolean	addMember(Member member)
boolean	addMemberConstraint(MemberConstraint memberConstraint) Adds a new MemberConstraint to the listOfMemberConstraints.
Group	clone()
Member	createMember(String id) Creates a new instance of Member and add it to this Group.
MemberConstraint	createMemberConstraint() Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list
MemberConstraint	createMemberConstraint(String id) Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list
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.
boolean	equals(Object obj)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
GroupKind	getKind()
ListOf<MemberConstraint>	getListOfMemberConstraints() Returns the listOfMemberConstraints.
ListOf<Member>	getListOfMembers()
Member	getMember(int i)
int	getMemberConstraintCount() Returns the number of MemberConstraints of this Group.
int	getMemberCount() Returns the number of Members of this Group.
int	getNumMemberConstraints() Returns the number of MemberConstraints of this Group.
int	getNumMembers() Returns the number of Members of this Group.
int	hashCode()
boolean	isIdMandatory()
boolean	isSetKind()
boolean	isSetListOfMemberConstraints() Returns true, if listOfMemberConstraints contains at least one element.
boolean	isSetListOfMembers()
boolean	readAttribute(String attributeName, String prefix, String value)
void	removeMemberConstraint(int i) Removes an element from the listOfMemberConstraints at the given index.
boolean	removeMemberConstraint(MemberConstraint memberConstraint) Removes an element from the listOfMemberConstraints.
void	removeMemberConstraint(String id)
void	setKind(GroupKind kind)
void	setListOfMemberConstraints(ListOfMemberConstraint listOfMemberConstraints) Sets the given ListOf<MemberConstraint>.
String	toString()
boolean	unsetListOfMemberConstraints() Returns true, if listOfMemberConstraints contain at least one element, otherwise false
boolean	unsetListOfMembers() Removes the listOfMembers from this Model and notifies all registered instances of TreeNodeChangeListener.
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

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

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, 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, isLeaf, 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, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, 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 ListOf<Member> listOfMembers

Constructor Detail

Group

public Group()

Group

public Group(Group group)

Parameters:

group -

Group

public Group(int level,
             int version)

Parameters:

level -

version -

Method Detail

addMember

public boolean addMember(Member member)

clone

public Group clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

createMember

public Member createMember(String id)

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

Parameters:

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

Returns:

the new Member instance.

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.

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 GroupKind getKind()

Returns:

getListOfMembers

public ListOf<Member> getListOfMembers()

Returns:

getMember

public Member getMember(int i)

Parameters:

i -

Returns:

getMemberCount

public int getMemberCount()

Returns the number of Members of this Group.

Returns:

the number of Members of this Group.

getMemberConstraintCount

public int getMemberConstraintCount()

Returns the number of MemberConstraints of this Group.

Returns:

the number of MemberConstraints 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()

getNumMemberConstraints

public int getNumMemberConstraints()

Returns the number of MemberConstraints of this Group.

Returns:

the number of MemberConstraints of this Group.

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

same as getMemberConstraintCount()

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

isSetKind

public boolean isSetKind()

Returns:

isSetListOfMembers

public boolean isSetListOfMembers()

Returns:

isSetListOfMemberConstraints

public boolean isSetListOfMemberConstraints()

Returns true, if listOfMemberConstraints contains at least one element.

Returns:

true, if listOfMemberConstraints contains at least one element, otherwise false

getListOfMemberConstraints

public ListOf<MemberConstraint> getListOfMemberConstraints()

Returns the listOfMemberConstraints. Creates it if it is not already existing.

Returns:

the listOfMemberConstraints

setListOfMemberConstraints

public void setListOfMemberConstraints(ListOfMemberConstraint listOfMemberConstraints)

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

Parameters:

listOfMemberConstraints -

unsetListOfMemberConstraints

public boolean unsetListOfMemberConstraints()

Returns true, if listOfMemberConstraints contain at least one element, otherwise false

Returns:

true, if listOfMemberConstraints contain at least one element, otherwise false

addMemberConstraint

public boolean addMemberConstraint(MemberConstraint memberConstraint)

Adds a new MemberConstraint to the listOfMemberConstraints.

The listOfMemberConstraints is initialized if necessary.

Parameters:

memberConstraint - the element to add to the list

Returns:

true (as specified by Collection#add)

removeMemberConstraint

public boolean removeMemberConstraint(MemberConstraint memberConstraint)

Removes an element from the listOfMemberConstraints.

Parameters:

memberConstraint - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List#remove(Object)

removeMemberConstraint

public void removeMemberConstraint(int i)

Removes an element from the listOfMemberConstraints at the given index.

Parameters:

i - the index where to remove the MemberConstraint

Throws:

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

removeMemberConstraint

public void removeMemberConstraint(String id)

createMemberConstraint

public MemberConstraint createMemberConstraint()

Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list

createMemberConstraint

public MemberConstraint createMemberConstraint(String id)

Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list

Returns:

a new MemberConstraint element

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractNamedSBase

setKind

public void setKind(GroupKind kind)

Parameters:

kind -

toString

public String toString()

Overrides:

toString in class AbstractNamedSBase

unsetListOfMembers

public boolean unsetListOfMembers()

Removes the listOfMembers from this Model and notifies all registered instances of TreeNodeChangeListener.

Returns:

true if calling this method lead to a change in this data structure.

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractNamedSBase

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 AbstractNamedSBase

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractNamedSBase