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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, UniqueNamedSBase, TreeNodeWithChangeSupport

public class Group
extends AbstractNamedSBase
implements UniqueNamedSBase

Since:

1.0

Version:

$Rev: 1714 $

Author:

Nicolas Rodriguez, Clemens Wrzodek

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private GroupKind	kind Defined in version 3 of the groups proposal.
private ListOfMemberConstraint	listOfMemberConstraints
protected ListOf<Member>	listOfMembers
private static long	serialVersionUID Generated serial version identifier.

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

Methods

Modifier and Type	Method and Description
boolean	addMember(Member member)
boolean	addMemberConstraint(MemberConstraint memberConstraint) Adds a new MemberConstraint to the listOfMemberConstraints.
Group	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
Member	createMember(java.lang.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(java.lang.String id) Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list
Member	createMemberWithIdRef(java.lang.String idRef) Creates a new instance of Member and add it to this Group.
Member	createMemberWithIdRef(java.lang.String id, java.lang.String idRef) Creates a new instance of Member and add it to this Group.
Member	createMemberWithMetaIdRef(java.lang.String metaIdRef) Creates a new instance of Member and add it to this Group.
Member	createMemberWithMetaIdRef(java.lang.String id, java.lang.String metaIdRef) Creates a new instance of Member and add it to this Group.
boolean	equals(java.lang.Object obj) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
boolean	getAllowsChildren()
javax.swing.tree.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() Returns a hash code value for this SBase instance.
private void	initDefaults()
boolean	isIdMandatory() This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isSetKind()
boolean	isSetListOfMemberConstraints() Returns true, if listOfMemberConstraints contains at least one element.
boolean	isSetListOfMembers()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
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(java.lang.String id)
void	setKind(GroupKind kind)
void	setListOfMemberConstraints(ListOfMemberConstraint listOfMemberConstraints) Sets the given ListOf<MemberConstraint>.
java.lang.String	toString() Returns the name of the component, if it is available.
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.
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes() Returns a map with all the attributes of this SBase that need to be written out in XML.

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

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

kind

private GroupKind kind

Defined in version 3 of the groups proposal.

listOfMembers

protected ListOf<Member> listOfMembers

listOfMemberConstraints

private ListOfMemberConstraint listOfMemberConstraints

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()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

createMember

public Member createMember(java.lang.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(java.lang.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(java.lang.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(java.lang.String id,
                           java.lang.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(java.lang.String id,
                               java.lang.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 javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.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.

getNumMemberConstraints

public int getNumMemberConstraints()

Returns the number of MemberConstraints of this Group.

Returns:

the number of MemberConstraints of this Group.

initDefaults

private void initDefaults()

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: NamedSBase

This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Returns:

true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.

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:

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

removeMemberConstraint

public void removeMemberConstraint(java.lang.String id)

createMemberConstraint

public MemberConstraint createMemberConstraint()

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

createMemberConstraint

public MemberConstraint createMemberConstraint(java.lang.String id)

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

Returns:

a new MemberConstraint element

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractNamedSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

setKind

public void setKind(GroupKind kind)

Parameters:

kind -

toString

public java.lang.String toString()

Description copied from class: AbstractNamedSBase

Returns the name of the component, if it is available. Otherwise, the identifier is returned. If both is not possible, the class name of this element is returned.

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 java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this SBase that need to be written out in XML.

The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractNamedSBase

Returns:

a Map containing the XML attributes of this object.

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractNamedSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

equals

public boolean equals(java.lang.Object obj)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractNamedSBase

Parameters:

obj - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.