Package 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, 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	Description
static class	Group.Kind	This is a collection of possible values for the kind attribute within a Group.

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

JSBML_WRONG_SBO_TERM

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
boolean	addMember(Member member)	Adds a new Member to the listOfMembers.
Group	clone()	Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
Member	createMember()	Creates a new Member element and adds it to the listOfMembers list.
Member	createMember(java.lang.String id)	Creates a new Member element and adds it to the listOfMembers list.
Member	createMember(java.lang.String id, SBase sbase)
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.
Member	creteMember(SBase sbase)
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()
Group.Kind	getKind()
ListOfMembers	getListOfMembers()	Returns the listOfMembers.
Member	getMember(int i)	Gets an element from the listOfMembers at the given index.
Member	getMember(java.lang.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()	Returns a hash code value for this SBase instance.
boolean	isIdMandatory()	Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isSetKind()
boolean	isSetListOfMembers()	Returns true if listOfMembers is not null.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)	Sets the given attribute in this SBase.
Member	removeMember(int i)	Removes an element from the listOfMembers at the given index.
Member	removeMember(java.lang.String id)	Removes an element from the listOfMembers.
boolean	removeMember(Member member)	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.
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

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, 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, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, 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, isLeaf, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

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, hasExtension, 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 javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

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

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()

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

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.

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(java.lang.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 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 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(java.lang.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:

java.lang.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(java.lang.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:

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

getMember

public Member getMember(java.lang.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()

Description copied from interface: SBase

Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

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:

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 AbstractSBase

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(Group.Kind kind)

Parameters:

kind -

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 AbstractSBase

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 AbstractSBase

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 AbstractSBase

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.