org.sbml.jsbml

Class ListOf<T extends SBase>

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ListOf<T>

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<T>, java.util.Collection<T>, java.util.List<T>, javax.swing.tree.TreeNode, SBase, UniqueSId, TreeNodeWithChangeSupport

Direct Known Subclasses:

ListOfWithName

public class ListOf<T extends SBase>
extends AbstractSBase
implements java.util.List<T>, UniqueSId

This list implementation is a Java List that extends AbstractSBase. It represents the listOfxxx XML elements in a SBML file. Unfortunately, there is no way for multiple inheritance in Java.

Since:

0.8

Author:

Nicolas Rodriguez, Marine Dumousseau, Andreas Dräger

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ListOf.Type This enum lists all the possible names of the listXXX components.

Field Summary

Fields

Modifier and Type	Field and Description
private static boolean	DEBUG_MODE Switches the behavior of the AbstractSBase.toString() method from displaying the ListOf.Type (default) to the complete content of all instances of ListOf
protected java.util.List<T>	listOf list containing all the SBase elements of this object.
protected ListOf.Type	listType name of the list at it appears in the SBMLFile.
private static org.apache.log4j.Logger	logger A Logger for this class.
protected java.lang.String	otherListName name of the list at it appears in the SBMLFile.
private static long	serialVersionUID Generated serial version identifier.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, lv, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
ListOf() Creates a ListOf instance.
ListOf(int level, int version) Creates a ListOf instance from a level and version.
ListOf(ListOf<? extends SBase> listOf) Creates a ListOf instance from a given ListOf.
ListOf(java.lang.String id) Creates a new ListOf instance with the given id.
ListOf(java.lang.String id, int level, int version) Creates a new ListOf instance.
ListOf(java.lang.String id, java.lang.String name, int level, int version) Creates a new ListOf instance.

Method Summary

Modifier and Type	Method and Description
void	add(int index, T element)
boolean	add(T element)
boolean	addAll(java.util.Collection<? extends T> c)
boolean	addAll(int index, java.util.Collection<? extends T> collection)
boolean	append(T element) Adds item to the end of this ListOf.
void	clear()
ListOf<T>	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	contains(java.lang.Object o)
boolean	containsAll(java.util.Collection<?> c)
boolean	equals(java.lang.Object o) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
java.util.List<T>	filterList(Filter f) Returns a new List that contains only those elements that satisfy a certain filter criterion.
T	firstHit(Filter f) Returns the first element in this list that satisfies a certain filter criterion.
T	get(int index) Returns the element at the specified position in this list or null if the index is negative or too big.
T	get(java.lang.String id) Gets the list element which has the id 'id'.
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
java.lang.String	getElementName() Returns the XML element name of this object.
T	getFirst() Returns the first element in this list.
T	getLast() Returns the last element in this list.
java.lang.String	getOtherListName() Returns the XML element name used when the ListOf type is set to ListOf.Type.other.
ListOf.Type	getSBaseListType() Returns the SBaseListType of this ListOf instance.
int	indexOf(java.lang.Object o)
static <T extends SBase> ListOf<T>	initListOf(SBase parent, ListOf<T> list, ListOf.Type type) Initializes newly created lists.
static boolean	isDebugMode() If this method returns true, the AbstractSBase.toString() method of this ListOf displays the whole content of the list.
boolean	isEmpty()
java.util.Iterator<T>	iterator()
int	lastIndexOf(java.lang.Object o)
java.util.ListIterator<T>	listIterator()
java.util.ListIterator<T>	listIterator(int index)
static <T extends SBase> ListOf<T>	newInstance(SBase parent, java.lang.Class<T> clazz) Initializes a new ListOf object for the given parent SBML object and with the given Class as the type of the list.
T	remove(int index)
boolean	remove(NamedSBase nsb) Removes a NamedSBase according to its unique id.
boolean	remove(java.lang.Object o)
T	remove(java.lang.String removeId) Specialized method to remove a named SBase according to its unique id.
boolean	removeAll(java.util.Collection<?> c)
boolean	removeAll(Filter f) Removes all elements from this list that are accepted by the Filter.accepts(Object) method of the given filter.
T	removeFirst(Filter f) Removes the first element from this list that is accepted by the Filter.accepts(Object) method of the given filter.
boolean	retainAll(java.util.Collection<?> c)
T	set(int index, T element)
static void	setDebugMode(boolean debugMode) Allows you to influence the behavior of the AbstractSBase.toString() method.
void	setListOf(java.util.List<T> listOf) Clears this ListOf if not empty and then adds all elements in the given List to this ListOf.
void	setOtherListName(java.lang.String otherListName) Sets the XML element name used when the ListOf type is set to ListOf.Type.other.
void	setPackageName(java.lang.String newPackageName) Sets the name of the package to which this SBase belong.
void	setSBaseListType(java.lang.Class<T> type) Sets the ListOf.Type of this ListOf instance to the ListOf.Type defined by the given Class.
void	setSBaseListType(ListOf.Type listType) Sets the ListOf.Type of this ListOf instance to 'listType'.
int	size()
java.util.List<T>	subList(int fromIndex, int toIndex)
java.lang.Object[]	toArray()
<T> T[]	toArray(T[] a)
void	unsetSBaseListType() Sets the SBaseListType of this ListOf to SBaseListType.none.

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, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, readAttribute, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setLevelAndVersion, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageNamespaceAndVersion, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm, writeXMLAttributes

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, 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 java.util.List

hashCode, replaceAll, sort, spliterator

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Methods inherited from interface org.sbml.jsbml.SBase

removeTreeNodeChangeListener

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

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

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, isLeaf

Field Detail

DEBUG_MODE

private static boolean DEBUG_MODE

Switches the behavior of the AbstractSBase.toString() method from displaying the ListOf.Type (default) to the complete content of all instances of ListOf

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

logger

private static final transient org.apache.log4j.Logger logger

A Logger for this class.

listOf

protected java.util.List<T extends SBase> listOf

list containing all the SBase elements of this object.

listType

protected ListOf.Type listType

name of the list at it appears in the SBMLFile. By default, it is SBaseListType.none.

otherListName

protected java.lang.String otherListName

name of the list at it appears in the SBMLFile. By default, it is null. This value is used only if the type of the ListOf is ListOf.Type.other.

Constructor Detail

ListOf

public ListOf()

Creates a ListOf instance. By default, the list containing the SBase elements is empty.

ListOf

public ListOf(int level,
              int version)

Creates a ListOf instance from a level and version. By default, the list containing the SBase elements is empty.

Parameters:

level - the SBML level

version - the SBML version

ListOf

public ListOf(ListOf<? extends SBase> listOf)

Creates a ListOf instance from a given ListOf.

Parameters:

listOf - the list to clone

ListOf

public ListOf(java.lang.String id)

Creates a new ListOf instance with the given id.

Parameters:

id - the ListOf id.

ListOf

public ListOf(java.lang.String id,
              int level,
              int version)

Creates a new ListOf instance.

Parameters:

id - the ListOf id.

level - the SBML level.

version - the SBML version.

ListOf

public ListOf(java.lang.String id,
              java.lang.String name,
              int level,
              int version)

Creates a new ListOf instance.

Parameters:

id - the ListOf id.

name - the ListOf name.

level - the SBML level.

version - the SBML version.

Method Detail

initListOf

public static <T extends SBase> ListOf<T> initListOf(SBase parent,
                                                     ListOf<T> list,
                                                     ListOf.Type type)

Initializes newly created lists.

Parameters:

parent - the list parent, used to set the SBML level and version

list - the list to initialize

type - the type of the list

Returns:

the initialized list for convenience

isDebugMode

public static boolean isDebugMode()

If this method returns true, the AbstractSBase.toString() method of this ListOf displays the whole content of the list. Otherwise, only the ListOf.Type is shown.

Returns:

the debugMode

newInstance

public static <T extends SBase> ListOf<T> newInstance(SBase parent,
                                                      java.lang.Class<T> clazz)

Initializes a new ListOf object for the given parent SBML object and with the given Class as the type of the list.

Parameters:

parent - the ListOf parent

clazz - the class of objects the new ListOf will contain

Returns:

a new ListOf object for the given parent SBML object and with the given Class as the type of the list.

setDebugMode

public static void setDebugMode(boolean debugMode)

Allows you to influence the behavior of the AbstractSBase.toString() method. If set to true, the whole content of this ListOf is displayed by the AbstractSBase.toString() method, just like it is done in other List implementations. The default for JSBML, however, is, to only display the ListOf.Type of this list.

Parameters:

debugMode - the debugMode to set

add

public void add(int index,
                T element)

Specified by:

add in interface java.util.List<T extends SBase>

add

public boolean add(T element)
            throws LevelVersionError

Specified by:

add in interface java.util.Collection<T extends SBase>

Specified by:

add in interface java.util.List<T extends SBase>

Throws:

LevelVersionError

addAll

public boolean addAll(java.util.Collection<? extends T> c)
               throws LevelVersionError

Specified by:

addAll in interface java.util.Collection<T extends SBase>

Specified by:

addAll in interface java.util.List<T extends SBase>

Throws:

LevelVersionError

addAll

public boolean addAll(int index,
                      java.util.Collection<? extends T> collection)
               throws LevelVersionError

Specified by:

addAll in interface java.util.List<T extends SBase>

Throws:

LevelVersionError

append

public boolean append(T element)
               throws LevelVersionError

Adds item to the end of this ListOf. This variant of the method makes a clone of the item handed to it. This means that when the ListOf is destroyed, the original items will not be destroyed.

Parameters:

element - the item to be added to the list.

Returns:

true if this could be successfully appended.

Throws:

LevelVersionError - if the SBML level and version of the new element is different from the SBML level and version of list.

See Also:

add(SBase)

clear

public void clear()

Specified by:

clear in interface java.util.Collection<T extends SBase>

Specified by:

clear in interface java.util.List<T extends SBase>

clone

public ListOf<T> 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

contains

public boolean contains(java.lang.Object o)

Specified by:

contains in interface java.util.Collection<T extends SBase>

Specified by:

contains in interface java.util.List<T extends SBase>

containsAll

public boolean containsAll(java.util.Collection<?> c)

Specified by:

containsAll in interface java.util.Collection<T extends SBase>

Specified by:

containsAll in interface java.util.List<T extends SBase>

equals

public boolean equals(java.lang.Object o)

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 java.util.Collection<T extends SBase>

Specified by:

equals in interface java.util.List<T extends SBase>

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

Parameters:

o - 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.

filterList

public java.util.List<T> filterList(Filter f)

Returns a new List that contains only those elements that satisfy a certain filter criterion.

Parameters:

f - A filter that defines the criterion for elements to be put into the list to be returned.

Returns:

A new list that can be empty if no element fulfills the filter criterion.

firstHit

public T firstHit(Filter f)

Returns the first element in this list that satisfies a certain filter criterion.

Parameters:

f - A filter defining the criterion for which to be filter.

Returns:

The first element of this list that satisfies the criterion or null if no such element exists in this list.

get

public T get(int index)

Returns the element at the specified position in this list or null if the index is negative or too big.

Specified by:

get in interface java.util.List<T extends SBase>

Parameters:

index - index of the element to return.

Returns:

the element at the specified position in this list or null if the index is negative or too big.

See Also:

List.get(int)

get

public T get(java.lang.String id)

Gets the list element which has the id 'id'.

The elements of the list have to implement NamedSBase, if they are not or if the id is not found, null is returned.

Parameters:

id - the id to search for.

Returns:

the list element which has the id 'id'.

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

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

getElementName

public java.lang.String getElementName()

Description copied from interface: SBase

Returns the XML element name of this object.

Specified by:

getElementName in interface SBase

Overrides:

getElementName in class AbstractSBase

Returns:

the XML element name of this object.

getFirst

public T getFirst()

Returns the first element in this list.

Returns:

the first element in this list.

Throws:

java.lang.IndexOutOfBoundsException - if there are no element in the list

getLast

public T getLast()

Returns the last element in this list.

Returns:

the last element in this list.

Throws:

java.lang.IndexOutOfBoundsException - if there are no element in the list

getSBaseListType

public ListOf.Type getSBaseListType()

Returns the SBaseListType of this ListOf instance.

Returns:

the SBaseListType of this ListOf instance

indexOf

public int indexOf(java.lang.Object o)

Specified by:

indexOf in interface java.util.List<T extends SBase>

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface java.util.Collection<T extends SBase>

Specified by:

isEmpty in interface java.util.List<T extends SBase>

iterator

public java.util.Iterator<T> iterator()

Specified by:

iterator in interface java.lang.Iterable<T extends SBase>

Specified by:

iterator in interface java.util.Collection<T extends SBase>

Specified by:

iterator in interface java.util.List<T extends SBase>

lastIndexOf

public int lastIndexOf(java.lang.Object o)

Specified by:

lastIndexOf in interface java.util.List<T extends SBase>

listIterator

public java.util.ListIterator<T> listIterator()

Specified by:

listIterator in interface java.util.List<T extends SBase>

listIterator

public java.util.ListIterator<T> listIterator(int index)

Specified by:

listIterator in interface java.util.List<T extends SBase>

remove

public T remove(int index)

Specified by:

remove in interface java.util.List<T extends SBase>

remove

public boolean remove(NamedSBase nsb)

Removes a NamedSBase according to its unique id.

Parameters:

nsb - the object to be removed.

Returns:

success or failure.

remove

public boolean remove(java.lang.Object o)

Specified by:

remove in interface java.util.Collection<T extends SBase>

Specified by:

remove in interface java.util.List<T extends SBase>

remove

public T remove(java.lang.String removeId)

Specialized method to remove a named SBase according to its unique id.

Parameters:

removeId - the id of the object to be removed.

Returns:

success or failure.

removeAll

public boolean removeAll(java.util.Collection<?> c)

Specified by:

removeAll in interface java.util.Collection<T extends SBase>

Specified by:

removeAll in interface java.util.List<T extends SBase>

removeAll

public boolean removeAll(Filter f)

Removes all elements from this list that are accepted by the Filter.accepts(Object) method of the given filter.

Parameters:

f - a Filter to apply

Returns:

true if this list changed as a result of the call

removeFirst

public T removeFirst(Filter f)

Removes the first element from this list that is accepted by the Filter.accepts(Object) method of the given filter.

Parameters:

f - a Filter to apply

Returns:

the removed element or null if no elements satisfied the filter

retainAll

public boolean retainAll(java.util.Collection<?> c)

Specified by:

retainAll in interface java.util.Collection<T extends SBase>

Specified by:

retainAll in interface java.util.List<T extends SBase>

set

public T set(int index,
             T element)
      throws LevelVersionError

Specified by:

set in interface java.util.List<T extends SBase>

Throws:

LevelVersionError

setListOf

public void setListOf(java.util.List<T> listOf)

Clears this ListOf if not empty and then adds all elements in the given List to this ListOf.

Parameters:

listOf - the list that contain all the elements to add to this ListOf

setPackageName

public void setPackageName(java.lang.String newPackageName)

Sets the name of the package to which this SBase belong.

This an internal method that should not be used outside of the main jsbml code (core + packages). One class should always belong to the same package. You have to know what you are doing when using this method.

Parameters:

newPackageName - the name of the package to which this SBase belong.

setSBaseListType

public void setSBaseListType(java.lang.Class<T> type)

Sets the ListOf.Type of this ListOf instance to the ListOf.Type defined by the given Class.

Parameters:

type - a class instance

setSBaseListType

public void setSBaseListType(ListOf.Type listType)

Sets the ListOf.Type of this ListOf instance to 'listType'.

Parameters:

listType - a list ListOf.Type

size

public int size()

Specified by:

size in interface java.util.Collection<T extends SBase>

Specified by:

size in interface java.util.List<T extends SBase>

subList

public java.util.List<T> subList(int fromIndex,
                                 int toIndex)

Specified by:

subList in interface java.util.List<T extends SBase>

toArray

public java.lang.Object[] toArray()

Specified by:

toArray in interface java.util.Collection<T extends SBase>

Specified by:

toArray in interface java.util.List<T extends SBase>

toArray

public <T> T[] toArray(T[] a)

Specified by:

toArray in interface java.util.Collection<T extends SBase>

Specified by:

toArray in interface java.util.List<T extends SBase>

unsetSBaseListType

public void unsetSBaseListType()

Sets the SBaseListType of this ListOf to SBaseListType.none.

getOtherListName

public java.lang.String getOtherListName()

Returns the XML element name used when the ListOf type is set to ListOf.Type.other.

This an internal method that should not be used outside of the main jsbml code (packages). You have to know what you are doing when using this method.

Returns:

the XML element name or null if it was not set.

setOtherListName

public void setOtherListName(java.lang.String otherListName)

Sets the XML element name used when the ListOf type is set to ListOf.Type.other.

This an internal method that should not be used outside of the main jsbml code (packages). You have to know what you are doing when using this method.

Parameters:

otherListName - the value of otherListName to be set.