org.annotation.wordfreak
Class AnnotationTree

java.lang.Object
  org.annotation.wordfreak.AnnotationTree

public class AnnotationTree

extends java.lang.Object

A data structure for storing extent-based annotations in a sorted tree structure and meta-information relating them. The sorting is based on the annoation's span. In cases where this does not indicate a unique location within the tree methods are available to specify which parent or sibling should be used or to prefer placing the annotation deeper or shallower in the tree.

Field Summary

static java.lang.String	ANNOTATION_SOURCE
static java.lang.String	DEFAULT
static java.lang.String	DEFAULT_VIEW
protected AnnotationFile	file The i/o file for this Tree.
protected java.util.List	heads List of chain head annotations.
static java.lang.String	ID
protected int	maxId Largest id being used in this tree.
protected boolean	messaging Specifies whether views should be notified of changes to this tree.
protected java.util.Map	nextMap Mapping between a head annotation and it's chained annotation.
protected java.util.Map	prevMap Mapping between a chained annotation and it's head annotation.
protected java.util.HashMap	relations_per_anchor Mapping between anchor annotation and their relation.
protected HashList	relations_per_annotation Mapping between annotation and every relation which references that annotation.
protected HashList	relations_per_type Mapping between a relation type and all the realtions of that type.
protected Annotation	root The root of this Tree.
protected AnnotationSource	source The data source that this Tree annotates.
protected java.util.Set	usedIds Set of id keys currently being used in this tree.
protected java.util.Map	views A list of various masked views of this Tree.
static java.lang.String	XML_TYPE

Constructor Summary

AnnotationTree(AnnotationFile f, AnnotationSource s)

Method Summary

boolean	add(Annotation annotation)
boolean	add(Annotation root, Annotation annotation) Adds a new annotation to root and updates dependent annotations adjusting it if necessary to maintain tree integrity.
boolean	add(Annotation root, Annotation annotation, Annotation above)
boolean	add(Annotation root, Annotation annotation, Annotation above, boolean strictContains)
boolean	add(Annotation root, Annotation annotation, Annotation above, boolean preferShallow, int start, int end) Adds the specified annotation below the specified root and above the specified above annotation prefering shallow insertion when the specified boolean is true.
boolean	addAbove(Annotation annotation, Annotation above)
AnnotationView	addAnnotationView(java.lang.Object key)
AnnotationView	addAnnotationView(java.lang.Object key, AnnotationFilter filter)
AnnotationView	addAnnotationView(java.lang.Object key, AnnotationFilter aFilter, AnnotationFilter bFilter)
AnnotationView	addAnnotationView(java.lang.Object key, AnnotationFilter aFilter, AnnotationFilter bFilter, SortedAnnotations s)
void	addAnnotationView(java.lang.Object key, AnnotationView view)
void	addAnnotator(java.lang.String annotator)
void	addFeature(java.lang.String feature)
int	adjacent(Annotation a, Annotation b)
void	chainAnnotations(Annotation a, Annotation b) Creates a chain between the two specified annotations.
void	clear()
boolean	contains(Annotation a)
Relation	createRelation(java.lang.String type, java.lang.Object key, java.lang.String[] frame, Annotation[] annotations) Returns a new releation with the specified type, anchor key, frame, and annotations.
boolean	deepAdd(Annotation annotation)
boolean	deepAdd(Annotation root, Annotation annotation)
void	deepInsert(Annotation a)
Annotation	deepInsert(java.lang.String type, int s, int e)
void	fireTreeNodesChanged(Annotation node, Annotation[] children)
void	fireTreeNodesInserted(Annotation node, Annotation[] children)
void	fireTreeNodesMoved(Annotation[] children, Annotation oldParent, Annotation newParent)
void	fireTreeNodesRemoved(Annotation node, Annotation[] children)
void	fireTreeStructureChanged(Annotation node)
AnnotationFile	getAnnotationFile()
AnnotationSource	getAnnotationSource()
AnnotationView	getAnnotationView(java.lang.Object key)
Annotation[]	getChain(Annotation a) Returns the chains associated with the specified annotation.
Annotation[]	getChains() Returns the head annotations associated with all chains in this tree.
java.lang.Object	getChild(Annotation a, int i) Returns the child at the specified index of the specified annotation.
java.lang.Object	getChild(java.lang.Object node, int i)
int	getChildCount(Annotation a) Returns the number of children that the specified annotation has.
int	getChildCount(java.lang.Object node)
Annotation	getContainingLeaf(int offset) Returns the leaf which contains the offset.
Annotation	getContainingNode(Span span) Returns the deepest annotation which contains the specified span.
byte[]	getData(int offset, int length)
int	getIndexOfChild(java.lang.Object node, java.lang.Object child)
java.util.List	getLeavesInRange(int s, int e)
java.lang.Object	getParent(Annotation a)
Relation	getRelation(Annotation a)
Relation	getRelation(java.lang.String type, Annotation a) Returns a relation which is of the specified type and has as its anchor the specified annotation.
Relation[]	getRelations() Returns all the relations in this tree.
Relation[]	getRelations(Annotation a) Returns all the relations which relate the specified annotation.
Relation[]	getRelations(java.lang.String type) Returns all the relations of a given type in this tree.
Relation[]	getRelations(java.lang.String type, Annotation a) Returns all relation which are of the specified type and which contain the specified annotation.
Annotation	getRoot()
AnnotationSource	getSource()
void	insert(Annotation a)
void	insert(Annotation parent, Annotation annotation) Inserts the specified annotation below the specified parent.
void	insert(Annotation root, Annotation annotation, Annotation above)
Annotation	insert(int s, int e)
Annotation	insert(int s, int e, Annotation parent)
Annotation	insert(java.lang.String type, Annotation s, Annotation e) Inserts and annotation which has s as its first child and e as its last child.
Annotation	insert(java.lang.String type, int s, int e) Inserts an annotation with specified type and span and returns that new annotation.
Annotation	insert(java.lang.String type, int s, int e, Annotation parent)
Annotation	insertParent(Annotation child) Creates a parent above an Annotation.
Annotation	insertParent(java.lang.String type, Annotation child) Creates a parent above an Annotation.
void	insertSubTree(Annotation a, Annotation p)
Annotation	insertZeroLengthAnnotationAfter(Annotation after)
Annotation	insertZeroLengthAnnotationAfter(java.lang.String type, Annotation after)
Annotation	insertZeroLengthAnnotationBefore(Annotation before)
Annotation	insertZeroLengthAnnotationBefore(java.lang.String type, Annotation before)
boolean	isAnchor(Annotation chainedAnnotation) Returns true of the specified annotation is the head of a chain.
boolean	isLeaf(java.lang.Object node)
boolean	isTerminalSpan(int start, int end) Returns true if the span given by the specified start and end values can be inserted into this tree as a leaf.
boolean	isTerminalSpan(Span span) Returns true if the specified span can be inserted into this tree as a leaf.
boolean	isValidSpan(int start, int end) Returns true if the span given by the specified start and end values can be inserted into this tree without crossing another annotation.
boolean	isValidSpan(Span span) Returns true if the specified span can be inserted into this tree without crossing another annotation.
java.util.Iterator	iterator()
void	move(Annotation node, Annotation dest) moves an Annotation from one place to another.
void	put(int roleIndex, Annotation ann, Relation relation) Puts the specified annotation at the specified role index in the specified relation.
void	put(java.lang.String role, Annotation ann, Relation relation) Puts the specified annotation the specified relation with the specified role name.
void	remove(Annotation annotation)
void	remove(Annotation annotation, boolean shrink)
void	remove(Annotation annotation, Relation relation) Removes the specified annotation from the specified relation or if the specified annotation is the anchor of the relation, removes the relation from this tree.
void	remove(Relation relation) Removes the specified relation from this tree.
void	remove(java.lang.String type, Annotation a, Relation relation)
void	removeAnnotationView(java.lang.Object key)
Annotation	removeFromChain(Annotation a) Removes the specified annotation from a chain and returns another annotation from the modified chain if such an annotation exists.
javax.swing.tree.TreeNode	removeSubTree(Annotation annotation)
void	setAnnotationSource(AnnotationSource s)
void	setRoot(Annotation r)
protected void	setSourceFileName(java.lang.String sfn)
boolean	shallowAdd(Annotation annotation)
boolean	shallowAdd(Annotation root, Annotation annotation)
Annotation	terminalInsert(java.lang.String type, int start, int end) Inserts a newly created annotation with the specified type and span in this tree and returns the newly created annotation.
void	update(Annotation a)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ID

public static final java.lang.String ID

See Also:

Constant Field Values

ANNOTATION_SOURCE

public static final java.lang.String ANNOTATION_SOURCE

See Also:

Constant Field Values

DEFAULT_VIEW

public static final java.lang.String DEFAULT_VIEW

See Also:

Constant Field Values

XML_TYPE

public static final java.lang.String XML_TYPE

See Also:

Constant Field Values

DEFAULT

public static final java.lang.String DEFAULT

See Also:

Constant Field Values

file

protected AnnotationFile file

The i/o file for this Tree.

source

protected AnnotationSource source

The data source that this Tree annotates.

root

protected Annotation root

The root of this Tree.

views

protected java.util.Map views

A list of various masked views of this Tree. This list is used for updating the views when changes to the tree are made.

usedIds

protected java.util.Set usedIds

Set of id keys currently being used in this tree.

maxId

protected int maxId

Largest id being used in this tree.

heads

protected java.util.List heads

List of chain head annotations.

nextMap

protected java.util.Map nextMap

Mapping between a head annotation and it's chained annotation.

prevMap

protected java.util.Map prevMap

Mapping between a chained annotation and it's head annotation.

relations_per_anchor

protected java.util.HashMap relations_per_anchor

Mapping between anchor annotation and their relation.

relations_per_annotation

protected HashList relations_per_annotation

Mapping between annotation and every relation which references that annotation.

relations_per_type

protected HashList relations_per_type

Mapping between a relation type and all the realtions of that type.

messaging

protected boolean messaging

Specifies whether views should be notified of changes to this tree. This is used to prevent views from updating when large changes are being made until after the changes are complete.

Constructor Detail

AnnotationTree

public AnnotationTree(AnnotationFile f,
                      AnnotationSource s)

Method Detail

setSourceFileName

protected void setSourceFileName(java.lang.String sfn)

setAnnotationSource

public void setAnnotationSource(AnnotationSource s)

getAnnotationSource

public AnnotationSource getAnnotationSource()

getAnnotationView

public AnnotationView getAnnotationView(java.lang.Object key)

addAnnotationView

public AnnotationView addAnnotationView(java.lang.Object key)

addAnnotationView

public AnnotationView addAnnotationView(java.lang.Object key,
                                        AnnotationFilter filter)

addAnnotationView

public AnnotationView addAnnotationView(java.lang.Object key,
                                        AnnotationFilter aFilter,
                                        AnnotationFilter bFilter)

addAnnotationView

public AnnotationView addAnnotationView(java.lang.Object key,
                                        AnnotationFilter aFilter,
                                        AnnotationFilter bFilter,
                                        SortedAnnotations s)

addAnnotationView

public void addAnnotationView(java.lang.Object key,
                              AnnotationView view)

removeAnnotationView

public void removeAnnotationView(java.lang.Object key)

getContainingLeaf

public Annotation getContainingLeaf(int offset)

Returns the leaf which contains the offset.

Parameters:

offset - The offset.

Returns:

A leaf annotation which contains the offset or null if no such annotation exists.

getContainingNode

public Annotation getContainingNode(Span span)

Returns the deepest annotation which contains the specified span.

Parameters:

span - The span which the returned node must contain.

Returns:

The deepest annotation which contains the span or null if no such annotation exists.

add

public boolean add(Annotation annotation)

add

public boolean add(Annotation root,
                   Annotation annotation)

Adds a new annotation to root and updates dependent annotations adjusting it if necessary to maintain tree integrity.

Parameters:

root - parent annotation into which new annotaiton will be inserted.

annotation - new annotation to be added.

Returns:

always returns true.

addAbove

public boolean addAbove(Annotation annotation,
                        Annotation above)

deepAdd

public boolean deepAdd(Annotation annotation)

deepAdd

public boolean deepAdd(Annotation root,
                       Annotation annotation)

shallowAdd

public boolean shallowAdd(Annotation annotation)

shallowAdd

public boolean shallowAdd(Annotation root,
                          Annotation annotation)

add

public boolean add(Annotation root,
                   Annotation annotation,
                   Annotation above)

add

public boolean add(Annotation root,
                   Annotation annotation,
                   Annotation above,
                   boolean strictContains)

add

public boolean add(Annotation root,
                   Annotation annotation,
                   Annotation above,
                   boolean preferShallow,
                   int start,
                   int end)

Adds the specified annotation below the specified root and above the specified above annotation prefering shallow insertion when the specified boolean is true.

Parameters:

root - the annotation below which the annotation is added.

annotation - The annotation to be added.

above - An annotation above which the specified annotation should be inserted.

preferShallow - specifies whether the addition should prefer shallower placement in the tree.

start -

end -

Returns:

true if this annotation was successfully inserted, false otherwise.

insert

public void insert(Annotation parent,
                   Annotation annotation)

Inserts the specified annotation below the specified parent.

Parameters:

parent - The parent annotation of the annotation to be inserted.

annotation - The annotation to insert into this tree.

insert

public void insert(Annotation root,
                   Annotation annotation,
                   Annotation above)

insert

public void insert(Annotation a)

deepInsert

public void deepInsert(Annotation a)

insert

public Annotation insert(int s,
                         int e)

insert

public Annotation insert(int s,
                         int e,
                         Annotation parent)

deepInsert

public Annotation deepInsert(java.lang.String type,
                             int s,
                             int e)

terminalInsert

public Annotation terminalInsert(java.lang.String type,
                                 int start,
                                 int end)

Inserts a newly created annotation with the specified type and span in this tree and returns the newly created annotation.

Parameters:

type - The type of annotation to create.

start - The start of the span of the new annotation.

end - The end of the span of the new annotation.

Returns:

the newly ceated annotation or null if the annotation would intersect with an exiting annotation.

isValidSpan

public boolean isValidSpan(int start,
                           int end)

Returns true if the span given by the specified start and end values can be inserted into this tree without crossing another annotation.

Parameters:

start - The start value of the span.

end - The end value of the span.

Returns:

true if the span given by the specified start and end values does not intersect any existing nodes, false otherwise or if the span is outside of this tree.

isValidSpan

public boolean isValidSpan(Span span)

Returns true if the specified span can be inserted into this tree without crossing another annotation.

Parameters:

span - The span to be tested.

Returns:

true if the specified span does not intersect any existing nodes, false otherwise or if the span is outside of this tree.

isTerminalSpan

public boolean isTerminalSpan(int start,
                              int end)

Returns true if the span given by the specified start and end values can be inserted into this tree as a leaf.

Parameters:

start - The start value of the span.

end - The end value of the span.

Returns:

true if the span given by the specified start and end values does not intersect any existing nodes, false otherwise.

isTerminalSpan

public boolean isTerminalSpan(Span span)

Returns true if the specified span can be inserted into this tree as a leaf.

Parameters:

span - The span to be tested.

Returns:

true if the specified span does not intersect any existing nodes, false otherwise.

insert

public Annotation insert(java.lang.String type,
                         int s,
                         int e,
                         Annotation parent)

insert

public Annotation insert(java.lang.String type,
                         int s,
                         int e)

Inserts an annotation with specified type and span and returns that new annotation.

Parameters:

type - the type.

s - the start of the span.

e - then end of the span.

Returns:

the newly inserted annotation.

insert

public Annotation insert(java.lang.String type,
                         Annotation s,
                         Annotation e)

Inserts and annotation which has s as its first child and e as its last child.

insertSubTree

public void insertSubTree(Annotation a,
                          Annotation p)

insertZeroLengthAnnotationBefore

public Annotation insertZeroLengthAnnotationBefore(Annotation before)

insertZeroLengthAnnotationBefore

public Annotation insertZeroLengthAnnotationBefore(java.lang.String type,
                                                   Annotation before)

insertZeroLengthAnnotationAfter

public Annotation insertZeroLengthAnnotationAfter(Annotation after)

insertZeroLengthAnnotationAfter

public Annotation insertZeroLengthAnnotationAfter(java.lang.String type,
                                                  Annotation after)

insertParent

public Annotation insertParent(Annotation child)

Creates a parent above an Annotation.

Parameters:

child - the annotation to create a parent above.

Returns:

the newly created parent.

insertParent

public Annotation insertParent(java.lang.String type,
                               Annotation child)

Creates a parent above an Annotation.

Parameters:

child - the annotation to create a parent above.

type - the type of annotation to create.

Returns:

the newly created parent.

move

public void move(Annotation node,
                 Annotation dest)

moves an Annotation from one place to another.

Parameters:

node - the annotation to move.

dest - the annotation to move it into.

remove

public void remove(Annotation annotation)

remove

public void remove(Annotation annotation,
                   boolean shrink)

removeSubTree

public javax.swing.tree.TreeNode removeSubTree(Annotation annotation)

update

public void update(Annotation a)

clear

public void clear()

contains

public boolean contains(Annotation a)

iterator

public java.util.Iterator iterator()

setRoot

public void setRoot(Annotation r)

getRoot

public Annotation getRoot()

getAnnotationFile

public AnnotationFile getAnnotationFile()

getLeavesInRange

public java.util.List getLeavesInRange(int s,
                                       int e)

getData

public byte[] getData(int offset,
                      int length)

getSource

public AnnotationSource getSource()

addAnnotator

public void addAnnotator(java.lang.String annotator)

addFeature

public void addFeature(java.lang.String feature)

fireTreeNodesInserted

public void fireTreeNodesInserted(Annotation node,
                                  Annotation[] children)

fireTreeNodesMoved

public void fireTreeNodesMoved(Annotation[] children,
                               Annotation oldParent,
                               Annotation newParent)

fireTreeNodesRemoved

public void fireTreeNodesRemoved(Annotation node,
                                 Annotation[] children)

fireTreeNodesChanged

public void fireTreeNodesChanged(Annotation node,
                                 Annotation[] children)

fireTreeStructureChanged

public void fireTreeStructureChanged(Annotation node)

chainAnnotations

public void chainAnnotations(Annotation a,
                             Annotation b)

Creates a chain between the two specified annotations.

Parameters:

a - The first annotation in the chain.

b - The second annotation in the chain.

getChains

public Annotation[] getChains()

Returns the head annotations associated with all chains in this tree.

Returns:

An array of head annotations associated with all chains in this tree.

getChain

public Annotation[] getChain(Annotation a)

Returns the chains associated with the specified annotation. Annotations can only be in one chain.

Parameters:

a - An annotation in a chain.

Returns:

The chains associated with the specified annotation. The returned array can be empty.

removeFromChain

public Annotation removeFromChain(Annotation a)

Removes the specified annotation from a chain and returns another annotation from the modified chain if such an annotation exists.

Parameters:

a - The annotation to be removed.

Returns:

A annotation from the modified chain or null if no such an annotation exists.

isAnchor

public boolean isAnchor(Annotation chainedAnnotation)

Returns true of the specified annotation is the head of a chain.

Parameters:

chainedAnnotation - Tha annotation to check.

Returns:

True of the specified annotation is the head of a chain, false otherwise.

createRelation

public Relation createRelation(java.lang.String type,
                               java.lang.Object key,
                               java.lang.String[] frame,
                               Annotation[] annotations)

Returns a new releation with the specified type, anchor key, frame, and annotations.

Parameters:

type - The type of the relations.

key - The anchor annotation of this relation.

frame - The names of the frame elements of the relation.

annotations - The annotation which occupy the frame elements.

Returns:

A new releation with the specified type, anchor key, frame, and annotations.

put

public void put(int roleIndex,
                Annotation ann,
                Relation relation)

Puts the specified annotation at the specified role index in the specified relation.

Parameters:

roleIndex - The position in the frame of the specified relation when the specified annotaiton will be placed.

ann - The annotation to be placed at the specified role Index in the specified relation.

relation - The annotation to be modified.

put

public void put(java.lang.String role,
                Annotation ann,
                Relation relation)

Puts the specified annotation the specified relation with the specified role name. Role names can be duplicated and this will always add anothor element to the relations frame.

Parameters:

role - The name of the role slot in the relation when the annotation will be placed.

ann - The annotation to put in the relation.

relation - The relation to be modified.

remove

public void remove(Relation relation)

Removes the specified relation from this tree.

Parameters:

relation - The relation to be removed.

remove

public void remove(Annotation annotation,
                   Relation relation)

Removes the specified annotation from the specified relation or if the specified annotation is the anchor of the relation, removes the relation from this tree.

Parameters:

annotation - The annotaiton to remove.

relation - The relation from which the spevified annotation is removed.

remove

public void remove(java.lang.String type,
                   Annotation a,
                   Relation relation)

getRelations

public Relation[] getRelations()

Returns all the relations in this tree.

Returns:

an array of all the relations this tree.

getRelations

public Relation[] getRelations(java.lang.String type)

Returns all the relations of a given type in this tree.

Parameters:

type - the type of Relation to return

Returns:

an array of all the relations of type type in this tree.

getRelations

public Relation[] getRelations(Annotation a)

Returns all the relations which relate the specified annotation.

Parameters:

a - the Annotation to find Relations for

getRelations

public Relation[] getRelations(java.lang.String type,
                               Annotation a)

Returns all relation which are of the specified type and which contain the specified annotation.

Parameters:

type - The type of relations to be returned.

a - The annotation which the returned relations contain.

Returns:

An array of all relation which are of the specified type and which contain the specified relation.

getRelation

public Relation getRelation(Annotation a)

getRelation

public Relation getRelation(java.lang.String type,
                            Annotation a)

Returns a relation which is of the specified type and has as its anchor the specified annotation.

Parameters:

type - The type of relation to be returned.

a - The anchor of the relations to be returned.

Returns:

A relation which is of the specified type and has as its anchor the specified annotation or null if not such relation exists.

adjacent

public int adjacent(Annotation a,
                    Annotation b)

getChild

public java.lang.Object getChild(java.lang.Object node,
                                 int i)

getChildCount

public int getChildCount(java.lang.Object node)

getIndexOfChild

public int getIndexOfChild(java.lang.Object node,
                           java.lang.Object child)

isLeaf

public boolean isLeaf(java.lang.Object node)

getParent

public java.lang.Object getParent(Annotation a)

getChild

public java.lang.Object getChild(Annotation a,
                                 int i)

Returns the child at the specified index of the specified annotation.

Parameters:

a - The annotation whose child is to be returned.

i - The index of the child to be returned.

Returns:

The child at the specified index of the specified annotation.

getChildCount

public int getChildCount(Annotation a)

Returns the number of children that the specified annotation has.

Parameters:

a - The annotation whose children count is being requested.

Returns:

the number of children that the specified annotation has.