gate.annotation
Class AnnotationSetImpl

java.lang.Object
  java.util.AbstractCollection
      java.util.AbstractSet
          gate.annotation.AnnotationSetImpl

All Implemented Interfaces:

AnnotationSet, SimpleAnnotationSet, Serializable, Cloneable, Iterable, Collection, Set

Direct Known Subclasses:

DatabaseAnnotationSetImpl

public class AnnotationSetImpl
extends AbstractSet
implements AnnotationSet

Implementation of AnnotationSet. Has a number of indices, all bar one of which are null by default and are only constructed when asked for. Has lots of get methods with various selection criteria; these return views into the set, which are nonetheless valid sets in their own right (but will not necesarily be fully indexed). Has a name, which is null by default; clients of Document can request named AnnotationSets if they so desire. Has a reference to the Document it is attached to. Contrary to Collections convention, there is no no-arg constructor, as this would leave the set in an inconsistent state.

There are five indices: annotation by id, annotations by type, annotations by start/end node and nodes by offset. The last three jointly provide positional indexing; construction of these is triggered by indexByStart/EndOffset(), or by calling a get method that selects on offset. The type index is triggered by indexByType(), or calling a get method that selects on type. The id index is always present.

See Also:

Serialized Form

Nested Class Summary

class

AnnotationSetImpl.VerboseHashMap This is a HashMap that fires events when elements are removed.

Field Summary

protected static AnnotationFactory	annFactory
protected Vector	annotationSetListeners
protected HashMap	annotsById Maps annotation ids (Integers) to Annotations

Constructor Summary

AnnotationSetImpl(Collection c)
Construction from Collection (which must be an AnnotationSet)

AnnotationSetImpl(Document doc)
Construction from Document.

AnnotationSetImpl(Document doc, String name)
Construction from Document and name.

Method Summary

void	add(Integer id, Long start, Long end, String type, FeatureMap features) Create and add an annotation from database read data In this case the id is already known being previously fetched from the database
Integer	add(Long start, Long end, String type, FeatureMap features) Create and add an annotation and return its id
Integer	add(Node start, Node end, String type, FeatureMap features) Create and add an annotation with pre-existing nodes, and return its id
boolean	add(Object o) Add an existing annotation.
boolean	addAll(Collection c) Adds multiple annotations to this set in one go.
protected boolean	addAllKeepIDs(Collection c) Adds multiple annotations to this set in one go.
void	addAnnotationSetListener(AnnotationSetListener l)
void	addGateListener(GateListener l)
Object	clone()
void	edit(Long start, Long end, DocumentContent replacement) Propagate changes to the document content.
protected void	fireAnnotationAdded(AnnotationSetEvent e)
protected void	fireAnnotationRemoved(AnnotationSetEvent e)
protected void	fireGateEvent(GateEvent e)
Node	firstNode() Get the node with the smallest offset
AnnotationSet	get() Get all annotations
Annotation	get(Integer id) Find annotations by id
AnnotationSet	get(Long offset) Select annotations by offset.
AnnotationSet	get(Long startOffset, Long endOffset) Select annotations by offset.
AnnotationSet	get(Set types) Select annotations by a set of types.
AnnotationSet	get(String type) Select annotations by type
AnnotationSet	get(String type, FeatureMap constraints) Select annotations by type and features This will return an annotation set containing just those annotations of a particular type (i.e. with a particular name) and which have features with specific names and values.
AnnotationSet	get(String type, FeatureMap constraints, Long offset) Select annotations by type, features and offset
AnnotationSet	get(String neededType, Long startOffset, Long endOffset) Select annotations by offset.
AnnotationSet	get(String type, Set featureNames) Select annotations by type and feature names
Set	getAllTypes() Get a set of java.lang.String objects representing all the annotation types present in this annotation set.
AnnotationSet	getContained(Long startOffset, Long endOffset) Select annotations by offset that start at a position between the start and end before the end offset
Document	getDocument() Get the document this set is attached to.
String	getName() Get the name of this set.
AnnotationSet	getStrict(Long startOffset, Long endOffset) Select annotations by offset.
protected void	indexByEndOffset() Construct the positional indices for annotation end
protected void	indexByStartOffset() Construct the positional indices for annotation start
protected void	indexByType() Construct the positional index.
Iterator	iterator() Get an iterator for this set
Node	lastNode() Get the node with the largest offset
Node	nextNode(Node node) Get the first node that is relevant for this annotation set and which has the offset larger than the one of the node provided.
boolean	remove(Object o) Remove an element from this set.
void	removeAnnotationSetListener(AnnotationSetListener l)
protected boolean	removeFromIdIndex(Annotation a) Remove from the ID index.
protected void	removeFromOffsetIndex(Annotation a) Remove from the offset indices.
protected void	removeFromTypeIndex(Annotation a) Remove from the type index.
void	removeGateListener(GateListener l)
static void	setAnnotationFactory(AnnotationFactory newFactory) Set the annotation factory used to create annotation objects.
int	size() The size of this set

Methods inherited from class java.util.AbstractSet

equals, hashCode, removeAll

Methods inherited from class java.util.AbstractCollection

clear, contains, containsAll, isEmpty, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Set

clear, contains, containsAll, equals, hashCode, isEmpty, removeAll, retainAll, toArray, toArray

Field Detail

annFactory

protected static AnnotationFactory annFactory

annotsById

protected HashMap annotsById

Maps annotation ids (Integers) to Annotations

annotationSetListeners

protected transient Vector annotationSetListeners

Constructor Detail

AnnotationSetImpl

public AnnotationSetImpl(Document doc)

Construction from Document.

AnnotationSetImpl

public AnnotationSetImpl(Document doc,
                         String name)

Construction from Document and name.

AnnotationSetImpl

public AnnotationSetImpl(Collection c)
                  throws ClassCastException

Construction from Collection (which must be an AnnotationSet)

Throws:

ClassCastException

Method Detail

iterator

public Iterator iterator()

Get an iterator for this set

Specified by:

iterator in interface SimpleAnnotationSet

Specified by:

iterator in interface Iterable

Specified by:

iterator in interface Collection

Specified by:

iterator in interface Set

Specified by:

iterator in class AbstractCollection

remove

public boolean remove(Object o)
               throws ClassCastException

Remove an element from this set.

Specified by:

remove in interface SimpleAnnotationSet

Specified by:

remove in interface Collection

Specified by:

remove in interface Set

Overrides:

remove in class AbstractCollection

Throws:

ClassCastException

removeFromIdIndex

protected boolean removeFromIdIndex(Annotation a)

Remove from the ID index.

removeFromTypeIndex

protected void removeFromTypeIndex(Annotation a)

Remove from the type index.

removeFromOffsetIndex

protected void removeFromOffsetIndex(Annotation a)

Remove from the offset indices.

size

public int size()

The size of this set

Specified by:

size in interface SimpleAnnotationSet

Specified by:

size in interface Collection

Specified by:

size in interface Set

Specified by:

size in class AbstractCollection

get

public Annotation get(Integer id)

Find annotations by id

Specified by:

get in interface SimpleAnnotationSet

get

public AnnotationSet get()

Get all annotations

Specified by:

get in interface SimpleAnnotationSet

get

public AnnotationSet get(String type)

Select annotations by type

Specified by:

get in interface SimpleAnnotationSet

get

public AnnotationSet get(Set types)
                  throws ClassCastException

Select annotations by a set of types. Expects a Set of String.

Specified by:

get in interface SimpleAnnotationSet

Throws:

ClassCastException

get

public AnnotationSet get(String type,
                         FeatureMap constraints)

Select annotations by type and features This will return an annotation set containing just those annotations of a particular type (i.e. with a particular name) and which have features with specific names and values. (It will also return annotations that have features besides those specified, but it will not return any annotations that do not have all the specified feature-value pairs.) However, if constraints contains a feature whose value is equal to gate.creole.ANNIEConstants.LOOKUP_CLASS_FEATURE_NAME (which is normally "class"), then GATE will attempt to match that feature using an ontology which it will try to retreive from a feature on the both the annotation and in constraints. If these do not return identical ontologies, or if either the annotation or constraints does not contain an ontology, then matching will fail, and the annotation will not be added. In summary, this method will not work normally for features with the name "class".

Specified by:

get in interface AnnotationSet

Parameters:

type - The name of the annotations to return.

constraints - A feature map containing all of the feature value pairs that the annotation must have in order for them to be returned.

Returns:

An annotation set containing only those annotations with the given name and which have the specified set of feature-value pairs.

get

public AnnotationSet get(String type,
                         Set featureNames)

Select annotations by type and feature names

Specified by:

get in interface AnnotationSet

get

public AnnotationSet get(Long offset)

Select annotations by offset. This returns the set of annotations whose start node is the least such that it is less than or equal to offset. If a positional index doesn't exist it is created. If there are no nodes at or beyond the offset param then it will return null.

Specified by:

get in interface AnnotationSet

get

public AnnotationSet get(Long startOffset,
                         Long endOffset)

Select annotations by offset. This returns the set of annotations that overlap totaly or partially with the interval defined by the two provided offsets.The result will include all the annotations that either:

• start before the start offset and end strictly after it
• OR
• start at a position between the start and the end offsets

Specified by:

get in interface AnnotationSet

getStrict

public AnnotationSet getStrict(Long startOffset,
                               Long endOffset)

Select annotations by offset. This returns the set of annotations that overlap strictly with the interval defined by the two provided offsets.The result will include all the annotations that start at the start offset and end strictly at the end offset

get

public AnnotationSet get(String neededType,
                         Long startOffset,
                         Long endOffset)

Select annotations by offset. This returns the set of annotations of the given type that overlap totaly or partially with the interval defined by the two provided offsets.The result will include all the annotations that either:

• start before the start offset and end strictly after it
• OR
• start at a position between the start and the end offsets

Specified by:

get in interface AnnotationSet

get

public AnnotationSet get(String type,
                         FeatureMap constraints,
                         Long offset)

Select annotations by type, features and offset

Specified by:

get in interface AnnotationSet

getContained

public AnnotationSet getContained(Long startOffset,
                                  Long endOffset)

Select annotations by offset that start at a position between the start and end before the end offset

Specified by:

getContained in interface AnnotationSet

firstNode

public Node firstNode()

Get the node with the smallest offset

Specified by:

firstNode in interface AnnotationSet

lastNode

public Node lastNode()

Get the node with the largest offset

Specified by:

lastNode in interface AnnotationSet

nextNode

public Node nextNode(Node node)

Get the first node that is relevant for this annotation set and which has the offset larger than the one of the node provided.

Specified by:

nextNode in interface AnnotationSet

setAnnotationFactory

public static void setAnnotationFactory(AnnotationFactory newFactory)

Set the annotation factory used to create annotation objects. The default factory is DefaultAnnotationFactory.

add

public Integer add(Node start,
                   Node end,
                   String type,
                   FeatureMap features)

Create and add an annotation with pre-existing nodes, and return its id

Specified by:

add in interface SimpleAnnotationSet

add

public boolean add(Object o)
            throws ClassCastException

Add an existing annotation. Returns true when the set is modified.

Specified by:

add in interface SimpleAnnotationSet

Specified by:

add in interface Collection

Specified by:

add in interface Set

Overrides:

add in class AbstractCollection

Throws:

ClassCastException

addAll

public boolean addAll(Collection c)

Adds multiple annotations to this set in one go. All the objects in the provided collection should be of Annotation type, otherwise a ClassCastException will be thrown. The provided annotations will be used to create new annotations using the appropriate add() methods from this set. The new annotations will have different IDs from the old ones (which is required in order to preserve the uniqueness of IDs inside an annotation set).

Specified by:

addAll in interface Collection

Specified by:

addAll in interface Set

Overrides:

addAll in class AbstractCollection

Parameters:

c - a collection of annotations

Returns:

true if the set has been modified as a result of this call.

addAllKeepIDs

protected boolean addAllKeepIDs(Collection c)

Adds multiple annotations to this set in one go. All the objects in the provided collection should be of Annotation type, otherwise a ClassCastException will be thrown. This method does not create copies of the annotations like addAll() does but simply adds the new annotations to the set. It is intended to be used solely by annotation sets in order to construct the results for various get(...) methods.

Parameters:

c - a collection of annotations

Returns:

true if the set has been modified as a result of this call.

add

public Integer add(Long start,
                   Long end,
                   String type,
                   FeatureMap features)
            throws InvalidOffsetException

Create and add an annotation and return its id

Specified by:

add in interface SimpleAnnotationSet

Throws:

InvalidOffsetException

add

public void add(Integer id,
                Long start,
                Long end,
                String type,
                FeatureMap features)
         throws InvalidOffsetException

Create and add an annotation from database read data In this case the id is already known being previously fetched from the database

Specified by:

add in interface AnnotationSet

Throws:

InvalidOffsetException

indexByType

protected void indexByType()

Construct the positional index.

indexByStartOffset

protected void indexByStartOffset()

Construct the positional indices for annotation start

indexByEndOffset

protected void indexByEndOffset()

Construct the positional indices for annotation end

edit

public void edit(Long start,
                 Long end,
                 DocumentContent replacement)

Propagate changes to the document content. Has, unfortunately, to be public, to allow DocumentImpls to get at it. Oh for a "friend" declaration. Doesn't throw InvalidOffsetException as DocumentImpl is the only client, and that checks the offsets before calling this method.

getName

public String getName()

Get the name of this set.

Specified by:

getName in interface SimpleAnnotationSet

getDocument

public Document getDocument()

Get the document this set is attached to.

Specified by:

getDocument in interface SimpleAnnotationSet

getAllTypes

public Set getAllTypes()

Get a set of java.lang.String objects representing all the annotation types present in this annotation set.

Specified by:

getAllTypes in interface SimpleAnnotationSet

clone

public Object clone()
             throws CloneNotSupportedException

Overrides:

clone in class Object

Returns:

a clone of this set.

Throws:

CloneNotSupportedException

removeAnnotationSetListener

public void removeAnnotationSetListener(AnnotationSetListener l)

Specified by:

removeAnnotationSetListener in interface AnnotationSet

Parameters:

l -

addAnnotationSetListener

public void addAnnotationSetListener(AnnotationSetListener l)

Specified by:

addAnnotationSetListener in interface AnnotationSet

Parameters:

l -

fireAnnotationAdded

protected void fireAnnotationAdded(AnnotationSetEvent e)

Parameters:

e -

fireAnnotationRemoved

protected void fireAnnotationRemoved(AnnotationSetEvent e)

Parameters:

e -

removeGateListener

public void removeGateListener(GateListener l)

Specified by:

removeGateListener in interface AnnotationSet

Parameters:

l -

addGateListener

public void addGateListener(GateListener l)

Specified by:

addGateListener in interface AnnotationSet

Parameters:

l -

fireGateEvent

protected void fireGateEvent(GateEvent e)

Parameters:

e -