com.ontotext.gate.ontology
Class TaxonomyImpl

java.lang.Object
  gate.util.AbstractFeatureBearer
      gate.creole.AbstractResource
          gate.creole.AbstractLanguageResource
              com.ontotext.gate.ontology.TaxonomyImpl

All Implemented Interfaces:

Taxonomy, LanguageResource, Resource, FeatureBearer, NameBearer, Serializable

Direct Known Subclasses:

OntologyImpl

public class TaxonomyImpl
extends AbstractLanguageResource
implements Taxonomy

A Taxonomy Implementation Class

Author:

borislav popov, Valentin Tablan

See Also:

Serialized Form

Field Summary

static byte	DIRECT_CLOSURE denotes a direct closure(no transitivity)
protected long	lastGeneratedId
protected boolean	modified Whether the ontology has been modified after loading. once it became true it stays true till a save takes place
protected boolean	nullBuffers Whether the ontology has been modified switches to true when null-ing and reinfering the subclasses and super classes and tops
static byte	TRANSITIVE_CLOSURE denotes atransitive closure

Fields inherited from class gate.creole.AbstractLanguageResource

dataStore, lrPersistentId

Fields inherited from class gate.util.AbstractFeatureBearer

features

Constructor Summary

TaxonomyImpl()

Method Summary

void	addClass(TClass theClass) Adds a class to the ontology.
void	addObjectModificationListener(ObjectModificationListener listener) Adds an object modification listener.
boolean	containsClassByName(String theName) Checks if the ontology contains a class with the given name.
TClass	createClass(String aName, String aComment) Creates a new OClass and returns it.
boolean	equals(Object o) Compares the id,uri and url of the ontology.
protected void	fireObjectModificationEvent(Object source) Fires an object modification event.
TClass	getClassByName(String theName) Retrieves a class by its name.
Set	getClasses() Retrieves all classes as a set.
Iterator	getClasses(Comparator comp) Retireves an iterator over the classes, ordered according to the comparator.
String	getComment() Gets the comment of this ontology.
String	getDefaultNameSpace() Gets the default name space for this ontology.
String	getId() Gets the id of this ontology.
String	getLabel() Retrieves the label of the ontology
static Taxonomy	getOntology(URL someUrl) Gets a taxonomy by URL.
int	getTaxonomicDistance(TClass class1, TClass class2) calculates the taxonomic distance between two classes. note that the method is relatively big, but in case similar methods are developed for graph traversal, some parts of this method would naturally become separate methods/members.
Set	getTopClasses() Gets the top classes.
URL	getURL() Gets the url of this ontology
String	getVersion() Gets the version of this ontology.
Resource	init() Initialises this resource, and returns it.
boolean	isDirectSubClassOf(String cls1, String cls2) Check for subclass relation with direct closure
boolean	isModified() Returns true of an LR has been modified since the last sync.
boolean	isSubClassOf(String cls1, String cls2) Check for subclass relation with transitive closure
void	load() Loads this ontology.
protected void	reinfer() Called when the ontology has been modified to re-infer all sub/super classes, tops, etc. currently could be implemented simpler but this implementation could be useful in the future
void	removeClass(TClass theClass) note: if a class is deleted and there aresome subclasses of this class which lack any other super classes : then they become top classes. this could be changed on request or made optional.
void	setComment(String theComment) Sets the comment of this ontology.
void	setDefaultNameSpace(String theURI) Sets the URI of the ontology
void	setId(String theID) Sets the id of this ontology.
void	setLabel(String theLabel) Sets the label of the ontology
void	setModified(boolean isModified) Sets the modified flag.
void	setURL(URL aUrl) Set the url of this ontology
void	setVersion(String theVersion) Sets version to this ontology.
void	store() Stores this ontology.
String	toString()

Methods inherited from class gate.creole.AbstractLanguageResource

cleanup, getDataStore, getLRPersistenceId, getParent, setDataStore, setLRPersistenceId, setParent, sync

Methods inherited from class gate.creole.AbstractResource

checkParameterValues, getBeanInfo, getName, getParameterValue, getParameterValue, removeResourceListeners, setName, setParameterValue, setParameterValue, setParameterValues, setParameterValues, setResourceListeners

Methods inherited from class gate.util.AbstractFeatureBearer

getFeatures, setFeatures

Methods inherited from class java.lang.Object

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

Methods inherited from interface gate.LanguageResource

getDataStore, getLRPersistenceId, getParent, setDataStore, setLRPersistenceId, setParent, sync

Methods inherited from interface gate.Resource

cleanup, getParameterValue, setParameterValue, setParameterValues

Methods inherited from interface gate.util.FeatureBearer

getFeatures, setFeatures

Methods inherited from interface gate.util.NameBearer

getName, setName

Field Detail

DIRECT_CLOSURE

public static final byte DIRECT_CLOSURE

denotes a direct closure(no transitivity)

See Also:

Constant Field Values

TRANSITIVE_CLOSURE

public static final byte TRANSITIVE_CLOSURE

denotes atransitive closure

See Also:

Constant Field Values

lastGeneratedId

protected long lastGeneratedId

nullBuffers

protected boolean nullBuffers

Whether the ontology has been modified switches to true when null-ing and reinfering the subclasses and super classes and tops

modified

protected boolean modified

Whether the ontology has been modified after loading. once it became true it stays true till a save takes place

Constructor Detail

TaxonomyImpl

public TaxonomyImpl()

Method Detail

addObjectModificationListener

public void addObjectModificationListener(ObjectModificationListener listener)

Adds an object modification listener.

Parameters:

listener - listener to be added.

fireObjectModificationEvent

protected void fireObjectModificationEvent(Object source)

Fires an object modification event.

Parameters:

event - the event to be fired

getOntology

public static Taxonomy getOntology(URL someUrl)
                            throws ResourceInstantiationException

Gets a taxonomy by URL. The taxonomy will be searched first among the existing LRs and afterwards loaded by the URL if not found

Parameters:

someUrl - the url of the taxonomy

Returns:

the retrieved or loaded taxonomy

Throws:

ResourceInstantiationException - if something gets wrong with the loading

init

public Resource init()
              throws ResourceInstantiationException

Initialises this resource, and returns it.

Specified by:

init in interface Resource

Overrides:

init in class AbstractResource

Throws:

ResourceInstantiationException

getURL

public URL getURL()

Description copied from interface: Taxonomy

Gets the url of this ontology

Specified by:

getURL in interface Taxonomy

Returns:

the url of this ontology

setURL

public void setURL(URL aUrl)

Description copied from interface: Taxonomy

Set the url of this ontology

Specified by:

setURL in interface Taxonomy

Parameters:

aUrl - the url to be set

setLabel

public void setLabel(String theLabel)

Sets the label of the ontology

Specified by:

setLabel in interface Taxonomy

Parameters:

theLabel - the label to be set

getLabel

public String getLabel()

Retrieves the label of the ontology

Specified by:

getLabel in interface Taxonomy

Returns:

the label of the ontology

load

public void load()
          throws ResourceInstantiationException

Description copied from interface: Taxonomy

Loads this ontology. According to different storages - different implementations are expected. Should take care of the modifiedAfterLoading member

Specified by:

load in interface Taxonomy

Throws:

ResourceInstantiationException

store

public void store()
           throws ResourceInstantiationException

Description copied from interface: Taxonomy

Stores this ontology. According to different storages - different implementations are expected. Should take care of the modifiedAfterLoading member

Specified by:

store in interface Taxonomy

Throws:

ResourceInstantiationException

setDefaultNameSpace

public void setDefaultNameSpace(String theURI)

Description copied from interface: Taxonomy

Sets the URI of the ontology

Specified by:

setDefaultNameSpace in interface Taxonomy

Parameters:

theURI - the URI to be set

getDefaultNameSpace

public String getDefaultNameSpace()

Description copied from interface: Taxonomy

Gets the default name space for this ontology. This value is prepended to local URIs (the ones not containing '#'.

Specified by:

getDefaultNameSpace in interface Taxonomy

Returns:

a String value.

setVersion

public void setVersion(String theVersion)

Description copied from interface: Taxonomy

Sets version to this ontology.

Specified by:

setVersion in interface Taxonomy

Parameters:

theVersion - the version to be set

getVersion

public String getVersion()

Description copied from interface: Taxonomy

Gets the version of this ontology.

Specified by:

getVersion in interface Taxonomy

Returns:

the version of this ontology

getId

public String getId()

Description copied from interface: Taxonomy

Gets the id of this ontology.

Specified by:

getId in interface Taxonomy

Returns:

the id of this ontology

setId

public void setId(String theID)

Description copied from interface: Taxonomy

Sets the id of this ontology.

Specified by:

setId in interface Taxonomy

Parameters:

theID - the id to be set

getComment

public String getComment()

Description copied from interface: Taxonomy

Gets the comment of this ontology.

Specified by:

getComment in interface Taxonomy

Returns:

the comment of this ontology

setComment

public void setComment(String theComment)

Description copied from interface: Taxonomy

Sets the comment of this ontology.

Specified by:

setComment in interface Taxonomy

Parameters:

theComment - the comment to be set

createClass

public TClass createClass(String aName,
                          String aComment)

Description copied from interface: Taxonomy

Creates a new OClass and returns it.

Specified by:

createClass in interface Taxonomy

Parameters:

aName - the name of this class

aComment - the comment of this class

Returns:

the newly created class

removeClass

public void removeClass(TClass theClass)

note: if a class is deleted and there aresome subclasses of this class which lack any other super classes : then they become top classes. this could be changed on request or made optional.

Specified by:

removeClass in interface Taxonomy

Parameters:

theClass - the class to be removed

addClass

public void addClass(TClass theClass)

Description copied from interface: Taxonomy

Adds a class to the ontology.

Specified by:

addClass in interface Taxonomy

Parameters:

theClass - the class to be added

getClassByName

public TClass getClassByName(String theName)

Description copied from interface: Taxonomy

Retrieves a class by its name.

Specified by:

getClassByName in interface Taxonomy

Parameters:

theName - the name of the class

Returns:

the class matching the name or null if no matches.

containsClassByName

public boolean containsClassByName(String theName)

Description copied from interface: Taxonomy

Checks if the ontology contains a class with the given name.

Specified by:

containsClassByName in interface Taxonomy

Parameters:

theName - name of a class

Returns:

true if the ontology contains a class with the name specified

getClasses

public Set getClasses()

Description copied from interface: Taxonomy

Retrieves all classes as a set.

Specified by:

getClasses in interface Taxonomy

Returns:

set of all the classes in this ontology

getClasses

public Iterator getClasses(Comparator comp)

Description copied from interface: Taxonomy

Retireves an iterator over the classes, ordered according to the comparator.

Specified by:

getClasses in interface Taxonomy

Parameters:

comp - a comparator defining the order of iterating the classes

Returns:

an iterator over the classes

getTopClasses

public Set getTopClasses()

Description copied from interface: Taxonomy

Gets the top classes.

Specified by:

getTopClasses in interface Taxonomy

Returns:

set of the top classes of this ontology

getTaxonomicDistance

public int getTaxonomicDistance(TClass class1,
                                TClass class2)

calculates the taxonomic distance between two classes. note that the method is relatively big, but in case similar methods are developed for graph traversal, some parts of this method would naturally become separate methods/members.

Specified by:

getTaxonomicDistance in interface Taxonomy

Parameters:

class1 - the first class

class2 - the second class

Returns:

the taxonomic distance between the 2 classes

equals

public boolean equals(Object o)

Compares the id,uri and url of the ontology.

Specified by:

equals in interface Taxonomy

Overrides:

equals in class Object

Parameters:

o - another ontology to compare with

Returns:

true if id,uri and url match

toString

public String toString()

Overrides:

toString in class Object

reinfer

protected void reinfer()

Called when the ontology has been modified to re-infer all sub/super classes, tops, etc. currently could be implemented simpler but this implementation could be useful in the future

setModified

public void setModified(boolean isModified)

Description copied from interface: Taxonomy

Sets the modified flag.

Specified by:

setModified in interface Taxonomy

Parameters:

isModified - sets this param as a value of the modified property of the ontology

isModified

public boolean isModified()

Description copied from class: AbstractLanguageResource

Returns true of an LR has been modified since the last sync. Always returns false for transient LRs.

Specified by:

isModified in interface Taxonomy

Specified by:

isModified in interface LanguageResource

Overrides:

isModified in class AbstractLanguageResource

Returns:

whether the ontology has been modified after the loading

isSubClassOf

public boolean isSubClassOf(String cls1,
                            String cls2)

Check for subclass relation with transitive closure

Specified by:

isSubClassOf in interface Taxonomy

Parameters:

cls1 - the first class

cls2 - the second class

isDirectSubClassOf

public boolean isDirectSubClassOf(String cls1,
                                  String cls2)

Check for subclass relation with direct closure

Specified by:

isDirectSubClassOf in interface Taxonomy

Parameters:

cls1 - the first class

cls2 - the second class