project35.soa.ontology.sources
Class AbstractTreeOntologySource

java.lang.Object
  project35.soa.ontology.sources.AbstractTreeOntologySource

All Implemented Interfaces:

java.io.Serializable, OntologySource, TreeOntologySource, ServiceClass

Direct Known Subclasses:

DefaultSubtreeOntologySource, TabIndentedTextSource, XMLOntologySource

public abstract class AbstractTreeOntologySource
extends java.lang.Object
implements TreeOntologySource

This class is used to manage a tree of terms. Subclasses construct tree elements from sources such as tab indented files and xml files. Also contains routines for searching through the tree.

Copyright (c) Kevin Garwood and University of Manchester 2007. All rights reserved. Licensed under the Academic Free License version 3.0. For more information on the terms and conditions, please see the file "LICENSE" that is included in this distribution.

Version:

1.0

Author:

Kevin Garwood (kgarwood@users.sourceforge.net), code contributions from 2002 - September 30, 2007.

See Also:

Serialized Form

Field Summary

protected java.util.ArrayList	anchorTerms
protected java.text.Collator	collator
protected java.io.File	file
protected java.lang.String	fileName
protected boolean	isSourceWorking
protected StringMaskValidator	maskValidator
protected OntologyContext	ontologyContext
protected OntologyServiceMetaData	ontologyServiceMetaData
protected Parameter[]	parameters
protected java.net.URL	resourceDirectory
protected TreeOntologyTerm	rootTerm
protected TreeOntologyTerm	searchResultTerm
protected java.lang.StringBuffer	status
protected java.net.URL	url

Constructor Summary

AbstractTreeOntologySource()

Method Summary

protected void	addAnchorTerm(java.lang.String anchorTerm)
boolean	containsTerm(Project35FormContext project35FormContext, OntologyTerm ontologyTerm) determines whether an ontology contains a given term
Parameter[]	getInitialisationParameters()
OntologyServiceMetaData	getOntologyServiceMetaData(Project35FormContext project35FormContext)
abstract OntologyTermProvenance	getOntologyTermProvenance(Project35FormContext project35FormContext, OntologyTerm ontologyTerm)
OntologyTerm[]	getRelatedTerms(Project35FormContext project35FormContext, OntologyRelationshipType relationshipType, OntologyTerm ontologyTerm)
OntologySource	getSubOntologySource(Project35FormContext project35FormContext, Parameter[] parameterList) returns a part of the original ontology
OntologyRelationshipType[]	getSupportedOntologyRelationships(Project35FormContext project35FormContext)
OntologyTerm[]	getTerms(Project35FormContext project35FormContext) returns a collection of terms
TreeOntologyTerm	getTreeRoot(Project35FormContext project35FormContext)
void	initialiseService(java.net.URL resourceDirectory, Parameter[] parameters)
boolean	isWorking() indicates whether the ontology source is ready for service
protected void	reviseTreeWithAnchorTerms()
protected TreeOntologyTerm	search(java.lang.String mask)
protected TreeOntologyTerm	search(java.lang.String mask, TreeOntologyTerm ontologyTerm) returns a subtree search result based on a search parameter and a root node
protected void	setDescription(java.lang.String fileName)
java.lang.String	test() diagnostic method that indicates whether the ontology source is working.

Methods inherited from class java.lang.Object

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

Field Detail

anchorTerms

protected java.util.ArrayList anchorTerms

collator

protected java.text.Collator collator

rootTerm

protected TreeOntologyTerm rootTerm

searchResultTerm

protected TreeOntologyTerm searchResultTerm

maskValidator

protected StringMaskValidator maskValidator

file

protected java.io.File file

status

protected java.lang.StringBuffer status

isSourceWorking

protected boolean isSourceWorking

fileName

protected java.lang.String fileName

url

protected java.net.URL url

parameters

protected Parameter[] parameters

ontologyContext

protected OntologyContext ontologyContext

resourceDirectory

protected java.net.URL resourceDirectory

ontologyServiceMetaData

protected OntologyServiceMetaData ontologyServiceMetaData

Constructor Detail

AbstractTreeOntologySource

public AbstractTreeOntologySource()

Method Detail

search

protected TreeOntologyTerm search(java.lang.String mask)

search

protected TreeOntologyTerm search(java.lang.String mask,
                                  TreeOntologyTerm ontologyTerm)

returns a subtree search result based on a search parameter and a root node

Parameters:

mask - the search criteria

ontologyTerm - the root term where the search begins

Returns:

a root term whose children represents the results of the search

addAnchorTerm

protected void addAnchorTerm(java.lang.String anchorTerm)

reviseTreeWithAnchorTerms

protected void reviseTreeWithAnchorTerms()

isWorking

public boolean isWorking()

Description copied from interface: OntologySource

indicates whether the ontology source is ready for service

Specified by:

isWorking in interface OntologySource

getInitialisationParameters

public Parameter[] getInitialisationParameters()

Specified by:

getInitialisationParameters in interface ServiceClass

initialiseService

public void initialiseService(java.net.URL resourceDirectory,
                              Parameter[] parameters)
                       throws java.lang.Exception

Specified by:

initialiseService in interface ServiceClass

Throws:

java.lang.Exception

setDescription

protected void setDescription(java.lang.String fileName)

test

public java.lang.String test()

Description copied from interface: OntologySource

diagnostic method that indicates whether the ontology source is working.

Specified by:

test in interface OntologySource

getOntologyServiceMetaData

public OntologyServiceMetaData getOntologyServiceMetaData(Project35FormContext project35FormContext)

Specified by:

getOntologyServiceMetaData in interface OntologySource

getOntologyTermProvenance

public abstract OntologyTermProvenance getOntologyTermProvenance(Project35FormContext project35FormContext,
                                                                 OntologyTerm ontologyTerm)

Specified by:

getOntologyTermProvenance in interface OntologySource

getSupportedOntologyRelationships

public OntologyRelationshipType[] getSupportedOntologyRelationships(Project35FormContext project35FormContext)

Specified by:

getSupportedOntologyRelationships in interface OntologySource

getRelatedTerms

public OntologyTerm[] getRelatedTerms(Project35FormContext project35FormContext,
                                      OntologyRelationshipType relationshipType,
                                      OntologyTerm ontologyTerm)

Specified by:

getRelatedTerms in interface OntologySource

getTerms

public OntologyTerm[] getTerms(Project35FormContext project35FormContext)

Description copied from interface: OntologySource

returns a collection of terms

Specified by:

getTerms in interface OntologySource

Returns:

the ontology terms as a sorted list

containsTerm

public boolean containsTerm(Project35FormContext project35FormContext,
                            OntologyTerm ontologyTerm)

determines whether an ontology contains a given term

Specified by:

containsTerm in interface OntologySource

Parameters:

ontologyTerm - an ontology term

Returns:

true if the ontology contains a term; else the ontology doesn't contain the term

getTreeRoot

public TreeOntologyTerm getTreeRoot(Project35FormContext project35FormContext)

Specified by:

getTreeRoot in interface TreeOntologySource

Parameters:

project35FormContext - a collection of environment variables that refer to different parts of the Project35 application

Returns:

the root term of the ontology

getSubOntologySource

public OntologySource getSubOntologySource(Project35FormContext project35FormContext,
                                           Parameter[] parameterList)

returns a part of the original ontology

Specified by:

getSubOntologySource in interface OntologySource

Parameters:

parameterList - an array containing multiple terms enclosed in double quotation marks

Returns:

another ontology source based on the parameters and the original ontology source