From 503f33d246c706eb2132d8884f9fdb27b519c8ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Mon, 31 Mar 2008 10:26:08 +0000
Subject: [PATCH] - fully implemented abstract ontology management
---
html/relnotes.html | 24 +-
html/up2to3.html | 85 +++--
lib/mappingapilite.jar | Bin 89807 -> 89807 bytes
.../exmo/align/impl/BasicAlignment.java | 65 +++-
.../inrialpes/exmo/align/impl/BasicCell.java | 14 +
.../exmo/align/impl/ConcatenatedIterator.java | 3 +-
.../exmo/align/impl/DistanceAlignment.java | 184 +++++-----
.../exmo/align/impl/MatrixMeasure.java | 98 +++--
.../exmo/align/impl/OWLAPIAlignment.java | 68 +---
.../inrialpes/exmo/align/impl/OWLAPICell.java | 32 +-
.../exmo/align/impl/ObjectAlignment.java | 188 ++++++++++
.../inrialpes/exmo/align/impl/ObjectCell.java | 115 ++++++
.../inrialpes/exmo/align/impl/Similarity.java | 28 +-
.../exmo/align/impl/eval/ExtPREvaluator.java | 159 ++++----
.../align/impl/eval/SymMeanEvaluator.java | 58 ++-
.../impl/method/ClassStructAlignment.java | 201 ++++------
.../impl/method/EditDistNameAlignment.java | 40 +-
.../impl/method/NameAndPropertyAlignment.java | 217 +++++------
.../align/impl/method/NameEqAlignment.java | 48 +--
.../align/impl/method/SMOANameAlignment.java | 45 +--
.../impl/method/StringDistAlignment.java | 51 +--
.../impl/method/StrucSubsDistAlignment.java | 347 +++++++-----------
.../impl/method/SubsDistNameAlignment.java | 56 +--
.../renderer/COWLMappingRendererVisitor.java | 61 ++-
.../renderer/OWLAxiomsRendererVisitor.java | 154 ++++----
.../impl/renderer/RDFRendererVisitor.java | 44 ++-
.../renderer/SEKTMappingRendererVisitor.java | 86 ++---
.../impl/renderer/SKOSRendererVisitor.java | 37 +-
.../impl/renderer/SWRLRendererVisitor.java | 112 +++---
.../impl/renderer/XSLTRendererVisitor.java | 30 +-
.../exmo/align/ling/JWNLAlignment.java | 39 +-
.../exmo/align/onto/HeavyLoadedOntology.java | 64 ++++
.../align/onto/owlapi10/OWLAPIOntology.java | 36 ++
.../onto/owlapi10/OWLAPIOntologyFactory.java | 2 +-
.../exmo/align/parser/AlignmentParser.java | 10 +-
.../align/service/AServProtocolManager.java | 18 +-
.../exmo/align/service/CacheImpl.java | 2 +-
.../align/service/CannotRenderAlignment.java | 4 +-
.../exmo/align/util/ExtGroupEval.java | 6 +-
.../exmo/align/util/ParserPrinter.java | 7 +-
.../inrialpes/exmo/align/util/Procalign.java | 2 +-
src/org/semanticweb/owl/align/Alignment.java | 12 +-
42 files changed, 1474 insertions(+), 1378 deletions(-)
create mode 100644 src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
create mode 100644 src/fr/inrialpes/exmo/align/impl/ObjectCell.java
create mode 100644 src/fr/inrialpes/exmo/align/onto/HeavyLoadedOntology.java
diff --git a/html/relnotes.html b/html/relnotes.html
index 59134f5c..d26a8174 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -17,23 +17,33 @@
<h2>Under development</h2>
<p><ul compact="1">
+<li>Output HTML in XHTML+RDFa (impl)</li>
<li>Online evaluation (server)</li>
<li>Upgrade to OWL 1.1 (impl)</li>
-<li>Restructuring language dependent alignments (impl)</li>
<li>Implementing database store for OMWG Language (server)</li>
-<li>Replacing <tt>Parameters</tt> with Java <tt>Property</tt> (api/impl)</li>
+<li>Implement ontology support database store (server)</li>
<li>Implement debug options with log4j</li>
<li>Use more for-each Java 1.5 construct</li>
+<li>Rendering alignments as module descriptions (impl)</li>
+<li>Replacing <tt>Parameters</tt> with Java <tt>Property</tt> (api/impl)[Version 4]</li>
</ul></p>
<h2>Current SVN trunk version</h2>
-<!--h2>Version 3.3 (): xx/yy/2008 - O sole mio</h2-->
+<!--h2>Version 3.3 (688): xx/yy/2008 - O sole mio</h2-->
<p><ul compact="1">
-<li>Added an abstract ontology interface (impl)</li>
+<li>Suppressed language dependent (OWLAPI) alignments (impl)</li>
+<li><a href="up2to3.html" style="color:red;">Deprecated</a>
+ <tt>OWLAPIAlignment</tt> to be replaced by <tt>ObjectAlignment</tt></li>
+<li>Reimplemented the whole API in function of the onto package (impl)</li>
+<li>Added an abstract ontology package allowing to change API (onto)</li>
+<li>Made <tt>Alignment</tt> iterable<Cell> (api/impl)</li>
+<li>Corrected a bug in AlignmentParser that overlooked formalism URI (parser)</li>
<li>Passed to Java 1.5 generics [incl. API modif] (dev/api)</li>
+<li>Added first unit tests (TestNG) (dev)</li>
<li>Passed all code through lint (dev)</li>
+<li>Corrected link to documentation (doc)</li>
</ul></p>
<h2>Version 3.2 (666): 29/02/2008 - Blejsko jezero</h2>
@@ -57,7 +67,7 @@
<li>MANIFEST generation in buildfile (distrib)</li>
<li>Improved version number management</li>
<li>Javadoc generation flawless in buildfile (distrib)</li>
-<li>Revised reference manual</li>
+<li>Revised reference manual (doc)</li>
</ul>
</p>
@@ -122,7 +132,9 @@ Other improvements include:
The main modification in this version is more independence from the
OWL API which is not anymore compulsory. Consequently, the existing
implementation of matching methods with Alignment API should undergo
- some modifications: <a href="up2to3.html">Here is how to do</a>.</p>
+ some modifications: <a href="up2to3.html">Here is how to do</a>
+ (this document has been updated to help migrating directly to
+ version 3.3 if necessary).</p>
<p>The Alignment API is now compiled in Java 1.5 (older versions
should still be able to run it).</p>
diff --git a/html/up2to3.html b/html/up2to3.html
index d3dfeba5..db5ef0a9 100644
--- a/html/up2to3.html
+++ b/html/up2to3.html
@@ -1,19 +1,56 @@
<html>
<head>
-<title>Alignment API: Upgrading from version 2.x to 3.0</title>
+<title>Alignment API: Upgrading from version 2.x to 3.3</title>
<!--style type="text/css">@import url(style.css);</style-->
<link rel="stylesheet" type="text/css" href="base.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body bgcolor="#ffffff">
-<center><h1>Upgrading an Alignment implementation from version 2.x to
- 3.0 of the Alignment API</h1></center>
-
-<p>The version 3.0 of the Alignment API has been designed to provide
- matching algorithm designers more flexibility. In particular, the
- version 3.0 does not necessarily rely on the OWL API, so designers
- who want to use another OWL API can do so at no cost.</p>
+<center><h1>Upgrading an Alignment implementation from version 2.x to 3.3 of the Alignment API</h1></center>
+
+<p>
+Version 3.0 of the Alignment API has been designed to provide
+matching algorithm designers more flexibility. In particular, the
+version 3.0 does not necessarily rely on the OWL API, so designers
+who want to use another OWL API, e.g., Jena, can do so at no cost.
+</p>
+
+<p>
+Version 3.3 goes one step further towards providing an API
+independent access to ontologies. Hence it is possible to switch from
+one API to another without changing code (see documentation).
+</p>
+
+<p>
+This has led to some changes over time in the API.
+</p>
+
+<h2>Since version 3.3, OWLAPIAlignment, OWLAPICell, getObjectXAsURI() are
+ deprecated</h2>
+
+<p>
+The <tt>OWLAPIAlignment</tt> and <tt>OWLAPICell</tt> introduced in
+version 3.0 and which were previously discussed below are now deprecated and
+replaced by <tt>ObjectAlignment</tt> and <tt>ObjectCell</tt>. However,
+for compatibility purposes, these classes are still available and have
+been reimplemented in function of the new ones. They still have the
+same structure, content and behavior as the old ones, but the
+remainder of the API does not use them anymore.
+</p>
+
+<p>
+Moreover, in most of the cases, these classes can be safely replaced
+by the new ones (bringing the benefit of changing Ontology API).</p>
+
+<p>The main exception is that the <tt>getObjectXAsURI()</tt> is not available
+in <tt>ObjectCell</tt>. So, call to this method on <tt>ObjectCell</tt>
+will return <tt>null</tt>. The <tt>Ontology</tt> of the object is
+necessary to obtain its URI, through the call to:
+<pre>
+ontology.getEntityURI( cell.getObjectX() );
+</pre>
+</p>
<h2>Don't panic</h2>
@@ -22,20 +59,20 @@
3. But first do not panic. This document aims at helping you in this
simple task.</p>
-<h2>From Basic to OWLAPI</h2>
+<h2>From BasicAlignments to ObjectAlignments</h2>
<p>Previously you certainly had your class
extending <tt>BasicAlignment</tt>. You must now have it
- extending <tt>OWLAPIAlignment</tt>. This guarantee that you will
+ extending <tt>ObjectAlignment</tt>. This guarantee that you will
still find all the features found in the
previous <tt>BasicAlignment</tt>.</p>
<p>If you create on the fly new <tt>Alignment</tt> or
- new <tt>Cell</tt>, if they must contain <tt>OWLEntity</tt>, then
- be sure that they are created as <tt>OWLAPIAlignment</tt>
- and <tt>OWLAPICell</tt> respectively.</p>
+ new <tt>Cell</tt>, if they must contain <tt>Object</tt>
+ (e.g., <tt>OWLEntity</tt>), then
+ be sure that they are created as <tt>ObjectAlignment</tt>
+ and <tt>ObjectCell</tt> respectively.</p>
<p>The new implementation of <tt>BasicAlignment</tt>
- and <tt>BasicCell</tt> provides additional new primitives such
- as <tt>getOntology1URI()</tt> and <tt>getObject1AsURI()</tt>.</p>
+ provides additional new primitives such as <tt>getOntology1URI()</tt>.</p>
<h2>Parsing alignments</h2>
@@ -43,9 +80,9 @@
used <tt>AlignmentParser</tt> which returned
a <tt>BasicAlignment</tt>. Now the <tt>AlignmentParser</tt> returns
a <tt>URIAlignment</tt>. To turn this <tt>URIAlignment</tt> into
- a <tt>OWLAPIAlignment</tt>, just
- invoke <tt>OWLAPIAlignment.toOWLAPIAlignment( URIAlignment )</tt>. It
- will return the corresponding <tt>OWLAPIAlignment</tt>.</p>
+ an <tt>ObjectAlignment</tt>, just
+ invoke <tt>ObjectAlignment.toObjectAlignment( URIAlignment )</tt>. It
+ will return the corresponding <tt>ObjectAlignment</tt>.</p>
<p>Moreover, <tt>AlignmentParser.parse( URI )</tt> used to take a
Hashtable as a second argument. This is not true anymore: you must
@@ -57,19 +94,19 @@
following:
<pre>
AlignmentProcess al = new MyAlignment();
-al.init( OWLOntology, OWLOntology );
+al.init( Ontology, Ontology );
al.align( Alignment, Parameters );
</pre>
-(You may have used a <tt>MyAlignment( OWLOntology, OWLOntology )</tt>
+(You may have used a <tt>MyAlignment( Ontology, Ontology )</tt>
constructor and no <tt>init</tt>. Now the sequence above is compulsory).
-From version 3, the sequence is the same except that the arguments for init() are
+Since version 3.0, the sequence is the same except that the arguments for init() are
the <tt>URL</tt> where to find the ontologies instead of the ontology
themselves. It is thus necessary for you to change your implementation
of <tt>init()</tt> so that it loads the ontologies. Moreover, the init
Alignment in <tt>align()</tt> is a <tt>URIAlignment</tt> and not
-a <tt>OWLAPIAlignment</tt> so it may be necessary to change it as well.</p>
+a <tt>ObjectAlignment</tt> so it may be necessary to change it as well.</p>
-<p>Fortunately, the <tt>OWLAPIAlignment</tt> class already provides
+<p>Fortunately, the <tt>OntologyFactory</tt> class already provides
the <tt>loadOntology( URI, OntologyCache )</tt> method that loads the
required ontology and a <tt>loadInit( URI )</tt> method that will
load the initial alignment.</p>
@@ -78,7 +115,7 @@ a <tt>OWLAPIAlignment</tt> so it may be necessary to change it as well.</p>
<p>If you manipulated the alignment through the attributes
(<tt>onto1</tt> and <tt>onto2</tt>), you must now explicitely cast
- them as <tt>(OWLOntology)onto1</tt> because they are now declared
+ them as <tt>(Ontology)onto1</tt> because they are now declared
as <tt>Object</tt>.</p>
<h2>Misc.</h2>
diff --git a/lib/mappingapilite.jar b/lib/mappingapilite.jar
index 4ad55c763d9058068646f6db89ab6fb74ff00590..739d91e2bb26edeb2342522d35490c9757235016 100644
GIT binary patch
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diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index a51155bb..b0af8666 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -21,6 +21,7 @@
package fr.inrialpes.exmo.align.impl;
+import java.lang.Iterable;
import java.util.Hashtable;
import java.util.HashSet;
import java.util.Enumeration;
@@ -93,11 +94,17 @@ public class BasicAlignment implements Alignment {
onto2 = new BasicOntology<Object>();
}
+ /**
+ * Initialises the Alignment object with two ontologies.
+ * These two ontologies can be either an instance of fr.inrialpes.exmo.align.onto.Ontology
+ * which will then replaced the one that was there at creation time
+ * or a "concrete" ontology which will be inserted in the fr.inrialpes.exmo.align.onto.Ontology
+ * object.
+ */
public void init( Object onto1, Object onto2, Object cache ) throws AlignmentException {
- // JE: Onto I am not sure this works
if ( onto1 instanceof Ontology ) {
- this.onto1 = (Ontology<Object>)onto1;
- this.onto2 = (Ontology<Object>)onto2;
+ this.onto1 = (Ontology<Object>)onto1; // [W:unchecked]
+ this.onto2 = (Ontology<Object>)onto2; // [W:unchecked]
} else {
this.onto1.setOntology( onto1 );
this.onto2.setOntology( onto2 );
@@ -129,11 +136,11 @@ public class BasicAlignment implements Alignment {
return onto2.getOntology();
};
- public Ontology getOntologyObject1() {
+ public Ontology<Object> getOntologyObject1() {
return onto1;
};
- public Ontology getOntologyObject2() {
+ public Ontology<Object> getOntologyObject2() {
return onto2;
};
@@ -195,6 +202,10 @@ public class BasicAlignment implements Alignment {
return new MEnumeration<Cell>( hash1 );
}
+ public Iterator<Cell> iterator() {
+ return new MIterator<Cell>( hash1 );
+ }
+
public ArrayList<Cell> getArrayElements() {
ArrayList<Cell> array = new ArrayList<Cell>();
for (Enumeration e = getElements(); e.hasMoreElements(); ) {
@@ -267,8 +278,7 @@ public class BasicAlignment implements Alignment {
}
/*
- * Deprecated: implement as the one retrieving the highest strength correspondence
- * @deprecated
+ * @deprecated implemented as the one retrieving the highest strength correspondence
*/
public Cell getAlignCell1(Object ob) throws AlignmentException {
if ( Annotations.STRICT_IMPLEMENTATION == true ){
@@ -635,3 +645,44 @@ class MEnumeration<T> implements Enumeration<T> {
return val;
}
}
+
+class MIterator<T> implements Iterator<T> {
+ // Because of the remove, the implentation should be different
+ // Keeping the last element at hand
+ private Enumeration<Set<T>> set = null; // The enumeration of sets
+ private Iterator<T> current = null; // The current set's enumeration
+ private Iterator<T> next = null; // The next set enumeration
+
+ MIterator( Hashtable<Object,Set<T>> s ){
+ set = s.elements();
+ if ( set.hasMoreElements() ) {
+ current = set.nextElement().iterator();
+ if ( current.hasNext() ) {
+ next = current;
+ } else {
+ while( set.hasMoreElements() && next == null ){
+ next = set.nextElement().iterator();
+ if( !next.hasNext() ) next = null;
+ }
+ }
+ }
+ }
+ public boolean hasNext(){
+ return ( next != null && next.hasNext() );
+ }
+ public T next(){
+ current = next;
+ T val = current.next();
+ if( !current.hasNext() ){
+ next = null;
+ while( set.hasMoreElements() && next == null ){
+ next = set.nextElement().iterator();
+ if( !next.hasNext() ) next = null;
+ }
+ }
+ return val;
+ }
+ public void remove(){
+ if ( current != null ) current.remove();
+ }
+}
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicCell.java b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
index 0e97b6db..c8b2952d 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicCell.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
@@ -92,6 +92,13 @@ public class BasicCell implements Cell, Comparable<Cell> {
public void setSemantics( String sem ){ semantics = sem; };
public Object getObject1(){ return object1; };
public Object getObject2(){ return object2; };
+ /**
+ * Since version 3.3, the interpretation of objects (and thus finding their
+ * URI) depends on the Ontology API which is used. This information is not
+ * stored in the Cells (this would cost two pointers per cell) and thus,
+ * most of the time, this will raise an exception.
+ * Use <tt>Ontology.getEntityURI( this )</tt> instead.
+ */
public URI getObject1AsURI() throws AlignmentException {
if ( object1 instanceof URI ) {
return (URI)object1;
@@ -99,6 +106,13 @@ public class BasicCell implements Cell, Comparable<Cell> {
throw new AlignmentException( "Cannot find URI for "+object1 );
}
}
+ /**
+ * Since version 3.3, the interpretation of objects (and thus finding their
+ * URI) depends on the Ontology API which is used. This information is not
+ * stored in the Cells (this would cost two pointers per cell) and thus,
+ * most of the time, this will raise an exception.
+ * Use <tt>Ontology.getEntityURI( this )</tt> instead.
+ */
public URI getObject2AsURI() throws AlignmentException {
if ( object2 instanceof URI ) {
return (URI)object2;
diff --git a/src/fr/inrialpes/exmo/align/impl/ConcatenatedIterator.java b/src/fr/inrialpes/exmo/align/impl/ConcatenatedIterator.java
index 76f9a056..89ac07a1 100644
--- a/src/fr/inrialpes/exmo/align/impl/ConcatenatedIterator.java
+++ b/src/fr/inrialpes/exmo/align/impl/ConcatenatedIterator.java
@@ -26,8 +26,7 @@ import java.lang.UnsupportedOperationException;
/**
* This class builds a composite iterator from two iterators
- * This helps writing more concise code especially since
- * the OWL API does not impements Iterator getProperties() in OWL Ontologies
+ * This helps writing more concise code.
*
* This is the naive implementation (can be optimized)
*
diff --git a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
index ee6f1c78..209b8a8c 100644
--- a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
@@ -27,12 +27,7 @@ import java.util.TreeSet;
import java.util.SortedSet;
import java.util.Comparator;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLEntity;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLException;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
@@ -46,17 +41,18 @@ import org.semanticweb.owl.align.Parameters;
* @version $Id$
*/
-public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProcess
+public class DistanceAlignment extends ObjectAlignment implements AlignmentProcess
{
Similarity sim;
/** Creation **/
public DistanceAlignment() {}
- public DistanceAlignment( OWLOntology onto1, OWLOntology onto2 ){
+ // JE: OntoRewr (LoadedOntology -> one step above)
+ //public DistanceAlignment( LoadedOntology onto1, LoadedOntology onto2 ){
// Init must now be triggered explicitely
// init( onto1, onto2 );
- };
+ //};
public void setSimilarity( Similarity s ) { sim = s; }
public Similarity getSimilarity() { return sim; }
@@ -67,7 +63,7 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
public double getAlignedDistance1( Object ob ) throws AlignmentException {
return (1 - getAlignedStrength1(ob));
};
- public double getAlignedDistance2( Object ob ) throws AlignmentException{
+ public double getAlignedDistance2( Object ob ) throws AlignmentException {
return (1 - getAlignedStrength2(ob));
};
@@ -86,7 +82,8 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
if ( sim == null )
throw new AlignmentException("DistanceAlignment: requires a similarity measure");
- sim.initialize( (OWLOntology)getOntology1(), (OWLOntology)getOntology2(), init );
+ sim.initialize( ontology1(), ontology2(), init );
+ //sim.initialize( getOntologyObject1(), getOntologyObject2(), init );
sim.compute( params );
if ( params.getParameter("printMatrix") != null ) printDistanceMatrix(params);
extract( getType(), params );
@@ -161,17 +158,17 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
try {
// Extract for properties
ConcatenatedIterator pit1 = new
- ConcatenatedIterator(((OWLOntology)(onto1.getOntology())).getObjectProperties().iterator(),
- ((OWLOntology)(onto1.getOntology())).getDataProperties().iterator());
+ ConcatenatedIterator(ontology1().getObjectProperties().iterator(),
+ ontology1().getDataProperties().iterator());
for ( ; pit1.hasNext(); ) {
- OWLProperty prop1 = (OWLProperty)pit1.next();
+ Object prop1 = pit1.next();
found = false; max = threshold; val = 0;
- OWLProperty prop2 = null;
+ Object prop2 = null;
ConcatenatedIterator pit2 = new
- ConcatenatedIterator(((OWLOntology)(onto2.getOntology())).getObjectProperties().iterator(),
- ((OWLOntology)(onto2.getOntology())).getDataProperties().iterator());
+ ConcatenatedIterator(ontology2().getObjectProperties().iterator(),
+ ontology2().getDataProperties().iterator());
for ( ; pit2.hasNext(); ) {
- OWLProperty current = (OWLProperty)pit2.next();
+ Object current = pit2.next();
val = 1 - sim.getPropertySimilarity(prop1,current);
if ( val > max) {
found = true; max = val; prop2 = current;
@@ -180,30 +177,30 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
if ( found ) addAlignCell(prop1,prop2, "=", max);
}
// Extract for classes
- for (Iterator it1 = ((OWLOntology)(onto1.getOntology())).getClasses().iterator(); it1.hasNext(); ) {
- OWLClass class1 = (OWLClass)it1.next();
+ for (Iterator it1 = ontology1().getClasses().iterator(); it1.hasNext(); ) {
+ Object class1 = it1.next();
found = false; max = threshold; val = 0;
- OWLClass class2 = null;
- for (Iterator it2 = ((OWLOntology)(onto2.getOntology())).getClasses().iterator(); it2.hasNext(); ) {
- OWLClass current = (OWLClass)it2.next();
+ Object class2 = null;
+ for (Iterator it2 = ontology2().getClasses().iterator(); it2.hasNext(); ) {
+ Object current = it2.next();
val = 1 - sim.getClassSimilarity(class1,current);
if (val > max) {
found = true; max = val; class2 = current;
}
}
- if ( found ) addAlignCell(class1,class2, "=", max);
+ if ( found ) addAlignCell(class1, class2, "=", max);
}
// Extract for individuals
// This does not work, at least for the OAEI 2005 tests
if ( params.getParameter("noinst") == null ){
- for (Iterator it1 = ((OWLOntology)(onto1.getOntology())).getIndividuals().iterator(); it1.hasNext();) {
- OWLIndividual ind1 = (OWLIndividual)it1.next();
- if ( ind1.getURI() != null ) {
+ for (Iterator it1 = ontology1().getIndividuals().iterator(); it1.hasNext();) {
+ Object ind1 = it1.next();
+ if ( ontology1().getEntityURI( ind1 ) != null ) {
found = false; max = threshold; val = 0;
- OWLIndividual ind2 = null;
- for (Iterator it2 = ((OWLOntology)(onto2.getOntology())).getIndividuals().iterator(); it2.hasNext(); ) {
- OWLIndividual current = (OWLIndividual)it2.next();
- if ( current.getURI() != null ) {
+ Object ind2 = null;
+ for (Iterator it2 = ontology2().getIndividuals().iterator(); it2.hasNext(); ) {
+ Object current = it2.next();
+ if ( ontology2().getEntityURI( current ) != null ) {
val = 1 - sim.getIndividualSimilarity(ind1,current);
if (val > max) {
found = true; max = val; ind2 = current;
@@ -214,8 +211,7 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
}
}
}
- } catch (OWLException owlex) { owlex.printStackTrace(); }
- catch (AlignmentException alex) { alex.printStackTrace(); }
+ } catch (AlignmentException alex) { alex.printStackTrace(); }
return((Alignment)this);
}
@@ -230,18 +226,18 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
// (redoing the matrix instead of getting it)
// For each kind of stuff (cl, pr, ind)
// Create a matrix
- int nbclasses1 = ((OWLOntology)(onto1.getOntology())).getClasses().size();
- int nbclasses2 = ((OWLOntology)(onto2.getOntology())).getClasses().size();
+ int nbclasses1 = ontology1().nbClasses();
+ int nbclasses2 = ontology2().nbClasses();
double[][] matrix = new double[nbclasses1][nbclasses2];
- OWLClass[] class1 = new OWLClass[nbclasses1];
- OWLClass[] class2 = new OWLClass[nbclasses2];
+ Object[] class1 = new Object[nbclasses1];
+ Object[] class2 = new Object[nbclasses2];
int i = 0;
- for (Iterator it1 = ((OWLOntology)(onto1.getOntology())).getClasses().iterator(); it1.hasNext(); i++) {
- class1[i] = (OWLClass)it1.next();
+ for (Iterator it1 = ontology1().getClasses().iterator(); it1.hasNext(); i++) {
+ class1[i] = it1.next();
}
int j = 0;
- for (Iterator it2 = ((OWLOntology)(onto2.getOntology())).getClasses().iterator(); it2.hasNext(); j++) {
- class2[j] = (OWLClass)it2.next();
+ for (Iterator it2 = ontology2().getClasses().iterator(); it2.hasNext(); j++) {
+ class2[j] = it2.next();
}
for( i = 0; i < nbclasses1; i++ ){
for( j = 0; j < nbclasses2; j++ ){
@@ -258,31 +254,30 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
// it means that alignments with 0. similarity
// will be excluded from the best match.
if( val > threshold ){
- addCell( new OWLAPICell( (String)null, class1[result[i][0]], class2[result[i][1]], BasicRelation.createRelation("="), val ) );
+ addCell( new ObjectCell( (String)null, class1[result[i][0]], class2[result[i][1]], BasicRelation.createRelation("="), val ) );
}
}
- } catch (OWLException owlex) { owlex.printStackTrace(); }
- catch (AlignmentException alex) { alex.printStackTrace(); }
+ } catch (AlignmentException alex) { alex.printStackTrace(); }
// For properties
try{
- int nbprop1 = ((OWLOntology)(onto1.getOntology())).getDataProperties().size() + ((OWLOntology)(onto1.getOntology())).getObjectProperties().size();
- int nbprop2 = ((OWLOntology)(onto2.getOntology())).getDataProperties().size() + ((OWLOntology)(onto2.getOntology())).getObjectProperties().size();
+ int nbprop1 = ontology1().nbProperties();
+ int nbprop2 = ontology2().nbProperties();
double[][] matrix = new double[nbprop1][nbprop2];
- OWLProperty[] prop1 = new OWLProperty[nbprop1];
- OWLProperty[] prop2 = new OWLProperty[nbprop2];
+ Object[] prop1 = new Object[nbprop1];
+ Object[] prop2 = new Object[nbprop2];
int i = 0;
ConcatenatedIterator pit1 = new
- ConcatenatedIterator(((OWLOntology)(onto1.getOntology())).getObjectProperties().iterator(),
- ((OWLOntology)(onto1.getOntology())).getDataProperties().iterator());
+ ConcatenatedIterator(ontology1().getObjectProperties().iterator(),
+ ontology1().getDataProperties().iterator());
for (; pit1.hasNext(); i++) {
- prop1[i] = (OWLProperty)pit1.next();
+ prop1[i] = pit1.next();
}
int j = 0;
ConcatenatedIterator pit2 = new
- ConcatenatedIterator(((OWLOntology)(onto2.getOntology())).getObjectProperties().iterator(),
- ((OWLOntology)(onto2.getOntology())).getDataProperties().iterator());
+ ConcatenatedIterator(ontology2().getObjectProperties().iterator(),
+ ontology2().getDataProperties().iterator());
for (; pit2.hasNext(); j++) {
- prop2[j] = (OWLProperty)pit2.next();
+ prop2[j] = pit2.next();
}
for( i = 0; i < nbprop1; i++ ){
for( j = 0; j < nbprop2; j++ ){
@@ -299,11 +294,10 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
// it means that alignments with 0. similarity
// will be excluded from the best match.
if( val > threshold ){
- addCell( new OWLAPICell( (String)null, prop1[result[i][0]], prop2[result[i][1]], BasicRelation.createRelation("="), val ) );
+ addCell( new ObjectCell( (String)null, prop1[result[i][0]], prop2[result[i][1]], BasicRelation.createRelation("="), val ) );
}
}
- }catch (OWLException owlex) { owlex.printStackTrace(); }
- catch (AlignmentException alex) { alex.printStackTrace(); }
+ } catch (AlignmentException alex) { alex.printStackTrace(); }
return((Alignment)this);
}
@@ -322,7 +316,7 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
* with overall of 1.8.
*/
public Alignment extractqqNaive( double threshold, Parameters params) {
- OWLEntity ent1=null, ent2=null;
+ Object ent1=null, ent2=null;
double val = 0;
//TreeSet could be replaced by something else
//The comparator must always tell that things are different!
@@ -348,21 +342,21 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
return -1;
} else if ( o1.getStrength() < o2.getStrength() ){
return 1;
- } else if ( (((OWLEntity)o1.getObject1()).getURI().getFragment() == null)
- || (((OWLEntity)o2.getObject1()).getURI().getFragment() == null) ) {
+ } else if ( ontology1().getEntityName( o1.getObject1() ) == null
+ || ontology2().getEntityName( o2.getObject1() ) == null ) {
return -1;
- } else if ( ((OWLEntity)o1.getObject1()).getURI().getFragment().compareTo(((OWLEntity)o2.getObject1()).getURI().getFragment()) > 0) {
+ } else if ( ontology1().getEntityName( o1.getObject1()).compareTo( ontology2().getEntityName( o2.getObject1() ) ) > 0 ) {
return -1;
- } else if ( ((OWLEntity)o1.getObject1()).getURI().getFragment().compareTo(((OWLEntity)o2.getObject1()).getURI().getFragment()) < 0 ) {
+ } else if ( ontology1().getEntityName( o1.getObject1()).compareTo( ontology2().getEntityName( o2.getObject1() ) ) < 0 ) {
return 1;
- } else if ( (((OWLEntity)o1.getObject2()).getURI().getFragment() == null)
- || (((OWLEntity)o2.getObject2()).getURI().getFragment() == null) ) {
+ } else if ( ontology1().getEntityName( o1.getObject2() ) == null
+ || ontology2().getEntityName( o2.getObject2() ) == null ) {
return -1;
- } else if ( ((OWLEntity)o1.getObject2()).getURI().getFragment().compareTo(((OWLEntity)o2.getObject2()).getURI().getFragment()) > 0) {
+ } else if ( ontology1().getEntityName( o1.getObject2()).compareTo( ontology2().getEntityName( o2.getObject2() ) ) > 0 ) {
return -1;
- // On va supposer qu'ils n'ont pas le meme nom
+ // Assume they have different names
} else { return 1; }
- } catch ( OWLException e) {
+ } catch ( AlignmentException e) {
e.printStackTrace(); return 0;}
}
}
@@ -373,46 +367,43 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
// Plus a map from the objects to the cells
// O(n^2.log n)
ConcatenatedIterator pit1 = new
- ConcatenatedIterator(((OWLOntology)(onto1.getOntology())).getObjectProperties().iterator(),
- ((OWLOntology)(onto1.getOntology())).getDataProperties().iterator());
+ ConcatenatedIterator(ontology1().getObjectProperties().iterator(),
+ ontology1().getDataProperties().iterator());
for (; pit1.hasNext(); ) {
- ent1 = (OWLProperty)pit1.next();
+ ent1 = pit1.next();
ConcatenatedIterator pit2 = new
- ConcatenatedIterator(((OWLOntology)(onto2.getOntology())).getObjectProperties().iterator(),
- ((OWLOntology)(onto2.getOntology())).getDataProperties().iterator());
+ ConcatenatedIterator(ontology2().getObjectProperties().iterator(),
+ ontology2().getDataProperties().iterator());
for (; pit2.hasNext(); ) {
- ent2 = (OWLProperty)pit2.next();
- val = 1 - sim.getPropertySimilarity((OWLProperty)ent1,(OWLProperty)ent2);
- //val = ((SimilarityMeasure)getSimilarity()).getSimilarity(ent1.getURI(),ent2.getURI());
+ ent2 = pit2.next();
+ val = 1 - sim.getPropertySimilarity( ent1, ent2 );
if ( val > threshold ){
- cellSet.add( new OWLAPICell( (String)null, ent1, ent2, BasicRelation.createRelation("="), val ) );
+ cellSet.add( new ObjectCell( (String)null, ent1, ent2, BasicRelation.createRelation("="), val ) );
}
}
}
- for (Iterator it1 = ((OWLOntology)(onto1.getOntology())).getClasses().iterator(); it1.hasNext(); ) {
- ent1 = (OWLClass)it1.next();
- for (Iterator it2 = ((OWLOntology)(onto2.getOntology())).getClasses().iterator(); it2.hasNext(); ) {
- ent2 = (OWLClass)it2.next();
- val = 1 - sim.getClassSimilarity((OWLClass)ent1,(OWLClass)ent2);
- //val = ((SimilarityMeasure)getSimilarity()).getSimilarity(ent1.getURI(),ent2.getURI());
+ for (Iterator it1 = ontology1().getClasses().iterator(); it1.hasNext(); ) {
+ ent1 = it1.next();
+ for (Iterator it2 = ontology2().getClasses().iterator(); it2.hasNext(); ) {
+ ent2 = it2.next();
+ val = 1 - sim.getClassSimilarity( ent1, ent2 );
if ( val > threshold ){
- cellSet.add( new OWLAPICell( (String)null, ent1, ent2, BasicRelation.createRelation("="), val ) );
+ cellSet.add( new ObjectCell( (String)null, ent1, ent2, BasicRelation.createRelation("="), val ) );
}
}
}
// OLA with or without instances
if ( params.getParameter("noinst") == null ){
- for (Iterator it1 = ((OWLOntology)(onto1.getOntology())).getIndividuals().iterator(); it1.hasNext();) {
- ent1 = (OWLIndividual)it1.next();
- if ( ent1.getURI() != null ) {
+ for (Iterator it1 = ontology1().getIndividuals().iterator(); it1.hasNext();) {
+ ent1 = it1.next();
+ if ( ontology1().getEntityURI( ent1 ) != null ) {
- for (Iterator it2 = ((OWLOntology)(onto2.getOntology())).getIndividuals().iterator(); it2.hasNext(); ) {
- ent2 = (OWLIndividual)it2.next();
- if ( ent2.getURI() != null ) {
- val = 1 - sim.getIndividualSimilarity((OWLIndividual)ent1,(OWLIndividual)ent2);
- //val = ((SimilarityMeasure)getSimilarity()).getSimilarity(ent1.getURI(),ent2.getURI());
+ for (Iterator it2 = ontology2().getIndividuals().iterator(); it2.hasNext(); ) {
+ ent2 = it2.next();
+ if ( ontology2().getEntityURI( ent2 ) != null ) {
+ val = 1 - sim.getIndividualSimilarity( ent1, ent2 );
if ( val > threshold ){
- cellSet.add( new OWLAPICell( (String)null, ent1, ent2, BasicRelation.createRelation("="), val ) );
+ cellSet.add( new ObjectCell( (String)null, ent1, ent2, BasicRelation.createRelation("="), val ) );
}
}
}
@@ -423,16 +414,17 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
// O(n^2)
for( Iterator it = cellSet.iterator(); it.hasNext(); ){
Cell cell = (Cell)it.next();
- ent1 = (OWLEntity)cell.getObject1();
- ent2 = (OWLEntity)cell.getObject2();
+ ent1 = cell.getObject1();
+ ent2 = cell.getObject2();
if ( (getAlignCells1( ent1 ) == null) && (getAlignCells2( ent2 ) == null) ){
// The cell is directly added!
addCell( cell );
}
};
- } catch (AlignmentException alex) { alex.printStackTrace(); }
- catch (OWLException owlex) { owlex.printStackTrace(); }
+ } catch (AlignmentException alex) {
+ alex.printStackTrace();
+ };
return((Alignment)this);
}
diff --git a/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java b/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java
index 4d231e86..0f0f6caa 100644
--- a/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java
+++ b/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java
@@ -24,17 +24,13 @@ import java.util.Iterator;
import java.util.HashMap;
import java.text.NumberFormat;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLException;
-
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Parameters;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
+
import fr.inrialpes.exmo.align.impl.Similarity;
/**
@@ -49,8 +45,8 @@ import fr.inrialpes.exmo.align.impl.Similarity;
public abstract class MatrixMeasure implements Similarity {
//Momentaneously public
- public OWLOntology onto1 = null;
- public OWLOntology onto2 = null;
+ public LoadedOntology onto1 = null;
+ public LoadedOntology onto2 = null;
public int nbclass1 = 0; // number of classes in onto1
public int nbclass2 = 0; // number of classes in onto2
public int nbprop1 = 0; // number of classes in onto1
@@ -59,12 +55,12 @@ public abstract class MatrixMeasure implements Similarity {
public int nbind2 = 0; // number of individuals in onto2
public int i, j = 0; // index for onto1 and onto2 classes
public int l1, l2 = 0; // length of strings (for normalizing)
- public HashMap<OWLClass,Integer> classlist2 = null; // onto2 classes
- public HashMap<OWLClass,Integer> classlist1 = null; // onto1 classes
- public HashMap<OWLProperty,Integer> proplist2 = null; // onto2 properties
- public HashMap<OWLProperty,Integer> proplist1 = null; // onto1 properties
- public HashMap<OWLIndividual,Integer> indlist2 = null; // onto2 individuals
- public HashMap<OWLIndividual,Integer> indlist1 = null; // onto1 individuals
+ public HashMap<Object,Integer> classlist2 = null; // onto2 classes
+ public HashMap<Object,Integer> classlist1 = null; // onto1 classes
+ public HashMap<Object,Integer> proplist2 = null; // onto2 properties
+ public HashMap<Object,Integer> proplist1 = null; // onto1 properties
+ public HashMap<Object,Integer> indlist2 = null; // onto2 individuals
+ public HashMap<Object,Integer> indlist1 = null; // onto1 individuals
private NumberFormat numFormat = null; // printing
@@ -72,88 +68,88 @@ public abstract class MatrixMeasure implements Similarity {
public double prmatrix[][]; // distance matrix
public double indmatrix[][]; // distance matrix
- public void initialize( OWLOntology onto1, OWLOntology onto2, Alignment align ){
+ public void initialize( LoadedOntology onto1, LoadedOntology onto2, Alignment align ){
initialize( onto1, onto2 );
// Set the values of the initial alignment in the cells
}
- public void initialize( OWLOntology o1, OWLOntology o2 ){
+ public void initialize( LoadedOntology o1, LoadedOntology o2 ){
onto1 = o1;
onto2 = o2;
- classlist2 = new HashMap<OWLClass,Integer>(); // onto2 classes
- classlist1 = new HashMap<OWLClass,Integer>(); // onto1 classes
- proplist2 = new HashMap<OWLProperty,Integer>(); // onto2 properties
- proplist1 = new HashMap<OWLProperty,Integer>(); // onto1 properties
- indlist2 = new HashMap<OWLIndividual,Integer>(); // onto2 instances
- indlist1 = new HashMap<OWLIndividual,Integer>(); // onto1 instances
+ classlist2 = new HashMap<Object,Integer>(); // onto2 classes
+ classlist1 = new HashMap<Object,Integer>(); // onto1 classes
+ proplist2 = new HashMap<Object,Integer>(); // onto2 properties
+ proplist1 = new HashMap<Object,Integer>(); // onto1 properties
+ indlist2 = new HashMap<Object,Integer>(); // onto2 instances
+ indlist1 = new HashMap<Object,Integer>(); // onto1 instances
try {
// Create class lists
for ( Iterator it = onto2.getClasses().iterator(); it.hasNext(); nbclass2++ ){
- classlist2.put( (OWLClass)it.next(), new Integer(nbclass2) );
+ classlist2.put( (Object)it.next(), new Integer(nbclass2) );
}
for ( Iterator it = onto1.getClasses().iterator(); it.hasNext(); nbclass1++ ){
- classlist1.put( (OWLClass)it.next(), new Integer(nbclass1) );
+ classlist1.put( (Object)it.next(), new Integer(nbclass1) );
}
clmatrix = new double[nbclass1+1][nbclass2+1];
// Create property lists
for ( Iterator it = onto2.getObjectProperties().iterator(); it.hasNext(); nbprop2++ ){
- proplist2.put( (OWLProperty)it.next(), new Integer(nbprop2) );
+ proplist2.put( (Object)it.next(), new Integer(nbprop2) );
}
for ( Iterator it = onto2.getDataProperties().iterator(); it.hasNext(); nbprop2++ ){
- proplist2.put( (OWLProperty)it.next(), new Integer(nbprop2) );
+ proplist2.put( (Object)it.next(), new Integer(nbprop2) );
}
for ( Iterator it = onto1.getObjectProperties().iterator(); it.hasNext(); nbprop1++ ){
- proplist1.put( (OWLProperty)it.next(), new Integer(nbprop1) );
+ proplist1.put( (Object)it.next(), new Integer(nbprop1) );
}
for ( Iterator it = onto1.getDataProperties().iterator(); it.hasNext(); nbprop1++ ){
- proplist1.put( (OWLProperty)it.next(), new Integer(nbprop1) );
+ proplist1.put( (Object)it.next(), new Integer(nbprop1) );
}
prmatrix = new double[nbprop1+1][nbprop2+1];
// Create individual lists
for ( Iterator it = onto2.getIndividuals().iterator(); it.hasNext(); ){
- OWLIndividual o = (OWLIndividual)it.next();
+ Object o = (Object)it.next();
//System.err.println( o );
// We suppress anonymous individuals... this is not legitimate
- if ( o.getURI() != null ) {
+ if ( onto2.getEntityURI(o) != null ) {
indlist2.put( o, new Integer(nbind2) );
nbind2++;
}
}
for ( Iterator it = onto1.getIndividuals().iterator(); it.hasNext(); ){
- OWLIndividual o = (OWLIndividual)it.next();
+ Object o = (Object)it.next();
//System.err.println( o );
// We suppress anonymous individuals... this is not legitimate
- if ( o.getURI() != null ) {
+ if ( onto2.getEntityURI(o) != null ) {
indlist1.put( o, new Integer(nbind1) );
nbind1++;
}
}
indmatrix = new double[nbind1+1][nbind2+1];
- } catch (OWLException e) { e.printStackTrace(); };
+ } catch (AlignmentException e) { e.printStackTrace(); };
}
public void compute( Parameters params ){
try {
// Compute distances on classes
for ( Iterator it2 = onto2.getClasses().iterator(); it2.hasNext(); ){
- OWLClass cl2 = (OWLClass)it2.next();
+ Object cl2 = (Object)it2.next();
for ( Iterator it1 = onto1.getClasses().iterator(); it1.hasNext(); ){
- OWLClass cl1 = (OWLClass)it1.next();
- clmatrix[((Integer)classlist1.get(cl1)).intValue()][((Integer)classlist2.get(cl2)).intValue()] = measure( cl1, cl2 );
+ Object cl1 = (Object)it1.next();
+ clmatrix[((Integer)classlist1.get(cl1)).intValue()][((Integer)classlist2.get(cl2)).intValue()] = classMeasure( cl1, cl2 );
}
}
// Compute distances on individuals
// (this comes first because otherwise, it2 is defined)
for ( Iterator it2 = onto2.getIndividuals().iterator(); it2.hasNext(); ){
- OWLIndividual ind2 = (OWLIndividual)it2.next();
+ Object ind2 = (Object)it2.next();
if ( indlist2.get(ind2) != null ) {
for ( Iterator it1 = onto1.getIndividuals().iterator(); it1.hasNext(); ){
- OWLIndividual ind1 = (OWLIndividual)it1.next();
+ Object ind1 = (Object)it1.next();
if ( indlist1.get(ind1) != null ) {
- indmatrix[((Integer)indlist1.get(ind1)).intValue()][((Integer)indlist2.get(ind2)).intValue()] = measure( ind1, ind2 );
+ indmatrix[((Integer)indlist1.get(ind1)).intValue()][((Integer)indlist2.get(ind2)).intValue()] = individualMeasure( ind1, ind2 );
}
}
}
@@ -163,26 +159,26 @@ public abstract class MatrixMeasure implements Similarity {
ConcatenatedIterator(onto2.getObjectProperties().iterator(),
onto2.getDataProperties().iterator());
for ( ; it2.hasNext(); ){
- OWLProperty pr2 = (OWLProperty)it2.next();
+ Object pr2 = (Object)it2.next();
ConcatenatedIterator it1 = new
ConcatenatedIterator(onto1.getObjectProperties().iterator(),
onto1.getDataProperties().iterator());
for ( ; it1.hasNext(); ){
- OWLProperty pr1 = (OWLProperty)it1.next();
- prmatrix[((Integer)proplist1.get(pr1)).intValue()][((Integer)proplist2.get(pr2)).intValue()] = measure( pr1, pr2 );
+ Object pr1 = (Object)it1.next();
+ prmatrix[((Integer)proplist1.get(pr1)).intValue()][((Integer)proplist2.get(pr2)).intValue()] = propertyMeasure( pr1, pr2 );
}
}
// What is caught is really Exceptions
} catch (Exception e) { e.printStackTrace(); }
}
- public double getIndividualSimilarity( OWLIndividual i1, OWLIndividual i2 ){
+ public double getIndividualSimilarity( Object i1, Object i2 ){
return indmatrix[((Integer)indlist1.get(i1)).intValue()][((Integer)indlist2.get(i2)).intValue()];
}
- public double getClassSimilarity( OWLClass c1, OWLClass c2 ){
+ public double getClassSimilarity( Object c1, Object c2 ){
return clmatrix[((Integer)classlist1.get(c1)).intValue()][((Integer)classlist2.get(c2)).intValue()];
}
- public double getPropertySimilarity( OWLProperty p1, OWLProperty p2 ){
+ public double getPropertySimilarity( Object p1, Object p2 ){
return prmatrix[((Integer)proplist1.get(p1)).intValue()][((Integer)proplist2.get(p2)).intValue()];
}
@@ -197,20 +193,20 @@ public abstract class MatrixMeasure implements Similarity {
System.out.println("}");
try {
for ( Iterator it1 = onto1.getClasses().iterator(); it1.hasNext(); ){
- OWLClass cl1 = (OWLClass)it1.next();
- System.out.print(" & \\rotatebox{90}{"+cl1.getURI().getFragment()+"}");
+ Object cl1 = (Object)it1.next();
+ System.out.print(" & \\rotatebox{90}{"+onto1.getEntityName( cl1 )+"}");
}
System.out.println(" \\\\ \\hline");
for ( Iterator it2 = onto2.getClasses().iterator(); it2.hasNext(); ){
- OWLClass cl2 = (OWLClass)it2.next();
- System.out.print(cl2.getURI().getFragment());
+ Object cl2 = (Object)it2.next();
+ System.out.print( onto2.getEntityName( cl2 ) );
for ( Iterator it1 = onto1.getClasses().iterator(); it1.hasNext(); ){
- OWLClass cl1 = (OWLClass)it1.next();
+ Object cl1 = (Object)it1.next();
System.out.print(" & "+numFormat.format(clmatrix[((Integer)classlist1.get(cl1)).intValue()][((Integer)classlist2.get(cl2)).intValue()]));
}
System.out.println("\\\\");
}
- } catch (OWLException e) { e.printStackTrace(); };
+ } catch (AlignmentException e) { e.printStackTrace(); };
System.out.println("\n\\end{tabular}");
}
diff --git a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
index e2e2a6cb..928df006 100644
--- a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
@@ -56,9 +56,13 @@ import fr.inrialpes.exmo.align.onto.LoadedOntology;
*
* @author Jérôme Euzenat
* @version $Id$
+ * @deprecated OWLAPIAlignment has been deprecated to the profit of ObjectAlignment
+ * It remains here for compatibility purposes and is reimplemented in terms
+ * of ObjectAlignment.
*/
-public class OWLAPIAlignment extends BasicAlignment {
+@Deprecated
+public class OWLAPIAlignment extends ObjectAlignment {
protected OWLAPIAlignment init = null;
@@ -126,7 +130,7 @@ public class OWLAPIAlignment extends BasicAlignment {
return super.addAlignCell( ob1, ob2 );
};
public Cell createCell(String id, Object ob1, Object ob2, Relation relation, double measure) throws AlignmentException {
- return (Cell)new OWLAPICell( id, (OWLEntity)ob1, (OWLEntity)ob2, relation, measure);
+ return (Cell)new OWLAPICell( id, (OWLEntity)ob1, (OWLEntity)ob2, relation, measure); //[W:Deprecated]
}
public Set<Cell> getAlignCells1(Object ob) throws AlignmentException {
@@ -144,7 +148,10 @@ public class OWLAPIAlignment extends BasicAlignment {
}
}
- // Deprecated: implement as the one retrieving the highest strength correspondence (
+ /**
+ * @deprecated implemented as the one retrieving the highest strength correspondence
+ */
+ @Deprecated
public Cell getAlignCell1(Object ob) throws AlignmentException {
if ( Annotations.STRICT_IMPLEMENTATION == true ){
throw new AlignmentException("deprecated (use getAlignCells1 instead)");
@@ -157,6 +164,10 @@ public class OWLAPIAlignment extends BasicAlignment {
}
}
+ /**
+ * @deprecated implemented as the one retrieving the highest strength correspondence
+ */
+ @Deprecated
public Cell getAlignCell2(Object ob) throws AlignmentException {
if ( Annotations.STRICT_IMPLEMENTATION == true ){
throw new AlignmentException("deprecated (use getAlignCells2 instead)");
@@ -210,17 +221,17 @@ public class OWLAPIAlignment extends BasicAlignment {
align.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
for (Enumeration e = getElements(); e.hasMoreElements();) {
- Cell c = (Cell)e.nextElement();
+ OWLAPICell c = (OWLAPICell)e.nextElement(); //[W:Deprecated]
try {
align.addAlignCell( c.getId(), c.getObject1AsURI(), c.getObject2AsURI(), c.getRelation(), c.getStrength() );
} catch (AlignmentException aex) {
- // Sometimes URIs are null, this is ignore
+ // Sometimes URIs are null, this is ignored
}
};
return align;
}
- // Here it becomes necessary to load OWL
+ // Here it becomes necessary to load OWL: This is done by init().
static public OWLAPIAlignment toOWLAPIAlignment( URIAlignment al, OntologyCache ontologies ) throws AlignmentException, SAXException, OWLException {
OWLAPIAlignment alignment = new OWLAPIAlignment();
alignment.init( al.getFile1(), al.getFile2(), ontologies );
@@ -246,13 +257,6 @@ public class OWLAPIAlignment extends BasicAlignment {
return alignment;
}
- private static LoadedOntology loadOntology( URI ref, OntologyCache ontologies ) {
- OntologyFactory factory = OntologyFactory.newInstance();
- LoadedOntology onto = factory.loadOntology( ref );
- if ( ontologies != null ) ontologies.recordOntology( ref, onto );
- return onto;
- }
-
// JE: newOnto --- Onto: should be discarded
private static OWLEntity getEntity( OWLOntology ontology, URI uri ) throws OWLException, SAXException {
OWLEntity result = (OWLEntity)ontology.getClass( uri );
@@ -261,43 +265,5 @@ public class OWLAPIAlignment extends BasicAlignment {
if ( result == null ) result = (OWLEntity)ontology.getIndividual( uri );
return result;
}
-
- // JE: newOnto --- Onto: should be discarded
- /** Can be used for loading the ontology if it is not available **/
- /*
- //private static OWLOntology loadOntology( URI ref, Hashtable ontologies ) throws SAXException, OWLException {
- private static OWLOntology loadOntology( URI ref, OntologyCache ontologies ) throws SAXException, OWLException {
- if ( (ontologies != null) && ( ontologies.getOntology( ref ) != null ) ) {
- return ontologies.getOntology( ref );
- } else {
- OWLOntology parsedOnt = null;
- OWLRDFParser parser = new OWLRDFParser();
- OWLRDFErrorHandler handler = new OWLRDFErrorHandler(){
- public void owlFullConstruct( int code, String message )
- throws SAXException {
- }
- public void owlFullConstruct(int code, String message, Object o)
- throws SAXException {
- }
- public void error( String message ) throws SAXException {
- throw new SAXException( message.toString() );
- }
- public void warning( String message ) throws SAXException {
- System.err.println("WARNING: " + message);
- }
- };
- Level lev = Logger.getLogger("org.semanticweb.owl").getLevel();
- Logger.getLogger("org.semanticweb.owl").setLevel(Level.ERROR);
- parser.setOWLRDFErrorHandler( handler );
- parser.setConnection( OWLManager.getOWLConnection() );
- parsedOnt = parser.parseOntology( ref );
- if ( ontologies != null )
- ontologies.recordOntology( ref, parsedOnt );
- // ontologies.put( ref.toString(), parsedOnt );
- Logger.getLogger("org.semanticweb.owl").setLevel(lev);
- return parsedOnt;
- }
- }
- */
}
diff --git a/src/fr/inrialpes/exmo/align/impl/OWLAPICell.java b/src/fr/inrialpes/exmo/align/impl/OWLAPICell.java
index 55327d07..15997729 100644
--- a/src/fr/inrialpes/exmo/align/impl/OWLAPICell.java
+++ b/src/fr/inrialpes/exmo/align/impl/OWLAPICell.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2007-2008
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -30,7 +30,6 @@ import java.net.URI;
import org.xml.sax.ContentHandler;
import org.xml.sax.SAXException;
-//import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLException;
@@ -46,27 +45,23 @@ import fr.inrialpes.exmo.align.impl.rel.*;
*
* @author Jérôme Euzenat
* @version $Id$
+ * @deprecated OWLAPICell as been deprecated to the profit of ObjectCell
+ * It remains here for compatibility purposes and is reimplemented in terms
+ * of ObjectCell.
*/
-public class OWLAPICell extends BasicCell {
+@Deprecated
+public class OWLAPICell extends ObjectCell {
public void accept( AlignmentVisitor visitor) throws AlignmentException {
visitor.visit( this );
}
- /** Creation **/
- //public OWLAPICell( Object ob1, Object ob2 ) throws AlignmentException {
- // super( ob1, ob2 );
- // };
-
- // public OWLAPICell( Object ob1, Object ob2, String rel, double m ) throws AlignmentException {
- // super( ob1, ob2, rel, m );
- // }
-
public OWLAPICell( String id, OWLEntity ob1, OWLEntity ob2, Relation rel, double m ) throws AlignmentException {
super( id, ob1, ob2, rel, m );
};
// the strength must be compared with regard to abstract types
+ // NOOWL
public boolean equals( Cell c ) {
if ( c instanceof OWLAPICell ){
return ( object1.equals(c.getObject1()) && object2.equals(c.getObject2()) && strength == c.getStrength() && (relation.equals( c.getRelation() )) );
@@ -75,6 +70,7 @@ public class OWLAPICell extends BasicCell {
}
}
+ // Only OWL
public URI getObject1AsURI() throws AlignmentException {
try {
return ((OWLEntity)object1).getURI();
@@ -82,6 +78,8 @@ public class OWLAPICell extends BasicCell {
throw new AlignmentException( "Cannot convert to URI "+object1, e );
}
}
+
+ // Only OWL
public URI getObject2AsURI() throws AlignmentException {
try {
return ((OWLEntity)object2).getURI();
@@ -89,16 +87,8 @@ public class OWLAPICell extends BasicCell {
throw new AlignmentException( "Cannot convert to URI "+object2, e );
}
}
- //public Object getObject1(){ return object1; };
- //public Object getObject2(){ return object2; };
- // We could check that the given values are URIs
- //public void setObject1( Object ob ) throws AlignmentException {
- // object1 = ob;
- //}
- //public void setObject2( Object ob ) throws AlignmentException {
- // object2 = ob;
- //}
+ // Only OWL
public Cell inverse() throws AlignmentException {
return (Cell)new OWLAPICell( (String)null, (OWLEntity)object2, (OWLEntity)object1, relation.inverse(), strength );
// The same should be done for the measure
diff --git a/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java b/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
new file mode 100644
index 00000000..34e14585
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
@@ -0,0 +1,188 @@
+/*
+ * $Id: ObjectAlignment.java 677 2008-03-23 22:58:22Z euzenat $
+ *
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2008
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 2.1 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+package fr.inrialpes.exmo.align.impl;
+
+import java.util.Hashtable;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Enumeration;
+import java.util.Set;
+import java.net.URI;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.Level;
+
+import org.xml.sax.SAXException;
+
+import org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentException;
+import org.semanticweb.owl.align.AlignmentVisitor;
+import org.semanticweb.owl.align.Cell;
+import org.semanticweb.owl.align.Relation;
+import org.semanticweb.owl.align.Parameters;
+
+import fr.inrialpes.exmo.align.onto.OntologyFactory;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
+import fr.inrialpes.exmo.align.onto.Ontology;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
+
+/**
+ * Represents an OWL ontology alignment. An ontology comprises a number of
+ * collections. Each ontology has a number of classes, properties and
+ * individuals, along with a number of axioms asserting information about those
+ * objects.
+ *
+ * @author Jérôme Euzenat
+ * @version $Id: ObjectAlignment.java 677 2008-03-23 22:58:22Z euzenat $
+ */
+
+public class ObjectAlignment extends BasicAlignment {
+
+ protected ObjectAlignment init = null;
+
+ public ObjectAlignment() {}
+
+ public void init(Object onto1, Object onto2) throws AlignmentException {
+ init( onto1, onto2, (OntologyCache)null );
+ }
+
+ public void init(Object o1, Object o2, Object ontologies) throws AlignmentException {
+ OntologyCache cache = null;
+ if ( ontologies instanceof OntologyCache ) cache = (OntologyCache)ontologies;
+ else cache = (OntologyCache)null;
+ if ( (o1 instanceof LoadedOntology && o2 instanceof LoadedOntology) ){
+ super.init( o1, o2, ontologies );
+ } else if ( o1 instanceof URI && o2 instanceof URI ) {
+ super.init( loadOntology( (URI)o1, cache ),
+ loadOntology( (URI)o2, cache ) );
+ } else {
+ throw new AlignmentException("Arguments must be LoadedOntology or URI");
+ };
+ }
+
+ public LoadedOntology<Object> ontology1(){
+ return (LoadedOntology<Object>)onto1;
+ }
+
+ public LoadedOntology<Object> ontology2(){
+ return (LoadedOntology<Object>)onto2;
+ }
+
+ public void loadInit( Alignment al ) throws AlignmentException {
+ loadInit( al, (OntologyCache)null );
+ }
+
+ public void loadInit( Alignment al, OntologyCache ontologies ) throws AlignmentException {
+ if ( al instanceof URIAlignment ) {
+ try { init = toObjectAlignment( (URIAlignment)al, ontologies );
+ } catch (SAXException e) { e.printStackTrace(); }
+ } else if ( al instanceof ObjectAlignment ) {
+ init = (ObjectAlignment)al;
+ }
+ }
+
+ public URI getOntology1URI() { return onto1.getURI(); };
+
+ public URI getOntology2URI() { return onto2.getURI(); };
+
+ public Cell createCell(String id, Object ob1, Object ob2, Relation relation, double measure) throws AlignmentException {
+ return new ObjectCell( id, ob1, ob2, relation, measure);
+ }
+
+ /**
+ * Generate a copy of this alignment object
+ */
+ // JE: this is a mere copy of the method in BasicAlignement
+ // It has two difficulties
+ // - it should call the current init() and not that of BasicAlignement
+ // - it should catch the AlignmentException that it is supposed to raise
+ public Object clone() {
+ ObjectAlignment align = new ObjectAlignment();
+ try {
+ align.init( onto1, onto2 );
+ } catch ( AlignmentException e ) {};
+ align.setType( getType() );
+ align.setLevel( getLevel() );
+ align.setFile1( getFile1() );
+ align.setFile2( getFile2() );
+ for ( Object ext : ((BasicParameters)extensions).getValues() ){
+ align.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
+ }
+ align.getExtensions().unsetParameter( Annotations.ALIGNNS+"id" );
+ try {
+ align.ingest( this );
+ } catch (AlignmentException ex) { ex.printStackTrace(); }
+ return align;
+ }
+
+ /**
+ * This is a clone with the URI instead of Object objects
+ *
+ */
+ public URIAlignment toURIAlignment() throws AlignmentException {
+ URIAlignment align = new URIAlignment();
+ align.init( getOntology1URI(), getOntology2URI() );
+ align.setType( getType() );
+ align.setLevel( getLevel() );
+ align.setFile1( getFile1() );
+ align.setFile2( getFile2() );
+ for ( Object ext : ((BasicParameters)extensions).getValues() ){
+ align.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
+ }
+ for (Enumeration e = getElements(); e.hasMoreElements();) {
+ Cell c = (Cell)e.nextElement();
+ try {
+ align.addAlignCell( c.getId(), c.getObject1AsURI(), c.getObject2AsURI(), c.getRelation(), c.getStrength() );
+ } catch (AlignmentException aex) {
+ // Sometimes URIs are null, this is ignore
+ }
+ };
+ return align;
+ }
+
+ static public ObjectAlignment toObjectAlignment( URIAlignment al, OntologyCache ontologies ) throws AlignmentException, SAXException {
+ ObjectAlignment alignment = new ObjectAlignment();
+ alignment.init( al.getFile1(), al.getFile2(), ontologies );
+ alignment.setType( al.getType() );
+ alignment.setLevel( al.getLevel() );
+ for ( Object ext : ((BasicParameters)al.getExtensions()).getValues() ){
+ alignment.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
+ }
+ LoadedOntology<Object> o1 = (LoadedOntology<Object>)alignment.getOntologyObject1(); // [W:unchecked]
+ LoadedOntology<Object> o2 = (LoadedOntology<Object>)alignment.getOntologyObject2(); // [W:unchecked]
+ for (Enumeration e = al.getElements(); e.hasMoreElements();) {
+ Cell c = (Cell)e.nextElement();
+ alignment.addAlignCell( c.getId(),
+ o1.getEntity( c.getObject1AsURI() ),
+ o2.getEntity( c.getObject2AsURI() ),
+ c.getRelation(),
+ c.getStrength(),
+ c.getExtensions() );
+ };
+ return alignment;
+ }
+
+ static LoadedOntology loadOntology( URI ref, OntologyCache ontologies ) throws AlignmentException {
+ OntologyFactory factory = OntologyFactory.newInstance();
+ return factory.loadOntology( ref, ontologies );
+ }
+}
+
diff --git a/src/fr/inrialpes/exmo/align/impl/ObjectCell.java b/src/fr/inrialpes/exmo/align/impl/ObjectCell.java
new file mode 100644
index 00000000..400286a3
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/impl/ObjectCell.java
@@ -0,0 +1,115 @@
+/*
+ * $Id: BasicCell.java 670 2008-03-02 00:06:16Z euzenat $
+ *
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007-2008
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ * USA.
+ */
+
+package fr.inrialpes.exmo.align.impl;
+
+import java.net.URI;
+import java.util.Enumeration;
+
+import org.xml.sax.ContentHandler;
+
+import org.semanticweb.owl.align.AlignmentException;
+import org.semanticweb.owl.align.AlignmentVisitor;
+import org.semanticweb.owl.align.Cell;
+import org.semanticweb.owl.align.Relation;
+import org.semanticweb.owl.align.Parameters;
+
+/**
+ * Represents an ontology alignment correspondence.
+ *
+ * @author Jérôme Euzenat
+ * @version $Id: BasicCell.java 670 2008-03-02 00:06:16Z euzenat $
+ */
+
+public class ObjectCell extends BasicCell {
+ // JE ??: implements Comparable<ObjectCell> {
+
+ // public void accept( AlignmentVisitor visitor) throws AlignmentException {
+ // visitor.visit( this );
+ //}
+
+ /** Creation **/
+ public ObjectCell( String id, Object ob1, Object ob2, Relation rel, double m ) throws AlignmentException {
+ super( id, ob1, ob2, rel, m );
+ };
+
+
+ // the strength must be compared with regard to abstract types
+ public boolean equals( Cell c ) {
+ if ( c instanceof ObjectCell ){
+ return ( object1 == c.getObject1() && object2 == c.getObject2() && strength == c.getStrength() && (relation.equals( c.getRelation() )) );
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * Used to order the cells in an alignment:
+ * -- this > c iff this.getStrength() < c.getStrength() --
+ public int compareTo( Cell c ){
+ //if ( ! (c instanceof Cell) ) return 1;
+ if ( c.getStrength() > getStrength() ) return 1;
+ if ( getStrength() > c.getStrength() ) return -1;
+ return 0;
+ }
+ */
+
+ public URI getObject1AsURI() throws AlignmentException {
+ if ( object1 instanceof URI ) {
+ return (URI)object1;
+ } else {
+ // TO BE DONE
+ return null;
+ }
+ }
+ public URI getObject2AsURI() throws AlignmentException {
+ if ( object2 instanceof URI ) {
+ return (URI)object2;
+ } else {
+ // TO BE DONE
+ return null;
+ }
+ }
+ public Cell inverse() throws AlignmentException {
+ Cell result = (Cell)new ObjectCell( (String)null, object2, object1, relation.inverse(), strength );
+ if ( extensions != null ) {
+ for ( Object ext : ((BasicParameters)extensions).getValues() ){
+ result.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
+ }
+ }
+ result.getExtensions().unsetParameter( Annotations.ALIGNNS+Annotations.ID );
+ // The sae should be done for the measure
+ return result;
+ }
+
+ public Cell compose(Cell c) throws AlignmentException {
+ if (!object2.equals(c.getObject1()) && relation.compose(c.getRelation())==null )
+ return null;
+ Cell result = (ObjectCell)new ObjectCell( (String)null, object1, c.getObject2(), relation.compose(c.getRelation()), strength*c.getStrength() );
+ // TODO : extension...
+ return result;
+ }
+
+ /** Housekeeping **/
+ public void dump( ContentHandler h ){};
+
+}
+
diff --git a/src/fr/inrialpes/exmo/align/impl/Similarity.java b/src/fr/inrialpes/exmo/align/impl/Similarity.java
index 327cfed1..5a7316f9 100644
--- a/src/fr/inrialpes/exmo/align/impl/Similarity.java
+++ b/src/fr/inrialpes/exmo/align/impl/Similarity.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2004, 2006-2007
+ * Copyright (C) INRIA Rhône-Alpes, 2004, 2006-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -20,14 +20,11 @@
package fr.inrialpes.exmo.align.impl;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-
import org.semanticweb.owl.align.Parameters;
import org.semanticweb.owl.align.Alignment;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
+
/**
* Represents the implementation of a similarity measure
*
@@ -42,12 +39,13 @@ public interface Similarity
// It would be better if they where explicit...
// Apparently the initialize also compute the similarity
- public void initialize( OWLOntology onto1, OWLOntology onto2 );
- public void initialize( OWLOntology onto1, OWLOntology onto2, Alignment align );
+ // JE: OntoRewr: This should not be in init
+ public void initialize( LoadedOntology<Object> onto1, LoadedOntology<Object> onto2 );
+ public void initialize( LoadedOntology<Object> onto1, LoadedOntology<Object> onto2, Alignment align );
public void compute( Parameters p );
- public double getClassSimilarity( OWLClass c1, OWLClass c2 );
- public double getPropertySimilarity( OWLProperty p1, OWLProperty p2);
- public double getIndividualSimilarity( OWLIndividual i1, OWLIndividual i2 );
+ public double getClassSimilarity( Object c1, Object c2 );
+ public double getPropertySimilarity( Object p1, Object p2);
+ public double getIndividualSimilarity( Object i1, Object i2 );
public void printClassSimilarityMatrix( String type );
public void printPropertySimilarityMatrix( String type );
@@ -59,8 +57,10 @@ public interface Similarity
// the abstract matrix class provides the get- accessors and the
// concrete classes implement measure as their computation function.
// This is not clean. What should be done is:
- public double measure( OWLClass c1, OWLClass c2 ) throws Exception;
- public double measure( OWLProperty p1, OWLProperty p2) throws Exception;
- public double measure( OWLIndividual i1, OWLIndividual i2 ) throws Exception;
+ // JE: OntoRewr: to be suppressed
+ public double measure( Object c1, Object c2 ) throws Exception;
+ public double classMeasure( Object c1, Object c2 ) throws Exception;
+ public double propertyMeasure( Object p1, Object p2) throws Exception;
+ public double individualMeasure( Object i1, Object i2 ) throws Exception;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java
index 1e0f3595..75e5baad 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java
@@ -25,15 +25,10 @@ import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Parameters;
-import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
import fr.inrialpes.exmo.align.impl.BasicEvaluator;
-
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLEntity;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLException;
+import fr.inrialpes.exmo.align.impl.ObjectAlignment;
+import fr.inrialpes.exmo.align.onto.HeavyLoadedOntology;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
import java.util.Enumeration;
import java.util.Iterator;
@@ -54,8 +49,8 @@ import java.net.URI;
public class ExtPREvaluator extends BasicEvaluator {
- private OWLOntology onto1;
- private OWLOntology onto2;
+ private HeavyLoadedOntology<Object> onto1;
+ private HeavyLoadedOntology<Object> onto2;
private double symALPHA = .5;
//private double editALPHA = .4;
@@ -106,28 +101,30 @@ public class ExtPREvaluator extends BasicEvaluator {
}
public double eval(Parameters params, Object cache) throws AlignmentException {
// Better to transform them instead...
- if ( !( align1 instanceof OWLAPIAlignment ) || !( align2 instanceof OWLAPIAlignment ) )
- throw new AlignmentException( "ExtPREvaluation: requires OWLAPIAlignments" );
- onto1 = (OWLOntology)align1.getOntology1();
- onto2 = (OWLOntology)align1.getOntology2();
+ if ( !( align1 instanceof ObjectAlignment ) || !( align2 instanceof ObjectAlignment ) )
+ throw new AlignmentException( "ExtPREvaluation: requires ObjectAlignments" );
+ LoadedOntology<Object> o1 = (LoadedOntology<Object>)((ObjectAlignment)align1).getOntologyObject1();
+ LoadedOntology<Object> o2 = (LoadedOntology<Object>)((ObjectAlignment)align1).getOntologyObject2();
+ if ( !( o1 instanceof HeavyLoadedOntology ) || !( o2 instanceof HeavyLoadedOntology ) )
+ throw new AlignmentException( "ExtPREvaluation: requires HeavyLoadedOntology" );
+ onto1 = (HeavyLoadedOntology<Object>)o1;
+ onto2 = (HeavyLoadedOntology<Object>)o2;
nbexpected = align1.nbCells();
nbfound = align2.nbCells();
for ( Enumeration e = align1.getElements(); e.hasMoreElements();) {
Cell c1 = (Cell)e.nextElement();
- Set s2 = (Set)align2.getAlignCells1((OWLEntity)c1.getObject1());
+ Set s2 = (Set)align2.getAlignCells1( c1.getObject1() );
if( s2 != null ){
for( Iterator it2 = s2.iterator(); it2.hasNext() && c1 != null; ){
Cell c2 = (Cell)it2.next();
- try {
- URI uri1 = ((OWLEntity)c1.getObject2()).getURI();
- URI uri2 = ((OWLEntity)c2.getObject2()).getURI();
- // if (c1.getobject2 == c2.getobject2)
- if ( uri1.toString().equals(uri2.toString()) ) {
- symsimilarity = symsimilarity + 1.;
- c1 = null; // out of the loop.
- }
- } catch (OWLException exc) { exc.printStackTrace(); }
+ URI uri1 = onto2.getEntityURI( c1.getObject2() );
+ URI uri2 = onto2.getEntityURI( c2.getObject2() );
+ // if (c1.getobject2 == c2.getobject2)
+ if ( uri1.toString().equals(uri2.toString()) ) {
+ symsimilarity = symsimilarity + 1.;
+ c1 = null; // out of the loop.
+ }
}
// if nothing has been found
// JE: Full implementation would require computing a matrix
@@ -157,73 +154,87 @@ public class ExtPREvaluator extends BasicEvaluator {
return (result);
}
+ /**
+ * This computes similarity depending on structural measures:
+ * the similarity is symALPHA^minval, symALPHA being lower than 1.
+ * minval is the length of the subclass chain.
+ */
protected double computeSymSimilarity( Cell c1, Enumeration s2 ){
int minval = 0;
int val = 0;
- try{
+ try {
for( ; s2.hasMoreElements(); ){
Cell c2 = (Cell)s2.nextElement();
- if ( ((OWLEntity)c1.getObject1()).getURI().toString().equals(((OWLEntity)c2.getObject1()).getURI().toString()) ){
- val = relativePosition( (OWLEntity)c1.getObject2(), (OWLEntity)c2.getObject2(), onto2 );
+ if ( onto1.getEntityURI( c1.getObject1() ).toString().equals(onto1.getEntityURI(c2.getObject1()).toString()) ){
+ val = relativePosition( c1.getObject2(), c2.getObject2(), onto2 );
if ( val != 0 && val < minval ) minval = val;
- } else if ( ((OWLEntity)c1.getObject2()).getURI().toString().equals(((OWLEntity)c2.getObject2()).getURI().toString()) ){
- val = relativePosition( (OWLEntity)c1.getObject1(), (OWLEntity)c2.getObject1(), onto1 );
+ } else if ( onto2.getEntityURI(c1.getObject2()).toString().equals(onto2.getEntityURI(c2.getObject2()).toString()) ){
+ val = relativePosition( c1.getObject1(), c2.getObject1(), onto1 );
if ( val != 0 && val < minval ) minval = val;
}
}
- return symALPHA; //^minval;
- } catch (OWLException e) { return 0; }
+ } catch( AlignmentException aex ) { return 0; }
+ //return symALPHA; //^minval;
+ return Math.pow( symALPHA, minval );
}
- protected int relativePosition( OWLEntity o1, OWLEntity o2, OWLOntology onto ){
- try {
- if ( o1 instanceof OWLClass && o2 instanceof OWLClass ){
- isSuperClass( (OWLClass)o2, (OWLClass)o1, onto );
- } else if ( o1 instanceof OWLProperty && o2 instanceof OWLProperty ){
- if ( isSuperProperty( (OWLProperty)o2, (OWLProperty)o1, onto ) ) { return -1; }
- else if ( isSuperProperty( (OWLProperty)o1, (OWLProperty)o2, onto ) ) { return 1; }
- else { return 0; }
- } else if ( o1 instanceof OWLIndividual && o2 instanceof OWLIndividual ){
- return 0;
- //if () { return -1; }
- //else if () { return 1; }
- //else return 0;
- }
- } catch (OWLException e) { e.printStackTrace(); }
+ protected int relativePosition( Object o1, Object o2, HeavyLoadedOntology<Object> onto ) throws AlignmentException {
+ if ( onto.isClass( o1 ) && onto.isClass( o2 ) ){
+ isSuperClass( o2, o1, onto ); // This is the level
+ } else if ( onto.isProperty( o1 ) && onto.isProperty( o2 ) ){
+ if ( isSuperProperty( o2, o1, onto ) ) { return -1; }
+ else if ( isSuperProperty( o1, o2, onto ) ) { return 1; }
+ else { return 0; }
+ } else if ( onto.isIndividual( o1 ) && onto.isIndividual( o2 ) ){
+ return 0;
+ //if () { return -1; }
+ //else if () { return 1; }
+ //else return 0;
+ }
return 0;
}
- public int superClassPosition( OWLClass class1, OWLClass class2, OWLOntology onto ) throws OWLException {
- int result = - isSuperClass( (OWLClass)class2, (OWLClass)class1, onto );
+ public boolean isSuperProperty( Object prop1, Object prop2, HeavyLoadedOntology<Object> ontology ) throws AlignmentException {
+ return ontology.getSuperProperties( prop2 ).contains( prop1 );
+ }
+
+
+ public int superClassPosition( Object class1, Object class2, HeavyLoadedOntology<Object> onto ) throws AlignmentException {
+ int result = - isSuperClass( class2, class1, onto );
if ( result == 0 )
- result = isSuperClass( (OWLClass)class1, (OWLClass)class2, onto );
+ result = isSuperClass( class1, class2, onto );
return result;
}
- public int isSuperClass( OWLClass class1, OWLClass class2, OWLOntology ontology ) throws OWLException {
- URI uri1 = class1.getURI();
- Set<OWLEntity> superclasses = new HashSet<OWLEntity>();
- // required for avoiding java.util.ConcurrentModificationException
- Set<OWLEntity> bufferedSuperClasses = null;
+ /**
+ * This is a strange method which returns an integer representing how
+ * directly a class is superclass of another or not.
+ *
+ * This would require coputing the transitive reduction of the superClass
+ * relation which is currently returned bu HeavyLoadedOntology.
+ *
+ * It would require to have a isDirectSubClassOf().
+ */
+ public int isSuperClass( Object class1, Object class2, HeavyLoadedOntology<Object> ontology ) throws AlignmentException {
+ URI uri1 = ontology.getEntityURI( class1 );
+ Set<Object> bufferedSuperClasses = null;
+ Set<Object> superclasses = ontology.getAssertedSuperClasses( class1 );
int level = 0;
- // [Warning:unchecked] due to OWL API not serving generic types
- superclasses.addAll( class2.getSuperClasses( ontology )); // [W:unchecked]
while ( !superclasses.isEmpty() ){
bufferedSuperClasses = superclasses;
- superclasses = new HashSet<OWLEntity>();
- Iterator it = bufferedSuperClasses.iterator();
+ superclasses = new HashSet<Object>();
level++;
- for( ; it.hasNext() ; ){
- Object entity = it.next();
- if ( entity instanceof OWLClass ){
- URI uri2 = ((OWLClass)entity).getURI();
+ for( Object entity : bufferedSuperClasses ) {
+ if ( ontology.isClass( entity ) ){
+ URI uri2 = ontology.getEntityURI( entity );
//if ( entity == class2 ) return true;
if ( uri1.toString().equals(uri2.toString()) ) {
return level;
} else {
- // [Warning:unchecked] due to OWL API not serving generic types
- superclasses.addAll(((OWLClass)entity).getSuperClasses( ontology )); // [W:unchecked]
+ // [W:unchecked] due to OWL API not serving generic types
+ //superclasses.addAll(((OWLClass)entity).getSuperClasses( ontology )); // [W:unchecked]
+ superclasses.addAll( ontology.getAssertedSuperClasses( entity ) );
}
}
}
@@ -232,20 +243,6 @@ public class ExtPREvaluator extends BasicEvaluator {
return 0;
}
- public boolean isSuperProperty( OWLProperty prop1, OWLProperty prop2, OWLOntology ontology ) throws OWLException {
- URI uri1 = prop1.getURI();
- for( Iterator it = prop2.getSuperProperties( ontology ).iterator(); it.hasNext() ; ){
- OWLEntity entity = (OWLEntity)it.next();
- //x.contains( prop2 );
- URI uri2 = entity.getURI();
- //if ( entity == prop2 ) return true;
- if ( uri1.toString().equals(uri2.toString()) ) {
- return true;
- }
- }
- return false;
- }
-
/**
* This now output the results in Lockheed format.
@@ -257,10 +254,8 @@ public class ExtPREvaluator extends BasicEvaluator {
//if ( ) {
// writer.println(" <map:algorithm rdf:resource=\"http://co4.inrialpes.fr/align/algo/"+align1.get+"\">");
//}
- try {
- writer.println(" <map:input1 rdf:resource=\""+((OWLOntology)(align1.getOntology1())).getURI()+"\">");
- writer.println(" <map:input2 rdf:resource=\""+((OWLOntology)(align1.getOntology2())).getURI()+"\">");
- } catch (OWLException e) { e.printStackTrace(); };
+ writer.println(" <map:input1 rdf:resource=\""+((ObjectAlignment)align1).getOntologyObject1().getURI()+"\">");
+ writer.println(" <map:input2 rdf:resource=\""+((ObjectAlignment)align1).getOntologyObject2().getURI()+"\">");
writer.print(" <map:symmetricprecision>");
writer.print(symprec);
writer.print("</map:symmetricprecision>\n <map:symmetricrecall>");
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/SymMeanEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/SymMeanEvaluator.java
index 9dd6358a..112655f8 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/SymMeanEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/SymMeanEvaluator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2004-2005, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2004-2005, 2007-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -26,10 +26,8 @@ import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.BasicEvaluator;
-
-import org.semanticweb.owl.model.OWLEntity;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
+import fr.inrialpes.exmo.align.impl.ObjectAlignment;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
import java.lang.Math;
import java.util.Enumeration;
@@ -52,15 +50,17 @@ import java.io.PrintWriter;
* @version $Id$
*/
-public class SymMeanEvaluator extends BasicEvaluator
-{
+public class SymMeanEvaluator extends BasicEvaluator {
private double classScore = 0.;
private double propScore = 0.;
private double indScore = 0.;
/** Creation **/
- public SymMeanEvaluator( Alignment align1, Alignment align2 ){
+ public SymMeanEvaluator( Alignment align1, Alignment align2 ) throws AlignmentException {
super(align1,align2);
+ if ( !( align1 instanceof ObjectAlignment ) ||
+ !( align2 instanceof ObjectAlignment ) )
+ throw new AlignmentException( "Alignments should be ObjectAlignments, try to " );
}
public double eval(Parameters params) throws AlignmentException {
@@ -74,40 +74,32 @@ public class SymMeanEvaluator extends BasicEvaluator
classScore = 0.;
propScore = 0.;
indScore = 0.;
+ LoadedOntology onto1 = (LoadedOntology)((ObjectAlignment)align1).getOntologyObject1();
+ LoadedOntology onto2 = (LoadedOntology)((ObjectAlignment)align2).getOntologyObject1();
+ //for ( Cell c1 : align1.getElements() ){
for (Enumeration e = align1.getElements() ; e.hasMoreElements() ;) {
Cell c1 = (Cell)e.nextElement();
- if ( c1.getObject1() instanceof OWLClass ) nbClassCell++;
- else if ( c1.getObject1() instanceof OWLProperty ) nbPropCell++;
+ if ( onto1.isClass( c1.getObject1() ) ) nbClassCell++;
+ else if ( onto1.isProperty( c1.getObject1() ) ) nbPropCell++;
else nbIndCell++;
- Set s2 = (Set)align2.getAlignCells1((OWLEntity)c1.getObject1());
+ Set<Cell> s2 = (Set<Cell>)align2.getAlignCells1( c1.getObject1() );
if( s2 != null ){
- for( Iterator it2 = s2.iterator(); it2.hasNext() && c1 != null; ){
- Cell c2 = (Cell)it2.next();
- if ( c1.getObject2() == c2.getObject2() ) {
- if ( c1.getObject2() instanceof OWLClass ) {
- classScore = classScore + 1 - Math.abs(c2.getStrength() - c1.getStrength());
- } else if ( c1.getObject2() instanceof OWLProperty ) {
- propScore = propScore + 1 - Math.abs(c2.getStrength() - c1.getStrength());
- } else {
- indScore = indScore + 1 - Math.abs(c2.getStrength() - c1.getStrength());}}}}}
+ for ( Cell c2: s2 ){
+ if ( c1.getObject2() == c2.getObject2() ) {
+ if ( onto2.isClass( c1.getObject2() ) ) {
+ classScore = classScore + 1 - Math.abs(c2.getStrength() - c1.getStrength());
+ } else if ( onto2.isProperty( c1.getObject2() ) ) {
+ propScore = propScore + 1 - Math.abs(c2.getStrength() - c1.getStrength());
+ } else {
+ indScore = indScore + 1 - Math.abs(c2.getStrength() - c1.getStrength());}}}}}
+ //for( Cell c2: align2.getElements() ) {
for (Enumeration e = align2.getElements() ; e.hasMoreElements() ;) {
Cell c2 = (Cell)e.nextElement();
- if ( c2.getObject1() instanceof OWLClass ) nbClassCell++ ;
- else if ( c2.getObject1() instanceof OWLProperty ) nbPropCell++;
+ if ( onto1.isClass( c2.getObject1() ) ) nbClassCell++ ;
+ else if ( onto1.isProperty( c2.getObject1() ) ) nbPropCell++;
else nbIndCell++;
- //Set s1 = (Set)align1.getAlignCells2((OWLEntity)c2.getObject1());
- //if( s1 != null ){
- // for( Iterator it1 = s1.iterator(); it1.hasNext() && c2 != null; ){
- // Cell c1 = (Cell)it1.next();
- // if ( c2.getObject1() == c1.getObject1() ) {
- // if ( c2.getObject1() instanceof OWLClass ) {
- // classScore = classScore + 1 - Math.abs(c1.getStrength() - c2.getStrength());
- // } else if ( c2.getObject1() instanceof OWLProperty ) {
- // propScore = propScore + 1 - Math.abs(c1.getStrength() - c2.getStrength());
- // } else {
- // indScore = indScore + 1 - Math.abs(c1.getStrength() - c2.getStrength());}}}}
}
// Beware, this must come first
diff --git a/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
index 065fbaf7..2081093e 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
@@ -18,24 +18,10 @@
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
-
package fr.inrialpes.exmo.align.impl.method;
-import java.util.Iterator;
import java.util.Vector;
import java.util.Set;
-import java.util.HashSet;
-import java.lang.reflect.Method;
-import java.lang.reflect.InvocationTargetException;
-
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLRestriction;
-import org.semanticweb.owl.model.OWLDescription;
-import org.semanticweb.owl.model.OWLNaryBooleanDescription;
-import org.semanticweb.owl.model.OWLException;
-import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
@@ -44,6 +30,7 @@ import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.DistanceAlignment;
+import fr.inrialpes.exmo.align.onto.HeavyLoadedOntology;
/** This class has been built for ISWC experiments with bibliography.
* It implements a non iterative (one step) OLA algorithms based on
@@ -62,153 +49,93 @@ import fr.inrialpes.exmo.align.impl.DistanceAlignment;
* @version $Id$
*/
+public class ClassStructAlignment extends DistanceAlignment implements AlignmentProcess {
+
+ private HeavyLoadedOntology<Object> honto1 = null;
+ private HeavyLoadedOntology<Object> honto2 = null;
-public class ClassStructAlignment extends DistanceAlignment implements AlignmentProcess
-{
/** Creation **/
public ClassStructAlignment(){};
/** Processing **/
public void align( Alignment alignment, Parameters params ) throws AlignmentException {
loadInit( alignment );
- //ignore alignment;
- //double threshold = 0.6; // threshold above which distances are to high
+ honto1 = (HeavyLoadedOntology<Object>)getOntologyObject1();
+ honto2 = (HeavyLoadedOntology<Object>)getOntologyObject2();
int i, j = 0; // index for onto1 and onto2 classes
- //int l1, l2 = 0; // length of strings (for normalizing)
int nbclass1 = 0; // number of classes in onto1
int nbclass2 = 0; // number of classes in onto2
- Vector<OWLClass> classlist2 = new Vector<OWLClass>(10); // onto2 classes
- Vector<OWLClass> classlist1 = new Vector<OWLClass>(10); // onto1 classes
+ Vector<Object> classlist2 = new Vector<Object>(10); // onto2 classes
+ Vector<Object> classlist1 = new Vector<Object>(10); // onto1 classes
double classmatrix[][]; // class distance matrix
double pic1 = 0.5; // class weigth for name
double pic2 = 0.5; // class weight for properties
ingest( alignment );
- try {
- // Create class lists
- for ( Iterator it = ((OWLOntology)onto2).getClasses().iterator(); it.hasNext(); nbclass2++ ){
- classlist2.add( (OWLClass)it.next() );
- }
- for ( Iterator it = ((OWLOntology)onto1).getClasses().iterator(); it.hasNext(); nbclass1++ ){
- classlist1.add( (OWLClass)it.next() );
- }
- classmatrix = new double[nbclass1+1][nbclass2+1];
+
+ // Create class lists
+ for ( Object cl : honto2.getClasses() ){
+ nbclass2++;
+ classlist2.add( cl );
+ }
+ for ( Object cl : honto1.getClasses() ){
+ nbclass1++;
+ classlist1.add( cl );
+ }
+ classmatrix = new double[nbclass1+1][nbclass2+1];
- if (debug > 0) System.err.println("Initializing class distances");
- // Initialize class distances
- for ( i=0; i<nbclass1; i++ ){
- OWLClass cl = (OWLClass)classlist1.get(i);
- for ( j=0; j<nbclass2; j++ ){
- classmatrix[i][j] = pic1 * StringDistances.subStringDistance(
- cl.getURI().getFragment().toLowerCase(),
- ((OWLClass)classlist2.get(j)).getURI().getFragment().toLowerCase());
- }
+ if (debug > 0) System.err.println("Initializing class distances");
+
+ // Initialize class distances
+ // JE: Here AlignmentException is raised if cl or classlist2.get(j)
+ // cannot be identified as an Entity, maybe this should be traped here
+ for ( i=0; i<nbclass1; i++ ){
+ Object cl = classlist1.get(i);
+ for ( j=0; j<nbclass2; j++ ){
+ classmatrix[i][j] = pic1 * StringDistances.subStringDistance(honto1.getEntityName( cl ).toLowerCase(),
+ honto2.getEntityName( classlist2.get(j) ).toLowerCase());
}
+ }
- if (debug > 0) System.err.print("Computing class distances\n");
- // Compute classes distances
- // -- for all of its attribute, find the best match if possible... easy
- // -- simply replace in the matrix the value by the value plus the
- // classmatrix[i][j] =
- // pic1 * classmatrix[i][j]
- // + pic2 * 2 *
- // (sigma (att in c[i]) getAllignCell... )
- // / nbatts of c[i] + nbatts of c[j]
- for ( i=0; i<nbclass1; i++ ){
- Set<OWLProperty> properties1 = getProperties( classlist1.get(i), ((OWLOntology)onto1) );
- int nba1 = properties1.size();
- if ( nba1 > 0 ) { // if not, keep old values...
- //Set correspondences = new HashSet();
- for ( j=0; j<nbclass2; j++ ){
- Set<OWLProperty> properties2 = getProperties( classlist2.get(j), ((OWLOntology)onto2) );
- int nba2 = properties1.size();
- double attsum = 0.;
- // check that there is a correspondance
- // in list of class2 atts and add their weights
- for ( OWLProperty prp : properties1 ){
- Set<Cell> s2 = (Set<Cell>)getAlignCells1( prp );
- // Find the property with the higest similarity
- // that is matched here
- double currentValue = 0.;
- for( Iterator<Cell> it2 = s2.iterator(); it2.hasNext(); ){
- Cell c2 = it2.next();
- if ( properties2.contains((Object)c2.getObject2() ) ) {
- double val = c2.getStrength();
- if ( val > currentValue )
- currentValue = val;
- }
+ if (debug > 0) System.err.print("Computing class distances\n");
+ // Compute classes distances
+ // -- for all of its attribute, find the best match if possible... easy
+ // -- simply replace in the matrix the value by the value plus the
+ // classmatrix[i][j] =
+ // pic1 * classmatrix[i][j]
+ // + pic2 * 2 *
+ // (sigma (att in c[i]) getAllignCell... )
+ // / nbatts of c[i] + nbatts of c[j]
+ for ( i=0; i<nbclass1; i++ ){
+ Set<Object> properties1 = honto1.getProperties( classlist1.get(i) );
+ int nba1 = properties1.size();
+ if ( nba1 > 0 ) { // if not, keep old values...
+ //Set correspondences = new HashSet();
+ for ( j=0; j<nbclass2; j++ ){
+ Set<Object> properties2 = honto2.getProperties( classlist2.get(j) );
+ int nba2 = properties1.size();
+ double attsum = 0.;
+ // check that there is a correspondance
+ // in list of class2 atts and add their weights
+ for ( Object prp : properties1 ){
+ Set<Cell> s2 = (Set<Cell>)getAlignCells1( prp );
+ // Find the property with the higest similarity
+ // that is matched here
+ double currentValue = 0.;
+ for( Cell c2 : s2 ){
+ if ( properties2.contains( c2.getObject2() ) ) {
+ double val = c2.getStrength();
+ if ( val > currentValue )
+ currentValue = val;
}
- attsum = attsum + 1 - currentValue;
}
- classmatrix[i][j] = classmatrix[i][j]
- + pic2 * (2 * attsum / (nba1 + nba2));
+ attsum = attsum + 1 - currentValue;
}
+ classmatrix[i][j] = classmatrix[i][j]
+ + pic2 * (2 * attsum / (nba1 + nba2));
}
- // Assess factor
- // -- FirstExp: nothing to be done: one pass
}
- //selectBestMatch( nbclass1, classlist1, nbclass2, classlist2, classmatrix, threshold, null);
- } catch (OWLException e) {
- throw new AlignmentException( "OWLException during alignment", e );
}
}
- public void getProperties( OWLDescription desc, OWLOntology o, Set<OWLProperty> list){
- // I am Jerome Euzenat and I am sure that there is some problem here...
- // DISPATCHING MANUALLY !
- try {
- Method mm = null;
- if ( Class.forName("org.semanticweb.owl.model.OWLRestriction").isInstance(desc) ){
- mm = this.getClass().getMethod("getProperties",
- new Class [] {Class.forName("org.semanticweb.owl.model.OWLRestriction"),Class.forName("org.semanticweb.owl.model.OWLOntology"),Class.forName("java.util.Set")});
- } else if (Class.forName("org.semanticweb.owl.model.OWLClass").isInstance(desc) ) {
- mm = this.getClass().getMethod("getProperties",
- new Class [] {Class.forName("org.semanticweb.owl.model.OWLClass"),Class.forName("org.semanticweb.owl.model.OWLOntology"),Class.forName("java.util.Set")});
- } else if (Class.forName("org.semanticweb.owl.model.OWLNaryBooleanDescription").isInstance(desc) ) {
- mm = this.getClass().getMethod("getProperties",
- new Class [] {Class.forName("org.semanticweb.owl.model.OWLNaryBooleanDescription"),Class.forName("org.semanticweb.owl.model.OWLOntology"),Class.forName("java.util.Set")});
- }
- if ( mm != null ) mm.invoke(this,new Object[] {desc,o,list});
- //Method mmm[] = this.getClass().getMethods();
- //for ( int i = 0; i < mmm.length ; i++ ){
- // if ( mmm[i].getName().equals("getProperties") ){
- // mmm[i].invoke(this,new Object[] {desc,o,list});
- // i = mmm.length;
- // }
- // }
- } catch (IllegalAccessException e) {
- e.printStackTrace();
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- } catch (NoSuchMethodException e) {
- e.printStackTrace();
- } catch (InvocationTargetException e) {
- e.printStackTrace();
- }
- }
- public void getProperties( OWLRestriction rest, OWLOntology o, Set<OWLProperty> list) throws OWLException {
- list.add( rest.getProperty() );
- }
- public void getProperties( OWLNaryBooleanDescription d, OWLOntology o, Set<OWLProperty> list) throws OWLException {
- for ( Iterator it = d.getOperands().iterator(); it.hasNext() ;){
- getProperties( (OWLDescription)it.next(), o, list );
- }
- }
- public void getProperties( OWLClass cl, OWLOntology o, Set<OWLProperty> list) throws OWLException {
- for ( Iterator it = cl.getSuperClasses(o).iterator(); it.hasNext(); ){
- OWLDescription dsc = (OWLDescription)it.next();
- getProperties( dsc, o, list );
- }
- // JE: I suspect that this can be a cause for looping!!
- for ( Iterator it = cl.getEquivalentClasses(o).iterator(); it.hasNext(); ){
- getProperties( (OWLDescription)it.next(), o, list );
- }
- }
-
- private Set<OWLProperty> getProperties( OWLClass cl, OWLOntology o ) throws OWLException {
- Set<OWLProperty> resultSet = new HashSet<OWLProperty>();
- getProperties( cl, o, resultSet );
- return resultSet;
- }
-
}
diff --git a/src/fr/inrialpes/exmo/align/impl/method/EditDistNameAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/EditDistNameAlignment.java
index 5ec11055..a4229b0a 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/EditDistNameAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/EditDistNameAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -20,14 +20,6 @@
package fr.inrialpes.exmo.align.impl.method;
-import java.util.Iterator;
-
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLException;
-
import org.semanticweb.owl.align.AlignmentProcess;
import fr.inrialpes.exmo.align.impl.DistanceAlignment;
@@ -42,34 +34,26 @@ import fr.inrialpes.exmo.align.impl.MatrixMeasure;
* @version $Id$
*/
-public class EditDistNameAlignment extends DistanceAlignment implements AlignmentProcess
-{
+public class EditDistNameAlignment extends DistanceAlignment implements AlignmentProcess {
/** Creation **/
public EditDistNameAlignment(){
setSimilarity( new MatrixMeasure() {
- public double measure( OWLClass cl1, OWLClass cl2 ) throws OWLException{
- String s1 = cl1.getURI().getFragment();
- String s2 = cl2.getURI().getFragment();
+ public double measure( Object o1, Object o2 ) throws Exception {
+ String s1 = ontology1().getEntityName( o1 );
+ String s2 = ontology2().getEntityName( o2 );
if ( s1 == null || s2 == null ) return 1.;
else return StringDistances.levenshteinDistance(
s1.toLowerCase(),
s2.toLowerCase()) / max(s1.length(),s2.length());
}
- public double measure( OWLProperty pr1, OWLProperty pr2 ) throws OWLException{
- String s1 = pr1.getURI().getFragment();
- String s2 = pr2.getURI().getFragment();
- if ( s1 == null || s2 == null ) return 1.;
- else return StringDistances.levenshteinDistance(
- s1.toLowerCase(),
- s2.toLowerCase()) / max(s1.length(),s2.length());
+ public double classMeasure( Object cl1, Object cl2 ) throws Exception {
+ return measure( cl1, cl2 );
}
- public double measure( OWLIndividual id1, OWLIndividual id2 ) throws OWLException{
- String s1 = id1.getURI().getFragment();
- String s2 = id2.getURI().getFragment();
- if ( s1 == null || s2 == null ) return 1.;
- else return StringDistances.levenshteinDistance(
- s1.toLowerCase(),
- s2.toLowerCase()) / max(s1.length(),s2.length());
+ public double propertyMeasure( Object pr1, Object pr2 ) throws Exception {
+ return measure( pr1, pr2 );
+ }
+ public double individualMeasure( Object id1, Object id2 ) throws Exception {
+ return measure( id1, id2 );
}
} );
};
diff --git a/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java
index e05fdff3..a53f0d18 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java
@@ -22,20 +22,8 @@
package fr.inrialpes.exmo.align.impl.method;
import java.lang.Integer;
-import java.util.Iterator;
import java.util.Vector;
import java.util.Set;
-import java.util.HashSet;
-import java.lang.reflect.Method;
-import java.lang.reflect.InvocationTargetException;
-
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLRestriction;
-import org.semanticweb.owl.model.OWLDescription;
-import org.semanticweb.owl.model.OWLNaryBooleanDescription;
-import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
@@ -43,7 +31,7 @@ import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.DistanceAlignment;
-
+import fr.inrialpes.exmo.align.onto.HeavyLoadedOntology;
/** This class has been built for ISWC experiments with bibliography.
* It implements a non iterative (one step) OLA algorithms based on
@@ -62,89 +50,95 @@ import fr.inrialpes.exmo.align.impl.DistanceAlignment;
* @version $Id$
*/
+public class NameAndPropertyAlignment extends DistanceAlignment implements AlignmentProcess {
+
+ private HeavyLoadedOntology<Object> honto1 = null;
+ private HeavyLoadedOntology<Object> honto2 = null;
-public class NameAndPropertyAlignment extends DistanceAlignment implements AlignmentProcess
-{
/** Creation **/
public NameAndPropertyAlignment(){
setType("**");
};
-
/** Processing **/
public void align( Alignment alignment, Parameters params ) throws AlignmentException {
loadInit( alignment );
- //ignore alignment;
+ honto1 = (HeavyLoadedOntology<Object>)getOntologyObject1();
+ honto2 = (HeavyLoadedOntology<Object>)getOntologyObject2();
double threshold = 1.; // threshold above which distances are too high
int i, j = 0; // index for onto1 and onto2 classes
- //int l1, l2 = 0; // length of strings (for normalizing)
int nbclass1 = 0; // number of classes in onto1
int nbclass2 = 0; // number of classes in onto2
- Vector<OWLClass> classlist2 = new Vector<OWLClass>(10); // onto2 classes
- Vector<OWLClass> classlist1 = new Vector<OWLClass>(10); // onto1 classes
+ Vector<Object> classlist2 = new Vector<Object>(10); // onto2 classes
+ Vector<Object> classlist1 = new Vector<Object>(10); // onto1 classes
double classmatrix[][]; // class distance matrix
int nbprop1 = 0; // number of properties in onto1
int nbprop2 = 0; // number of properties in onto2
- Vector<OWLProperty> proplist2 = new Vector<OWLProperty>(10); // onto2 properties
- Vector<OWLProperty> proplist1 = new Vector<OWLProperty>(10); // onto1 properties
+ Vector<Object> proplist2 = new Vector<Object>(10); // onto2 properties
+ Vector<Object> proplist1 = new Vector<Object>(10); // onto1 properties
double propmatrix[][]; // properties distance matrix
double pic1 = 0.5; // class weigth for name
- //double pic2 = 0.5; // class weight for properties
double pia1 = 1.; // relation weight for name
- //double pia2 = 0.; // relation weight for domain
- //double pia3 = 0.; // relation weight for range
double epsillon = 0.05; // stoping condition
if ( params.getParameter("debug") != null )
debug = ((Integer)params.getParameter("debug")).intValue();
- try {
// Create property lists and matrix
- for ( Iterator it = ((OWLOntology)getOntology1()).getObjectProperties().iterator(); it.hasNext(); nbprop1++ ){
- proplist1.add( (OWLProperty)it.next() );
+ for ( Object prop : honto1.getObjectProperties() ){
+ nbprop1++;
+ proplist1.add( prop );
}
- for ( Iterator it = ((OWLOntology)getOntology1()).getDataProperties().iterator(); it.hasNext(); nbprop1++ ){
- proplist1.add( (OWLProperty)it.next() );
+ for ( Object prop : honto1.getDataProperties() ){
+ nbprop1++;
+ proplist1.add( prop );
}
- for ( Iterator it = ((OWLOntology)getOntology2()).getObjectProperties().iterator(); it.hasNext(); nbprop2++ ){
- proplist2.add( (OWLProperty)it.next() );
+ for ( Object prop : honto2.getObjectProperties() ){
+ nbprop2++;
+ proplist2.add( prop );
}
- for ( Iterator it = ((OWLOntology)getOntology2()).getDataProperties().iterator(); it.hasNext(); nbprop2++ ){
- proplist2.add( (OWLProperty)it.next() );
+ for ( Object prop : honto2.getDataProperties() ){
+ nbprop2++;
+ proplist2.add( prop );
}
propmatrix = new double[nbprop1+1][nbprop2+1];
// Create class lists
- for ( Iterator it = ((OWLOntology)getOntology2()).getClasses().iterator(); it.hasNext(); nbclass2++ ){
- classlist2.add( (OWLClass)it.next() );
+ for ( Object cl : honto1.getClasses() ){
+ nbclass1++;
+ classlist1.add( cl );
}
- for ( Iterator it = ((OWLOntology)getOntology1()).getClasses().iterator(); it.hasNext(); nbclass1++ ){
- classlist1.add( (OWLClass)it.next() );
+ for ( Object cl : honto2.getClasses() ){
+ nbclass2++;
+ classlist2.add( cl );
}
classmatrix = new double[nbclass1+1][nbclass2+1];
if (debug > 0) System.err.println("Initializing property distances");
+
for ( i=0; i<nbprop1; i++ ){
- OWLProperty cl = (OWLProperty)proplist1.get(i);
- String st1=new String();
- String st2=new String();
- if (cl.getURI().getFragment()!=null){ st1 = cl.getURI().getFragment().toLowerCase();}
+ Object cl1 = proplist1.get(i);
+ String st1 = honto1.getEntityName( cl1 );
+ if ( st1 != null) st1 = st1.toLowerCase();
for ( j=0; j<nbprop2; j++ ){
- cl = (OWLProperty)proplist2.get(j);
- if(cl.getURI().getFragment()!=null){st2 = cl.getURI().getFragment().toLowerCase() ;}
- propmatrix[i][j] = pia1 * StringDistances.subStringDistance( st1, st2 );
-
+ Object cl2 = proplist2.get(j);
+ String st2 = honto2.getEntityName( cl2 );
+ if( st2 != null ) st2 = st2.toLowerCase();
+ if ( st1 != null || st2 != null ) {
+ propmatrix[i][j] = pia1 * StringDistances.subStringDistance( st1, st2 );
+ } else {
+ propmatrix[i][j] = 1.;
+ }
}
}
if (debug > 0) System.err.println("Initializing class distances");
+
// Initialize class distances
for ( i=0; i<nbclass1; i++ ){
- OWLClass cl = (OWLClass)classlist1.get(i);
+ Object cl1 = classlist1.get(i);
for ( j=0; j<nbclass2; j++ ){
- classmatrix[i][j] = pic1*StringDistances.subStringDistance(
- cl.getURI().getFragment().toLowerCase(),
- ((OWLClass)classlist2.get(j)).getURI().getFragment().toLowerCase());
+ classmatrix[i][j] = pic1*StringDistances.subStringDistance( honto1.getEntityName( cl1 ).toLowerCase(), honto2.getEntityName( classlist2.get(j) ).toLowerCase());
}
}
@@ -168,7 +162,7 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
max = propmatrix[i][j];
}
}
- if ( found && max < 0.5) { addAlignDistanceCell( (OWLProperty)proplist1.get(i), (OWLProperty)proplist2.get(best), "=", max ); }
+ if ( found && max < 0.5) { addAlignDistanceCell( proplist1.get(i), proplist2.get(best), "=", max ); }
}
if (debug > 0) System.err.print("Computing class distances\n");
// Compute classes distances
@@ -181,13 +175,13 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
// / nbatts of c[i] + nbatts of c[j]
for ( i=0; i<nbclass1; i++ ){
- Set properties1 = getProperties( (OWLClass)classlist1.get(i), ((OWLOntology)getOntology1()) );
+ Set<Object> properties1 = honto1.getProperties( classlist1.get(i) );
int nba1 = properties1.size();
if ( nba1 > 0 ) { // if not, keep old values...
//Set correspondences = new HashSet();
for ( j=0; j<nbclass2; j++ ){
- Set properties2 = getProperties( (OWLClass)classlist2.get(j), ((OWLOntology)getOntology2()) );
+ Set<Object> properties2 = honto2.getProperties( classlist2.get(j) );
//int nba2 = properties1.size();
//double attsum = 0.;
// check that there is a correspondance
@@ -196,7 +190,7 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
// Make a local alignment with the properties.
double moy_align_loc = alignLocal(properties1,properties2);
- if (moy_align_loc>0.7){
+ if (moy_align_loc > 0.7){
classmatrix[i][j] = (classmatrix[i][j] + 2* moy_align_loc)/3;
}
}
@@ -207,9 +201,6 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
// -- FirstExp: nothing to be done: one pass
factor = 0.;
}
- } catch (OWLException e) {
- throw new AlignmentException( "OWLException during alignment", e );
- }
// This mechanism should be parametric!
// Select the best match
// There can be many algorithm for these:
@@ -230,95 +221,51 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
max = classmatrix[i][j];
}
}
- if ( found && max < 0.5) { addAlignDistanceCell( (OWLClass)classlist1.get(i), (OWLClass)classlist2.get(best), "=", max ); }
+ if ( found && max < 0.5) { addAlignDistanceCell( classlist1.get(i), classlist2.get(best), "=", max ); }
}
}
- public void getProperties( OWLDescription desc, OWLOntology o, Set<OWLProperty> list){
- // I am Jerome Euzenat and I am sure that there is some problem here...
- // DISPATCHING MANUALLY !
- try {
- Method mm = null;
- if ( Class.forName("org.semanticweb.owl.model.OWLRestriction").isInstance(desc) ){
- mm = this.getClass().getMethod("getProperties",
- new Class [] {Class.forName("org.semanticweb.owl.model.OWLRestriction"),Class.forName("org.semanticweb.owl.model.OWLOntology"),Class.forName("java.util.Set")});
- } else if (Class.forName("org.semanticweb.owl.model.OWLClass").isInstance(desc) ) {
- mm = this.getClass().getMethod("getProperties",
- new Class [] {Class.forName("org.semanticweb.owl.model.OWLClass"),Class.forName("org.semanticweb.owl.model.OWLOntology"),Class.forName("java.util.Set")});
- } else if (Class.forName("org.semanticweb.owl.model.OWLNaryBooleanDescription").isInstance(desc) ) {
- mm = this.getClass().getMethod("getProperties",
- new Class [] {Class.forName("org.semanticweb.owl.model.OWLNaryBooleanDescription"),Class.forName("org.semanticweb.owl.model.OWLOntology"),Class.forName("java.util.Set")});
- }
- if ( mm != null ) mm.invoke(this,new Object[] {desc,o,list});
- } catch (IllegalAccessException e) {
- e.printStackTrace();
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- } catch (NoSuchMethodException e) {
- e.printStackTrace();
- } catch (InvocationTargetException e) {
- e.printStackTrace();
- }
- }
- public void getProperties( OWLRestriction rest, OWLOntology o, Set<OWLProperty> list) throws OWLException {
- list.add( rest.getProperty() );
- }
- public void getProperties( OWLNaryBooleanDescription d, OWLOntology o, Set<OWLProperty> list) throws OWLException {
- for ( Iterator it = d.getOperands().iterator(); it.hasNext() ;){
- getProperties( (OWLDescription)it.next(), o, list );
- }
- }
- public void getProperties( OWLClass cl, OWLOntology o, Set<OWLProperty> list) throws OWLException {
- for ( Iterator it = cl.getSuperClasses(o).iterator(); it.hasNext(); ){
- OWLDescription dsc = (OWLDescription)it.next();
- getProperties( dsc, o, list );
- }
- // JE: I suspect that this can be a cause for looping!!
- for ( Iterator it = cl.getEquivalentClasses(o).iterator(); it.hasNext(); ){
- getProperties( (OWLDescription)it.next(), o, list );
- }
- }
-
- private Set<OWLProperty> getProperties( OWLClass cl, OWLOntology o ) throws OWLException {
- Set<OWLProperty> resultSet = new HashSet<OWLProperty>();
- getProperties( cl, o, resultSet );
- return resultSet;
- }
-
- private double alignLocal( Set prop1, Set prop2) throws OWLException {
- // make a local alignement
- // return an average of all the property alignement
-
- double propmatrix[] [];
- int nbprop1=prop1.size();
- int nbprop2=prop2.size();
- //int best=0;
- double max =0.0;
- double moy=0.0;
- int i=0;
- int j=0;
- propmatrix = new double[nbprop1+1][nbprop2+1];
+ /**
+ * Make a local alignement
+ * @return an average of all the property alignement
+ */
+ private double alignLocal( Set<Object> prop1, Set<Object> prop2) {
+ int nbprop1 = prop1.size();
+ int nbprop2 = prop2.size();
+ double max = 0.0;
+ double moy= 0.0;
+ int i = 0;
+ int j = 0;
+ String s1 = null;
+ String s2 = null;
+ double[][] propmatrix = new double[nbprop1+1][nbprop2+1];
- for ( Iterator prp1 = prop1.iterator(); prp1.hasNext();i++ ){
- OWLProperty property1 = (OWLProperty)prp1.next();
- String s1 = property1.getURI().getFragment().toLowerCase();
- for ( Iterator prp2 = prop2.iterator(); prp2.hasNext();j++ ){
- OWLProperty property2 = (OWLProperty)prp2.next();
- String s2 = property2.getURI().getFragment().toLowerCase();
- propmatrix[i][j] = StringDistances.subStringDistance( s1, s2 );
+ for ( Object property1 : prop1 ){
+ i++;
+ try {
+ s1 = honto1.getEntityName( property1 ).toLowerCase();
+ } catch (AlignmentException aex) { s1 = null; };
+ for ( Object property2 : prop2 ) {
+ j++;
+ try {
+ s2 = honto2.getEntityName( property2 ).toLowerCase();
+ propmatrix[i][j] = 1.0-StringDistances.subStringDistance( s1, s2 );
+ } catch (AlignmentException aex) {
+ propmatrix[i][j] = 0.0;
+ }
}
j=0;
}
- for (i=0; i< nbprop1; i++){
- for(j=0;j<nbprop2;j++){
- if (1.0-propmatrix[i][j]>max){
- max=1.0-propmatrix[i][j];
+ for ( i=0; i< nbprop1; i++ ) {
+ for ( j=0; j<nbprop2; j++ ) {
+ if ( propmatrix[i][j] > max ) {
+ max = propmatrix[i][j];
}
}
- moy=moy+max;
- max=0.0;
+ moy = moy+max;
+ max = 0.0;
}
return moy;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/method/NameEqAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/NameEqAlignment.java
index 49dbea91..3c24c7f7 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/NameEqAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/NameEqAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -20,59 +20,19 @@
package fr.inrialpes.exmo.align.impl.method;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLException;
-
-import org.semanticweb.owl.align.Alignment;
-import org.semanticweb.owl.align.AlignmentProcess;
-import org.semanticweb.owl.align.AlignmentException;
-import org.semanticweb.owl.align.Parameters;
-
-import fr.inrialpes.exmo.align.impl.DistanceAlignment;
-import fr.inrialpes.exmo.align.impl.MatrixMeasure;
-
/**
* Matches two oontologies based on the equality of the name of their entities.
+ * THIS CLASS IS ONLY HERE FOR COMPATIBILITY PURPOSES
*
* @author Jérôme Euzenat
* @version $Id$
*/
-public class NameEqAlignment extends DistanceAlignment implements AlignmentProcess {
+public class NameEqAlignment extends StringDistAlignment {
/** Creation **/
public NameEqAlignment(){
- setSimilarity( new MatrixMeasure() {
- public double measure( OWLClass cl1, OWLClass cl2 ) throws OWLException{
- String s1 = cl1.getURI().getFragment();
- String s2 = cl2.getURI().getFragment();
- if ( s1 != null && s2 != null && s1.toLowerCase().equals(s2.toLowerCase()) ) return 0.;
- else return 1.;
- }
- public double measure( OWLProperty pr1, OWLProperty pr2 ) throws OWLException{
- String s1 = pr1.getURI().getFragment();
- String s2 = pr2.getURI().getFragment();
- if ( s1 != null && s2 != null && s1.toLowerCase().equals(s2.toLowerCase()) ) return 0.;
- else return 1.;
- }
- public double measure( OWLIndividual id1, OWLIndividual id2 ) throws OWLException{
- String s1 = id1.getURI().getFragment();
- String s2 = id2.getURI().getFragment();
- if ( s1 != null && s2 != null && s1.toLowerCase().equals(s2.toLowerCase()) ) return 0.;
- else return 1.;
- }
- } );
- setType("**");
+ methodName = "equalDistance";
};
- /** Processing **/
- public void align( Alignment alignment, Parameters params ) throws AlignmentException {
- loadInit( alignment );
- getSimilarity().initialize( (OWLOntology)getOntology1(), (OWLOntology)getOntology2(), alignment );
- getSimilarity().compute( params );
- extract( type, params );
- }
}
diff --git a/src/fr/inrialpes/exmo/align/impl/method/SMOANameAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/SMOANameAlignment.java
index da41a525..0ce23cb6 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/SMOANameAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/SMOANameAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -20,55 +20,20 @@
package fr.inrialpes.exmo.align.impl.method;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLException;
-
-import fr.inrialpes.exmo.align.impl.DistanceAlignment;
-import fr.inrialpes.exmo.align.impl.MatrixMeasure;
-
-import org.semanticweb.owl.align.AlignmentProcess;
-
/**
* This class aligns ontology with regard to the editing distance between
* class names.
+ * THIS CLASS IS ONLY HERE FOR COMPATIBILITY PURPOSES
*
* @author Jérôme Euzenat
* @version $Id$
*/
-public class SMOANameAlignment extends DistanceAlignment implements AlignmentProcess
-{
+public class SMOANameAlignment extends StringDistAlignment {
+
/** Creation **/
public SMOANameAlignment(){
- setSimilarity( new MatrixMeasure() {
- public double measure( OWLClass cl1, OWLClass cl2 ) throws OWLException{
- String s1 = cl1.getURI().getFragment();
- String s2 = cl2.getURI().getFragment();
- if ( s1 == null || s2 == null ) return 1.;
- else return StringDistances.smoaDistance(
- s1.toLowerCase(),
- s2.toLowerCase());
- }
- public double measure( OWLProperty pr1, OWLProperty pr2 ) throws OWLException{
- String s1 = pr1.getURI().getFragment();
- String s2 = pr2.getURI().getFragment();
- if ( s1 == null || s2 == null ) return 1.;
- else return StringDistances.smoaDistance(
- s1.toLowerCase(),
- s2.toLowerCase());
- }
- public double measure( OWLIndividual id1, OWLIndividual id2 ) throws OWLException{
- String s1 = id1.getURI().getFragment();
- String s2 = id2.getURI().getFragment();
- if ( s1 == null || s2 == null ) return 1.;
- else return StringDistances.smoaDistance(
- s1.toLowerCase(),
- s2.toLowerCase());
- }
- } );
+ methodName = "smoaDistance";
};
}
diff --git a/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
index 0c293071..89c536f0 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -23,12 +23,6 @@ package fr.inrialpes.exmo.align.impl.method;
import java.net.URI;
import java.lang.reflect.Method;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLException;
-
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentException;
@@ -54,35 +48,29 @@ import fr.inrialpes.exmo.align.impl.BasicParameters;
public class StringDistAlignment extends DistanceAlignment implements AlignmentProcess {
Method dissimilarity = null;
+ String methodName = "equalDistance";
/** Creation **/
public StringDistAlignment() {
setSimilarity( new MatrixMeasure() {
- public double measure( OWLClass cl1, OWLClass cl2 ) throws Exception{
- Object[] params = { cl1.getURI().getFragment(), cl2.getURI().getFragment() };
- if ( debug > 4 )
- System.err.println( "CL:"+cl1.getURI().getFragment()+" ++ "+cl2.getURI().getFragment());
- return ((Double)dissimilarity.invoke( null, params )).doubleValue();
+ public double classMeasure( Object cl1, Object cl2 ) throws Exception {
+ return measure( cl1, cl2 );
}
- public double measure( OWLProperty pr1, OWLProperty pr2 ) throws Exception{
- Object[] params = { pr1.getURI().getFragment(), pr2.getURI().getFragment() };
+ public double measure( Object o1, Object o2 ) throws Exception {
+ String s1 = ontology1().getEntityName( o1 );
+ String s2 = ontology2().getEntityName( o2 );
+ // Unnamed entity = max distance
+ if ( s1 == null || s2 == null ) return 1.;
+ Object[] params = { s1.toLowerCase(), s2.toLowerCase() };
if ( debug > 4 )
- System.err.println( "PR:"+pr1.getURI().getFragment()+" ++ "+pr2.getURI().getFragment());
+ System.err.println( "OB:"+ontology1().getEntityName( o1 )+" ++ "+ontology2().getEntityName( o2 )+" ==> "+dissimilarity.invoke( null, params ));
return ((Double)dissimilarity.invoke( null, params )).doubleValue();
}
- public double measure( OWLIndividual id1, OWLIndividual id2 ) throws Exception{
- if ( debug > 4 )
- System.err.println( "ID:"+id1+" -- "+id2);
- URI URI1 = id1.getURI();
- String name1;
- if ( URI1 != null ) name1 = URI1.getFragment();
- else name1 = "";
- URI URI2 = id2.getURI();
- String name2;
- if ( URI2 != null ) name2 = URI2.getFragment();
- else name2 = "";
- Object[] params = { name1, name2 };
- return ((Double)dissimilarity.invoke( null, params )).doubleValue();
+ public double propertyMeasure( Object pr1, Object pr2 ) throws Exception{
+ return measure( pr1, pr2 );
+ }
+ public double individualMeasure( Object id1, Object id2 ) throws Exception{
+ return measure( id1, id2 );
}
} );
setType("**");
@@ -95,11 +83,10 @@ public class StringDistAlignment extends DistanceAlignment implements AlignmentP
// Get function from params
String f = (String)params.getParameter("stringFunction");
try {
- String fname = "equalDistance";
- if ( f != null ) fname = f.trim();
+ if ( f != null ) methodName = f.trim();
Class sClass = Class.forName("java.lang.String");
Class[] mParams = { sClass, sClass };
- dissimilarity = Class.forName("fr.inrialpes.exmo.align.impl.method.StringDistances").getMethod( fname, mParams );
+ dissimilarity = Class.forName("fr.inrialpes.exmo.align.impl.method.StringDistances").getMethod( methodName, mParams );
} catch (ClassNotFoundException e) {
e.printStackTrace();
} catch (NoSuchMethodException e) {
@@ -107,7 +94,7 @@ public class StringDistAlignment extends DistanceAlignment implements AlignmentP
}
// Initialize matrix
- getSimilarity().initialize( (OWLOntology)getOntology1(), (OWLOntology)getOntology2(), alignment );
+ getSimilarity().initialize( ontology1(), ontology2(), alignment );
// Compute similarity/dissimilarity
getSimilarity().compute( params );
diff --git a/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
index 04a1d5c0..a9083218 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2007-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -21,22 +21,9 @@
package fr.inrialpes.exmo.align.impl.method;
-import java.util.Iterator;
import java.util.Vector;
import java.util.Set;
-import java.util.HashSet;
import java.lang.Integer;
-import java.lang.reflect.Method;
-import java.lang.reflect.InvocationTargetException;
-
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLRestriction;
-import org.semanticweb.owl.model.OWLDescription;
-import org.semanticweb.owl.model.OWLNaryBooleanDescription;
-import org.semanticweb.owl.model.OWLException;
-import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
@@ -45,6 +32,7 @@ import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.DistanceAlignment;
+import fr.inrialpes.exmo.align.onto.HeavyLoadedOntology;
/** This class has been built for ISWC experiments with bibliography.
* It implements a non iterative (one step) OLA algorithms based on
@@ -63,9 +51,11 @@ import fr.inrialpes.exmo.align.impl.DistanceAlignment;
* @version $Id$
*/
+public class StrucSubsDistAlignment extends DistanceAlignment implements AlignmentProcess {
+
+ private HeavyLoadedOntology<Object> honto1 = null;
+ private HeavyLoadedOntology<Object> honto2 = null;
-public class StrucSubsDistAlignment extends DistanceAlignment implements AlignmentProcess
-{
/** Creation **/
public StrucSubsDistAlignment() {
setType("**");
@@ -74,235 +64,174 @@ public class StrucSubsDistAlignment extends DistanceAlignment implements Alignme
/** Processing **/
public void align( Alignment alignment, Parameters params ) throws AlignmentException {
loadInit( alignment );
- //ignore alignment;
+ honto1 = (HeavyLoadedOntology<Object>)getOntologyObject1();
+ honto2 = (HeavyLoadedOntology<Object>)getOntologyObject2();
double threshold = 1.; // threshold above which distances are too high
int i, j = 0; // index for onto1 and onto2 classes
- //int l1, l2 = 0; // length of strings (for normalizing)
int nbclass1 = 0; // number of classes in onto1
int nbclass2 = 0; // number of classes in onto2
- Vector<OWLClass> classlist2 = new Vector<OWLClass>(10); // onto2 classes
- Vector<OWLClass> classlist1 = new Vector<OWLClass>(10); // onto1 classes
+ Vector<Object> classlist2 = new Vector<Object>(10); // onto2 classes
+ Vector<Object> classlist1 = new Vector<Object>(10); // onto1 classes
double classmatrix[][]; // class distance matrix
int nbprop1 = 0; // number of properties in onto1
int nbprop2 = 0; // number of properties in onto2
- Vector<OWLProperty> proplist2 = new Vector<OWLProperty>(10); // onto2 properties
- Vector<OWLProperty> proplist1 = new Vector<OWLProperty>(10); // onto1 properties
+ Vector<Object> proplist2 = new Vector<Object>(10); // onto2 properties
+ Vector<Object> proplist1 = new Vector<Object>(10); // onto1 properties
double propmatrix[][]; // properties distance matrix
double pic1 = 0.5; // class weigth for name
double pic2 = 0.5; // class weight for properties
double pia1 = 1.; // relation weight for name
- //double pia2 = 0.; // relation weight for domain
- //double pia3 = 0.; // relation weight for range
double epsillon = 0.05; // stoping condition
if ( params.getParameter("debug") != null )
debug = ((Integer)params.getParameter("debug")).intValue();
- try {
- // Create property lists and matrix
- for ( Iterator it = ((OWLOntology)onto1).getObjectProperties().iterator(); it.hasNext(); nbprop1++ ){
- proplist1.add( (OWLProperty)it.next() );
- }
- for ( Iterator it = ((OWLOntology)onto1).getDataProperties().iterator(); it.hasNext(); nbprop1++ ){
- proplist1.add( (OWLProperty)it.next() );
- }
- for ( Iterator it = ((OWLOntology)onto2).getObjectProperties().iterator(); it.hasNext(); nbprop2++ ){
- proplist2.add( (OWLProperty)it.next() );
- }
- for ( Iterator it = ((OWLOntology)onto2).getDataProperties().iterator(); it.hasNext(); nbprop2++ ){
- proplist2.add( (OWLProperty)it.next() );
- }
- propmatrix = new double[nbprop1+1][nbprop2+1];
+ // Create property lists and matrix
+ for ( Object prop : honto1.getObjectProperties() ){
+ nbprop1++;
+ proplist1.add( prop );
+ }
+ for ( Object prop : honto1.getDataProperties() ){
+ nbprop1++;
+ proplist1.add( prop );
+ }
+ for ( Object prop : honto2.getObjectProperties() ){
+ nbprop2++;
+ proplist2.add( prop );
+ }
+ for ( Object prop : honto2.getDataProperties() ){
+ nbprop2++;
+ proplist2.add( prop );
+ }
+ propmatrix = new double[nbprop1+1][nbprop2+1];
+
+ // Create class lists
+ for ( Object cl : honto1.getClasses() ){
+ nbclass1++;
+ classlist1.add( cl );
+ }
+ for ( Object cl : honto2.getClasses() ){
+ nbclass2++;
+ classlist2.add( cl );
+ }
+ classmatrix = new double[nbclass1+1][nbclass2+1];
- // Create class lists
- for ( Iterator it = ((OWLOntology)onto1).getClasses().iterator(); it.hasNext(); nbclass1++ ){
- classlist1.add( (OWLClass)it.next() );
+ if (debug > 0) System.err.println("Initializing property distances");
+
+ for ( i=0; i<nbprop1; i++ ){
+ Object cl1 = proplist1.get(i);
+ String st1 = honto1.getEntityName( cl1 );
+ if ( st1 != null) st1 = st1.toLowerCase();
+ for ( j=0; j<nbprop2; j++ ){
+ Object cl2 = proplist2.get(j);
+ String st2 = honto2.getEntityName( cl2 );
+ if( st2 != null ) st2 = st2.toLowerCase();
+ if ( st1 != null || st2 != null ) {
+ propmatrix[i][j] = pia1 * StringDistances.subStringDistance( st1, st2 );
+ } else {
+ propmatrix[i][j] = pia1;
+ }
}
- for ( Iterator it = ((OWLOntology)onto2).getClasses().iterator(); it.hasNext(); nbclass2++ ){
- classlist2.add( (OWLClass)it.next() );
+ }
+
+ if (debug > 0) System.err.println("Initializing class distances");
+
+ // Initialize class distances
+ for ( i=0; i<nbclass1; i++ ){
+ Object cl1 = classlist1.get(i);
+ for ( j=0; j<nbclass2; j++ ){
+ classmatrix[i][j] = pic1*StringDistances.subStringDistance( honto1.getEntityName( cl1 ).toLowerCase(), honto2.getEntityName( classlist2.get(j) ).toLowerCase());
}
- classmatrix = new double[nbclass1+1][nbclass2+1];
+ }
- if (debug > 0) System.err.println("Initializing property distances");
+ // Iterate until completion
+ double factor = 1.0;
+ while ( factor > epsillon ){
+ // Compute property distances
+ // -- FirstExp: nothing to be done: one pass
+ // Here create the best matches for property distance already
+ // -- FirstExp: goes directly in the alignment structure
+ // since it will never be refined anymore...
+ if (debug > 0) System.err.print("Storing property alignment\n");
for ( i=0; i<nbprop1; i++ ){
- OWLProperty cl = proplist1.get(i);
- String s1 = cl.getURI().getFragment();
- if ( s1 != null ) s1 = s1.toLowerCase();
+ boolean found = false;
+ int best = 0;
+ double max = threshold;
for ( j=0; j<nbprop2; j++ ){
- cl = proplist2.get(j);
- String s2 = cl.getURI().getFragment();
- if ( s2 != null ) s2 = s2.toLowerCase();
- if ( s1 == null || s2 == null ) { propmatrix[i][j] = pia1; }
- else {
- propmatrix[i][j] = pia1 * StringDistances.subStringDistance( s1, s2 );
+ if ( propmatrix[i][j] < max) {
+ found = true;
+ best = j;
+ max = propmatrix[i][j];
}
}
+ if ( found ) { addAlignDistanceCell( proplist1.get(i), proplist2.get(best), "=", max ); }
}
-
- if (debug > 0) System.err.println("Initializing class distances");
- // Initialize class distances
+
+ if (debug > 0) System.err.print("Computing class distances\n");
+ // Compute classes distances
+ // -- for all of its attribute, find the best match if possible... easy
+ // -- simply replace in the matrix the value by the value plus the
+ // classmatrix[i][j] =
+ // pic1 * classmatrix[i][j]
+ // + pic2 * 2 *
+ // (sigma (att in c[i]) getAllignCell... )
+ // / nbatts of c[i] + nbatts of c[j]
for ( i=0; i<nbclass1; i++ ){
- OWLClass cl = classlist1.get(i);
- for ( j=0; j<nbclass2; j++ ){
- classmatrix[i][j] = pic1 * StringDistances.subStringDistance(
- cl.getURI().getFragment().toLowerCase(),
- classlist2.get(j).getURI().getFragment().toLowerCase());
- }
- }
-
- // Iterate until completion
- double factor = 1.0;
- while ( factor > epsillon ){
- // Compute property distances
- // -- FirstExp: nothing to be done: one pass
- // Here create the best matches for property distance already
- // -- FirstExp: goes directly in the alignment structure
- // since it will never be refined anymore...
- if (debug > 0) System.err.print("Storing property alignment\n");
- for ( i=0; i<nbprop1; i++ ){
- boolean found = false;
- int best = 0;
- double max = threshold;
- for ( j=0; j<nbprop2; j++ ){
- if ( propmatrix[i][j] < max) {
- found = true;
- best = j;
- max = propmatrix[i][j];
- }
- }
- if ( found ) { addAlignDistanceCell( proplist1.get(i), proplist2.get(best), "=", max ); }
- }
-
- if (debug > 0) System.err.print("Computing class distances\n");
- // Compute classes distances
- // -- for all of its attribute, find the best match if possible... easy
- // -- simply replace in the matrix the value by the value plus the
- // classmatrix[i][j] =
- // pic1 * classmatrix[i][j]
- // + pic2 * 2 *
- // (sigma (att in c[i]) getAllignCell... )
- // / nbatts of c[i] + nbatts of c[j]
- for ( i=0; i<nbclass1; i++ ){
- Set properties1 = getProperties( classlist1.get(i), ((OWLOntology)onto1) );
- int nba1 = properties1.size();
- if ( nba1 > 0 ) { // if not, keep old values...
- //Set correspondences = new HashSet();
- for ( j=0; j<nbclass2; j++ ){
- Set properties2 = getProperties( classlist2.get(j), ((OWLOntology)onto2) );
- int nba2 = properties2.size();
- double attsum = 0.;
- // check that there is a correspondance
- // in list of class2 atts and add their weights
- for ( Iterator prp = properties1.iterator(); prp.hasNext(); ){
- Set s2 = getAlignCells1( (OWLEntity)prp.next() );
- // Find the property with the higest similarity
- // that is matched here
- double currentValue = 0.;
- for( Iterator it2 = s2.iterator(); it2.hasNext(); ){
- Cell c2 = (Cell)it2.next();
- if ( properties2.contains((Object)c2.getObject2() ) ) {
- double val = c2.getStrength();
- if ( val > currentValue )
- currentValue = val;
- }
+ Set<Object> properties1 = honto1.getProperties( classlist1.get(i) );
+ int nba1 = properties1.size();
+ if ( nba1 > 0 ) { // if not, keep old values...
+ //Set correspondences = new HashSet();
+ for ( j=0; j<nbclass2; j++ ){
+ Set<Object> properties2 = honto2.getProperties( classlist2.get(j) );
+ int nba2 = properties2.size();
+ double attsum = 0.;
+ // check that there is a correspondance
+ // in list of class2 atts and add their weights
+ for ( Object prp : properties1 ){
+ Set<Cell> s2 = getAlignCells1( prp );
+ // Find the property with the higest similarity
+ // that is matched here
+ double currentValue = 0.;
+ for( Cell c2 : s2 ){
+ if ( properties2.contains( c2.getObject2() ) ) {
+ double val = c2.getStrength();
+ if ( val > currentValue )
+ currentValue = val;
}
- attsum = attsum + 1 - currentValue;
}
- classmatrix[i][j] = classmatrix[i][j]
- + pic2 * (2 * attsum / (nba1 + nba2));
+ attsum = attsum + 1 - currentValue;
}
+ classmatrix[i][j] = classmatrix[i][j]
+ + pic2 * (2 * attsum / (nba1 + nba2));
}
}
- // Assess factor
- // -- FirstExp: nothing to be done: one pass
- factor = 0.;
}
+ // Assess factor
+ // -- FirstExp: nothing to be done: one pass
+ factor = 0.;
+ }
- // This mechanism should be parametric!
- // Select the best match
- // There can be many algorithm for these:
- // n:m: get all of those above a threshold
- // 1:1: get the best discard lines and columns and iterate
- // Here we basically implement ?:* because the algorithm
- // picks up the best matching object above threshold for i.
- if (debug > 0) System.err.print("Storing class alignment\n");
+ // This mechanism should be parametric!
+ // Select the best match
+ // There can be many algorithm for these:
+ // n:m: get all of those above a threshold
+ // 1:1: get the best discard lines and columns and iterate
+ // Here we basically implement ?:* because the algorithm
+ // picks up the best matching object above threshold for i.
+ if (debug > 0) System.err.print("Storing class alignment\n");
- for ( i=0; i<nbclass1; i++ ){
- boolean found = false;
- int best = 0;
- double max = threshold;
- for ( j=0; j<nbclass2; j++ ){
- if ( classmatrix[i][j] < max) {
- found = true;
- best = j;
- max = classmatrix[i][j];
- }
+ for ( i=0; i<nbclass1; i++ ){
+ boolean found = false;
+ int best = 0;
+ double max = threshold;
+ for ( j=0; j<nbclass2; j++ ){
+ if ( classmatrix[i][j] < max) {
+ found = true;
+ best = j;
+ max = classmatrix[i][j];
}
- if ( found ) { addAlignDistanceCell( classlist1.get(i), classlist2.get(best), "=", max ); }
}
- } catch (OWLException e) {
- throw new AlignmentException( "OWLException during alignment", e );
+ if ( found ) { addAlignDistanceCell( classlist1.get(i), classlist2.get(best), "=", max ); }
}
}
-
- public void getProperties( OWLDescription desc, OWLOntology o, Set<OWLProperty> list, Set<Object> accu){
- // I am Jerome Euzenat and I am sure that there is some problem here...
- // DISPATCHING MANUALLY !
- try {
- Method mm = null;
- if ( Class.forName("org.semanticweb.owl.model.OWLRestriction").isInstance(desc) ){
- mm = this.getClass().getMethod("getProperties",
- new Class [] {Class.forName("org.semanticweb.owl.model.OWLRestriction"),Class.forName("org.semanticweb.owl.model.OWLOntology"),Class.forName("java.util.Set"),Class.forName("java.util.Set")});
- } else if (Class.forName("org.semanticweb.owl.model.OWLClass").isInstance(desc) ) {
- mm = this.getClass().getMethod("getProperties",
- new Class [] {Class.forName("org.semanticweb.owl.model.OWLClass"),Class.forName("org.semanticweb.owl.model.OWLOntology"),Class.forName("java.util.Set"),Class.forName("java.util.Set")});
- } else if (Class.forName("org.semanticweb.owl.model.OWLNaryBooleanDescription").isInstance(desc) ) {
- mm = this.getClass().getMethod("getProperties",
- new Class [] {Class.forName("org.semanticweb.owl.model.OWLNaryBooleanDescription"),Class.forName("org.semanticweb.owl.model.OWLOntology"),Class.forName("java.util.Set"),Class.forName("java.util.Set")});
- }
- if ( mm != null ) mm.invoke(this,new Object[] {desc,o,list,accu});
- } catch (IllegalAccessException e) {
- e.printStackTrace();
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- } catch (NoSuchMethodException e) {
- e.printStackTrace();
- } catch (InvocationTargetException e) {
- e.printStackTrace();
- }
- }
- public void getProperties( OWLRestriction rest, OWLOntology o, Set<OWLProperty> list, Set<Object> accu) throws OWLException {
- if ( !accu.contains( (Object)rest ) ) {
- accu.add((Object)rest);
- list.add( rest.getProperty() );
- }
- }
- public void getProperties( OWLNaryBooleanDescription d, OWLOntology o, Set<OWLProperty> list, Set<Object> accu) throws OWLException {
- if ( !accu.contains( (Object)d ) ) {
- accu.add((Object)d);
- for ( Iterator it = d.getOperands().iterator(); it.hasNext() ;){
- getProperties( (OWLDescription)it.next(), o, list, accu );
- }
- }
- }
- public void getProperties( OWLClass cl, OWLOntology o, Set<OWLProperty> list, Set<Object> accu) throws OWLException {
- if ( !accu.contains( (Object)cl ) ) {
- accu.add((Object)cl);
- for ( Iterator it = cl.getSuperClasses(o).iterator(); it.hasNext(); ){
- OWLDescription dsc = (OWLDescription)it.next();
- getProperties( dsc, o, list, accu );
- }
- // avoid loops
- //for ( Iterator it = cl.getEquivalentClasses(o).iterator(); it.hasNext(); ){
- // getProperties( (OWLDescription)it.next(), o, list, accu );
- //}
- }
- }
-
- private Set<OWLProperty> getProperties( OWLClass cl, OWLOntology o ) throws OWLException {
- Set<OWLProperty> resultSet = new HashSet<OWLProperty>();
- Set<Object> accu = new HashSet<Object>();
- getProperties( cl, o, resultSet, accu );
- return resultSet;
- }
}
diff --git a/src/fr/inrialpes/exmo/align/impl/method/SubsDistNameAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/SubsDistNameAlignment.java
index eb96bf67..08155174 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/SubsDistNameAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/SubsDistNameAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -20,66 +20,20 @@
package fr.inrialpes.exmo.align.impl.method;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLException;
-
-import fr.inrialpes.exmo.align.impl.MatrixMeasure;
-import fr.inrialpes.exmo.align.impl.Similarity;
-
-import org.semanticweb.owl.align.Alignment;
-import org.semanticweb.owl.align.AlignmentProcess;
-import org.semanticweb.owl.align.AlignmentException;
-import org.semanticweb.owl.align.Parameters;
-
-import fr.inrialpes.exmo.align.impl.DistanceAlignment;
-
/**
* This class implements alignment based on substring distance
* of class and property labels
+ * THIS CLASS IS ONLY HERE FOR COMPATIBILITY PURPOSES
*
* @author Jérôme Euzenat
* @version $Id$
*/
-public class SubsDistNameAlignment extends DistanceAlignment implements AlignmentProcess
-{
+public class SubsDistNameAlignment extends StringDistAlignment {
+
/** Creation **/
public SubsDistNameAlignment(){
- setSimilarity( new MatrixMeasure() {
- public double measure( OWLClass cl1, OWLClass cl2 ) throws OWLException{
- String s1 = cl1.getURI().getFragment();
- String s2 = cl2.getURI().getFragment();
- if ( s1 != null && s2 != null )
- return StringDistances.subStringDistance(s1.toLowerCase(),s2.toLowerCase());
- else return 1.;
- }
- public double measure( OWLProperty pr1, OWLProperty pr2 ) throws OWLException{
- String s1 = pr1.getURI().getFragment();
- String s2 = pr2.getURI().getFragment();
- if ( s1 != null && s2 != null )
- return StringDistances.subStringDistance(s1.toLowerCase(),s2.toLowerCase());
- else return 1.;
- }
- public double measure( OWLIndividual id1, OWLIndividual id2 ) throws OWLException{
- String s1 = id1.getURI().getFragment();
- String s2 = id2.getURI().getFragment();
- if ( s1 != null && s2 != null )
- return StringDistances.subStringDistance(s1.toLowerCase(),s2.toLowerCase());
- else return 1.;
- }
- } );
- setType("**");
+ methodName = "subStringDistance";
};
- /** Processing **/
- public void align( Alignment alignment, Parameters params ) throws AlignmentException {
- loadInit( alignment );
- getSimilarity().initialize( (OWLOntology)getOntology1(), (OWLOntology)getOntology2(), alignment );
- getSimilarity().compute( params );
- extract( type, params );
- }
-
}
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java
index a2008b23..0c137e00 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java
@@ -26,18 +26,15 @@ import java.io.PrintWriter;
import java.lang.reflect.Method;
import java.lang.reflect.InvocationTargetException;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLEntity;
-import org.semanticweb.owl.model.OWLException;
-
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
-import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
+import fr.inrialpes.exmo.align.impl.ObjectAlignment;
import fr.inrialpes.exmo.align.impl.rel.*;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
/**
* Renders an alignment as a new ontology merging these.
@@ -51,6 +48,8 @@ public class COWLMappingRendererVisitor implements AlignmentVisitor
{
PrintWriter writer = null;
Alignment alignment = null;
+ LoadedOntology onto1 = null;
+ LoadedOntology onto2 = null;
Cell cell = null;
public COWLMappingRendererVisitor( PrintWriter writer ){
@@ -58,9 +57,11 @@ public class COWLMappingRendererVisitor implements AlignmentVisitor
}
public void visit( Alignment align ) throws AlignmentException {
- if ( !(align instanceof OWLAPIAlignment) )
- throw new AlignmentException("COWLMappingRenderer: cannot render simple alignment. Turn them into OWLAlignment, by toOWLAPIAlignement()");
+ if ( !(align instanceof ObjectAlignment) )
+ throw new AlignmentException("COWLMappingRenderer: cannot render simple alignment. Turn them into ObjectAlignment, by toObjectAlignement()");
alignment = align;
+ onto1 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject1();
+ onto2 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject2();
writer.print("<rdf:RDF\n");
writer.print(" xmlns:owl=\"http://www.w3.org/2002/07/owl#\"\n");
writer.print(" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n");
@@ -70,10 +71,10 @@ public class COWLMappingRendererVisitor implements AlignmentVisitor
writer.print(" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema#\">\n\n");
writer.print(" <cowl:Mapping rdf:ID=\"\">\n");
writer.print(" <cowl:sourceOntology>\n");
- writer.print(" <owl:Ontology rdf:about=\""+align.getOntology1URI()+"\"/>\n");
+ writer.print(" <owl:Ontology rdf:about=\""+onto1.getURI()+"\"/>\n");
writer.print(" </cowl:sourceOntology>\n");
writer.print(" <cowl:targetOntology>\n");
- writer.print(" <owl:Ontology rdf:about=\""+align.getOntology2URI()+"\"/>\n");
+ writer.print(" <owl:Ontology rdf:about=\""+onto2.getURI()+"\"/>\n");
writer.print(" </cowl:targetOntology>\n");
for( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
Cell c = (Cell)e.nextElement();
@@ -89,53 +90,45 @@ public class COWLMappingRendererVisitor implements AlignmentVisitor
writer.print(" </cowl:bridgeRule>\n");
}
public void visit( EquivRelation rel ) throws AlignmentException {
- try {
writer.print(" <cowl:Equivalent>\n");
writer.print(" <cowl:source>\n");
- printObject(cell.getObject1AsURI(),(OWLOntology)alignment.getOntology1());
+ printObject(cell.getObject1(),onto1);
writer.print(" </cowl:source>\n");
writer.print(" <cowl:target>\n");
- printObject(cell.getObject2AsURI(),(OWLOntology)alignment.getOntology2());
+ printObject(cell.getObject2(),onto2);
writer.print(" </cowl:target>\n");
writer.print(" </cowl:Equivalent>\n");
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); };
}
public void visit( SubsumeRelation rel ) throws AlignmentException {
- try {
writer.print(" <cowl:Into>\n");
writer.print(" <cowl:source>\n");
- printObject(cell.getObject1AsURI(),(OWLOntology)alignment.getOntology1());
+ printObject(cell.getObject1(),onto1);
writer.print(" </cowl:source>\n");
writer.print(" <cowl:target>\n");
- printObject(cell.getObject2AsURI(),(OWLOntology)alignment.getOntology2());
+ printObject(cell.getObject2(),onto2);
writer.print(" </cowl:target>\n");
writer.print(" </cowl:Into>\n");
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); };
}
public void visit( SubsumedRelation rel ) throws AlignmentException {
- try {
writer.print(" <cowl:Onto>\n");
writer.print(" <cowl:source>\n");
- printObject(cell.getObject1AsURI(),(OWLOntology)alignment.getOntology1());
+ printObject(cell.getObject1(),onto1);
writer.print(" </cowl:source>\n");
writer.print(" <cowl:target>\n");
- printObject(cell.getObject2AsURI(),(OWLOntology)alignment.getOntology2());
+ printObject(cell.getObject2(),onto2);
writer.print(" </cowl:target>\n");
writer.print(" </cowl:Onto>\n");
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); };
}
public void visit( IncompatRelation rel ) throws AlignmentException {
- try {
writer.print(" <cowl:INCOMPATIBLE>\n");
writer.print(" <cowl:source>\n");
- printObject(cell.getObject1AsURI(),(OWLOntology)alignment.getOntology1());
+ printObject(cell.getObject1(),onto1);
writer.print(" </cowl:source>\n");
writer.print(" <cowl:target>\n");
- printObject(cell.getObject2AsURI(),(OWLOntology)alignment.getOntology2());
+ printObject(cell.getObject2(),onto2);
writer.print(" </cowl:target>\n");
writer.print(" </cowl:INCOMPATIBLE>\n");
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); };
}
public void visit( Relation rel ) throws AlignmentException {
// JE: I do not understand why I need this,
@@ -167,15 +160,15 @@ public class COWLMappingRendererVisitor implements AlignmentVisitor
}
}
- public void printObject( URI uri, OWLOntology onto ) throws OWLException {
- if ( (OWLEntity)onto.getClass( uri ) != null ) { // A class
- writer.print(" <owl:Class rdf:about=\""+uri.toString()+"\"/>\n");
- } else if ( (OWLEntity)onto.getDataProperty( uri ) != null ) { // A Dataproperty
- writer.print(" <owl:DataProperty rdf:about=\""+uri.toString()+"\"/>\n");
- } else if ( (OWLEntity)onto.getObjectProperty( uri ) != null ) { // An ObjectProperty
- writer.print(" <owl:ObjectProperty rdf:about=\""+uri.toString()+"\"/>\n");
- } else if ( (OWLEntity)onto.getIndividual( uri ) != null ) { // An individual (but check this)
- writer.print(" <owl:Individual rdf:about=\""+uri.toString()+"\"/>\n");
+ public void printObject( Object ob, LoadedOntology onto ) throws AlignmentException {
+ if ( onto.isClass( ob ) ) {
+ writer.print(" <owl:Class rdf:about=\""+onto.getEntityURI(ob)+"\"/>\n");
+ } else if ( onto.isDataProperty( ob ) ) {
+ writer.print(" <owl:DataProperty rdf:about=\""+onto.getEntityURI(ob)+"\"/>\n");
+ } else if ( onto.isObjectProperty( ob ) ) {
+ writer.print(" <owl:ObjectProperty rdf:about=\""+onto.getEntityURI(ob)+"\"/>\n");
+ } else if ( onto.isIndividual( ob ) ) {
+ writer.print(" <owl:Individual rdf:about=\""+onto.getEntityURI(ob)+"\"/>\n");
}
}
}
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
index 5f3ffb98..0a0308ee 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2007-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -26,17 +26,14 @@ import java.net.URI;
import java.lang.reflect.Method;
import java.lang.reflect.InvocationTargetException;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLEntity;
-import org.semanticweb.owl.model.OWLException;
-
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
-import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
+import fr.inrialpes.exmo.align.impl.ObjectAlignment;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
import fr.inrialpes.exmo.align.impl.rel.*;
/**
@@ -46,11 +43,11 @@ import fr.inrialpes.exmo.align.impl.rel.*;
* @version $Id$
*/
-
-public class OWLAxiomsRendererVisitor implements AlignmentVisitor
-{
+public class OWLAxiomsRendererVisitor implements AlignmentVisitor {
PrintWriter writer = null;
Alignment alignment = null;
+ LoadedOntology onto1 = null;
+ LoadedOntology onto2 = null;
Cell cell = null;
public OWLAxiomsRendererVisitor( PrintWriter writer ){
@@ -58,9 +55,14 @@ public class OWLAxiomsRendererVisitor implements AlignmentVisitor
}
public void visit( Alignment align ) throws AlignmentException {
- if ( !( align instanceof OWLAPIAlignment ) )
- throw new AlignmentException("OWLAxiomsRenderer: cannot render simple alignment. Turn them into OWLAlignment, by toOWLAPIAlignement()");
+ if ( !( align instanceof ObjectAlignment )) {
+ throw new AlignmentException("OWLAxiomsRenderer: cannot render simple alignment. Turn them into ObjectAlignment, by toObjectAlignement()");
+ }
alignment = align;
+ if ( align instanceof ObjectAlignment ){
+ onto1 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject1();
+ onto2 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject2();
+ }
writer.print("<rdf:RDF\n");
writer.print(" xmlns:owl=\"http://www.w3.org/2002/07/owl#\"\n");
writer.print(" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n");
@@ -81,86 +83,77 @@ public class OWLAxiomsRendererVisitor implements AlignmentVisitor
public void visit( Cell cell ) throws AlignmentException {
this.cell = cell;
- OWLOntology onto1 = null;
- URI entity1URI = null;
- try {
- // Not very good but we failed to think subsumed from the first shot.
- if ( cell.getRelation() instanceof SubsumedRelation ){
- onto1 = (OWLOntology)alignment.getOntology2();
- entity1URI = cell.getObject2AsURI();
- } else {
- onto1 = (OWLOntology)alignment.getOntology1();
- entity1URI = cell.getObject1AsURI();
- }
- if ( (OWLEntity)onto1.getClass( entity1URI ) != null ) { // A class
- writer.print(" <owl:Class rdf:about=\""+entity1URI.toString()+"\">\n");
- cell.getRelation().accept( this );
- writer.print(" </owl:Class>\n");
- } else if ( (OWLEntity)onto1.getDataProperty( entity1URI ) != null ) { // A Dataproperty
- writer.print(" <owl:DatatypeProperty rdf:about=\""+entity1URI.toString()+"\">\n");
- cell.getRelation().accept( this );
- writer.print(" </owl:DatatypeProperty>\n");
- } else if ( (OWLEntity)onto1.getObjectProperty( entity1URI ) != null ) { // An ObjectProperty
- writer.print(" <owl:ObjectProperty rdf:about=\""+entity1URI.toString()+"\">\n");
- cell.getRelation().accept( this );
- writer.print(" </owl:ObjectProperty>\n");
- } else if ( (OWLEntity)onto1.getIndividual( entity1URI ) != null ) { // An individual (but check this)
- writer.print(" <owl:Thing rdf:about=\""+entity1URI.toString()+"\">\n");
- cell.getRelation().accept( this );
- writer.print(" </owl:Thing>\n");
- }
- writer.print("\n");
+ Object ob1 = cell.getObject1();
+ URI u1;
+ if ( cell.getRelation() instanceof SubsumedRelation ){
+ u1 = onto2.getEntityURI( cell.getObject2() );
+ } else {
+ u1 = onto1.getEntityURI( ob1 );
+ }
+ if ( onto1.isClass( ob1 ) ) {
+ writer.print(" <owl:Class rdf:about=\""+u1+"\">\n");
+ cell.getRelation().accept( this );
+ writer.print(" </owl:Class>\n");
+ } else if ( onto1.isDataProperty( ob1 ) ) {
+ writer.print(" <owl:DatatypeProperty rdf:about=\""+u1+"\">\n");
+ cell.getRelation().accept( this );
+ writer.print(" </owl:DatatypeProperty>\n");
+ } else if ( onto1.isObjectProperty( ob1 ) ) {
+ writer.print(" <owl:ObjectProperty rdf:about=\""+u1+"\">\n");
+ cell.getRelation().accept( this );
+ writer.print(" </owl:ObjectProperty>\n");
+ } else if ( onto1.isIndividual( ob1 ) ) {
+ writer.print(" <owl:Thing rdf:about=\""+u1+"\">\n");
+ cell.getRelation().accept( this );
+ writer.print(" </owl:Thing>\n");
}
- catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
}
+
public void visit( EquivRelation rel ) throws AlignmentException {
- OWLOntology onto2 = (OWLOntology)alignment.getOntology2();
- try {
- URI entity2URI = cell.getObject2AsURI();
- if ( (OWLEntity)onto2.getClass( entity2URI ) != null ) { // A class
- writer.print(" <owl:equivalentClass rdf:resource=\""+entity2URI.toString()+"\"/>\n");
- } else if ( (OWLEntity)onto2.getDataProperty( entity2URI ) != null ) { // A Dataproperty
- writer.print(" <owl:equivalentProperty rdf:resource=\""+entity2URI.toString()+"\"/>\n");
- } else if ( (OWLEntity)onto2.getObjectProperty( entity2URI ) != null ) { // An ObjectProperty
- writer.print(" <owl:equivalentProperty rdf:resource=\""+entity2URI.toString()+"\"/>\n");
- } else if ( (OWLEntity)onto2.getIndividual( entity2URI ) != null ) { // An individual (but check this)
- writer.print(" <owl:sameAs rdf:resource=\""+entity2URI.toString()+"\"/>\n");
- }
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); };
+ Object ob2 = cell.getObject2();
+ URI u2 = onto2.getEntityURI( ob2 );
+ if ( onto1.isClass( ob2 ) ) {
+ writer.print(" <owl:equivalentClass rdf:resource=\""+u2+"\"/>\n");
+ } else if ( onto1.isDataProperty( ob2 ) ) {
+ writer.print(" <owl:equivalentProperty rdf:resource=\""+u2+"\"/>\n");
+ } else if ( onto1.isObjectProperty( ob2 ) ) {
+ writer.print(" <owl:equivalentProperty rdf:resource=\""+u2+"\"/>\n");
+ } else if ( onto1.isIndividual( ob2 ) ) {
+ writer.print(" <owl:sameAs rdf:resource=\""+u2+"\"/>\n");
+ }
}
-
public void visit( SubsumeRelation rel ) throws AlignmentException {
- OWLOntology onto2 = (OWLOntology)alignment.getOntology2();
- try {
- URI entity2URI = cell.getObject2AsURI();
- if ( (OWLEntity)onto2.getClass( entity2URI ) != null ) { // A class
- writer.print(" <rdfs:subClassOf rdf:resource=\""+entity2URI.toString()+"\"/>\n");
- } else if ( (OWLEntity)onto2.getDataProperty( entity2URI ) != null ) { // A Dataproperty
- writer.print(" <rdfs:subPropertyOf rdf:resource=\""+entity2URI.toString()+"\"/>\n");
- } else if ( (OWLEntity)onto2.getObjectProperty( entity2URI ) != null ) { // An ObjectProperty
- writer.print(" <rdfs:subPropertyOf rdf:resource=\""+entity2URI.toString()+"\"/>\n");
- }
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); };
+ Object ob2 = cell.getObject2();
+ URI u2 = onto2.getEntityURI( ob2 );
+ if ( onto1.isClass( ob2 ) ) {
+ writer.print(" <rdfs:subClassOf rdf:resource=\""+u2+"\"/>\n");
+ } else if ( onto1.isDataProperty( ob2 ) ) {
+ writer.print(" <rdfs:subPropertyOf rdf:resource=\""+u2+"\"/>\n");
+ } else if ( onto1.isObjectProperty( ob2 ) ) {
+ writer.print(" <rdfs:subPropertyOf rdf:resource=\""+u2+"\"/>\n");
+ }
}
+
public void visit( SubsumedRelation rel ) throws AlignmentException {
- OWLOntology onto1 = (OWLOntology)alignment.getOntology1();
- try {
- URI entity1URI = cell.getObject1AsURI();
- if ( (OWLEntity)onto1.getClass( entity1URI ) != null ) { // A class
- writer.print(" <rdfs:subClassOf rdf:resource=\""+entity1URI.toString()+"\"/>\n");
- } else if ( (OWLEntity)onto1.getDataProperty( entity1URI ) != null ) { // A Dataproperty
- writer.print(" <rdfs:subPropertyOf rdf:resource=\""+entity1URI.toString()+"\"/>\n");
- } else if ( (OWLEntity)onto1.getObjectProperty( entity1URI ) != null ) { // An ObjectProperty
- writer.print(" <rdfs:subPropertyOf rdf:resource=\""+entity1URI.toString()+"\"/>\n");
- }
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); };
+ Object ob1 = cell.getObject1();
+ URI u1 = onto1.getEntityURI( ob1 );
+ if ( onto1.isClass( ob1 ) ) {
+ writer.print(" <rdfs:subClassOf rdf:resource=\""+u1+"\"/>\n");
+ } else if ( onto1.isDataProperty( ob1 ) ) {
+ writer.print(" <rdfs:subPropertyOf rdf:resource=\""+u1+"\"/>\n");
+ } else if ( onto1.isObjectProperty( ob1 ) ) {
+ writer.print(" <rdfs:subPropertyOf rdf:resource=\""+u1+"\"/>\n");
+ }
}
+
+ // JE: I assume this is incorrect
public void visit( IncompatRelation rel ) throws AlignmentException {
- //OWLOntology onto2 = (OWLOntology)alignment.getOntology2();
- URI entity2URI = cell.getObject2AsURI();
- writer.print(" <owl:inverseOf rdf:resource=\""+entity2URI.toString()+"\"/>\n");
+ Object ob2 = cell.getObject2();
+ URI u2 = onto2.getEntityURI( ob2 );
+ writer.print(" <owl:inverseOf rdf:resource=\""+u2+"\"/>\n");
}
+
public void visit( Relation rel ) throws AlignmentException {
// JE: I do not understand why I need this,
// but this seems to be the case...
@@ -189,6 +182,5 @@ public class OWLAxiomsRendererVisitor implements AlignmentVisitor
} catch (InvocationTargetException e) {
e.printStackTrace();
}
- // } catch (Exception e) { throw new AlignmentException("Dispatching problem ", e); };
};
}
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
index 6743eb74..1f2bc160 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2006, 2007-2008
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -21,8 +21,9 @@
package fr.inrialpes.exmo.align.impl.renderer;
import java.util.Enumeration;
-import java.io.PrintWriter;
import java.util.Hashtable;
+import java.io.PrintWriter;
+import java.net.URI;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
@@ -32,7 +33,9 @@ import org.semanticweb.owl.align.Relation;
import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.ObjectCell;
import fr.inrialpes.exmo.align.impl.BasicParameters;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
import org.omwg.mediation.language.export.omwg.OmwgSyntaxFormat;
import org.omwg.mediation.parser.alignment.NamespaceDefs;
@@ -132,21 +135,25 @@ public class RDFRendererVisitor implements AlignmentVisitor
writer.print("\n <location>"+align.getFile2()+"</location>");
if ( align instanceof BasicAlignment && ((BasicAlignment)align).getOntologyObject2().getFormalism() != null ) {
writer.print("\n <formalism>\n <Formalism align:name=\""+((BasicAlignment)align).getOntologyObject2().getFormalism()+"\" align:uri=\""+((BasicAlignment)align).getOntologyObject2().getFormURI()+"\"/>\n </formalism>");
-
}
writer.print("\n </Ontology>\n </onto2>\n");
- for( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
- Cell c = (Cell)e.nextElement();
- c.accept( this );
- } //end for
+ for( Cell c : align ){ c.accept( this ); };
writer.print("</Alignment>\n");
writer.print("</rdf:RDF>\n");
}
public void visit( Cell cell ) throws AlignmentException {
this.cell = cell;
- if ( ( cell.getObject1AsURI() != null &&
- cell.getObject2AsURI() != null) ||
- alignment.getLevel().equals("2OMWG") ){
+ URI u1, u2;
+ if ( cell instanceof ObjectCell ) {
+ u1 = ((LoadedOntology)((BasicAlignment)alignment).getOntologyObject1()).getEntityURI( cell.getObject1() );
+ u2 = ((LoadedOntology)((BasicAlignment)alignment).getOntologyObject2()).getEntityURI( cell.getObject2() );
+ } else {
+ System.err.println( cell );
+ u1 = cell.getObject1AsURI();
+ u2 = cell.getObject2AsURI();
+ }
+ if ( ( u1 != null && u2 != null)
+ || alignment.getLevel().equals("2OMWG") ){
writer.print(" <map>\n");
writer.print(" <Cell");
if ( cell.getId() != null ){
@@ -158,22 +165,19 @@ public class RDFRendererVisitor implements AlignmentVisitor
if ( alignment.getLevel().equals("2OMWG") ) {
writer.print(" <entity1>");
writer.print( oMWGformatter.export( (Expression)cell.getObject1() ) );
- //writer.print( oMWGformatter.getExprNode( (Expression)cell.getObject1(), model ) );
writer.print("\n </entity1>\n <entity2>");
writer.print( oMWGformatter.export( (Expression)cell.getObject2() ) );
- //writer.print( oMWGformatter.getExprNode( (Expression)cell.getObject2(), model ) );
- writer.print("\n </entity2>\n <relation>");
- cell.getRelation().accept( this );
- writer.print("</relation>\n");
+ writer.print("\n </entity2>\n");
} else {
writer.print(" <entity1 rdf:resource='");
- writer.print( cell.getObject1AsURI().toString() );
+ writer.print( u1.toString() );
writer.print("'/>\n <entity2 rdf:resource='");
- writer.print( cell.getObject2AsURI().toString() );
- writer.print("'/>\n <relation>");
- cell.getRelation().accept( this );
- writer.print("</relation>\n");
+ writer.print( u2.toString() );
+ writer.print("'/>\n");
}
+ writer.print(" <relation>");
+ cell.getRelation().accept( this );
+ writer.print("</relation>\n");
writer.print(" <measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>");
writer.print( cell.getStrength() );
writer.print("</measure>\n");
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SEKTMappingRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SEKTMappingRendererVisitor.java
index c8ed350f..4badb16d 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SEKTMappingRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SEKTMappingRendererVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -27,18 +27,15 @@ import java.net.URI;
import java.lang.reflect.Method;
import java.lang.reflect.InvocationTargetException;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLEntity;
-import org.semanticweb.owl.model.OWLException;
-
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
-import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
+import fr.inrialpes.exmo.align.impl.ObjectAlignment;
import fr.inrialpes.exmo.align.impl.rel.*;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
/**
* Renders an alignment as a new ontology merging these.
@@ -47,11 +44,11 @@ import fr.inrialpes.exmo.align.impl.rel.*;
* @version $Id$
*/
-
-public class SEKTMappingRendererVisitor implements AlignmentVisitor
-{
+public class SEKTMappingRendererVisitor implements AlignmentVisitor {
PrintWriter writer = null;
Alignment alignment = null;
+ LoadedOntology onto1 = null;
+ LoadedOntology onto2 = null;
Cell cell = null;
// I hate using random generator for generating symbols (address would be better)
Random generator = null;
@@ -62,12 +59,14 @@ public class SEKTMappingRendererVisitor implements AlignmentVisitor
}
public void visit( Alignment align ) throws AlignmentException {
+ if ( !(align instanceof ObjectAlignment) )
+ throw new AlignmentException("SEKTMappingRenderer: cannot render simple alignment. Turn them into ObjectAlignment, by toObjectAlignement()");
alignment = align;
- if ( !(align instanceof OWLAPIAlignment) )
- throw new AlignmentException("SEKTMappingRenderer: cannot render simple alignment. Turn them into OWLAlignment, by toOWLAPIAlignement()");
+ onto1 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject1();
+ onto2 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject2();
writer.print("MappingDocument(<\""+"\">\n");
- writer.print(" source(<\""+align.getOntology1URI().toString()+"\">)\n");
- writer.print(" target(<\""+align.getOntology2URI().toString()+"\">)\n");
+ writer.print(" source(<\""+onto1.getURI()+"\">)\n");
+ writer.print(" target(<\""+onto2.getURI()+"\">)\n");
for( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
Cell c = (Cell)e.nextElement();
@@ -78,39 +77,34 @@ public class SEKTMappingRendererVisitor implements AlignmentVisitor
public void visit( Cell cell ) throws AlignmentException {
this.cell = cell;
String id = "s"+generator.nextInt(100000);
- OWLOntology onto1 = (OWLOntology)alignment.getOntology1();
- //OWLOntology onto2 = (OWLOntology)alignment.getOntology2();
- try {
- URI entity1URI = cell.getObject1AsURI();
- URI entity2URI = cell.getObject2AsURI();
- if ( (OWLEntity)onto1.getClass( entity1URI ) != null ) { // A class
- writer.print(" classMapping( <\"#"+id+"\">\n");
- cell.getRelation().accept( this );
- writer.print(" <\""+entity1URI.toString()+"\">\n");
- writer.print(" <\""+entity2URI.toString()+"\">\n");
-
- writer.print(" )\n");
- } else if ( (OWLEntity)onto1.getDataProperty( entity1URI ) != null ) { // A Dataproperty
- writer.print(" relationMapping( <\"#"+id+"\">\n");
- cell.getRelation().accept( this );
- writer.print(" <\""+entity1URI.toString()+"\">\n");
- writer.print(" <\""+entity2URI.toString()+"\">\n");
- writer.print(" )\n");
- } else if ( (OWLEntity)onto1.getObjectProperty( entity1URI ) != null ) { // An ObjectProperty
- writer.print(" attributeMapping( <\"#"+id+"\">\n");
- cell.getRelation().accept( this );
- writer.print(" <\""+entity1URI.toString()+"\">\n");
- writer.print(" <\""+entity2URI.toString()+"\">\n");
- writer.print(" )\n");
- } else if ( (OWLEntity)onto1.getIndividual( entity1URI ) != null ) { // An individual (but check this)
- writer.print(" instanceMapping( <\"#"+id+"\">\n");
- cell.getRelation().accept( this );
- writer.print(" <\""+entity1URI.toString()+"\">\n");
- writer.print(" <\""+entity2URI.toString()+"\">\n");
- writer.print(" )\n");
- }
- writer.print("\n");
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); };
+ Object ob1 = cell.getObject1();
+ Object ob2 = cell.getObject2();
+ if ( onto1.isClass( ob1 ) ) {
+ writer.print(" classMapping( <\"#"+id+"\">\n");
+ cell.getRelation().accept( this );
+ writer.print(" <\""+onto1.getEntityURI( ob1 )+"\">\n");
+ writer.print(" <\""+onto2.getEntityURI( ob2 )+"\">\n");
+ writer.print(" )\n");
+ } else if ( onto1.isDataProperty( ob1 ) ) {
+ writer.print(" relationMapping( <\"#"+id+"\">\n");
+ cell.getRelation().accept( this );
+ writer.print(" <\""+onto1.getEntityURI( ob1 )+"\">\n");
+ writer.print(" <\""+onto2.getEntityURI( ob2 )+"\">\n");
+ writer.print(" )\n");
+ } else if ( onto1.isObjectProperty( ob1 ) ) {
+ writer.print(" attributeMapping( <\"#"+id+"\">\n");
+ cell.getRelation().accept( this );
+ writer.print(" <\""+onto1.getEntityURI( ob1 )+"\">\n");
+ writer.print(" <\""+onto2.getEntityURI( ob2 )+"\">\n");
+ writer.print(" )\n");
+ } else if ( onto1.isIndividual( ob1 ) ) {
+ writer.print(" instanceMapping( <\"#"+id+"\">\n");
+ cell.getRelation().accept( this );
+ writer.print(" <\""+onto1.getEntityURI( ob1 )+"\">\n");
+ writer.print(" <\""+onto2.getEntityURI( ob2 )+"\">\n");
+ writer.print(" )\n");
+ }
+ writer.print("\n");
}
public void visit( EquivRelation rel ) throws AlignmentException {
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SKOSRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SKOSRendererVisitor.java
index 2a11c5b9..691ba69c 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SKOSRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SKOSRendererVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2006-2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2006-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -33,19 +33,21 @@ import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
import fr.inrialpes.exmo.align.impl.rel.*;
+import fr.inrialpes.exmo.align.impl.ObjectAlignment;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
/**
* Renders an alignment as a new ontology merging these.
*
* @author Jérôme Euzenat
- * @version $$
+ * @version $Id$
*/
-
-public class SKOSRendererVisitor implements AlignmentVisitor
-{
+public class SKOSRendererVisitor implements AlignmentVisitor {
PrintWriter writer = null;
Alignment alignment = null;
+ LoadedOntology onto1 = null;
+ LoadedOntology onto2 = null;
Cell cell = null;
public SKOSRendererVisitor( PrintWriter writer ){
@@ -54,6 +56,10 @@ public class SKOSRendererVisitor implements AlignmentVisitor
// This must be considered
public void visit( Alignment align ) throws AlignmentException {
+ if ( align instanceof ObjectAlignment ) {
+ onto1 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject1();
+ onto2 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject2();
+ }
alignment = align;
writer.print("<rdf:RDF\n");
writer.print(" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n");
@@ -66,20 +72,32 @@ public class SKOSRendererVisitor implements AlignmentVisitor
writer.print("</rdf:RDF>\n");
}
+ public URI getURI2() throws AlignmentException {
+ if ( onto2 != null ) {
+ return onto2.getEntityURI( cell.getObject2() );
+ } else {
+ return cell.getObject2AsURI();
+ }
+ }
+
public void visit( Cell cell ) throws AlignmentException {
this.cell = cell;
- writer.print(" <skos:Concept rdf:about=\""+cell.getObject1AsURI().toString()+"\">\n");
+ if ( onto1 != null ) {
+ writer.print(" <skos:Concept rdf:about=\""+onto1.getEntityURI( cell.getObject1() )+"\">\n");
+ } else {
+ writer.print(" <skos:Concept rdf:about=\""+cell.getObject1AsURI()+"\">\n");
+ }
cell.getRelation().accept( this );
writer.print(" </skos:Concept>\n\n");
}
public void visit( EquivRelation rel ) throws AlignmentException {
- writer.print(" <skos:related rdf:resource=\""+cell.getObject2AsURI().toString()+"\"/>\n");
+ writer.print(" <skos:related rdf:resource=\""+getURI2()+"\"/>\n");
}
public void visit( SubsumeRelation rel ) throws AlignmentException {
- writer.print(" <skos:narrower rdf:resource=\""+cell.getObject2AsURI().toString()+"\"/>\n");
+ writer.print(" <skos:narrower rdf:resource=\""+getURI2()+"\"/>\n");
}
public void visit( SubsumedRelation rel ) throws AlignmentException {
- writer.print(" <skos:broader rdf:resource=\""+cell.getObject2AsURI().toString()+"\"/>\n");
+ writer.print(" <skos:broader rdf:resource=\""+getURI2()+"\"/>\n");
}
public void visit( IncompatRelation rel ) throws AlignmentException {
throw new AlignmentException("Cannot translate in SKOS"+rel);
@@ -112,6 +130,5 @@ public class SKOSRendererVisitor implements AlignmentVisitor
} catch (InvocationTargetException e) {
e.printStackTrace();
}
- // } catch (Exception e) { throw new AlignmentException("Dispatching problem ", e); };
};
}
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SWRLRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SWRLRendererVisitor.java
index e7cf95d1..fe848b6b 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SWRLRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SWRLRendererVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2007-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -27,17 +27,15 @@ import java.net.URI;
import java.lang.reflect.Method;
import java.lang.reflect.InvocationTargetException;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLException;
-
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
-import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
+import fr.inrialpes.exmo.align.impl.ObjectAlignment;
import fr.inrialpes.exmo.align.impl.rel.*;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
/**
* Renders an alignment as a SWRL rule set interpreting
@@ -47,11 +45,11 @@ import fr.inrialpes.exmo.align.impl.rel.*;
* @version $Id$
*/
-
-public class SWRLRendererVisitor implements AlignmentVisitor
-{
+public class SWRLRendererVisitor implements AlignmentVisitor {
PrintWriter writer = null;
Alignment alignment = null;
+ LoadedOntology onto1 = null;
+ LoadedOntology onto2 = null;
Cell cell = null;
public SWRLRendererVisitor( PrintWriter writer ){
@@ -59,15 +57,17 @@ public class SWRLRendererVisitor implements AlignmentVisitor
}
public void visit( Alignment align ) throws AlignmentException {
- if ( !( align instanceof OWLAPIAlignment) )
- throw new AlignmentException("SWRLRenderer: cannot render simple alignment. Turn them into OWLAlignment, by toOWLAPIAlignement()");
+ if ( !( align instanceof ObjectAlignment) )
+ throw new AlignmentException("SWRLRenderer: cannot render simple alignment. Turn them into ObjectAlignment, by toObjectAlignement()");
alignment = align;
+ onto1 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject1();
+ onto2 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject2();
writer.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
writer.println("<swrlx:Ontology swrlx:name=\"generatedAl\"");
writer.println(" xmlns:swrlx=\"http://www.w3.org/2003/11/swrlx#\"");
writer.println(" xmlns:owlx=\"http://www.w3.org/2003/05/owl-xml\"");
writer.println(" xmlns:ruleml=\"http://www.w3.org/2003/11/ruleml#\">");
- writer.println(" <owlx:Imports rdf:resource=\""+align.getOntology1URI().toString()+"\"/>\n");
+ writer.println(" <owlx:Imports rdf:resource=\""+onto1.getURI()+"\"/>\n");
for( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
Cell c = (Cell)e.nextElement();
c.accept( this );
@@ -77,58 +77,53 @@ public class SWRLRendererVisitor implements AlignmentVisitor
public void visit( Cell cell ) throws AlignmentException {
this.cell = cell;
- URI entity1URI = cell.getObject1AsURI();
cell.getRelation().accept( this );
}
public void visit( EquivRelation rel ) throws AlignmentException {
- // JE: It sounds that the alignment and cell variables are taken as global...
- // But it seems that this is not the case...
// JE: We should send warnings when dataproperties are mapped to individual properties and vice versa...
- try {
- writer.println(" <ruleml:imp>");
- writer.println(" <ruleml:_body>");
- OWLOntology onto1 = (OWLOntology)alignment.getOntology1();
- URI uri1 = cell.getObject1AsURI();
- if ( onto1.getClass( uri1 ) != null ){
- writer.println(" <swrl:classAtom>");
- writer.println(" <owllx:Class owllx:name=\""+uri1.toString()+"\"/>");
- writer.println(" <ruleml:var>x</ruleml:var>");
- writer.println(" </swrl:classAtom>");
- } else if ( onto1.getDataProperty( uri1 ) != null ){
- writer.println(" <swrl:datavaluedPropertyAtom swrlx:property=\""+uri1.toString()+"\"/>");
- writer.println(" <ruleml:var>x</ruleml:var>");
- writer.println(" <ruleml:var>y</ruleml:var>");
- writer.println(" <swrl:datavaluedPropertyAtom>");
- } else {
- writer.println(" <swrl:individualPropertyAtom swrlx:property=\""+uri1.toString()+"\"/>");
- writer.println(" <ruleml:var>x</ruleml:var>");
- writer.println(" <ruleml:var>y</ruleml:var>");
- writer.println(" </swrl:individualPropertyAtom>");
- }
- writer.println(" </ruleml:_body>");
- writer.println(" <ruleml:_head>");
- OWLOntology onto2 = (OWLOntology)alignment.getOntology2();
- URI uri2 = cell.getObject2AsURI();
- if ( onto2.getClass( uri2 ) != null ){
- writer.println(" <swrlx:classAtom>");
- writer.println(" <owllx:Class owllx:name=\""+uri2.toString()+"\"/>");
- writer.println(" <ruleml:var>x</ruleml:var>");
- writer.println(" </swrl:classAtom>");
- } else if ( onto2.getDataProperty( uri2 ) != null ){
- writer.println(" <swrl:datavaluedPropertyAtom swrlx:property=\""+uri2.toString()+"\"/>");
- writer.println(" <ruleml:var>x</ruleml:var>");
- writer.println(" <ruleml:var>y</ruleml:var>");
- writer.println(" </swrl:datavaluedPropertyAtom>");
- } else {
- writer.println(" <swrl:individualPropertyAtom swrlx:property=\""+uri2.toString()+"\"/>");
- writer.println(" <ruleml:var>x</ruleml:var>");
- writer.println(" <ruleml:var>y</ruleml:var>");
- writer.println(" </swrl:individualPropertyAtom>");
- }
- writer.println(" </ruleml:_head>");
- writer.println(" </ruleml:imp>\n");
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); };
+ Object ob1 = cell.getObject1();
+ URI uri1 = onto1.getEntityURI( ob1 );
+ writer.println(" <ruleml:imp>");
+ writer.println(" <ruleml:_body>");
+ if ( onto1.isClass( ob1 ) ){
+ writer.println(" <swrl:classAtom>");
+ writer.println(" <owllx:Class owllx:name=\""+uri1+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" </swrl:classAtom>");
+ } else if ( onto1.isDataProperty( ob1 ) ){
+ writer.println(" <swrl:datavaluedPropertyAtom swrlx:property=\""+uri1+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" <ruleml:var>y</ruleml:var>");
+ writer.println(" <swrl:datavaluedPropertyAtom>");
+ } else {
+ writer.println(" <swrl:individualPropertyAtom swrlx:property=\""+uri1+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" <ruleml:var>y</ruleml:var>");
+ writer.println(" </swrl:individualPropertyAtom>");
+ }
+ writer.println(" </ruleml:_body>");
+ writer.println(" <ruleml:_head>");
+ Object ob2 = cell.getObject2();
+ URI uri2 = onto2.getEntityURI( ob2 );
+ if ( onto2.isClass( ob2 ) ){
+ writer.println(" <swrlx:classAtom>");
+ writer.println(" <owllx:Class owllx:name=\""+uri2+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" </swrl:classAtom>");
+ } else if ( onto2.isDataProperty( ob2 ) ){
+ writer.println(" <swrl:datavaluedPropertyAtom swrlx:property=\""+uri2+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" <ruleml:var>y</ruleml:var>");
+ writer.println(" </swrl:datavaluedPropertyAtom>");
+ } else {
+ writer.println(" <swrl:individualPropertyAtom swrlx:property=\""+uri2+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" <ruleml:var>y</ruleml:var>");
+ writer.println(" </swrl:individualPropertyAtom>");
+ }
+ writer.println(" </ruleml:_head>");
+ writer.println(" </ruleml:imp>\n");
}
public void visit( SubsumeRelation rel ){};
@@ -163,6 +158,5 @@ public class SWRLRendererVisitor implements AlignmentVisitor
} catch (InvocationTargetException e) {
e.printStackTrace();
}
- // } catch (Exception e) { throw new AlignmentException("Dispatching problem ", e); };
};
}
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
index effb03bc..56b500bc 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
@@ -34,6 +34,8 @@ import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
import fr.inrialpes.exmo.align.impl.rel.*;
+import fr.inrialpes.exmo.align.impl.ObjectAlignment;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
/**
* Renders an alignment as a XSLT stylesheet transforming
@@ -43,11 +45,12 @@ import fr.inrialpes.exmo.align.impl.rel.*;
* @version $Id$
*/
-public class XSLTRendererVisitor implements AlignmentVisitor
-{
+public class XSLTRendererVisitor implements AlignmentVisitor {
PrintWriter writer = null;
Alignment alignment = null;
Cell cell = null;
+ LoadedOntology onto1 = null;
+ LoadedOntology onto2 = null;
Hashtable<String,String> namespaces = null;
int nsrank = 0;
@@ -61,6 +64,10 @@ public class XSLTRendererVisitor implements AlignmentVisitor
}
public void visit( Alignment align ) throws AlignmentException {
+ if ( align instanceof ObjectAlignment ) {
+ onto1 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject1();
+ onto2 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject2();
+ }
for( Enumeration e = align.getElements(); e.hasMoreElements(); ){
collectURIs( (Cell)e.nextElement() );
}
@@ -99,8 +106,14 @@ public class XSLTRendererVisitor implements AlignmentVisitor
}
private void collectURIs ( Cell cell ) throws AlignmentException {
- URI entity1URI = cell.getObject1AsURI();
- URI entity2URI = cell.getObject2AsURI();
+ URI entity1URI, entity2URI;
+ if ( onto1 != null ){
+ entity1URI = onto1.getEntityURI( cell.getObject1() );
+ entity2URI = onto2.getEntityURI( cell.getObject2() );
+ } else {
+ entity1URI = cell.getObject1AsURI();
+ entity2URI = cell.getObject2AsURI();
+ }
if ( entity1URI != null ) {
String ns1 = entity1URI.getScheme()+":"+entity1URI.getSchemeSpecificPart()+"#";
if ( namespaces.get( ns1 ) == null ){
@@ -117,8 +130,13 @@ public class XSLTRendererVisitor implements AlignmentVisitor
public void visit( EquivRelation rel ) throws AlignmentException {
// The code is exactly the same for properties and classes
- writer.println(" <xsl:template match=\""+namespacify(cell.getObject1AsURI())+"\">");
- writer.println(" <xsl:element name=\""+namespacify(cell.getObject2AsURI())+"\">");
+ if ( onto1 != null ){
+ writer.println(" <xsl:template match=\""+namespacify(onto1.getEntityURI( cell.getObject1() ))+"\">");
+ writer.println(" <xsl:element name=\""+namespacify(onto2.getEntityURI( cell.getObject2() ))+"\">");
+ } else {
+ writer.println(" <xsl:template match=\""+namespacify(cell.getObject1AsURI())+"\">");
+ writer.println(" <xsl:element name=\""+namespacify(cell.getObject2AsURI())+"\">");
+ }
writer.println(" <xsl:apply-templates select=\"*|@*|text()\"/>");
writer.println(" </xsl:element>");
writer.println(" </xsl:template>\n");
diff --git a/src/fr/inrialpes/exmo/align/ling/JWNLAlignment.java b/src/fr/inrialpes/exmo/align/ling/JWNLAlignment.java
index 4703f83a..398b27cf 100644
--- a/src/fr/inrialpes/exmo/align/ling/JWNLAlignment.java
+++ b/src/fr/inrialpes/exmo/align/ling/JWNLAlignment.java
@@ -20,12 +20,6 @@
package fr.inrialpes.exmo.align.ling;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLException;
-
import fr.inrialpes.exmo.align.impl.DistanceAlignment;
import fr.inrialpes.exmo.align.impl.MatrixMeasure;
@@ -61,33 +55,22 @@ public class JWNLAlignment extends DistanceAlignment implements AlignmentProcess
public void init( String wndict ) throws AlignmentException {
Dist.Initialize( wndict, WNVERS );
}
- public double measure( OWLClass cl1, OWLClass cl2 ) throws OWLException{
- String s1 = cl1.getURI().getFragment();
- String s2 = cl2.getURI().getFragment();
+ public double measure( Object o1, Object o2 ) throws Exception {
+ String s1 = ontology1().getEntityName( o1 );
+ String s2 = ontology2().getEntityName( o2 );
if ( s1 == null || s2 == null ) return 1.;
return Dist.BasicSynonymDistance(s1.toLowerCase(),s2.toLowerCase());
}
- public double measure( OWLProperty pr1, OWLProperty pr2 ) throws OWLException{
- String s1 = pr1.getURI().getFragment();
- String s2 = pr2.getURI().getFragment();
- if ( s1 == null || s2 == null ) return 1.;
- return Dist.BasicSynonymDistance(s1.toLowerCase(),s2.toLowerCase());
+ public double classMeasure( Object cl1, Object cl2 ) throws Exception {
+ return measure( cl1, cl2 );
}
- public double measure( OWLIndividual id1, OWLIndividual id2 ) throws OWLException{
+ public double propertyMeasure( Object pr1, Object pr2 ) throws Exception {
+ return measure( pr1, pr2 );
+ }
+ public double individualMeasure( Object id1, Object id2 ) throws Exception {
if ( debug > 4 )
System.err.println( "ID:"+id1+" -- "+id2);
- URI URI1 = id1.getURI();
- String s1;
- if ( URI1 != null ) s1 = URI1.getFragment();
- else s1 = "";
- URI URI2 = id2.getURI();
- String s2;
- if ( URI2 != null ) s2 = URI2.getFragment();
- else s2 = "";
- if ( s1 == null || s2 == null ) return 1.;
- // String s1 = id1.getURI().getFragment();
- // String s2 = id2.getURI().getFragment();
- return Dist.BasicSynonymDistance(s1.toLowerCase(),s2.toLowerCase());
+ return measure( id1, id2 );
}
}
@@ -104,7 +87,7 @@ public class JWNLAlignment extends DistanceAlignment implements AlignmentProcess
String wnvers = (String)params.getParameter("wnvers");
if ( wnvers == null ) wnvers = WNVERS;
sim.init( (String)params.getParameter("wndict"), wnvers );
- sim.initialize( (OWLOntology)getOntology1(), (OWLOntology)getOntology2(), alignment );
+ sim.initialize( ontology1(), ontology2(), alignment );
getSimilarity().compute( params );
if ( params.getParameter("printMatrix") != null ) printDistanceMatrix(params);
extract( type, params );
diff --git a/src/fr/inrialpes/exmo/align/onto/HeavyLoadedOntology.java b/src/fr/inrialpes/exmo/align/onto/HeavyLoadedOntology.java
new file mode 100644
index 00000000..bd31761d
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/onto/HeavyLoadedOntology.java
@@ -0,0 +1,64 @@
+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA Rhône-Alpes, 2008
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 2.1 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+package fr.inrialpes.exmo.align.onto;
+
+import java.util.Set;
+
+import org.semanticweb.owl.align.AlignmentException;
+
+/**
+ * Encapsulate deep access to an ontology through some Ontology API
+ *
+ * Asserted methods corresponds to the information explicitely given or stored about the entity.
+ * Non-asserted corresponds to the information that can be deduced from it.
+ * So asserted methods are related to a syntactic view while the others are related to the semantics
+ */
+public interface HeavyLoadedOntology<O> extends LoadedOntology<O> {
+
+ /* Class methods */
+ public Set<Object> getSubClasses( Object c );
+ public Set<Object> getAssertedSubClasses( Object c );
+ public Set<Object> getSuperClasses( Object c );
+ public Set<Object> getAssertedSuperClasses( Object c );
+ public Set<Object> getProperties( Object c );
+ public Set<Object> getAssertedProperties( Object c );
+ public Set<Object> getDataProperties( Object c );
+ public Set<Object> getAssertedDataProperties( Object c );
+ public Set<Object> getObjectProperties( Object c );
+ public Set<Object> getAssertedObjectProperties( Object c );
+ public Set<Object> getInstances( Object c );
+ public Set<Object> getAssertedInstances( Object c );
+
+ /* Property methods */
+ public Set<Object> getSubProperties( Object p );
+ public Set<Object> getAssertedSubProperties( Object p );
+ public Set<Object> getSuperProperties( Object p );
+ public Set<Object> getAssertedSuperProperties( Object p );
+ public Set<Object> getRange( Object p );
+ public Set<Object> getAssertedRange( Object p );
+ public Set<Object> getDomain( Object p );
+ public Set<Object> getAssertedDomain( Object p );
+
+ /* Individual methods */
+ public Set<Object> getClasses( Object i );
+ public Set<Object> getAssertedClasses( Object i );
+
+}
diff --git a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
index d4093a9a..ade34980 100644
--- a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
+++ b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
@@ -18,10 +18,18 @@
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
+/*
+ * This should be turned into an HeavyLoadedOntology.
+ * Some primitives are already avalible below
+ *
+ *
+ */
+
package fr.inrialpes.exmo.align.onto.owlapi10;
import java.net.URI;
import java.util.Set;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.lang.UnsupportedOperationException;
@@ -38,6 +46,9 @@ import org.semanticweb.owl.model.OWLObjectProperty;
import org.semanticweb.owl.model.OWLDataProperty;
import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLEntity;
+import org.semanticweb.owl.model.OWLRestriction;
+import org.semanticweb.owl.model.OWLDescription;
+import org.semanticweb.owl.model.OWLNaryBooleanDescription;
import org.semanticweb.owl.model.OWLException;
/*
@@ -279,6 +290,31 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
}
}
+ /* HeavyLoadedOntology specifics */
+
+ public Set<Object> getProperties( OWLDescription desc ) {
+ Set<Object> list = new HashSet<Object>();
+ try {
+ if ( desc instanceof OWLRestriction ){
+ list.add( ((OWLRestriction)desc).getProperty() );
+ } else if ( desc instanceof OWLClass ) {
+ // JE: I suspect that this can be a cause for looping!!
+ for ( Object cl : ((OWLClass)desc).getEquivalentClasses((OWLOntology)onto) ){
+ // JE: strange casting
+ Set<Object> res = getProperties( (OWLDescription)cl );
+ if ( res != null ) list.add( res );
+ }
+ } else if ( desc instanceof OWLNaryBooleanDescription ) {
+ for ( Object d : ((OWLNaryBooleanDescription)desc).getOperands() ){
+ // JE: strange casting
+ Set<Object> res = getProperties( (OWLDescription)d );
+ if ( res != null ) list.add( res );
+ }
+ }
+ } catch (OWLException e) { e.printStackTrace(); }
+ return list;
+ }
+
public void unload() {
try {
((OWLOntology)onto).getOWLConnection().notifyOntologyDeleted( ((OWLOntology)onto) );
diff --git a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
index deeb5cfd..8004be83 100644
--- a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
+++ b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
@@ -67,7 +67,7 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
public LoadedOntology loadOntology( URI uri ) throws AlignmentException {
OWLConnection connection = null;
Map parameters = new HashMap();
- parameters.put(OWLManager.OWL_CONNECTION,
+ parameters.put(OWLManager.OWL_CONNECTION, // [W:unchecked]
"org.semanticweb.owl.impl.model.OWLConnectionImpl");
try {
connection = OWLManager.getOWLConnection(parameters);
diff --git a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
index b474d046..b8bf6e6f 100644
--- a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
@@ -272,9 +272,13 @@ public class AlignmentParser extends DefaultHandler {
throw new SAXException("Catched alignment exception", e );
}
} else if (pName.equals("Formalism")) {
- // JE: OMWG1 leave it alone for the moment
- //if ( atts.getValue("uri") != null )
- // curronto.setFormalismURI( new URI(atts.getValue("uri")) );
+ // JE: Check that this is OK with OMWG
+ if ( atts.getValue("uri") != null )
+ try {
+ curronto.setFormURI( new URI(atts.getValue("uri")) );
+ } catch (Exception e) {
+ throw new SAXException("Malformed URI"+atts.getValue("uri"), e );
+ };
if ( atts.getValue("name") != null )
curronto.setFormalism( atts.getValue("name") );
} else if (pName.equals("formalism")) {
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index c2dcc6f8..982a2564 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -549,20 +549,10 @@ public class AServProtocolManager {
*********************************************************************/
public LoadedOntology reachable( URI uri ){
- try { return loadOntology( uri ); }
- catch (Exception e) {
- e.printStackTrace();
- return null;
- }
- }
-
- public LoadedOntology loadOntology( URI uri ) {
- // Test if not loaded...
- OntologyFactory factory = OntologyFactory.newInstance();
- LoadedOntology onto = factory.loadOntology( uri );
- if ( loadedOntologies != null )
- loadedOntologies.recordOntology( uri, onto );
- return onto;
+ try {
+ OntologyFactory factory = OntologyFactory.newInstance();
+ return factory.loadOntology( uri, loadedOntologies );
+ } catch (Exception e) { return null; }
}
/*********************************************************************
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index ed58e2bc..888c9eb2 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -161,7 +161,7 @@ public class CacheImpl {
* in an alignment object
*
* Beware, the Alignment API has two attributes:
- * onto1 is the OWLOntology object
+ * onto1 is the Ontology object
* uri1 is the URI object from which loading the ontologies
* In the database we store:
* owlontology1 the URI string of the ontology
diff --git a/src/fr/inrialpes/exmo/align/service/CannotRenderAlignment.java b/src/fr/inrialpes/exmo/align/service/CannotRenderAlignment.java
index 21d7ca68..fdcc00ab 100644
--- a/src/fr/inrialpes/exmo/align/service/CannotRenderAlignment.java
+++ b/src/fr/inrialpes/exmo/align/service/CannotRenderAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2006-2007
+ * Copyright (C) INRIA Rhône-Alpes, 2006-2008
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -31,6 +31,6 @@ public class CannotRenderAlignment extends ErrorMsg {
super( surr, rep, from, to, cont, param );
}
public String HTMLString(){
- return "Cannot render alignment "+content+": turn it to a OWLAPIAlignment with OWLAPIAlignement.toOWLAPIAlignement( al )";
+ return "Cannot render alignment "+content+": turn it to an ObjectAlignment with ObjectAlignement.toOkbjectAlignement( al )";
}
}
diff --git a/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java b/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
index 3a5b7274..7850c188 100644
--- a/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
@@ -33,7 +33,7 @@ import org.semanticweb.owl.align.Parameters;
import org.semanticweb.owl.align.Evaluator;
import fr.inrialpes.exmo.align.impl.BasicParameters;
-import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
+import fr.inrialpes.exmo.align.impl.ObjectAlignment;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.impl.eval.ExtPREvaluator;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
@@ -240,8 +240,8 @@ public class ExtGroupEval {
Alignment align2 = aparser2.parse( alignName2 );
if ( debug > 1 ) System.err.println(" Alignment structure2 parsed");
// Create evaluator object
- eval = new ExtPREvaluator(OWLAPIAlignment.toOWLAPIAlignment( (URIAlignment)align1, loaded ),
- OWLAPIAlignment.toOWLAPIAlignment( (URIAlignment)align2, loaded ) );
+ eval = new ExtPREvaluator(ObjectAlignment.toObjectAlignment( (URIAlignment)align1, loaded ),
+ ObjectAlignment.toObjectAlignment( (URIAlignment)align2, loaded ) );
// Compare
params.setParameter( "debug", new Integer( nextdebug ) );
eval.eval( params, loaded ) ;
diff --git a/src/fr/inrialpes/exmo/align/util/ParserPrinter.java b/src/fr/inrialpes/exmo/align/util/ParserPrinter.java
index 09fe449c..24bc304a 100644
--- a/src/fr/inrialpes/exmo/align/util/ParserPrinter.java
+++ b/src/fr/inrialpes/exmo/align/util/ParserPrinter.java
@@ -32,7 +32,7 @@ import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
-import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
+import fr.inrialpes.exmo.align.impl.ObjectAlignment;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.onto.OntologyCache;
@@ -167,7 +167,6 @@ public class ParserPrinter {
// Create parser
AlignmentParser aparser = null;
if ( parserClass == null ) aparser = new AlignmentParser( debug );
- // JE: I would be surprised that it works for the moment
else {
try {
Object[] mparams = { (Object)debug };
@@ -223,9 +222,9 @@ public class ParserPrinter {
try {
result.render( renderer );
} catch ( AlignmentException aex ) {
- // if the renderer needs an OWLAPIALignment: give it
+ // if the renderer needs an ObjectALignment: give it
//aex.printStackTrace();
- result = OWLAPIAlignment.toOWLAPIAlignment( (URIAlignment)result, (OntologyCache)null );
+ result = ObjectAlignment.toObjectAlignment( (URIAlignment)result, (OntologyCache)null );
result.render( renderer );
}
writer.flush();
diff --git a/src/fr/inrialpes/exmo/align/util/Procalign.java b/src/fr/inrialpes/exmo/align/util/Procalign.java
index 0613657a..9df7b236 100644
--- a/src/fr/inrialpes/exmo/align/util/Procalign.java
+++ b/src/fr/inrialpes/exmo/align/util/Procalign.java
@@ -252,7 +252,7 @@ public class Procalign {
// Thresholding
if (threshold != 0) result.cut( cutMethod, threshold );
- if (debug > 0) System.err.println(" Alignment performed");
+ if (debug > 0) System.err.println(" Matching performed");
// Set output file
OutputStream stream;
diff --git a/src/org/semanticweb/owl/align/Alignment.java b/src/org/semanticweb/owl/align/Alignment.java
index eef89eb7..c4ed3fc1 100644
--- a/src/org/semanticweb/owl/align/Alignment.java
+++ b/src/org/semanticweb/owl/align/Alignment.java
@@ -21,7 +21,9 @@
package org.semanticweb.owl.align;
import java.lang.Cloneable;
+import java.lang.Iterable;
import java.util.Enumeration;
+import java.util.Iterator;
import java.util.Set;
import java.net.URI;
@@ -35,8 +37,7 @@ import org.xml.sax.ContentHandler;
*/
-public interface Alignment extends Cloneable
-{
+public interface Alignment extends Cloneable, Iterable<Cell> {
/** Initialize the alignement before using it **/
@@ -112,8 +113,14 @@ public interface Alignment extends Cloneable
* Reason: this applies only for 1:1 alignments
* Some implementations might act cleverly (retrieving the best value).
* Basic implementations may raise the exception
+ * //@deprecated There is more than one cell about one object
*/
+ //@Deprecated
public Cell getAlignCell1( Object ob ) throws AlignmentException;
+ /**
+ * //@deprecated There is more than one cell about one object
+ */
+ //@Deprecated
public Cell getAlignCell2( Object ob ) throws AlignmentException;
/**
* Each part of the cell can be queried independently.
@@ -150,6 +157,7 @@ public interface Alignment extends Cloneable
public void setExtension( String uri, String label, String value );
public Enumeration<Cell> getElements();
+ public Iterator<Cell> iterator();
public int nbCells();
public void cut( String method, double threshold ) throws AlignmentException;
--
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