From f80dfce563b67b77dc25fcf32e3ee82debfa31ed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Thu, 15 May 2014 15:42:25 +0000
Subject: [PATCH] - improved implementation of the algebraic manipulation
---
html/relnotes.html | 1 +
.../exmo/align/impl/BasicOntologyNetwork.java | 91 ++++++++++++++-----
2 files changed, 68 insertions(+), 24 deletions(-)
diff --git a/html/relnotes.html b/html/relnotes.html
index 136669dd..b246055c 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -87,6 +87,7 @@ with a warning:
<li>Added httpcore library necessary for tutorial4 (tutorial/lib)</li>
<li>Added extensions to <tt>BasicOntologyNetwork</tt> (impl)</li>
<li>Added read/write to <tt>BasicOntologyNetwork</tt> (impl)</li>
+<li>Added algebraic manipulation of <tt>BasicOntologyNetwork</tt> (impl)</li>
<li>Added storage support for networks of ontologies (serv)</li>
<li>Genericised storage <tt>Cache</tt> and implemented <tt>VolatilCache</tt> which contains a full Cache implementation without storage (serv)</li>
</ul></p>
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java b/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
index fed9dc98..65d89d2b 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
@@ -20,7 +20,7 @@
package fr.inrialpes.exmo.align.impl;
-import java.lang.Cloneable;
+//import java.lang.Cloneable; // JE: what happens when I do a clone() ??
import java.lang.Iterable;
import java.util.Collections;
import java.util.Collection;
@@ -135,13 +135,44 @@ public class BasicOntologyNetwork implements OntologyNetwork {
return ontologies.keySet(); // ??
};
public Set<Alignment> getTargetingAlignments( URI onto ){
- if (!ontologies.containsKey(onto)) return Collections.emptySet();
- return ontologies.get( onto ).targettingAlignments;
- };
+ OntologyTriple ot = ontologies.get( onto );
+ if ( ot == null ) return Collections.emptySet();
+ return ot.targettingAlignments;
+ }
public Set<Alignment> getSourceAlignments( URI onto ){
- if (!ontologies.containsKey(onto)) return Collections.emptySet();
- return ontologies.get( onto ).sourceAlignments;
- };
+ OntologyTriple ot = ontologies.get( onto );
+ if ( ot == null ) return Collections.emptySet();
+ return ot.sourceAlignments;
+ }
+ /*
+ The one below is more efficient (as soon as the structure is maintained)
+ Thus structure is not necessary... it should have been put rather in ontoTriple!
+ public Set<Alignment> getAlignments( URI onto1, URI onto2 ){
+ OntologyTriple ot1 = ontologies.get( onto1 );
+ OntologyTriple ot2 = ontologies.get( onto2 );
+ if ( ot1 == null || ot2 == null ) return Collections.emptySet();
+ return intersectAlignments( ot1.sourceAlignments, ot2.targettingAlignments );
+ }
+ */
+ public Set<Alignment> getAlignments(URI srcOnto, URI dstOnto) {
+ Map<URI,Set<Alignment>> m = onto2Align.get(srcOnto);
+ if (m!=null) {
+ Set<Alignment> aligns = m.get(dstOnto);
+ if (aligns!=null) return Collections.unmodifiableSet(aligns);
+ }
+ return Collections.emptySet();
+ }
+
+
+ /**
+ * Clone?
+ */
+ //public BasicOntologyNetwork clone() {}
+
+ /**
+ * Normalizes an ontology network for it to have exactly one alignment between each pair of ontologies.
+ * Creates a new network
+ */
public void invert() throws AlignmentException {
HashSet<Alignment> newal = new HashSet<Alignment>();
for ( Alignment al : alignments ) newal.add( al.inverse() );
@@ -155,7 +186,7 @@ public class BasicOntologyNetwork implements OntologyNetwork {
public void normalize() throws AlignmentException {
for ( OntologyTriple ot1 : ontologies.values() ) {
for ( OntologyTriple ot2 : ontologies.values() ) {
- Set<Alignment> als = intersect( ot1.sourceAlignments, ot2.targettingAlignments );
+ Set<Alignment> als = intersectAlignments( ot1.sourceAlignments, ot2.targettingAlignments );
// Suppress them
if ( als.size() != 1 ) {
Alignment norm = normalizeAlignmentSet( als, ot1.onto, ot2.onto );
@@ -169,7 +200,7 @@ public class BasicOntologyNetwork implements OntologyNetwork {
}
}
- protected Alignment normalizeAlignmentSet( Set<Alignment> als, URI onto1, URI onto2 ) {
+ protected static Alignment normalizeAlignmentSet( Set<Alignment> als, URI onto1, URI onto2 ) throws AlignmentException {
Alignment result = null;
if ( als.size() == 0 ) { // If no element, create new
result = new BasicAlignment();
@@ -189,7 +220,7 @@ public class BasicOntologyNetwork implements OntologyNetwork {
return result;
}
- protected Set<Alignment> intersect( Set<Alignment> s1, Set<Alignment> s2 ) {
+ protected static Set<Alignment> intersectAlignments( Set<Alignment> s1, Set<Alignment> s2 ) {
Set<Alignment> result = new HashSet<Alignment>();
for ( Alignment x : s1 ) {
if ( s2.contains( x ) ) result.add( x );
@@ -201,13 +232,16 @@ public class BasicOntologyNetwork implements OntologyNetwork {
* Match ontologies in a network, using existing ontologies as input...
* Modifies the network
* TODO
+ * Alternative definition!
+ * public void match( Class<? extends AlignmentProcess> method, boolean reflexive ) throws AlignmentException {
+ }
*/
public void match( String method, boolean reflexive, boolean symmetric) throws AlignmentException {
for ( OntologyTriple ot1 : ontologies.values() ) {
for ( OntologyTriple ot2 : ontologies.values() ) {
if ( ( ot1 == ot2 && reflexive )
|| symmetric ) {
- Set<Alignment> als = intersect( ot1.sourceAlignments, ot2.targettingAlignments );
+ Set<Alignment> als = intersectAlignments( ot1.sourceAlignments, ot2.targettingAlignments );
Alignment init = normalizeAlignmentSet( als, ot1.onto, ot2.onto );
for ( Alignment al : als ) {
remAlignment( al );
@@ -224,10 +258,20 @@ public class BasicOntologyNetwork implements OntologyNetwork {
}
}
+ /**
+ * Applies a threshold to all alignments in a network
+ * Modifies the network
+ */
+ public void trim( String method, double threshold ) throws AlignmentException {
+ for ( Alignment al : alignments ) {
+ al.cut( method, threshold );
+ }
+ }
+
/**
* Intersection of two ontology networks...
* Creates a new network
- * TODO
+ * TODO: add extensions? i.e., partial clone as BasicAlignment
*/
public static BasicOntologyNetwork meet( OntologyNetwork on1, OntologyNetwork on2 ) throws AlignmentException {
BasicOntologyNetwork result = new BasicOntologyNetwork();
@@ -242,8 +286,13 @@ public class BasicOntologyNetwork implements OntologyNetwork {
for ( URI onto1 : result.getOntologies() ) {
for ( URI onto2 : result.getOntologies() ) {
// Get the alignments from both networks
+ Set<Alignment> als1 = on1.getAlignments( onto1, onto2 );
+ Set<Alignment> als2 = on2.getAlignments( onto1, onto2 );
// Normalise them (yes because it is join)
+ Alignment init1 = normalizeAlignmentSet( als1, onto1, onto2 );
+ Alignment init2 = normalizeAlignmentSet( als2, onto1, onto2 );
// Meet them
+ result.addAlignment( init1.meet( init2 ) );
}
}
return result;
@@ -252,25 +301,19 @@ public class BasicOntologyNetwork implements OntologyNetwork {
/**
* Union of two ontology networks...
* Creates a new network
- * TODO
+ * TODO: same as before
*/
public static BasicOntologyNetwork join( OntologyNetwork on1, OntologyNetwork on2 ) throws AlignmentException {
return (BasicOntologyNetwork)null;
}
/**
- * Add alignments only if there is no existing alignments
- public void match( Class<? extends AlignmentProcess> method, boolean reflexive ) throws AlignmentException {
- }
+ * Difference between two ontology networks...
+ * Creates a new network
+ * TODO: same as before
*/
-
- public Set<Alignment> getAlignments(URI srcOnto, URI dstOnto) {
- Map<URI,Set<Alignment>> m = onto2Align.get(srcOnto);
- if (m!=null) {
- Set<Alignment> aligns = m.get(dstOnto);
- if (aligns!=null) return Collections.unmodifiableSet(aligns);
- }
- return Collections.emptySet();
+ public static BasicOntologyNetwork diff( OntologyNetwork on1, OntologyNetwork on2 ) throws AlignmentException {
+ return (BasicOntologyNetwork)null;
}
public Collection<String[]> getExtensions(){ return extensions.getValues(); }
--
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