diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index 6dc265371d0de918e64ab2dc7275ff9df6f41334..c84a8d31ff723a505e5d5a74c44a7976012cc14f 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -1,7 +1,8 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rh�ne-Alpes, 2003-2004
+ * Copyright (C) INRIA Rh�ne-Alpes, 2003-2005
+ * Copyright (C) CNR Pisa, 2005
*
* 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
@@ -18,19 +19,16 @@
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
-//Raph: are things to change for dealing with multiple cell
-// for one objects
-
package fr.inrialpes.exmo.align.impl;
import java.lang.ClassNotFoundException;
import java.util.Hashtable;
-//Raph:
import java.util.HashSet;
import java.util.Enumeration;
import java.util.Iterator;
import java.util.Collections;
import java.util.List;
+import java.util.Set;
import java.util.ArrayList;
import java.io.PrintStream;
import java.io.PrintWriter;
@@ -55,8 +53,11 @@ import org.semanticweb.owl.align.Relation;
* collections. Each ontology has a number of classes, properties and
* individuals, along with a number of axioms asserting information about those
* objects.
+ *
+ * NOTE(JE): hashtabale are indexed by URI.
+ * This is strange, but there might be a reason
*
- * @author J�r�me Euzenat, David Loup
+ * @author J�r�me Euzenat, David Loup, Rapha�l Troncy
* @version $Id$
*/
@@ -65,6 +66,9 @@ public class BasicAlignment implements Alignment {
visitor.visit(this);
}
+ /* Set to true for rejecting the use of deprecated (non deterministic) primitives */
+ private boolean STRICT_IMPLEMENTATION = false;
+
protected int debug = 0;
protected String level = "0";
@@ -102,8 +106,12 @@ public class BasicAlignment implements Alignment {
}
public int nbCells() {
- // Raph: this is now wrong: I need multi-enumeration
- return hash1.size();
+ //-return hash1.size();
+ int sum = 0;
+ for ( Enumeration e = hash1.elements(); e.hasMoreElements(); ) {
+ sum = sum + ((HashSet)e.nextElement()).size();
+ }
+ return sum;
}
/** Alignment methods * */
@@ -148,153 +156,260 @@ public class BasicAlignment implements Alignment {
public void setFile2(URI u) { uri2 = u; };
public Enumeration getElements() {
- //Raph: This should be a multi Enumeration:
- return hash1.elements();
+ //-return hash1.elements();
+ return new MEnumeration( hash1 );
+ }
+
+ public ArrayList getArrayElements() {
+ ArrayList array = new ArrayList();
+ for (Enumeration e = getElements(); e.hasMoreElements(); ) {
+ array.add( (BasicCell)e.nextElement() );
+ }
+ return array;
}
- /*
- * Please note that all the following methods must be changed because they
- * consider that only ONE Entity can be aligned with another !!
- * A number of modifications are considered in the //Raph:
- */
/** Cell methods **/
- public Cell addAlignCell(Object ob1, Object ob2, String relation,
- double measure) throws AlignmentException {
- if ( !( ob1 instanceof OWLEntity && ob2 instanceof OWLEntity ) )
- throw new AlignmentException("addAlignCell: arguments must be OWLEntities");
- Cell cell = (Cell) new BasicCell((OWLEntity)ob1, (OWLEntity)ob2,
- relation, measure);
- addCell( (OWLEntity)ob1, (OWLEntity)ob2, cell );
- return cell;
+ //-public Cell addAlignCell(Object ob1, Object ob2, String relation,
+ // double measure) throws AlignmentException {
+ // if ( !( ob1 instanceof OWLEntity && ob2 instanceof OWLEntity ) )
+ // throw new AlignmentException("addAlignCell: arguments must be OWLEntities");
+ // Cell cell = (Cell) new BasicCell((OWLEntity)ob1, (OWLEntity)ob2,
+ // relation, measure);
+ // addCell( (OWLEntity)ob1, (OWLEntity)ob2, cell );
+ // return cell;
+ //};
+ public Cell addAlignCell(Object ob1, Object ob2, String relation, double measure) throws AlignmentException {
+
+ if ( !( ob1 instanceof OWLEntity && ob2 instanceof OWLEntity ) )
+ throw new AlignmentException("addAlignCell: arguments must be OWLEntities");
+ try {
+ Cell cell = (Cell) new BasicCell((OWLEntity) ob1, (OWLEntity) ob2, relation, measure);
+ HashSet s1 = (HashSet)hash1.get((Object)(((OWLEntity)ob1).getURI()));
+ if (s1 == null) {
+ s1 = new HashSet();
+ hash1.put((Object)(((OWLEntity)ob1).getURI()),s1);
+ }
+ s1.add(cell);
+ HashSet s2 = (HashSet)hash2.get((Object)(((OWLEntity)ob2).getURI()));
+ if (s2 == null) {
+ s2 = new HashSet();
+ hash2.put((Object)(((OWLEntity)ob2).getURI()),s2);
+ }
+ s2.add(cell);
+ return cell;
+ } catch (OWLException e) {
+ throw new AlignmentException("getURI problem", e);
+ }
};
public Cell addAlignCell(Object ob1, Object ob2) throws AlignmentException {
return addAlignCell( ob1, ob2, "=", 1. );
}
- public void addCell( OWLEntity ob1, OWLEntity ob2, Cell cell ) throws AlignmentException {
- try {
- //Raph:
- //HashSet s1 = hash1.get((Object)(((OWLEntity)ob1).getURI()));
- //if ( s1 == null ){
- // s1 = new HashSet();
- // hash1.put((Object)(((OWLEntity)ob1).getURI()),s1);
- //}
- //s1.add(cell);
- hash1.put((Object)(((OWLEntity)ob1).getURI()), cell);
- //Raph:
- //HashSet s1 = hash1.get((Object)(((OWLEntity)ob1).getURI()));
- //if ( s2 == null ){
- // s2 = new HashSet();
- // hash2.put((Object)(((OWLEntity)ob2).getURI()),s2);
- //}
- //s2.add(cell);
- hash2.put((Object)(((OWLEntity)ob2).getURI()), cell);
- } catch (OWLException e) {
- throw new AlignmentException("getURI problem", e);
- }
+ //-
+ //public void addCell( OWLEntity ob1, OWLEntity ob2, Cell cell ) throws AlignmentException {
+ // try {
+ // hash1.put((Object)(((OWLEntity)ob1).getURI()), cell);
+ // hash2.put((Object)(((OWLEntity)ob2).getURI()), cell);
+ // } catch (OWLException e) {
+ // throw new AlignmentException("getURI problem", e);
+ // }
+ //}
+ protected void addCell( Cell c ) throws AlignmentException {
+ try {
+ HashSet s1 = (HashSet)hash1.get(((OWLEntity)c.getObject1()).getURI());
+ if( s1 != null ){
+ s1.add( c ); // I must check that there is no one here
+ } else {
+ s1 = new HashSet();
+ hash1.put(((OWLEntity)c.getObject1()).getURI(),s1);
+ s1.add( c );
+ }
+
+ HashSet s2 = (HashSet)hash2.get(((OWLEntity)c.getObject2()).getURI());
+ if( s2 != null ){
+ s2.add( c ); // I must check that there is no one here
+ } else {
+ s2 = new HashSet();
+ hash2.put(((OWLEntity)c.getObject2()).getURI(),s2);
+ s2.add( c );
+ }
+
+ } catch (OWLException ex) {
+ throw new AlignmentException("getURI problem", ex);
+ }
}
- // Raph:
- public Iterator getAlignCells1(Object ob) throws AlignmentException {
+ // Beware, the catch applies both for getURI and OWLException
+ public Set getAlignCells1(Object ob) throws AlignmentException {
if ( ob instanceof OWLEntity ){
- HashSet s = null;
- try { s = (HashSet)hash1.get(((OWLEntity)ob).getURI()); }
- catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
- if ( s == null ) { return null; }
- else { return s.iterator(); }
+ try{ return (HashSet)hash1.get(((OWLEntity)ob).getURI());
+ } catch (Exception e) { return null;}
} else {
- throw new AlignmentException("getAlignCell1: argument must be OWLEntity");
+ throw new AlignmentException("getAlignCells1: argument must be OWLEntity");
+ }
+ }
+ public Set getAlignCells2(Object ob) throws AlignmentException {
+ if ( ob instanceof OWLEntity ){
+ try{ return (HashSet)hash2.get(((OWLEntity)ob).getURI());
+ } catch (Exception e) { return null;}
+ } else {
+ throw new AlignmentException("getAlignCells1: argument must be OWLEntity");
}
}
+ // Deprecated: implement as the one retrieving the highest strength correspondence (
public Cell getAlignCell1(Object ob) throws AlignmentException {
- if ( ob instanceof OWLEntity ){
- try { return (Cell) hash1.get(((OWLEntity) ob).getURI()); }
- catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
+ if ( STRICT_IMPLEMENTATION == true ){
+ throw new AlignmentException("getAlignCell1: deprecated (use getAlignCells1 instead)");
} else {
- throw new AlignmentException("getAlignCell1: argument must be OWLEntity");
+ if ( ob instanceof OWLEntity ){
+ try {
+ Set s2 = (Set)hash1.get(((OWLEntity) ob).getURI());
+ Cell bestCell = null;
+ double bestStrength = 0.;
+ if ( s2 != null ) {
+ for( Iterator it2 = s2.iterator(); it2.hasNext(); ){
+ Cell c = (Cell)it2.next();
+ double val = c.getStrength();
+ if ( val > bestStrength ) {
+ bestStrength = val;
+ bestCell = c;
+ }
+ }
+ }
+ return bestCell;
+ } catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
+ } else {
+ throw new AlignmentException("getAlignCell1: argument must be OWLEntity");
+ }
}
}
public Cell getAlignCell2(Object ob) throws AlignmentException {
- if ( ob instanceof OWLEntity ){
- try { return (Cell) hash2.get(((OWLEntity) ob).getURI()); }
- catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
+ if ( STRICT_IMPLEMENTATION == true ){
+ throw new AlignmentException("getAlignCell2: deprecated (use getAlignCells2 instead)");
} else {
- throw new AlignmentException("getAlignCell2: argument must be OWLEntity");
+ if ( ob instanceof OWLEntity ){
+ try {
+ Set s1 = (Set)hash2.get(((OWLEntity) ob).getURI());
+ Cell bestCell = null;
+ double bestStrength = 0.;
+ if ( s1 != null ){
+ for( Iterator it1 = s1.iterator(); it1.hasNext(); ){
+ Cell c = (Cell)it1.next();
+ double val = c.getStrength();
+ if ( val > bestStrength ) {
+ bestStrength = val;
+ bestCell = c;
+ }
+ }
+ }
+ return bestCell;
+ } catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
+ } else {
+ throw new AlignmentException("getAlignCell2: argument must be OWLEntity");
+ }
}
}
+ //- Deprecated
public Object getAlignedObject1(Object ob) throws AlignmentException {
Cell c = getAlignCell1(ob);
if (c != null) return c.getObject2();
else return null;
};
+ //- Deprecated
public Object getAlignedObject2(Object ob) throws AlignmentException {
Cell c = getAlignCell2(ob);
if (c != null) return c.getObject1();
else return null;
};
+ //- Deprecated
public Relation getAlignedRelation1(Object ob) throws AlignmentException {
Cell c = getAlignCell1(ob);
if (c != null) return c.getRelation();
else return (Relation) null;
};
+ //- Deprecated
public Relation getAlignedRelation2(Object ob) throws AlignmentException {
Cell c = getAlignCell2(ob);
if (c != null) return c.getRelation();
else return (Relation) null;
};
+ //- Deprecated
public double getAlignedStrength1(Object ob) throws AlignmentException {
Cell c = getAlignCell1(ob);
if (c != null) return c.getStrength();
else return 0;
};
+ //- Deprecated
public double getAlignedStrength2(Object ob) throws AlignmentException {
Cell c = getAlignCell2(ob);
if (c != null) return c.getStrength();
else return 0;
};
- //Raph:
+ //-
+ //public void removeAlignCell(Cell c) throws AlignmentException {
+ //try {
+ // HashSet s1 = (HashSet)hash1.get(((OWLEntity)c.getObject1()).getURI());
+ // HashSet s2 = (HashSet)hash2.get(((OWLEntity)c.getObject2()).getURI());
+ // s1.remove(c);
+ // s2.remove(c);
+ //} catch (OWLException ex) {
+ // throw new AlignmentException("getURI problem", ex);
+ //}
+ //}
+
public void removeAlignCell(Cell c) throws AlignmentException {
- try {
- HashSet s1 = (HashSet)hash1.get(((OWLEntity)c.getObject1()).getURI());
- HashSet s2 = (HashSet)hash2.get(((OWLEntity)c.getObject2()).getURI());
- s1.remove(c);
- s2.remove(c);
- } catch (OWLException ex) {
- throw new AlignmentException("getURI problem", ex);
- }
+ try {
+ HashSet s1 = (HashSet)hash1.get(((OWLEntity)c.getObject1()).getURI());
+ HashSet s2 = (HashSet)hash2.get(((OWLEntity)c.getObject2()).getURI());
+ s1.remove(c);
+ s2.remove(c);
+ if (s1.isEmpty())
+ hash1.remove(((OWLEntity) c.getObject1()).getURI());
+ if (s2.isEmpty())
+ hash2.remove(((OWLEntity) c.getObject2()).getURI());
+ } catch (OWLException ex) {
+ throw new AlignmentException("getURI problem", ex);
+ }
}
/***************************************************************************
* The cut function suppresses from an alignment all the cell over a
* particulat threshold
**************************************************************************/
+ //-public void cut2(double threshold) throws AlignmentException {
+ // for (Enumeration e = hash1.keys(); e.hasMoreElements();) {
+ // Cell c = (Cell) hash1.get(e.nextElement());
+ // if (c.getStrength() < threshold) {
+ // // Beware, this suppresses all cells with these keys
+ // // There is only one of them
+ // try {
+ // //Raph:
+ // //removeAlignCell( c );
+ // hash1.remove(((OWLEntity) c.getObject1()).getURI());
+ // hash2.remove(((OWLEntity) c.getObject2()).getURI());
+ // } catch (OWLException ex) {
+ // throw new AlignmentException("getURI problem", ex);
+ // }
+ // }
+ // } //end for
+ // };
public void cut2(double threshold) throws AlignmentException {
- for (Enumeration e = hash1.keys(); e.hasMoreElements();) {
- Cell c = (Cell) hash1.get(e.nextElement());
- if (c.getStrength() < threshold) {
- // Beware, this suppresses all cells with these keys
- // There is only one of them
- try {
- //Raph:
- //removeAlignCell( c );
- hash1.remove(((OWLEntity) c.getObject1()).getURI());
- hash2.remove(((OWLEntity) c.getObject2()).getURI());
- } catch (OWLException ex) {
- throw new AlignmentException("getURI problem", ex);
- }
- }
- } //end for
- };
+ for (Enumeration e = getElements(); e.hasMoreElements(); ) {
+ Cell c = (Cell)e.nextElement();
+ if (c.getStrength() < threshold)
+ removeAlignCell( c );
+ }
+ }
/***************************************************************************
@@ -313,13 +428,63 @@ public class BasicAlignment implements Alignment {
* - getting the under n% of the best (prop)
* - getting the n best values
**************************************************************************/
- public void cut( String method, double threshold ) throws AlignmentException {
+ //-public void cut( String method, double threshold ) throws AlignmentException {
+ // // Check that threshold is a percent
+ // if ( threshold > 1. || threshold < 0. )
+ // throw new AlignmentException( "Not a percentage or threshold : "+threshold );
+ // // Create a sorted list of cells
+ // // Raph: this will not work anymore
+ // List buffer = new ArrayList( hash1.values() );
+ // Collections.sort( buffer );
+ // int size = buffer.size();
+ // boolean found = false;
+ // int i = 0;
+ // // Depending on the method, find the limit
+ // if ( method.equals("hard") ){
+ // for( i=0; i < size && !found ; i++ ) {
+ // if ( ((Cell)buffer.get(i)).getStrength() <= threshold ) found = true;
+ // }
+ // } else if ( method.equals("span") ){
+ // double max = ((Cell)buffer.get(0)).getStrength() -threshold;
+ // for( i=0; i < size && !found ; i++ ) {
+ // if ( ((Cell)buffer.get(i)).getStrength() <= max ) found = true;
+ // }
+ // } else if ( method.equals("prop") ){
+ // double max = ((Cell)buffer.get(0)).getStrength() * (1-threshold);
+ // for( i=0; i < size && !found ; i++ ) {
+ // if ( ((Cell)buffer.get(i)).getStrength() <= max ) found = true;
+ // }
+ // } else if ( method.equals("perc") ){
+ // i = (new Double(size*threshold)).intValue();
+ // } else if ( method.equals("best") ){
+ // i=(new Double(threshold)).intValue();
+ // } else throw new AlignmentException( "Not a cut specification : "+method );
+ // // Flush the structure
+ // for( size-- ; size > i ; size-- ) buffer.remove(size);
+ // // Introduce the result back in the structure
+ // size = i;
+ // hash1.clear();
+ // hash2.clear();
+ // try {
+ // for( i = 0; i < size; i++ ) {
+ // Cell c = (Cell)buffer.get(i);
+ // hash1.put((Object) (((OWLEntity)c.getObject1()).getURI()), c);
+ // hash2.put((Object) (((OWLEntity)c.getObject2()).getURI()), c);
+ // }
+ // } catch (OWLException e) {
+ // throw new AlignmentException("getURI problem", e);
+ // }
+ // };
+ public void cut( String method, double threshold ) throws AlignmentException
+ {
// Check that threshold is a percent
if ( threshold > 1. || threshold < 0. )
throw new AlignmentException( "Not a percentage or threshold : "+threshold );
// Create a sorted list of cells
+ // For sure with sorted lists, we could certainly do far better
// Raph: this will not work anymore
- List buffer = new ArrayList( hash1.values() );
+ //List buffer = new ArrayList( hash1.values() );
+ List buffer = getArrayElements();
Collections.sort( buffer );
int size = buffer.size();
boolean found = false;
@@ -350,37 +515,43 @@ public class BasicAlignment implements Alignment {
size = i;
hash1.clear();
hash2.clear();
- try {
- for( i = 0; i < size; i++ ) {
- Cell c = (Cell)buffer.get(i);
- hash1.put((Object) (((OWLEntity)c.getObject1()).getURI()), c);
- hash2.put((Object) (((OWLEntity)c.getObject2()).getURI()), c);
- }
- } catch (OWLException e) {
- throw new AlignmentException("getURI problem", e);
+ for( i = 0; i < size; i++ ) {
+ addCell( (Cell)buffer.get(i) );
+ // OLD Stuff pre-v2
+ //hash1.put((Object) (((OWLEntity)c.getObject1()).getURI()), c);
+ //hash2.put((Object) (((OWLEntity)c.getObject2()).getURI()), c);
}
};
/***************************************************************************
* The harden function acts like threshold but put all weights to 1.
**************************************************************************/
+ //-public void harden(double threshold) throws AlignmentException {
+ // for (Enumeration e = hash1.keys(); e.hasMoreElements();) {
+ // Cell c = (Cell) hash1.get(e.nextElement());
+ // if (c.getStrength() < threshold) {
+ // // Beware, this suppresses all cells with these keys
+ // // There is only one of them
+ // try {
+ // hash1.remove(((OWLEntity) c.getObject1()).getURI());
+ // hash2.remove(((OWLEntity) c.getObject2()).getURI());
+ // } catch (OWLException ex) {
+ // throw new AlignmentException("getURI problem", ex);
+ // }
+ // } else {
+ // c.setStrength(1.);
+ // }
+ // } //end for
+ // };
public void harden(double threshold) throws AlignmentException {
- for (Enumeration e = hash1.keys(); e.hasMoreElements();) {
- Cell c = (Cell) hash1.get(e.nextElement());
- if (c.getStrength() < threshold) {
- // Beware, this suppresses all cells with these keys
- // There is only one of them
- try {
- hash1.remove(((OWLEntity) c.getObject1()).getURI());
- hash2.remove(((OWLEntity) c.getObject2()).getURI());
- } catch (OWLException ex) {
- throw new AlignmentException("getURI problem", ex);
- }
- } else {
+ for (Enumeration e = getElements(); e.hasMoreElements();) {
+ Cell c = (Cell)e.nextElement();
+ if (c.getStrength() < threshold)
+ removeAlignCell( c );
+ else
c.setStrength(1.);
- }
- } //end for
- };
+ }
+ }
/**
* The second alignment is meet with the first one meaning that for
@@ -446,22 +617,28 @@ public class BasicAlignment implements Alignment {
};
/**
- * Incorporate the cell of the alignment into it own alignment. Note: for
+ * Incorporate the cells of the alignment into its own alignment. Note: for
* the moment, this does not copy but really incorporates. So, if hardening
* or cutting, are applied, then the ingested alignmment will be modified as
* well.
*/
+ //-
+ //protected void ingest(Alignment alignment) throws AlignmentException {
+ // for (Enumeration e = alignment.getElements(); e.hasMoreElements();) {
+ // Cell c = (Cell) e.nextElement();
+ // try {
+ // hash1.put((Object) ((OWLEntity) c.getObject1()).getURI(), c);
+ // hash2.put((Object) ((OWLEntity) c.getObject2()).getURI(), c);
+ // } catch (OWLException ex) {
+ // throw new AlignmentException("getURI problem", ex);
+ // }
+ // }
+ // };
protected void ingest(Alignment alignment) throws AlignmentException {
for (Enumeration e = alignment.getElements(); e.hasMoreElements();) {
- Cell c = (Cell) e.nextElement();
- try {
- hash1.put((Object) ((OWLEntity) c.getObject1()).getURI(), c);
- hash2.put((Object) ((OWLEntity) c.getObject2()).getURI(), c);
- } catch (OWLException ex) {
- throw new AlignmentException("getURI problem", ex);
- }
- }
- };
+ addCell((Cell)e.nextElement());
+ };
+ }
/**
* This should be rewritten in order to generate the axiom ontology instead
@@ -472,3 +649,30 @@ public class BasicAlignment implements Alignment {
accept(renderer);
}
}
+
+class MEnumeration implements Enumeration {
+ private Enumeration set = null; // The enumeration of sets
+ private Iterator current = null; // The current set's enumeration
+
+ MEnumeration( Hashtable s ){
+ set = s.elements();
+ while( set.hasMoreElements() && current == null ){
+ current = ((Set)set.nextElement()).iterator();
+ if( !current.hasNext() ) current = null;
+ }
+ }
+ public boolean hasMoreElements(){
+ return ( current != null);
+ }
+ public Object nextElement(){
+ Object val = current.next();
+ if( !current.hasNext() ){
+ current = null;
+ while( set.hasMoreElements() && current == null ){
+ current = ((Set)set.nextElement()).iterator();
+ if( !current.hasNext() ) current = null;
+ }
+ }
+ return val;
+ }
+}