From 181d2673555a8005089dc8e8a8bb26e6e1695b1f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Fri, 17 Feb 2006 12:00:00 +0000
Subject: [PATCH] - introduced/corrected/etc. Raphael Troncy's ingest -
corrected addCell (which accepted cells twice)
---
.../exmo/align/impl/BasicAlignment.java | 315 +++++-------------
src/org/semanticweb/owl/align/Alignment.java | 2 +-
src/org/semanticweb/owl/align/Cell.java | 2 +-
3 files changed, 85 insertions(+), 234 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index 9104f0b4..0943d318 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2005
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2006
* Copyright (C) CNR Pisa, 2005
*
* This program is free software; you can redistribute it and/or modify
@@ -104,16 +104,12 @@ public class BasicAlignment implements Alignment {
setExtension( "method", getClass().getName() );
}
- // Note: protected is a problem outside of package
- // but everything else is public
- // JE[15/5/2005]: This does not seem to be a problem indeed
protected void init(OWLOntology onto1, OWLOntology onto2) {
this.onto1 = onto1;
this.onto2 = onto2;
}
public int nbCells() {
- //-return hash1.size();
int sum = 0;
for ( Enumeration e = hash1.elements(); e.hasMoreElements(); ) {
sum = sum + ((HashSet)e.nextElement()).size();
@@ -173,7 +169,6 @@ public class BasicAlignment implements Alignment {
};
public Enumeration getElements() {
- //-return hash1.elements();
return new MEnumeration( hash1 );
}
@@ -186,90 +181,59 @@ public class BasicAlignment implements Alignment {
}
/** 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");
- 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);
- }
+ Cell cell = (Cell) new BasicCell((OWLEntity) ob1, (OWLEntity) ob2, relation, measure);
+ addCell( cell );
+ return cell;
};
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 {
- // 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 );
+ boolean found = false;
+ HashSet s1 = (HashSet)hash1.get((OWLEntity)c.getObject1());
+ if ( s1 != null ) {
+ // I must check that there is no one here
+ for (Iterator i = s1.iterator(); !found && i.hasNext(); ) {
+ if ( c.equals((BasicCell)i.next()) ) found = true;
}
-
- 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 );
+ if (!found) s1.add( c );
+ } else {
+ s1 = new HashSet();
+ s1.add( c );
+ hash1.put((OWLEntity)c.getObject1(),s1);
+ }
+ found = false;
+ HashSet s2 = (HashSet)hash2.get((OWLEntity)c.getObject2());
+ if( s2 != null ){
+ // I must check that there is no one here
+ for (Iterator i=s2.iterator(); !found && i.hasNext(); ) {
+ if ( c.equals((BasicCell)i.next()) ) found = true;
}
-
- } catch (OWLException ex) {
- throw new AlignmentException("getURI problem", ex);
- }
+ if (!found) s2.add( c );
+ } else {
+ s2 = new HashSet();
+ s2.add( c );
+ hash2.put((OWLEntity)c.getObject2(),s2);
+ }
}
// Beware, the catch applies both for getURI and OWLException
public Set getAlignCells1(Object ob) throws AlignmentException {
if ( ob instanceof OWLEntity ){
- try{ return (HashSet)hash1.get(((OWLEntity)ob).getURI());
- } catch (Exception e) { return null;}
+ return (HashSet)hash1.get((OWLEntity)ob);
} else {
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;}
+ return (HashSet)hash2.get((OWLEntity)ob);
} else {
throw new AlignmentException("getAlignCells1: argument must be OWLEntity");
}
@@ -281,22 +245,20 @@ public class BasicAlignment implements Alignment {
throw new AlignmentException("getAlignCell1: deprecated (use getAlignCells1 instead)");
} else {
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;
- }
+ Set s2 = (Set)hash1.get((OWLEntity) ob);
+ 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); }
+ }
+ return bestCell;
} else {
throw new AlignmentException("getAlignCell1: argument must be OWLEntity");
}
@@ -308,22 +270,20 @@ public class BasicAlignment implements Alignment {
throw new AlignmentException("getAlignCell2: deprecated (use getAlignCells2 instead)");
} else {
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;
- }
+ Set s1 = (Set)hash2.get((OWLEntity) ob);
+ 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); }
+ }
+ return bestCell;
} else {
throw new AlignmentException("getAlignCell2: argument must be OWLEntity");
}
@@ -372,63 +332,31 @@ public class BasicAlignment implements Alignment {
else return 0;
};
- //-
- //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);
- //}
- //}
-
+ // JE: beware this does only remove the exact equal cell
+ // not those with same value
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);
- 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);
- }
+ HashSet s1 = (HashSet)hash1.get((OWLEntity)c.getObject1());
+ HashSet s2 = (HashSet)hash2.get((OWLEntity)c.getObject2());
+ s1.remove(c);
+ s2.remove(c);
+ if (s1.isEmpty())
+ hash1.remove((OWLEntity) c.getObject1());
+ if (s2.isEmpty())
+ hash2.remove((OWLEntity) c.getObject2());
}
/***************************************************************************
* 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 = getElements(); e.hasMoreElements(); ) {
Cell c = (Cell)e.nextElement();
- if (c.getStrength() < threshold)
+ if ( c.getStrength() < threshold )
removeAlignCell( c );
}
}
-
/***************************************************************************
* Default cut implementation
* For compatibility with API until version 1.1
@@ -445,53 +373,6 @@ 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 {
- // // 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
@@ -500,7 +381,7 @@ public class BasicAlignment implements Alignment {
// 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() );
+ // JE**: did we know if it still works???
List buffer = getArrayElements();
Collections.sort( buffer );
int size = buffer.size();
@@ -534,39 +415,17 @@ public class BasicAlignment implements Alignment {
hash2.clear();
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 = getElements(); e.hasMoreElements();) {
Cell c = (Cell)e.nextElement();
- if (c.getStrength() < threshold)
- removeAlignCell( c );
- else
- c.setStrength(1.);
+ if (c.getStrength() < threshold) removeAlignCell( c );
+ else c.setStrength(1.);
}
}
@@ -613,20 +472,24 @@ public class BasicAlignment implements Alignment {
* any pair (o, o', n, r) in O the resulting alignment will contain:
* ( o', o, n, inverse(r)) iff compose(r) exists.
*/
- public void inverse () {
- OWLOntology o = onto1;
- onto1 = onto2;
- onto2 = o;
+
+ public Alignment inverse () throws AlignmentException {
+ BasicAlignment result = new BasicAlignment();
+ result.init( onto2, onto1 );
+ result.setFile1( getFile2() );
+ result.setFile2( getFile1() );
// We must inverse getType
- URI u = uri1;
- uri1 = uri2;
- uri2 = u;
- Hashtable h = hash1;
- hash1 = hash2;
- hash2 = h;
+ result.setType( getType() );
+ result.setLevel( getLevel() );
+ // Must add an inverse to the method extension
+ for ( Enumeration e = extensions.getNames() ; e.hasMoreElements(); ){
+ String label = (String)e.nextElement();
+ result.setExtension( label, getExtension( label ) );
+ }
for ( Enumeration e = getElements() ; e.hasMoreElements(); ){
- ((Cell)e.nextElement()).inverse();
+ result.addCell(((Cell)e.nextElement()).inverse());
}
+ return (Alignment)result;
};
/** Housekeeping **/
@@ -639,18 +502,6 @@ public class BasicAlignment implements Alignment {
* 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();) {
addCell((Cell)e.nextElement());
diff --git a/src/org/semanticweb/owl/align/Alignment.java b/src/org/semanticweb/owl/align/Alignment.java
index 535b1029..4878663d 100644
--- a/src/org/semanticweb/owl/align/Alignment.java
+++ b/src/org/semanticweb/owl/align/Alignment.java
@@ -152,7 +152,7 @@ public interface Alignment
/**
* Algebra of alignment manipulation operations: compose, join, meet.
*/
- public void inverse() throws AlignmentException;
+ public Alignment inverse() throws AlignmentException;
public Alignment meet(Alignment align) throws AlignmentException;
public Alignment join(Alignment align) throws AlignmentException;
public Alignment compose(Alignment align) throws AlignmentException;
diff --git a/src/org/semanticweb/owl/align/Cell.java b/src/org/semanticweb/owl/align/Cell.java
index 45b7eae3..da8fc1cc 100644
--- a/src/org/semanticweb/owl/align/Cell.java
+++ b/src/org/semanticweb/owl/align/Cell.java
@@ -59,7 +59,7 @@ public interface Cell
public void setStrength( double m );
public boolean equals( Cell c );
- public void inverse();
+ public Cell inverse() throws AlignmentException;
/** Housekeeping **/
public void dump(ContentHandler h);
--
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