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Commit 181d2673 authored by Jérôme Euzenat's avatar Jérôme Euzenat
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- introduced/corrected/etc. Raphael Troncy's ingest 

- corrected addCell (which accepted cells twice)
parent f6b433c0
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src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+ 83
− 232
View file @ 181d2673
/*
* $Id$
*
* Copyright (C) INRIA Rhne-Alpes, 2003-2005
* Copyright (C) INRIA Rhne-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());
......
src/org/semanticweb/owl/align/Alignment.java
+ 1
− 1
View file @ 181d2673
......@@ -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;
......
src/org/semanticweb/owl/align/Cell.java
+ 1
− 1
View file @ 181d2673
......@@ -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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