diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
index ee8ffa9cdc1a76aa34304dce3c573a6fc477dbfc..f3224f1ffb52fcaa4c5d2376dd75aaba887b8e43 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2004-2005, 2007-2009
+ * Copyright (C) INRIA, 2004-2005, 2007-2009
*
* 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
@@ -148,16 +148,15 @@ public class PRGraphEvaluator extends BasicEvaluator {
);
// Set the found cells in the sorted structure
- for (Enumeration e = align2.getElements(); e.hasMoreElements();) {
- cellSet.add( (Cell)e.nextElement() );
+ for ( Cell c : align2 ) {
+ cellSet.add( c );
}
// Collect the points that change recall
// (the other provide lower precision from the same recall and are not considered)
points.add( new Pair( 0., 1. ) ); // [R=0%]
- for( Iterator it = cellSet.iterator(); it.hasNext(); ){
+ for( Cell c2 : cellSet ){
nbfound++;
- Cell c2 = (Cell)it.next();
Set s1 = (Set)align1.getAlignCells1( c2.getObject1() );
if( s1 != null ){ // for all cells matching our first entity
for( Iterator it1 = s1.iterator(); it1.hasNext() && c2 != null; ){
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 9336063926a29a47fd7b5e60b70b03731f62c113..829d5914a9288773ed818ccf6a3fb7189794dc24 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -61,6 +61,7 @@ import java.net.JarURLConnection;
import java.util.Hashtable;
import java.util.Set;
import java.util.HashSet;
+import java.util.Collection;
import java.util.Enumeration;
import java.util.Iterator;
import java.util.StringTokenizer;
@@ -156,9 +157,14 @@ public class AServProtocolManager {
return evaluators;
}
+ /*
public Enumeration alignments(){
return alignmentCache.listAlignments();
}
+ */
+ public Collection<Alignment> alignments() {
+ return alignmentCache.alignments();
+ }
public String query( String query ){
//return alignmentCache.query( query );
@@ -215,7 +221,9 @@ public class AServProtocolManager {
Message result = null;
Parameters p = mess.getParameters();
// These are added to the parameters wich are in the message
- for (Enumeration<String> e = commandLineParams.getNames(); e.hasMoreElements();) {
+ //for ( String key : commandLineParams ) {
+ // Unfortunately non iterable
+ for ( Enumeration<String> e = commandLineParams.getNames(); e.hasMoreElements();) {
String key = e.nextElement();
if ( p.getParameter( key ) == null ){
p.setParameter( key , commandLineParams.getParameter( key ) );
@@ -271,10 +279,9 @@ public class AServProtocolManager {
// Try to retrieve first
Set alignments = alignmentCache.getAlignments( onto1.getURI(), onto2.getURI() );
*/
- Set alignments = alignmentCache.getAlignments( uri1, uri2 );
+ Set<Alignment> alignments = alignmentCache.getAlignments( uri1, uri2 );
if ( alignments != null && params.getParameter("force") == null ) {
- for ( Iterator it = alignments.iterator(); it.hasNext() ; ){
- Alignment al = ((Alignment)it.next());
+ for ( Alignment al: alignments ){
if ( al.getExtension( Annotations.ALIGNNS, Annotations.METHOD ).equals(method) ) {
return new AlignmentId(newId(),mess,myId,mess.getSender(),
al.getExtension( Annotations.ALIGNNS, Annotations.ID ),(Parameters)null,
@@ -815,6 +822,7 @@ public class AServProtocolManager {
// in the path or at the local place?
//classPath += File.pathSeparator+file.getParent()+File.separator + path.replaceAll("[ \t]+",File.pathSeparator+file.getParent()+File.separator);
// This replaces the replaceAll which is not tolerant on Windows in having "\" as a separator
+ // Is there a way to make it iterable???
for( StringTokenizer token = new StringTokenizer(path," \t"); token.hasMoreTokens(); )
classPath += File.pathSeparator+file.getParent()+File.separator+token.nextToken();
}
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index e0c7d1e7aeaabe404ed3bdc2be027ef8d7454264..d8da7434ab2e04d8d28ebc34ffa5178848cc0a39 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -282,7 +282,6 @@ public class CacheImpl {
protected Alignment retrieveAlignment( String id, Alignment alignment ) throws SQLException, AlignmentException, URISyntaxException {
String query;
URI ent1 = null, ent2 = null;
- Cell cell = null;
Statement st = createStatement();
@@ -296,15 +295,14 @@ public class CacheImpl {
ent1 = new URI(rs.getString("uri1"));
ent2 = new URI(rs.getString("uri2"));
if(ent1 == null || ent2 == null) break;
- cell = alignment.addAlignCell(ent1, ent2, rs.getString("relation"), Double.parseDouble(rs.getString("measure")));
+ Cell cell = alignment.addAlignCell(ent1, ent2, rs.getString("relation"), Double.parseDouble(rs.getString("measure")));
cell.setId(rs.getString("cell_id"));
cell.setSemantics(rs.getString("semantics"));
}
// JE: I must now retrieve all the extensions of the cells
- for( Enumeration e = alignment.getElements() ; e.hasMoreElements(); ){
- cell = (Cell)e.nextElement();
+ for ( Cell cell: alignment ){
String cid = cell.getId();
if ( cid != null && !cid.equals("") ){
query = "SELECT * FROM extension WHERE id = '" + cid + "'";
@@ -591,8 +589,7 @@ public class CacheImpl {
st.executeUpdate(query);
}
- for( Enumeration e = alignment.getElements() ; e.hasMoreElements(); ){
- Cell c = (Cell)e.nextElement();
+ for( Cell c : alignment ) {
String cellid = null;
if ( c.getObject1() != null && c.getObject2() != null ){
cellid = c.getId();
diff --git a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
index d158d8a1460b55fa15c6b4894ee3651406cfe2fd..157bf40267fa4d35d38811b4dfca903740c72f39 100644
--- a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
@@ -403,8 +403,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
String msg = "";
if ( perf.equals("listalignments") ){
msg = "<h1>Available alignments</h1><ul compact=\"1\">";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- Alignment al = (Alignment)e.nextElement();
+ for ( Alignment al : manager.alignments() ) {
String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID );
String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
@@ -496,11 +495,11 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Store an alignment</h1><form action=\"store\">";
msg += "Alignment id: <select name=\"id\">";
// JE: only those non stored please (retrieve metadata + stored)
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
+ for ( Alignment al : manager.alignments() ) {
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
params.setParameter("id", id);
if ( !manager.storedAlignment( new Message(newId(),(Message)null,myId,serverId,"", params ) ) ){
- String pid = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
msg += "<option value=\""+id+"\">"+pid+"</option>";
}
@@ -532,8 +531,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
String sel = (String)params.getParameter("id");
msg ="<h1>Trim alignments</h1><form action=\"cut\">";
msg += "Alignment id: <select name=\"id\">";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- Alignment al = (Alignment)e.nextElement();
+ for( Alignment al: manager.alignments() ){
String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
@@ -560,8 +558,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("prminv") ) {
msg ="<h1>Invert alignment</h1><form action=\"inv\">";
msg += "Alignment id: <select name=\"id\">";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- Alignment al = (Alignment)e.nextElement();
+ for( Alignment al: manager.alignments() ){
String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
@@ -596,8 +593,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "</select><br />Initial alignment id: <select name=\"id\"><option value=\"\" selected=\"1\"></option>";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- Alignment al = (Alignment)e.nextElement();
+ for( Alignment al: manager.alignments() ){
String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
@@ -630,8 +626,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
String sel = (String)params.getParameter("id");
msg = "<h1>Retrieve alignment</h1><form action=\"retrieve\">";
msg += "Alignment id: <select name=\"id\">";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- Alignment al = (Alignment)e.nextElement();
+ for( Alignment al: manager.alignments() ){
String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
@@ -660,8 +655,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("prmmetadata") ) {
msg = "<h1>Retrieve alignment metadata</h1><form action=\"metadata\">";
msg += "Alignment id: <select name=\"id\">";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- Alignment al = (Alignment)e.nextElement();
+ for( Alignment al: manager.alignments() ){
String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
@@ -706,8 +700,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("prmtranslate") ) {
msg = "<h1>Translate query</h1><form action=\"translate\">";
msg += "Alignment id: <select name=\"id\">";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- Alignment al = (Alignment)e.nextElement();
+ for( Alignment al: manager.alignments() ){
String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
@@ -729,8 +722,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("prmmetadata") ) {
msg = "<h1>Retrieve alignment metadata</h1><form action=\"metadata\">";
msg += "Alignment id: <select name=\"id\">";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- Alignment al = (Alignment)e.nextElement();
+ for( Alignment al: manager.alignments() ){
String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
@@ -752,8 +744,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg ="<h1>Evaluate alignment</h1><form action=\"eval\">";
msg += "Alignment to evaluate: ";
msg += "<select name=\"id\">";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- Alignment al = (Alignment)e.nextElement();
+ for( Alignment al: manager.alignments() ){
String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
@@ -762,8 +753,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "</select><br />";
msg +="Reference alignment: ";
msg += "<select name=\"ref\">";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- Alignment al = (Alignment)e.nextElement();
+ for( Alignment al: manager.alignments() ){
String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
diff --git a/src/fr/inrialpes/exmo/align/service/QueryMediator.java b/src/fr/inrialpes/exmo/align/service/QueryMediator.java
index 572dbc35bdccda2594f8c055ea9a13219d28f75c..c4fc23d7fe1ad1ba88e50fc6248103e73380e5ee 100644
--- a/src/fr/inrialpes/exmo/align/service/QueryMediator.java
+++ b/src/fr/inrialpes/exmo/align/service/QueryMediator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2006-2008
+ * Copyright (C) INRIA, 2006-2009
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -186,8 +186,7 @@ public class QueryMediator implements QueryProcessor {
}
} else mainQuery = aQuery;
// The second part replaces the named items by their counterparts
- for( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
- Cell cell = (Cell)e.nextElement();
+ for( Cell cell : align ){
mainQuery = mainQuery.replaceAll(
cell.getObject1AsURI(align).toString(),
cell.getObject2AsURI(align).toString() );
diff --git a/src/fr/inrialpes/exmo/align/service/WSAServProfile.java b/src/fr/inrialpes/exmo/align/service/WSAServProfile.java
index d1ac5210ed955f16a37754511356bc7f0f42b542..61a9081464ec8737117882fefe2af129d5f25380 100644
--- a/src/fr/inrialpes/exmo/align/service/WSAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/WSAServProfile.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2007-2008.
+ * Copyright (C) INRIA, 2007-2009
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -231,29 +231,28 @@ public class WSAServProfile implements AlignmentServiceProfile {
msg += wsdlAnswer();
} else if ( method.equals("listalignmentsRequest") || method.equals("listalignments") ) {
msg += " <listalignmentsResponse>\n <alignmentList>";
- for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension(Annotations.ALIGNNS, Annotations.ID);
+ for( Alignment al: manager.alignments() ){
+ String id = al.getExtension(Annotations.ALIGNNS, Annotations.ID);
msg += " <alid>"+id+"</alid>\n";
}
msg += " </alignmentList>\n </listalignmentsResponse>\n";
// -> List of URI
} else if ( method.equals("listmethodsRequest") || method.equals("listmethods") ) { // -> List of String
msg += " <listmethodsResponse>\n <classList>\n";
- for( Iterator it = manager.listmethods().iterator(); it.hasNext(); ) {
- String mt = (String) it.next();
+ for( String mt: manager.listmethods() ) {
msg += " <method>"+mt+"</method>\n";
}
msg += " </classList>\n </listmethodsResponse>\n";
} else if ( method.equals("listrenderersRequest") || method.equals("listrenderers") ) { // -> List of String
msg += " <listrenderersResponse>\n <classList>\n";
- for( Iterator it = manager.listrenderers().iterator(); it.hasNext(); ) {
- msg += " <renderer>"+it.next()+"</renderer>\n";
+ for( String m: manager.listrenderers() ) {
+ msg += " <renderer>"+m+"</renderer>\n";
}
msg += " </classList>\n </listrenderersResponse>\n";
} else if ( method.equals("listservicesRequest") || method.equals("listservices") ) { // -> List of String
msg += " <listservicesResponse>\n <classList>\n";
- for( Iterator it = manager.listservices().iterator(); it.hasNext(); ) {
- msg += " <service>"+it.next()+"</service>\n";
+ for( String m: manager.listservices() ) {
+ msg += " <service>"+m+"</service>\n";
}
msg += " </classList>\n </listservicesResponse>\n";
} else if ( method.equals("storeRequest") || method.equals("store") ) { // URI -> URI
diff --git a/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java b/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
index 271ea4c6fe007f63f14b5bf5c501f67c0f5cb08a..fe0dd1ea5c5373d019c9eb61f44f69fc1b68692d 100644
--- a/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2005, 2007-2008 INRIA
+ * Copyright (C) 2003-2005, 2007-2009 INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -192,8 +192,8 @@ public class ExtGroupEval {
print( iterateDirectories() );
}
- public Vector<Object> iterateDirectories (){
- Vector<Object> result = null;
+ public Vector<Vector> iterateDirectories (){
+ Vector<Vector> result = null;
File [] subdir = null;
try {
if (ontoDir == null) {
@@ -207,14 +207,14 @@ public class ExtGroupEval {
}
int size = subdir.length;
Arrays.sort(subdir);
- result = new Vector<Object>(size);
+ result = new Vector<Vector>(size);
int i = 0;
for ( int j=0 ; j < size; j++ ) {
if( subdir[j].isDirectory() ) {
if ( debug > 0 ) System.err.println("\nEntering directory "+subdir[j]);
// eval the alignments in a subdirectory
// store the result
- Object vect = (Object)iterateAlignments( subdir[j] );
+ Vector vect = (Vector)iterateAlignments( subdir[j] );
if ( vect != null ){
result.add(i, vect);
i++;
@@ -229,14 +229,15 @@ public class ExtGroupEval {
Vector<Object> result = new Vector<Object>();
boolean ok = false;
result.add(0,(Object)dir.getName().toString());
- int i = 1;
+ int i = 0;
// for all alignments there,
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
+ for ( String m : listAlgo ) {
+ i++;
// call eval
// store the result in a record
// return the record.
if ( debug > 1) System.err.println(" Considering result "+i);
- Evaluator evaluator = (Evaluator)eval( prefix+reference, prefix+e.nextElement()+".rdf");
+ Evaluator evaluator = (Evaluator)eval( prefix+reference, prefix+m+".rdf");
if ( evaluator != null ) ok = true;
result.add( i, evaluator );
}
@@ -280,7 +281,7 @@ public class ExtGroupEval {
/**
* This does not only print the results but compute the average as well
*/
- public void print( Vector result ) {
+ public void print( Vector<Vector> result ) {
// variables for computing iterative harmonic means
int expected = 0; // expected so far
int foundVect[]; // found so far
@@ -301,18 +302,18 @@ public class ExtGroupEval {
writer.println("<table border='2' frame='sides' rules='groups'>");
writer.println("<colgroup align='center' />");
// for each algo <td spancol='2'>name</td>
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ;e.nextElement()) {
+ for ( String m : listAlgo ) {
writer.println("<colgroup align='center' span='"+fsize+"' />");
}
// For each file do a
writer.println("<thead valign='top'><tr><th>algo</th>");
// for each algo <td spancol='2'>name</td>
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ;) {
- writer.println("<th colspan='"+(fsize+1)+"'>"+e.nextElement()+"</th>");
+ for ( String m : listAlgo ) {
+ writer.println("<th colspan='"+(fsize+1)+"'>"+m+"</th>");
}
writer.println("</tr></thead><tbody><tr><td>test</td>");
// for each algo <td>Prec.</td><td>Rec.</td>
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ;e.nextElement()) {
+ for ( String m : listAlgo ) {
for ( int i = 0; i < fsize; i++){
if ( format.charAt(i) == 's' ) {
writer.println("<td colspan='2'>Symmetric</td>");
@@ -334,9 +335,8 @@ public class ExtGroupEval {
// </tr>
// For each directory <tr>
boolean colored = false;
- for ( Enumeration e = result.elements() ; e.hasMoreElements() ;) {
+ for ( Vector test : result ) {
int nexpected = -1;
- Vector test = (Vector)e.nextElement();
if ( colored == true && color != null ){
colored = false;
writer.println("<tr bgcolor=\""+color+"\">");
@@ -392,8 +392,7 @@ public class ExtGroupEval {
}
writer.print("<tr bgcolor=\"yellow\"><td>H-mean</td>");
int k = 0;
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ; k++) {
- e.nextElement();
+ for ( String m : listAlgo ) {
if ( foundVect[k] != -1 ){
double precision = (double)correctVect[k]/foundVect[k];
double recall = (double)correctVect[k]/expected;
@@ -407,6 +406,7 @@ public class ExtGroupEval {
writer.println("<td colspan='2'><center>Error</center></td>");
}
//};
+ k++;
}
writer.println("</tr>");
writer.println("</tbody></table>");
diff --git a/src/fr/inrialpes/exmo/align/util/GenPlot.java b/src/fr/inrialpes/exmo/align/util/GenPlot.java
index 952320faf2759d3f168e63178dd58856f118ee8c..0e9cde8dd022adce44c59050ebb8293f65440100 100644
--- a/src/fr/inrialpes/exmo/align/util/GenPlot.java
+++ b/src/fr/inrialpes/exmo/align/util/GenPlot.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2008, INRIA
+ * Copyright (C) 2003-2009, INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -224,8 +224,7 @@ public class GenPlot {
if( debug > 0 ) System.err.println("Directory : "+dir);
// for all alignments there,
- for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
- String algo = (String)e.nextElement();
+ for ( String algo : listAlgo ) {
// call eval
if ( debug > 0 ) System.err.println(" Considering result "+algo+" ("+i+")");
PRGraphEvaluator evaluator = eval( prefix+"refalign.rdf", prefix+algo+".rdf");
@@ -235,6 +234,7 @@ public class GenPlot {
result[i][j] = result[i][j] + evaluator.getPrecision(j);
}
}
+ i++;
}
// Unload the ontologies.
OntologyFactory.clear();
@@ -303,23 +303,24 @@ public class GenPlot {
output.println("\\draw (-0.3,5) node[rotate=90] {$precision$}; ");
output.println("\\draw (-0.3,10) node {1.}; ");
output.println("% Plots");
- for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
- output.println("\\draw["+colortable[i%7]+"] plot[mark="+marktable[i%19]+",smooth] file {"+(String)e.nextElement()+".table};");
+ for ( String m : listAlgo ) {
+ output.println("\\draw["+colortable[i%7]+"] plot[mark="+marktable[i%19]+",smooth] file {"+m+".table};");
+ i++;
}
// And a legend
output.println("% Legend");
i = 0;
- for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
+ for ( String m : listAlgo ) {
output.println("\\draw["+colortable[i%7]+"] plot[mark="+marktable[i%19]+",smooth] coordinates {("+((i%3)*3+1)+","+(-(i/3)*.8-1)+") ("+((i%3)*3+3)+","+(-(i/3)*.8-1)+")};");
- output.println("\\draw["+colortable[i%7]+"] ("+((i%3)*3+2)+","+(-(i/3)*.8-.8)+") node {"+(String)e.nextElement()+"};");
+ output.println("\\draw["+colortable[i%7]+"] ("+((i%3)*3+2)+","+(-(i/3)*.8-.8)+") node {"+m+"};");
+ i++;
}
output.println("\\end{tikzpicture}");
output.println();
output.println("\\end{document}");
i = 0;
- for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
- String algo = (String)e.nextElement();
+ for ( String algo : listAlgo ) {
// Open one file
PrintWriter writer;
try {
@@ -346,13 +347,14 @@ public class GenPlot {
writer.close();
} catch (Exception ex) { ex.printStackTrace(); }
// UnsupportedEncodingException + FileNotFoundException
+ i++;
}
}
public void printTSV( double[][] result ) {
// Print first line
- for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; ) {
- output.print("\t"+(String)e.nextElement() );
+ for ( String m : listAlgo ) {
+ output.print("\t"+m );
}
output.println();
diff --git a/src/fr/inrialpes/exmo/align/util/GroupEval.java b/src/fr/inrialpes/exmo/align/util/GroupEval.java
index 0ef5540ed289b8f9546e24097ab5372526141be0..51cb486b283e81b5072c0067e38eda20fe0a6ae7 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupEval.java
@@ -226,14 +226,15 @@ public class GroupEval {
Vector<Object> result = new Vector<Object>();
boolean ok = false;
result.add(0,(Object)dir.getName().toString());
- int i = 1;
+ int i = 0;
// for all alignments there,
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
+ for ( String m: listAlgo ) {
+ i++;
// call eval
// store the result in a record
// return the record.
if ( debug > 2) System.err.println(" Considering result "+i);
- Evaluator evaluator = (Evaluator)eval( prefix+reference, prefix+(String)e.nextElement()+".rdf");
+ Evaluator evaluator = (Evaluator)eval( prefix+reference, prefix+m+".rdf");
if ( evaluator != null ) ok = true;
result.add( i, evaluator );
}
@@ -282,7 +283,7 @@ public class GroupEval {
else if ( type.equals("triangle") ) printTRIANGLE( result );
}
- public void printTRIANGLE( Vector result ) {
+ public void printTRIANGLE( Vector<Vector> result ) {
// variables for computing iterative harmonic means
int expected = 0; // expected so far
int foundVect[]; // found so far
@@ -296,10 +297,10 @@ public class GroupEval {
correctVect[k] = 0;
timeVect[k] = 0;
}
- for ( Enumeration e = result.elements() ; e.hasMoreElements() ;) {
+ for ( Vector test : result ) {
int nexpected = -1;
- Vector test = (Vector)e.nextElement();
Enumeration f = test.elements();
+ // Too bad the first element must be skipped
f.nextElement();
for( int k = 0 ; f.hasMoreElements() ; k++) {
PRecEvaluator eval = (PRecEvaluator)f.nextElement();
@@ -338,7 +339,7 @@ public class GroupEval {
//System.out.println("\\draw (10,-0.3) node {1.}; ");
System.out.println("% Plots");
int k = 0;
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ; k++) {
+ for ( String m: listAlgo ) {
double precision = (double)correctVect[k]/foundVect[k];
double recall = (double)correctVect[k]/expected;
double prec2 = precision*precision;
@@ -346,7 +347,8 @@ public class GroupEval {
double b = java.lang.Math.sqrt( prec2 - (a*a) );
a = a*10; b = b*10; //for printing scale 10.
System.out.println("\\draw plot[mark=+,] coordinates {("+a+","+b+")};");
- System.out.println("\\draw ("+(a+.01)+","+(b+.01)+") node[anchor=south west] {"+(String)e.nextElement()+"};");
+ System.out.println("\\draw ("+(a+.01)+","+(b+.01)+") node[anchor=south west] {"+m+"};");
+ k++;
}
System.out.println("\\end{tikzpicture}");
System.out.println();
@@ -402,7 +404,7 @@ and
which the program does...
*/
- public void printHTML( Vector result ) {
+ public void printHTML( Vector<Vector> result ) {
// variables for computing iterative harmonic means
int expected = 0; // expected so far
int foundVect[]; // found so far
@@ -426,18 +428,18 @@ which the program does...
writer.println("<table border='2' frame='sides' rules='groups'>");
writer.println("<colgroup align='center' />");
// for each algo <td spancol='2'>name</td>
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ;e.nextElement()) {
+ for ( String m : listAlgo ) {
writer.println("<colgroup align='center' span='"+fsize+"' />");
}
// For each file do a
writer.println("<thead valign='top'><tr><th>algo</th>");
// for each algo <td spancol='2'>name</td>
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ;) {
- writer.println("<th colspan='"+fsize+"'>"+e.nextElement()+"</th>");
+ for ( String m : listAlgo ) {
+ writer.println("<th colspan='"+fsize+"'>"+m+"</th>");
}
writer.println("</tr></thead><tbody><tr><td>test</td>");
// for each algo <td>Prec.</td><td>Rec.</td>
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ;e.nextElement()) {
+ for ( String m : listAlgo ) {
for ( int i = 0; i < fsize; i++){
writer.print("<td>");
if ( format.charAt(i) == 'p' ) {
@@ -469,9 +471,8 @@ which the program does...
// </tr>
// For each directory <tr>
boolean colored = false;
- for ( Enumeration e = result.elements() ; e.hasMoreElements() ;) {
+ for ( Vector test : result ) {
int nexpected = -1;
- Vector test = (Vector)e.nextElement();
if ( colored == true && color != null ){
colored = false;
writer.println("<tr bgcolor=\""+color+"\">");
@@ -530,8 +531,8 @@ which the program does...
// here we use the real values, i.e., add 0 to both correctVect and
// foundVect, so this is OK for computing the average.
int k = 0;
- for ( Enumeration<String> e = listAlgo.elements() ; e.hasMoreElements() ; k++) {
- e.nextElement();
+ // ???
+ for ( String m : listAlgo ) {
double precision = (double)correctVect[k]/foundVect[k];
double recall = (double)correctVect[k]/expected;
for ( int i = 0 ; i < fsize; i++){
@@ -555,6 +556,7 @@ which the program does...
}
writer.println("</td>");
};
+ k++;
}
writer.println("</tr>");
writer.println("</tbody></table>");
diff --git a/src/fr/inrialpes/exmo/align/util/GroupOutput.java b/src/fr/inrialpes/exmo/align/util/GroupOutput.java
index dd26188bf58a6f5f1a2d5bd76104d27f6da244ba..11f27109e49fb4de1ee0f931b28c05f0fe3421c5 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupOutput.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupOutput.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2008, INRIA
+ * Copyright (C) 2003-2009, INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -217,8 +217,7 @@ public class GroupOutput {
public void iterateAlgorithm(){
// for all alignments there,
- for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; ) {
- String algo = (String)e.nextElement();
+ for ( String algo : listAlgo ) {
if ( debug > 0 ) System.err.println("Algorithm: "+algo);
// type
if ( type.equals("tex") ) {