- A few cosmetic fixes (server interface+code indentation and comments)

src/fr/inrialpes/exmo/align/impl/BasicAlignment.java

@@ -636,8 +636,8 @@ public class BasicAlignment implements Alignment, Extensible {
 		Cell cell = s.iterator().next(); // yes dangerous
 		Object o1 = cell.getObject1();
 		Object o2 = cell.getObject2();
-		Relation rel = cell.getRelation();
-		// Aggregate them depending on iterator
+		Relation rel = cell.getRelation(); // This assumes that the relation is the same.
+		// Aggregate them depending on modality
 		double val = 0.;
 		if ( modality.equals("min") ) {
 		    if ( size <= s.size() ) {
@@ -711,7 +711,7 @@ public class BasicAlignment implements Alignment, Extensible {
      * ( o, o", join(n,n'), r)
      * any pair which is in only one alignment is discarded.
      */
-    public Alignment join(Alignment align) throws AlignmentException {
+    public Alignment join( Alignment align ) throws AlignmentException {
 	// Could also test: onto1 == getOntologyObject1();
 	if ( onto1.getURI() != align.getOntology1URI() )
 	    throw new AlignmentException("Can only join alignments with same ontologies");
@@ -747,12 +747,10 @@ public class BasicAlignment implements Alignment, Extensible {
 	BasicAlignment result = createNewAlignment( onto1, ((BasicAlignment)align).getOntologyObject2() );
 	for ( Cell c1 : this ) {
 	    Set<Cell> cells2 = align.getAlignCells1(c1.getObject2());
-	    if (cells2 !=null) {
-		for (Cell c2 : cells2) {
+	    if ( cells2 != null ) {
+		for ( Cell c2 : cells2 ) {
 		    Cell newCell = c1.compose(c2);
-		    if (newCell != null) {
-			result.addCell(newCell);
-		    }
+		    if ( newCell != null ) result.addCell( newCell );
 		}
 	    }
 	}

src/fr/inrialpes/exmo/align/service/AServProtocolManager.java

@@ -895,21 +895,16 @@ public class AServProtocolManager implements Service {
 	}
 	result = "<h1>" + id+ " ("+pidON+")" +"</h1>";
 	result += "<table border=\"0\">\n";
-	result += "<h2>Ontologies</h2>\n";
     	Collection<URI> networkOntology = noo.getOntologies();
-	result += "<p><tr><th><b>Total ontologies: </b>" + networkOntology.size() + "</th></tr></p>";
-	result += "<table>\n";
+	result += "<h2>Ontologies ("+networkOntology.size()+")</h2>\n";
 	result += "<ul>";
 	for ( URI onto : networkOntology ) {
 	    result += "<li><a href=\"" + onto.toString() +"\">"+ onto.toString() + "</a></li>";
 	}
 	result += "</ul>";
-	result += "</table>\n";
 	
-    	result += "<h2>Alignments</h2>\n"; 
 	Set<Alignment> networkAlignments = noo.getAlignments();
-	result += "<p><tr><th><b>Total alignments: </b>" + networkAlignments.size() + "</th></tr></p>";
-	result += "<table>\n";
+    	result += "<h2>Alignments ("+networkAlignments.size()+")</h2>\n"; 
 	result += "<ul>";
 	for (Alignment al : networkAlignments) {	
 	    String idAl = al.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
@@ -918,8 +913,8 @@ public class AServProtocolManager implements Service {
 	    result += "<li><a href=\""+idAl+"\">"+pidAl+"</a></li>";
 	}
 	result += "</ul>";
-	result += "</table>\n";
-    	return new RenderedAlignment( params, newId(), serverId, result );
+	// was renderedAlignement!
+    	return new RenderedNetwork( params, newId(), serverId, result );
     }
     
     /*

src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java

@@ -73,6 +73,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
 
     private AServProtocolManager manager;
 
+    private Properties parameters = null;
+
     private String serverURL;
     private int localId = 0;
 
@@ -81,6 +83,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
     public static final String HEADER = "<style type=\"text/css\">body { font-family: sans-serif } button {background-color: #DDEEFF; margin-left: 1%; border: #CCC 1px solid;}</style>";
 
     public void init( Properties params, AServProtocolManager manager ) throws AServException {
+	parameters = params;
 	this.manager = manager;
 	serverURL = manager.serverURL()+"/html/";
     }
@@ -108,11 +111,18 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
     // ==================================================
 
     protected static String about() {
-	return "<h1>Alignment server</h1><center>"+AlignmentService.class.getPackage().getImplementationTitle()+" "+AlignmentService.class.getPackage().getImplementationVersion()+"<br />"
-	    + "<center><a href=\"html/\">Access</a></center>"
-	    + "(C) INRIA, 2006-2014<br />"
+	String result = "<h1>Alignment server</h1><center><div>"+AlignmentService.class.getPackage().getImplementationTitle()+" "+AlignmentService.class.getPackage().getImplementationVersion()+"</div>"
+	    //+ "<center><a href=\"html/\">Access</a></center>"
+	    + "<div style=\"align: center;\"><br />"
+	    + "<form style=\"height: 15px; width: 150px; position: relative;\" action=\"html/\"><button style=\"background-color: lightblue;\" title=\"Alignment menu\" type=\"submit\">Alignments</button></form>"
+	    + "<form style=\"height: 15px; width: 150px; margin-left: 5px; position: relative;\" action=\"noo/\"><button style=\"background-color: lightgreen;\" title=\"Network of ontologies menu\" type=\"submit\">Ontology networks</button></form>"
+	    + "<form style=\"height: 15px; width: 150px; margin-left: 5px; position: relative;\" action=\"../admin/\"><button style=\"background-color: lightpink;\" title=\"Server management functions\" type=\"submit\">Server management</button></form>"
+	    + "</div>"
+	    + "<div style=\"align: center;\"><br />(C) INRIA, 2006-2014<br />"
 	    + "<a href=\"http://alignapi.gforge.inria.fr\">http://alignapi.gforge.inria.fr</a><br />"
-	    + "</center>";
+	    + "</div></center>";
+	// reading parameters here will raise static problem
+	return result;
     }
 
     /**