- comment changes

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

@@ -84,7 +84,7 @@ public class BasicAlignment implements Alignment {
     /**
      * This is the URI of the place from which the ontology has been loaded!
      * This is NOT the Ontology URI which can be obtained by
-     * onto1.getLogicalURI();
+     * getOntology1URI()
      */
     protected URI uri1 = null;
 

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

@@ -76,7 +76,7 @@ public class OWLAPIAlignment extends BasicAlignment {
 	if ( onto1 instanceof OWLOntology && onto2 instanceof OWLOntology ){
 	    super.init( onto1, onto2, ontologies );
 	} else if ( onto1 instanceof URI && onto2 instanceof URI ) {
-	    // JE: This apprently contains the File and not the URI!
+	    // JE: This contains the File and not the URI!
 	    setFile1( (URI)onto1 );
 	    setFile2( (URI)onto2 );
 	    try {

src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java

@@ -90,8 +90,6 @@ public class StringDistAlignment extends DistanceAlignment implements AlignmentP
     /* Processing */
     public void align( Alignment alignment, Parameters params ) throws AlignmentException {
 	loadInit( alignment );
-	//ignore alignment;
-	//double threshold = 1.; // threshold above which distances are to high
 
 	// Get function from params
 	String f = (String)params.getParameter("stringFunction");