- changed the parameter reading function so that it preserves parameters

src/fr/inrialpes/exmo/align/util/GroupAlign.java

@@ -158,11 +158,7 @@ public class GroupAlign {
 	    case 'p' :
 		/* Read parameters from filename */
 		paramfile = g.getOptarg();
-		//try {
-		//    FileInputStream fis = new FileInputStream( paramfile );
-		//    System.setIn( fis );
-		//} catch (Exception e) { e.printStackTrace(); }
-		params = (Parameters)BasicParameters.read(paramfile);
+		BasicParameters.read( params, paramfile );
 		break;
 	    case 'r' :
 		/* Use the given class for rendering */
@@ -215,6 +211,7 @@ public class GroupAlign {
 	if (debug == 0 && params.getParameter("debug") != null) {
 	    debug = Integer.parseInt((String)params.getParameter("debug"));
 	}
+	// Exception to the parameter as string rule
 	if (debug > 0) params.setParameter("debug", new Integer(debug-1));
 
 	iterateDirectories();

src/fr/inrialpes/exmo/align/util/GroupEval.java

@@ -63,7 +63,7 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
 
 /** A basic class for synthesizing the results of a set of alignments provided by
     different algorithms. The output is a table showing various classical measures
-    for each test and for each algorithm. Average is also computed.
+    for each test and for each algorithm. Average is also computed as Harmonic means.
     
     <pre>
     java -cp procalign.jar fr.inrialpes.exmo.align.util.GroupEval [options]

src/fr/inrialpes/exmo/align/util/Procalign.java

@@ -169,7 +169,7 @@ public class Procalign {
 		//    FileInputStream fis = new FileInputStream( paramfile );
 		//    System.setIn( fis );
 		//} catch (Exception e) { e.printStackTrace(); }
-		params = (Parameters)BasicParameters.read(paramfile);
+		BasicParameters.read( params, paramfile);
 		break;
 	    case 'r' :
 		/* Use the given class for rendering */