- added a parameter argument to the read method

- corrected a bug that made -p and -D option optional
- corrected a bug that made erasing the debug option with parameter file

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

@@ -94,9 +94,10 @@ public class BasicParameters implements Parameters {
     }
 
     public static Parameters read(String filename){
-	Parameters p = new BasicParameters();
-	//	String filename = "params.xml";
+	return read(new BasicParameters(), filename);
+    }
 
+    public static Parameters read(Parameters p, String filename){
 	try {
 	    // open the stream
 	    DocumentBuilderFactory docBuilderFactory =

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

@@ -137,7 +137,7 @@ public class GroupAlign {
 	// Is there a way for that in LongOpt ???
 	longopts[11] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
 
-	Getopt g = new Getopt("", args, "ho:a:d::n:u:r:i:s:t:p::D::", longopts);
+	Getopt g = new Getopt("", args, "ho:a:d::n:u:r:i:s:t:p:D:", longopts);
 	int c;
 	String arg;
 
@@ -212,6 +212,9 @@ public class GroupAlign {
 
 	int i = g.getOptind();
 
+	if (debug == 0 && params.getParameter("debug") != null) {
+	    debug = Integer.parseInt((String)params.getParameter("debug"));
+	}
 	if (debug > 0) params.setParameter("debug", new Integer(debug-1));
 
 	iterateDirectories();

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

@@ -148,7 +148,7 @@ public class Procalign {
 	// Is there a way for that in LongOpt ???
 	longopts[9] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
 
-	Getopt g = new Getopt("", args, "ho:a:p:d::r:t:T:i:D::", longopts);
+	Getopt g = new Getopt("", args, "ho:a:p:d::r:t:T:i:D:", longopts);
 	int c;
 	String arg;
 
@@ -215,6 +215,12 @@ public class Procalign {
 	
 	int i = g.getOptind();
 
+	if (debug > 0) {
+	    params.setParameter("debug", new Integer(debug));
+	} else if ( params.getParameter("debug") != null ) {
+	    debug = Integer.parseInt((String)params.getParameter("debug"));
+	}
+
 	loadedOntologies = new Hashtable();
 	if (debug > 0) {
 	    params.setParameter("debug", new Integer(debug));

src/org/semanticweb/owl/align/Parameters.java

@@ -43,5 +43,6 @@ public interface Parameters {
     public Enumeration getNames();
 
     public void write();
-    //public static Parameters read();
+    //public static Parameters read(String filename);
+    //public static Parameters read(Parameters params, String filename);
 }