From 662afd2e62a0d775b823e886e3e7a217ff807733 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Wed, 20 Jul 2005 14:40:21 +0000
Subject: [PATCH] - 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 | 5 +++--
 src/fr/inrialpes/exmo/align/util/GroupAlign.java      | 5 ++++-
 src/fr/inrialpes/exmo/align/util/Procalign.java       | 8 +++++++-
 src/org/semanticweb/owl/align/Parameters.java         | 3 ++-
 4 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/src/fr/inrialpes/exmo/align/impl/BasicParameters.java b/src/fr/inrialpes/exmo/align/impl/BasicParameters.java
index 61be6c92..df214b77 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicParameters.java
+++ b/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 =
diff --git a/src/fr/inrialpes/exmo/align/util/GroupAlign.java b/src/fr/inrialpes/exmo/align/util/GroupAlign.java
index 78ab22b8..812b54a1 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupAlign.java
+++ b/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();
diff --git a/src/fr/inrialpes/exmo/align/util/Procalign.java b/src/fr/inrialpes/exmo/align/util/Procalign.java
index 52091c61..2de765ef 100644
--- a/src/fr/inrialpes/exmo/align/util/Procalign.java
+++ b/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));
diff --git a/src/org/semanticweb/owl/align/Parameters.java b/src/org/semanticweb/owl/align/Parameters.java
index 383c2c29..da0183f0 100644
--- a/src/org/semanticweb/owl/align/Parameters.java
+++ b/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);
 }
-- 
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