FormatAdapter throws exception

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index a26b9d0..c4e17fb 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -127,8 +127,13 @@ public class JalviewLite extends Applet
       }\r
 \r
       String format = jalview.io.IdentifyFile.Identify(args[0],"File");\r
-      SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);\r
-\r
+      SequenceI[] sequences = null;\r
+     try{\r
+       sequences = new AppletFormatAdapter().readFile(args[0], "File", format);\r
+     }catch(java.io.IOException ex)\r
+     {\r
+       ex.printStackTrace();\r
+     }\r
       if ( (sequences != null) && (sequences.length > 0))\r
       {\r
         AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);\r
@@ -247,8 +252,13 @@ public class JalviewLite extends Applet
         public void run()\r
         {\r
             SequenceI[] sequences = null;\r
-            sequences = new AppletFormatAdapter().readFile(file, protocol, format);\r
-\r
+            try{\r
+              sequences = new AppletFormatAdapter().readFile(file, protocol,\r
+                  format);\r
+            }catch(java.io.IOException ex)\r
+            {\r
+              ex.printStackTrace();\r
+            }\r
             if ((sequences != null) && (sequences.length > 0))\r
             {\r
               currentAlignFrame = new AlignFrame(new Alignment(sequences),\r
@@ -263,12 +273,11 @@ public class JalviewLite extends Applet
                 if (treeFile != null)\r
                 {\r
                   if (treeFile.indexOf("://") == -1)\r
-                  treeFile = getCodeBase() + treeFile;\r
+                    treeFile = getCodeBase() + treeFile;\r
 \r
                   try\r
                   {\r
-                    jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
-                        getCodeBase() + treeFile, "URL");\r
+                    jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, "URL");\r
                     fin.parse();\r
 \r
                     if (fin.getTree() != null)\r
@@ -276,7 +285,7 @@ public class JalviewLite extends Applet
                       TreePanel tp = null;\r
                       tp = new TreePanel(currentAlignFrame.viewport,\r
                                          currentAlignFrame.viewport.getAlignment().getSequences(),\r
-                                         fin, "FromFile", applet.getCodeBase() + treeFile);\r
+                                         fin, "FromFile", treeFile);\r
                       addFrame(tp, treeFile, 600, 500);\r
                       currentAlignFrame.addTreeMenuItem(tp, treeFile);\r
                     }\r