X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=c4e17fb3cb08752cfea40df0f82fa05282b52f61;hb=98e5ebe726c30cca66c22541ddb98228d914805a;hp=a26b9d05b83c26ac560cbbeb3f33fb2dccdc5537;hpb=8f8dbc28e40a7e23e984882191ef2f9772bb1dbb;p=jalview.git

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