X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;fp=src%2Fjalview%2Fbin%2FCommands.java;h=9cacc837471f45eac13647aa85ffa2b3798b9ac6;hp=b1b8288f3bb7220b352a1b7d4c4451320fa31143;hb=a36a254c3edbac394449bb7c9e01e2f93111ee30;hpb=e93bc0a7b2def06392a2f6b0f563c1e07fb917a1

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index b1b8288..9cacc83 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -247,9 +247,24 @@ public class Commands
           Console.debug(
                   "Opening '" + openFile + "' in new alignment frame");
           FileLoader fileLoader = new FileLoader(!headless);
-
-          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
-                  format);
+          boolean xception=false;
+          try {
+            af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+                    format);
+          } catch (Throwable thr)
+          {
+            xception=true;
+            Console.error("Couldn't open '"+openFile+"' as "+format+" "+thr.getLocalizedMessage()+ " (Enable debug for full stack trace)");
+            Console.debug("Exception when opening '"+openFile+"'",thr);
+          }
+          finally
+          {
+            if (af==null && !xception)
+            {
+              Console.info("Ignoring '"+openFile+"' - no alignment data found.");
+              continue;
+            }
+          }
 
           // colour alignment?
           String colour = ArgParser.getFromSubValArgOrPref(avm, av,