From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 7 Sep 2023 15:26:40 +0000 (+0100)
Subject: JAL-4279 catch exceptions with fileLoader and report when we don’t get an alignment... 
X-Git-Tag: Release_2_11_3_0~8^2~15
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a36a254c3edbac394449bb7c9e01e2f93111ee30;hp=e93bc0a7b2def06392a2f6b0f563c1e07fb917a1;p=jalview.git

JAL-4279 catch exceptions with fileLoader and report when we don’t get an alignment frame after trying to import a given file before moving on.
---

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,