JAL-4196 report an error if structure view doesn’t get created (for whatever reason...

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

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index b9c04f5..7f493e0 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -569,9 +569,20 @@ public class Commands
                           structureFilepath, tft, paeFilepath, false,
                           ssFromStructure, false, viewerType);
 
-          if (headless)
+          if (sv==null)
+          {
+            Console.error("Failed to import and open structure view.");
+            continue;
+          }
+          while (sv.isBusy())
           {
-            sv.setAsync(false);
+            try {
+              Thread.sleep(25);
+            }
+            catch (Exception x)
+            {
+              
+            }
           }
 
           String structureImageFilename = ArgParser.getValueFromSubValOrArg(
@@ -629,8 +640,15 @@ public class Commands
               if (sview instanceof AppJmol)
               {
                 AppJmol jmol = (AppJmol) sview;
-                jmol.makePDBImage(structureImageFile, imageType, renderer,
+                try { 
+                  jmol.makePDBImage(structureImageFile, imageType, renderer,
                         userBis);
+                }
+                catch (ImageOutputException ioexc)
+                {
+                  Console.warn("Unexpected error whilst exporting image to "+structureImageFile,ioexc);
+                }
+
               }
               break;
             default: