bugfix

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index c2c02d1..0896975 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -97,15 +97,22 @@ public class Finder extends GFinder
     }
   }
 
+  /**
+   * gets the topmost alignment window and sets av and ap accordingly
+   * @return false if no alignment window was found
+   */
   boolean getFocusedViewport()
   {
-    JInternalFrame frame = Desktop.desktop.getAllFrames()[1];
-
-    if (frame != null && frame instanceof AlignFrame)
-    {
-      av = ((AlignFrame) frame).viewport;
-      ap = ((AlignFrame) frame).alignPanel;
-      return true;
+    // now checks further down the window stack to fix bug https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    for (int f=0;f<frames.length; f++) {
+      JInternalFrame frame = frames[f];
+      if (frame != null && frame instanceof AlignFrame)
+      {
+        av = ((AlignFrame) frame).viewport;
+        ap = ((AlignFrame) frame).alignPanel;
+        return true;
+      }
     }
     return false;
   }