X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=7c0c55cc3835dad954a7b81094299a0a169157d0;hb=23acdc937f2eb189a4736f8a4c3dba924e1ebbce;hp=0297a74c9108a8eee753b281ee0fc6e73ed1edf9;hpb=1b378087ec2d5be9b290cd63c45bfdb9e75269fb;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0297a74..7c0c55c 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1479,9 +1479,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           closeView(alignPanel);
         }
       }
-
       if (closeAllTabs)
       {
+        if (featureSettings != null && featureSettings.isOpen())
+        {
+          featureSettings.close();
+          featureSettings = null;
+        }
         /*
          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
          * be called recursively, with the frame now in 'closed' state
@@ -4691,6 +4695,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             if (parseFeaturesFile(file, sourceType))
             {
               alignPanel.paintAlignment(true, true);
+              SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
+              if (splitFrame != null)
+              {
+                splitFrame.repaint();
+              }
             }
           }
           else