X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=eaf93c274e5b671092d515cf2dd101cc1a6b3ea7;hb=ae21643b1d2aa912f1de8b7b0ce3e388860a5493;hp=a14da77d76681e4e951a8fcfd40f26ee9c87f934;hpb=2a9991ef1eb02d97e9c8ed1644f292117ae6f600;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index a14da77..eaf93c2 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -210,7 +210,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (hiddenSeqs != null && hiddenSeqs.length > 0)
     {
       viewport.hideSequence(hiddenSeqs);
-      viewport.setHasHiddenRows(true);
     }
     if (columnSelection != null)
     {
@@ -928,7 +927,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               : showForSequences);
         aa.visible = visible;
     }
-    alignPanel.validateAnnotationDimensions(false);
+    alignPanel.validateAnnotationDimensions(true);
   }
 
   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
@@ -1341,9 +1340,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             { e.getActionCommand() }), 600, 500);
 
     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
-    viewport.setFeatureRenderer(fr);
-    viewport.setIncludeHiddenRegion(false);
-    cap.setText(new AppletFormatAdapter(viewport).formatSequences(
+    cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
             viewport.getShowJVSuffix()));
   }