X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=850a09a0aa1c7a140c52ac87569a7a181ef648aa;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=2ef71cce5d6fff162391756b1425434754dcce56;hpb=6d06be2714c9cba8c69148d5e2d26b50b7051840;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2ef71cc..850a09a 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1743,7 +1743,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
 
       sequence.setName(dialog.getName().replace(' ', '_'));
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
 
     sequence.setDescription(dialog.getDescription());
@@ -1946,8 +1946,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       if (start <= end)
       {
         seqs.add(sg.getSequenceAt(i).getDatasetSequence());
-        features.add(
-                new SequenceFeature(null, null, null, start, end, null));
+        features.add(new SequenceFeature(null, null, start, end, null));
       }
     }
 
@@ -1960,7 +1959,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               .amendFeatures(seqs, features, true, ap))
       {
         ap.alignFrame.setShowSeqFeatures(true);
-        ap.highlightSearchResults(null);
+        ap.av.setSearchResults(null); // clear highlighting
+        ap.repaint(); // draw new/amended features
       }
     }
   }