X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;fp=src%2Fjalview%2Fgui%2FSeqPanel.java;h=531eca654e8ac9168314fdbe1728c959bf8ee84b;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=e99e5774dc47d606815fd01e330aaee483da32dc;hpb=98558735e9208afa98bb155bd5350ad0a680ca24;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index e99e577..531eca6 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -484,7 +484,7 @@ public class SeqPanel extends JPanel
       av.setSelectionGroup(sg);
     }
 
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -1057,7 +1057,7 @@ public class SeqPanel extends JPanel
         }
         if (newWidth > 0)
         {
-          ap.paintAlignment(false);
+          ap.paintAlignment(false, false);
           if (copyChanges)
           {
             /*
@@ -1841,7 +1841,9 @@ public class SeqPanel extends JPanel
       }
     }
     PaintRefresher.Refresh(this, av.getSequenceSetId());
-    ap.paintAlignment(needOverviewUpdate);
+    // TODO: structure colours only need updating if stretchGroup used to or now
+    // does contain sequences with structure views
+    ap.paintAlignment(needOverviewUpdate, needOverviewUpdate);
     needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;