JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...

[jalview.git] / src / jalview / gui / SeqPanel.java

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index e99e577..531eca6 100644 (file)
--- 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;