X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=9a61f5fc350998c2a81a637ae530c427b9e5f20b;hb=refs%2Fheads%2Fbug%2FJAL-2842;hp=f36a8e29791f59323b4739b5c0219143d56fcfa1;hpb=b5a209613f14ad6e75f43aa537a96484d847ce0a;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index f36a8e2..9a61f5f 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -335,7 +335,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
     }
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -417,7 +417,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    *          alignment column
    * @param seq
    *          index of sequence in alignment
-   * @return position of column in sequence or -1 if at gap
    */
   void setStatusMessage(SequenceI sequence, int column, int seq)
   {
@@ -983,7 +982,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       lastMousePress = evt.getPoint();
 
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
       ap.annotationPanel.image = null;
       return;
     }
@@ -1450,7 +1449,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           if (links == null)
           {
-            links = new Vector<String>();
+            links = new Vector<>();
           }
           links.addAll(sf.links);
         }
@@ -1524,7 +1523,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
     PaintRefresher.Refresh(ap, av.getSequenceSetId());
-    ap.paintAlignment(needOverviewUpdate);
+    ap.paintAlignment(needOverviewUpdate, needOverviewUpdate);
     needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;