X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FScalePanel.java;h=a1d0bf72c914933bd4c03a84eee88fba22a48a0f;hb=16af141746661052f9902fe1ee2872ed07929667;hp=b35fa6c9497b27cf7efd303a415443c40a86d1b4;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index b35fa6c..a1d0bf7 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -189,7 +189,7 @@ public class ScalePanel
 
     if (!stretchingGroup)
     {
-      ap.paintAlignment(true);
+      ap.paintAlignment(false);
 
       return;
     }
@@ -206,7 +206,7 @@ public class ScalePanel
     }
 
     stretchingGroup = false;
-    ap.paintAlignment(true);
+    ap.paintAlignment(false);
   }
 
   public void mouseDragged(MouseEvent evt)
@@ -259,19 +259,22 @@ public class ScalePanel
         sg.setStartRes(res);
       }
 
+      int col;
       for (int i = min; i <= max; i++)
       {
-        if ( (i < sg.getStartRes()) || (i > sg.getEndRes()))
+        col = av.getColumnSelection().adjustForHiddenColumns(i);
+
+        if ( (col < sg.getStartRes()) || (col > sg.getEndRes()))
         {
-          av.getColumnSelection().removeElement(i);
+          av.getColumnSelection().removeElement(col);
         }
         else
         {
-          av.getColumnSelection().addElement(i);
+          av.getColumnSelection().addElement(col);
         }
       }
 
-      ap.paintAlignment(true);
+      ap.paintAlignment(false);
     }
   }