patch for JAL-695 - need to test if this is observed in applet

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 6d4c63b..0519f47 100755 (executable)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -224,6 +224,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
   }
 
+  /**
+   * Highlight the given results on the alignment.
+   * 
+   */
   public void highlightSearchResults(SearchResults results)
   {
     seqPanel.seqCanvas.highlightSearchResults(results);
@@ -261,6 +265,19 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return;
       }
+      if (av.hasHiddenColumns)
+      {
+        start = av.getColumnSelection().findColumnPosition(start);
+        end = av.getColumnSelection().findColumnPosition(end);
+        if (start==end)
+        {
+          if (!av.colSel.isVisible(r[0]))
+          {
+            // don't scroll - position isn't visible
+            return;
+          }
+        }
+      }
       if (!av.wrapAlignment)
       {
         if ((av.getStartRes() > end)