search result highlighting and scrolling and some patches for JAL-695

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 0519f47..2d2f4bb 100755 (executable)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -230,16 +230,33 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
    */
   public void highlightSearchResults(SearchResults results)
   {
+    scrollToPosition(results);
     seqPanel.seqCanvas.highlightSearchResults(results);
   }
 
   /**
    * scroll the view to show the position of the highlighted region in results
+   * (if any) and redraw the overview
+   * 
+   * @param results
+   * @return false if results were not found
+   */
+  public boolean scrollToPosition(SearchResults results)
+  {
+    return scrollToPosition(results, true);
+  }
+
+  /**
+   * scroll the view to show the position of the highlighted region in results
    * (if any)
    * 
    * @param results
+   * @param redrawOverview
+   *          - when set, the overview will be recalculated (takes longer)
+   * @return false if results were not found
    */
-  public void scrollToPosition(SearchResults results)
+  public boolean scrollToPosition(SearchResults results,
+          boolean redrawOverview)
   {
     // do we need to scroll the panel?
     if (results != null && results.getSize() > 0)
@@ -247,34 +264,34 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       int seqIndex = av.alignment.findIndex(results);
       if (seqIndex == -1)
       {
-        return;
+        return false;
       }
       SequenceI seq = av.alignment.getSequenceAt(seqIndex);
       int[] r = results.getResults(seq, seq.getStart(), seq.getEnd());
       if (r == null)
       {
-        return;
+        return false;
       }
       int start = r[0];
       int end = r[1];
       if (start < 0)
       {
-        return;
+        return false;
       }
       if (end == seq.getEnd())
       {
-        return;
+        return false;
       }
       if (av.hasHiddenColumns)
       {
         start = av.getColumnSelection().findColumnPosition(start);
         end = av.getColumnSelection().findColumnPosition(end);
-        if (start==end)
+        if (start == end)
         {
           if (!av.colSel.isVisible(r[0]))
           {
             // don't scroll - position isn't visible
-            return;
+            return false;
           }
         }
       }
@@ -308,8 +325,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
         scrollToWrappedVisible(start);
       }
     }
-
-    repaint();
+    if (redrawOverview && overviewPanel != null)
+    {
+      overviewPanel.setBoxPosition();
+    }
+    paintAlignment(redrawOverview);
+    return true;
   }
 
   void scrollToWrappedVisible(int res)