From ecf2d49dbf1d62c024845715f141a596cff8b065 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 18 Jan 2011 17:43:16 +0000
Subject: [PATCH] patch for JAL-695

---
 src/jalview/gui/AlignmentPanel.java |   33 ++++++++++++++++++++-------------
 1 file changed, 20 insertions(+), 13 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index efefeaf..d06251c 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -223,10 +223,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Highlight the given results on the alignment.
    * 
-   * @param results
-   *          DOCUMENT ME!
    */
   public void highlightSearchResults(SearchResults results)
   {
@@ -271,12 +269,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
         return false;
       }
       SequenceI seq = av.alignment.getSequenceAt(seqIndex);
-
-      int[] r = results.getResults(seq, 0, av.alignment.getWidth()); // results.getResults(seq,
-      // seq.getStart(),
-      // seq.getEnd());
-      // TODO: VAMSAS: fix hidden column issue where scroll to left from C
-      // terminus is not visible
+      
+      int[] r=results.getResults(seq, 0, av.alignment.getWidth());
       if (r == null)
       {
         return false;
@@ -293,6 +287,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         return false;
       }
+      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 false;
+          }
+        }
+      }
       if (!av.wrapAlignment)
       {
         if ((startv = av.getStartRes()) >= start)
@@ -501,12 +508,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Adjust row/column scrollers to show a visible position in the alignment.
    * 
-   * @param x
-   *          DOCUMENT ME!
-   * @param y
+   * @param x visible column to scroll to
    *          DOCUMENT ME!
+   * @param y visible row to scroll to
+   *          
    */
   public void setScrollValues(int x, int y)
   {
-- 
1.7.10.2