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

[jalview.git] / src / jalview / appletgui / AlignmentPanel.java

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 7e42d34..0519f47 100755 (executable)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.appletgui;
 
@@ -225,41 +224,60 @@ 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);
   }
+
   /**
-   * scroll the view to show the position of the highlighted
-   * region in results (if any)
+   * scroll the view to show the position of the highlighted region in results
+   * (if any)
+   * 
    * @param results
    */
   public void scrollToPosition(SearchResults results)
   {
     // do we need to scroll the panel?
-    if (results != null && results.getSize()>0)
+    if (results != null && results.getSize() > 0)
     {
       int seqIndex = av.alignment.findIndex(results);
-      if (seqIndex==-1)
+      if (seqIndex == -1)
       {
         return;
       }
       SequenceI seq = av.alignment.getSequenceAt(seqIndex);
-      int [] r = results.getResults(seq, seq.getStart(), seq.getEnd());
-      if (r==null)
+      int[] r = results.getResults(seq, seq.getStart(), seq.getEnd());
+      if (r == null)
       {
         return;
       }
       int start = r[0];
       int end = r[1];
-      if (start<0)
+      if (start < 0)
       {
         return;
       }
-      if (end==seq.getEnd())
+      if (end == seq.getEnd())
       {
         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)
@@ -417,8 +435,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     }
 
     av.setStartRes(x);
-    av
-            .setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+    av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
 
     hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
     vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;