update author list in license for (JAL-826)

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index c41c35f..caf20ee 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
 
@@ -23,7 +22,7 @@ import java.awt.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 
-public class SequenceRenderer
+public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
   AlignViewport av;
 
@@ -50,7 +49,7 @@ public class SequenceRenderer
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void prepare(Graphics g, boolean renderGaps)
   {
@@ -220,6 +219,12 @@ public class SequenceRenderer
           getBoxColour(currentSequenceGroup.cs, seq, i);
           graphics.setColor(resBoxColour.darker());
         }
+        if (currentSequenceGroup.getShowNonconserved())
+        {
+          // cheat - use this if we have a consensus for each group: s =
+          // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
+          s = getDisplayChar(av.consensus, i, s, '.');
+        }
       }
       else
       {
@@ -240,6 +245,11 @@ public class SequenceRenderer
             graphics.setColor(resBoxColour);
           }
         }
+        if (av.getShowunconserved())
+        {
+          s = getDisplayChar(av.consensus, i, s, '.');
+
+        }
       }
 
       if (av.upperCasebold)
@@ -269,6 +279,18 @@ public class SequenceRenderer
 
   }
 
+  private char getDisplayChar(AlignmentAnnotation consensus, int position,
+          char s, char c)
+  {
+    char conschar = consensus.annotations[position].displayCharacter
+            .charAt(0);
+    if (conschar != '-' && s == conschar)
+    {
+      s = c;
+    }
+    return s;
+  }
+
   boolean inCurrentSequenceGroup(int res)
   {
     if (allGroups == null)