X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=697c0d179c6539e4b91635af9a3d9789b6386098;hb=72b3f05a1157da32ada5aea139139996dddea219;hp=c41c35fa9f02c3a2a29e6c3c60dbb5c88077d688;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index c41c35f..697c0d1 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,29 +1,36 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
 
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
 
-public class SequenceRenderer
+public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
   AlignViewport av;
 
@@ -50,7 +57,7 @@ public class SequenceRenderer
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void prepare(Graphics g, boolean renderGaps)
   {
@@ -62,7 +69,7 @@ public class SequenceRenderer
 
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
-    allGroups = av.alignment.findAllGroups(seq);
+    allGroups = av.getAlignment().findAllGroups(seq);
 
     if (inCurrentSequenceGroup(i))
     {
@@ -73,7 +80,7 @@ public class SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.getGlobalColourScheme(), seq, i);
     }
 
     return resBoxColour;
@@ -83,7 +90,7 @@ public class SequenceRenderer
   {
     if (cs != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@ -99,7 +106,7 @@ public class SequenceRenderer
 
   public Color findSequenceColour(SequenceI seq, int i)
   {
-    allGroups = av.alignment.findAllGroups(seq);
+    allGroups = av.getAlignment().findAllGroups(seq);
     drawBoxes(seq, i, i, 0);
     return resBoxColour;
   }
@@ -220,6 +227,13 @@ 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.getAlignmentConsensusAnnotation(), i, s,
+                  '.');
+        }
       }
       else
       {
@@ -240,6 +254,12 @@ public class SequenceRenderer
             graphics.setColor(resBoxColour);
           }
         }
+        if (av.getShowUnconserved())
+        {
+          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+                  '.');
+
+        }
       }
 
       if (av.upperCasebold)
@@ -269,6 +289,18 @@ 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)