JAL-1065 - Visualize T-Coffee quality scores for an alignment

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 86c8490..15f1928 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,10 +17,14 @@
  */
 package jalview.gui;
 
-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.FontMetrics;
+import java.awt.Graphics;
 
 /**
  * DOCUMENT ME!
@@ -28,7 +32,7 @@ import jalview.schemes.*;
  * @author $author$
  * @version $Revision$
  */
-public class SequenceRenderer
+public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
   AlignViewport av;
 
@@ -111,7 +115,7 @@ public class SequenceRenderer
   {
     if (cs != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq.getIndex());
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@ -325,7 +329,7 @@ public class SequenceRenderer
           {
             graphics.setColor(currentSequenceGroup.textColour);
           }
-          if (currentSequenceGroup.getShowunconserved()) // todo optimize
+          if (currentSequenceGroup.getShowNonconserved()) // todo optimize
           {
             // todo - use sequence group consensus
             s = getDisplayChar(av.consensus, i, s, '.');
@@ -466,10 +470,8 @@ public class SequenceRenderer
         }
 
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics
-                .drawString(String.valueOf(s), charOffset + x1
-                        + (av.charWidth * (i - start)),
-                        (y1 + av.charHeight) - pady);
+        graphics.drawString(String.valueOf(s), charOffset + x1
+                + (av.charWidth * (i - start)), (y1 + av.charHeight) - pady);
       }
     }
   }