X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=044fcbe431a72bb1abe798668793be05e08d2046;hb=af563e083b2a94e50f23d317f260fb734c52c266;hp=0215e55609dd6bc7cb596dafe224101ecac01817;hpb=3e62000c93de12ce4e4a2282d8f020e21a278292;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 0215e55..044fcbe 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,10 +17,15 @@
  */
 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 implements jalview.api.SequenceRenderer
 {
@@ -61,7 +66,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
-    allGroups = av.alignment.findAllGroups(seq);
+    allGroups = av.getAlignment().findAllGroups(seq);
 
     if (inCurrentSequenceGroup(i))
     {
@@ -72,7 +77,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.getGlobalColourScheme(), seq, i);
     }
 
     return resBoxColour;
@@ -82,7 +87,7 @@ public class SequenceRenderer implements jalview.api.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)))
@@ -98,7 +103,7 @@ public class SequenceRenderer implements jalview.api.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;
   }
@@ -223,7 +228,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         {
           // cheat - use this if we have a consensus for each group: s =
           // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
-          s = getDisplayChar(av.consensus, i, s, '.');
+          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
         }
       }
       else
@@ -245,9 +250,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
             graphics.setColor(resBoxColour);
           }
         }
-        if (av.getShowunconserved())
+        if (av.getShowUnconserved())
         {
-          s = getDisplayChar(av.consensus, i, s, '.');
+          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
 
         }
       }