(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 857472b..afbc7e3 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -61,7 +61,7 @@ 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 +72,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.getGlobalColourScheme(), seq, i);
     }
 
     return resBoxColour;
@@ -98,7 +98,7 @@ 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 +223,7 @@ 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 +245,9 @@ 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, '.');
 
         }
       }