X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=afbc7e365e811e47664676c804005092d0d89237;hb=cf2e3cf08db12cd9b1ad97d2c2b7e97d9c126ce7;hp=caf20ee7cfe6b8989555fb47533c11ca7c15f15d;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index caf20ee..afbc7e3 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -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, '.');
 
         }
       }