X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=b29428266360884f64c726491623b350831c6d1c;hb=af563e083b2a94e50f23d317f260fb734c52c266;hp=e94fba41742996b73fb37829f07c4d36d14d42c3;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index e94fba4..b294282 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -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!
@@ -80,7 +84,7 @@ 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))
     {
@@ -91,7 +95,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.getGlobalColourScheme(), seq, i);
     }
 
     return resBoxColour;
@@ -111,7 +115,7 @@ 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)))
@@ -205,7 +209,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.globalColourScheme, seq, i);
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
         }
 
       }
@@ -328,7 +332,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (currentSequenceGroup.getShowNonconserved()) // todo optimize
           {
             // todo - use sequence group consensus
-            s = getDisplayChar(av.consensus, i, s, '.');
+            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
 
           }
 
@@ -343,7 +347,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (av.getColourText())
           {
             getboxColour = true;
-            getBoxColour(av.globalColourScheme, seq, i);
+            getBoxColour(av.getGlobalColourScheme(), seq, i);
 
             if (av.getShowBoxes())
             {
@@ -359,7 +363,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             if (!getboxColour)
             {
-              getBoxColour(av.globalColourScheme, seq, i);
+              getBoxColour(av.getGlobalColourScheme(), seq, i);
             }
 
             if (resBoxColour.getRed() + resBoxColour.getBlue()
@@ -368,9 +372,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
               graphics.setColor(av.textColour2);
             }
           }
-          if (av.showUnconserved)
+          if (av.getShowUnconserved())
           {
-            s = getDisplayChar(av.consensus, i, s, '.');
+            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
 
           }