JAL-845 applet colour by tree; translate as cDNA; pull up history list

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index e700fb3..fc0a758 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import jalview.analysis.Conservation;
 import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -892,11 +893,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
           aps[a].av.getAlignment().deleteAllGroups();
           aps[a].av.clearSequenceColours();
         }
-        if (av.getSlave() != null)
+        if (av.getCodingComplement() != null)
         {
-          av.getSlave().setSelectionGroup(null);
-          av.getSlave().getAlignment().deleteAllGroups();
-          av.getSlave().clearSequenceColours();
+          av.getCodingComplement().setSelectionGroup(null);
+          av.getCodingComplement().getAlignment().deleteAllGroups();
+          av.getCodingComplement().clearSequenceColours();
         }
         colourGroups();
       }
@@ -954,7 +955,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         if (cs != null)
         {
           cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.getIgnoreGapsConsensus());
+                  av.isIgnoreGapsConsensus());
         }
       }
       sg.cs = cs;
@@ -981,21 +982,20 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
       // TODO can we push all of the below into AlignViewportI?
       av.getAlignment().addGroup(sg);
-      if (av.getSlave() != null)
+      final AlignViewportI codingComplement = av.getCodingComplement();
+      if (codingComplement != null)
       {
         SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
-                av.getSlave());
+                codingComplement);
         if (mappedGroup.getSequences().size() > 0)
         {
-          av.getSlave().getAlignment().addGroup(mappedGroup);
+          codingComplement.getAlignment().addGroup(mappedGroup);
           for (SequenceI seq : mappedGroup.getSequences())
           {
-            av.getSlave().setSequenceColour(seq,
-                    mappedGroup.getIdColour().brighter());
+            codingComplement.setSequenceColour(seq, col.brighter());
           }
         }
       }
-
     }
 
     // notify the panel to redo any group specific stuff.
@@ -1006,9 +1006,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       // to any Jmols listening in
     }
 
-    if (av.getSlave() != null)
+    if (av.getCodingComplement() != null)
     {
-      ((AlignViewport) av.getSlave()).getAlignPanel().updateAnnotation();
+      ((AlignViewport) av.getCodingComplement()).getAlignPanel().updateAnnotation();
       /*
        * idPanel. repaint ()
        */