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 e90f867..fc0a758 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -955,7 +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;
@@ -992,8 +992,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
           codingComplement.getAlignment().addGroup(mappedGroup);
           for (SequenceI seq : mappedGroup.getSequences())
           {
-            codingComplement.setSequenceColour(seq,
-                    mappedGroup.getIdColour().brighter());
+            codingComplement.setSequenceColour(seq, col.brighter());
           }
         }
       }