todo for JAL-1106

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 47aebd1..1063f8b 100644 (file)
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -72,12 +72,17 @@ public class TCoffeeColourScheme extends ResidueColourScheme {
               seqMap.put(al.sequenceRef, scores);
             }
           }
+    // TODO: compute average colour for each symbol type in each column - gives
+    // a second order colourscheme for colouring a sequence logo derived from
+    // the alignment (colour reflects quality of alignment for each residue
+    // class)
        }
        @Override
        public Color findColour(char c, int j, SequenceI seq) {
           Color[] cols;
 
          if( seqMap==null || (cols=seqMap.get(seq))==null) {
+//      see above TODO about computing a colour for each residue in each column:           cc = _rcols[i][indexFor[c]];
            return Color.white;
          }