From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 23 May 2012 19:09:01 +0000 (+0100)
Subject: todo for JAL-1106
X-Git-Tag: Jalview_2_9~513
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ec1d08cc67adaf89176114f7011d5484cc1ff350;p=jalview.git

todo for JAL-1106
---

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 47aebd1..1063f8b 100644
--- 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;
 	  }