From ec1d08cc67adaf89176114f7011d5484cc1ff350 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 23 May 2012 20:09:01 +0100 Subject: [PATCH] todo for JAL-1106 --- src/jalview/schemes/TCoffeeColourScheme.java | 5 +++++ 1 file changed, 5 insertions(+) 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; } -- 1.7.10.2