+public class TCoffeeColourScheme extends ResidueColourScheme
+{
+
+ static final Color[] colors =
+ { new Color(102, 102, 255), // #6666FF
+ new Color(0, 255, 0), // #00FF00
+ new Color(102, 255, 0), // #66FF00
+ new Color(204, 255, 0), // #CCFF00
+ new Color(255, 255, 0), // #FFFF00
+ new Color(255, 204, 0), // #FFCC00
+ new Color(255, 153, 0), // #FF9900
+ new Color(255, 102, 0), // #FF6600
+ new Color(255, 51, 0), // #FF3300
+ new Color(255, 34, 0) // #FF2000
+ };
+
+ IdentityHashMap<SequenceI, Color[]> seqMap;
+
+ /**
+ * the color scheme needs to look at the alignment to get and cache T-COFFEE
+ * scores
+ *
+ * @param alignment
+ * - annotated sequences to be searched
+ */
+ public TCoffeeColourScheme(AnnotatedCollectionI alignment)
+ {
+ alignmentChanged(alignment, null);
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ // TODO: if sequences have been represented and they have scores, could
+ // compute an average sequence score for the representative