+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
+
+ // assume only one set of TCOFFEE scores - but could have more than one
+ // potentially.
+ ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
+ // Search alignment to get all tcoffee annotation and pick one set of
+ // annotation to use to colour seqs.
+ seqMap = new IdentityHashMap<SequenceI, Color[]>();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
+ int w = 0;
+ for (AlignmentAnnotation al : alcontext
+ .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
+ {
+ if (al.sequenceRef != null && !al.belowAlignment)
+ {
+ annots.add(al);
+ if (w < al.annotations.length)
+ {
+ w = al.annotations.length;
+ }
+ Color[] scores = new Color[al.annotations.length];
+ int i = 0;
+ for (Annotation an : al.annotations)
+ {
+ scores[i++] = (an != null) ? an.colour : Color.white;
+ }
+ 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)
+ }