+public class TCoffeeColourScheme extends ResidueColourScheme
+{
+ IdentityHashMap<SequenceI, Color[]> seqMap;
+
+ /**
+ * Default constructor (required for Class.newInstance())
+ */
+ public TCoffeeColourScheme()
+ {
+
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * Finds the TCoffeeScore annotation (if any) for each sequence and notes the
+ * annotation colour for each column position. The colours are fixed for
+ * scores 0-9 and are set when annotation is parsed.
+ *
+ * @see TCoffeeScoreFile#annotateAlignment(AlignmentI, boolean)
+ */
+ @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.
+ List<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();
+ if (alcontext == null)
+ {
+ return;
+ }
+ 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)
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ if (seqMap == null)
+ {
+ return Color.WHITE;
+ }
+ Color[] cols = seqMap.get(seq);
+ if (cols == null)
+ {
+ // see above TODO about computing a colour for each residue in each
+ // column: cc = _rcols[i][indexFor[c]];
+ return Color.white;
+ }
+
+ if (j < 0 || j >= cols.length)
+ {
+ return Color.white;
+ }
+ return cols[j];
+ }