- 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[]>();
- int w=0;
- for (AlignmentAnnotation al:alignment.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);
- }
- }
+ /**
+ * 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<>();
+ // Search alignment to get all tcoffee annotation and pick one set of
+ // annotation to use to colour seqs.
+ seqMap = new IdentityHashMap<>();
+ 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);
+ }
+ }