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[]>();
- for (AlignmentAnnotation al:alignment.getAlignmentAnnotation())
+ int w=0;
+ for (AlignmentAnnotation al:alignment.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
{
- if (al.sequenceRef!=null && !al.belowAlignment && al.label!=null && (al.label==TCoffeeScoreFile.TCOFFEE_SCORE || al.label.equals(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)