// 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();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
int w = 0;
for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
}
return cols[j];
}
-
+
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)