+
+ /**
+ * return pruned visible sequences in each group in alignment view
+ *
+ * @param c
+ * @return
+ */
+ public Collection<? extends AnnotatedCollectionI> getVisibleGroups(char c)
+ {
+ ArrayList<SequenceGroup> groups = new ArrayList<>();
+ for (ScGroup sc : scGroups)
+ {
+ SequenceGroup sg = sc.getNewSequenceGroup(c);
+ groups.add(sg);
+ }
+ return groups;
+ }