+ // look for other sequences represented by this hit and create rep groups
+ // could be in "pdbs", or ..
+ addRedundantSeqGroup(firsthit, alisqfrom, alisqto,
+ (JSONArray) hmmrhit.get("seqs"), true);
+ }
+ }
+
+ /**
+ * series of operations to perform for the viewpanel associated with the
+ * alignment
+ */
+ private List<Runnable> viewOps = new ArrayList<Runnable>();
+
+ public void updateView(AlignmentViewport view)
+ {
+ viewAl = view;
+ for (Runnable op : viewOps)
+ {
+ op.run();
+ }
+ }
+
+ private void addRedundantSeqGroup(final SequenceI firsthit,
+ long alisqfrom, long alisqto, JSONArray others, boolean justDelete)
+ {
+ if (others != null)
+ {
+ final SequenceGroup repgroup = new SequenceGroup();
+ repgroup.setSeqrep(firsthit);
+ repgroup.addOrRemove(firsthit, false);
+ repgroup.setStartRes(0);
+ repgroup.setEndRes(resultAl.getWidth() - 1);
+ for (Object otherseq : others.toArray(new JSONObject[0]))