+ addLine(al, (StringTokenizer) _deferred_args[1], // st
+ (SequenceI) _deferred_args[2], // refSeq
+ (_deferred_args[3] == null) ? null
+ : groupRefLookup.get(_deferred_args[3]) // the
+ // reference
+ // group, or
+ // null
+ );
+ }
+ }
+
+ // finally, combine all the annotation rows within each context.
+ /**
+ * number of combine statements in this annotation file. Used to create new
+ * groups for combined annotation graphs without disturbing existing ones
+ */
+ int combinecount = 0;
+ for (Object[] _combine_args : combineAnnotation_calls)
+ {
+ combineAnnotations(al, ++combinecount,
+ (StringTokenizer) _combine_args[0], // st
+ (SequenceI) _combine_args[1], // refSeq
+ (_combine_args[2] == null) ? null
+ : groupRefLookup.get(_combine_args[2]) // the reference
+ // group,
+ // or null
+ );
+ }
+
+ return modified;
+ }
+
+ private void parseHideCols(HiddenColumns hidden, String nextToken)
+ {
+ StringTokenizer inval = new StringTokenizer(nextToken, ",");
+ while (inval.hasMoreTokens())
+ {
+ String range = inval.nextToken().trim();
+ int from, to = range.indexOf("-");
+ if (to == -1)
+ {
+ from = to = Integer.parseInt(range);
+ if (from >= 0)
+ {
+ hidden.hideColumns(from, to);
+ }
+ }
+ else
+ {
+ from = Integer.parseInt(range.substring(0, to));
+ if (to < range.length() - 1)