+ // process any deferred attribute settings for each context
+ for (Object[] _deferred_args : deferredAnnotation_calls)
+ {
+ if (_deferred_args[0] == GRAPHLINE)
+ {
+ addLine(al,
+ (StringTokenizer) _deferred_args[1], // st
+ (SequenceI) _deferred_args[2], // refSeq
+ (_deferred_args[3] == null) ? null : groupRefLookup
+ .get((String) _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((String) _combine_args[2]) // the reference group,
+ // or null
+ );
+ }