- // 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(_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
+ groupRefRows.get(groupRef).removeAllElements();
+ }
+ // 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(_deferred_args[3]) // the
+ // reference
+ // group, or
+ // null