+ // TODO devise way of merging new annotation onto (identical) existing annotation that was used as input
+ // delete all input annotation
+ if (contextAl.getAlignmentAnnotation()!=null) {
+ for (AlignmentAnnotation alan: contextAl.getAlignmentAnnotation()) {
+ contextAl.deleteAnnotation(alan);
+ }
+ }
+ // TODO devise way of merging new groups onto (identical) existing groups when they were used as input to service
+ // delete all existing groups
+ if (contextAl.getGroups()!=null)
+ {
+ contextAl.deleteAllGroups();
+ }