JAL-2154 belt-and-braces patch:

JAL-2154 belt-and-braces patch:
* when dataset XML doc is read in, all vamsasSet sequences should be processed in sync with the ‘view’ JSeq entries containing start/end metadata
* features, dbrefs and pdbentrys are now added direct to dataset sequences, but old behaviour should be preserved for reading alignment views containing dbrefs that get propagated to dataset.