copy the .gen files from $birch/tutorials/bioLegato/sequence
to the current directory

bldna

read in PBI101TD.gen and X5331.gen
select X52331 in name pane
File --> SaveAs (GenBank) X52331.bldna.gen

This file will contain the GenBank entries for both files, 
despite the fact that only X52331 was selected.

read in PEACAB15.gen
select PEACAB15 in name pane
file --> SaveAs (GenBank) PEACAB15.bldna.gen
This file will contain all three GenBank entries

select PEACAB15
File --> SaveAs (fasta) PEACAB15.bldna.fsa
This file saves all three sequences in fasta format


read in pBSGUS.wrp (a fasta file)
select pBSGUS in name pane
File --> SaveAs (GenBank) pBSGUS.bldna.gen
This file contains all four sequences in GenBank format.
since pBSGUS has no GenBank annotation, its annotation
is generated, correctly by Biolegato.

CONCLUSION:
It appears that there is a bug in SaveAs that ignores the
selection and just saves all sequences.