[Bioperl-l] Bio::Tools:Sim4::Results

[Miroslava Cuperlovic-Culf]

Dear All,
I am trying to parse output from sim4  to gff format using something like:
    while(my $exonset = $sim4->next_exonset()) {

       foreach my $exon ( $exonset->sub_SeqFeature() ) {
.....
}
}

This works fine if exon alignment is in the the first group of seq1/seq2  :
seq1 = ..
seq2 = ..

 >fasta info
 >fasta info

1-66  (31346313-31346378)   100% ->
67-222  (31372915-31373070)   100% ->
223-798  (31376360-31376935)   100%

But  if the sim4 outputs shows alignment to multiple sections of the 
Chromosome input and if the exon info is not in the first group of data 
(seq1 \n seq2 ...) this loop doesn't find it. parse_next_alignment 
didn't seem to be able to solve this problem either.
Is there any way to loop around all seq1/seq2 parts of the input from 
Bioperl or not to write the empty alignments from sim4?
Sorry for this most likely trivial question!
Thanks for the on-going help
Mira