[Bioperl-l] Bio::Variation::SeqDiff, Bio::Variation::VariantI

[Eckhard Lehmann]

Heikki,

I think the best way is to initiate a private (or public?) method
"_set_dnamut()" which sets up the dna_mut in the way described. It can
be called in the current "dna_mut()" method and can be changed
afterwards by someone else.
So I don't need to change too much of the existing methods. 

The code at the end of this mail works fine for now.

Eckhard

#------------------------------------------------------------------
sub _set_dnamut {
  my $self = shift;

  return 0 unless $self->dna_ori && $self->each_Variant;

  $self->dna_mut($self->dna_ori);
  foreach ($self->each_Variant) {
    next unless $_->isMutation;

    my ($s, $la, $le);
    #lies the mutation lesser than 25 bases after the start of sequence?
    if ($_->start < 25) {$s = 0; $la = $_->start;}
    else {$s = $_->start - 25; $la = 25;}

    #is the mutation an insertion?
    $_->end($_->start) unless $_->allele_ori->seq;

    #does the mutation end greater than 25 bases before the end of 
    #sequence? 
    if (($_->end + 25) > length($self->dna_mut)) {
      $le = length($self->dna_mut) - $_->end;
    } else {$le = 25;}

    $_->dnStreamSeq(substr($self->dna_mut, $s, $la));
    $_->upStreamSeq(substr($self->dna_mut, $_->end, $le));
    
    my $s_ori = $_->dnStreamSeq . $_->allele_ori->seq . $_->upStreamSeq;
    my $s_mut = $_->dnStreamSeq . $_->allele_mut->seq . $_->upStreamSeq;
    (my $str = $self->dna_mut) =~ s/$s_ori/$s_mut/;
    $self->dna_mut($str);
  }
}