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lib/Bio/AlignIO/stockholm.pm  view on Meta::CPAN

=head2 new

 Title   : new
 Usage   : my $alignio = Bio::AlignIO->new(-format => 'stockholm'
					  -file   => '>file');
 Function: Initialize a new L<Bio::AlignIO::stockholm> reader or writer
 Returns : L<Bio::AlignIO> object
 Args    : -line_length :  length of the line for the alignment block
           -alphabet    :  symbol alphabet to set the sequences to.  If not set,
                           the parser will try to guess based on the alignment
                           accession (if present), defaulting to 'dna'.
           -spaces      :  (optional, def = 1) boolean to add a space in between
                           the "# STOCKHOLM 1.0" header and the annotation and
                           the annotation and the alignment.

=cut

sub _initialize {
    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);