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lib/Bio/App/SELEX/Stockholm.pm  view on Meta::CPAN

    push @out, "# STOCKHOLM 1.0";

    # determine alignment columns, legend columns & effective columns per line
    my $acols   = $self->columns;
    my $lcols   = $self->lcols;
    my $colstep = $maxcols < 1 ? $acols : $maxcols - $lcols - 1;
    $colstep = $maxcols
      if $colstep < 1;    # protect against negative and 0 colstep...

    # GF lines
    # check for gfOrder (insane, fragile Stockholm line ordering strikes again)
    if ( @{ $self->gfOrder } == map { (@$_) } values %{ $self->gf } )
    {                     # gfOrder same number of lines as #=GF block?
        my %gfCursor = map ( ( $_ => 0 ), keys %{ $self->gf } );
        foreach my $feature ( @{ $self->gfOrder } ) {
            push @out,
              $self->prettify(
                $lcols,
                "#=GF $feature",
                $self->gf_($feature)->[ $gfCursor{$feature}++ ]
              );