my ($self, @args) = @_;

}

# convert object from Bio::EnsEMBL::RepeatFeature
# to Bio::SeqFeature::FeaturePair

    my ($self, $ens_repeat) = @_;
    
    my $feature1 = new Bio::SeqFeature::Generic(
        -start => $ens_repeat->start,
        -end => $ens_repeat->end,
        -strand => $ens_repeat->strand,
        -source_tag => $ens_repeat->source_tag
        -primary_tag => $ens_repeat->repeat_class,
        -seq_id => $ens_repeat->seqname
    );
    
    my ($start2, $end2);
    if($ens_repeat->strand == 1){
        $start2 = $ens_repeat->hstart;
        $end2 = $ens_repeat->hend;
    }elsif($ens_repeat->strand == -1){
        $start2 = $ens_repeat->hend;
        $end2 = $ens_repeat->hstart;
    }else{
        $self->throw("strand cannot be out of range (1, -1)");
    }
        
    my $feature2 = new Bio::SeqFeature::Generic(
        -start => $start2,
        -end => $end2,
        -source_tag => $ens_repeat->source_tag,
        -primary_tag => $ens_repeat->repeat_class,
        -seq_id => $ens_repeat->repeat_name
    );
    
    my $output_module = $self->out;
    require "$output_module";
    return new Bio::SeqFeature::FeaturePair(
        -feature1 => $feature1,
        -feature2 => $feature2
    );
}

1;

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  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html

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