bio_ens_predictionExon.pm

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=head1 LICENSE
 
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regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
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distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
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  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=head1 AUTHOR
 
Juguang Xiao <juguang@tll.org.sg>
 
=cut
 
=head1 NAME
 
Bio::EnsEMBL::Utils::Converter::bio_ens_predictionExon
 
=head1 SYNOPISIS
 
  my $converter = new Bio::EnsEMBL::Utils::Converter(
    -in     => 'Bio::Tools::Prediction::Exon',
    -out    => 'Bio::EnsEMBL::Exon',
    -contig => $ens_contig
  );
 
=head1 DESCRIPTION
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::Utils::Converter::bio_ens_predictionExon;
 
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Utils::Converter;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Utils::Converter::bio_ens;
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
 
sub _convert_single {
    my ($self, $input) = @_;
    
 
    $input || $self->throw("a input object needed");
    $self->throw("a Bio::Tools::Prediction::Exon object needed")
        unless($input->isa("Bio::Tools::Prediction::Exon"));
 
    my $output = Bio::EnsEMBL::Exon->new(
        -start => $input->start,
        -end => $input->end,
        -strand => $input->strand
    );
 
    $output->score($input->score);
    $output->p_value($input->significance);
 
    $output->phase($input->get_tag_values("phase")); # only first element is used
    $output->end_phase($input->get_tag_values("end_phase"));
 
    $output->contig($self->contig);
 
    return $output;
}
 
 
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