bio_ens_transcript.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
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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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_transcript - the instance converter
 
=head1 SYNOPISIS
 
=head1 DESCRIPTION
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::Utils::Converter::bio_ens_transcript;
 
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Utils::Converter::bio_ens;
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
 
sub _convert_single {
    my ($self, $arg) = @_;
    unless($arg->isa('Bio::SeqFeature::Gene::Transcript')){
        $self->throw("A Bio::SeqFeature::Gene::Transcript object needed");
    }
    my $transcript = $arg;
 
    my @exons = $transcript->exons_ordered;
    $self->{_converter_for_exons}->contig($self->contig);
    $self->{_converter_for_exons}->analysis($self->analysis);
    
    my $ens_exons = $self->{_converter_for_exons}->convert(\@exons);
    
    my $ens_transcript = Bio::EnsEMBL::Transcript->new(@{$ens_exons});
    $ens_transcript->start($transcript->start);
    $ens_transcript->end($transcript->end);
#    $ens_transcript->strand($transcript->strand);
    return $ens_transcript;
}
 
 
sub _initialize {
    my ($self, @args) = @_;
    $self->SUPER::_initialize(@args);
 
    $self->{_converter_for_exons} = new Bio::EnsEMBL::Utils::Converter(
        -in => 'Bio::SeqFeature::Gene::Exon',
        -out => 'Bio::EnsEMBL::Exon'
    );
 
}