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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

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut


=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

=cut

=head1 NAME

Bio::EnsEMBL::ExonTranscript - An Exon feature in relation to a transcript

=head1 SYNOPSIS

  use Bio::EnsEMBL::ExonTranscript;

  $feature = Bio::EnsEMBL::ExonTranscript->new(-exon => $exon, -transcript => $transcript);

=head1 DESCRIPTION

This is a feature which extends the Exon class to add
the relation to a specific transcript.

=head1 METHODS

=cut

use strict;

package Bio::EnsEMBL::ExonTranscript;
$Bio::EnsEMBL::ExonTranscript::VERSION = '114.0.0';
use vars qw(@ISA);

use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Scalar::Util qw(weaken isweak);

@ISA = qw(Bio::EnsEMBL::Exon);


=head2 new

  Arg [Exon]: The Exon object
  Arg [Transcript]: The Transcript object the exon belongs to
  Example    : $feature = Bio::EnsEMBL::ExonTranscript->new(-exon => $exon, -transcript => $transcript);
  Description: Constructs a new Bio::EnsEMBL::ExonTranscript.
  Returntype : Bio::EnsEMBL::ExonTranscript
  Exceptions : Thrown on invalid -SLICE, -STRAND arguments
  Caller     : general, subclass constructors
  Status     : Stable

=cut

sub new {
  my $caller = shift;

  #allow this to be called as class or object method
  my $class = ref($caller) || $caller;
  my $self = $class->SUPER::new(@_);

  my ($exon, $transcript, $rank) = rearrange(['EXON','TRANSCRIPT', 'RANK'],@_);

  $self->{'exon'} = $exon;
  $self->{'transcript'} = $transcript;
  $self->{'rank'} = $rank;

  foreach my $attribute (keys %$exon) {
    $self->{$attribute} = $exon->{$attribute};
  }

  return $self;
}


=head2 exon

  Arg [1]    : (optional) Bio::EnsEMBL::Exon
  Example    : $exon = $exon_transcript->exon();
  Description: Getter/Setter for the exon forming this
               ExonTranscript.
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub exon {
  my $self = shift;
  $self->{'exon'} = shift if(@_);
  return $self->{'exon'};
}


=head2 transcript