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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::CDS - Object representing a CDS

=head1 SYNOPSIS

  use Bio::EnsEMBL::CDS;

  $feature = Bio::EnsEMBL::CDS->new(
    -start         => 100,
    -end           => 220,
    -strand        => -1,
    -slice         => $slice,
    -phase         => 1,
    -transcript    => $transcript
  );

=head1 DESCRIPTION

This is a CDS feature within the Ensembl CDS.
It represents the coding regions of a transcript.

=head1 METHODS

=cut

use strict;

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

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

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

use constant SEQUENCE_ONTOLOGY => {
  acc  => 'SO:0000316',
  term => 'CDS',
};

=head2 new

  Arg [...]  : Named arguments passed to superclass
  Example    : $feature = Bio::EnsEMBL::CDS->new
                        (-start   => 1,
                         -end     => 100,
                         -strand  => 1,
                         -slice   => $slice,
                         -dbID    => 10,
                         -transcript  => $transcript,
                         -phase   => 1);
  Description: Constructs a new Bio::EnsEMBL::CDS.
  Returntype : Bio::EnsEMBL::CDS
  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 ($transcript, $phase, $translation_id, $seq_region_start, $seq_region_end) = rearrange(['TRANSCRIPT','PHASE', 'TRANSLATION_ID', 'SEQ_REGION_START', 'SEQ_REGION_END'],@_);

  $self->{'transcript'} = $transcript;
  $self->{'phase'} = $phase;
  $self->{'translation_id'} = $translation_id;
  $self->{'seq_region_start'} = $seq_region_start;
  $self->{'seq_region_end'} = $seq_region_end;

  return $self;
}


=head2 transcript

  Arg [1]    : (optional) Bio::EnsEMBL::Transcript
  Example    : $transcript = $cds->transcript();
  Description: Getter/Setter for the transcript associated with this
               CDS.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub transcript {