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     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.
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::Translation - A class representing the translation of a
transcript

=head1 SYNOPSIS

  my $translation = Bio::EnsEMBL::Translation->new(
    -START_EXON => $exon1,
    -END_EXON   => $exon2,
    -SEQ_START  => 98,
    -SEQ_END    => 39
  );

  # stable ID setter
  $translation->stable_id('ENSP00053458');

  # get start and end position in start/end exons
  my $start = $translation->start;
  my $end   = $translation->end;

=head1 DESCRIPTION

A Translation object defines the CDS and UTR regions of a Transcript
through the use of start_Exon/end_Exon, and start/end attributes.

=cut


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

use Bio::EnsEMBL::Utils::Exception qw(throw warning );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref wrap_array );
use Scalar::Util qw(weaken);

use Bio::EnsEMBL::Storable;

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


=head2 new

  Arg [-START_EXON] : The Exon object in which the translation (CDS) starts
  Arg [-END_EXON]   : The Exon object in which the translation (CDS) ends
  Arg [-SEQ_START]  : The offset in the start_Exon indicating the start
                      position of the CDS.
  Arg [-SEQ_END]    : The offset in the end_Exon indicating the end
                      position of the CDS.
  Arg [-STABLE_ID]  : The stable identifier for this Translation
  Arg [-VERSION]    : The version of the stable identifier
  Arg [-DBID]       : The internal identifier of this Translation
  Arg [-ADAPTOR]    : The TranslationAdaptor for this Translation
  Arg [-SEQ]        : Manually sets the peptide sequence of this translation.
                      May be useful if this translation is not stored in
                      a database.
  Arg [-CREATED_DATE]: the date the translation was created
  Arg [-MODIFIED_DATE]: the date the translation was modified
  Example    : my $tl = Bio::EnsEMBL::Translation->new
                   (-START_EXON => $ex1,
                    -END_EXON   => $ex2,
                    -SEQ_START  => 98,
                    -SEQ_END    => 39);
  Description: Constructor.  Creates a new Translation object
  Returntype : Bio::EnsEMBL::Translation
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub new {
  my $caller = shift;

  my $class = ref($caller) || $caller;

  my ( $start_exon, $end_exon, $seq_start, $seq_end,
       $stable_id, $version, $dbID, $adaptor, $seq,
       $created_date, $modified_date ) =
	   rearrange( [ "START_EXON", "END_EXON", "SEQ_START", "SEQ_END",
			"STABLE_ID", "VERSION", "DBID", "ADAPTOR",
			"SEQ", "CREATED_DATE", "MODIFIED_DATE" ], @_ );
      
  # Default version
  if ( !defined($version) ) { $version = 1 }

  my $self = bless {
		    'start_exon' => $start_exon,
		    'end_exon'   => $end_exon,
		    'dbID'       => $dbID,
		    'start'      => $seq_start,
		    'end'        => $seq_end,
		    'stable_id'  => $stable_id,
		    'version'    => $version,
		    'created_date' => $created_date,
		    'modified_date' => $modified_date,
                    'seq'        => $seq
		   }, $class;

  $self->adaptor($adaptor);

  return $self;
}



=head2 transcript

  Arg [1]       : Transcript object (optional)
  Description   : Sets or retrieves the transcript object associated
                  with this translation object.
  Exceptions    : Throws if there is no adaptor or no dbID defined for
                  the translation object.
  Returntype    : Bio::EnsEMBL::Transcript
=cut

sub transcript {
  my ( $self, $transcript ) = @_;

  if ( defined($transcript) ) {
    assert_ref( $transcript, 'Bio::EnsEMBL::Transcript' );

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

    weaken( $self->{'transcript'} );    # Avoid circular references.

  } elsif ( @_ > 1 ) {
    # Break connection to transcript.
    delete( $self->{'transcript'} );
  } elsif ( !defined( $self->{'transcript'} ) ) {
    my $adaptor = $self->adaptor;
    if ( !defined($adaptor) ) {
      throw(   "Adaptor is not set for translation, "
             . "can not fetch its transcript." );
    }

    my $dbID = $self->{'dbID'};
    if ( !defined($dbID) ) {
      throw(   "dbID is not set for translation, "
             . " can not fetch its transcript." );
    }

    $self->{'transcript'} =
      $adaptor->db()->get_TranscriptAdaptor()
      ->fetch_by_translation_id($dbID);

  # Do not weaken the reference if we had to get the transcript from the
  # database.  The user is probably working on translations directly,
  # not going through transcripts.
  #weaken( $self->{'transcript'} );    # Avoid circular references.
  }

  return $self->{'transcript'};
} ## end sub transcript


=head2 start

  Arg [1]    : (optional) int $start - start position to set
  Example    : $translation->start(17);
  Description: Getter/setter for the value of start, which is a position within
               the exon given by start_Exon.

               If you need genomic coordinates, use the genomic_start()
               method.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub start{
   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      
      $obj->{'start'} = $value;
    }
    return $obj->{'start'};

}


=head2 end

  Arg [1]    : (optional) int $end - end position to set
  Example    : $translation->end(8);
  Description: Getter/setter for the value of end, which is a position within
               the exon given by end_Exon.

               If you need genomic coordinates, use the genomic_end()
               method.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

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

}