Translation.pm 27.9 KB
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=head1 LICENSE

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  Copyright (c) 1999-2010 The European Bioinformatics Institute and
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  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

=cut
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=head1 NAME

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Bio::EnsEMBL::Translation - A class representing the translation of a
transcript
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=head1 SYNOPSIS

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  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;
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  my $end   = $translation->end;
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=head1 DESCRIPTION

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


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package Bio::EnsEMBL::Translation;

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use vars qw($AUTOLOAD @ISA);
use strict;

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use Scalar::Util qw(weaken);

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use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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use Bio::EnsEMBL::Storable;
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@ISA = qw(Bio::EnsEMBL::Storable);
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=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.
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  Arg [-CREATED_DATE]: the date the translation was created
  Arg [-MODIFIED_DATE]: the date the translation was modified
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  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
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  Status     : Stable
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=cut

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sub new {
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  my $caller = shift;
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  my $class = ref($caller) || $caller;
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  my ( $start_exon, $end_exon, $seq_start, $seq_end,
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       $stable_id, $version, $dbID, $adaptor, $seq,
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       $created_date, $modified_date ) =
	   rearrange( [ "START_EXON", "END_EXON", "SEQ_START", "SEQ_END",
			"STABLE_ID", "VERSION", "DBID", "ADAPTOR",
			"SEQ", "CREATED_DATE", "MODIFIED_DATE" ], @_ );
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  my $self = bless {
		    'start_exon' => $start_exon,
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		    'end_exon'   => $end_exon,
		    'adaptor'    => $adaptor,
		    'dbID'       => $dbID,
		    'start'      => $seq_start,
		    'end'        => $seq_end,
		    'stable_id'  => $stable_id,
		    'version'    => $version,
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		    'created_date' => $created_date,
		    'modified_date' => $modified_date,
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        'seq'        => $seq
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		   }, $class;

  return $self;
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}

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=head2 new_fast

  Arg [1]    : hashref to be blessed
  Description: Construct a new Bio::EnsEMBL::Translation using the hashref.
  Exceptions : none
  Returntype : Bio::EnsEMBL::Translation
  Caller     : general, subclass constructors
  Status     : Stable

=cut


sub new_fast {
  my $class = shift;
  my $hashref = shift;
  return bless $hashref, $class;
}

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=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.

=cut

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

  if ( defined($transcript) ) {
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    if (    !ref($transcript)
         || !$transcript->isa('Bio::EnsEMBL::Transcript') )
    {
      throw("Argument is not a transcript");
    }
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    $self->{'transcript'} = $transcript;

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    weaken( $self->{'transcript'} );    # Avoid circular references.
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  } elsif ( !defined( $self->{'transcript'} ) ) {
    my $adaptor = $self->{'adaptor'};
    if ( !defined($adaptor) ) {
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      throw(   "Adaptor is not set for translation, "
             . "can not fecth its transcript." );
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    }

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

    $self->{'transcript'} =
      $adaptor->db()->get_TranscriptAdaptor()
      ->fetch_by_translation_id($dbID);
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    weaken( $self->{'transcript'} );    # Avoid circular references.
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  }

  return $self->{'transcript'};
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} ## end sub transcript
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=head2 start

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  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.

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

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

}


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=head2 end

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

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

}


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=head2 start_Exon
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  Arg [1]    : (optional) Bio::EnsEMBL::Exon - start exon to assign
  Example    : $translation->start_Exon($exon1);
  Description: Getter/setter for the value of start_Exon, which denotes the
               exon at which translation starts (and within this exon, at the
               position indicated by start, see above).
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : thrown on wrong argument type
  Caller     : general
  Status     : Stable
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=cut

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sub start_Exon {
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   my $self = shift;
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   if( @_ ) {
      my $value = shift;
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      if( !ref $value || !$value->isa('Bio::EnsEMBL::Exon') ) {
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         throw("Got to have an Exon object, not a $value");
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      }
      $self->{'start_exon'} = $value;
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    }
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   return $self->{'start_exon'};
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}


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=head2 end_Exon
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  Arg [1]    : (optional) Bio::EnsEMBL::Exon - start exon to assign
  Example    : $translation->start_Exon($exon1);
  Description: Getter/setter for the value of end_Exon, which denotes the
               exon at which translation ends (and within this exon, at the
               position indicated by end, see above).
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : thrown on wrong argument type
  Caller     : general
  Status     : Stable
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=cut

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sub end_Exon {
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   my $self = shift;
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   if( @_ ) {
      my $value = shift;
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      if( !ref $value || !$value->isa('Bio::EnsEMBL::Exon') ) {
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         throw("Got to have an Exon object, not a $value");
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      }
      $self->{'end_exon'} = $value;
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    } 
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    return $self->{'end_exon'};
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}

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=head2 cdna_start

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    Arg  [1]    : (optional) Bio::EnsEMBL::Transcript $transcript
                  The transcript which this is a translation of.
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    Example     : $translation_cdna_start = $translation->cdna_start();
    Description : Returns the start position of the translation in cDNA
                  coordinates.
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                  If no transcript is given, the method will use
                  TranscriptAdaptor->fetch_by_translation_id() to locate
                  the correct transcript.
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    Return type : Integer
    Exceptions  : Throws if the given (optional) argument is not a
                  transcript.
    Caller      : General
    Status      : At Risk (Under Development)

=cut

sub cdna_start {
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  my ( $self, $transcript ) = @_;
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  if ( defined($transcript)
       && (    !ref($transcript)
            || !$transcript->isa('Bio::EnsEMBL::Transcript') ) )
  {
    throw("Argument is not a transcript");
  }
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  if ( !exists( $self->{'cdna_start'} ) ) {
    if ( !defined($transcript) ) {
      # We were not given a transcript, get the transcript out of
      # the database.
      $transcript = $self->transcript();
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    }

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    $self->{'cdna_start'} =
      $self->start_Exon()->cdna_coding_start($transcript);
  }

  return $self->{'cdna_start'};
}
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=head2 cdna_end

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    Arg  [1]    : (optional) Bio::EnsEMBL::Transcript $transcript
                  The transcript which this is a translation of.
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    Example     : $translation_cdna_end = $translation->cdna_end();
    Description : Returns the end position of the translation in cDNA
                  coordinates.
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                  If no transcript is given, the method will use
                  TranscriptAdaptor->fetch_by_translation_id() to locate
                  the correct transcript.
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    Return type : Integer
    Exceptions  : Throws if the given (optional) argument is not a
                  transcript.
    Caller      : General
    Status      : At Risk (Under Development)

=cut

sub cdna_end {
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  my ( $self, $transcript ) = @_;
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  if ( defined($transcript)
       && (    !ref($transcript)
            || !$transcript->isa('Bio::EnsEMBL::Transcript') ) )
  {
    throw("Argument is not a transcript");
  }
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  if ( !exists( $self->{'cdna_end'} ) ) {
    if ( !defined($transcript) ) {
      # We were not given a transcript, get the transcript out of
      # the database.
      $transcript = $self->transcript();
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    }

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    $self->{'cdna_end'} =
      $self->end_Exon()->cdna_coding_end($transcript);
  }

  return $self->{'cdna_end'};
}
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=head2 genomic_start

    Args        : None
    Example     : $translation_genomic_start =
                      $translation->genomic_start();
    Description : Returns the start position of the translation in
                  genomic coordinates on the forward strand.
    Return type : Integer
    Exceptions  : None
    Caller      : General
    Status      : At Risk (Under Development)

=cut

sub genomic_start {
    my $self = shift;

    if ( !exists $self->{'genomic_start'} ) {
        if ( $self->start_Exon()->strand() >= 0 ) {
            $self->{'genomic_start'} =
              $self->start_Exon()->start() + ( $self->start() - 1 );
        } else {
            $self->{'genomic_start'} =
              $self->end_Exon()->end() - ( $self->end() - 1 );
        }
    }

    return $self->{'genomic_start'};
}

=head2 genomic_end

    Args        : None
    Example     : $translation_genomic_end = $translation->genomic_end();
    Description : Returns the end position of the translation in genomic
                  coordinates on the forward strand.
    Return type : Integer
    Exceptions  : None
    Caller      : General
    Status      : At Risk (Under Development)

=cut

sub genomic_end {
    my $self = shift;

    if ( !exists $self->{'genomic_end'} ) {
        if ( $self->end_Exon()->strand() >= 0 ) {
            $self->{'genomic_end'} =
              $self->end_Exon()->start() + ( $self->end() - 1 );
        } else {
            $self->{'genomic_end'} =
              $self->start_Exon()->end() - ( $self->start() - 1 );
        }
    }

    return $self->{'genomic_end'};
}
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=head2 version
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  Arg [1]    : (optional) string $version - version to set
  Example    : $translation->version(2);
  Description: Getter/setter for attribute version
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  Returntype : string
  Exceptions : none
  Caller     : general
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  Status     : Stable
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=cut

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sub version {
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   my $self = shift;
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  $self->{'version'} = shift if( @_ );
  return $self->{'version'};
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}
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=head2 stable_id
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  Arg [1]    : (optional) string $stable_id - stable ID to set
  Example    : $translation->stable_id('ENSP0059890');
  Description: Getter/setter for attribute stable_id
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  Returntype : string
  Exceptions : none
  Caller     : general
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  Status     : Stable
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=cut

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

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=head2 created_date

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  Arg [1]    : (optional) string $created_date - created date to set
  Example    : $translation->created_date('2007-01-10 20:52:00');
  Description: Getter/setter for attribute created date
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  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut 

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


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=head2 modified_date

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  Arg [1]    : (optional) string $modified_date - modification date to set
  Example    : $translation->modified_date('2007-01-10 20:52:00');
  Description: Getter/setter for attribute modified date
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  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut 

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

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=head2 transform

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  Arg [1]    : hashref $old_new_exon_map
               a hash that maps old to new exons for a whole gene
  Description: maps start end end exon according to mapping table.
              If an exon is not mapped, just keep the old one.
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  Returntype: none
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  Exceptions : none
  Caller     : Transcript->transform() 
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  Status     : Stable
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=cut

sub transform {
  my $self = shift;
  my $href_exons = shift;

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  my $start_exon = $self->start_Exon();
  my $end_exon = $self->end_Exon();
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  if ( exists $href_exons->{$start_exon} ) {
    $self->start_Exon($href_exons->{$start_exon});
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  } else {
    # do nothing, the start exon wasnt mapped
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  }

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  if ( exists $href_exons->{$end_exon} ) {
    $self->end_Exon($href_exons->{$end_exon});
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  } else { 
    # do nothing, the end exon wasnt mapped
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  }
}

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=head2 get_all_DBEntries

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  Arg [1]    : (optional) $ex_db_exp - external db name
  Example    : @dbentries = @{$translation->get_all_DBEntries()};
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  Description: Retrieves DBEntries (xrefs) for this translation.  

               This method will attempt to lazy-load DBEntries from a
               database if an adaptor is available and no DBEntries are present
               on the translation (i.e. they have not already been added or 
               loaded).
  Returntype : list reference to Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : get_all_DBLinks, TranslationAdaptor::store
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  Status     : Stable
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=cut

sub get_all_DBEntries {
  my $self = shift;
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  my $ex_db_exp = shift;
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  my $ex_db_type = shift;
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  my $cache_name = "dbentries";

  if(defined($ex_db_exp)){
    $cache_name .= $ex_db_exp;
  }
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  if(defined($ex_db_type)){
    $cache_name .= $ex_db_type;
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  }
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  # if not cached, retrieve all of the xrefs for this gene
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  if(!defined $self->{$cache_name}) {
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    my $adaptor = $self->adaptor();
    my $dbID    = $self->dbID();
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    return [] if(!$adaptor || !$dbID);
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    $self->{$cache_name} =
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      $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Translation($self, $ex_db_exp, $ex_db_type);
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  }

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  $self->{$cache_name} ||= [];
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  return $self->{$cache_name};
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}


=head2 add_DBEntry

  Arg [1]    : Bio::EnsEMBL::DBEntry $dbe
               The dbEntry to be added
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  Example    : $translation->add_DBEntry($xref);
  Description: Associates a DBEntry with this translation. Note that adding
               DBEntries will prevent future lazy-loading of DBEntries for this
               translation (see get_all_DBEntries).
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  Returntype : none
  Exceptions : thrown on incorrect argument type
  Caller     : general
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  Status     : Stable
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=cut

sub add_DBEntry {
  my $self = shift;
  my $dbe = shift;

  unless($dbe && ref($dbe) && $dbe->isa('Bio::EnsEMBL::DBEntry')) {
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    throw('Expected DBEntry argument');
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  }

  $self->{'dbentries'} ||= [];
  push @{$self->{'dbentries'}}, $dbe;
}


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=head2 get_all_DBLinks

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  Arg [1]    : see get_all_DBEntries
  Example    : see get_all_DBEntries
  Description: This is here for consistancy with the Transcript and Gene 
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               classes. It is a synonym for the get_all_DBEntries method.
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  Returntype : see get_all_DBEntries
  Exceptions : none
  Caller     : general
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  Status     : Stable
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=cut

sub get_all_DBLinks {
  my $self = shift;
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  return $self->get_all_DBEntries(@_);
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}

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=head2 get_all_ProteinFeatures

  Arg [1]    : (optional) string $logic_name
               The analysis logic_name of the features to retrieve.  If not
               specified, all features are retrieved instead.
  Example    : $features = $self->get_all_ProteinFeatures('PFam');
  Description: Retrieves all ProteinFeatures associated with this 
               Translation. If a logic_name is specified, only features with 
               that logic_name are returned.  If no logic_name is provided all
               associated protein_features are returned.
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               ProteinFeatures are lazy-loaded from the database unless they
               added manually to the Translation or had already been loaded.
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  Returntype : Bio::EnsEMBL::ProteinFeature
  Exceptions : none
  Caller     : general
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  Status     : Stable
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=cut

sub get_all_ProteinFeatures {
  my $self = shift;
  my $logic_name = shift;

  if(!$self->{'protein_features'}) {
    my $adaptor = $self->adaptor();
    my $dbID    = $self->dbID();
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    return [] if (!$adaptor || !$dbID);
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    my %hash;
    $self->{'protein_features'} = \%hash;

    my $pfa = $adaptor->db()->get_ProteinFeatureAdaptor();
    my $name;
    foreach my $f (@{$pfa->fetch_all_by_translation_id($dbID)}) {
      my $analysis = $f->analysis();
      if($analysis) {
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        $name = lc($f->analysis->logic_name());
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      } else {
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        warning("ProteinFeature has no attached analysis\n");
        $name = '';
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      }
      $hash{$name} ||= [];
      push @{$hash{$name}}, $f;
    }
  }

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  # a specific type of protein feature was requested
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  if(defined($logic_name)) {
    $logic_name = lc($logic_name);
    return $self->{'protein_features'}->{$logic_name} || [];
  }

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  my @features = ();
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  # all protein features were requested
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  foreach my $type (keys %{$self->{'protein_features'}}) {
    push @features, @{$self->{'protein_features'}->{$type}};
  }

  return \@features;    
}


=head2 get_all_DomainFeatures

  Example    : @domain_feats = @{$translation->get_all_DomainFeatures};
  Description: A convenience method which retrieves all protein features
               that are considered to be 'Domain' features.  Features which
               are 'domain' features are those with analysis logic names:
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               'pfscan', 'scanprosite', 'superfamily', 'pfam', 'prints',
               'smart', 'pirsf', 'tigrfam'.
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  Returntype : listref of Bio::EnsEMBL::ProteinFeatures
  Exceptions : none
  Caller     : webcode (protview)
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  Status     : Stable
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=cut

sub get_all_DomainFeatures{
 my ($self) = @_;

 my @features;

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 my @types = ('pfscan',      #profile (prosite or pfam motifs)
              'scanprosite', #prosite
              'superfamily',
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              'pfam',
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              'smart',
              'tigrfam',
              'pirsf',
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              'prints');

 foreach my $type (@types) {
   push @features, @{$self->get_all_ProteinFeatures($type)};
 }

 return \@features;
}

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=head2 add_ProteinFeature

  Arg [1]    : Bio::EnsEMBL::ProteinFeature $pf
               The ProteinFeature to be added
  Example    : $translation->add_ProteinFeature($pf);
  Description: Associates a ProteinFeature with this translation. Note that
               adding ProteinFeatures will prevent future lazy-loading of
               ProteinFeatures for this translation (see
               get_all_ProteinFeatures).
  Returntype : none
  Exceptions : thrown on incorrect argument type
  Caller     : general
  Status     : Stable

=cut

sub add_ProteinFeature {
  my $self = shift;
  my $pf = shift;

  unless ($pf && ref($pf) && $pf->isa('Bio::EnsEMBL::ProteinFeature')) {
    throw('Expected ProteinFeature argument');
  }

  my $analysis = $pf->analysis;
  throw("ProteinFeature has no attached Analysis.") unless $analysis;

  push @{ $self->{'protein_features'}->{$analysis->logic_name} }, $pf;
}


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=head2 display_id

  Example    : print $translation->display_id();
  Description: This method returns a string that is considered to be
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               the 'display' identifier. For translations this is (depending on
               availability and in this order) the stable Id, the dbID or an
               empty string.
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  Returntype : string
  Exceptions : none
  Caller     : web drawing code
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  Status     : Stable
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=cut

sub display_id {
  my $self = shift;
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  return $self->{'stable_id'} || $self->dbID || '';
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}


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=head2 length

  Example    : print "Peptide length =", $translation->length();
  Description: Retrieves the length of the peptide sequence (i.e. number of
               amino acids) represented by this Translation object.
  Returntype : int
  Exceptions : none
  Caller     : webcode (protview etc.)
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  Status     : Stable
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=cut

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sub length {
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  my $self = shift;
  my $seq = $self->seq();
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  return ($seq) ? CORE::length($seq) : 0;
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}


=head2 seq

  Example    : print $translation->seq();
  Description: Retrieves a string representation of the peptide sequence
               of this Translation.  This retrieves the transcript from the
               database and gets its sequence, or retrieves the sequence which
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               was set via the constructor.
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  Returntype : string
  Exceptions : warning if the sequence is not set and cannot be retrieved from
               the database.
  Caller     : webcode (protview etc.)
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  Status     : Stable
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=cut

sub seq {
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  my ( $self, $sequence ) = @_;
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  if ( defined($sequence) ) {
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    $self->{'seq'} = $sequence;
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  } elsif ( !defined( $self->{'seq'} ) ) {
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    my $transcript = $self->transcript();
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    my $canonical_translation = $transcript->translation();
    my $is_alternative =
      ( $canonical_translation->stable_id() ne $self->stable_id() );
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    if ($is_alternative) {
      # To deal with non-canonical (alternative) translations, subsitute
      # the canonical translation in the transcript with $self for a
      # while.
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      $transcript->translation($self);
    }

    my $seq = $transcript->translate();
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    if ( defined($seq) ) {
      $self->{'seq'} = $seq->seq();
    }
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    if ($is_alternative) {
      # Reinstate the real canonical translation.

      $transcript->translation($canonical_translation);
    }

  } ## end elsif ( !defined( $self->...))
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  if ( !defined( $self->{'seq'} ) ) {
    return '';    # Empty string
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  }
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  return $self->{'seq'};

} ## end sub seq
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=head2 get_all_Attributes

  Arg [1]    : optional string $attrib_code
               The code of the attribute type to retrieve values for.
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  Example    : ($sc_attr) = @{$tl->get_all_Attributes('_selenocysteine')};
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               @tl_attributes = @{$translation->get_all_Attributes()};
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  Description: Gets a list of Attributes of this translation.
               Optionally just get Attrubutes for given code.
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               Recognized attribute "_selenocysteine"
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  Returntype : listref Bio::EnsEMBL::Attribute
  Exceptions : warning if translation does not have attached adaptor and 
               attempts lazy load.
  Caller     : general, modify_translation
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  Status     : Stable
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=cut

sub get_all_Attributes {
  my $self = shift;
  my $attrib_code = shift;

  if( ! exists $self->{'attributes' } ) {
    if(!$self->adaptor() ) {
#      warning('Cannot get attributes without an adaptor.');
      return [];
    }

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    my $aa = $self->adaptor->db->get_AttributeAdaptor();
    $self->{'attributes'} = $aa->fetch_all_by_Translation( $self );
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  }

  if( defined $attrib_code ) {
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    my @results = grep { uc($_->code()) eq uc($attrib_code) }
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    @{$self->{'attributes'}};
    return \@results;
  } else {
    return $self->{'attributes'};
  }
}


=head2 add_Attributes

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  Arg [1..N] : Bio::EnsEMBL::Attribute $attribute
               Attributes to add.
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  Example    : $translation->add_Attributes($selenocysteine_attribute);
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  Description: Adds an Attribute to the Translation. Usefull to 
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               do _selenocysteine.
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               If you add an attribute before you retrieve any from database, 
               lazy load will be disabled.
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  Returntype : none
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  Exceptions : throw on incorrect arguments
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  Caller     : general
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  Status     : Stable
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=cut

sub add_Attributes {
  my $self = shift;
  my @attribs = @_;

  if( ! exists $self->{'attributes'} ) {
    $self->{'attributes'} = [];
  }

  for my $attrib ( @attribs ) {
    if( ! $attrib->isa( "Bio::EnsEMBL::Attribute" )) {
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      throw( "Argument to add_Attribute must be a Bio::EnsEMBL::Attribute" );
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    }
    push( @{$self->{'attributes'}}, $attrib );
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    $self->{seq}=undef;
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  }
}

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=head2 get_all_SeqEdits
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  Example    : my @seqeds = @{$transcript->get_all_SeqEdits()};
  Description: Retrieves all post transcriptional sequence modifications for
               this transcript.
  Returntype : Bio::EnsEMBL::SeqEdit
  Exceptions : none
  Caller     : spliced_seq()
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  Status     : Stable
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=cut

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sub get_all_SeqEdits {
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  my $self = shift;

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  my @seqeds;
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  my $attribs;
  
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  my @edits = ('initial_met', '_selenocysteine', 'amino_acid_sub');
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  foreach my $edit(@edits){
    $attribs = $self->get_all_Attributes($edit);
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    # convert attributes to SeqEdit objects
    foreach my $a (@$attribs) {
      push @seqeds, Bio::EnsEMBL::SeqEdit->new(-ATTRIB => $a);
    }
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  }
  return \@seqeds;
}
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=head2 modify_translation

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  Arg [1]    : Bio::Seq $peptide 
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  Example    : my $seq = Bio::Seq->new(-SEQ => $dna)->translate();
               $translation->modify_translation($seq);
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  Description: Applies sequence edits such as selenocysteines to the Bio::Seq 
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               peptide thats passed in
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  Returntype : Bio::Seq
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  Exceptions : none
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  Caller     : Bio::EnsEMBL::Transcript->translate
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  Status     : Stable
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=cut

sub modify_translation {
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  my ( $self, $seq ) = @_;
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  my @seqeds = @{ $self->get_all_SeqEdits() };
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  # Sort in reverse order to avoid complication of adjusting
  # downstream edits.
  @seqeds = sort { $b->start() <=> $a->start() } @seqeds;
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  # Apply all edits.
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  my $peptide = $seq->seq();
  foreach my $se (@seqeds) {
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    $se->apply_edit( \$peptide );
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  }
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  $seq->seq($peptide);
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  return $seq;
}


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=head2 temporary_id

  Description: DEPRECATED This method should not be needed. Use dbID,
               stable_id or something else.

=cut

sub temporary_id {
   my $self = shift;
   deprecate( "I cant see what a temporary_id is good for, please use " .
               "dbID or stableID or\n try without an id." );
  $self->{'temporary_id'} = shift if( @_ );
  return $self->{'temporary_id'};
}


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=head2 get_all_DASFactories

  Function  : Retrieves a listref of registered DAS objects
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  Returntype: DAS objects
  Exceptions: none
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  Caller    : webcode
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  Example   : $dasref = $prot->get_all_DASFactories;
  Status    : Stable