Inheritance diagram for Bio::EnsEMBL::DBSQL::TranslationAdaptor:

Public Member Functions
public Listref	fetch_all_alternative_by_Transcript ()

public Bio::EnsEMBL::Translation	fetch_by_Transcript ()

public Reference	fetch_all_by_external_name ()


public Listref	fetch_all_by_GOTerm ()

public Listref	fetch_all_by_GOTerm_accession ()

public Int	store ()

public void	remove ()

public List	list_dbIDs ()

public Reference	list_stable_ids ()

protected ArrayRef	_list_dbIDs ()

public Bio::EnsEMBL::Translation	fetch_by_dbID ()

public Bio::EnsEMBL::Translation	fetch_by_stable_id ()

public Bio::EnsEMBL::Gene	fetch_by_stable_id_version ()

public Reference	fetch_all_by_Transcript_list ()

public Listref	fetch_all ()

protected	_tables ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()

public DBI::StatementHandle	prepare ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()

public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()

public Boolean	is_multispecies ()

public Int	species_id ()

protected	_list_dbIDs ()

protected	_straight_join ()

protected	_can_straight_join ()

public Listref	bind_param_generic_fetch ()

protected	_bind_param_generic_fetch ()

public String	generate_in_constraint ()

public Listref	generic_fetch ()

public Int	generic_count ()

protected	_generate_sql ()

public Bio::EnsEMBL::Feature	fetch_by_dbID ()

protected	_uncached_fetch_by_dbID ()

public Listref	fetch_all_by_dbID_list ()

protected	_uncached_fetch_all_by_dbID_list ()

protected ArrayRef	_uncached_fetch_all_by_id_list ()

public	fetch_all ()

public Scalar	last_insert_id ()

public	insert_ignore_clause ()

protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()

protected Boolean	_no_id_cache ()

public Boolean	ignore_cache_override ()

public Int	schema_version ()

protected	_tables ()

protected	_columns ()

protected	_default_where_clause ()

protected	_left_join ()

protected	_final_clause ()

protected	_objs_from_sth ()

protected	_build_id_cache ()

protected	_logic_name_to_constraint ()

Detailed Description

Description

This adaptor provides a means to retrieve and store
Bio::EnsEMBL::Translation objects from/in a database.

Translation objects only truly make sense in the context of their
transcripts so the recommended means to retrieve Translations is
by retrieving the Transcript object first, and then fetching the
Translation.

Synopsis

use Bio::EnsEMBL::Registry;
 
Bio::EnsEMBL::Registry->load_registry_from_db(
  -host => 'ensembldb.ensembl.org',
  -user => 'anonymous'
);
 
$transcript_adaptor =
  Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
  "transcript" );
 
$translation_adaptor =
  Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
  "translation" );
 
my $transcript = $transcript_adaptor->fetch_by_dbID(131243);
my $translation =
  $translation_adaptor->fetch_by_Transcript($transcript);
 
print("Translation Start Site: "
    . $translation->start_Exon()->stable_id() . " "
    . $translation->start()
    . "\n" );
print("Translation Stop: "
    . $translation->end_Exon()->stable_id() . " "
    . $translation->end() );

Definition at line 50 of file TranslationAdaptor.pm.

Member Function Documentation

◆ _list_dbIDs()

protected ArrayRef Bio::EnsEMBL::DBSQL::TranslationAdaptor::_list_dbIDs ( )

  Arg[1]      : String $table
  Arg[2]      : String $column
  Example     :

$transl_adaptor->_list_dbIDs('translation','translation_id');

  Description : Local reimplementation to ensure multi-species translations
                are limited to their species alone
  Returntype  : ArrayRef of specified IDs
  Caller      : Internal
  Status      : Unstable

Code:

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◆ _tables()

protected Bio::EnsEMBL::DBSQL::TranslationAdaptor::_tables ( )

Undocumented method

Code:

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◆ fetch_all()

public Listref Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all ( )

  Example     :

$translations = $translation_adaptor->fetch_all();

  Description : Retrieves all canonical and alternative translations 
                stored in the database.
  Returntype  : listref of Bio::EnsEMBL::Translation
  Caller      : general
  Status      : At Risk

Code:

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◆ fetch_all_alternative_by_Transcript()

public Listref Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all_alternative_by_Transcript ( )

  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
  Example    :

@tl = @{
  $translation_adaptor->fetch_all_alternative_by_Transcript(
                                                        $transcript)
  };

  Description: Retrieves all alternative translations associated with a
               particular transcript.  If no alternative translation is
               found, a reference to an empty list is returned.

  Returntype : listref of Bio::EnsEMBL::Translation
  Exceptions : throw on incorrect argument
  Caller     : Transcript
  Status     : Stable

Code:

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sub fetch_all_alternative_by_Transcript {
  my ( $self, $transcript ) = @_;
 
  assert_ref($transcript, 'Bio::EnsEMBL::Transcript');
 
  my $tl_created_date =
    $self->db()->dbc()->from_date_to_seconds('tl.created_date');
  my $tl_modified_date =
    $self->db()->dbc()->from_date_to_seconds('tl.modified_date');
 
  my $sql =
    sprintf( "SELECT tl.translation_id, tl.start_exon_id, "
      . "tl.end_exon_id, tl.seq_start, tl.seq_end, "
      . "tl.stable_id, tl.version, %s, %s "
      . "FROM translation tl "
      . "JOIN transcript t "
      . "ON (t.transcript_id = tl.transcript_id) "
      . "WHERE tl.transcript_id = ? "
      . "AND tl.translation_id != t.canonical_translation_id",
    $tl_created_date, $tl_modified_date );
 
  my $transcript_id = $transcript->dbID();
  my $sth           = $self->prepare($sql);
  $sth->bind_param( 1, $transcript_id, SQL_INTEGER );
 
  $sth->execute();
 
  my (
    $translation_id, $start_exon_id, $end_exon_id,
    $seq_start,      $seq_end,       $stable_id,
    $version,        $created_date,  $modified_date
  );
 
  $sth->bind_columns(
    \(
      $translation_id, $start_exon_id, $end_exon_id,
      $seq_start,      $seq_end,       $stable_id,
      $version,        $created_date,  $modified_date
    ) );
 
  # Get all alternative translations.
  my $translations = [];
  while ( $sth->fetch() ) {
    if ( !defined($translation_id) ) { next }
 
    my ( $start_exon, $end_exon );
 
    # this will load all the exons whenever we load the translation
    # but I guess thats ok ....
 
    foreach my $exon ( @{ $transcript->get_all_Exons() } ) {
      if ( $exon->dbID() == $start_exon_id ) { $start_exon = $exon }
      if ( $exon->dbID() == $end_exon_id )   { $end_exon   = $exon }
    }
 
    if ( !( defined($start_exon) && defined($end_exon) ) ) {
      throw(
        sprintf(
          "Could not find start or end exon in transcript_id=%d\n",
          $transcript->dbID() ) );
    }
 
    my $translation =
      Bio::EnsEMBL::Translation->new_fast( {
                             'dbID'          => $translation_id,
                             'adaptor'       => $self,
                             'start'         => $seq_start,
                             'end'           => $seq_end,
                             'start_exon'    => $start_exon,
                             'end_exon'      => $end_exon,
                             'stable_id'     => $stable_id,
                             'version'       => $version,
                             'created_date'  => $created_date || undef,
                             'modified_date' => $modified_date || undef,
                           } );
 
    $translation->transcript($transcript);
 
    push( @{$translations}, $translation );
 
  } ## end while ( $sth->fetch() )
 
  return $translations;
} ## end sub fetch_all_by_Transcript

◆ fetch_all_by_external_name()

public Reference Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all_by_external_name ( )

  Arg [1]    : string $external_name
               The external identifier for the translation(s) to be
               obtained.
  Arg [2]    : (optional) string $external_db_name
               The name of the external database from which the
               identifier originates.
  Arg [3]    : Boolean override. Force SQL regex matching for users
               who really do want to find all 'NM'
  Example    :

my @translations =
                 @{ $trl_adaptor->fetch_all_by_external_name('BRCA2') };
              my @many_translations = 
                 @{ $trl_adaptor->fetch_all_by_external_name('BRCA%') };

  Description: Retrieves a list of translations fetched via an
               external identifier.  Note that this may not be a
               particularly useful method, because translations
               do not make much sense out of the context of
               their transcript.  It may be better to use the
               TranscriptAdaptor::fetch_all_by_external_name instead.
               SQL wildcards % and _ are supported in the $external_name
               but their use is somewhat restricted for performance reasons.
               Users that really do want % and _ in the first three characters
               should use argument 3 to prevent optimisations
  Returntype : reference to a list of Translations
  Exceptions : none
  Caller     : general
  Status     : Medium Risk

Code:

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◆ fetch_all_by_GOTerm()

public Listref Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all_by_GOTerm ( )

  Arg [1]   : Bio::EnsEMBL::OntologyTerm
              The GO term for which translations should be fetched.

  Example:  @translations =
              $translation_adaptor->fetch_all_by_GOTerm(
                $go_adaptor->fetch_by_accession('GO:0030326') ) };

  Description   : Retrieves a list of translations that are
                  associated with the given GO term, or with any of
                  its descendent GO terms.

  Return type   : listref of Bio::EnsEMBL::Translation
  Exceptions    : Throws of argument is not a GO term
  Caller        : general
  Status        : Stable

Code:

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◆ fetch_all_by_GOTerm_accession()

public Listref Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all_by_GOTerm_accession ( )

  Arg [1]   : String
              The GO term accession for which genes should be
              fetched.

  Example   :

@genes =

 $gene_adaptor->fetch_all_by_GOTerm_accession('GO:0030326') };

  Description   : Retrieves a list of genes that are associated with
                  the given GO term, or with any of its descendent
                  GO terms.  The genes returned are in their native
                  coordinate system, i.e. in the coordinate system
                  in which they are stored in the database.  If
                  another coordinate system is required then the
                  Gene::transfer or Gene::transform method can be
                  used.

  Return type   : listref of Bio::EnsEMBL::Gene
  Exceptions    : Throws of argument is not a GO term accession
  Caller        : general
  Status        : Stable

Code:

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◆ fetch_all_by_Transcript_list()

public Reference Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all_by_Transcript_list ( )

  Arg [1]    : reference to list of Bio::EnsEMBL::Transcripts $transcripts
               The list of $transcripts to obtain Translation object for.
  Example    :

@translations = @{$tla->fetch_all_by_Transcript_list([$t1,$t2]);

  Description: Fetches all translations associated with the list of transcripts
               passed to this method.  The passed transcripts will also have
               their translation set by this method.
  Returntype : Reference to list of Bio::EnsEMBL::Translations
  Exceptions : None
  Caller     : general
  Status     : Stable

Code:

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sub fetch_all_by_Transcript_list {
  my ($self,$transcripts) = @_;
 
  if(!defined($transcripts) || ref($transcripts) ne 'ARRAY') {
    throw("reference to list of Transcripts argument is required");
  }
 
  return [] if(!@$transcripts);
 
  my %trans_hash = map {$_->dbID() => $_} @$transcripts;
  my @id_list = keys %trans_hash;
 
  my @out;
 
  # mysql is faster and we ensure that we do not exceed the max query size by
  # splitting large queries into smaller queries of 200 ids
  my $max_size = 200;
 
  my ( $transcript_id, $translation_id, $start_exon_id, $end_exon_id,
       $seq_start, $seq_end, $stable_id, $version, 
       $created_date, $modified_date );
 
  my %ex_hash;
 
  while(@id_list) {
    my @ids;
    if(@id_list > $max_size) {
      @ids = splice(@id_list, 0, $max_size);
    } else {
      @ids = splice(@id_list, 0);
    }
 
    my $id_str;
    if(@ids > 1)  {
      $id_str = " IN (" . join(',', @ids). ")";
    } else {
      $id_str = " = " . $ids[0];
    }
    
    my $canonical_lookup = $self->dbc()->sql_helper()->execute_into_hash(
      -SQL => 'SELECT transcript_id, canonical_translation_id FROM transcript WHERE transcript_id '.$id_str
    );
 
    my $created_date = $self->db->dbc->from_date_to_seconds("tl.created_date");
    my $modified_date = $self->db->dbc->from_date_to_seconds("tl.modified_date");
 
    my $sth = $self->prepare
      ("SELECT tl.transcript_id, tl.translation_id, tl.start_exon_id,
           tl.end_exon_id, tl.seq_start, tl.seq_end,
           tl.stable_id, tl.version, " . $created_date . "," .
       $modified_date . 
       " FROM translation tl
         WHERE tl.transcript_id $id_str");
 
    $sth->execute();
 
    $sth->bind_columns( \$transcript_id, \$translation_id, \$start_exon_id, \$end_exon_id,
                        \$seq_start, \$seq_end, \$stable_id, \$version,
            \$created_date, \$modified_date );
 
    while($sth->fetch()) {
      my ($start_exon, $end_exon);
 
      # this will load all the exons whenever we load the translation
      # but I guess thats ok ....
 
      my $tr = $trans_hash{$transcript_id};
 
      foreach my $exon (@{$tr->get_all_Exons()}) {
        if(!$start_exon && $exon->dbID() == $start_exon_id ) {
          $start_exon = $exon;
          last if($end_exon);
        }
 
        if(!$end_exon && $exon->dbID() == $end_exon_id ) {
          $end_exon = $exon;
          last if($start_exon);
        }
      }
 
      unless($start_exon && $end_exon) {
        throw("Could not find start or end exon in transcript\n");
      }
 
      my $tl =  Bio::EnsEMBL::Translation->new
        (-dbID => $translation_id,
         -seq_start => $seq_start,
         -seq_end => $seq_end,
         -start_exon => $start_exon,
         -end_exon => $end_exon,
         -stable_id => $stable_id,
         -version => $version,
     -created_date => $created_date || undef,
     -modified_date => $modified_date || undef);
 
      # Calling the new method will set $tl->version to '1' if $version is not defined.
      # But if the version in the database is NULL, $version will be undef; and so we
      # need to override the default version of '1', and set it back to undef.
      $tl->{version} = undef unless defined $version;
      
      $tl->adaptor($self);
      my $canonical_translation_id = $canonical_lookup->{$transcript_id};
      $tr->translation($tl) if $translation_id == $canonical_translation_id;
 
      push @out, $tl;
    }
  }
 
  return \@out;
}

◆ fetch_by_dbID()

public Bio::EnsEMBL::Translation Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_by_dbID ( )

  Arg [1]    : int $dbID
               The internal identifier of the Translation to obtain
  Example    :

$translation = $translation_adaptor->fetch_by_dbID(1234);

  Description: This fetches a Translation object via its internal id.
               This is only debatably useful since translations do
               not make much sense outside of the context of their
               Transcript.  Consider using fetch_by_Transcript instead.
  Returntype : Bio::EnsEMBL::Translation, or undef if the translation is not
               found.
  Exceptions : warning if an additional (old style) Transcript argument is
               provided
  Caller     : ?
  Status     : Stable

Code:

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◆ fetch_by_stable_id()

public Bio::EnsEMBL::Translation Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_by_stable_id ( )

  Arg [1]    : string $stable_id
               The stable identifier of the Translation to obtain
  Example    :

$translation = $translation_adaptor->fetch_by_stable_id("ENSP00001");

  Description: This fetches a Translation object via its stable id.
               This is only debatably useful since translations do
               not make much sense outside of the context of their
               Transcript.  Consider using fetch_by_Transcript instead.
  Returntype : Bio::EnsEMBL::Translation or undef if the translation is not
               found.
  Exceptions : warning if an additional (old style) Transcript argument is
               provided
  Caller     : ?
  Status     : Stable

Code:

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◆ fetch_by_stable_id_version()

public Bio::EnsEMBL::Gene Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_by_stable_id_version ( )

  Arg [1]    : String $id 
               The stable ID of the gene to retrieve
  Arg [2]    : Integer $version
               The version of the stable_id to retrieve
  Example    :

$gene = $gene_adaptor->fetch_by_stable_id('ENSG00000148944', 14);

  Description: Retrieves a gene object from the database via its stable id and version.
               The gene will be retrieved in its native coordinate system (i.e.
               in the coordinate system it is stored in the database). It may
               be converted to a different coordinate system through a call to
               transform() or transfer(). If the gene or exon is not found
               undef is returned instead.
  Returntype : Bio::EnsEMBL::Gene or undef
  Exceptions : if we cant get the gene in given coord system
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_Transcript()

public Bio::EnsEMBL::Translation Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_by_Transcript ( )

  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
  Example    :

$tl = $translation_adaptor->fetch_by_Transcript($transcript);

  Description: Retrieves a Translation via its associated transcript.
               If the Translation is not found, undef is returned.
  Returntype : Bio::EnsEMBL::Translation
  Exceptions : throw on incorrect argument
  Caller     : Transcript
  Status     : Stable

Code:

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sub fetch_by_Transcript {
  my ( $self, $transcript ) = @_;
 
  assert_ref( $transcript, 'Bio::EnsEMBL::Transcript' );
 
  my $tl_created_date =
    $self->db()->dbc()->from_date_to_seconds('tl.created_date');
  my $tl_modified_date =
    $self->db()->dbc()->from_date_to_seconds('tl.modified_date');
 
  my $sql =
    sprintf( "SELECT tl.translation_id, tl.start_exon_id, "
      . "tl.end_exon_id, tl.seq_start, tl.seq_end, "
      . "tl.stable_id, tl.version, %s, %s "
      . "FROM translation tl "
      . "JOIN transcript tr "
      . "ON (tl.translation_id = tr.canonical_translation_id) "
      . "WHERE tr.transcript_id = ?",
    $tl_created_date, $tl_modified_date );
 
  my $transcript_id = $transcript->dbID();
  my $sth           = $self->prepare($sql);
  $sth->bind_param( 1, $transcript_id, SQL_INTEGER );
 
  $sth->execute();
 
  my (
    $translation_id, $start_exon_id, $end_exon_id,
    $seq_start,      $seq_end,       $stable_id,
    $version,        $created_date,  $modified_date
  ) = $sth->fetchrow_array();
  $sth->finish();
 
  if ( !defined($translation_id) ) { return undef }
 
  my ( $start_exon, $end_exon );
 
  # this will load all the exons whenever we load the translation
  # but I guess thats ok ....
 
  foreach my $exon ( @{ $transcript->get_all_Exons() } ) {
    if ( $exon->dbID() == $start_exon_id ) { $start_exon = $exon }
    if ( $exon->dbID() == $end_exon_id )   { $end_exon   = $exon }
  }
 
  if ( !( defined($start_exon) && defined($end_exon) ) ) {
    throw(
      sprintf( "Could not find start or end exon in transcript_id=%d\n",
        $transcript->dbID() ) );
  }
 
  my $translation =
    Bio::EnsEMBL::Translation->new_fast( {
                             'dbID'          => $translation_id,
                             'adaptor'       => $self,
                             'start'         => $seq_start,
                             'end'           => $seq_end,
                             'start_exon'    => $start_exon,
                             'end_exon'      => $end_exon,
                             'stable_id'     => $stable_id,
                             'version'       => $version,
                             'created_date'  => $created_date || undef,
                             'modified_date' => $modified_date || undef,
                           } );
 
  $translation->transcript($transcript);
 
  return $translation;
} ## end sub fetch_by_Transcript

◆ list_dbIDs()

public List Bio::EnsEMBL::DBSQL::TranslationAdaptor::list_dbIDs ( )

  Arg [1]    : none
  Example    :

@translation_ids = @{$translation_adaptor->list_dbIDs()};

  Description: Gets an array of internal ids for all translations in the current db
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable

Code:

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◆ list_stable_ids()

public Reference Bio::EnsEMBL::DBSQL::TranslationAdaptor::list_stable_ids ( )

  Arg [1]    : none
  Example    :

@transl_stable_ids = @{$transl_adaptor->list_stable_dbIDs()};

  Description: Gets an array of stable ids for all translations in the current 
               db
  Returntype : reference to a list of strings
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ remove()

public void Bio::EnsEMBL::DBSQL::TranslationAdaptor::remove ( )

  Arg [1]    : Bio::EnsEMBL::Translation $translation
  Example    :

$translation_adaptor->remove($translation);

  Description: Removes a translation completely from the database, and all
               associated information including protein features etc.
  Returntype : none
  Exceptions : throw on incorrect arguments
               warning if translation is not in this database
  Caller     : TranscriptAdaptor::remove
  Status     : Stable

Code:

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◆ store()

public Int Bio::EnsEMBL::DBSQL::TranslationAdaptor::store ( )

  Arg [1]    : Bio::EnsEMBL::Translation $translation
               The translation object to be stored in the database 
  Example    :

$transl_id = $translation_adaptor->store($translation);

  Description: Stores a translation object in the database
  Returntype : int - the new dbID of the stored translation
  Exceptions : thrown if the dbID of the start_Exon or end_Exon is not 
               defined.
               thrown if only partial stable id information is present (e.g.
               identifier but not version number)
  Caller     : Transcript::store
  Status     : Stable

Code:

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sub store {
  my ( $self, $translation, $transcript_id )  = @_;
  
  my $start_exon = $translation->start_Exon();
  my $end_exon   = $translation->end_Exon();
 
  if(!$start_exon) {
    throw("Translation must define a start_Exon to be stored.");
  }
 
  if(!$end_exon) {
    throw("Translation must define an end_Exon to be stored.");
  }
 
  if(!$start_exon->dbID) {
    throw("start_Exon must have a dbID for Translation to be stored.");
  }
 
  if(!$end_exon->dbID) {
    throw("end_Exon must have a dbID for Translation to be stored.");
  }
 
  my @columns = qw(
                 seq_start
                 start_exon_id
                 seq_end
                 end_exon_id
                 transcript_id
  );
 
  my @canned_columns;
  my @canned_values;
 
  if (defined($translation->stable_id)) {
      push @columns, 'stable_id', 'version';
 
      my $created = $self->db->dbc->from_seconds_to_date($translation->created_date());
      my $modified = $self->db->dbc->from_seconds_to_date($translation->modified_date());
 
      if ($created) {
    push @canned_columns, 'created_date';
    push @canned_values,  $created;
      }
      if ($modified) {
    push @canned_columns, 'modified_date';
    push @canned_values,  $modified;
      }
  }
 
  my $columns = join(', ', @columns, @canned_columns);
  my $values  = join(', ', ('?') x @columns, @canned_values);
  my $store_translation_sql = qq(
        INSERT INTO translation ( $columns ) VALUES ( $values )
  );
 
  my $sth = $self->prepare($store_translation_sql);
  $sth->bind_param(1,$translation->start,SQL_INTEGER);
  $sth->bind_param(2,$translation->start_Exon->dbID,SQL_INTEGER);
  $sth->bind_param(3,$translation->end,SQL_INTEGER);
  $sth->bind_param(4,$translation->end_Exon->dbID,SQL_INTEGER);
  $sth->bind_param(5,$transcript_id,SQL_INTEGER);
 
 
  if (defined($translation->stable_id)) {
 
    $sth->bind_param(6, $translation->stable_id,SQL_VARCHAR);
    $sth->bind_param(7, $translation->version,SQL_VARCHAR);
  }
 
  $sth->execute();
 
  my $transl_dbID = $self->last_insert_id('translation_id', undef, 'translation');
 
  #
  # store object xref mappings to translations
  #
 
  my $dbEntryAdaptor = $self->db()->get_DBEntryAdaptor();
  # store each of the xrefs for this translation
  foreach my $dbl ( @{$translation->get_all_DBEntries} ) {
     $dbEntryAdaptor->store( $dbl, $transl_dbID, "Translation", 1 );
  }
 
  #storing the protein features associated with the translation
  my $pfadaptor = $self->db->get_ProteinFeatureAdaptor();
  foreach my $pf(@{$translation->get_all_ProteinFeatures}){
    $pfadaptor->store($pf, $transl_dbID);
  }
 
  $translation->get_all_Attributes();
 
  # store any translation attributes that are defined
  my $attr_adaptor = $self->db->get_AttributeAdaptor();
  $attr_adaptor->store_on_Translation($transl_dbID,
                                      $translation->get_all_Attributes());
 
  $translation->dbID($transl_dbID);
  $translation->adaptor($self);
 
  return $transl_dbID;
}

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm

Public Member Functions

Detailed Description

Description

Synopsis

Member Function Documentation

◆ _list_dbIDs()

◆ _tables()

◆ fetch_all()

◆ fetch_all_alternative_by_Transcript()

◆ fetch_all_by_external_name()

◆ fetch_all_by_GOTerm()

◆ fetch_all_by_GOTerm_accession()

◆ fetch_all_by_Transcript_list()

◆ fetch_by_dbID()

◆ fetch_by_stable_id()

◆ fetch_by_stable_id_version()

◆ fetch_by_Transcript()

◆ list_dbIDs()

◆ list_stable_ids()

◆ remove()

◆ store()