Inheritance diagram for Bio::EnsEMBL::DBSQL::TranscriptAdaptor:

Class Summary

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' );

  $transcript = $transcript_adaptor-\>fetch_by_dbID(1234);

  $transcript =
    $transcript_adaptor-\>fetch_by_stable_id('ENST00000201961');

  $slice =
    $slice_adaptor-\>fetch_by_region( 'Chromosome', '3', 1, 1000000 );
  @transcripts = @{ $transcript_adaptor-\>fetch_all_by_Slice($slice) };

  ($transcript) =
    @{ $transcript_adaptor-\>fetch_all_by_external_name('NP_065811.1') };

Description

This adaptor provides a means to retrieve and store information related
to Transcripts.  Primarily this involves the retrieval or storage of
Bio::EnsEMBL::Transcript objects from a database.

See Bio::EnsEMBL::Transcript for details of the Transcript class.

Definition at line 46 of file TranscriptAdaptor.pm.

Available Methods
protected	_check_start_end_strand ()
protected	_columns ()
protected	_create_feature ()
protected	_create_feature_fast ()
protected	_default_where_clause ()
protected	_final_clause ()
protected	_left_join ()
protected	_list_dbIDs ()
protected	_list_seq_region_ids ()
protected	_logic_name_to_constraint ()
protected	_max_feature_length ()
protected	_objs_from_sth ()
protected	_pre_store ()
protected	_pre_store_userdata ()
protected	_remap ()
protected Bio::EnsEMBL::Utils::Cache	_slice_feature_cache ()
protected	_slice_fetch ()
protected	_straight_join ()
protected	_tables ()
public Listref	bind_param_generic_fetch ()
public void	clear_cache ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public	dump_data ()
public	fetch_all ()
public	fetch_all_by_DBEntry ()
public Listref	fetch_all_by_dbID_list ()
public Listref	fetch_all_by_exon_stable_id ()
public Listref	fetch_all_by_exon_supporting_evidence ()
public Listref	fetch_all_by_external_name ()
public Listref	fetch_all_by_Gene ()
public Listref	fetch_all_by_GOTerm ()
public Listref	fetch_all_by_GOTerm_accession ()
public Listref	fetch_all_by_logic_name ()
public	fetch_all_by_RawContig ()
public	fetch_all_by_RawContig_and_score ()
public	fetch_all_by_RawContig_constraint ()
public Listref	fetch_all_by_Slice ()
public Listref	fetch_all_by_Slice_and_score ()
public Listref	fetch_all_by_Slice_constraint ()
public Listref	fetch_all_by_transcript_supporting_evidence ()
public Listref	fetch_all_versions_by_stable_id ()
public Bio::EnsEMBL::Feature	fetch_by_dbID ()
public Bio::EnsEMBL::Transcript	fetch_by_display_label ()
public Bio::EnsEMBL::Transcript	fetch_by_stable_id ()
public Bio::EnsEMBL::Transcript	fetch_by_translation_id ()
public Bio::EnsEMBL::Transcript	fetch_by_translation_stable_id ()
public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice ()
public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice_method ()
public Listref	generic_fetch ()
public	get_display_xref ()
public	get_dumped_data ()
public Listref	get_Interpro_by_transid ()
public	get_seq_region_id_external ()
public	get_seq_region_id_internal ()
public	get_stable_entry_info ()
public Boolean	is_multispecies ()
public Boolean	is_Transcript_canonical ()
public Scalar	last_insert_id ()
public	list_dbIDs ()
public Listref	list_stable_ids ()
public Bio::EnsEMBL::BaseFeatureAdaptor	new ()
public DBI::StatementHandle	prepare ()
public void	remove ()
public	remove_by_analysis_id ()
public	remove_by_feature_id ()
public	remove_by_RawContig ()
public void	remove_by_Slice ()
public Int	species_id ()
public Boolean	start_equals_end ()
public Int	store ()
public void	update ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_check_start_end_strand ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::TranscriptAdaptor::_columns ( )

Undocumented method

Code:

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_create_feature ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_create_feature_fast ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause ( ) [inherited]

Undocumented method

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause ( ) [inherited]

Undocumented method

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, and Bio::EnsEMBL::DBSQL::PredictionExonAdaptor.

protected Bio::EnsEMBL::DBSQL::TranscriptAdaptor::_left_join ( )

Undocumented method

Code:

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_list_dbIDs ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_list_seq_region_ids ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_logic_name_to_constraint ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_max_feature_length ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::TranscriptAdaptor::_objs_from_sth ( )

Undocumented method

Code:

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sub _objs_from_sth {
  my ($self, $sth, $mapper, $dest_slice) = @_;

  #
  # This code is ugly because an attempt has been made to remove as many
  # function calls as possible for speed purposes.  Thus many caches and
  # a fair bit of gymnastics is used.
  #

  my $sa = $self->db()->get_SliceAdaptor();
  my $aa = $self->db->get_AnalysisAdaptor();
  my $dbEntryAdaptor = $self->db()->get_DBEntryAdaptor();

  my @transcripts;
  my %analysis_hash;
  my %slice_hash;
  my %sr_name_hash;
  my %sr_cs_hash;

  my (
    $transcript_id,  $seq_region_id,      $seq_region_start,
    $seq_region_end, $seq_region_strand,  $analysis_id,
    $gene_id,        $is_current,         $stable_id,
    $version,        $created_date,       $modified_date,
    $description,    $biotype,            $status,
    $external_db,    $external_status,    $external_db_name,
    $xref_id,        $xref_display_label, $xref_primary_acc,
    $xref_version,   $xref_description,   $xref_info_type,
    $xref_info_text
  );

  $sth->bind_columns(
    \(
      $transcript_id,  $seq_region_id,      $seq_region_start,
      $seq_region_end, $seq_region_strand,  $analysis_id,
      $gene_id,        $is_current,         $stable_id,
      $version,        $created_date,       $modified_date,
      $description,    $biotype,            $status,
      $external_db,    $external_status,    $external_db_name,
      $xref_id,        $xref_display_label, $xref_primary_acc,
      $xref_version,   $xref_description,   $xref_info_type,
      $xref_info_text
    ) );

  my $asm_cs;
  my $cmp_cs;
  my $asm_cs_vers;
  my $asm_cs_name;
  my $cmp_cs_vers;
  my $cmp_cs_name;
  if($mapper) {
    $asm_cs = $mapper->assembled_CoordSystem();
    $cmp_cs = $mapper->component_CoordSystem();
    $asm_cs_name = $asm_cs->name();
    $asm_cs_vers = $asm_cs->version();
    $cmp_cs_name = $cmp_cs->name();
    $cmp_cs_vers = $cmp_cs->version();
  }

  my $dest_slice_start;
  my $dest_slice_end;
  my $dest_slice_strand;
  my $dest_slice_length;
  my $dest_slice_cs;
  my $dest_slice_sr_name;
  my $dest_slice_sr_id;

  my $asma;
  if($dest_slice) {
    $dest_slice_start  = $dest_slice->start();
    $dest_slice_end    = $dest_slice->end();
    $dest_slice_strand = $dest_slice->strand();
    $dest_slice_length = $dest_slice->length();
    $dest_slice_cs     = $dest_slice->coord_system();
    $dest_slice_sr_name = $dest_slice->seq_region_name();
    $dest_slice_sr_id   = $dest_slice->get_seq_region_id();
    $asma              = $self->db->get_AssemblyMapperAdaptor();
  }

  FEATURE: while($sth->fetch()) {

    #get the analysis object
    my $analysis = $analysis_hash{$analysis_id} ||=
      $aa->fetch_by_dbID($analysis_id);
    #need to get the internal_seq_region, if present
    $seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
    my $slice = $slice_hash{"ID:".$seq_region_id};
    my $dest_mapper = $mapper;

    if(!$slice) {
      $slice = $sa->fetch_by_seq_region_id($seq_region_id);
      $slice_hash{"ID:".$seq_region_id} = $slice;
      $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
      $sr_cs_hash{$seq_region_id} = $slice->coord_system();
    }

    #obtain a mapper if none was defined, but a dest_seq_region was
    if(!$dest_mapper && $dest_slice && 
       !$dest_slice_cs->equals($slice->coord_system)) {
      $dest_mapper = $asma->fetch_by_CoordSystems($dest_slice_cs,
                                                 $slice->coord_system);
      $asm_cs = $dest_mapper->assembled_CoordSystem();
      $cmp_cs = $dest_mapper->component_CoordSystem();
      $asm_cs_name = $asm_cs->name();
      $asm_cs_vers = $asm_cs->version();
      $cmp_cs_name = $cmp_cs->name();
      $cmp_cs_vers = $cmp_cs->version();
    }

    my $sr_name = $sr_name_hash{$seq_region_id};
    my $sr_cs   = $sr_cs_hash{$seq_region_id};
    #
    # remap the feature coordinates to another coord system 
    # if a mapper was provided
    #
    if($dest_mapper) {

      ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
        $dest_mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
                              $seq_region_strand, $sr_cs);

      #skip features that map to gaps or coord system boundaries
      next FEATURE if(!defined($seq_region_id));

      #get a slice in the coord system we just mapped to
      if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
        $slice = $slice_hash{"ID:".$seq_region_id} ||=
          $sa->fetch_by_seq_region_id($seq_region_id);
      } else {
        $slice = $slice_hash{"ID:".$seq_region_id} ||=
          $sa->fetch_by_seq_region_id($seq_region_id);
      }
    }

    #
    # If a destination slice was provided convert the coords.
    #
    if (defined($dest_slice)) {
      if ( $dest_slice_strand == 1 ) {
        $seq_region_start = $seq_region_start - $dest_slice_start + 1;
        $seq_region_end   = $seq_region_end - $dest_slice_start + 1;

        if ( $dest_slice->is_circular ) {
          if ( $seq_region_start > $seq_region_end ) {
            # Looking at a feature overlapping the chromsome origin.
            if ( $seq_region_end > $dest_slice_start ) {
              # Looking at the region in the beginning of the chromosome
              $seq_region_start -= $dest_slice->seq_region_length();
            }
            if ( $seq_region_end < 0 ) {
              $seq_region_end += $dest_slice->seq_region_length();
            }
          } else {
            if (    $dest_slice_start > $dest_slice_end
                 && $seq_region_end < 0 )
            {
              # Looking at the region overlapping the chromosome
              # origin and a feature which is at the beginning of the
              # chromosome.
              $seq_region_start += $dest_slice->seq_region_length();
              $seq_region_end   += $dest_slice->seq_region_length();
            }
          }
        }
      } else {
        if (    $dest_slice->is_circular()
             && $seq_region_start > $seq_region_end )
        {
          if ( $seq_region_end > $dest_slice_start ) {
            # Looking at the region in the beginning of the chromosome.
            $seq_region_start = $dest_slice_end - $seq_region_end + 1;
            $seq_region_end =
              $seq_region_end -
              $dest_slice->seq_region_length() -
              $dest_slice_start + 1;
          } else {
            my $tmp_seq_region_start = $seq_region_start;
            $seq_region_start =
              $dest_slice_end -
              $seq_region_end -
              $dest_slice->seq_region_length() + 1;
            $seq_region_end =
              $dest_slice_end - $tmp_seq_region_start + 1;
          }

        } else {
          my $tmp_seq_region_start = $seq_region_start;
          $seq_region_start = $dest_slice_end - $seq_region_end + 1;
          $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
        }

        $seq_region_strand = -$seq_region_strand;
      } ## end else [ if ( $dest_slice_strand...)]

      # Throw away features off the end of the requested slice
      if (    $seq_region_end < 1
           || $seq_region_start > $dest_slice_length
           || ( $dest_slice_sr_id ne $seq_region_id ) )
      {
        next FEATURE;
      }

      $slice = $dest_slice;
    }

    my $display_xref;

    if ($xref_id) {
      $display_xref = Bio::EnsEMBL::DBEntry->new_fast( {
          'dbID'            => $xref_id,
          'display_id'      => $xref_display_label,
          'primary_id'      => $xref_primary_acc,
          'version'         => $xref_version,
          'description'     => $xref_description,
          'info_type'       => $xref_info_type,
          'info_text'       => $xref_info_text,
          'adaptor'         => $dbEntryAdaptor,
          'db_display_name' => $external_db_name,
          'dbname'          => $external_db
      } );
    }


    # Finally, create the new Transcript.
    push(
      @transcripts,
      $self->_create_feature_fast(
        'Bio::EnsEMBL::Transcript',
        {
          'analysis'              => $analysis,
          'start'                 => $seq_region_start,
          'end'                   => $seq_region_end,
          'strand'                => $seq_region_strand,
          'adaptor'               => $self,
          'slice'                 => $slice,
          'dbID'                  => $transcript_id,
          'stable_id'             => $stable_id,
          'version'               => $version,
          'created_date'          => $created_date || undef,
          'modified_date'         => $modified_date || undef,
          'external_name'         => $xref_display_label,
          'external_db'           => $external_db,
          'external_status'       => $external_status,
          'external_display_name' => $external_db_name,
          'display_xref'          => $display_xref,
          'description'           => $description,
          'biotype'               => $biotype,
          'status'                => $status,
          'is_current'            => $is_current,
          'edits_enabled'         => 1
        } ) );

  }

  return \@transcripts;
}

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_pre_store ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_pre_store_userdata ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_remap ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::Utils::Cache Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_slice_feature_cache ( ) [inherited]

 
  Description	: Returns the feature cache if we are allowed to cache and
                will build it if we need to. We will never return a reference
                to the hash to avoid unintentional auto-vivfying caching
  Returntype 	: Bio::EnsEMBL::Utils::Cache
  Exceptions 	: None
  Caller     	: Internal

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_slice_fetch ( ) [inherited]

Undocumented method

Code:

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sub _slice_fetch {
  my ( $self, $slice, $orig_constraint ) = @_;

  my $slice_start         = $slice->start();
  my $slice_end           = $slice->end();
  my $slice_strand        = $slice->strand();
  my $slice_cs            = $slice->coord_system();
  my $slice_seq_region    = $slice->seq_region_name();
  my $slice_seq_region_id = $slice->get_seq_region_id();

  #get the synonym and name of the primary_table
  my @tabs = $self->_tables;
  my ( $tab_name, $tab_syn ) = @{ $tabs[0] };

  #find out what coordinate systems the features are in
  my $mcc      = $self->db->get_MetaCoordContainer();
  my @feat_css = ();

  my $mca        = $self->db->get_MetaContainer();
  my $value_list = $mca->list_value_by_key( $tab_name . "build.level" );
  if ( @$value_list and $slice->is_toplevel() ) {
    push @feat_css, $slice_cs;
  } else {
    @feat_css =
      @{ $mcc->fetch_all_CoordSystems_by_feature_type($tab_name) };
  }

  my $asma = $self->db->get_AssemblyMapperAdaptor();
  my @features;

  # fetch the features from each coordinate system they are stored in
COORD_SYSTEM: foreach my $feat_cs (@feat_css) {
    my $mapper;
    my @coords;
    my @ids;

    if ( $feat_cs->equals($slice_cs) ) {
      # no mapping is required if this is the same coord system

      my $max_len = $self->_max_feature_length()
        || $mcc->fetch_max_length_by_CoordSystem_feature_type( $feat_cs,
                                                            $tab_name );

      my $constraint = $orig_constraint;

      my $sr_id;
      if ( $slice->adaptor() ) {
        $sr_id = $slice->adaptor()->get_seq_region_id($slice);
      } else {
        $sr_id =
          $self->db()->get_SliceAdaptor()->get_seq_region_id($slice);
      }

      # If there is mapping information, use the external_seq_region_id
      # to get features.

      my @sr_ids = ($sr_id);

      while (1) {
        my $ext_sr_id = $self->get_seq_region_id_external($sr_id);

        if ( $ext_sr_id == $sr_id ) { last }

        push( @sr_ids, $ext_sr_id );
        $sr_id = $ext_sr_id;
      }

      $constraint .= " AND " if ($constraint);

      
      $constraint .= "${tab_syn}.seq_region_id IN ("
          . join( ',', @sr_ids ) . ") AND";

      #faster query for 1bp slices where SNP data is not compressed
      if ( $self->start_equals_end && $slice_start == $slice_end ) {
      $constraint .=
          " AND ${tab_syn}.seq_region_start = $slice_end" .
          " AND ${tab_syn}.seq_region_end = $slice_start";

      } else {

      if ( !$slice->is_circular() ) {
          # Deal with the default case of a non-circular chromosome.
          $constraint .= " ${tab_syn}.seq_region_start <= $slice_end AND "
          . "${tab_syn}.seq_region_end >= $slice_start";

          if ( $max_len ) {
          my $min_start = $slice_start - $max_len;
          $constraint .= " AND ${tab_syn}.seq_region_start >= $min_start";
          }

      } else {
          # Deal with the case of a circular chromosome.
          if ( $slice_start > $slice_end ) {
          $constraint .= " ( ${tab_syn}.seq_region_start >= $slice_start "
              . "OR ${tab_syn}.seq_region_start <= $slice_end "
              . "OR ${tab_syn}.seq_region_end >= $slice_start "
              . "OR ${tab_syn}.seq_region_end <= $slice_end "
              . "OR ${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end)";

          } else {
          $constraint .= " ((${tab_syn}.seq_region_start <= $slice_end "
              . "AND ${tab_syn}.seq_region_end >= $slice_start) "
              . "OR (${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end "
              . "AND (${tab_syn}.seq_region_start <= $slice_end "
              . "OR ${tab_syn}.seq_region_end >= $slice_start)))";
          }
      }

      }

      my $fs = $self->generic_fetch( $constraint, undef, $slice );

    # features may still have to have coordinates made relative to slice
    # start
      $fs = $self->_remap( $fs, $mapper, $slice );

      push @features, @$fs;
    } else {
      $mapper = $asma->fetch_by_CoordSystems( $slice_cs, $feat_cs );

      next unless defined $mapper;

      # Get list of coordinates and corresponding internal ids for
      # regions the slice spans
      @coords =
        $mapper->map( $slice_seq_region, $slice_start, $slice_end,
                      $slice_strand, $slice_cs );

      @coords = grep { !$_->isa('Bio::EnsEMBL::Mapper::Gap') } @coords;

      next COORD_SYSTEM if ( !@coords );

      @ids = map { $_->id() } @coords;
      #coords are now id rather than name
      #      @ids = @{$asma->seq_regions_to_ids($feat_cs, \@ids)};

      # When regions are large and only partially spanned
      # by slice it is faster to to limit the query with
      # start and end constraints.  Take simple approach:
      # use regional constraints if there are less than a
      # specific number of regions covered.

      if ( @coords > $MAX_SPLIT_QUERY_SEQ_REGIONS ) {
        my $constraint = $orig_constraint;
        my $id_str = join( ',', @ids );
        $constraint .= " AND " if ($constraint);
        $constraint .= "${tab_syn}.seq_region_id IN ($id_str)";
        my $fs = $self->generic_fetch( $constraint, $mapper, $slice );

        $fs = $self->_remap( $fs, $mapper, $slice );

        push @features, @$fs;

      } else {
        # do multiple split queries using start / end constraints

        my $max_len = (
                $self->_max_feature_length()
                  || $mcc->fetch_max_length_by_CoordSystem_feature_type(
                                                     $feat_cs, $tab_name
                  ) );

        my $len = @coords;
        for ( my $i = 0; $i < $len; $i++ ) {
          my $constraint = $orig_constraint;
          $constraint .= " AND " if ($constraint);
          $constraint .=
              "${tab_syn}.seq_region_id = "
            . $ids[$i] . " AND "
            . "${tab_syn}.seq_region_start <= "
            . $coords[$i]->end() . " AND "
            . "${tab_syn}.seq_region_end >= "
            . $coords[$i]->start();

          if ($max_len) {
            my $min_start = $coords[$i]->start() - $max_len;
            $constraint .=
              " AND ${tab_syn}.seq_region_start >= $min_start";
          }
          my $fs = $self->generic_fetch( $constraint, $mapper, $slice );

          $fs = $self->_remap( $fs, $mapper, $slice );

          push @features, @$fs;
        }
      } ## end else [ if ( @coords > $MAX_SPLIT_QUERY_SEQ_REGIONS)]
    } ## end else [ if ( $feat_cs->equals(...))]
  } ## end foreach my $feat_cs (@feat_css)

  return \@features;
} ## end sub _slice_fetch

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join ( ) [inherited]

Undocumented method

Code:

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

Undocumented method

Code:

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::bind_param_generic_fetch ( ) [inherited]

 Arg [1]   : (optional)  scalar $param
              This is the parameter to bind
 Arg [2]   : (optional) int $sql_type
              Type of the parameter (from DBI (:sql_types))
 Example   :  $adaptor->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
              $adaptor->generic_fetch();
 Description:  When using parameters for the query, will call the bind_param to avoid
               some security issues. If there are no arguments, will return the bind_parameters
 ReturnType : listref
 Exceptions:  if called with one argument

Code:

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public void Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::clear_cache ( ) [inherited]

  Args      : None
  Example   : my $sa =
                $registry->get_adaptor( 'Mus musculus', 'Core',
                                        'Slice' );
              my $ga =
                $registry->get_adaptor( 'Mus musculus', 'Core',
                                        'Gene' );

              my $slice =
                $sa->fetch_by_region( 'Chromosome', '1', 1e8,
                                      1.05e8 );

              my $genes = $ga->fetch_all_by_Slice($slice);

              $ga->clear_cache();

  Description   : Empties the feature cache associated with this
                  feature adaptor.
  Return type   : None
  Exceptions    : None
  Caller        : General
  Status        : At risk (under development)

Code:

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public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::db ( ) [inherited]

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $obj 
               the database this adaptor is using.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::DBSQL::BaseAdaptor::dbc ( ) [inherited]

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBConnection $obj 
               the database this adaptor is using.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBConnection
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::BaseAdaptor::dump_data ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all ( )

Undocumented method

Code:

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_DBEntry ( )

  Description:
Deprecated:
. Use fetch_all_by_external_name() instead.

Code:

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public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all_by_dbID_list ( ) [inherited]

  Arg [1]    : listref of integers $id_list
               The unique database identifiers for the features to
               be obtained.
  Arg [2]    : optional - Bio::EnsEMBL::Slice to map features onto.
  Example    : @feats = @{$adaptor->fetch_all_by_dbID_list([1234, 2131, 982]))};
  Description: Returns the features created from the database
               defined by the the IDs in contained in the provided
               ID list $id_list.  The features will be returned
               in their native coordinate system.  That is, the
               coordinate system in which they are stored in the
               database.  In order to convert the features to a
               particular coordinate system use the transfer() or
               transform() method.  If none of the features are
               found in the database a reference to an empty list is
               returned.
  Returntype : listref of Bio::EnsEMBL::Features
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::OntologyTermAdaptor.

public Listref Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_exon_stable_id ( )

  Arg [1]    : String $stable_id 
               The stable id of an exon in a transcript
  Example    : my $tr = $tr_adaptor->fetch_all_by_exon_stable_id
                  ('ENSE00000309301');
  Description: Retrieves a list of transcripts via an exon stable id.
  Returntype : Listref of Bio::EnsEMBL::Transcript objects
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_exon_supporting_evidence ( )

  Arg [1]    : String $hit_name
               Name of supporting feature
  Arg [2]    : String $feature_type 
               one of "dna_align_feature" or "protein_align_feature"
  Arg [3]    : (optional) Bio::Ensembl::Analysis
  Example    : $tr = $tr_adaptor->fetch_all_by_exon_supporting_evidence
                  ('XYZ', 'dna_align_feature');
  Description: Gets all the transcripts with exons which have a specified hit
               on a particular type of feature. Optionally filter by analysis.
  Returntype : Listref of Bio::EnsEMBL::Transcript objects
  Exceptions : If feature_type is not of correct type.
  Caller     : general
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_external_name ( )

  Arg [1]    : String $external_name
               An external identifier of the transcript to be obtained
  Arg [2]    : (optional) String $external_db_name
               The name of the external database from which the
               identifier originates.
  Example    : my @transcripts =
                  @{ $tr_adaptor->fetch_all_by_external_name( 'NP_065811.1') };
               my @more_transcripts = 
                  @{$tr_adaptor->fetch_all_by_external_name( 'NP_0658__._')};
  Description: Retrieves all transcripts which are associated with
               an external identifier such as a GO term, Swissprot
               identifer, etc.  Usually there will only be a single
               transcript returned in the list reference, but not
               always.  Transcripts are returned in their native
               coordinate system, i.e. the coordinate system in which
               they are stored in the database.  If they are required
               in another coordinate system the Transcript::transfer or
               Transcript::transform method can be used to convert them.
               If no transcripts with the external identifier are found,
               a reference to an empty list is returned.
               SQL wildcards % and _ are supported in the $external_name
  Returntype : listref of Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_Gene ( )

  Arg [1]    : Bio::EnsEMBL::Gene $gene
               The gene to fetch transcripts of
  Example    : my $gene = $gene_adaptor->fetch_by_stable_id('ENSG0000123');
               my @transcripts = { $tr_adaptor->fetch_all_by_Gene($gene) };
  Description: Retrieves Transcript objects for given gene. Puts Genes slice
               in each Transcript. 
  Returntype : Listref of Bio::EnsEMBL::Transcript objects
  Exceptions : none
  Caller     : Gene->get_all_Transcripts()
  Status     : Stable

Code:

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

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

  Example:  @transcripts = @{
              $transcript_adaptor->fetch_all_by_GOTerm(
                $go_adaptor->fetch_by_accession('GO:0030326') ) };

  Description   : Retrieves a list of transcripts that are
                  associated with the given GO term, or with any of
                  its descendent GO terms.  The transcripts 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 Transcript::transfer or
                  Transcript::transform method can be used.

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

Code:

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public Listref Bio::EnsEMBL::DBSQL::TranscriptAdaptor::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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public Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_logic_name ( ) [inherited]

  Arg [3]    : string $logic_name
               the logic name of the type of features to obtain
  Example    : $fs = $a->fetch_all_by_logic_name('foobar');
  Description: Returns a listref of features created from the database.
               only features with an analysis of type $logic_name will
               be returned.  If the logic name is invalid (not in the
               analysis table), a reference to an empty list will be
               returned.
  Returntype : listref of Bio::EnsEMBL::SeqFeatures
  Exceptions : thrown if no $logic_name
  Caller     : General
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig ( ) [inherited]

Description:

Deprecated:: use fetch_all_by_Slice instead

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_and_score ( ) [inherited]

Description:

Deprecated:: use fetch_all_by_Slice_and_score instead

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_constraint ( ) [inherited]

Description:

Deprecated:: use fetch_all_by_RawContig_constraint instead

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public Listref Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_Slice ( )

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice to fetch transcripts on
  Arg [2]    : (optional) Boolean $load_exons
               If true, exons will be loaded immediately rather than
               lazy loaded later
  Arg [3]    : (optional) String $logic_name
               The logic name of the type of features to obtain
  ARG [4]    : (optional) String $constraint
               An extra contraint.
  Example    : my @transcripts = @{ $tr_adaptor->fetch_all_by_Slice($slice) };
  Description: Overrides superclass method to optionally load exons
               immediately rather than lazy-loading them later. This
               is more efficient when there are a lot of transcripts whose
               exons are going to be used.
  Returntype : Listref of Bio::EnsEMBL::Transcript objects
  Exceptions : thrown if exon cannot be placed on transcript slice
  Caller     : Slice::get_all_Transcripts
  Status     : Stable

Code:

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sub fetch_all_by_Slice {
  my ( $self, $slice, $load_exons, $logic_name, $constraint ) = @_;

  my $transcripts;
  if ( defined($constraint) && $constraint ne '' ) {
    $transcripts = $self->SUPER::fetch_all_by_Slice_constraint( $slice,
      't.is_current = 1 AND ' . $constraint, $logic_name );
  } else {
    $transcripts = $self->SUPER::fetch_all_by_Slice_constraint( $slice,
      't.is_current = 1', $logic_name );
  }

  # if there are 0 or 1 transcripts still do lazy-loading
  if ( !$load_exons || @$transcripts < 2 ) {
    return $transcripts;
  }

  # preload all of the exons now, instead of lazy loading later
  # faster than 1 query per transcript

  # first check if the exons are already preloaded
  # @todo FIXME: Should test all exons.
  if ( exists( $transcripts->[0]->{'_trans_exon_array'} ) ) {
    return $transcripts;
  }

  # get extent of region spanned by transcripts
  my ( $min_start, $max_end );
  foreach my $tr (@$transcripts) {
    if ( !defined($min_start) || $tr->seq_region_start() < $min_start )
    {
      $min_start = $tr->seq_region_start();
    }
    if ( !defined($max_end) || $tr->seq_region_end() > $max_end ) {
      $max_end = $tr->seq_region_end();
    }
  }

  my $ext_slice;

  if ( $min_start >= $slice->start() && $max_end <= $slice->end() ) {
    $ext_slice = $slice;
  } else {
    my $sa = $self->db()->get_SliceAdaptor();
    $ext_slice = $sa->fetch_by_region(
      $slice->coord_system->name(), $slice->seq_region_name(),
      $min_start,                   $max_end,
      $slice->strand(),             $slice->coord_system->version() );
  }

  # associate exon identifiers with transcripts

  my %tr_hash = map { $_->dbID => $_ } @{$transcripts};

  my $tr_id_str = join( ',', keys(%tr_hash) );

  my $sth =
    $self->prepare( "SELECT transcript_id, exon_id, rank "
      . "FROM exon_transcript "
      . "WHERE transcript_id IN ($tr_id_str)" );

  $sth->execute();

  my ( $tr_id, $ex_id, $rank );
  $sth->bind_columns( \( $tr_id, $ex_id, $rank ) );

  my %ex_tr_hash;

  while ( $sth->fetch() ) {
    $ex_tr_hash{$ex_id} ||= [];
    push( @{ $ex_tr_hash{$ex_id} }, [ $tr_hash{$tr_id}, $rank ] );
  }

  my $ea    = $self->db()->get_ExonAdaptor();
  my $exons = $ea->fetch_all_by_Slice_constraint(
    $ext_slice,
    sprintf( "e.exon_id IN (%s)",
      join( ',', sort { $a <=> $b } keys(%ex_tr_hash) ) ) );

  # move exons onto transcript slice, and add them to transcripts
  foreach my $ex ( @{$exons} ) {
    my $new_ex;
    if ( $slice != $ext_slice ) {
      $new_ex = $ex->transfer($slice);
      if ( !defined($new_ex) ) {
        throw("Unexpected. "
            . "Exon could not be transfered onto Transcript slice." );
      }
    } else {
      $new_ex = $ex;
    }

    foreach my $row ( @{ $ex_tr_hash{ $new_ex->dbID() } } ) {
      my ( $tr, $rank ) = @{$row};
      $tr->add_Exon( $new_ex, $rank );
    }
  }

  my $tla = $self->db()->get_TranslationAdaptor();

  # load all of the translations at once
  $tla->fetch_all_by_Transcript_list($transcripts);

  return $transcripts;
} ## end sub fetch_all_by_Slice

Reimplemented from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_and_score ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) float $score
               lower bound of the the score of the features retrieved
  Arg [3]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Example    : $fts = $a->fetch_all_by_Slice_and_score($slice,90,'Swall');
  Description: Returns a list of features created from the database which are 
               are on the Slice defined by $slice and which have a score 
               greater than $score. If $logic_name is defined, 
               only features with an analysis of type $logic_name will be 
               returned. 
  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
  Exceptions : none
  Caller     : Bio::EnsEMBL::Slice
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_constraint ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [3]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Example    : $fs = $a->fetch_all_by_Slice_constraint($slc, 'perc_ident > 5');
  Description: Returns a listref of features created from the database which 
               are on the Slice defined by $slice and fulfill the SQL 
               constraint defined by $constraint. If logic name is defined, 
               only features with an analysis of type $logic_name will be 
               returned. 
  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
  Exceptions : thrown if $slice is not defined
  Caller     : Bio::EnsEMBL::Slice
  Status     : Stable

Code:

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sub fetch_all_by_Slice_constraint {
  my ( $self, $slice, $constraint, $logic_name ) = @_;


  my @result = ();

  if ( !ref($slice)
       || !(    $slice->isa('Bio::EnsEMBL::Slice')
             or $slice->isa('Bio::EnsEMBL::LRGSlice') ) )
  {
    throw("Bio::EnsEMBL::Slice argument expected.");
  }

  $constraint ||= '';
  $constraint =
    $self->_logic_name_to_constraint( $constraint, $logic_name );

  # If the logic name was invalid, undef was returned
  if ( !defined($constraint) ) { return [] }

  my $key;
  my $cache;

  # Will only use feature_cache if hasn't been no_cache attribute set
  if (
    !( defined( $self->db()->no_cache() ) && $self->db()->no_cache() ) )
  {

    #strain test and add to constraint if so to stop caching.
    if ( $slice->isa('Bio::EnsEMBL::StrainSlice') ) {
      my $string =
        $self->dbc()->db_handle()->quote( $slice->strain_name() );

      if ( $constraint ne "" ) {
        $constraint .= " AND $string = $string ";
      } else {
        $constraint .= " $string = $string ";
      }
    }

    # Check the cache and return the cached results if we have already
    # done this query.  The cache key is the made up from the slice
    # name, the constraint, and the bound parameters (if there are any).
    $key = uc( join( ':', $slice->name(), $constraint ) );

    my $bind_params = $self->bind_param_generic_fetch();

    if ( defined($bind_params) ) {
      $key .= ':'
        . join( ':', map { $_->[0] . '/' . $_->[1] } @{$bind_params} );
    }

    $cache = $self->_slice_feature_cache();
    if ( exists( $cache->{$key} ) ) {
      # Clear the bound parameters and return the cached data.
      $self->{'_bind_param_generic_fetch'} = ();
      return $cache->{$key};
    }
  } ## end if ( !( defined( $self...)))

  my $sa = $slice->adaptor();

  # Hap/PAR support: retrieve normalized 'non-symlinked' slices.
  my @proj = @{ $sa->fetch_normalized_slice_projection($slice) };


 
  if ( !@proj ) {
    throw( 'Could not retrieve normalized Slices. '
         . 'Database contains incorrect assembly_exception information.'
    );
  }

  # Want to get features on the FULL original slice as well as any
  # symlinked slices.

  # Filter out partial slices from projection that are on same
  # seq_region as original slice.

  my $sr_id = $slice->get_seq_region_id();

  @proj = grep { $_->to_Slice->get_seq_region_id() != $sr_id } @proj;

  my $segment = bless( [ 1, $slice->length(), $slice ],
                       'Bio::EnsEMBL::ProjectionSegment' );
  push( @proj, $segment );

  # construct list of Hap/PAR boundaries for entire seq region
  my @bounds;

  my $ent_slice = $sa->fetch_by_seq_region_id($sr_id);
  if ( $slice->strand() == -1 ) {
    $ent_slice = $ent_slice->invert();
  }

  my @ent_proj =
    @{ $sa->fetch_normalized_slice_projection($ent_slice) };
  shift(@ent_proj);    # skip first

  @bounds = map { $_->from_start() - $slice->start() + 1 } @ent_proj;


  # fetch features for the primary slice AND all symlinked slices
  foreach my $seg (@proj) {


    my $offset    = $seg->from_start();
    my $seg_slice = $seg->to_Slice();
    my $features =
      $self->_slice_fetch( $seg_slice, $constraint );

    # If this was a symlinked slice offset the feature coordinates as
    # needed.
    if ( $seg_slice->name() ne $slice->name() ) {

    FEATURE:
      foreach my $f ( @{$features} ) {
        if ( $offset != 1 ) {
          $f->{'start'} += $offset - 1;
          $f->{'end'}   += $offset - 1;
        }

        # discard boundary crossing features from symlinked regions
        foreach my $bound (@bounds) {
          if ( $f->{'start'} < $bound && $f->{'end'} >= $bound ) {
            next FEATURE;
          }
        }

        $f->{'slice'} = $slice;
        push( @result, $f );
      }
    } else {
      push( @result, @{$features} );
    }
  } ## end foreach my $seg (@proj)

  # Will only use feature_cache when set attribute no_cache in DBAdaptor
  if ( defined($key) ) {
    $cache->{$key} = \@result;
  }

  return \@result;
} ## end sub fetch_all_by_Slice_constraint

public Listref Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_transcript_supporting_evidence ( )

  Arg [1]    : String $hit_name
               Name of supporting feature
  Arg [2]    : String $feature_type 
               one of "dna_align_feature" or "protein_align_feature"
  Arg [3]    : (optional) Bio::Ensembl::Analysis
  Example    : $transcripts = $transcript_adaptor->fetch_all_by_transcript_supporting_evidence('XYZ', 'dna_align_feature');
  Description: Gets all the transcripts with evidence from a specified hit_name on a particular type of feature, stored in the  
               transcript_supporting_feature table. Optionally filter by analysis.  For hits stored in the supporting_feature 
               table (linked to exons) use fetch_all_by_exon_supporting_evidence instead.
  Returntype : Listref of Bio::EnsEMBL::Transcript objects
  Exceptions : If feature_type is not of correct type.
  Caller     : general
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_versions_by_stable_id ( )

  Arg [1]     : String $stable_id 
                The stable ID of the transcript to retrieve
  Example     : my $tr = $tr_adaptor->fetch_all_version_by_stable_id
                  ('ENST00000309301');
  Description : Similar to fetch_by_stable_id, but retrieves all versions of a
                transcript stored in the database.
  Returntype  : listref of Bio::EnsEMBL::Transcript objects
  Exceptions  : if we cant get the gene in given coord system
  Caller      : general
  Status      : At Risk

Code:

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public Bio::EnsEMBL::Feature Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_by_dbID ( ) [inherited]

  Arg [1]    : int $id
               The unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234));
               $feat = $feat->transform('contig');
  Description: Returns the feature created from the database defined by the
               the id $id.  The feature will be returned in its native
               coordinate system.  That is, the coordinate system in which it
               is stored in the database.  In order to convert it to a
               particular coordinate system use the transfer() or transform()
               method.  If the feature is not found in the database then
               undef is returned instead
  Returntype : Bio::EnsEMBL::Feature or undef
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Transcript Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_by_display_label ( )

  Arg [1]    : String $label - display label of transcript to fetch
  Example    : my $tr = $tr_adaptor->fetch_by_display_label("BRCA2");
  Description: Returns the transcript which has the given display label or
               undef if there is none. If there are more than 1, only the first
               is reported.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Transcript Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_by_stable_id ( )

  Arg [1]    : String $stable_id 
               The stable id of the transcript to retrieve
  Example    : my $tr = $tr_adaptor->fetch_by_stable_id('ENST00000309301');
  Description: Retrieves a transcript via its stable id.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Transcript Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_by_translation_id ( )

  Arg [1]    : Int $id
               The internal identifier of the translation whose transcript
               is to be retrieved
  Example    : my $tr = $tr_adaptor->fetch_by_translation_id($transl->dbID);
  Description: Given the internal identifier of a translation this method 
               retrieves the transcript associated with that translation.
               If the transcript cannot be found undef is returned instead.
  Returntype : Bio::EnsEMBL::Transcript or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Transcript Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_by_translation_stable_id ( )

  Arg [1]    : String $transl_stable_id
               The stable identifier of the translation of the transcript to 
               retrieve
  Example    : my $tr = $tr_adaptor->fetch_by_translation_stable_id
                  ('ENSP00000311007');
  Description: Retrieves a Transcript object using the stable identifier of
               its translation.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_Iterator_by_Slice ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : Optional string: logic name of analysis
  Arg [3]    : Optional int: Chunk size to iterate over. Default is 500000
  Example    : my $slice_iter = $feature_adaptor->fetch_Iterator_by_Slice($slice);

               while(my $feature = $slice_iter->next && defined $feature){
                 #Do something here
               }

  Description: Creates an Iterator which chunks the query Slice to facilitate
               large Slice queries which would have previously run out of memory
  Returntype : Bio::EnsEMBL::Utils::Iterator
  Exceptions : None
  Caller     : general
  Status     : at risk

Code:

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public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_Iterator_by_Slice_method ( ) [inherited]

  Arg [1]    : CODE ref of Slice fetch method
  Arg [2]    : ARRAY ref of parameters for Slice fetch method
  Arg [3]    : Optional int: Slice index in parameters array
  Arg [4]    : Optional int: Slice chunk size. Default=500000
  Example    : my $slice_iter = $feature_adaptor->fetch_Iterator_by_Slice_method
                               	      ($feature_adaptor->can('fetch_all_by_Slice_Arrays'),
	                                   \@fetch_method_params,
	                                   0,#Slice idx
	                                  );

               while(my $feature = $slice_iter->next && defined $feature){
                 #Do something here
               }

  Description: Creates an Iterator which chunks the query Slice to facilitate
               large Slice queries which would have previously run out of memory
  Returntype : Bio::EnsEMBL::Utils::Iterator
  Exceptions : Throws if mandatory params not valid
  Caller     : general
  Status     : at risk

Code:

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public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch ( ) [inherited]

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) Bio::EnsEMBL::AssemblyMapper $mapper
               A mapper object used to remap features
               as they are retrieved from the database
  Arg [3]    : (optional) Bio::EnsEMBL::Slice $slice
               A slice that features should be remapped to
  Example    : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch
  Status     : Stable

Code:

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sub generic_fetch {
  my ($self, $constraint, $mapper, $slice) = @_;

  my @tabs = $self->_tables();

  my $extra_default_where;

  # Hack for feature types that needs to be restricted to species_id (in
  # coord_system).
  if (    $self->is_multispecies()
       && $self->isa('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor')
       && !$self->isa('Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor') )
  {
    # We do a check to see if there is already seq_region
    # and coord_system defined to ensure we get the right
    # alias.  We then do the extra query irrespectively of
    # what has already been specified by the user.
    my %thash = map { $_->[0] => $_->[1] } @tabs;

    my $sr_alias =
      ( exists( $thash{seq_region} ) ? $thash{seq_region} : 'sr' );
    my $cs_alias =
      ( exists( $thash{coord_system} ) ? $thash{coord_system} : 'cs' );

    if ( !exists( $thash{seq_region} ) ) {
      push( @tabs, [ 'seq_region', $sr_alias ] );
    }
    if ( !exists( $thash{coord_system} ) ) {
      push( @tabs, [ 'coord_system', $cs_alias ] );
    }

    $extra_default_where = sprintf(
                      '%s.seq_region_id = %s.seq_region_id '
                        . 'AND %s.coord_system_id = %s.coord_system_id '
                        . 'AND %s.species_id = ?',
                      $tabs[0]->[1], $sr_alias, $sr_alias,
                      $cs_alias,     $cs_alias );

    $self->bind_param_generic_fetch( $self->species_id(), SQL_INTEGER );
  } ## end if ( $self->is_multispecies...)

  my $columns = join(', ', $self->_columns());

  my $db = $self->db();

  #
  # Construct a left join statement if one was defined, and remove the
  # left-joined table from the table list
  #
  my @left_join_list = $self->_left_join();
  my $left_join_prefix = '';
  my $left_join = '';
  my @tables;
  if(@left_join_list) {
    my %left_join_hash = map { $_->[0] => $_->[1] } @left_join_list;
    while(my $t = shift @tabs) {
        my $t_alias = $t->[0] . " " . $t->[1];
      if( exists $left_join_hash{ $t->[0] } || exists $left_join_hash{$t_alias}) {
        my $condition = $left_join_hash{ $t->[0] };
        $condition ||= $left_join_hash{$t_alias};
        my $syn = $t->[1];
        $left_join .=
          "\n  LEFT JOIN " . $t->[0] . " $syn ON $condition ) ";
        $left_join_prefix .= '(';
      } else {
        push @tables, $t;
      }
    }
  } else {
    @tables = @tabs;
  }

  my $straight_join = '';

  if($self->_straight_join()) {
    $straight_join = "STRAIGHT_JOIN";
  }

  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));

  my $sql =
      "SELECT $straight_join $columns\n"
    . "FROM $left_join_prefix ($tablenames) $left_join";

  my $default_where = $self->_default_where_clause();
  my $final_clause = $self->_final_clause;

  if ($extra_default_where) {
    if ($default_where) {
      $default_where .= "\n AND $extra_default_where";
    } else {
      $default_where = $extra_default_where;
    }
  }

  #append a where clause if it was defined
  if ($constraint) {
    $sql .= "\n WHERE $constraint ";
    if ($default_where) {
      $sql .= " AND\n       $default_where ";
    }
  } elsif ($default_where) {
    $sql .= "\n WHERE $default_where ";
  }

  #append additional clauses which may have been defined
  $sql .= "\n$final_clause";


  # FOR DEBUG:
  #printf(STDERR "SQL:\n%s\n", $sql);
  
  
  my $sth = $db->dbc->prepare($sql);
  my $bind_parameters = $self->bind_param_generic_fetch();
  if (defined $bind_parameters){
      #if we have bind the parameters, call the DBI to bind them
      my $i = 1;
      foreach my $param (@{$bind_parameters}){
        $sth->bind_param($i,$param->[0],$param->[1]);
        $i++;
      }
      #after binding parameters, undef for future queries
      $self->{'_bind_param_generic_fetch'} = ();
  }
  eval { $sth->execute() };
  if ($@) {
    throw("Detected an error whilst executing SQL '${sql}': $@");
  }

  my $res = $self->_objs_from_sth($sth, $mapper, $slice);
  $sth->finish();
  return $res;
}

Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor.

public Bio::EnsEMBL::DBSQL::TranscriptAdaptor::get_display_xref ( )

  Description:
Deprecated:
. Use $transcript->display_xref() instead.

Code:

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public Bio::EnsEMBL::DBSQL::BaseAdaptor::get_dumped_data ( ) [inherited]

Undocumented method

Code:

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public Listref Bio::EnsEMBL::DBSQL::TranscriptAdaptor::get_Interpro_by_transid ( )

  Arg [1]    : String $trans_stable_id
               The stable if of the transcript to obtain
  Example    : @i = $tr_adaptor->get_Interpro_by_transid($trans->stable_id()); 
  Description: Gets interpro accession numbers by transcript stable id.
               A hack really - we should have a much more structured 
               system than this.
  Returntype : listref of strings (Interpro_acc:description)
  Exceptions : none 
  Caller     : domainview? , GeneView
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::get_seq_region_id_external ( ) [inherited]

Undocumented method

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::get_seq_region_id_internal ( ) [inherited]

Undocumented method

Code:

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public Bio::EnsEMBL::DBSQL::TranscriptAdaptor::get_stable_entry_info ( )

  Description:
Deprecated:
. Use $transcript->stable_id() instead.

Code:

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public Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::is_multispecies ( ) [inherited]

  Arg [1]    : (optional) boolean $arg
  Example    : if ($adaptor->is_multispecies()) { }
  Description: Getter/Setter for the is_multispecies boolean of
               to use for this adaptor.
  Returntype : boolean
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Boolean Bio::EnsEMBL::DBSQL::TranscriptAdaptor::is_Transcript_canonical ( )

  Arg [1]     : Bio::EnsEMBL::Transcript $transcript
                The transcript to query with
  Example     : $tr_adaptor->is_Transcript_canonical($transcript);
  Description : Returns a boolean if the given transcript is considered
                canonical with respect to a gene
  Returntype  : Boolean
  Exceptions  : None
  Caller      : Bio::EnsEMBL::Transcript
  Status      : Beta

Code:

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public Scalar Bio::EnsEMBL::DBSQL::BaseAdaptor::last_insert_id ( ) [inherited]

  Arg [1]     : (optional) $field the name of the field the inserted ID was pushed 
                into
  Arg [2]     : (optional) HashRef used to pass extra attributes through to the 
                DBD driver
  Description : Delegating method which uses DBI to extract the last inserted 
                identifier. If using MySQL we just call the DBI method 
                DBI::last_insert_id() since MySQL ignores any extra
                arguments. See DBI for more information about this 
                delegated method. 
  Example     : my $id = $self->last_insert_id('my_id'); my $other_id = $self->last_insert_id();
  Returntype  : Scalar or undef

Code:

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public Bio::EnsEMBL::DBSQL::TranscriptAdaptor::list_dbIDs ( )

  Example    : @transcript_ids = @{ $t_adaptor->list_dbIDs };
  Description: Gets a list of internal ids for all transcripts in the db.
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.  Returntype : Listref of Ints
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::DBSQL::TranscriptAdaptor::list_stable_ids ( )

  Example    : @stable_trans_ids = @{ $transcript_adaptor->list_stable_ids };
  Description: Gets a list of stable ids for all transcripts in the current
               database.
  Returntype : Listref of Strings
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::BaseFeatureAdaptor Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::new ( ) [inherited]

  Arg [1]    : list of args @args
               Superclass constructor arguments
  Example    : none
  Description: Constructor which warns if caching has been switched off
  Returntype : Bio::EnsEMBL::BaseFeatureAdaptor
  Exceptions : none
  Caller     : implementing subclass constructors
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

Reimplemented in Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, and Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor.

public DBI::StatementHandle Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare ( ) [inherited]

  Arg [1]    : string $string
               a SQL query to be prepared by this adaptors database
  Example    : $sth = $adaptor->prepare("select yadda from blabla")
  Description: provides a DBI statement handle from the adaptor. A convenience
               function so you dont have to write $adaptor->db->prepare all the
               time
  Returntype : DBI::StatementHandle
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::SliceAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

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

  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
               The transcript to remove from the database
  Example    : $tr_adaptor->remove($transcript);
  Description: Removes a transcript completely from the database, and all
               associated information.
               This method is usually called by the GeneAdaptor::remove method
               because this method will not preform the removal of genes
               which are associated with this transcript. Do not call this
               method directly unless you know there are no genes associated
               with the transcript!
  Returntype : none
  Exceptions : throw on incorrect arguments
               warning if transcript is not in this database
  Caller     : GeneAdaptor::remove
  Status     : Stable

Code:

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sub remove {
  my $self = shift;
  my $transcript = shift;

  if(!ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript')) {
    throw("Bio::EnsEMBL::Transcript argument expected");
  }

  # sanity check: make sure nobody tries to slip past a prediction transcript
  # which inherits from transcript but actually uses different tables
  if($transcript->isa('Bio::EnsEMBL::PredictionTranscript')) {
    throw("TranscriptAdaptor can only remove Transcripts " .
          "not PredictionTranscripts");
  }

  if ( !$transcript->is_stored($self->db()) ) {
    warning("Cannot remove transcript ". $transcript->dbID .". Is not stored ".
            "in this database.");
    return;
  }

  # remove the supporting features of this transcript

  my $prot_adp = $self->db->get_ProteinAlignFeatureAdaptor;
  my $dna_adp = $self->db->get_DnaAlignFeatureAdaptor;

  my $sfsth = $self->prepare("SELECT feature_type, feature_id  " .
                             "FROM transcript_supporting_feature " .
                             "WHERE transcript_id = ?");

  $sfsth->bind_param(1, $transcript->dbID, SQL_INTEGER);
  $sfsth->execute();

  # statements to check for shared align_features
  my $sth1 = $self->prepare("SELECT count(*) FROM supporting_feature " .
                "WHERE feature_type = ? AND feature_id = ?");
  my $sth2 = $self->prepare("SELECT count(*) " .
                            "FROM transcript_supporting_feature " .
                "WHERE feature_type = ? AND feature_id = ?");

  SUPPORTING_FEATURE:
  while(my ($type, $feature_id) = $sfsth->fetchrow()){
    
    # only remove align_feature if this is the last reference to it
    $sth1->bind_param(1, $type, SQL_VARCHAR);
    $sth1->bind_param(2, $feature_id, SQL_INTEGER);
    $sth1->execute;
    $sth2->bind_param(1, $type, SQL_VARCHAR);
    $sth2->bind_param(2, $feature_id, SQL_INTEGER);
    $sth2->execute;
    my ($count1) = $sth1->fetchrow;
    my ($count2) = $sth2->fetchrow;
    if ($count1 + $count2 > 1) {
      #warn "transcript: shared feature, not removing $type|$feature_id\n";
      next SUPPORTING_FEATURE;
    }
    
    #warn "transcript: removing $type|$feature_id\n";
  
    if($type eq 'protein_align_feature'){
      my $f = $prot_adp->fetch_by_dbID($feature_id);
      $prot_adp->remove($f);
    }
    elsif($type eq 'dna_align_feature'){
      my $f = $dna_adp->fetch_by_dbID($feature_id);
      $dna_adp->remove($f);
    }
    else {
      warning("Unknown supporting feature type $type. Not removing feature.");
    }
  }
  $sfsth->finish();
  $sth1->finish();
  $sth2->finish();

  # delete the association to supporting features

  $sfsth = $self->prepare("DELETE FROM transcript_supporting_feature WHERE transcript_id = ?");
  $sfsth->bind_param(1, $transcript->dbID, SQL_INTEGER);
  $sfsth->execute();
  $sfsth->finish();

  # remove all xref linkages to this transcript

  my $dbeAdaptor = $self->db->get_DBEntryAdaptor();
  foreach my $dbe (@{$transcript->get_all_DBEntries}) {
    $dbeAdaptor->remove_from_object($dbe, $transcript, 'Transcript');
  }

  # remove the attributes associated with this transcript
  my $attrib_adp = $self->db->get_AttributeAdaptor;  
  $attrib_adp->remove_from_Transcript($transcript);

  # remove the translation associated with this transcript

  my $translationAdaptor = $self->db->get_TranslationAdaptor();
  if( defined($transcript->translation()) ) {
    $translationAdaptor->remove( $transcript->translation );
  }

  # remove exon associations to this transcript

  my $exonAdaptor = $self->db->get_ExonAdaptor();
  foreach my $exon ( @{$transcript->get_all_Exons()} ) {
    # get the number of transcript references to this exon
    # only remove the exon if this is the last transcript to
    # reference it

    my $sth = $self->prepare( "SELECT count(*)
                               FROM   exon_transcript
                               WHERE  exon_id = ?" );
    $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
    $sth->execute();
    my ($count) = $sth->fetchrow_array();
    $sth->finish();

    if($count == 1){
      $exonAdaptor->remove( $exon );
    }
  }

  my $sth = $self->prepare( "DELETE FROM exon_transcript
                             WHERE transcript_id = ?" );
  $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
  $sth->execute();
  $sth->finish();


  $sth = $self->prepare( "DELETE FROM transcript
                          WHERE transcript_id = ?" );
  $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
  $sth->execute();
  $sth->finish();

  $transcript->dbID(undef);
  $transcript->adaptor(undef);

  return;
}

Reimplemented from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor.

public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_analysis_id ( ) [inherited]

Undocumented method

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_feature_id ( ) [inherited]

Undocumented method

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_RawContig ( ) [inherited]

Description:

Deprecated:: use remove_by_Slice instead

Code:

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public void Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_Slice ( ) [inherited]

  Arg [1]    : Bio::Ensembl::Slice $slice
  Example    : $feature_adaptor->remove_by_Slice($slice);
  Description: This removes features from the database which lie on a region
               represented by the passed in slice.  Only features which are
               fully contained by the slice are deleted; features which overlap
               the edge of the slice are not removed.
               The table the features are removed from is defined by
               the abstract method_tablename.
  Returntype : none
  Exceptions : thrown if no slice is supplied
  Caller     : general
  Status     : Stable

Code:

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public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::species_id ( ) [inherited]

  Arg [1]    : (optional) int $species_id
               The internal ID of the species in a multi-species database.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the internal ID of the species in a
               multi-species database.  The default species ID is 1.
  Returntype : Integer
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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public Boolean Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::start_equals_end ( ) [inherited]

  Arg [1]    : (optional) boolean $newval
  Example    : $bfa->start_equals_end(1);
  Description: Getter/Setter for the start_equals_end flag.  If set
               to true sub _slice_fetch will use a simplified sql to retrieve 1bp slices.
  Returntype : boolean
  Exceptions : none
  Caller     : EnsemblGenomes variation DB build
  Status     : Stable

Code:

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

Arg [1] : Bio::EnsEMBL::Transcript $transcript The transcript to be written to the database Arg [2] : Int $gene_dbID The identifier of the gene that this transcript is associated with Arg [3] :

Deprecated:: (optional) Int $analysis_id The analysis_id to use when storing this gene. This is for backward compatibility only and used to fall back to the gene analysis_id if no analysis object is attached to the transcript (which you should do for new code). Example : $transID = $tr_adaptor->store($transcript, $gene->dbID); Description: Stores a transcript in the database and returns the new internal identifier for the stored transcript. Returntype : Int Exceptions : none Caller : general Status : Stable

Code:

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

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

  my $db = $self->db();

  if ( $transcript->is_stored($db) ) {
    return $transcript->dbID();
  }

  # Force lazy-loading of exons and ensure coords are correct.
  $transcript->recalculate_coordinates();

  my $is_current = ( defined( $transcript->is_current() )
                     ? $transcript->is_current()
                     : 1 );

  # store analysis
  my $analysis = $transcript->analysis();
  my $new_analysis_id;

  if ($analysis) {
    if ( $analysis->is_stored($db) ) {
      $new_analysis_id = $analysis->dbID;
    } else {
      $new_analysis_id = $db->get_AnalysisAdaptor->store($analysis);
    }
  } elsif ($analysis_id) {
    # Fall back to analysis passed in (usually from gene) if analysis
    # wasn't set explicitely for the transcript. This is deprectated
    # though.
    warning(   "You should explicitely attach "
             . "an analysis object to the Transcript. "
             . "Will fall back to Gene analysis, "
             . "but this behaviour is deprecated." );
    $new_analysis_id = $analysis_id;
  } else {
    throw("Need an analysis_id to store the Transcript.");
  }

  #
  # Store exons - this needs to be done before the possible transfer
  # of the transcript to another slice (in _prestore()).  Transfering
  # results in copies being made of the exons and we need to preserve
  # the object identity of the exons so that they are not stored twice
  # by different transcripts.
  #
  my $exons       = $transcript->get_all_Exons();
  my $exonAdaptor = $db->get_ExonAdaptor();
  foreach my $exon ( @{$exons} ) {
    $exonAdaptor->store($exon);
  }

  my $original_translation = $transcript->translation();
  my $original             = $transcript;
  my $seq_region_id;
  ( $transcript, $seq_region_id ) = $self->_pre_store($transcript);

  # First store the transcript without a display xref.  The display xref
  # needs to be set after xrefs are stored which needs to happen after
  # transcript is stored.

  #
  # Store transcript
  #
  my $store_transcript_sql = qq(
      INSERT INTO transcript 
        SET gene_id = ?, 
            analysis_id = ?, 
            seq_region_id = ?, 
            seq_region_start = ?,
            seq_region_end = ?, 
            seq_region_strand = ?, 
            biotype = ?, 
            status = ?, 
            description = ?,
            is_current = ?, 
            canonical_translation_id = ? 
  );

  if ( defined( $transcript->stable_id() ) ) {

      my $created = $self->db->dbc->from_seconds_to_date($transcript->created_date());
      my $modified = $self->db->dbc->from_seconds_to_date($transcript->modified_date());
      $store_transcript_sql .= ", stable_id = ?, version = ?, created_date = " . $created . " , modified_date = " . $modified;

  }

  my $tst = $self->prepare($store_transcript_sql);
  $tst->bind_param( 1,  $gene_dbID,                 SQL_INTEGER );
  $tst->bind_param( 2,  $new_analysis_id,           SQL_INTEGER );
  $tst->bind_param( 3,  $seq_region_id,             SQL_INTEGER );
  $tst->bind_param( 4,  $transcript->start(),       SQL_INTEGER );
  $tst->bind_param( 5,  $transcript->end(),         SQL_INTEGER );
  $tst->bind_param( 6,  $transcript->strand(),      SQL_TINYINT );
  $tst->bind_param( 7,  $transcript->biotype(),     SQL_VARCHAR );
  $tst->bind_param( 8,  $transcript->status(),      SQL_VARCHAR );
  $tst->bind_param( 9,  $transcript->description(), SQL_LONGVARCHAR );
  $tst->bind_param( 10, $is_current,                SQL_TINYINT );

  # If the transcript has a translation, this is updated later:
  $tst->bind_param( 11, undef, SQL_INTEGER );

  if ( defined( $transcript->stable_id() ) ) {

    $tst->bind_param( 12, $transcript->stable_id(), SQL_VARCHAR );
    my $version = ($transcript->version()) ? $transcript->version() : 1;
    $tst->bind_param( 13, $version,                 SQL_INTEGER );
  }


  $tst->execute();
  $tst->finish();

  my $transc_dbID = $tst->{'mysql_insertid'};

  #
  # Store translation
  #

  my $alt_translations =
    $transcript->get_all_alternative_translations();
  my $translation = $transcript->translation();

  if ( defined($translation) ) {
    # Make sure that the start and end exon are set correctly.
    my $start_exon = $translation->start_Exon();
    my $end_exon   = $translation->end_Exon();

    if ( !defined($start_exon) ) {
      throw("Translation does not define a start exon.");
    }

    if ( !defined($end_exon) ) {
      throw("Translation does not defined an end exon.");
    }

    # If the dbID is not set, this means the exon must have been a
    # different object in memory than the the exons of the transcript.
    # Try to find the matching exon in all of the exons we just stored.
    if ( !defined( $start_exon->dbID() ) ) {
      my $key = $start_exon->hashkey();
      ($start_exon) = grep { $_->hashkey() eq $key } @$exons;

      if ( defined($start_exon) ) {
        $translation->start_Exon($start_exon);
      } else {
        throw(   "Translation's start_Exon does not appear "
               . "to be one of the exons in "
               . "its associated Transcript" );
      }
    }

    if ( !defined( $end_exon->dbID() ) ) {
      my $key = $end_exon->hashkey();
      ($end_exon) = grep { $_->hashkey() eq $key } @$exons;

      if ( defined($end_exon) ) {
        $translation->end_Exon($end_exon);
      } else {
        throw(   "Translation's end_Exon does not appear "
               . "to be one of the exons in "
               . "its associated Transcript." );
      }
    }

    my $old_dbid = $translation->dbID();
    $db->get_TranslationAdaptor()->store( $translation, $transc_dbID );

    # Need to update the canonical_translation_id for this transcript.

    my $sth = $self->prepare(
      q(
      UPDATE transcript
      SET canonical_translation_id = ?
      WHERE transcript_id = ?)
    );

    $sth->bind_param( 1, $translation->dbID(), SQL_INTEGER );
    $sth->bind_param( 2, $transc_dbID,         SQL_INTEGER );

    $sth->execute();

    # Set values of the original translation, we may have copied it when
    # we transformed the transcript.
    $original_translation->dbID( $translation->dbID() );
    $original_translation->adaptor( $translation->adaptor() );
  } ## end if ( defined($translation...))

  #
  # Store the alternative translations, if there are any.
  #

  if ( defined($alt_translations)
       && scalar( @{$alt_translations} ) > 0 )
  {
    foreach my $alt_translation ( @{$alt_translations} ) {
      my $start_exon = $alt_translation->start_Exon();
      my $end_exon   = $alt_translation->end_Exon();

      if ( !defined($start_exon) ) {
        throw("Translation does not define a start exon.");
      } elsif ( !defined($end_exon) ) {
        throw("Translation does not defined an end exon.");
      }

      if ( !defined( $start_exon->dbID() ) ) {
        my $key = $start_exon->hashkey();
        ($start_exon) = grep { $_->hashkey() eq $key } @{$exons};

        if ( defined($start_exon) ) {
          $alt_translation->start_Exon($start_exon);
        } else {
          throw(   "Translation's start_Exon does not appear "
                 . "to be one of the exon in"
                 . "its associated Transcript" );
        }
      } elsif ( !defined( $end_exon->dbID() ) ) {
        my $key = $end_exon->hashkey();
        ($end_exon) = grep { $_->hashkey() eq $key } @$exons;

        if ( defined($end_exon) ) {
          $translation->end_Exon($end_exon);
        } else {
          throw(   "Translation's end_Exon does not appear "
                 . "to be one of the exons in "
                 . "its associated Transcript." );
        }
      }

      $db->get_TranslationAdaptor()
        ->store( $alt_translation, $transc_dbID );
    } ## end foreach my $alt_translation...
  } ## end if ( defined($alt_translations...))

  #
  # Store the xrefs/object xref mapping.
  #
  my $dbEntryAdaptor = $db->get_DBEntryAdaptor();

  foreach my $dbe ( @{ $transcript->get_all_DBEntries() } ) {
    $dbEntryAdaptor->store( $dbe, $transc_dbID, "Transcript", 1 );
  }

  #
  # Update transcript to point to display xref if it is set.
  #
  if ( my $dxref = $transcript->display_xref() ) {
    my $dxref_id;

    if ( $dxref->is_stored($db) ) {
      $dxref_id = $dxref->dbID();
    } else {
      $dxref_id = $dbEntryAdaptor->exists($dxref);
    }

    if ( defined($dxref_id) ) {
      my $sth =
        $self->prepare(   "UPDATE transcript "
                        . "SET display_xref_id = ? "
                        . "WHERE transcript_id = ?" );
      $sth->bind_param( 1, $dxref_id,    SQL_INTEGER );
      $sth->bind_param( 2, $transc_dbID, SQL_INTEGER );
      $sth->execute();
      $dxref->dbID($dxref_id);
      $dxref->adaptor($dbEntryAdaptor);
      $sth->finish();
    } else {
      warning(sprintf(
                     "Display_xref %s:%s is not stored in database.\n"
                       . "Not storing relationship to this transcript.",
                     $dxref->dbname(), $dxref->display_id() ) );
      $dxref->dbID(undef);
      $dxref->adaptor(undef);
    }
  } ## end if ( my $dxref = $transcript...)

  #
  # Link transcript to exons in exon_transcript table
  #
  my $etst = $self->prepare(
             "INSERT INTO exon_transcript (exon_id,transcript_id,rank) "
               . "VALUES (?,?,?)" );
  my $rank = 1;
  foreach my $exon ( @{ $transcript->get_all_Exons } ) {
    $etst->bind_param( 1, $exon->dbID,  SQL_INTEGER );
    $etst->bind_param( 2, $transc_dbID, SQL_INTEGER );
    $etst->bind_param( 3, $rank,        SQL_INTEGER );
    $etst->execute();
    $rank++;
  }

  $etst->finish();

  # Now the supporting evidence
  my $tsf_adaptor = $db->get_TranscriptSupportingFeatureAdaptor();
  $tsf_adaptor->store( $transc_dbID,
                       $transcript->get_all_supporting_features() );

  # store transcript attributes if there are any
  my $attr_adaptor = $db->get_AttributeAdaptor();

  $attr_adaptor->store_on_Transcript( $transc_dbID,
                                    $transcript->get_all_Attributes() );

  # Update the original transcript object - not the transfered copy that
  # we might have created.
  $original->dbID($transc_dbID);
  $original->adaptor($self);

  return $transc_dbID;
} ## end sub store

Reimplemented from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor.

public void Bio::EnsEMBL::DBSQL::TranscriptAdaptor::update ( )

  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
               The transcript to update
  Example    : $tr_adaptor->update($transcript);
  Description: Updates a transcript in the database.
  Returntype : None
  Exceptions : thrown if the $transcript is not a Bio::EnsEMBL::Transcript.
               warn if the method is called on a transcript that does not exist 
               in the database.
               Should warn if trying to update the number of attached exons, but
               this is a far more complex process and is not yet implemented.
  Caller     : general
  Status     : Stable

Code:

click to view

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

Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

Class Summary

Synopsis

Description

Available Methods

Method Documentation