Inheritance diagram for Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor:

Public Member Functions
protected	_tables ()

protected	_columns ()

public Listref	list_dbIDs ()

public Reference	list_stable_ids ()

public	list_seq_region_ids ()

public Bio::EnsEMBL::OperonTranscript	fetch_by_stable_id ()

public Bio::EnsEMBL::OperonTranscript	fetch_by_stable_id_version ()

public Bio::EnsEMBL::OperonTranscript	fetch_by_name ()

public Listref	fetch_all ()

public Listref	fetch_all_versions_by_stable_id ()

public Reference	fetch_all_by_Slice ()

public	fetch_all_by_Operon ()

public Arrayref	fetch_by_operon_id ()

public Arrayref	fetch_genes_by_operon_transcript ()

public Arrayref	fetch_genes_by_operon_transcript_id ()

public Arrayref	fetch_all_by_gene ()

public Arrayref	fetch_all_by_gene_id ()

public The	store ()

public void	store_genes_on_OperonTranscript ()

public void	remove ()

protected	_objs_from_sth ()

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

public Boolean	start_equals_end ()

public void	clear_cache ()

protected	_clear_slice_feature_cache ()

protected Bio::EnsEMBL::Utils::Cache	_slice_feature_cache ()

public Listref	fetch_all_by_Slice ()

public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice_method ()

public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice ()

public Listref	fetch_all_by_Slice_and_score ()

public Listref	fetch_all_by_Slice_constraint ()

public Listref	fetch_all_by_logic_name ()

public Listref	fetch_all_by_stable_id_list ()

protected	_create_feature ()

protected	_create_feature_fast ()

public Int	count_by_Slice_constraint ()

protected ArrayRef	_get_and_filter_Slice_projections ()

protected ArrayRef	_generate_feature_bounds ()

protected Listref	_get_by_Slice ()

protected	_slice_fetch ()

public	get_seq_region_id_external ()

public	get_seq_region_id_internal ()

protected	_pre_store ()

protected	_pre_store_userdata ()

protected	_check_start_end_strand ()

protected	_remap ()

protected	_seq_region_boundary_from_db ()

public void	store ()

public void	remove ()

public void	remove_by_Slice ()

protected	_max_feature_length ()

protected	_list_seq_region_ids ()

public	remove_by_analysis_id ()

public	remove_by_feature_id ()

public Bio::EnsEMBL::Feature	fetch_nearest_by_Feature ()

public Listref	fetch_all_by_outward_search ()

public Listref	fetch_all_nearest_by_Feature ()

public Listref	select_nearest ()

protected Int	_compute_nearest_end ()

protected Int	_compute_prime_distance ()

protected Int	_compute_midpoint ()

protected	_discard_excess_features_from_matrix ()

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

Synopsis

my $operon_transcript_adaptor =  Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor->new($dba);
$operon_transcript_adaptor->store($operon_transcript);
my $operon_transcript2 = $operon_transcript_adaptor->fetch_by_dbID( $operon->dbID() );
my $operon_transcripts = $operon_transcript_adaptor->fetch_all_by_gene( $gene );

Description

This is a database aware adaptor for the retrieval and storage of operon
transcript objects.

Definition at line 28 of file OperonTranscriptAdaptor.pm.

Member Function Documentation

◆ _columns()

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

Undocumented method

Code:

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◆ _objs_from_sth()

protected Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::_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 @operons;
  my %analysis_hash;
  my %slice_hash;
  my %sr_name_hash;
  my %sr_cs_hash;
 
  my (
     $operon_transcript_id, $seq_region_id,     $seq_region_start,
     $seq_region_end,       $seq_region_strand, $display_label,
     $analysis_id,          $stable_id,         $version,
     $created_date,         $modified_date );
 
  $sth->bind_columns( \(
            $operon_transcript_id, $seq_region_id,     $seq_region_start,
            $seq_region_end,       $seq_region_strand, $display_label,
            $analysis_id,          $stable_id,         $version,
            $created_date,         $modified_date ));
 
  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();
  }
 
  OPERON: while ( $sth->fetch() ) {
 
    #get the analysis object
    my $analysis = $analysis_hash{$analysis_id} ||= $aa->fetch_by_dbID($analysis_id);
    $analysis_hash{$analysis_id} = $analysis;
 
    #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};
 
    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(!$mapper && $dest_slice && !$dest_slice_cs->equals($slice->coord_system)) {
      $mapper = $asma->fetch_by_CoordSystems($dest_slice_cs, $slice->coord_system);
    }
 
    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 ($mapper) {
 
      if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
        ($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand) =
         $mapper->map($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs, 1, $dest_slice);
 
      } else {
        ($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand) =
         $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs);
      }
 
      #skip features that map to gaps or coord system boundaries
      next OPERON if ( !defined($seq_region_id) );
 
      #get a slice in the coord system we just mapped to
      $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)) {
      my $seq_region_len = $dest_slice->seq_region_length();
 
      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 ) {
        # Handle circular chromosomes.
 
          if ( $seq_region_start > $seq_region_end ) {
            # Looking at a feature overlapping the chromosome origin.
 
            if ( $seq_region_end > $dest_slice_start ) {
              # Looking at the region in the beginning of the chromosome
              $seq_region_start -= $seq_region_len;
            }
            if ( $seq_region_end < 0 ) {
              $seq_region_end += $seq_region_len;
            }
          } else {
            if ($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 += $seq_region_len;
              $seq_region_end   += $seq_region_len;
            }
          }
        }
      } else {
 
        my $start = $dest_slice_end - $seq_region_end + 1;
        my $end = $dest_slice_end - $seq_region_start + 1;
 
        if ($dest_slice->is_circular()) {
 
          if ($dest_slice_start > $dest_slice_end) {
            # slice spans origin or replication
 
            if ($seq_region_start >= $dest_slice_start) {
              $end += $seq_region_len;
              $start += $seq_region_len if $seq_region_end > $dest_slice_start;
 
            } elsif ($seq_region_start <= $dest_slice_end) {
              # do nothing
            } elsif ($seq_region_end >= $dest_slice_start) {
              $start += $seq_region_len;
              $end += $seq_region_len;
 
            } elsif ($seq_region_end <= $dest_slice_end) {
              $end += $seq_region_len if $end < 0;
 
            } elsif ($seq_region_start > $seq_region_end) {
              $end += $seq_region_len;
            }
 
          } else {
 
            if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
              # do nothing
            } elsif ($seq_region_start > $seq_region_end) {
              if ($seq_region_start <= $dest_slice_end) {
                $start -= $seq_region_len;
              } elsif ($seq_region_end >= $dest_slice_start) {
                $end += $seq_region_len;
              }
            }
          }
        }
 
        $seq_region_start = $start;
        $seq_region_end = $end;
        $seq_region_strand *= -1;
 
      } ## end else [ if ( $dest_slice_strand...)]
 
      # Throw away features off the end of the requested slice or on
      # different seq_region.
      if ($seq_region_end < 1
          || $seq_region_start > $dest_slice_length
          || ($dest_slice_sr_id != $seq_region_id)) {
        next OPERON;
      }
      $slice = $dest_slice;
    }
 
    push( @operons,
        Bio::EnsEMBL::OperonTranscript->new(
                    -START         => $seq_region_start,
                    -END           => $seq_region_end,
                    -STRAND        => $seq_region_strand,
                    -SLICE         => $slice,
                    -DISPLAY_LABEL => $display_label,
                    -ADAPTOR       => $self,
                    -DBID          => $operon_transcript_id,
                    -STABLE_ID     => $stable_id,
                    -VERSION       => $version,
                    -CREATED_DATE  => $created_date || undef,
                    -MODIFIED_DATE => $modified_date || undef,
                    -ANALYSIS      => $analysis ) );
 
  } ## end while ( $sth->fetch() )
 
  return \@operons;
} ## end sub _objs_from_sth

◆ _tables()

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

Undocumented method

Code:

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◆ fetch_all()

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

  Example     :

$operon_transcripts = $operon_adaptor->fetch_all();

  Description : Retrieves all operon transcripts stored in the database.
  Returntype  : listref of Bio::EnsEMBL::OperonTranscript
  Caller      : general
  Status      : At Risk

Code:

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◆ fetch_all_by_gene()

public Arrayref Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::fetch_all_by_gene ( )

  Arg [1]    : Bio::EnsEMBL::Gene
  Example    :

$ots = $ot_adaptor->fetch_all_by_gene($gene);

  Description: Retrieves all operon transcripts attached to a given gene
  Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_all_by_gene_id()

public Arrayref Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::fetch_all_by_gene_id ( )

  Arg [1]    : Int id of Bio::EnsEMBL::Gene
  Example    :

$ots = $ot_adaptor->fetch_all_by_gene($gene);

  Description: Retrieves all operon transcripts attached to a given gene
  Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_all_by_Operon()

public Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::fetch_all_by_Operon ( )

Undocumented method

Code:

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◆ fetch_all_by_Slice()

public Reference Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::fetch_all_by_Slice ( )

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice to fetch operon_transcripts on.
  Arg [2]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Arg [3]    : (optional) boolean $load_transcripts
               if true, transcripts will be loaded immediately rather than
               lazy loaded later.
  Arg [4]    : (optional) string $source
               the source name of the features to obtain.
  Arg [5]    : (optional) string biotype
                the biotype of the features to obtain.
  Example    :

@operon_transcripts = @{$operon_transcript_adaptor->fetch_all_by_Slice()};

  Description: Overrides superclass method to optionally load transcripts
               immediately rather than lazy-loading them later.  This
               is more efficient when there are a lot of operon_transcripts whose
               transcripts are going to be used.
  Returntype : reference to list of operon_transcripts 
  Exceptions : thrown if exon cannot be placed on transcript slice
  Caller     : Slice::get_all_OperonTranscripts
  Status     : Stable

Code:

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sub fetch_all_by_Slice {
  my ( $self, $slice, $logic_name, $load_transcripts ) = @_;
 
  my $constraint = '';
 
  my $operons =
    $self->SUPER::fetch_all_by_Slice_constraint( $slice, $constraint,
                         $logic_name );
 
  # If there are less than two operons, still do lazy-loading.
  if ( !$load_transcripts || @$operons < 2 ) {
    return $operons;
  }
 
  # Preload all of the transcripts now, instead of lazy loading later,
  # faster than one query per transcript.
 
  # First check if transcripts are already preloaded.
  # FIXME: Should check all transcripts.
  if ( exists( $operons->[0]->{'_operon_transcript_array'} ) ) {
    return $operons;
  }
 
  # Get extent of region spanned by transcripts.
  my ($min_start, $max_end);
  my $ext_slice;
 
  unless ($slice->is_circular()) {
    foreach my $o (@$operons) {
      if (!defined($min_start) || $o->seq_region_start() < $min_start) {
    $min_start = $o->seq_region_start();
      }
      if (!defined($max_end) || $o->seq_region_end() > $max_end) {
    $max_end = $o->seq_region_end();
      }
    }
 
    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());
    }
 
  } else {
    # feature might be crossing the origin of replication (i.e. seq_region_start > seq_region_end)
    # the computation of min_start|end based on seq_region_start|end is not safe
    # use feature start/end relative to the slice instead
    my ($min_start_feature, $max_end_feature);
    foreach my $o (@$operons) {
      if (!defined($min_start) || ($o->start() >= 0 && $o->start() < $min_start)) {
    $min_start = $o->start();
    $min_start_feature = $o;
      }
      if (!defined($max_end) || ($o->end() >= 0 && $o->end() > $max_end)) {
    $max_end = $o->end();
    $max_end_feature = $o;
      }
    }
    
    # now we can reassign min_start|end to seq_region_start|end of
    # the feature which spans the largest region
    $min_start = $min_start_feature->seq_region_start();
    $max_end = $max_end_feature->seq_region_end();
 
    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 transcript identifiers with operon_transcripts.
 
  my %o_hash = map { $_->dbID => $_ } @{$operons};
 
  my $o_id_str = join( ',', keys(%o_hash) );
 
  my $sth =
    $self->prepare(   "SELECT operon_id, operon_transcript_id "
              . "FROM   operon_transcript "
              . "WHERE  operon_id IN ($o_id_str)" );
 
  $sth->execute();
 
  my ( $o_id, $tr_id );
  $sth->bind_columns( \( $o_id, $tr_id ) );
 
  my %tr_o_hash;
 
  while ( $sth->fetch() ) {
    $tr_o_hash{$tr_id} = $o_hash{$o_id};
  }
 
  my $ta = $self->db()->get_OperonTranscriptAdaptor();
  my $transcripts =
    $ta->fetch_all_by_Slice( $ext_slice,
                 1, undef,
                 sprintf( "ot.operon_transcript_id IN (%s)",
                      join( ',',
                        sort { $a <=> $b }
                        keys(%tr_o_hash) ) ) );
 
  # Move transcripts onto operon_transcript slice, and add them to operon_transcripts.
  foreach my $tr ( @{$transcripts} ) {
    if ( !exists( $tr_o_hash{ $tr->dbID() } ) ) {
      next;
    }
 
    my $new_tr;
    if ( $slice != $ext_slice ) {
      $new_tr = $tr->transfer($slice);
      if ( !defined($new_tr) ) {
    throw("Unexpected. "
          . "Transcript could not be transfered onto OperonTranscript slice."
         );
      }
    } else {
      $new_tr = $tr;
    }
 
    $tr_o_hash{ $tr->dbID() }->add_OperonTranscript($new_tr);
  }
 
  return $operons;
}               ## end sub fetch_all_by_Slice

◆ fetch_all_versions_by_stable_id()

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

  Arg [1]     : String $stable_id 
                The stable ID of the operon_transcript to retrieve
  Example     :

$operon_transcript = $operon_transcript_adaptor->fetch_all_versions_by_stable_id

('ENSG00000148944');

  Description : Similar to fetch_by_stable_id, but retrieves all versions of a
                operon_transcript stored in the database.
  Returntype  : listref of Bio::EnsEMBL::OperonTranscript
  Exceptions  : if we cant get the operon_transcript in given coord system
  Caller      : general
  Status      : At Risk

Code:

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◆ fetch_by_name()

public Bio::EnsEMBL::OperonTranscript Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::fetch_by_name ( )

  Arg [1]    : String $label - name of operon transcript to fetch
  Example    :

my $operon_transcript = $operonAdaptor->fetch_by_name("ECK0012121342");

  Description: Returns the operon 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::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_operon_id()

public Arrayref Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::fetch_by_operon_id ( )

  Arg [1]    : Int id
  Example    :

$ot = $ot_adaptor->fetch_by_operon_transcript($operon);

  Description: Retrieves all operon transcripts belonging to an operon
  Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_stable_id()

public Bio::EnsEMBL::OperonTranscript Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::fetch_by_stable_id ( )

  Arg [1]    : String $id 
               The stable ID of the operon_transcript to retrieve
  Example    :

$operon_transcript = $operon_transcript_adaptor->fetch_by_stable_id('T16152-16153-4840');

  Description: Retrieves a operon_transcript object from the database via its stable id.
               The operon_transcript 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 operon_transcript is not found
               undef is returned instead.
  Returntype : Bio::EnsEMBL::OperonTranscript or undef
  Exceptions : if we cant get the operon_transcript in given coord system
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_stable_id_version()

public Bio::EnsEMBL::OperonTranscript Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::fetch_by_stable_id_version ( )

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

$operon_transcript = $operon_transcript_adaptor->fetch_by_stable_id('T16152-16153-4840', 2);

  Description: Retrieves an operon_transcript object from the database via its stable id and version.
               The operon_transcript 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 operon_transcript is not found
               undef is returned instead.
  Returntype : Bio::EnsEMBL::OperonTranscript or undef
  Exceptions : if we cant get the operon_transcript in given coord system
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_genes_by_operon_transcript()

public Arrayref Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::fetch_genes_by_operon_transcript ( )

  Arg [1]    : Bio::EnsEMBL::OperonTranscript
  Example    :

$ot = $ot_adaptor->fetch_genes_by_operon_transcript($operon_transcript);

  Description: Retrieves all genes attached to an operon transcript
  Returntype : arrayref of Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_genes_by_operon_transcript_id()

public Arrayref Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::fetch_genes_by_operon_transcript_id ( )

  Arg [1]    : Int id
  Example    :

$ot = $ot_adaptor->fetch_genes_by_operon_transcript($operon_transcript_id);

  Description: Retrieves all genes attached to an operon transcript
  Returntype : arrayref of Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ list_dbIDs()

public Listref Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::list_dbIDs ( )

  Example    :

@ot_ids = @{$ot_adaptor->list_dbIDs()};

  Description: Gets an array of internal ids for all operon_transcripts in the current 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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◆ list_seq_region_ids()

public Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::list_seq_region_ids ( )

Undocumented method

Code:

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◆ list_stable_ids()

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

  Example    :

@stable_ot_ids = @{$ot_adaptor->list_stable_ids()};

  Description: Gets an listref of stable ids for all operon_transcripts 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::OperonTranscriptAdaptor::remove ( )

  Arg [1]    : Bio::EnsEMBL::OperonTranscript $ot
               the operon_transcript to remove from the database
  Example    :

$ot_adaptor->remove($ot);

  Description: Removes a operon transcript completely from the database.
  Returntype : none
  Exceptions : throw on incorrect arguments 
               warning if operon_transcript is not stored in this database
  Caller     : general
  Status     : Stable

Code:

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◆ store()

public The Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::store ( )

  Arg [1]    : Bio::EnsEMBL::OperonTranscript $gene
               The gene to store in the database
  Arg [2]    : ignore_release in xrefs [default 1] set to 0 to use release info 
               in external database references
  Example    :

$gene_adaptor->store($gene);

  Description: Stores a gene in the database.
  Returntype : the database identifier (dbID) of the newly stored gene
  Exceptions : thrown if the $gene is not a Bio::EnsEMBL::OperonTranscript or if 
               $gene does not have an analysis object
  Caller     : general
  Status     : Stable

Code:

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sub store {
    my ( $self, $operon_transcript, $operon_id ) = @_;
 
    assert_ref( $operon_transcript, 'Bio::EnsEMBL::OperonTranscript' );
 
    my $db = $self->db();
 
    if ( $operon_transcript->is_stored($db) ) {
        return $operon_transcript->dbID();
    }
 
    # ensure coords are correct before storing
    #$operon->recalculate_coordinates();
 
    my $seq_region_id;
 
    ( $operon_transcript, $seq_region_id ) =
      $self->_pre_store($operon_transcript);
    my $analysis = $operon_transcript->analysis();
    throw("OperonTranscripts must have an analysis object.")
      if ( !defined($analysis) );
    my $analysis_id;
    if ( $analysis->is_stored($db) ) {
        $analysis_id = $analysis->dbID();
    } else {
        $analysis_id = $db->get_AnalysisAdaptor->store($analysis);
    }
    my @columns = qw(
               seq_region_id
               seq_region_start
               seq_region_end
               seq_region_strand
               display_label
               operon_id
               analysis_id
        );
  my @canned_columns;
  my @canned_values;
    if ( defined($operon_transcript->stable_id()) ) {
        push @columns, qw(
      stable_id
      version
    );
        my $created = $self->db->dbc->from_seconds_to_date($operon_transcript->created_date());
        my $modified = $self->db->dbc->from_seconds_to_date($operon_transcript->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 $i_columns = join(', ', @columns, @canned_columns);
  my $i_values  = join(', ', (('?') x scalar(@columns)), @canned_values);
  my $store_operon_transcript_sql = qq(
    INSERT INTO operon_transcript ( ${i_columns} ) VALUES ( $i_values )
  );
 
    my $sth = $self->prepare($store_operon_transcript_sql);
    $sth->bind_param( 1, $seq_region_id,                      SQL_INTEGER );
    $sth->bind_param( 2, $operon_transcript->start(),         SQL_INTEGER );
    $sth->bind_param( 3, $operon_transcript->end(),           SQL_INTEGER );
    $sth->bind_param( 4, $operon_transcript->strand(),        SQL_TINYINT );
    $sth->bind_param( 5, $operon_transcript->display_label(), SQL_VARCHAR );
    $sth->bind_param( 6, $operon_id,                          SQL_INTEGER );
    $sth->bind_param( 7, $analysis_id,                        SQL_INTEGER );
 
    if ( defined($operon_transcript->stable_id()) ) {
        $sth->bind_param( 8, $operon_transcript->stable_id(), SQL_VARCHAR );
        my $version = ($operon_transcript->version()) ? $operon_transcript->version() : 1;
        $sth->bind_param( 9, $version,  SQL_INTEGER );
    }
 
    $sth->execute();
    $sth->finish();
 
    my $operon_transcript_dbID = $self->last_insert_id('operon_transcript_id', undef, 'operon_transcript');
 
    # store the dbentries associated with this gene
    my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
 
    foreach my $dbe ( @{ $operon_transcript->get_all_DBEntries } ) {
        $dbEntryAdaptor->store( $dbe, $operon_transcript_dbID,
                                "OperonTranscript" );
    }
 
    # store operon attributes if there are any
    my $attrs = $operon_transcript->get_all_Attributes();
    if ( $attrs && scalar @$attrs ) {
        my $attr_adaptor = $db->get_AttributeAdaptor();
        $attr_adaptor->store_on_OperonTranscript( $operon_transcript, $attrs );
    }
 
    # set the adaptor and dbID on the original passed in gene not the
    # transfered copy
    $operon_transcript->adaptor($self);
    $operon_transcript->dbID($operon_transcript_dbID);
 
    if ( defined $operon_transcript->{_gene_array} ) {
        $self->store_genes_on_OperonTranscript( $operon_transcript,
                                            $operon_transcript->{_gene_array} );
    }
 
    return $operon_transcript_dbID;
} ## end sub store

◆ store_genes_on_OperonTranscript()

public void Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor::store_genes_on_OperonTranscript ( )

  Arg [1]    : Bio::EnsEMBL::OperonTranscript $ot
               the operon_transcript to store genes on
  Arg [2]    : arrayref of Bio::EnsEMBL::Gene $gene
               the genes to store on operon transcript
  Example    :

$ot_adaptor->store_genes_on_OperonTranscript(\@genes);

  Description: Associates genes with operon transcript
  Returntype : none
  Exceptions : throw on incorrect arguments 
               warning if operon_transcript is not stored in this database
  Caller     : general, store
  Status     : Stable

Code:

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

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

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _columns()

◆ _objs_from_sth()

◆ _tables()

◆ fetch_all()

◆ fetch_all_by_gene()

◆ fetch_all_by_gene_id()

◆ fetch_all_by_Operon()

◆ fetch_all_by_Slice()

◆ fetch_all_versions_by_stable_id()

◆ fetch_by_name()

◆ fetch_by_operon_id()

◆ fetch_by_stable_id()

◆ fetch_by_stable_id_version()

◆ fetch_genes_by_operon_transcript()

◆ fetch_genes_by_operon_transcript_id()

◆ list_dbIDs()

◆ list_seq_region_ids()

◆ list_stable_ids()

◆ remove()

◆ store()

◆ store_genes_on_OperonTranscript()