Inheritance diagram for Bio::EnsEMBL::DBSQL::ExonAdaptor:

Public Member Functions
protected	_tables ()

protected	_columns ()

protected	_final_clause ()

public	fetch_all ()

public Bio::EnsEMBL::Exon	fetch_by_stable_id ()

public Bio::EnsEMBL::Exon	fetch_by_stable_id_version ()

public Listref	fetch_all_versions_by_stable_id ()

public Listref	fetch_all_by_Transcript ()

public void	store ()

public void	remove ()

public List	list_dbIDs ()

public List	list_stable_ids ()

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 $exon_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Exon' );
 
my $exon = $exon_adaptor->fetch_by_dbID($dbID);

Description

The ExonAdaptor is responsible for retrieving and storing Exon objects
from an Ensembl database.  Most of the ExonAdaptor functionality is
inherited from the Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor class.

Definition at line 22 of file ExonAdaptor.pm.

Member Function Documentation

◆ _columns()

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

Undocumented method

Code:

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◆ _final_clause()

protected Bio::EnsEMBL::DBSQL::ExonAdaptor::_final_clause ( )

Undocumented method

Code:

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◆ _objs_from_sth()

protected Bio::EnsEMBL::DBSQL::ExonAdaptor::_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 @exons;
  my %slice_hash;
  my %sr_name_hash;
  my %sr_cs_hash;
 
  my ( $exon_id,        $seq_region_id,     $seq_region_start,
       $seq_region_end, $seq_region_strand, $phase,
       $end_phase,      $is_current,        $is_constitutive,
       $stable_id,      $version,           $created_date,
       $modified_date );
 
  $sth->bind_columns( \( $exon_id, $seq_region_id, $seq_region_start,
                         $seq_region_end, $seq_region_strand, $phase,
                         $end_phase, $is_current, $is_constitutive,
                         $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();
  }
 
  FEATURE: while($sth->fetch()) {
 
    #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 FEATURE 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 FEATURE;
      }
      $slice = $dest_slice;
    }
 
    # Finally, create the new exon.
    push( @exons,
          $self->_create_feature_fast(
                           'Bio::EnsEMBL::Exon', {
                             'start'         => $seq_region_start,
                             'end'           => $seq_region_end,
                             'strand'        => $seq_region_strand,
                             'adaptor'       => $self,
                             'slice'         => $slice,
                             'dbID'          => $exon_id,
                             'stable_id'     => $stable_id,
                             'version'       => $version,
                             'created_date'  => $created_date || undef,
                             'modified_date' => $modified_date || undef,
                             'phase'         => $phase,
                             'end_phase'     => $end_phase,
                             'is_current'    => $is_current,
                             'is_constitutive' => $is_constitutive } )
    );
 
  } ## end while ( $sth->fetch() )
 
  return \@exons;
} ## end sub _objs_from_sth

◆ _tables()

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

Undocumented method

Code:

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◆ fetch_all()

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

Undocumented method

Code:

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◆ fetch_all_by_Transcript()

public Listref Bio::EnsEMBL::DBSQL::ExonAdaptor::fetch_all_by_Transcript ( )

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

none

  Description: Retrieves all Exons for the Transcript in 5-3 order
  Returntype : listref Bio::EnsEMBL::Exon on Transcript slice 
  Exceptions : throws if transcript has no slice
  Caller     : Transcript->get_all_Exons()
  Status     : Stable

Code:

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◆ fetch_all_versions_by_stable_id()

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

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

my $exon = $exon_adaptor->fetch_all_version_by_stable_id

('ENSE00000309301');

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

Code:

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◆ fetch_by_stable_id()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::DBSQL::ExonAdaptor::fetch_by_stable_id ( )

  Arg [1]    : string $stable_id
               the stable id of the exon to retrieve
  Example    :

$exon = $exon_adaptor->fetch_by_stable_id('ENSE0000988221');

  Description: Retrieves an Exon from the database via its stable id
  Returntype : Bio::EnsEMBL::Exon in native coordinates.
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_stable_id_version()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::DBSQL::ExonAdaptor::fetch_by_stable_id_version ( )

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

$exon = $exon_adaptor->fetch_by_stable_id('ENSE0000988221', 3);

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

Code:

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◆ list_dbIDs()

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

  Arg [1]    : none
  Example    :

@exon_ids = @{$exon_adaptor->list_dbIDs()};

  Description: Gets an array of internal ids for all exons in the current db
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable

Code:

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◆ list_stable_ids()

public List Bio::EnsEMBL::DBSQL::ExonAdaptor::list_stable_ids ( )

  Arg [1]    : none
  Example    :

@stable_exon_ids = @{$exon_adaptor->list_stable_dbIDs()};

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

Code:

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◆ remove()

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

  Arg [1]    : Bio::EnsEMBL::Exon $exon
               the exon to remove from the database
  Example    :

$exon_adaptor->remove($exon);

  Description: Removes an exon from the database.  This method is generally
               called by the TranscriptAdaptor::store method. Database
               integrity will not be maintained if this method is simply
               called on its own without taking into account transcripts which
               may refer to the exon being removed.
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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sub remove {
  my $self = shift;
  my $exon = shift;
 
  if(!ref($exon) || !$exon->isa('Bio::EnsEMBL::Exon')) {
    throw('Bio::EnsEMBL::Exon argument expected.');
  }
 
  if(!$exon->is_stored($self->db())) {
    warning("Cannot remove exon " .$exon->dbID.
            "Is not stored in this database.");
    return;
  }
 
  # sanity check: make sure nobdody tries to slip past a prediction exon
  # which inherits from exon but actually uses different tables
  if($exon->isa('Bio::EnsEMBL::PredictionExon')) {
    throw("ExonAdaptor can only remove Exons not PredictionExons.");
  }
 
  # Remove the supporting features of this exon
 
  my $prot_adp = $self->db->get_ProteinAlignFeatureAdaptor;
  my $dna_adp = $self->db->get_DnaAlignFeatureAdaptor;
 
  my $sth = $self->prepare("SELECT feature_type, feature_id  " .
                           "FROM supporting_feature " .            
               "WHERE exon_id = ?");
  $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
  $sth->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) = $sth->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 "shared feature, not removing $type|$feature_id\n";
      next SUPPORTING_FEATURE;
    }
    
    #warn "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.");
    }
  }
  $sth->finish();
  $sth1->finish();
  $sth2->finish();
 
  # delete the association to supporting features
 
  $sth = $self->prepare("DELETE FROM supporting_feature WHERE exon_id = ?");
  $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
  $sth->execute();
  $sth->finish();
 
 
  # delete the exon
 
  $sth = $self->prepare( "DELETE FROM exon WHERE exon_id = ?" );
  $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
  $sth->execute();
  $sth->finish();
 
  $exon->dbID(undef);
  $exon->adaptor(undef);
 
  return;
}

◆ store()

public void Bio::EnsEMBL::DBSQL::ExonAdaptor::store ( )

  Arg [1]    : Bio::EnsEMBL::Exon $exon
               the exon to store in this database
  Example    :

$exon_adaptor->store($exon);

  Description: Stores an exon in the database
  Returntype : none
  Exceptions : thrown if exon (or component exons) do not have a contig_id
               or if $exon->start, $exon->end, $exon->strand, or $exon->phase 
               are not defined or if $exon is not a Bio::EnsEMBL::Exon
  Caller     : general
  Status     : Stable

Code:

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sub store {
  my ($self, $exon) = @_;
 
  if( ! $exon->isa('Bio::EnsEMBL::Exon') ) {
    throw("$exon is not a EnsEMBL exon - not storing.");
  }
 
  my $db = $self->db();
 
  if($exon->is_stored($db)) {
    return $exon->dbID();
  }
 
  if( ! $exon->start || ! $exon->end ||
      ! $exon->strand || ! defined $exon->phase ) {
    throw("Exon does not have all attributes to store");
  }
 
  # Default to is_current = 1 if this attribute is not set
  my $is_current = $exon->is_current();
  if ( !defined($is_current) ) { $is_current = 1 }
 
  # Default to is_constitutive = 0 if this attribute is not set
  my $is_constitutive = $exon->is_constitutive();
  if ( !defined($is_constitutive) ) { $is_constitutive = 0 }
 
  my $exon_sql = q{
    INSERT into exon ( seq_region_id, seq_region_start,
               seq_region_end, seq_region_strand, phase,
               end_phase, is_current, is_constitutive                      
  };
  if ( defined($exon->stable_id) ) {
      my $created = $self->db->dbc->from_seconds_to_date($exon->created_date());
      my $modified = $self->db->dbc->from_seconds_to_date($exon->modified_date());
 
      $exon_sql .= sprintf ", stable_id, version%s%s) VALUES ( ?,?,?,?,?,?,?,?,?,?%s%s)", $created?", created_date":'', $modified?", modified_date":'', $created?",$created":'', $modified?",$modified":'';
     
  } else {
      $exon_sql .= q{
         ) VALUES ( ?,?,?,?,?,?,?,?)
      };
  }
 
 
  my $exonst = $self->prepare($exon_sql);
 
  my $exonId = undef;
 
  my $original = $exon;
  my $seq_region_id;
  ($exon, $seq_region_id) = $self->_pre_store($exon);
 
  #store the exon
  $exonst->bind_param( 1, $seq_region_id,   SQL_INTEGER );
  $exonst->bind_param( 2, $exon->start,     SQL_INTEGER );
  $exonst->bind_param( 3, $exon->end,       SQL_INTEGER );
  $exonst->bind_param( 4, $exon->strand,    SQL_TINYINT );
  $exonst->bind_param( 5, $exon->phase,     SQL_TINYINT );
  $exonst->bind_param( 6, $exon->end_phase, SQL_TINYINT );
  $exonst->bind_param( 7, $is_current,      SQL_TINYINT );
  $exonst->bind_param( 8, $is_constitutive, SQL_TINYINT );
 
  if ( defined($exon->stable_id) ) {
 
     $exonst->bind_param(  9, $exon->stable_id, SQL_VARCHAR );
     $exonst->bind_param( 10, $exon->version,   SQL_INTEGER ); 
  }
 
  $exonst->execute();
  $exonId = $self->last_insert_id('exon_id', undef, 'exon');
 
  # Now the supporting evidence
  my $esf_adaptor = $db->get_SupportingFeatureAdaptor;
  $esf_adaptor->store($exonId, $exon->get_all_supporting_features);
 
  #
  # Finally, update the dbID and adaptor of the exon (and any component exons)
  # to point to the new database
  #
 
  $original->adaptor($self);
  $original->dbID($exonId);
 
  return $exonId;
}

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

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

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _columns()

◆ _final_clause()

◆ _objs_from_sth()

◆ _tables()

◆ fetch_all()

◆ fetch_all_by_Transcript()

◆ fetch_all_versions_by_stable_id()

◆ fetch_by_stable_id()

◆ fetch_by_stable_id_version()

◆ list_dbIDs()

◆ list_stable_ids()

◆ remove()

◆ store()