comparison variant_effect_predictor/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm @ 0:1f6dce3d34e0

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=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

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

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

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=cut

=head1 NAME

Bio::EnsEMBL::DBSQL::ExonAdaptor - An adaptor responsible for the retrieval and
storage of exon objects

=head1 SYNOPSIS

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

  my $exon = $exon_adaptor->fetch_by_dbID($dbID);

=head1 DESCRIPTION

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

=head1 METHODS

=cut

package Bio::EnsEMBL::DBSQL::ExonAdaptor;

use strict;

use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
 
use vars qw( @ISA );
@ISA = qw( Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor );


#_tables
#
#  Arg [1]    : none
#  Example    : none
#  Description: PROTECTED implementation of superclass abstract method
#               returns the names, aliases of the tables to use for queries
#  Returntype : list of listrefs of strings
#  Exceptions : none
#  Caller     : internal

sub _tables {
  my $self = shift;

  # Allow the table definition to be overridden by certain methods.
  if ( defined( $self->{'tables'} ) ) {
    return @{ $self->{'tables'} };
  }

  return ( [ 'exon', 'e' ] );
}


# _columns
#
#  Arg [1]    : none
#  Example    : none
#  Description: PROTECTED implementation of superclass abstract method
#               returns a list of columns to use for queries
#  Returntype : list of strings
#  Exceptions : none
#  Caller     : internal

sub _columns {
  my $self = shift;

  my $created_date =
    $self->db->dbc->from_date_to_seconds("created_date");
  my $modified_date =
    $self->db->dbc->from_date_to_seconds("modified_date");

  return (
    'e.exon_id',        'e.seq_region_id',     'e.seq_region_start',
    'e.seq_region_end', 'e.seq_region_strand', 'e.phase',
    'e.end_phase',      'e.is_current',        'e.is_constitutive',
    'e.stable_id',      'e.version',           $created_date,
    $modified_date
  );
}



# _final_clause
#
#  Arg [1]    : none
#  Example    : none
#  Description: PROTECTED implementation of superclass abstract method
#               returns a default end for the SQL-query (ORDER BY)
#  Returntype : string
#  Exceptions : none
#  Caller     : internal

sub _final_clause {
  my $self = shift;
  return $self->{'final_clause'} || '';
}


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

  my $constraint = 'e.is_current = 1';
  my @exons  = @{ $self->generic_fetch($constraint) };
  return \@exons ;
}

=head2 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

=cut

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

  my $constraint = "e.stable_id = ? AND e.is_current = 1";

  $self->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
  my ($exon) = @{ $self->generic_fetch($constraint) };

  return $exon;
}


=head2 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

=cut

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

  my $constraint = "e.stable_id = ?";

  $self->bind_param_generic_fetch($stable_id,SQL_VARCHAR);

  return $self->generic_fetch($constraint);
}


=head2 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

=cut

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

  my $tslice = $transcript->slice();
  my $slice;

  if ( !defined($tslice) ) {
    throw("Transcript must have attached slice to retrieve exons.");
  }

  # use a small slice the same size as the transcript
  if ( !$tslice->is_circular() ) {
    $slice =
      $self->db()->get_SliceAdaptor()->fetch_by_Feature($transcript);
  } else {
    # Circular.
    $slice = $tslice;
  }

  # Override the tables definition to provide an additional join to the
  # exon_transcript table.  For efficiency we cannot afford to have this
  # in as a left join every time.
  my @tables = $self->_tables();

  # Be extra cautious so that we do not add 'exon_transcript' twice.
  my $found = 0;
  foreach my $table (@tables) {
    if ( $table->[0] eq 'exon_transcript' ) {
      $found = 1;
      last;
    }
  }
  if ( !$found ) {
    push @tables, [ 'exon_transcript', 'et' ];
  }

  $self->{'tables'}       = \@tables;
  $self->{'final_clause'} = "ORDER BY et.transcript_id, et.rank";

  my $constraint =
      "et.transcript_id = "
    . $transcript->dbID()
    . " AND e.exon_id = et.exon_id";

  # fetch all of the exons
  my $exons = $self->fetch_all_by_Slice_constraint($slice, $constraint);

  # un-override the table definition
  delete( $self->{'tables'} );
  delete( $self->{'final_clause'} );

  # remap exon coordinates if necessary
  if($slice->name() ne $tslice->name()) {
    my @out;
    foreach my $ex (@$exons) {
      push @out, $ex->transfer($tslice);
    }
    $exons = \@out;
  }

  return $exons;
}


=head2 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

=cut

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 .= ", stable_id, version, created_date, modified_date) VALUES ( ?,?,?,?,?,?,?,?,?,?,". $created . ",". $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 );
     my $version = ($exon->version()) ? $exon->version() : 1;
     $exonst->bind_param( 10, $version, SQL_INTEGER ); 
  }

  $exonst->execute();
  $exonId = $exonst->{'mysql_insertid'};

  # 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;
}


=head2 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

=cut

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;
}


=head2 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

=cut

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

   return $self->_list_dbIDs("exon",undef, $ordered);
}


=head2 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

=cut

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

   return $self->_list_dbIDs("exon", "stable_id");
}

#_objs_from_sth
#
#  Arg [1]    : StatementHandle $sth
#  Example    : none 
#  Description: PROTECTED implementation of abstract superclass method.
#               responsible for the creation of Exons
#  Returntype : listref of Bio::EnsEMBL::Exons in target coordinate system
#  Exceptions : none
#  Caller     : internal

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 $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() ) {
    #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 ( defined($dest_mapper) ) {

      if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
	    ( $seq_region_id,  $seq_region_start,
	      $seq_region_end, $seq_region_strand )
		=
		$dest_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 )
		= $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.
      if ( !defined($seq_region_id) ) { next FEATURE }

      # 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) ) {
      if ( $dest_slice_strand == 1 ) {
        # On the positive strand.

        $seq_region_start = $seq_region_start - $dest_slice_start + 1;
        $seq_region_end   = $seq_region_end - $dest_slice_start + 1;

	if ( ( $seq_region_end > $dest_slice_start || $seq_region_end < 0 || ( $dest_slice_start > $dest_slice_end
                 && $seq_region_end < 0 ) )  && $dest_slice->is_circular() ) {
          # Handle circular chromosomes.

          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 {
        # On the negative strand.

        if ( $seq_region_start > $seq_region_end && $dest_slice->is_circular() )
        {
          # Handle circular chromosomes.

          if ( $dest_slice_start > $dest_slice_end ) {
            my $tmp_seq_region_start = $seq_region_start;
            $seq_region_start = $dest_slice_end - $seq_region_end + 1;
            $seq_region_end =
              $dest_slice_end +
              $dest_slice->seq_region_length() -
              $tmp_seq_region_start + 1;
          } else {

            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 {
          # Non-circular chromosome.

          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 != $seq_region_id ) )
      {
        next FEATURE;
      }

      $slice = $dest_slice;
    } ## end if ( defined($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

=head1 DEPRECATED METHODS

=cut


=head2 get_stable_entry_info

  Description: DEPRECATED. This method is no longer necessary.  Exons are
               always fetched with their stable identifiers (if they exist) and
               no lazy loading is necessary.

=cut

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

  deprecated( "This method call shouldnt be necessary" );

  if( !$exon || !ref $exon || !$exon->isa('Bio::EnsEMBL::Exon') ) {
     $self->throw("Needs a exon object, not a $exon");
  }
  if(!$exon->dbID){
    #$self->throw("can't fetch stable info with no dbID");
    return;
  }

  my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
  my $modified_date = $self->db->dbc->from_date_to_seconds("modified_date");
  my $sth = $self->prepare("SELECT stable_id, " . $created_date . ",
                                   " . $modified_date . ", version 
                            FROM   exon
                            WHERE  exon_id = ");

  $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
  $sth->execute();

  # my @array = $sth->fetchrow_array();
  if( my $aref = $sth->fetchrow_arrayref() ) {
    $exon->{'_stable_id'} = $aref->[0];
    $exon->{'_created'}   = $aref->[1];
    $exon->{'_modified'}  = $aref->[2];
    $exon->{'_version'}   = $aref->[3];
  }

  return 1;
}


=head2 fetch_all_by_gene_id

  Description: DEPRECATED. This method should not be needed - Exons can
               be fetched by Transcript.

=cut

sub fetch_all_by_gene_id {
  my ( $self, $gene_id ) = @_;
  my %exons;
  my $hashRef;
  my ( $currentId, $currentTranscript );

  deprecated( "Hopefully this method is not needed any more. Exons should be fetched by Transcript" );

  if( !$gene_id ) {
      $self->throw("Gene dbID not defined");
  }
  
  $self->{rchash} = {};
  
  my $query = qq {
    SELECT 
      STRAIGHT_JOIN 
	e.exon_id
      , e.contig_id
      , e.contig_start
      , e.contig_end
      , e.contig_strand
      , e.phase
      , e.end_phase
      , e.sticky_rank
    FROM transcript t
      , exon_transcript et
      , exon e
    WHERE t.gene_id = ?
      AND et.transcript_id = t.transcript_id
      AND e.exon_id = et.exon_id
    ORDER BY t.transcript_id,e.exon_id
      , e.sticky_rank DESC
  };

  my $sth = $self->prepare( $query );
  $sth->bind_param(1,$gene_id,SQL_INTEGER);
  $sth->execute();

  while( $hashRef = $sth->fetchrow_hashref() ) {
    if( ! exists $exons{ $hashRef->{exon_id} } ) {

      my $exon = $self->_exon_from_sth( $sth, $hashRef );

      $exons{$exon->dbID} = $exon;
    }
  }
  delete $self->{rchash};
  
  my @out = ();

  push @out, values %exons;

  return \@out;
}


1;