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Summary

Bio::EnsEMBL::Compara::DBSQL::DnaFragRegionAdaptor - DESCRIPTION of Object

Package variables

Included modules

Inherit

Bio::EnsEMBL::DBSQL::BaseAdaptor

Synopsis

Give standard usage here

Description

Describe the object here

Methods

Methods description

None available.

Methods code

sub fetch_by_synteny_region_id {

  my ($self, $synteny_region_id) = @_;
  
  if( !defined $synteny_region_id ) {
    throw("fetch_by_synteny_region_id with no synteny_region_id!");
  }
#  print "synteny_region_id : $synteny_region_id\n";
  my $sth = $self->prepare("select synteny_region_id, dnafrag_id, dnafrag_start, dnafrag_end, dnafrag_strand from dnafrag_region where synteny_region_id = $synteny_region_id");
  $sth->execute;

  
  my ($dnafrag_id, $dnafrag_start, $dnafrag_end, $dnafrag_strand);
  $sth->bind_columns(\$synteny_region_id,\$ dnafrag_id,\$ dnafrag_start,\$ dnafrag_end,\$ dnafrag_strand);
  
  my $dfrs;
  while ($sth->fetch()) {
    my $dfr = new Bio::EnsEMBL::Compara::DnaFragRegion;
    $dfr->synteny_region_id($synteny_region_id);
    $dfr->dnafrag_id($dnafrag_id);
    $dfr->dnafrag_start($dnafrag_start);
    $dfr->dnafrag_end($dnafrag_end);
    $dfr->dnafrag_strand($dnafrag_strand);
    $dfr->adaptor($self);
    push @{$dfrs}, $dfr;
  }
  return $dfrs;

}

sub store {

   my ($self,$dfr) = @_;

   if( !ref $dfr || !$dfr->isa("Bio::EnsEMBL::Compara::DnaFragRegion") ) {
       throw("$dfr is not a DnaFragRegion object");
   }

   my $sth = $self->prepare("insert into dnafrag_region (synteny_region_id, dnafrag_id, dnafrag_start, dnafrag_end, dnafrag_strand) VALUES (?,?,?,?,?)");
   
   $sth->execute($dfr->synteny_region_id, $dfr->dnafrag_id, $dfr->dnafrag_start, $dfr->dnafrag_end, $dfr->dnafrag_strand);
   $dfr->adaptor($self);
   
   return 1;
}

1;

}

General documentation

Ensembl - ensembl-dev@ebi.ac.uk

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _