Bio::EnsEMBL::ExternalData::Mole::DBSQL SequenceAdaptor
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Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::DBSQL::BaseAdaptor
Bio::EnsEMBL::ExternalData::Mole::DBSQL::DBAdaptor
Bio::EnsEMBL::ExternalData::Mole::Sequence
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( deprecate throw warning stack_trace_dump )
Inherit
Bio::EnsEMBL::DBSQL::BaseAdaptor
Synopsis
No synopsis!
Description
No description!
Methods
_columns
No description
Code
_objs_from_sth
No description
Code
_tables
No description
Code
fetch_by_Entry
No description
Code
fetch_by_entry_id
No description
Code
fetch_by_sequence
No description
Code
Methods description
None available.
Methods code
_columnsdescriptionprevnextTop
sub _columns {
  my $self = shift;
  return ( 'seq.entry_id',
           'seq.split_counter', 'seq.sequence');
}
_objs_from_sthdescriptionprevnextTop
sub _objs_from_sth {
  my ($self, $sth) = @_;

  my @out;
  my ( $entry_id, $split_counter, $sequence );
  $sth->bind_columns(\$ entry_id,\$ split_counter,\$ sequence );

  while($sth->fetch()) {
    push @out, Bio::EnsEMBL::ExternalData::Mole::Sequence->new(
              -entry_id       => $entry_id,
              -adaptor        => $self,
              -split_counter  => $split_counter,
              -sequence       => $sequence,
              );
  }
  return\@ out;
}


1;
}
_tablesdescriptionprevnextTop
sub _tables {
  my $self = shift;
  return (['sequence' , 'seq']);
}
fetch_by_EntrydescriptionprevnextTop
sub fetch_by_Entry {
  my $self = shift;
  my $entry = shift;

  my $sequence_object = $self->fetch_by_entry_id($entry->dbID);
  return $sequence_object;
}
fetch_by_entry_iddescriptionprevnextTop
sub fetch_by_entry_id {
  my ($self, $entry_id) = @_;
  my $constraint = "seq.entry_id = '$entry_id'";
  my ($sequence_obj) = @{ $self->generic_fetch($constraint) };
  return $sequence_obj;
}
fetch_by_sequencedescriptionprevnextTop
sub fetch_by_sequence {
  my ($self, $seq) = @_;
  my $constraint = "seq.sequence = '$seq'";
  my ($sequence_obj) = @{ $self->generic_fetch($constraint) };
  return $sequence_obj;
}
General documentation
No general documentation available.