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lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

 Function: fetch feature from database
 Returns : feature
 Args    : primary id
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

This method is the back end for fetch(). It accepts a primary_id and
returns a feature object. It must be implemented by the adaptor.

In practice, the implementation will retrieve the serialized
Bio::SeqfeatureI object from the database and pass it to the thaw()
method to unserialize it and synchronize the primary_id.

=cut

# _fetch($id)
sub _fetch { shift->throw_not_implemented }

=head2 _fetch_many

 Title   : _fetch_many
 Usage   : $feature = $db->_fetch_many(@primary_ids)

lib/Bio/DB/SeqFeature/Store/DBI/SQLite.pm  view on Meta::CPAN

  $writeable    = 1 if $is_temporary or $dump_dir;

  $dsn or $self->throw("Usage: ".__PACKAGE__."->init(-dsn => \$dbh || \$dsn)");

  my $dbh;
  if (ref $dsn) {
    $dbh = $dsn;
  } else {
    $dsn = "dbi:SQLite:$dsn" unless $dsn =~ /^dbi:/;
    $dbh = DBI->connect($dsn,$user,$pass,$dbi_options) or $self->throw($DBI::errstr);
    $dbh->do("PRAGMA synchronous = OFF;"); # makes writes much faster
    $dbh->do("PRAGMA temp_store = MEMORY;"); # less disk I/O; some speedup
    $dbh->do("PRAGMA cache_size = 20000;"); # less disk I/O; some speedup
    # Keep track of database file location
    my $cwd = getcwd;
    my ($db_file) = ($dsn =~ m/(?:db(?:name)?|database)=(.+)$/);
    $self->{dbh_file} = "$cwd/$db_file";
  }
  $self->{dbh}       = $dbh;
  $self->{fts}       = $fts;
  $self->{is_temp}   = $is_temporary;