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

	my $binend   = int $end/$bin;
	return $binstart+$BINS{$bin} if $binstart == $binend;
    }

    die "unreasonable coordinates ",$start+1,"..$end";
}

sub search_bins {
    my $self = shift;
    my ($start,$end) = @_;
    my @results;

    for my $bin (@BINS) {
	my $binstart = int $start/$bin;
	my $binend   = int $end/$bin;
	push @results,$binstart+$BINS{$bin}..$binend+$BINS{$bin};
    }
    return @results;
}


###
# object initialization
#
sub init {
  my $self          = shift;
  my ($dsn,
      $is_temporary,
      $autoindex,
      $namespace,
      $dump_dir,
      $user,
      $pass,
      $dbi_options,
      $writeable,
      $fts,
      $create,
     ) = rearrange(['DSN',
		    ['TEMP','TEMPORARY'],
		    'AUTOINDEX',
		    'NAMESPACE',
		    ['DUMP_DIR','DUMPDIR','TMP','TMPDIR'],
		    'USER',
		    ['PASS','PASSWD','PASSWORD'],
		    ['OPTIONS','DBI_OPTIONS','DBI_ATTR'],
		    ['WRITE','WRITEABLE'],
		    'FTS',
		    'CREATE',
		   ],@_);
  $dbi_options  ||= {};
  $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;
  $self->{namespace} = $namespace;
  $self->{writeable} = $writeable;

  $self->default_settings;
  $self->autoindex($autoindex)                   if defined $autoindex;
  $self->dumpdir($dump_dir)                      if $dump_dir;
  if ($self->is_temp) {
    $self->init_tmp_database();
  } elsif ($create) {
    $self->init_database('erase');
  }
}

sub table_definitions {
  my $self = shift;
  my $defs =
      {
	  feature => <<END,
(
  id        integer primary key autoincrement,
  typeid    integer not null,
  strand    integer default 0,
  "indexed" integer default 1,
  object    blob not null
)
END

	  locationlist => <<END,
(
  id      integer primary key autoincrement,
  seqname text    not null
);
create index index_locationlist on locationlist (seqname);
END

	  typelist => <<END,
(
  id  integer primary key autoincrement,
  tag text    not null collate nocase
);
create index index_typelist on typelist (tag);
END
	  name => <<END,
(
  id           integer not null,
  name         text    not null collate nocase,
  display_name integer default 0
);
create index index_name_id on name(id);
create index index_name_name on name(name);