Bio::DB BioDB
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::DB::BioDB - class creating the adaptor factory for a particular database
Package variables
Privates (from "my" definitions)
$default_prefix = "Bio::DB::"
$initrc_name = ".bioperldb"
%db_map = ("biosql" => "Bio::DB::BioSQL::", "map" => "Bio::DB::Map::")
@DBC_MODULES = ("DBAdaptor", "dbadaptor")
Included modules
Scalar::Util qw ( blessed )
    $dbadp = Bio::DB::BioDB->new(
-database => 'biosql',
-user => 'root',
-dbname => 'pog',
-host => 'caldy',
-port => 3306, # optional
-driver => 'mysql'
This object represents a database that is implemented somehow (you
should not care much as long as you can get the object). From the
object you can pull out other adapters, such as the BioSeqAdapter etc.
Methods description
newcode    nextTop
 Title   : new
Usage : $db = Bio::DB::BioDB->new(-database => 'biosql');
Function: Load and instantiate the encapsulating adaptor for the given
This module acts as a factory, similar in spirit to Bio::SeqIO, but instead of a sequence stream it returns the adaptor object for the specified database. Example : Returns : a Bio::DB::DBAdaptorI implementing object Args : Named parameters. Currently recognized are -database the name of the database for which the encapsulating adaptor is sought (biosql|markerdb) -dbcontext a Bio::DB::DBContextI implementing object -initrc a scalar denoting a file which when evaluated by perl results in a hash reference or an array reference (to an array with an even number of elements) representing the arguments for this method and for creating an instance of Bio::DB::SimpleDBContext. The special value DEFAULT means to use the file .bioperldb in either the current directory or the home directory, in this order. -printerror whether or not the database and statement handles to be created when necessary should print all errors (the adaptor modules will handle errors themselves, too) Instead of -dbcontext, you can also pass all parameters accepted by Bio::DB::SimpleDBContext::new(), and this module will create the context for you and set the dbadaptor property to the returned value. Note that if you do pass in your own DBContextI object, as a side effect the dbadaptor() property will be changed by this method to reflect the created adaptor. Note also that if using the -initrc argument any separately supplied arguments will override and supplement the arguments defined in that file.
 Title   : _load_dbadaptor
Usage : $self->_load_dbadaptor("Bio::DB::BioSQL::");
Function: Loads up (like use) the DBAdaptorI implementing module for a
database at run time on demand.
Example :
Returns : TRUE on success
Args : The prefix of the database implementing modules.
 Title   : add_db_mapping
Usage : $self->add_db_mapping(key, value)
Function: Adds another package path mapping to the static private hash %db_map.
Example : add_db_mapping("FastBioSQL", "Bio::Das::BioSQL::");
Returns : None
Args : key - arbitrary identifier, value - Perl package path ending in "::"
Methods code
    %LOADED = ();
sub new {
    my($pkg, @args) = @_;
    my $self = $pkg->SUPER::new(@args);

    my ($biodb, $dbc, $prerr, $initrc) = 
                           ], @args);

    # first check whether we need to read an initialization record
if ($initrc && ($initrc eq "DEFAULT")) { foreach my $dir (".",$ENV{HOME}) { $initrc = Bio::Root::IO->catfile($dir,$initrc_name); last if -e $initrc; # the default behavior is to ignore if the file isn't
# present in any of the possible locations
$initrc = undef; } } if ($initrc) { eval { $initrc = do $initrc; }; $self->throw("error in evaluating '$initrc': $@") if $@; $self->throw("unable to read file '$initrc': $!") if $!; $self->throw("'$initrc' failed to return an array ref or hash ref") unless $initrc || !ref($initrc); if (blessed($initrc) && $initrc->isa("Bio::DB::DBContextI")) { # we allow this too
$dbc = $initrc; $initrc = undef; } else { # if necessary convert to array reference
if (ref($initrc) eq "HASH") { $initrc = [%$initrc]; } # append explicitly supplied arguments
push(@$initrc, @args); # build parameter hash while lower-casing all keys; this will
# also let supplied arguments override those read from file
my %params = (); while (@$initrc) { my $key = lc(shift(@$initrc)); my $val = shift(@$initrc); # don't let undefs override values possibly defined in %initrc
$params{$key} = $val if defined($val); } # check for our arguments; they may have come through the file
$biodb = $params{-database} unless $biodb; $prerr = $params{-printerror} unless defined($prerr); $self->verbose($params{-verbose}) unless defined($self->verbose) || !exists($params{-verbose}); # restore argument list from consolidated parameter map
@args = %params; } } # all arguments should be there now
$self->throw("you must provide the database (schema)") unless $biodb; if(exists($db_map{lc($biodb)})) { $biodb = $db_map{lc($biodb)}; } else { $biodb = $default_prefix . $biodb . "::"; } my $dbadp_class = $self->_load_dbadaptor($biodb); if(! $dbadp_class) { $self->throw("fatal: unable to load DBAdaptor for database: $biodb". "{" . join(",", @DBC_MODULES) . "} all failed to load"); } my $mydbc = $dbc || Bio::DB::SimpleDBContext->new(@args); my $dbadp = $dbadp_class->new(-dbcontext => $mydbc, -printerror => $prerr, -verbose => $self->verbose); # store the adaptor in the context
$mydbc->dbadaptor($dbadp); # success - we hope
return $dbadp;
sub _load_dbadaptor {
    my ($self, $db) = @_;
    my @msgs = ();

    # check if it's successfully been loaded already before
return $LOADED{$db} if(exists($LOADED{$db})); # try all possibilities
foreach my $dbadp_name (@DBC_MODULES) { eval { $self->_load_module($db . $dbadp_name); }; if($@) { push(@msgs, $@); } else { $LOADED{$db} = $db . $dbadp_name; last; } } $self->warn("failed to load dbadaptor: " . join("\n", @msgs)) if ! $LOADED{$db}; return $LOADED{$db};
sub add_db_mapping {
      my ($self, $key, $value) = @_;
      $db_map{lc $key} = $value;

General documentation
    Hilmar Lapp, hlapp at
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _