NAME

Bio::DB::Map::SQL::DBAdaptor - Object representing an instance of a bioperl Map Database

SYNOPSIS

    use Bio::DB::Map::SQL::DBAdaptor;
    my $db = new Bio::DB::Map::SQL::DBAdaptor 
    ( -user   => 'user',
      -dbname => 'markermap',
      -host   => 'localhost',
      -driver => 'mysql' );
                                                

DESCRIPTION

This object represents a database that is implemented somehow (you shouldn\'t care much as long as you can get the object). From the object you can pull out other adapters, such as MarkerAdaptor or MapAdaptor.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org             - General discussion
  http://bioperl.org/MailList.shtml - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@chg.mc.duke.edu

APPENDIX

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

new

 Title   : new
 Usage   : my $db = new Bio::DB::Map::SQL::DBAdaptor(%params);
 Function: instantiates a new DBAdaptor object
 Returns : new Bio::DB::Map::SQL::DBAdaptor object
 Args    : -user   => username
           -pass   => password to use
           -dbname => database name to use
           -host   => host where db is running
           -driver => db driver to use     
 Throws  : Exception if db connection cannot be established

prepare

 Title   : prepare
 Usage   : $sth = $dbobj->prepare("select seq_start,seq_end from feature where analysis = \" \" ");
 Function: prepares a SQL statement on the DBI handle
 Example :
 Returns : A DBI statement handle object
 Args    : a SQL string

get_MapAdaptorAdaptor

 Title   : get_MapAdaptor
 Usage   :
 Function: get a MapAdaptor object
 Returns : Bio::DB::Map::SQL::MapAdaptor object
 Args    : none

get_MarkerAdaptor

 Title   : get_MarkerAdaptor
 Usage   :
 Function: get a MarkerAdaptor object
 Returns : Bio::DB::Map::SQL::MarkerAdaptor object
 Args    : none

_db_handle

 Title   : _db_handle
 Usage   : $obj->_db_handle($newval)
 Function: 
 Example : 
 Returns : value of _db_handle
 Args    : newvalue (optional)

DESTROY

 Title   : DESTROY
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :