NAME

Bio::DB::BioDB - class creating the adaptor factory for a particular database

SYNOPSIS

            

              
              
$dbadp = Bio::DB::BioDB->new(
           -database => 'biosql',
                    -user     => 'root',
                    -dbname   => 'pog',
                    -host     => 'caldy',
              -port     => 3306,    # optional
                    -driver   => 'mysql'
 );
            
          

DESCRIPTION

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.

CONTACT

            

              
              
Hilmar Lapp, hlapp at gmx.net
            
          

APPENDIX

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

new

            

              
              
Title   : new
Usage   : $db = Bio::DB::BioDB->new(-database => 'biosql');
Function: Load and instantiate the encapsulating adaptor for the given
          database.
          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.
            
          

_load_dbadaptor

            

              
              
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.
            
          

add_db_mapping

            

              
              
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 "::"