/ 
bioperl-db-1.5.2_005-RC
/ Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver

NAME

Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver - DESCRIPTION of Object

SYNOPSIS

#

DESCRIPTION

This is basically a copy-and-paste job from the mysql-specific file
of the very same name.

FEEDBACK

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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/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

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

bioperl-bugs@bioperl.org
http://bugzilla.open-bio.org/

AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

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

new

Title   : new
Usage   : my $obj = new Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver();
Function: Builds a new Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver object 
Returns : an instance of Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver
Args    :

prepare_findbypk_sth

Title   : prepare_findbypk_sth
Usage   :
Function: Prepares and returns a DBI statement handle with one
          placeholder for the primary key. The statement is expected
          to return the primary key as the first and then as many
          columns as $adp->get_persistent_slots() returns, and in
          that order.

Example :
Returns : A DBI prepared statement handle with one placeholder
Args    : The Bio::DB::BioSQL::BasePersistenceAdaptor derived object 
          (basically, it needs to implement dbh() and get_persistent_slots()).
          A reference to an array of foreign key slots (class names).
          The name class for the taxon name table (default is
          'scientific name').

prepare_findbyuk_sth

Title   : prepare_findbyuk_sth
Usage   :
Function: Prepares and returns a DBI SELECT statement handle with as many
          placeholders as necessary for the given unique key.

          The statement is expected to return the primary key as the
          first and then as many columns as
          $adp->get_persistent_slots() returns, and in that order.

Example :
Returns : A DBI prepared statement handle with as many placeholders as 
          necessary for the given unique key

Args    : The calling Bio::DB::BioSQL::BasePersistenceAdaptor derived
          object (basically, it needs to implement dbh() and
          get_persistent_slots()).

          A reference to a hash with the names of the object''s slots
          in the unique key as keys and their values as values.  

          A reference to an array of foreign key objects or slots
          (class names if slot).

prepare_delete_sth

Title   : prepare_delete_sth
Usage   :
Function: Creates a prepared statement with one placeholder variable
          suitable to delete one row from the respective table the
          given class maps to.

          We override this here in order to delete from the taxon
          node table, not the taxon name table. The node table will
          cascade to the name table.

Example :
Returns : A DBI statement handle for a prepared statement with one placeholder
Args    : The calling adaptor (basically, it needs to implement dbh()).
          Optionally, additional arguments.

insert_object

 Title   : insert_object
 Usage   :
 Function:
 Example :
 Returns : The primary key of the newly inserted record.
 Args    : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object
           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).

	   The object to be inserted.

           A reference to an array of foreign key objects; if any of
           those foreign key values is NULL (some foreign keys may be
           nullable), then give the class name.

update_object

 Title   : update_object
 Usage   :
 Function:
 Example :
 Returns : The number of updated rows
 Args    : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object
           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           A reference to an array of foreign key objects; if any of those
           foreign key values is NULL (some foreign keys may be nullable),
           then give the class name.

_build_select_list

Title   : _build_select_list
Usage   :
Function: Builds and returns the select list for an object query. The list
          contains those columns, in the right order, that are necessary to
          populate the object.
Example :
Returns : An array of strings (column names, not prefixed)
Args    : The calling persistence adaptor.
          A reference to an array of foreign key entities (objects, class
          names, or adaptors) the object must attach.
          A reference to a hash table mapping entity names to aliases (if
          omitted, aliases will not be used, and SELECT columns can only be
          from one table)

get_classification

Title   : get_classification
Usage   :
Function: Returns the classification array for a taxon as identified by
          its primary key.
Example :
Returns : a reference to an array of two-element arrays, where the first
          element contains the name of the node and the second element
          denotes its rank
Args    : the calling adaptor, the primary key of the taxon

get_common_name

Title   : get_common_name
Usage   :
Function: Get the common name for a taxon as identified by its primary
          key.
Example :
Returns : a string denoting the common name
Args    : the calling adaptor, and the primary key of the taxon