Christopher Fields > BioPerl-DB > Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver

Download:
BioPerl-DB-1.006900.tar.gz

Dependencies

Annotate this POD

CPAN RT

Open  0
View/Report Bugs
Source  

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 ^

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/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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://redmine.open-bio.org/projects/bioperl/

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 = Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver->new();
 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
syntax highlighting: