NAME
Bio::DB::BioSQL::Pg::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 listsSupport
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::Pg::SpeciesAdaptorDriver->new();
Function: Builds a new Bio::DB::BioSQL::Pg::SpeciesAdaptorDriver object
Returns : an instance of Bio::DB::BioSQL::Pg::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 taxonget_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