Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver - DESCRIPTION of Object
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This is basically a copy-and-paste job from the mysql-specific file of the very same name.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
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').
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 $adp->get_persistent_slots() returns, and in that order. Example : Returns : A DBI prepared statement handle with as many placeholders as necessary for the given unique key Args : The calling Bio::DB::BioSQL::BasePersistenceAdaptor derived object (basically, it needs to implement dbh() and get_persistent_slots()). A reference to a hash with the names of the object''s slots in the unique key as keys and their values as values. A reference to an array of foreign key objects or slots (class names if slot).
Title : prepare_delete_sth Usage : Function: Creates a prepared statement with one placeholder variable suitable to delete one row from the respective table the given class maps to. We override this here in order to delete from the taxon node table, not the taxon name table. The node table will cascade to the name table. Example : Returns : A DBI statement handle for a prepared statement with one placeholder Args : The calling adaptor (basically, it needs to implement dbh()). Optionally, additional arguments.
Title : insert_object Usage : Function: Example : Returns : The primary key of the newly inserted record. Args : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object (basically, it needs to implement dbh(), sth($key, $sth), dbcontext(), and get_persistent_slots()). The object to be inserted. A reference to an array of foreign key objects; if any of those foreign key values is NULL (some foreign keys may be nullable), then give the class name.
Title : update_object Usage : Function: Example : Returns : The number of updated rows Args : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object (basically, it needs to implement dbh(), sth($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.
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)
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
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
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::BioEntry
CPAN shell
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.