/ 
bioperl-db-1.5.2_100
/ Bio::DB::BioSQL::SpeciesAdaptor

NAME

Bio::DB::BioSQL::SpeciesAdaptor - DESCRIPTION of Object

SYNOPSIS

Give standard usage here

DESCRIPTION

Species DB adaptor

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 one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bio.perl.org

Reporting Bugs

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

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

AUTHOR - Ewan Birney, Hilmar Lapp

Email birney@ebi.ac.uk Email 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   :
Function: Instantiates the persistence adaptor.
Example :
Returns : 
Args    :

get_persistent_slots

Title   : get_persistent_slots
Usage   :
Function: Get the slots of the object that map to attributes in its respective
          entity in the datastore.

          Slots should be methods callable without an argument.

          This is a strictly abstract method. A derived class MUST override
          it to return something meaningful.
Example :
Returns : an array of method names constituting the serializable slots
Args    : the object about to be inserted or updated

get_persistent_slot_values

Title   : get_persistent_slot_values
Usage   :
Function: Obtain the values for the slots returned by get_persistent_slots(),
          in exactly that order.

          The reason this method is here is that sometimes the actual slot
          values need to be post-processed to yield the value that gets
          actually stored in the database. E.g., slots holding arrays
          will need some kind of join function applied. Another example is if
          the method call needs additional arguments. Supposedly the
          adaptor for a specific interface knows exactly what to do here.

          Since there is also populate_from_row() the adaptor has full
          control over mapping values to a version that is actually stored.
Example :
Returns : A reference to an array of values for the persistent slots of this
          object. Individual values may be undef.
Args    : The object about to be serialized.
          A reference to an array of foreign key objects if not retrievable 
          from the object itself.

instantiate_from_row

Title   : instantiate_from_row
Usage   :
Function: Instantiates the class this object is an adaptor for, and populates
          it with values from columns of the row.

          This implementation call populate_from_row() to do the real job.
Example :
Returns : An object, or undef, if the row contains no values
Args    : A reference to an array of column values. The first column is the
          primary key, the other columns are expected to be in the order 
          returned by get_persistent_slots().
          Optionally, the object factory to be used for instantiating the
          proper class. The adaptor must be able to instantiate a default
          class if this value is undef.

populate_from_row

Title   : populate_from_row
Usage   :
Function: Instantiates the class this object is an adaptor for, and populates
          it with values from columns of the row.

          Usually a derived class will instantiate the proper class and pass
          it on to populate_from_row().

          This method MUST be overridden by a derived object.
Example :
Returns : An object, or undef, if the row contains no values
Args    : The object to be populated.
          A reference to an array of column values. The first column is the
          primary key, the other columns are expected to be in the order 
          returned by get_persistent_slots().

get_unique_key_query

Title   : get_unique_key_query
Usage   :
Function: Obtain the suitable unique key slots and values as determined by the
          attribute values of the given object and the additional foreign
          key objects, in case foreign keys participate in a UK. 

Example :
Returns : One or more references to hash(es) where each hash
          represents one unique key, and the keys of each hash
          represent the names of the object's slots that are part of
          the particular unique key and their values are the values
          of those slots as suitable for the key.
Args    : The object with those attributes set that constitute the chosen
          unique key (note that the class of the object will be suitable for
          the adaptor).
          A reference to an array of foreign key objects if not retrievable 
          from the object itself.

remove_children

Title   : remove_children
Usage   :
Function: This method is to cascade deletes in maintained objects.

          We just return TRUE here.

Example :
Returns : TRUE on success and FALSE otherwise
Args    : The persistent object that was just removed from the database.
          Additional (named) parameter, as passed to remove().

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 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 primary key of the taxon