Christopher Fields
and 1 contributors

NAME

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

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the object here

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

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 the bugs and their resolution. Bug reports can be submitted via the web:

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

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   : my $obj = Bio::DB::BioSQL::AnnotationCollectionAdaptor->new();
 Function: Builds a new Bio::DB::BioSQL::AnnotationCollectionAdaptor object 
 Returns : an instance of Bio::DB::BioSQL::AnnotationCollectionAdaptor
 Args    :

get_foreign_key_objects

 Title   : get_foreign_key_objects
 Usage   :
 Function: Gets the objects referenced by this object, and which therefore need
           to be referenced as foreign keys in the datastore.

           Note that the objects are expected to implement
           Bio::DB::PersistentObjectI.

           An implementation may obtain the values either through the
           object to be serialized, or through the additional
           arguments. An implementation should also make sure that the
           order of foreign key objects returned is always the same.

 Example :
 Returns : an array of Bio::DB::PersistentObjectI implementing objects
 Args    : The object about to be inserted or updated, or undef if the call
           is for a SELECT query. In the latter case return class or interface
           names that are mapped to the foreign key tables.
           Optionally, additional named parameters. A common parameter will
           be -fkobjs, with a reference to an array of foreign key objects
           that are not retrievable from the persistent object itself.

store_children

 Title   : store_children
 Usage   :
 Function: Inserts or updates the child entities of the given object in the 
           datastore.
 Example :
 Returns : TRUE on success, and FALSE otherwise
 Args    : The Bio::DB::PersistentObjectI implementing object for which the
           child objects shall be made persistent.
           A reference to an array of foreign key values, in the order of
           foreign keys returned by get_foreign_key_objects().

attach_children

 Title   : attach_children
 Usage   :
 Function: Possibly retrieve and attach child objects of the given object.

           This is called by the find_by_XXXX() methods once the base
           object has been built.

 Example :
 Returns : TRUE on success, and FALSE otherwise.
 Args    : The object for which to find and to which to attach the child
           objects.
           Foreign key objects by which to find the entries to be attached
           (as an array ref).

Inherited methods

 We override a couple of inherited methods here because an
 AnnotationCollection currently is only a virtual entity in the
 database. Hence, a number of operations greatly reduce or don't make
 sense at all.

remove

 Title   : remove
 Usage   : $objectstoreadp->remove($persistent_obj, @params)
 Function: Removes the persistent object from the datastore.
 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The object to be removed, and optionally additional (named) 
           parameters.

find_by_primary_key

 Title   : find_by_primary_key
 Usage   : $objectstoreadp->find_by_primary_key($pk)
 Function: Locates the entry associated with the given primary key and
           initializes a persistent object with that entry.

           AnnotationCollection is not an entity in the database and hence
           this method doesn''t make sense. We just throw an exception here.
 Example :
 Returns : 
 Args    : 

find_by_unique_key

 Title   : find_by_unique_key
 Usage   :
 Function: Locates the entry matching the unique key attributes as set in the
           passed object, and populates a persistent object with this entry.

           AnnotationCollection is not an entity in the database and hence
           this method doesn''t make sense. We just throw an exception here.
 Example :
 Returns : 
 Args    : 

add_association

 Title   : add_assocation
 Usage   :
 Function: Stores the association between given objects in the datastore.

           We override this here in order to propagate associations of the
           AnnotationCollection to all the annotations it contains.
 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : Named parameters. At least the following must be recognized:
               -objs   a reference to an array of objects to be associated with
                       each other
               -values a reference to a hash the keys of which are abstract
                       column names and the values are values of those columns.
                       These columns are generally those other than
                       the ones for foreign keys to the entities to be
                       associated
  Caveats: Make sure you *always* give the objects to be associated in the
           same order.

find_by_association

 Title   : find_by_association
 Usage   :
 Function: Locates those records associated between a number of
           objects. The focus object (the type to be instantiated)
           depends on the adaptor class that inherited from this
           class.

           We override this here to propagate this to all possible
           annotations.

 Example :
 Returns : A Bio::DB::Query::QueryResultI implementing object 
 Args    : Named parameters. At least the following must be recognized:
               -objs   a reference to an array of objects to be
                       associated with each other
               -obj_factory the factory to use for instantiating the
                       AnnotationCollectionI implementation.
  Caveats: Make sure you *always* give the objects to be associated in
           the same order.

remove_children

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

           We need to undefine the primary keys of all contained
           children objects 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().

Internal Methods

 These are mostly private or 'protected.' Methods which are in the
 latter class have this explicitly stated in their
 documentation. 'Protected' means you may call these from derived
 classes, but not from outside.

 Most of these methods cache certain adaptors or otherwise reduce call
 path and object creation overhead. There's no magic here.

_anntype_assoc_args

 Title   : _anntype_assoc_args
 Usage   :
 Function: Get the arguments to be passed to the annotation object
           adaptor''s add_association method, based on the type of
           annotation to be associated.

           This is an internal method.

 Example :
 Returns : an array of arguments in the format of named parameters
 Args    : the adaptor for the annotation object
           the type of the annotation object (a string)

_supported_annotation_map

 Title   : _supported_annotation_map
 Usage   : $obj->_supported_annotation_map($newval)
 Function: Get/set the map of supported annotation types (implementing
           classes) to annotation keys and persistence arguments.

           The values of the map are anonymous hashes themselves with
           currently the following keys and values.
             key     the annotation collection key for this type of
                     annotation
             link    the type of link between the collection and the
                     annotation object (child or association)

 Example : 
 Returns : value of _supported_annotation_map (a reference to hash map)
 Args    : new value (a reference to a hash map)