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.orgSupport
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)