NAME
Bio::DB::BioSQL::CommentAdaptor - DESCRIPTION of Object
SYNOPSIS
Give standard usage here
DESCRIPTION
Adaptor for Comment objects inside bioperl db
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 email or the web:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/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 _
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.
Slot name generally refers to a method name, but is not
required to do so, since determining the values is under
the control of get_persistent_slot_values().
Example :
Returns : an array of method names constituting the serializable slots
Args : the object about to be inserted or updatedget_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.
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.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.
A Bio::Annotation::Comment will reference a bioentry.
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.attach_foreign_key_objects
Title : attach_foreign_key_objects
Usage :
Function: Attaches foreign key objects to the given object as far as
necessary.
This method is called after find_by_XXX() queries, not for
INSERTs or UPDATEs.
Bio::Annotation::Comment objects have a Bio::SeqI as
foreign key, but it is not referenced by the object. So we
do nothing here.
Example :
Returns : TRUE on success, and FALSE otherwise.
Args : The object to which to attach foreign key objects.
A reference to an array of foreign key values, in the order of
foreign keys returned by get_foreign_key_objects().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().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 calls 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().
Example :
Returns : An object, or undef, if the row contains no values
Args : The object to be populated, or the class to be instantiated.
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._seq_adaptor
Title : _seq_adaptor
Usage : $obj->_seq_adaptor($newval)
Function: Get/set cached persistence adaptor for a bioperl seq object.
In OO speak, consider the access class of this method protected.
I.e., call from descendants, but not from outside.
Example :
Returns : value of _seq_adaptor (a Bio::DB::PersistenceAdaptorI
instance)
Args : new value (a Bio::DB::PersistenceAdaptorI instance, optional)