NAME
Bio::DB::Persistent::PersistentObject - makes a given object persistent
SYNOPSIS
# obtain a PersistentObject somehow, e.g.
$pobj = $dbadaptor->create_persistent("Bio::Seq");
# manipulate and query as if it were the wrapped object itself
print $pobj->isa("Bio::PrimarySeqI"), "\n";
$pobj->display_id("O238356");
$pobj->seq("ATCATCGACTGACAGGCAGTATCGACTAGCA");
$fea = Bio::SeqFeature::Generic->new(-start => 3, -end => 15);
$fea->attach_seq($pobj);
# and so on and so forth
# and, finally, or whenever suitable, make it persistent in the datastore
$pobj->create();
# change it
$pobj->desc("not a useful description");
# and update it in the datastore
$pobj->store();
# you may also want it to disappear
$pobj->remove();DESCRIPTION
This class takes any Bioperl object for which an adaptor exists for a certain datastore and makes it implement Bio::DB::PersistentObjectI.
There is one single caveat though. The wrapped object must not use any of the method names defined in Bio::DB::PersistentObjectI, nor obj() or adaptor(). If it does, calls of these methods will never get routed to the wrapped object.
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 the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing listsSupport
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 of the bugs and their resolution. Bug reports can be submitted via the web:
http://redmine.open-bio.org/projects/bioperl/AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
Describe contact details here
CONTRIBUTORS
Additional contributors names and emails here
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::Persistent::PersistentObject->new();
Function: Builds a new Bio::DB::Persistent::PersistentObject object
Returns : an instance of Bio::DB::Persistent::PersistentObject
Args : -object => $obj_to_be_wrapped (mandatory)
-adaptor => $adaptor_for_obj (optional, may be set later)create
Title : create
Usage : $obj->create()
Function: Creates the object as a persistent object in the datastore. This
is equivalent to an insert.
Note that you will be able to retrieve the primary key at any time
by calling primary_key() on the object.
Example :
Returns : The newly assigned primary key.
Args : 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
Title : store
Usage : $obj->store()
Function: Updates the persistent object in the datastore to reflect its
attribute values.
Example :
Returns : TRUE on success and FALSE otherwise
Args : 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.remove
Title : remove
Usage : $obj->remove()
Function: Removes the persistent object from the datastore.
Example :
Returns : TRUE on success and FALSE otherwise
Args : noneprimary_key
Title : primary_key
Usage : $obj->primary_key($newval)
Function: Get the primary key of the persistent object in the datastore.
Note that this implementation does not permit changing the
primary key once it has been set. This is for sanity
reasons, and may or may not be relaxed in the future. The
only exception is changing it to undef.
Example :
Returns : value of primary_key (a scalar)
Args : new value (a scalar, optional)obj
Title : obj
Usage : $obj->obj()
Function: Get/set the object that is made persistent through this adaptor.
Note that this implementation does not allow to change the
value once it has been set. This is for sanity reasons, and
may or may not be relaxed in the future.
Example :
Returns : The object made persistent through this adaptor
Args : On set, the new value. Read above for caveat.adaptor
Title : adaptor
Usage : $obj->adaptor($newval)
Function: Get/set of the PersistenceAdaptorI compliant object that actually
implements persistence for this object
Example :
Returns : A Bio::DB::PersistenceAdaptorI compliant object
Args : Optionally, on set a Bio::DB::PersistenceAdaptorI compliant objectis_dirty
Title : is_dirty
Usage : $obj->is_dirty($newval)
Function: Get/set whether this persistent object is to be considered
dirty.
An object is considered dirty if one or more of it's
properties has been altered since it was last obtained
from, stored in, or created in the database, or if the
create() (insert) or the last store() (update) hasn't been
committed or rolled back yet.
There are currently 3 known states of this attribute. A
value of zero (or false) means the object has not been
modified since it either came from the database, or since
the changes have been serialized (via store()) and
committed (via commit()). A negative value means changes
have been serialized, but not yet committed. A positive
value means there have been unserialized changes on the
object.
Example :
Returns : value of is_dirty (a scalar)
Args : on set, new value (a scalar or undef, optional)Methods for transactional control
Rollback and commitcommit
Title : commit
Usage :
Function: Commits the current transaction, if the underlying driver
supports transactions.
Example :
Returns : TRUE
Args : nonerollback
Title : rollback
Usage :
Function: Triggers a rollback of the current transaction, if the
underlying driver supports transactions.
Example :
Returns : TRUE
Args : noneMethods to mimic the wrapped object
isa
Title : isa
Usage :
Function: This is a standard perl object method. We override it here in order
to generically claim we implement everything that the wrapped
object does.
Example :
Returns : TRUE if this object is an instance of the given class, or inherits
from the given class, and FALSE otherwise
Args : the class to query for (a scalar string)can
Title : can
Usage :
Function: This is a standard perl object method. We override it here in order
to generically claim we 'can' everything that the wrapped
object does.
Example :
Returns : TRUE if this object is has the named method, and FALSE otherwise
Args : the method to query for (a scalar string)Implementation of the decorating methods
See Bio::DB::PersistentObjectI for further documentation of the methods.
rank
Title : rank
Usage : $obj->rank($newval)
Function: Get/set the rank of this persistent object in a 1:n or n:n
relationship.
Example :
Returns : value of rank (a scalar)
Args : new value (a scalar or undef, optional)foreign_key_slot
Title : foreign_key_slot
Usage : $obj->foreign_key_slot($newval)
Function: Get/set of the slot name that is referring to this persistent
object as a foreign key.
Example :
Returns : value of foreign_key_slot (a scalar)
Args : new value (a scalar or undef, optional)