15 Apr 2011 19:35:57 UTC
- Distribution: BioPerl-DB
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- License: perl_5
- Perl: v5.6.1
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- This version
- Latest versionCJFIELDS Christopher Fieldsand 1 contributors
- BioPerl Team
- AUTHOR - Hilmar Lapp
- Methods for managing persistence of this object
- Methods for transactional control
- Decorating methods
Bio::DB::PersistentObjectI - DESCRIPTION of Interface
Give standard usage here
Describe the interface here
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
Email hlapp at gmx.net
Describe contact details here
Additional contributors names and emails here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Create (insert), store (update), remove (delete), and the primary key
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.
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.
Title : remove Usage : $obj->remove() Function: Removes the persistent object from the datastore. Example : Returns : TRUE on success and FALSE otherwise Args : none
Title : primary_key Usage : $obj->primary_key($newval) Function: Get the primary key of the persistent object in the datastore. Note that an implementation may not permit changing the primary key once it has been set. For most applications, changing an existing primary key value to another one is a potentially very hazardous operation and will hence be prohibited. Example : Returns : value of primary_key (a scalar) Args : new value (a scalar, optional)
Title : obj Usage : $obj->obj() Function: Get/set the object that is made persistent through this adaptor. Note that an implementation is not required to allow setting a value. In fact, an implementation is encouraged to disallow changing the value once it has been set. Implementations based on inheriting from the class to be made persistent will just return $self here. Example : Returns : The object made persistent through this adaptor Args : On set, the new value. Read above for caveat.
Rollback and commit
Title : commit Usage : Function: Commits the current transaction, if the underlying driver supports transactions. Example : Returns : TRUE Args : none
Title : rollback Usage : Function: Triggers a rollback of the current transaction, if the underlying driver supports transactions. Example : Returns : TRUE Args : none
These methods aren't intrinsically necessary on this interface, but rather ease recurrent tasks when serializing objects and translate from object model to relational model.
Title : rank Usage : $obj->rank($newval) Function: Get/set the rank of this persistent object in a 1:n or n:n relationship. This method is here in order to ease maintaining the order of objects in an array property or cardinality-n association. Unless the schema mandates the corresponding attribute as NOT NULL, derived classes may override the implementation given here with an empty one. In practice it may only pertain to few objects and hence could be just as well stuck onto those classes instead of also on the interface. This design decision is up for debate - if people don''t like it, it can be changed without too much effort. Example : Returns : value of rank (a scalar) Args : new value (a scalar or undef, optional)
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. This should come in a fully-qualified form. The fully qualified form is the class name (or adaptor name for the class) that defines the slot, followed by a double-colon and the name of the slot (method) itself. I.e., it is the name of the method as class method. Without this method, the name of the foreign key may be determined automatically based on naming convention, or based on a full mapping table. Neither is always possible because the situation can be ambiguous, e.g., if an entity references another instance of itself as foreign key, or if an entity references the same other entity via multiple foreign keys (e.g. entity associated to itself). This method is here only to aid ferrying this value from adaptors to schema drivers and mappers who need to actually figure the name of the foreign key column in the physical schema. An adaptor is not required to use it, and everyone else other than the intended sender and recipient should know what he/she is doing before tampering with it. Example : Returns : value of foreign_key_slot (a scalar) Args : new value (a scalar or undef, optional)
Module Install Instructions
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.