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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- AUTHOR - Ewan Birney, Hilmar Lapp
- Internal methods
Bio::DB::BioSQL::PrimarySeqAdaptor - DESCRIPTION of Object
Give standard usage here
Describe the object here
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.
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 the bugs and their resolution. Bug reports can be submitted via the web:
Email email@example.com Email hlapp at gmx.net
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_persistent_slots Usage : Function: Get the slots of the object that map to attributes in its respective entity in the datastore. Slots should be methods callable without an argument. Example : Returns : an array of method names constituting the serializable slots Args : the object about to be inserted or updated
Title : get_persistent_slot_values Usage : Function: Obtain the values for the slots returned by get_persistent_slots(), in exactly that order. 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.
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::PrimarySeqI references a namespace with authority. 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.
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. PrimarySeqIs have a BioNamespace as foreign key. 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().
Title : store_children Usage : Function: Inserts or updates the child entities of the given object in the datastore. Bio::PrimarySeqI has a sequence as child. Example : Returns : TRUE on success, and FALSE otherwise Args : The Bio::DB::PersistentObjectI implementing object for which the child objects shall be made persistent.
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().
Title : attach_children Usage : Function: Possibly retrieve and attach child objects of the given object. This is needed when whole object trees are supposed to be built when a base object is queried for and returned. An example would be Bio::SeqI objects and all the annotation objects that hang off of it. This is called by the find_by_XXXX() methods once the base object has been built. For Bio::PrimarySeqIs, we need to get the biosequence attributes as well. Example : Returns : TRUE on success, and FALSE otherwise. Args : The object for which to find and to which to attach the child objects.
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. 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, a Bio::Factory::SequenceFactoryI compliant object to be used for creating the object.
Title : populate_from_row Usage : Function: Populates an object with values from columns of the row. Example : Returns : The object populated, or undef, if the row contains no values Args : The object to be populated. 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().
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.
Title : get_biosequence Usage : Function: Returns the actual sequence for a bioentry, or a substring of it. Example : Returns : A string (the sequence or subsequence) Args : The primary key of the bioentry for which to obtain the sequence. Optionally, start and end position if only a subsequence is to be returned (for long sequences, obtaining the subsequence from the database may be much faster than obtaining it from the complete in-memory string, because the latter has to be retrieved first).
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.
Title : _bioseq_adaptor Usage : $obj->_bioseq_adaptor($newval) Function: Get/set cached persistence adaptor for the biosequence. In OO speak, consider the access class of this method protected. I.e., call from descendants, but not from outside. Example : Returns : value of _bioseq_adaptor (a Bio::DB::PersistenceAdaptorI instance) Args : new value (a Bio::DB::PersistenceAdaptorI instance, optional)
Title : _bionamespace_adaptor Usage : $obj->_bionamespace_adaptor($newval) Function: Get/set cached persistence adaptor for the bionamespace. In OO speak, consider the access class of this method protected. I.e., call from descendants, but not from outside. Example : Returns : value of _bionamespace_adaptor (a Bio::DB::PersistenceAdaptorI instance) Args : new value (a Bio::DB::PersistenceAdaptorI instance, 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.
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