Bio::DB::BioSQL::SimpleValueAdaptor - DESCRIPTION of Object
Give standard usage here
SimpleValue DB adaptor
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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. Note that the objects are expected to implement Bio::DB::PersistentObjectI. 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.
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. 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. Usually, those child objects will reference the given object as a foreign key. We override this here from the ontology term adaptor because there is no synonyms or dbxrefs for SimpleValue tags. I.e., we revert to the default behaviour of doing nothing. 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().
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. We override this here from the ontology term adaptor because there is no synonyms or dbxrefs for SimpleValue tags. I.e., we revert to the default behaviour of doing nothing. Example : Returns : TRUE on success, and FALSE otherwise. Args : The object for which to find and to which to attach the child objects.
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 : 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 call 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.
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. Example : Returns : An object, 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 : 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.
Title : add_assocation Usage : Function: Stores the association between given objects in the datastore. We override this here to make sure the value slot gets stored in associations. 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.
Title : find_by_association Usage : Function: Locates those records associated between a SimpleValue annotation and another object. We override this here in order to be able to constrain by the ontology of a term (which is the category of the tag). 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 object from the found rows -constraints a reference to an array of additional L<Bio::DB::Query::QueryConstraint> objects -values the values to bind to the constraint clauses, as a hash reference keyed by the constraints Caveats: Make sure you *always* give the objects to be associated in the same order.
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. SimpleValues are not identifiable by primary key. It is suspicious if someone calls this method, so we throw an exception until we know better. Example : Returns : An instance of the class this adaptor adapts, represented by an object implementing Bio::DB::PersistentObjectI, or undef if no matching entry was found. Args : The primary key. Optionally, the Bio::Factory::ObjectFactoryI compliant object factory to be used for instantiating the proper class. If the object does not implement Bio::Factory::ObjectFactoryI, it is assumed to be the object to be populated with the query results.
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 : _ontology_fk Usage : $obj->_ontology_fk($svann) Function: Get/set the ontology foreign key constant. This is a private method. Example : Returns : value of _ontology_fk (a Bio::Ontology::OntologyI compliant object) Args : the L<Bio::Annotation::SimpleValue> object for which to return the ontology new value (a Bio::Ontology::OntologyI compliant object, optional)
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::BioEntry
CPAN shell
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.