Bio::DB::BioSQL::SeqFeatureAdaptor - DESCRIPTION of Object
Give standard usage here
Describe the object here
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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. The reason this method is here is that sometimes the actual slot values need to be post-processed to yield the value that gets actually stored in the database. E.g., slots holding arrays will need some kind of join function applied. Another example is if the method call needs additional arguments. Supposedly the adaptor for a specific interface knows exactly what to do here. 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.
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::SeqFeatureI 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. SeqFeatureIs have a bioentry, a key and a source as foreign keys (the two latter are ontology terms). We don''t fetch the bioentry for seqfeatures, as that may easily result in infinite loops (because the seq will look for its features). 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::SeqFeatureI has a location, annotation, and possibly sub-seqfeatures as children. The latter is not implemented yet. 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 : 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::SeqFeatureIs, we need to get the location, tag/value pairs and other annotation, and possibly sub-seqfeatures. The latter is not implemented yet. 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 need to undefine the primary keys of location objects 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 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, a Bio::Factory::SequenceFactoryI compliant object to be used for creating the object.
Title : populate_from_row Usage : Function: Populates the 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.
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 : _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)
Title : _term_adaptor Usage : $obj->_term_adaptor($newval) Function: Get/set cached persistence adaptor for an Ontology::TermI 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 _term_adaptor (a Bio::DB::PersistenceAdaptorI instance) Args : new value (a Bio::DB::PersistenceAdaptorI instance, optional)
Title : _loc_adaptor Usage : $obj->_loc_adaptor($newval) Function: Get/set cached persistence adaptor for a bioperl location 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 _loc_adaptor (a Bio::DB::PersistenceAdaptorI instance) Args : new value (a Bio::DB::PersistenceAdaptorI instance, optional)
Title : _anncoll_adaptor Usage : $obj->_anncoll_adaptor($newval) Function: Get/set cached persistence adaptor for a bioperl AnnotationCollectionI 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 _anncoll_adaptor (a Bio::DB::PersistenceAdaptorI instance) Args : new value (a Bio::DB::PersistenceAdaptorI instance, optional)
Title : _ontology_term_fk Usage : $term_fk = $obj->_ontology_term_fk($slot, $value) Function: Obtain the persistent ontology term representation of certain slots that map to ontology terms (e.g. source tag, primary tag). This is an internal method. Example : Returns : A persistent Bio::Ontology::TermI object Args : The slot for which to obtain the FK term object. The value of the slot.
Title : _featann_adaptor Usage : $anncoll = $obj->_featann_adaptor() Function: Obtains the adaptor that adapts SeqFeatureI objects to annotation collections. This is an internal method. Example : Returns : A Bio::AnnotationI compliant object that adapts a feature''s annotation Args : none
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.