NAME
Bio::DB::BioSQL::SeqFeatureAdaptor - DESCRIPTION of Object
SYNOPSIS
Give standard usage here
DESCRIPTION
Describe the object here
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 one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bio.perl.orgSupport
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 the bugs and their resolution. Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://redmine.open-bio.org/projects/bioperl/AUTHOR - Ewan Birney, Hilmar Lapp
Email birney@ebi.ac.uk Email hlapp at gmx.net
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
get_persistent_slots
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 updatedget_persistent_slot_values
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.get_foreign_key_objects
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.attach_foreign_key_objects
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().store_children
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.attach_children
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.remove_children
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().instantiate_from_row
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.populate_from_row
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().get_unique_key_query
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.Internal methods
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._seq_adaptor
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)_term_adaptor
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)_loc_adaptor
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)_anncoll_adaptor
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)_ontology_term_fk
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._featann_adaptor
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