NAME
Bio::DB::BioSQL::TermAdaptor - DESCRIPTION of Object
SYNOPSIS
Give standard usage here
DESCRIPTION
Term DB adaptor
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@bioperl.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
Describe contact details here
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage :
Function: Instantiates the persistence adaptor.
Example :
Returns :
Args :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.
Note that the objects are expected to implement
Bio::DB::PersistentObjectI.
An implementation may obtain the values either through the
object to be serialized, or through the additional
arguments. An implementation should also make sure that the
order of foreign key objects returned is always the same.
Note also that in order to indicate a NULL value for a
nullable foreign key, either put an object returning undef
from primary_key(), or put the name of the class
instead. DO NOT SIMPLY LEAVE IT OUT.
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.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.
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.
The implementation can assume that all of the child objects
are already Bio::DB::PersistentObjectI.
Ontology terms have synonyms and dbxrefs as children.
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().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.
An ontology term has synonyms and dbxrefs as children.
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.
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, 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.populate_from_row
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().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.Methods overriden from BasePersistenceAdaptor
Public methods specific to this module
remove_synonyms
Title : remove_synonyms
Usage :
Function: Removes synonyms for the given ontology term.
Example :
Returns : TRUE on success, and FALSE otherwise.
Args : The persistent term object for which to remove the synonyms
(a Bio::DB::PersistentObjectI compliant object with defined
primary key).store_synonym
Title : store_synonym
Usage :
Function: Stores a synonym for an ontology term.
Example :
Returns : TRUE on success, and FALSE otherwise.
Args : The persistent term object for which to store the synonym
(a Bio::DB::PersistentObjectI compliant object with defined
primary key).
The synonym to store (a scalar). get_synonyms
Title : get_synonyms
Usage :
Function: Retrieves the synonyms for an ontology term and adds them
the term's synonyms.
Example :
Returns : TRUE on success, and FALSE otherwise.
Args : The persistent term object for which to retrieve the synonyms
(a Bio::DB::PersistentObjectI compliant object with defined
primary key).Private methods
These are mostly convenience and/or shorthand methods._ont_adaptor
Title : _ont_adaptor
Usage : $obj->_ont_adaptor($newval)
Function: Get/set the ontology persistence adaptor.
Example :
Returns : value of _ont_adaptor (a Bio::DB::PersistenceAdaptorI object)
Args : on set, new value (a Bio::DB::PersistenceAdaptorI object
or undef, optional)_build_dblink
Title : _build_dblink
Usage :
Function: Create a Bio::Annotation::DBLink object for a flat
dbxref string.
Example :
Returns : A Bio::Annotation::DBLink instance
Args : The dbxref as a flat string (DB:acc.version format)