NAME
Bio::DB::BioSQL::PrimarySeqAdaptor - 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 the web:
http://bio.perl.org/bioperl-bugs/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 _
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.
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::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.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.
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().store_children
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.remove_children
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().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::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.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.
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 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().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.get_biosequence
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).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._bioseq_adaptor
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)_bionamespace_adaptor
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)