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Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

This method is the back end for init_database(). It must be
implemented by an adaptor that inherits from
Bio::DB::SeqFeature::Store. It returns true on success. @features = $db->features(-seqid=>'Chr1');

=cut

sub _init_database { shift->throw_not_implemented }

=head2 _store

 Title   : _store
 Usage   : $success = $db->_store($indexed,@objects)
 Function: store seqfeature objects into database
 Returns : true on success
 Args    : a boolean flag indicating whether objects are to be indexed,
           and one or more objects
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

This method is the back end for store() and store_noindex(). It should
write the seqfeature objects into the database. If indexing is
requested, the features should be indexed for query and
retrieval. Otherwise the features should be stored without indexing
(it is not required that adaptors respect this).

If the object has no primary_id (undef), then the object is written
into the database and assigned a new primary_id. If the object already
has a primary_id, then the system will perform an update, replacing
whatever was there before.

In practice, the implementation will serialize each object using the
freeze() method and then store it in the database under the
corresponding primary_id. The object is then updated with the
primary_id.

=cut

# _store($indexed,@objs)
sub _store {
  my $self    = shift;
  my $indexed = shift;
  my @objs    = @_;
  $self->throw_not_implemented;
}

=head2 _fetch

 Title   : _fetch
 Usage   : $feature = $db->_fetch($primary_id)
 Function: fetch feature from database
 Returns : feature
 Args    : primary id
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

This method is the back end for fetch(). It accepts a primary_id and
returns a feature object. It must be implemented by the adaptor.

In practice, the implementation will retrieve the serialized
Bio::SeqfeatureI object from the database and pass it to the thaw()
method to unserialize it and synchronize the primary_id.

=cut

# _fetch($id)
sub _fetch { shift->throw_not_implemented }

=head2 _fetch_many

 Title   : _fetch_many
 Usage   : $feature = $db->_fetch_many(@primary_ids)
 Function: fetch many features from database
 Returns : feature
 Args    : primary id
 Status  : private -- does not need to be implemented

This method fetches many features specified by a list of IDs. The
default implementation simply calls _fetch() once for each
primary_id. Implementors can override it if needed for efficiency.

=cut

# _fetch_many(@ids)
# this one will fall back to many calls on fetch() if you don't
# override it
sub _fetch_many {
  my $self = shift;
  return map {$self->_fetch($_)} @_;
}

=head2 _update_indexes

 Title   : _update_indexes
 Usage   : $success = $db->_update_indexes($feature)
 Function: update the indexes for a feature
 Returns : true on success
 Args    : A seqfeature object
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

This method is called by reindex() to update the searchable indexes
for a feature object that has changed.

=cut

# this is called to index a feature
sub _update_indexes { shift->throw_not_implemented }

=head2 _start_reindexing, _end_reindexing

 Title   : _start_reindexing, _end_reindexing
 Usage   : $db->_start_reindexing()
           $db->_end_reindexing
 Function: flag that a series of reindexing operations is beginning/ending
 Returns : true on success
 Args    : none
 Status  : MAY BE IMPLEMENTED BY AN ADAPTOR (optional)

These methods are called by reindex() before and immediately after a
series of reindexing operations. The default behavior is to do
nothing, but these methods can be overridden by an adaptor in order to
perform optimizations, turn off autocommits, etc.