# $Id$
#
# BioPerl module for Bio::DB::BioSQL::LocationAdaptor
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
#
# The previous Location adaptor was SeqLocationAdaptor by Ewan Birney. This
# module evidently is similar in purpose ...
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::BioSQL::LocationAdaptor - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 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.org
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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://bio.perl.org/bioperl-bugs/
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::BioSQL::LocationAdaptor;
use vars qw(@ISA);
use strict;
use Bio::DB::BioSQL::BasePersistenceAdaptor;
use Bio::Ontology::Term;
use Bio::Location::Simple;
@ISA = qw(Bio::DB::BioSQL::BasePersistenceAdaptor);
#our %slot_cat_map = ();
# new inherited from base adaptor.
#
# if we wanted caching we'd have to override new here - but don't do caching
# for locations of features ...
=head2 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.
Example :
Returns : an array of method names constituting the serializable slots
Args : the object about to be inserted or updated
=cut
sub get_persistent_slots{
my ($self,@args) = @_;
return ("start","end","strand","rank");
}
=head2 get_persistent_slot_values
Title : get_persistent_slot_values
Usage :
Function: Obtain the values for the slots returned by get_persistent_slots(),
in exactly that order.
The reason this method is here is that sometimes the actual slot
values need to be post-processed to yield the value that gets
actually stored in the database. E.g., slots holding arrays
will need some kind of join function applied. Another example is if
the method call needs additional arguments. Supposedly the
adaptor for a specific interface knows exactly what to do here.
Since there is also populate_from_row() the adaptor has full
control over mapping values to a version that is actually stored.
Example :
Returns : A reference to an array of values for the persistent slots of this
object. Individual values may be undef.
Args : The object about to be serialized.
A reference to an array of foreign key objects if not retrievable
from the object itself.
=cut
sub get_persistent_slot_values {
my ($self,$obj,$fkobjs) = @_;
my @vals = ($obj->start(),
$obj->end(),
defined($obj->strand) ? $obj->strand : 0,
$obj->can('rank') ? $obj->rank() : undef
);
return \@vals;
}
=head2 get_foreign_key_objects
Title : get_foreign_key_objects
Usage :
Function: Gets the objects referenced by this object, and which therefore need
to be referenced as foreign keys in the datastore.
A Bio::LocationI references a Bio::SeqFeatureI.
Example :
Returns : an array of Bio::DB::PersistentObjectI implementing objects
Args : The object about to be inserted or updated, or undef if the call
is for a SELECT query. In the latter case return class or interface
names that are mapped to the foreign key tables.
Additional named parameters, with -fkobjs being recognized and
pointing to a reference to an array of foreign key objects (the
Bio::SeqFeatureI object) not retrievable from the object itself.
=cut
sub get_foreign_key_objects{
my ($self,$obj,@args) = @_;
my ($feat,$dblink);
# Bio::LocationI doesn't have a pointer to the feature. Hence, we need to
# get this from the arguments.
my ($fkobjs) = $self->_rearrange([qw(FKOBJS)], @args);
if($fkobjs && @$fkobjs) {
($feat) = grep { ref($_) && $_->isa("Bio::SeqFeatureI"); } @$fkobjs;
if(ref($obj) && $obj->is_remote()) {
# construct DBLink on-the-fly
$dblink = $self->_seq_id_as_dblink($obj, $feat);
}
}
$feat = "Bio::SeqFeatureI" unless $feat;
# default for dblink is this is not a remote location
$dblink = "Bio::Annotation::DBLink" unless $dblink;
return ($feat,$dblink);
}
=head2 attach_foreign_key_objects
Title : attach_foreign_key_objects
Usage :
Function: Attaches foreign key objects to the given object as far as
necessary.
This method is called after find_by_XXX() queries, not for
INSERTs or UPDATEs.
LocationIs don''t really have a foreign key object attached
-- it would be the SeqFeatureI if they had one.
Example :
Returns : TRUE on success, and FALSE otherwise.
Args : The object to which to attach foreign key objects.
A reference to an array of foreign key values, in the order
of foreign keys returned by get_foreign_key_objects().
=cut
sub attach_foreign_key_objects{
my ($self,$obj,$fks) = @_;
my $ok = 1;
# remote location reference?
if($fks->[1]) {
my $dbl = $self->_dblink_adaptor->find_by_primary_key($fks->[1]);
$obj->is_remote(1);
$obj->seq_id($dbl->namespace_string) if $dbl;
$ok = $dbl && $ok;
}
return $ok;
}
=head2 store_children
Title : store_children
Usage :
Function: Inserts or updates the child entities of the given object in the
datastore.
Bio::LocationI may have qualifier/value pairs as children. This is
not implemented yet.
Example :
Returns : TRUE on success, and FALSE otherwise
Args : The Bio::DB::PersistentObjectI implementing object for which the
child objects shall be made persistent.
=cut
sub store_children{
my ($self,$obj) = @_;
return 1;
}
=head2 remove_children
Title : remove_children
Usage :
Function: This method is to cascade deletes in maintained objects.
We just return TRUE here.
Example :
Returns : TRUE on success and FALSE otherwise
Args : The persistent object that was just removed from the database.
Additional (named) parameter, as passed to remove().
=cut
sub remove_children{
return 1;
}
=head2 attach_children
Title : attach_children
Usage :
Function: Possibly retrieve and attach child objects of the given object.
This is needed when whole object trees are supposed to be built
when a base object is queried for and returned. An example would
be Bio::SeqI objects and all the annotation objects that hang off
of it.
This is called by the find_by_XXXX() methods once the base object
has been built.
For Bio::LocationIs, we need to get the qualifier/value pairs
possibly associated with it. Not implemented yet.
Example :
Returns : TRUE on success, and FALSE otherwise.
Args : The object for which to find and to which to attach the child
objects.
=cut
sub attach_children{
my ($self,$obj) = @_;
return 1;
}
=head2 instantiate_from_row
Title : instantiate_from_row
Usage :
Function: Instantiates the class this object is an adaptor for, and populates
it with values from columns of the row.
This implementation calls populate_from_row() to do the real job.
Example :
Returns : An object, or undef, if the row contains no values
Args : A reference to an array of column values. The first column is the
primary key, the other columns are expected to be in the order
returned by get_persistent_slots().
Optionally, a Bio::Factory::SequenceFactoryI compliant object to
be used for creating the object.
=cut
sub instantiate_from_row{
my ($self,$row,$fact) = @_;
my $obj;
if($row && @$row) {
if($fact) {
$obj = $fact->create_object();
} else {
$obj = Bio::Location::Simple->new();
}
$self->populate_from_row($obj, $row);
}
return $obj;
}
=head2 populate_from_row
Title : populate_from_row
Usage :
Function: Populates the object with values from columns of the row.
Example :
Returns : The object populated, or undef, if the row contains no values
Args : The object to be populated.
A reference to an array of column values. The first column is the
primary key, the other columns are expected to be in the order
returned by get_persistent_slots().
=cut
sub populate_from_row{
my ($self,$obj,$rows) = @_;
if(! ref($obj)) {
$self->throw("\"$obj\" is not an object. Probably internal error.");
}
if($rows && @$rows) {
$obj->start($rows->[1]) if $rows->[1];
$obj->end($rows->[2]) if $rows->[2];
$obj->strand($rows->[3]) if $rows->[3];
$obj->rank($rows->[4]) if $rows->[4] && $obj->can('rank');
if($obj->isa("Bio::DB::PersistentObjectI")) {
$obj->primary_key($rows->[0]);
}
return $obj;
}
return undef;
}
=head2 get_unique_key_query
Title : get_unique_key_query
Usage :
Function: Obtain the suitable unique key slots and values as determined by the
attribute values of the given object and the additional foreign
key objects, in case foreign keys participate in a UK.
Example :
Returns : One or more references to hash(es) where each hash
represents one unique key, and the keys of each hash
represent the names of the object's slots that are part of
the particular unique key and their values are the values
of those slots as suitable for the key.
Args : The object with those attributes set that constitute the chosen
unique key (note that the class of the object will be suitable for
the adaptor).
A reference to an array of foreign key objects if not retrievable
from the object itself.
=cut
sub get_unique_key_query{
my ($self,$obj,$fkobjs) = @_;
my $uk_h = {};
# UK for LocationIs is (seqfeature,rank)
# that is, we need the seqfeature or otherwise there's no point
my $feat;
if($fkobjs && @$fkobjs) {
($feat) = grep { $_->isa("Bio::SeqFeatureI"); } @$fkobjs;
if($feat &&
(! ($feat->isa("Bio::DB::PersistentObjectI") &&
$feat->primary_key()))) {
$feat = $self->_feat_adaptor()->find_by_unique_key($feat);
}
}
# we only need to continue with the feature FK in hand
if($feat) {
$uk_h->{'Bio::SeqFeatureI'} = $feat->primary_key();
$uk_h->{'rank'} = $obj->rank() if $obj->can('rank');
}
return $uk_h;
}
=head2 _seq_id_as_dblink
Title : _seq_id_as_dblink
Usage :
Function:
Example :
Returns : L<Bio::Annotation::DBLink> object
Args : L<Bio::LocationI> object, L<Bio::SeqFeatureI> object
=cut
sub _seq_id_as_dblink{
my ($self,$loc,$feat) = @_;
my $seqid = $loc->seq_id;
my ($ns,$v);
if( # this is an Ensembl artifact
$seqid !~ /^Chr(X|Y|Un|\d+|Chr)/) {
if($seqid =~ /^(\w+?):(.+)/) {
$ns = $1;
$seqid = $2;
}
}
if($seqid =~ /^([0-9\w]+)\.([0-9]{1,3})\s*$/) {
$seqid = $1;
$v = $2;
}
if(! $ns) {
if(! $feat) {
$self->throw("need feature FK for remote location on ".
$loc->seq_id());
}
# default namespace is the one from the attached seq
$ns = $feat->entire_seq()->namespace();
}
# create DBLink object
my $dblink = Bio::Annotation::DBLink->new(-database => $ns,
-primary_id => $seqid,
-version => $v);
# return the persistent version of it
return $self->_dblink_adaptor->create_persistent($dblink);
}
=head2 _feat_adaptor
Title : _feat_adaptor
Usage : $obj->_feat_adaptor($newval)
Function: Get/set cached persistence adaptor for a bioperl feature 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 _feat_adaptor (a Bio::DB::PersistenceAdaptorI
instance)
Args : new value (a Bio::DB::PersistenceAdaptorI instance, optional)
=cut
sub _feat_adaptor{
my ($self,$adp) = @_;
if( defined $adp) {
$self->{'_feat_adaptor'} = $adp;
}
if(! exists($self->{'_feat_adaptor'})) {
$self->{'_feat_adaptor'} =
$self->db()->get_object_adaptor("Bio::SeqFeatureI");
}
return $self->{'_feat_adaptor'};
}
=head2 _dblink_adaptor
Title : _dblink_adaptor
Usage : $obj->_dblink_adaptor($newval)
Function: Get/set cached persistence adaptor for a bioperl DBLink 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 _dblink_adaptor (a Bio::DB::PersistenceAdaptorI
instance)
Args : new value (a Bio::DB::PersistenceAdaptorI instance, optional)
=cut
sub _dblink_adaptor{
my ($self,$adp) = @_;
if( defined $adp) {
$self->{'_dblink_adaptor'} = $adp;
}
if(! exists($self->{'_dblink_adaptor'})) {
$self->{'_dblink_adaptor'} =
$self->db()->get_object_adaptor("Bio::Annotation::DBLink");
}
return $self->{'_dblink_adaptor'};
}
1;