# $Id$ # # BioPerl module for Bio::DB::BioSQL::PathAdaptor # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # # (c) Hilmar Lapp, hlapp at gmx.net, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003. # # 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::PathAdaptor - DESCRIPTION of Object =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Bio::Ontology::PathI DB adaptor =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 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@bioperl.org http://redmine.open-bio.org/projects/bioperl/ =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =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::PathAdaptor; use vars qw(@ISA); use strict; # Object preamble use Bio::DB::BioSQL::RelationshipAdaptor; use Bio::DB::PersistentObjectI; use Bio::Ontology::Path; @ISA = qw(Bio::DB::BioSQL::RelationshipAdaptor); # new is inherited =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. 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 updated =cut sub get_persistent_slots{ my ($self,@args) = @_; return ($self->SUPER::get_persistent_slots(@args), "distance"); } =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. 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,$fkobjs) = @_; my @vals = (@{$self->SUPER::get_persistent_slot_values($obj,$fkobjs)}, $obj->distance()); return \@vals; } =head2 instantiate_from_row Title : instantiate_from_row Usage : Function: Instantiates the class this object is an adaptor for, and populates it with values from columns of the row. This implementation call populate_from_row() to do the real job. We override this here in order to create a Bio::Ontology::Path object by default. Example : Returns : An object, or undef, if the row contains no values Args : A reference to an array of column values. The first column is the primary key, the other columns are expected to be in the order returned by get_persistent_slots(). Optionally, the object factory to be used for instantiating the proper class. The adaptor must be able to instantiate a default class if this value is undef. =cut sub instantiate_from_row{ my ($self,$row,$fact) = @_; my $obj; if($row && @$row) { if($fact) { $obj = $fact->create_object(); } else { $obj = Bio::Ontology::Path->new(); } $self->populate_from_row($obj, $row); } return $obj; } =head2 populate_from_row Title : populate_from_row Usage : Function: Instantiates the class this object is an adaptor for, and populates it with values from columns of the row. Example : Returns : An object, or undef, if the row contains no values Args : The object to be populated. A reference to an array of column values. The first column is the primary key, the other columns are expected to be in the order returned by get_persistent_slots(). =cut sub populate_from_row{ my ($self,$obj,$row) = @_; $obj = $self->SUPER::populate_from_row($obj, $row); if($obj && $row && @$row) { $obj->distance($row->[1]) if defined($row->[1]); } return $obj; } =head1 Methods specific to this adaptor =cut =head2 compute_transitive_closure Title : compute_transitive_closure Usage : Function: Compute the transitive closure over a given ontology and populate the respective path table in the relational schema. There are options that allow one to create certain necessary relationships between predicates on-the-fly. Read below. Example : Returns : TRUE on success, and FALSE otherwise Args : The ontology over which to create the transitive closure (a Bio::Ontology::OntologyI compliant object). In addition, named parameters. Currently, the following are recognized. -truncate If assigned a true value, will cause an existing transitive closure for the ontology be deleted from the path table. Usually, this option should be enabled. -predicate_superclass A Bio::Ontology::TermI compliant object that specifies a common ancestor predicate for all predicates in the ontology. If this is specified, the method will create and serialize relationships between all predicates in the ontology and the ancestor predicate, where the ancestor predicate is the object, the predicate is either the one given by -subclass_predicate or the term 'implies', and the ontology is the ontology referenced by the ancestor predicate. If this is not provided, the aforementioned relationships should be present in an ontology in the database already, unless the ontology over which to compute the transitive closure has only one predicate, or if paths over mixed predicates are void. Otherwise the transitive closure will not be complete for mixed predicate paths. -subclass_predicate A Bio::Ontology::TermI compliant object that represents the predicate for the relationship between predicate A and predicate B if predicate A can be considered to subclass, or imply, predicate B. -identity_predicate A Bio::Ontology::TermI compliant object that represents the predicate for the identity of a predicate with itself. If provided, the method will create relationships for all predicates in the ontology, where subject and object are the predicate of the ontology, the predicate is the supplied identity predicate, and the ontology is the ontology referenced by the supplied term object. If this is not provided, the aforementioned relationships should be present in an ontology in the database already. Otherwise the transitive closure will be incomplete. The predicate will also be used for indicating identity between a term and itself for the paths of distance zero between a term and itself. If undef the zero distance paths will not be created. =cut sub compute_transitive_closure{ my ($self,$ont,@args) = @_; # check whether we need to create predicate relationships on the fly my ($trunc, $ancestor_pred, $subclass_pred, $identity_pred) = $self->_rearrange([qw(TRUNCATE PREDICATE_SUPERCLASS SUBCLASS_PREDICATE IDENTITY_PREDICATE )], @args); # need to create identity relationships? if (defined($identity_pred)) { # set up the relationship object we'll reuse my $rel = Bio::Ontology::Relationship->new( -ontology => $identity_pred->ontology()); $rel = $self->db->create_persistent($rel); # set the constant(s) (only one here) $rel->predicate_term($identity_pred); # create an identity rel.ship for each predicate my @preds = $ont->get_predicate_terms(); # if there is a superclass predicate, we need to create an identity # relationship for that, too push(@preds, $ancestor_pred) if $ancestor_pred; # now loop over the list of predicates foreach my $pred (@preds) { $rel->primary_key(undef); $rel->subject_term($pred); $rel->object_term($pred); $rel->create(); } } # need to create subclass relationships? if (defined($ancestor_pred)) { # set up the relationship object we'll reuse my $rel = Bio::Ontology::Relationship->new( -ontology => $ancestor_pred->ontology()); $rel = $self->db->create_persistent($rel); # create a subclasses predicate if none supplied $subclass_pred = Bio::Ontology::Term->new( -name => "subclasses", -ontology => $ancestor_pred->ontology()) unless $subclass_pred; # and make it persistent if it isn't already $subclass_pred = $self->db->create_persistent($subclass_pred) unless $subclass_pred->isa("Bio::DB::PersistentObjectI"); # set the constants $rel->object_term($ancestor_pred); $rel->predicate_term($subclass_pred); # create one subclass rel.ship for each predicate foreach my $pred ($ont->get_predicate_terms()) { $rel->primary_key(undef); $rel->subject_term($pred); $rel->create(); } } # make sure the ontology object is a persistent object $ont = $self->db->create_persistent($ont) unless $ont->isa("Bio::DB::PeristentObjectI"); # now delegate to the driver return $self->dbd->compute_transitive_closure($self, $ont, $identity_pred, $trunc); } 1;