Bio::DB::BioSQL PathAdaptor
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Summary
Bio::DB::BioSQL::PathAdaptor - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::DB::BioSQL::RelationshipAdaptor
Bio::DB::PersistentObjectI
Bio::Ontology::Path
Inherit
Bio::DB::BioSQL::RelationshipAdaptor
Synopsis
Give standard usage here
Description
Bio::Ontology::PathI DB adaptor
Methods
get_persistent_slotsDescriptionCode
get_persistent_slot_valuesDescriptionCode
instantiate_from_rowDescriptionCode
populate_from_rowDescriptionCode
compute_transitive_closureDescriptionCode
Methods description
get_persistent_slotscode    nextTop
 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
get_persistent_slot_valuescodeprevnextTop
 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.
instantiate_from_rowcodeprevnextTop
 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.
populate_from_rowcodeprevnextTop
 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().
compute_transitive_closurecodeprevnextTop
 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.
Methods code
get_persistent_slotsdescriptionprevnextTop
sub get_persistent_slots {
    my ($self,@args) = @_;

    return ($self->SUPER::get_persistent_slots(@args), "distance");
}
get_persistent_slot_valuesdescriptionprevnextTop
sub get_persistent_slot_values {
    my ($self,$obj,$fkobjs) = @_;
    my @vals = (@{$self->SUPER::get_persistent_slot_values($obj,$fkobjs)},
		$obj->distance());
    return\@ vals;
}
instantiate_from_rowdescriptionprevnextTop
sub instantiate_from_row {
    my ($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 $obj;
}
populate_from_rowdescriptionprevnextTop
sub populate_from_row {
    my ($self,$obj,$row) = @_;

    $obj = $self->SUPER::populate_from_row($obj, $row);
    if($obj && $row && @$row) {
	$obj->distance($row->[1]) if defined($row->[1]);
    }
    return $obj;
}
compute_transitive_closuredescriptionprevnextTop
sub compute_transitive_closure {
    my ($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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
 
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 BugsTop
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://bugzilla.open-bio.org/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Methods specific to this adaptorTop