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lib/Bio/DB/BioSQL/SpeciesAdaptor.pm  view on Meta::CPAN

	# an explicit variant overwrites
	$obj->variant($rows->[5]) if $rows->[5] && ($rows->[5] ne "-");
	# check for common name if not already in the result
	if(! $obj->common_name()) {
	    my $cname = $self->get_common_name($rows->[0]);
	    $obj->common_name($cname) if $cname;
	}
	# primary key
	if($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 = {};

    # UKs for species are full binomial with variant, and ncbi_taxid
    if($obj->ncbi_taxid()) {
	$uk_h->{'ncbi_taxid'} = $obj->ncbi_taxid();
	$uk_h->{'name_class'} = "scientific name";
    } elsif($obj->binomial()) {
	$uk_h->{'binomial'} = $obj->binomial('full');
	$uk_h->{'binomial'} .= " ".$obj->variant() if $obj->variant();
	$uk_h->{'name_class'} = "scientific name";
    }
    
    return $uk_h;
}

=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 get_classification

 Title   : get_classification
 Usage   :
 Function: Returns the classification array for a taxon as identified by
           its primary key.
 Example :
 Returns : a reference to an array of two-element arrays, where the first
           element contains the name of the node and the second element
           denotes its rank
 Args    : the primary key of the taxon


=cut

sub get_classification{
    my $self = shift;
    return $self->dbd->get_classification($self,@_);
}

=head2 get_common_name

 Title   : get_common_name
 Usage   :
 Function: Get the common name for a taxon as identified by its primary
           key.
 Example :
 Returns : a string denoting the common name
 Args    : the primary key of the taxon


=cut

sub get_common_name{
    my $self = shift;
    return $self->dbd->get_common_name($self,@_);
}

1;