Bio::DB::BioSQL SpeciesAdaptor
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Summary
Bio::DB::BioSQL::SpeciesAdaptor - DESCRIPTION of Object
Package variables
Privates (from "my" definitions)
%rank_attr_map = ("no rank" => "variant", "subspecies" => "sub_species", "varietas" => "variant", "tribe" => "variant", "subtribe" => "variant")
Included modules
Bio::DB::BioSQL::BasePersistenceAdaptor
Bio::DB::PersistentObjectI
Bio::Species
Inherit
Bio::DB::BioSQL::BasePersistenceAdaptor
Synopsis
Give standard usage here
Description
Species DB adaptor
Methods
newDescriptionCode
get_persistent_slotsDescriptionCode
get_persistent_slot_valuesDescriptionCode
instantiate_from_rowDescriptionCode
populate_from_rowDescriptionCode
get_unique_key_queryDescriptionCode
remove_childrenDescriptionCode
get_classificationDescriptionCode
get_common_nameDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage :
Function: Instantiates the persistence adaptor.
Example :
Returns :
Args :
get_persistent_slotscodeprevnextTop
 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. This is a strictly abstract method. A derived class MUST override it to return something meaningful. 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.
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.
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. 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.
Usually a derived class will instantiate the proper class and pass it on to populate_from_row(). This method MUST be overridden by a derived object. 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().
get_unique_key_querycodeprevnextTop
 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.
remove_childrencodeprevnextTop
 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().
get_classificationcodeprevnextTop
 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
get_common_namecodeprevnextTop
 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
Methods code
newdescriptionprevnextTop
sub new {
   my ($class,@args) = @_;

   # we want to enable object caching
push(@args, "-cache_objects", 1) unless grep { /cache_objects/i; } @args; my $self = $class->SUPER::new(@args); return $self;
}
get_persistent_slotsdescriptionprevnextTop
sub get_persistent_slots {
    my ($self,@args) = @_;

    return ("common_name", "classification",
	    "ncbi_taxid", "binomial", "variant");
}
get_persistent_slot_valuesdescriptionprevnextTop
sub get_persistent_slot_values {
    my ($self,$obj,$fkobjs) = @_;
    my @vals = ($obj->common_name(),
		join(":", $obj->classification()),
		$obj->ncbi_taxid(),
		$obj->binomial('full'),
		$obj->variant() ? $obj->variant() : "-"
		);
    return\@ vals;
}
instantiate_from_rowdescriptionprevnextTop
sub instantiate_from_row {
    my ($self,$row,$fact) = @_;
    my $obj;

    if($row && @$row) {
	if($fact) {
	    $obj = $fact->create_object();
	} else {
	    $obj = Bio::Species->new();
	}
	$self->populate_from_row($obj, $row);
    }
    return $obj;
}
populate_from_rowdescriptionprevnextTop
sub populate_from_row {
    my ($self,$obj,$rows) = @_;

    if(! ref($obj)) {
	$self->throw("\"$obj\" is not an object. Probably internal error.");
    }
    if($rows && @$rows) {
	$obj->common_name($rows->[1]) if $rows->[1];
	$obj->ncbi_taxid($rows->[3]) if $rows->[3];
	# get the classification array in a separate query
my $clf = $self->get_classification($rows->[0]); if($clf && @$clf) { # for the species object we do not maintain the nodes that don't
# correspond to a standard rank, so remove them (e.g., 'root')
while($clf->[0]->[1] && ($clf->[0]->[1] eq "no rank")) { shift(@$clf); } # in the species object we store the species element without the
# genus, and similarly for the sub-species and variant
for(my $i = scalar(@$clf)-2; $i >= 0; $i--) { # if this node's name matches the start of the previous one,
# remove this portion from the previous one's name
if(index($clf->[$i+1]->[0], $clf->[$i]->[0]) == 0) { $clf->[$i+1]->[0] = substr($clf->[$i+1]->[0], length($clf->[$i]->[0])+1); } # don't do this stuff beyond genus and species
last if $clf->[$i]->[1] eq "genus"; } # we do not store the variant nor subspecies etc in the species
# object's classification array, so we need to sort those out
my $rank = $clf->[scalar(@$clf)-1]->[1]; while(grep { $rank eq $_; } keys %rank_attr_map) { my $meth = $rank_attr_map{$rank}; $obj->$meth($clf->[scalar(@$clf)-1]->[0]); pop(@$clf); $rank = $clf->[scalar(@$clf)-1]->[1]; } # done massaging, store away
$obj->classification([reverse(map { $_->[0]; } @$clf)], "FORCE"); } if($rows->[4] && (! $obj->classification)) { # poor man's binomial
my @clf = split(' ',$rows->[4]); $obj->classification([$clf[1],$clf[0]], "FORCE"); # remove genus and species
splice(@clf,0,2); # what remains goes under variant
$obj->variant(join(" ",@clf)) if @clf; } # 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 $obj; } return undef;
}
get_unique_key_querydescriptionprevnextTop
sub get_unique_key_query {
    my ($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;
}
remove_childrendescriptionprevnextTop
sub remove_children {
    return 1;
}
get_classificationdescriptionprevnextTop
sub get_classification {
    my $self = shift;
    return $self->dbd->get_classification($self,@_);
}
get_common_namedescriptionprevnextTop
sub get_common_name {
    my $self = shift;
    return $self->dbd->get_common_name($self,@_);
}

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@bio.perl.org
http://bugzilla.open-bio.org/
AUTHOR - Ewan Birney, Hilmar LappTop
Email birney@ebi.ac.uk
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _