Bio::DB::BioSQL SeqAdaptor
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::DB::BioSQL::SeqAdaptor - DESCRIPTION of Object
Package variables
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Included modules
Give standard usage here
Describe the object here
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
 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.
 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.
This implementation takes care of the species. 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.
 Title   : attach_foreign_key_objects
Usage :
Function: Attaches foreign key objects to the given object as far as
This method is called after find_by_XXX() queries, not for INSERTs or UPDATEs. SeqIs have Species in addition. 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().
 Title   : store_children
Usage :
Function: Inserts or updates the child entities of the given object in the
A Bio::SeqI has annotation and seqfeatures as children. Example : Returns : TRUE on success, and FALSE otherwise Args : The Bio::DB::PersistentObjectI implementing object for which the child objects shall be made persistent.
 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. A Bio::SeqI has annotation and seqfeatures as children. Example : Returns : TRUE on success, and FALSE otherwise. Args : The object for which to find and to which to attach the child objects.
 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.
 Title   : populate_from_row
Usage :
Function: Populates an 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().
 Title   : remove_children
Usage :
Function: This method is to cascade deletes in maintained objects.
We need to undefine the primary keys of all contained feature objects 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().
 Title   : _feat_adaptor
Usage : $obj->_feat_adaptor($newval)
Function: Get/set cached persistence adaptor for a Bio::SeqFeatureI 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)
Methods code
sub get_persistent_slots {
    my $self = shift;

    return ($self->SUPER::get_persistent_slots(@_), "division");
sub get_persistent_slot_values {
    my $self = shift;
    my $obj = shift;

    my $vals = $self->SUPER::get_persistent_slot_values($obj, @_);
    push(@$vals, $obj->isa("Bio::Seq::RichSeqI") ? $obj->division() : undef);
    return $vals;
sub get_foreign_key_objects {
    my ($self,$obj) = @_;
    my @fkobjs = $self->SUPER::get_foreign_key_objects($obj);

    # we have an additional optional FK object, namely species.
push(@fkobjs, ($obj && $obj->species() ? $obj->species() : "Bio::Species")); return @fkobjs;
sub attach_foreign_key_objects {
    my ($self,$obj,$fks) = @_;
    # do what we inherit from PrimarySeqAdaptor
my $ok = $self->SUPER::attach_foreign_key_objects($obj, $fks); # there's also possibly a species
if($ok && $fks && $fks->[1]) { my $adp = $self->db()->get_object_adaptor("Bio::Species"); my $species = $adp->find_by_primary_key($fks->[1]); $ok = $species ? 1 : 0; $obj->species($species); } return $ok;
sub store_children {
    my ($self,$obj) = @_;

    my $ok = $self->SUPER::store_children($obj);
    # we need to store the annotations, and associate ourselves with them
my $ac = $obj->annotation(); # the annotation object might just have been created on the fly, and hence
# may not be a PersistentObjectI (if that's the case we'll assume it's
# empty, and there's no point storing anything)
if($ac->isa("Bio::DB::PersistentObjectI")) { $ok = $ac->store(-fkobjs => [$obj]) && $ok; $ac->adaptor()->add_association(-objs => [$ac, $obj]); } # store the features
# re-sync the attached seq of the features with this seq object
if(! $obj->primary_seq->isa("Bio::DB::PersistentObjectI")) { $self->throw("PrimarySeq object is not a persistent object. ". "This is alarming - probably an internal bug."); } $obj->add_SeqFeature($obj->remove_SeqFeatures()); # loop over the seqfeatures and store
my $i = 0; foreach my $feat ($obj->get_SeqFeatures()) { # we need to assign a rank if there isn't one already -- likewise,
# if there is one already make sure we don't clash with that
if(my $rank = $feat->rank()) { $i = $rank+1 if $i <= $rank; } else { $feat->rank(++$i); } $ok = $feat->store() && $ok; } # done
return $ok;
sub attach_children {
    my ($self,$obj) = @_;

    my $ok = $self->SUPER::attach_children($obj);
    # we need to associate annotation
my $annadp = $self->db()->get_object_adaptor("Bio::AnnotationCollectionI"); my $qres = $annadp->find_by_association(-objs => [$annadp,$obj]); my $ac = $qres->next_object(); if($ac) { $obj->annotation($ac); } # there may be features for this seq: search for those having a FK to
# the seq
my $query = Bio::DB::Query::BioQuery->new( -datacollections => ["Bio::SeqFeatureI t1"], -where => ["t1.entire_seq = ?"], -order => ["t1.rank"], ); $qres = $self->_feat_adaptor()->find_by_query( $query, -name => "FIND FEATURE BY SEQ", -values => [$obj->primary_key()]); while(my $feat = $qres->next_object()) { $obj->add_SeqFeature($feat); # try to cleanup a possibly redundant namespace in remote location
# seq IDs - we don't usually print that although we should
if(my $ns = $obj->namespace()) { my @locs = $feat->location->each_Location(); foreach my $subloc (@locs) { if($subloc->is_remote()) { my $seqid = $subloc->seq_id(); if($seqid =~ s/^$ns://) { $subloc->seq_id($seqid); } } } # set top object seqid
my $toploc = $feat->location(); if($toploc && (! $toploc->is_remote()) && (! $toploc->seq_id())) { $toploc->seq_id($obj->accession_number(). ($obj->version ? ".".$obj->version : "")); } } } # done
return $ok;
sub instantiate_from_row {
    my ($self,$row,$fact) = @_;
    my $obj;

    if($row && @$row) {
	if(! $fact) {
	    # we need to create at least Bio::SeqI implementing objects here;
# as a default catch-all we upgrade that to Bio::Seq::RichSeqI
$fact = Bio::Seq::SeqFactory->new(-type => "Bio::Seq::RichSeq"); } $obj = $fact->create_object(); $self->populate_from_row($obj, $row); } return $obj;
sub populate_from_row {
    my ($self,$obj,$rows) = @_;

    $obj = $self->SUPER::populate_from_row($obj,$rows);
    if($obj && $rows && @$rows && $obj->isa("Bio::Seq::RichSeqI")) {
	$obj->division($rows->[6]) if $rows->[6];
    return $obj;
sub remove_children {
    my $self = shift;
    my $obj = shift;

    # features
foreach my $feat ($obj->top_SeqFeatures()) { if($feat->isa("Bio::DB::PersistentObjectI")) { $feat->primary_key(undef); # cascade to feature's children
$self->_feat_adaptor->remove_children($feat); } } # annotation collection
my $ac = $obj->annotation(); if($ac->isa("Bio::DB::PersistentObjectI")) { $ac->primary_key(undef); $ac->adaptor()->remove_children($ac); } # done
return 1;
sub _feat_adaptor {
    my ($self,$adp) = @_;
    if( defined $adp) {
	$self->{'_feat_adaptor'} = $adp;
    if(! exists($self->{'_feat_adaptor'})) {
	$self->{'_feat_adaptor'} =
    return $self->{'_feat_adaptor'};

General documentation
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Your participation is much appreciated.
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Please direct usage questions or support issues to the mailing list:

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 the web:
AUTHOR - Ewan Birney, Hilmar LappTop
Email hlapp at
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Internal methodsTop
 These are mostly private or 'protected.' Methods which are in the
latter class have this explicitly stated in their
documentation. 'Protected' means you may call these from derived
classes, but not from outside.
Most of these methods cache certain adaptors or otherwise reduce call path and object creation overhead. There's no magic here.