Bio::DB::BioSQL PrimarySeqAdaptor
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Summary
Bio::DB::BioSQL::PrimarySeqAdaptor - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::DB::BioSQL::BasePersistenceAdaptor
Bio::DB::Persistent::BioNamespace
Bio::PrimarySeq
Inherit
Bio::DB::BioSQL::BasePersistenceAdaptor
Synopsis
Give standard usage here
Description
Describe the object here
Methods
get_persistent_slotsDescriptionCode
get_persistent_slot_valuesDescriptionCode
get_foreign_key_objectsDescriptionCode
attach_foreign_key_objectsDescriptionCode
store_childrenDescriptionCode
remove_childrenDescriptionCode
attach_childrenDescriptionCode
instantiate_from_rowDescriptionCode
populate_from_rowDescriptionCode
get_unique_key_queryDescriptionCode
get_biosequenceDescriptionCode
_bioseq_adaptorDescriptionCode
_bionamespace_adaptorDescriptionCode
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.
get_foreign_key_objectscodeprevnextTop
 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.
A Bio::PrimarySeqI references a namespace with authority. 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.
attach_foreign_key_objectscodeprevnextTop
 Title   : attach_foreign_key_objects
Usage :
Function: Attaches foreign key objects to the given object as far as
necessary.
This method is called after find_by_XXX() queries, not for INSERTs or UPDATEs. PrimarySeqIs have a BioNamespace as foreign key. 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().
store_childrencodeprevnextTop
 Title   : store_children
Usage :
Function: Inserts or updates the child entities of the given object in the
datastore.
Bio::PrimarySeqI has a sequence as child. Example : Returns : TRUE on success, and FALSE otherwise Args : The Bio::DB::PersistentObjectI implementing object for which the child objects shall be made persistent.
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().
attach_childrencodeprevnextTop
 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. For Bio::PrimarySeqIs, we need to get the biosequence attributes as well. Example : Returns : TRUE on success, and FALSE otherwise. Args : The object for which to find and to which to attach the child objects.
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.
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.
populate_from_rowcodeprevnextTop
 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().
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.
get_biosequencecodeprevnextTop
 Title   : get_biosequence
Usage :
Function: Returns the actual sequence for a bioentry, or a substring of it.
Example :
Returns : A string (the sequence or subsequence)
Args : The primary key of the bioentry for which to obtain the sequence.
Optionally, start and end position if only a subsequence is to be
returned (for long sequences, obtaining the subsequence from the
database may be much faster than obtaining it from the complete
in-memory string, because the latter has to be retrieved first).
_bioseq_adaptorcodeprevnextTop
 Title   : _bioseq_adaptor
Usage : $obj->_bioseq_adaptor($newval)
Function: Get/set cached persistence adaptor for the biosequence.
In OO speak, consider the access class of this method protected. I.e., call from descendants, but not from outside. Example : Returns : value of _bioseq_adaptor (a Bio::DB::PersistenceAdaptorI instance) Args : new value (a Bio::DB::PersistenceAdaptorI instance, optional)
_bionamespace_adaptorcodeprevnextTop
 Title   : _bionamespace_adaptor
Usage : $obj->_bionamespace_adaptor($newval)
Function: Get/set cached persistence adaptor for the bionamespace.
In OO speak, consider the access class of this method protected. I.e., call from descendants, but not from outside. Example : Returns : value of _bionamespace_adaptor (a Bio::DB::PersistenceAdaptorI instance) Args : new value (a Bio::DB::PersistenceAdaptorI instance, optional)
Methods code
get_persistent_slotsdescriptionprevnextTop
sub get_persistent_slots {
    my ($self,@args) = @_;

    return ("display_id", "primary_id", "accession_number",
	    "desc", "version");
}
get_persistent_slot_valuesdescriptionprevnextTop
sub get_persistent_slot_values {
    my ($self,$obj,$fkobjs) = @_;
    my @vals = ($obj->display_id(),
		$obj->primary_id() =~ /=(HASH|ARRAY)\(0x/ ?
		    undef : $obj->primary_id(),
		$obj->accession_number(),
		$obj->description(),
		$obj->version() || 0);
    return\@ vals;
}
get_foreign_key_objectsdescriptionprevnextTop
sub get_foreign_key_objects {
    my ($self,$obj) = @_;
    my $ns;

    if($obj) {
	# there is no "namespace" or Bio::Identifiable object in bioperl, so
# we need to create one here
$ns = Bio::DB::Persistent::BioNamespace->new(-identifiable => $obj); $ns->adaptor($self->_bionamespace_adaptor()); } else { $ns = "Bio::DB::Persistent::BioNamespace"; } return ($ns);
}
attach_foreign_key_objectsdescriptionprevnextTop
sub attach_foreign_key_objects {
    my ($self,$obj,$fks) = @_;
    
    # retrieve namespace by primary key
my $nsadp = $self->_bionamespace_adaptor(); my $ns = $nsadp->find_by_primary_key($fks->[0]); if($ns) { $obj->namespace($ns->namespace()) if $ns->namespace(); $obj->authority($ns->authority()) if $ns->authority(); return 1; } return 0;
}
store_childrendescriptionprevnextTop
sub store_children {
    my ($self,$obj) = @_;

    # delegate to Biosequence adaptor
return $self->_bioseq_adaptor()->store($obj);
}
remove_childrendescriptionprevnextTop
sub remove_children {
    return 1;
}
attach_childrendescriptionprevnextTop
sub attach_children {
    my ($self,$obj) = @_;

    my $adp = $self->_bioseq_adaptor();
    # This will find the biosequence by its foreign key to bioentry, since
# that's the UK. Subsequently, it will populate the biosequence-specific
# slots of $obj with the found record.
my $o = $adp->find_by_unique_key($obj); # on success, $o == $obj, and $o == undef otherwise
# however, some SeqI objects may legally lack any of those attributes
# and hence may not have an entry here, so we'll have to be permissive
return 1; #$o ? 1 : 0;
}
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::PrimarySeq->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) {
	$obj->display_id($rows->[1]) if $rows->[1];
	$obj->primary_id($rows->[2]) if $rows->[2];
	$obj->accession_number($rows->[3]) if $rows->[3];
	$obj->desc($rows->[4]) if $rows->[4];
	$obj->version($rows->[5]) if $rows->[5];
	if($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 @ukqueries = ();

    # UKs for PrimarySeqIs are (accession number,namespace,version)
# and (primary_id,namespace).
# all of the UKs include the namespace if provided, so get
# this right away.
my $ns; if($obj->namespace()) { $ns = Bio::BioEntry->new(-namespace => $obj->namespace()); $ns = $self->_bionamespace_adaptor()->find_by_unique_key($ns); } if($obj->primary_id() && ($obj->primary_id() !~ /=(HASH|ARRAY)\(0x/)) { my $uk_h = { 'primary_id' => $obj->primary_id(), }; # For the identifier we'll be graceful if the namespace was not
# provided, as in some earlier definitions of the schema the
# namespace wasn't necessarily part of the UK constraint. OTOH, if
# the namespace was provided but not found, we won't silently allow
# for typos etc.
if ($obj->namespace()) { $uk_h->{'bionamespace'} = $ns ? $ns->primary_key() : undef; } push(@ukqueries, $uk_h); } if($obj->accession_number()) { my $uk_h = { 'accession_number' => $obj->accession_number(),}; # we'll be graceful on the version if it was omitted, allowing any
# version to be matched, as opposed to only version 0 (the equivalent
# in the schema of 'no version')
$uk_h->{'version'} = $obj->version() if defined($obj->version); $uk_h->{'bionamespace'} = $ns ? $ns->primary_key() : undef; push(@ukqueries, $uk_h); } return @ukqueries;
}
get_biosequencedescriptionprevnextTop
sub get_biosequence {
    my ($self,@args) = @_;

    # delegate to Biosequence adaptor
return $self->_bioseq_adaptor()->get_biosequence(@args);
}
_bioseq_adaptordescriptionprevnextTop
sub _bioseq_adaptor {
    my ($self,$adp) = @_;
    if( defined $adp) {
	$self->{'_bioseq_adaptor'} = $adp;
    }
    if(! exists($self->{'_bioseq_adaptor'})) {
	$self->{'_bioseq_adaptor'} =
	    $self->db()->get_object_adaptor("Biosequence");
    }
    return $self->{'_bioseq_adaptor'};
}
_bionamespace_adaptordescriptionprevnextTop
sub _bionamespace_adaptor {
    my ($self,$adp) = @_;
    if( defined $adp) {
	$self->{'_bions_adaptor'} = $adp;
    }
    if(! exists($self->{'_bions_adaptor'})) {
	$self->{'_bions_adaptor'} =
	    $self->db->get_object_adaptor("BioNamespace");
    }
    return $self->{'_bions_adaptor'};
}

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 the web:
  http://bio.perl.org/bioperl-bugs/
AUTHOR - Ewan Birney, Hilmar LappTop
Email birney@ebi.ac.uk
Email hlapp at gmx.net
Describe contact details here
APPENDIXTop
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.