Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

276 lines (219 sloc) 8.826 kb
# $Id$
#
# BioPerl module for Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver
#
# Cut&pasted by Yves Bastide <ybastide at irisa.fr> from mysql/Oracle ones
#
# Copyright INRIA
#
# You may distribute this module under the same terms as perl itself
#
# Original:
# (c) Hilmar Lapp, hlapp at gmx.net, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<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.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://bugzilla.open-bio.org/
=head1 AUTHOR - Yves Bastide
Email ybastide at irisa.fr
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver;
use vars qw(@ISA);
use strict;
use DBI qw(:sql_types);
# Object preamble - inherits from Bio::Root::Root
use Bio::DB::BioSQL::Pg::BasePersistenceAdaptorDriver;
@ISA = qw(Bio::DB::BioSQL::Pg::BasePersistenceAdaptorDriver);
# new() is inherited
=head2 insert_object
Title : insert_object
Usage :
Function: We override this here in order to omit the insert if there are
no values. This is because this entity basically represents a
derived class, and we may simply be dealing with the base class.
Example :
Returns : The primary key of the newly inserted record.
Args : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object
(basically, it needs to implement dbh(), sth($key, $sth),
dbcontext(), and get_persistent_slots()).
The object to be inserted.
A reference to an array of foreign key objects; if any of those
foreign key values is NULL (some foreign keys may be nullable),
then give the class name.
=cut
sub insert_object{
my $self = shift;
my ($adp,$obj,$fkobjs) = @_;
# obtain the object's slot values to be serialized
my $slotvals = $adp->get_persistent_slot_values($obj, $fkobjs);
# any value present?
my $isdef = $slotvals->[0];
for(my $i = 1; $i < @$slotvals; $i++) {
$isdef ||= $slotvals->[$i];
last if $isdef;
}
return $self->SUPER::insert_object(@_) if $isdef;
return -1;
}
=head2 update_object
Title : update_object
Usage :
Function: See parent class. We need to override this here because there is
no Biosequence object separate from PrimarySeq that would hold a
primary key. Hence, store()s cannot recognize when the Biosequence
for a Bioentry already exists and needs to be updated, or when it
needs to be created. The way the code is currently wired, the
presence of the primary key (stemming from the bioentry) will always
trigger an update.
So, what we need to do here is check whether the entry already
exists and if not delegate to insert_object().
Example :
Returns : The number of updated rows
Args : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object
(basically, it needs to implement dbh(), sth($key, $sth),
dbcontext(), and get_persistent_slots()).
The object to be updated.
A reference to an array of foreign key objects; if any of those
foreign key values is NULL (some foreign keys may be nullable),
then give the class name.
=cut
sub update_object{
my ($self,$adp,$obj,$fkobjs) = @_;
my $cache_key = 'SELECT UK '.ref($self);
my $sth = $adp->sth($cache_key);
if(! $sth) {
# create and prepare sql
my $table = $self->table_name($adp);
my $ukname = $self->foreign_key_name("Bio::PrimarySeqI");
my $sql = "SELECT $ukname FROM $table WHERE $ukname = ?";
$adp->debug("preparing SELECT statement: $sql\n");
$sth = $adp->dbh()->prepare($sql);
# and cache it
$adp->sth($cache_key, $sth);
}
# bind parameters
$sth->bind_param(1, $obj->primary_key(), SQL_INTEGER);
# execute and fetch
$sth->execute();
my $row = $sth->fetchall_arrayref();
if(@$row) {
# exists already, this is an update
return $self->SUPER::update_object($adp,$obj,$fkobjs);
} else {
# doesn't exist yet, this is in fact an insert
return $self->insert_object($adp,$obj,$fkobjs);
}
}
=head2 get_biosequence
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 calling persistence adaptor.
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).
=cut
sub get_biosequence{
my ($self,$adp,$bioentryid,$start,$end) = @_;
# statement cached?
my $cache_key = defined($start)
? "SELECT BIOSEQ SUBSTR ".(defined($end) ? "2POS " : "").ref($adp)
: "SELECT BIOSEQ ".ref($adp);
my $sth = $adp->sth($cache_key);
if(! $sth) {
my $table = $self->table_name($adp);
my $seqcol = $self->slot_attribute_map($table)->{"seq"};
if(! $seqcol) {
$self->throw("no mapping for column seq in table $table");
}
my $ukname = $self->foreign_key_name("Bio::PrimarySeqI");
# we need to create this
my $sql = defined($start)
? "SELECT SUBSTRING($seqcol FROM ?".(defined($end) ? " FOR ?" : "")
. ") FROM $table WHERE $ukname = ?"
: "SELECT $seqcol FROM $table WHERE $ukname = ?";
$adp->debug("preparing SELECT statement: $sql\n");
$sth = $adp->dbh()->prepare($sql);
# cache it
if ($sth) {
$adp->sth($cache_key, $sth);
} else {
$self->throw("failed to prepare SQL statement '$sql': "
.$adp->dbh->errstr);
}
}
# bind parameters
my $i = 1;
if (defined($start)) {
# note that the SQL type specification is absolutely necessary
# here as otherwise the server will complain about an escaped string
$sth->bind_param($i, $start, SQL_INTEGER);
$i++;
if (defined($end)) {
$sth->bind_param($i, $end-$start+1, SQL_INTEGER);
$i++;
}
}
$sth->bind_param($i, $bioentryid, SQL_INTEGER);
# execute and fetch
$adp->debug(substr(ref($self),rindex(ref($self),"::")+2)
.": executing SELECT SUBSTRING with ("
.(defined($start) ? "$start;" : "")
.(defined($end) ? ($end-$start+1).";" : "")
.$bioentryid.")\n")
if $adp->verbose > 0;
if (! $sth->execute()) {
$self->throw("error while executing query $cache_key with values ("
.(defined($start) ? "$start;" : "")
.(defined($end) ? ($end-$start+1).";" : "")
.$bioentryid."):\n"
.$sth->errstr." (".$sth->state.")");
}
my $row = $sth->fetchall_arrayref();
return (@$row ? $row->[0]->[0] : undef);
}
1;
Jump to Line
Something went wrong with that request. Please try again.