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# $Id: BiosequenceAdaptorDriver.pm,v 1.6 2006/07/04 22:23:12 mauricio Exp $
#
# BioPerl module for Bio::DB::BioSQL::mysql::BiosequenceAdaptorDriver
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
#
# (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
HideShow 49 lines of Pod
=head1 NAME
Bio::DB::BioSQL::mysql::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 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
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
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::mysql::BiosequenceAdaptorDriver;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver;
@ISA = qw(Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver);
# new() is inherited
HideShow 21 lines of Pod
=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 $isdef;
    foreach (@$slotvals) { $isdef ||= $_; last if $isdef; }
    return $self->SUPER::insert_object(@_) if $isdef;
    return -1;
}
HideShow 27 lines of Pod
=head2 update_object
 Title   : update_object
 Usage   :
 Function: See parent class. We need to override this here because there is
           no Biosequence object separate from PrimarySeq that would hold a
           primary key. Hence, store()s cannot recognize when the Biosequence
           for a Bioentry already exists and needs to be updated, or when it
           needs to be created. The way the code is currently wired, the
           presence of the primary key (stemming from the bioentry) will always
           trigger an update.
           So, what we need to do here is check whether the entry already
           exists and if not delegate to insert_object().
 Example :
 Returns : The number of updated rows
 Args    : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object
           (basically, it needs to implement dbh(), sth($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 $cache_key = 'SELECT UK '.$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());
    # 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);
    }
}
HideShow 17 lines of Pod
=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,$end) = @_;
    my ($sth, $cache_key, $i, $row);
    my $seqstr;
    if(defined($start)) {
        # statement cached?
        $cache_key = "SELECT BIOSEQ SUBSTR".$adp.(defined($end) ?" 2POS":"");
        $sth = $adp->sth($cache_key);
        if(! $sth) {
            # we need to create this
            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");
            my $sql = "SELECT SUBSTRING($seqcol, ?" .
                (defined($end) ? ", ?" : "") .
                ") 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, $start);
        $i = 2;
        if(defined($end)) {
            $sth->bind_param(2, $end-$start+1);
            $i = 3;
        }
        $sth->bind_param($i, $bioentryid);
    } else {
        # statement cached?
        $cache_key = "SELECT BIOSEQ ".$adp;
        $sth = $adp->sth($cache_key);
        if(! $sth) {
            # we need to create this
            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");
            my $sql = "SELECT $seqcol 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, $bioentryid);
    }
    # execute and fetch
    $sth->execute();
    $row = $sth->fetchall_arrayref();
    return (@$row ? $row->[0]->[0] : undef);
}
1;