Raw content of Bio::EnsEMBL::Funcgen::DBSQL::ChannelAdaptor
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Funcgen::DBSQL::ChannelAdaptor
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::Funcgen::DBSQL::ChannelAdaptor - A database adaptor for fetching and
storing Funcgen Channel objects.
=head1 SYNOPSIS
my $chan_a = $db->get_ChannelAdaptor();
my @channels = @{$chan_a->fetch_all_by_ExperimentalChip($exp)};
=head1 DESCRIPTION
The ChannelAdaptor is a database adaptor for storing and retrieving
Funcgen Channel objects.
=head1 AUTHOR
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::DBSQL::ChannelAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( warning throw );
use Bio::EnsEMBL::Funcgen::Channel;
use Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor;
use vars qw(@ISA);
#May need to our this?
@ISA = qw(Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor);
=head2 fetch_by_type_experimental_chip_id
Arg [1] : string - type
Arg [2] : Bio::EnsEMBL::Funcgen::ExperimentalChip
Example : my $chan = $chan_a->fetch_by_type_experimental_chip_dbID('EXPERIMENTAL', $ec_dbid);
Description: Does what it says on the tin
Returntype : Bio::EnsEMBL::Funcgen::Channel object
Exceptions : Throws if args not met
Caller : General
Status : At risk
=cut
sub fetch_by_type_experimental_chip_id {
my ($self, $type, $ec_id) = @_;
throw("Must specify a channel type e.g. EXPERIMENTAL, TOTAL and an ExperimentalChip id") if(! ($type && $ec_id));
my $sth = $self->prepare("
SELECT c.channel_id
FROM channel c
WHERE c.experimental_chip_id = ?
AND c.type = ?
");
$sth->bind_param(1, $ec_id, SQL_INTEGER);
$sth->bind_param(2, $type, SQL_VARCHAR);
$sth->execute();
my ($chan_id) = $sth->fetchrow();
return $self->fetch_by_dbID($chan_id) if $chan_id;
}
=head2 fetch_by_dye_experimental_chip_id
Arg [1] : string - dye
Arg [1] : int - dbID of Experiment
Example : my $chan = $chan_a->fetch_by_type_experimental_chip_dbID('Cy5', $ec_dbid);
Description: Does what it says on the tin
Returntype : Bio::EnsEMBL::Funcgen::Channel object
Exceptions : Throws is experiment dbID or dye not passed
Caller : General
Status : At Risk
=cut
sub fetch_by_dye_experimental_chip_dbID {
my $self = shift;
my $dye = shift;
my $ec_dbid = shift;
throw("not yet impemented");
my ($chan_id, @results);
throw("Must specify an experiemntal dbID") if(! $ec_dbid);
#Need to validate dye against VendorDefs? Or leave and just return whatever is in DB e.g. nothing if dye name is wrong.
my $sth = $self->prepare("
SELECT c.channel_id
FROM experimental_chip ec, channel c
WHERE c.experimental_chip_id = ec.experimental_chip_id
AND ec.experimental_chip_id = $ec_dbid
");
#can we do a generic fetch here?
$sth->execute();
while ($chan_id = $sth->fetchrow()){
push @results, $self->fetch_by_dbID($chan_id);
}
return \@results;
}
=head2 fetch_all_by_experimental_chip_dbID
Arg [1] : int - dbID of Experiment
Example : my @chans = @{$ec_a->fetch_all_by_experimental_chip_dbID($ac_dbid);
Description: Does what it says on the tin
Returntype : Listref of Bio::EnsEMBL::Funcgen::Channel object
Exceptions : None
Caller : General
Status : At Risk
=cut
sub fetch_all_by_experimental_chip_dbID {
my $self = shift;
my $ec_dbid = shift;
my ($chan_id, @results);
throw("Must specify an experiemntal dbID") if(! $ec_dbid);
#my $sth = $self->prepare("
#SELECT c.channel_id
# FROM experimental_chip ec, channel c
# WHERE c.experimental_chip_id = ec.experimental_chip_id
# AND ec.experimental_chip_id = $ec_dbid
# ");
my $constraint = "c.experimental_chip_id=$ec_dbid";
#can we do a generic fetch here?
#$sth->execute();
#while ($chan_id = $sth->fetchrow()){
# push @results, $self->fetch_by_dbID($chan_id);
# }
return $self->generic_fetch($constraint);
}
=head2 fetch_all_by_ExperimentalChip
Arg [1] : Bio::EnsEMBL::Funcgen::ExperimentalChip
Example : my @chans = @{$ec_a->fetch_all_by_ExperimentalChip($echip);
Description: Returns all channels associated with a given ExperimentalChip
Returntype : Listref of Bio::EnsEMBL::Funcgen::Channel objects
Exceptions : Throws if no ExperimentalChip defined
Caller : General
Status : At Risk
=cut
sub fetch_all_by_ExperimentalChip{
my ($self, $exp) = @_;
throw("Must provide an ExperimentChip object") if(! $exp->isa('Bio::EnsEMBL::Funcgen::ExperimentalChip'));
return $self->fetch_all_by_experimental_chip_dbID($exp->dbID());
}
=head2 fetch_attributes
Arg [1] : Bio::EnsEMBL::Funcgen::Array - array to fetch attributes for
Example : None
Description: This function is solely intended to lazy load attributes into
empty Array objects. You should not need to call this.
Returntype : None
Exceptions : None
Caller : Bio::EnsEMBL::Funcgen::Array getters
Status : Medium Risk
=cut
sub fetch_attributes {
my $self = shift;
my $array = shift;
my $tmp_array = $self->fetch_by_dbID( $array->dbID() );
%$array = %$tmp_array;
}
=head2 _tables
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns the names and aliases of the tables to use for queries.
Returntype : List of listrefs of strings
Exceptions : None
Caller : Internal
Status : At Risk
=cut
sub _tables {
my $self = shift;
return ['channel', 'c'];
}
=head2 _columns
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns a list of columns to use for queries.
Returntype : List of strings
Exceptions : None
Caller : Internal
Status : At Risk
=cut
sub _columns {
my $self = shift;
return qw( c.channel_id c.experimental_chip_id c.sample_id c.dye c.type);
}
=head2 _objs_from_sth
Arg [1] : DBI statement handle object
Example : None
Description: PROTECTED implementation of superclass abstract method.
Creates Channel objects from an executed DBI statement
handle.
Returntype : Listref of Bio::EnsEMBL::Funcgen::Channel objects
Exceptions : None
Caller : Internal
Status : At Risk
=cut
sub _objs_from_sth {
my ($self, $sth) = @_;
my (@result, $ec_id, $chan_id, $sample_id, $type, $dye);
$sth->bind_columns(\$chan_id, \$ec_id, \$sample_id, \$dye, \$type);
while ( $sth->fetch() ) {
my $chan = Bio::EnsEMBL::Funcgen::Channel->new(
-DBID => $chan_id,
-EXPERIMENTAL_CHIP_ID => $ec_id,
-SAMPLE_ID => $sample_id,
-TYPE => $type,
-DYE => $dye,
-ADAPTOR => $self,
);
push @result, $chan;
}
return \@result;
}
=head2 store
Args : List of Bio::EnsEMBL::Funcgen::Channel objects
Example : $chan_a->store($c1, $c2, $c3);
Description: Stores given Channel objects in the database. Should only be
called once per array because no checks are made for duplicates.
Sets dbID and adaptor on the objects that it stores.
Returntype : None
Exceptions : Throws if object is not a Bio::EnsEMBL::Funcgen::Channel
Throws if object is already present in the DB but has no dbID
Caller : General
Status : At Risk
=cut
sub store {
my $self = shift;
my @args = @_;
my $sth = $self->prepare("
INSERT INTO channel
(experimental_chip_id, sample_id, dye, type)
VALUES (?, ?, ?, ?)");
foreach my $chan (@args) {
throw('Can only store Channel objects') if ( ! $chan->isa('Bio::EnsEMBL::Funcgen::Channel'));
if (!( $chan->dbID() && $chan->adaptor() == $self )){#use is_stored?
my $s_chan = $self->fetch_by_type_experimental_chip_id($chan->type(), $chan->experimental_chip_id());
throw("Channel already exists in the database with dbID:".$s_chan->dbID().
"\nTo reuse/update this Channel you must retrieve it using the ChannelAdaptor".
"\nMaybe you want to use the -recover option?") if $s_chan;
#if(! $s_chan){
$sth->bind_param(1, $chan->experimental_chip_id(), SQL_INTEGER);
$sth->bind_param(2, $chan->sample_id(), SQL_VARCHAR);
$sth->bind_param(3, $chan->dye() , SQL_VARCHAR);
$sth->bind_param(4, $chan->type(), SQL_VARCHAR);
$sth->execute();
my $dbID = $sth->{'mysql_insertid'};
$chan->dbID($dbID);
$chan->adaptor($self);
#}
#else{
# #do some status checks here, check IMPORTED
# #Need to account for recover in Importer?
# $chan = $s_chan;
# my @states = @{$self->db->fetch_all_states('channel', $chan->dbID())};
# #need better id than dbID?
# warn("Using previously stored Channel (".$chan->experimental_chip_id().":".$chan->type().") with states\t@states\n");
#}
}else{
#assume we want to update the states
warn('You may want to use $chan->adaptor->store_states($chan)');
$self->store_states($chan);
}
}
return \@args;
}
=head2 list_dbIDs
Args : None
Example : my @array_ids = @{$ec_a->list_dbIDs()};
Description: Gets an array of internal IDs for all ExperimentalChip objects in the
current database.
Returntype : List of ints
Exceptions : None
Caller : ?
Status : At risk
=cut
sub list_dbIDs {
my ($self) = @_;
return $self->_list_dbIDs('channel');
}
1;
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