Raw content of Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor
#
# Copyright Javier Herrero
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
#
=head1 NAME
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor - Object to access data in genomic_align_group table
=head1 SYNOPSIS
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
my $db = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor (
-host => $host,
-user => $dbuser,
-pass => $dbpass,
-port => $port,
-dbname => $dbname,
-conf_file => $conf_file);
my $genomic_align_group_adaptor = $db->get_GenomicAlignGroupAdaptor();
$genomic_align_group_adaptor->store($genomic_align_group);
$genomic_align_groups = $genomic_align_group_adaptor->fetch_all_by_GenomicAlign($genomic_align);
$genomic_align_groups = $genomic_align_group_adaptor->fetch_all_by_genomic_align_id(11223);
$genomic_align_group = $genomic_align_group_adaptor->fetch_by_GenomicAlign_type($genomic_align,
"default");
$genomic_align_group = $genomic_align_group_adaptor->fetch_by_genomic_align_id_type(11223,
"default");
=head1 DESCRIPTION
This class is intended to access data in genomic_align_group table
=head1 AUTHOR
Javier Herrero (jherrero@ebi.ac.uk)
This modules is part of the Ensembl project
=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::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Compara::GenomicAlignGroup;
use Bio::EnsEMBL::Compara::GenomicAlign;
use Bio::EnsEMBL::Compara::DnaFrag;
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 new
Arg [1] : list of args to super class constructor
Example : $gag_a = new Bio::EnsEMBL::Compara::GenomicAlignGroupAdaptor($dbobj);
Description: Creates a new GenomicAlignGroupAdaptor. This
class should be instantiated through the get method on the
DBAdaptor rather than calling this method directly.
Returntype : none
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::DBConnection
Status : Stable
=cut
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
$self->{_use_autoincrement} = 1;
return $self;
}
=head2 store
Arg 1 : Bio::EnsEMBL::Compara::GenomicAlignGroup
The things you want to store
Example : $gen_ali_grp_adaptor->store($genomic_align_group);
Description: It stores the given GenomicAlginGroup in the database
Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup object
Exceptions : not stored linked Bio::EnsEMBL::Compara::GenomicAlign objects throw.
Caller : general
Status : Stable
=cut
sub store {
my ($self, $genomic_align_group) = @_;
my $genomic_align_block_sql =
qq{INSERT INTO genomic_align_group (
group_id,
type,
genomic_align_id
) VALUES (?,?,?)};
my @values;
## CHECKING
my $all_genomic_aligns = $genomic_align_group->get_all_GenomicAligns;
foreach my $genomic_align (@$all_genomic_aligns) {
# check if every GenomicAlgin has a dbID
if (!defined($genomic_align->dbID)) {
throw("GenomicAlign [$genomic_align] in GenomicAlignGroup is not in DB");
}
}
my $group_id = $genomic_align_group->dbID;
if (!$group_id) {
my $method_link_species_set_id;
# Get common method_link_species_set_id
foreach my $genomic_align (@$all_genomic_aligns) {
if (!$genomic_align->method_link_species_set_id()) {
## undef value and exit loop if method_link_species_set_id does not match
$method_link_species_set_id = undef;
last;
} elsif (!$method_link_species_set_id) {
$method_link_species_set_id = $genomic_align->method_link_species_set_id();
} elsif ($method_link_species_set_id != $genomic_align->method_link_species_set_id()) {
## undef value and exit loop if method_link_species_set_id does not match
$method_link_species_set_id = undef;
last;
}
}
if ($method_link_species_set_id && !$self->use_autoincrement()) {
## Only if method_link_species_set_id is the same for all the GenomicAligns
my $sql =
"SELECT MAX(group_id) FROM genomic_align_group WHERE".
" group_id > ".$method_link_species_set_id.
"0000000000 AND group_id < ".
($method_link_species_set_id + 1)."0000000000";
my $sth = $self->prepare($sql);
$sth->execute();
$group_id = $sth->fetchrow_array();
if (defined $group_id) {
$group_id++;
} else {
$group_id = $method_link_species_set_id * 10000000000 + 1;
}
}
}
## Stores data, all of them with the same id
my $sth = $self->prepare($genomic_align_block_sql);
for (my $i = 0; $i < @$all_genomic_aligns; $i++) {
my $genomic_align = $all_genomic_aligns->[$i];
$sth->execute(
($group_id or "NULL"),
$genomic_align_group->type,
$genomic_align->dbID
);
if (!$group_id) {$group_id = $sth->{'mysql_insertid'};}
info("Stored Bio::EnsEMBL::Compara::GenomicAlignGroup ".
"(".($i+1)."/".scalar(@$all_genomic_aligns).") ".
($group_id or "NULL").", ".$genomic_align_group->type.", ".
$genomic_align->dbID, );
}
$genomic_align_group->dbID($group_id);
return $genomic_align_group;
}
=head2 fetch_by_dbID
Arg 1 : integer group_id
Example : my $genomic_align_group =
$genomic_align_group_adaptor->fetch_by_dbID(12413)
Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
to the given group_id.
Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
Exceptions : none
Caller : object::methodname
Status : Stable
=cut
sub fetch_by_dbID {
my ($self, $group_id) = @_;
my $genomic_align_group;
my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
my $genomic_align_block_sql = qq{
SELECT
group_id,
type,
genomic_align_id
FROM
genomic_align_group
WHERE
group_id = ?
};
my @values;
my $sth = $self->prepare($genomic_align_block_sql);
$sth->execute($group_id);
# Group results in order to be able to build Bio::EnsEMBL::Compara::GenomicAlignGroupAdaptor objects
my $group;
while (my $values = $sth->fetchrow_arrayref) {
my ($group_id, $type, $genomic_align_id) = @$values;
$group->{'group_id'} = $group_id;
$group->{'type'} = $type;
my $this_genomic_align = new Bio::EnsEMBL::Compara::GenomicAlign(
-dbID => $genomic_align_id,
-adaptor => $genomic_align_adaptor
);
push(@{$group->{'genomic_align_array'}}, $this_genomic_align);
}
#return undef if no genomic_align_groups have been found
if (!defined $group->{'group_id'}) {
return $genomic_align_group;
}
$genomic_align_group = new Bio::EnsEMBL::Compara::GenomicAlignGroup(
-dbID => $group->{'group_id'},
-adaptor => $self,
-type => $group->{'type'},
-genomic_align_array => $group->{'genomic_align_array'}
);
foreach my $this_genomic_align (@{$genomic_align_group->genomic_align_array}) {
$this_genomic_align->genomic_align_group_by_type($genomic_align_group->type, $genomic_align_group);
}
return $genomic_align_group;
}
=head2 fetch_all_by_GenomicAlign
Arg 1 : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
Example : my $genomic_align_groups =
$genomic_align_group_adaptor->fetch_all_by_GenomicAlign(
$genomic_align)
Description: Returns all the Bio::EnsEMBL::Compara::GenomicAlignGroup
corresponding to the given Bio::EnsEMBL::Compara::GenomicAlign.
Returntype : a ref. to an array of Bio::EnsEMBL::Compara::GenomicAlignGroup
objects.
Exceptions : none
Caller : object::methodname
Status : Stable
=cut
sub fetch_all_by_GenomicAlign {
my ($self, $genomic_align) = @_;
my $genomic_align_groups = [];
my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
# Check Bio::EnsEMBL::Compara::GenomicAlign object
unless($genomic_align && ref $genomic_align &&
$genomic_align->isa('Bio::EnsEMBL::Compara::GenomicAlign')) {
throw("genomic_align argument must be a Bio::EnsEMBL::Compara::GenomicAlign not a [$genomic_align]");
}
my $genomic_align_block_sql = qq{
SELECT
group_id,
type
FROM
genomic_align_group
WHERE
genomic_align_id = ?
};
my $sth = $self->prepare($genomic_align_block_sql);
$sth->execute($genomic_align->dbID);
my $groups;
while (my $values = $sth->fetchrow_arrayref) {
my ($group_id, $type) = @$values;
$groups->{$group_id}->{'type'} = $type;
}
foreach my $group_id (keys %$groups) {
my $genomic_align_group = new Bio::EnsEMBL::Compara::GenomicAlignGroup(
-dbID => $group_id,
-adaptor => $self,
-type => $groups->{$group_id}->{'type'},
);
push(@{$genomic_align_groups}, $genomic_align_group);
}
return $genomic_align_groups;
}
=head2 fetch_all_by_genomic_align_id
Arg 1 : integer $genomic_align_id
Example : my $genomic_align_groups =
$genomic_align_group_adaptor->fetch_all_by_genomic_align_id(
124214)
Description: Returns all the Bio::EnsEMBL::Compara::GenomicAlignGroup
corresponding to the given Bio::EnsEMBL::Compara::GenomicAlign.
Returntype : a ref. to an array of Bio::EnsEMBL::Compara::GenomicAlignGroup
objects.
Exceptions : none
Caller : object->methodname
Status : Stable
=cut
sub fetch_all_by_genomic_align_id {
my ($self, $genomic_align_id) = @_;
my $genomic_align_groups = [];
my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
my $genomic_align_block_sql = qq{
SELECT
group_id,
type
FROM
genomic_align_group
WHERE
genomic_align_id = ?
};
my $sth = $self->prepare($genomic_align_block_sql);
$sth->execute($genomic_align_id);
my $groups;
while (my $values = $sth->fetchrow_arrayref) {
my ($group_id, $type) = @$values;
$groups->{$group_id}->{'type'} = $type;
}
foreach my $group_id (keys %$groups) {
my $genomic_align_group = new Bio::EnsEMBL::Compara::GenomicAlignGroup(
-dbID => $group_id,
-adaptor => $self,
-type => $groups->{$group_id}->{'type'},
);
push(@{$genomic_align_groups}, $genomic_align_group);
}
return $genomic_align_groups;
}
# # =head2 fetch_by_GenomicAlign_and_type
# #
# # Arg 1 : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
# # - or -
# # integer $genomic_align_id
# # Arg 2 : string $genomic_align_group_type
# # Example : my $genomic_align_group =
# # $genomic_align_group_adaptor->fetch_by_GenomicAlign_and_type(
# # $genomic_align, "default")
# # Example : my $genomic_align_groups =
# # $genomic_align_group_adaptor->fetch_all_by_GenomicAlign(
# # 124214, "default")
# # Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
# # to the given Bio::EnsEMBL::Compara::GenomicAlign and group_type.
# # Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
# # Exceptions : none
# # Caller : object::methodname
# #
# # =cut
=head2 fetch_by_GenomicAlign_and_type
DEPRECATED: Use the fetch_by_GenomicAlign_type method instead
=cut
sub fetch_by_GenomicAlign_and_type {
my ($self, $genomic_align, $type) = @_;
my $genomic_align_group;
deprecate("Use fetch_by_GenomicAlign_type method instead");
my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
# Get Bio::EnsEMBL::Compara::GenomicAlign object from dbID if needed
if ($genomic_align =~ /^\d+$/) {
$genomic_align = $genomic_align_adaptor->fetch_by_dbID($genomic_align);
}
return $self->fetch_by_GenomicAlign_type($genomic_align, $type);
}
=head2 fetch_by_GenomicAlign_type
Arg 1 : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
Arg 2 : string $genomic_align_group_type
Example : my $genomic_align_group =
$genomic_align_group_adaptor->fetch_by_GenomicAlign_and_type(
$genomic_align, "default")
Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
to the given Bio::EnsEMBL::Compara::GenomicAlign and group_type.
Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
Exceptions : none
Caller : object::methodname
Status : Stable
=cut
sub fetch_by_GenomicAlign_type {
my ($self, $genomic_align, $type) = @_;
my $genomic_align_group;
my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
# Check Bio::EnsEMBL::Compara::GenomicAlign object
unless($genomic_align && ref $genomic_align &&
$genomic_align->isa('Bio::EnsEMBL::Compara::GenomicAlign')) {
throw("[$genomic_align] must be a Bio::EnsEMBL::Compara::GenomicAlign object");
}
my $genomic_align_block_sql = qq{
SELECT
b.group_id,
b.type,
b.genomic_align_id
FROM
genomic_align_group a, genomic_align_group b
WHERE
a.group_id = b.group_id
AND a.genomic_align_id = ?
AND a.type = ?
};
my @values;
my $sth = $self->prepare($genomic_align_block_sql);
$sth->execute($genomic_align->dbID, $type);
# Group results in order to be able to build Bio::EnsEMBL::Compara::GenomicAlignGroupAdaptor objects
my $group;
while (my $values = $sth->fetchrow_arrayref) {
my ($group_id, $type, $genomic_align_id) = @$values;
$group->{'group_id'} = $group_id;
$group->{'type'} = $type;
my $this_genomic_align;
if ($genomic_align_id == $genomic_align->dbID) {
# Use Bio::EnsEMBL::Compara::GenomicAlign object given by argument if possible
$this_genomic_align = $genomic_align;
} else {
# Create a new Bio::EnsEMBL::Compara::GenomicAlign object otherwise
$this_genomic_align = new Bio::EnsEMBL::Compara::GenomicAlign(
-dbID => $genomic_align_id,
-adaptor => $genomic_align_adaptor
);
}
push(@{$group->{'genomic_align_array'}}, $this_genomic_align);
}
$genomic_align_group = new Bio::EnsEMBL::Compara::GenomicAlignGroup(
-dbID => $group->{'group_id'},
-adaptor => $self,
-type => $group->{'type'},
-genomic_align_array => $group->{'genomic_align_array'}
);
foreach my $this_genomic_align (@{$genomic_align_group->genomic_align_array}) {
$this_genomic_align->genomic_align_group_by_type($genomic_align_group->type, $genomic_align_group);
}
return $genomic_align_group;
}
=head2 fetch_by_genomic_align_id_type
Arg 1 : integer $genomic_align_id
Arg 2 : string $genomic_align_group_type
Example : my $genomic_align_group =
$genomic_align_group_adaptor->fetch_by_genomic_align_id_type(
12322, "default")
Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
to the given Bio::EnsEMBL::Compara::GenomicAlign defined by the
$genomic_align_id and to the group_type.
Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
Exceptions : none
Caller : object::methodname
Status : Stable
=cut
sub fetch_by_genomic_align_id_type {
my ($self, $genomic_align_id, $type) = @_;
my $genomic_align_group;
my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
# Get Bio::EnsEMBL::Compara::GenomicAlign object
my $genomic_align = $genomic_align_adaptor->fetch_by_dbID($genomic_align_id);
unless($genomic_align && ref $genomic_align &&
$genomic_align->isa('Bio::EnsEMBL::Compara::GenomicAlign')) {
throw("[$genomic_align] must be a Bio::EnsEMBL::Compara::GenomicAlign object");
}
return $self->fetch_by_GenomicAlign_type($genomic_align, $type);
}
=head2 retrieve_all_direct_attributes
Arg 1 : Bio::EnsEMBL::Compara::GenomicAlignGroup $genomic_align_group
Example : $genomic_align_group_adaptor->retrieve_all_direct_attributes($genomic_align_group)
Description: Retrieve the all the direct attibutes corresponding to the dbID of the
Bio::EnsEMBL::Compara::GenomicAlignGroup object. It is used after lazy fetching
of the object for populating it when required.
Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
Exceptions :
Caller : none
Status : Stable
=cut
sub retrieve_all_direct_attributes {
my ($self, $genomic_align_group) = @_;
my $sql_tmp = "SELECT type FROM genomic_align_group WHERE group_id = ?";
my $sql = $self->dbc->add_limit_clause($sql_tmp,1);
# my $sql = qq{
# SELECT
# type
# FROM
# genomic_align_group
# WHERE
# group_id = ?
# LIMIT 1
# };
my $sth = $self->prepare($sql);
$sth->execute($genomic_align_group->dbID);
my ($type) = $sth->fetchrow_array();
## Populate the object
$genomic_align_group->adaptor($self);
$genomic_align_group->type($type) if (defined($type));
return $genomic_align_group;
}
=head2 use_autoincrement
[Arg 1] : (optional)int value
Example : $genomic_align_adaptor->use_autoincrement(0);
Description: Getter/setter for the _use_autoincrement flag. This flag
is used when storing new objects with no dbID in the
database. If the flag is ON (default), the adaptor will
let the DB set the dbID using the AUTO_INCREMENT ability.
If you unset the flag, then the adaptor will look for the
first available dbID after 10^10 times the
method_link_species_set_id.
Returntype : integer
Exceptions :
Caller : none
Status : Stable
=cut
sub use_autoincrement {
my ($self, $value) = @_;
if (defined $value) {
$self->{_use_autoincrement} = $value;
}
return $self->{_use_autoincrement};
}
1;
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