Raw content of Bio::EnsEMBL::Compara::DBSQL::SitewiseOmegaAdaptor
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# Ensembl module for Bio::EnsEMBL::Compara::DBSQL::SitewiseOmegaAdaptor
#
# Cared for by Albert Vilella <avilella@ebi.ac.uk>
#
# Copyright Albert Vilella
#
# 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::SitewiseOmegaAdaptor - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 AUTHOR - Albert Vilella
This modules is part of the Ensembl project
Email aVilella@ebi.ac.uk
Describe contact details 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::EnsEMBL::Compara::DBSQL::SitewiseOmegaAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Compara::SitewiseOmega;
use Bio::EnsEMBL::Utils::Exception;
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
sub fetch_all_by_ProteinTreeId {
my ($self, $protein_tree_id) = @_;
my $sitewise_dnds_values = [];
my $sql = qq{
SELECT
sitewise_id,
aln_position,
node_id,
tree_node_id,
omega,
omega_lower,
omega_upper,
optimal,
threshold_on_branch_ds,
type
FROM
sitewise_aln
WHERE
node_id = ?
};
my $sth = $self->prepare($sql);
$sth->execute($protein_tree_id);
my $sitewise_dnds;
while (my ($sitewise_id,$aln_position,$node_id,$tree_node_id,
$omega,$omega_lower,$omega_upper,$optimal,
$threshold_on_branch_ds,$type) = $sth->fetchrow_array()) {
$sitewise_dnds = Bio::EnsEMBL::Compara::SitewiseOmega->new_fast(
{'adaptor' => $self,
'_dbID' => $sitewise_id,
'aln_position' => $aln_position,
'node_id' => $node_id,
'tree_node_id' => $tree_node_id,
'omega' => $omega,
'omega_lower' => $omega_lower,
'omega_upper' => $omega_upper,
'optimal' => $optimal,
'threshold_on_branch_ds' => $threshold_on_branch_ds,
'type' => $type});
push(@$sitewise_dnds_values, $sitewise_dnds);
}
#sort into numerical order based on aln_position
my @sorted_values = sort {$a->{aln_position} <=> $b->{aln_position}} @$sitewise_dnds_values;
return \@sorted_values;
}
1;
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