Bio::Das::ProServer::SourceAdaptor::grouped_db - Bio::Das::ProServer::SourceAdaptor::grouped_db documentation
Index
Code Index:
NAME
Bio::Das::ProServer::SourceAdaptor::grouped_db
VERSION
$LastChangedRevision: 548 $
SYNOPSIS
DESCRIPTION
SUBROUTINES/METHODS
capabilities
build_features
build_types
build_entry_points
segment_version
DIAGNOSTICS
CONFIGURATION AND ENVIRONMENT
DEPENDENCIES
Bio::Das::ProServer::SourceAdaptor
INCOMPATIBILITIES
BUGS AND LIMITATIONS
AUTHOR
LICENSE AND COPYRIGHT
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
#########
# Author: jws
# Maintainer: jws, dj3
# Created: 2005-04-19
# Last Modified: $Date: 2008-12-03 23:14:25 +0000 (Wed, 03 Dec 2008) $ $Author: zerojinx $
# Id: $Id: grouped_db.pm 548 2008-12-03 23:14:25Z zerojinx $
# Source: $Source: /nfs/team117/rmp/tmp/Bio-Das-ProServer/Bio-Das-ProServer/lib/Bio/Das/ProServer/SourceAdaptor/grouped_db.pm,v $
# $HeadURL: https://proserver.svn.sf.net/svnroot/proserver/trunk/lib/Bio/Das/ProServer/SourceAdaptor/grouped_db.pm $
# Builds DAS features from ProServer mysql database
# schema at eof
#
## no critic (ValuesAndExpressions::ProhibitImplicitNewlines)
#
package Bio::Das::ProServer::SourceAdaptor::grouped_db;
use strict;
use warnings;
use base qw(Bio::Das::ProServer::SourceAdaptor);
use Readonly;
our $VERSION = do { my ($v) = (q$Revision: 548 $ =~ /\d+/mxg); $v; };
Readonly::Scalar our $SHORT_SEG_LEN => 4;
sub capabilities {
return {
features => '1.0',
stylesheet => '1.0',
entry_points => '1.0',
types => '1.0',
};
}
sub build_features {
my ($self, $opts) = @_;
my $seg = $opts->{segment};
my $start = $opts->{start};
my $end = $opts->{end};
my $shortsegnamehack = (defined $self->config->{'shortsegnamehack'})?$self->config->{'shortsegnamehack'}:1; #e.g. 1 (default) or 0
if($shortsegnamehack && (CORE::length($seg) > $SHORT_SEG_LEN)) {
return;
}
my $qbounds = q();
if(defined $start && $start ne q() && defined $end && $end ne q()) {
$start = $self->transport->dbh->quote($start);
$end = $self->transport->dbh->quote($end);
$qbounds = qq(AND start <= $end AND end >= $start);
}
my $query = qq(SELECT * FROM feature, fgroup
WHERE segment = ? $qbounds
AND feature.group_id = fgroup.group_id
ORDER BY start);
my @results;
for ( @{$self->transport->query($query, $seg)} ) {
push @results, {
id => $_->{id},
start => $_->{start},
end => $_->{end},
label => $_->{label},
score => $_->{score},
ori => $_->{orient},
phase => $_->{phase},
type => $_->{type_id},
typecategory => $_->{type_category},
method => $_->{method},
group => $_->{group_id},
grouptype => $_->{group_type},
grouplabel => $_->{group_label},
groupnote => $_->{group_note},
grouplink => $_->{group_link_url},
grouplinktxt => $_->{group_link_text},
target_start => $_->{target_start},
target_stop => $_->{target_end},
target_id => $_->{target_id},
link => $_->{link_url},
linktxt => $_->{link_text},
note => $_->{note},
};
}
return @results;
}
sub build_types {
my ($self, @args) = @_;
if(!scalar @args) {
my $query = q(SELECT DISTINCT type_id type, method FROM feature);
return @{$self->transport->query($query)};
}
my @r;
for (@args) {
my ($seg, $start, $end) = @{$_}{qw(segment start end)};
my $qbounds = q();
if(defined $start && $start ne q() && defined $end && $end ne q()) {
$start = $self->transport->dbh->quote($start);
$end = $self->transport->dbh->quote($end);
$qbounds = qq(AND start <= $end AND end >= $start);
}
my $query = qq(SELECT DISTINCT type_id type, method FROM feature
WHERE segment = ? $qbounds);
push @r, map { $qbounds?$self->_build_types_population($_, $seg, $start, $end):$_; }
@{$self->transport->query($query, $seg)};
}
return @r;
}
sub _build_types_population {
my ($self, $ref, $seg, $start, $end) = @_;
$ref->{segment} = $seg;
@{$ref}{qw(start end)} = ($start, $end);
return $ref;
}
sub build_entry_points {
my ($self) = @_;
my $query = q(SELECT DISTINCT segment FROM feature);
return map { $self->_build_ep_population($_); }
@{$self->transport->query($query)};
}
sub _build_ep_population {
my ($self, $ref) = @_;
$ref->{subparts} = 'no';
if(exists $self->{config}->{assembly}) {
$ref->{version} = $self->{config}->{assembly};
}
return $ref;
}
sub segment_version {
my $self = shift;
return (exists $self->{config}->{assembly})?$self->{config}->{assembly}:undef;
}
1;
# SCHEMA
# Generic MySQL schema to hold DAS feature data for ProServer
#
# feature
# id varchar(30)
# label varchar(30)
# segment varchar(30)
# start int(11)
# end int(11)
# score float
# orient enum('0', '+', '-')
# phase enum('0','1','2')
# type_id varchar(30)
# type_category varchar(30)
# method varchar(30)
# group_id varchar(30)
# target_id varchar(30)
# target_start int(11)
# target_end int(11)
# link_url varchar(255)
# link_text varchar(30)
# note text
#
# fgroup
# group_id varchar(30)
# label varchar(30)
# type varchar(30)
# note text
# link_url varchar(255)
# link_text varchar(30)
#
# Note that spec allows multiple groups, targets, and links per feature,
# but these aren't implemented here.
#
__END__