# $Id$
#
# BioPerl module for Bio::DB::SoapEUtilities::GQueryAdaptor
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark A. Jensen <maj -at- fortinbras -dot- us>
#
# Copyright Mark A. Jensen
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::SoapEUtilities::GQueryAdaptor - Handle for Entrez SOAP GlobalQuery items
=head1 SYNOPSIS
my $fac = Bio::DB::SoapEUtilities->new();
# run a query, returning a GQueryAdaptor
my $queries = $fac->egquery( -term => 'BRCA and human' )->run(-auto_adapt=>1);
# all databases with hits
my @dbs = $queries->found_in_dbs;
# queries by database
my $prot_count = $queries->query_by_db('prot')->count;
# iterate over gquery
while ( my $q = $queries->next_query ) {
my $db = $q->db;
my $count = $q->count;
my $status = $q->status;
}
=head1 DESCRIPTION
This adaptor provides an iterator (C<next_query()>) and other
convenience functions for parsing NCBI Entrez EUtility C<egquery>
SOAP results.
=head1 SEE ALSO
L<Bio::DB::SoapEUtilities>
=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 Support
Please direct usage questions or support issues to the mailing list:
L<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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
the web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
=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::SoapEUtilities::GQueryAdaptor;
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use base qw(Bio::Root::Root );
=head2 new
Title : new
Usage : my $obj = new Bio::DB::SoapEUtilities::GQueryAdaptor();
Function: Builds a new Bio::DB::SoapEUtilities::GQueryAdaptor object
Returns : an instance of Bio::DB::SoapEUtilities::GQueryAdaptor
Args :
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($result) = $self->_rearrange([qw(RESULT)], @args);
$self->throw("GQueryAdaptor requires a SoapEUtilities::Result argument")
unless $result;
$self->throw("GQueryAdaptor only works with egquery results") unless
$result->util eq 'egquery';
$self->{'_result'} = $result;
$self->{'_query_by_db'} = {};
$self->{'_idx'} = 1;
return $self;
}
sub result { shift->{'_result'} }
=head2 next_query()
Title : next_query
Usage :
Function: return the next global query from the attached Result
Returns :
Args :
=cut
sub next_query {
my $self = shift;
# my $stem = "//Body/".$self->result->result_type."/[".$self->{'_idx'}."]";
# not consistent, kludge as follows:
my $stem = "//eGQueryResult/[".$self->{'_idx'}."]";
my $som = $self->result->som;
return unless $som->valueof($stem);
my ($ret, %params);
my $get = sub { $som->valueof("$stem/".shift) };
my $toplev = $get->('');
my $get_tl = sub { $toplev->{ shift @_ } };
$params{'-term'} = $som->valueof("//Term");
my $names = [];
$params{'-count'} = $get_tl->('Count');
$params{'-db'} = $get_tl->('DbName');
$params{'-status'} = $get_tl->('Status');
my $class = ref($self)."::gquery";
$ret = $class->new(%params);
$self->{_query_by_db}->{$params{'-db'}} = $ret;
($self->{'_idx'})++;
return $ret;
}
sub next_obj { shift->next_query(@_) }
sub rewind { shift->{'_idx'} = 1; };
=head2 found_in_dbs()
Title : found_in_dbs
Usage :
Function: Return list of db names containing hits for
the query term
Returns : array of scalar strings
Args : none
=cut
sub found_in_dbs {
my $self = shift;
return @{$self->{'_found_in_dbs'}} if $self->{'_found_in_dbs'};
my $som = $self->result->som;
$self->{'_found_in_dbs'} = [];
foreach ($som->valueof("//eGQueryResult/*")) {
push @{$self->{'_found_in_dbs'}}, $_->{'DbName'} if
$_->{'Count'};
}
return @{$self->{'_found_in_dbs'}};
}
=head2 query_by_db()
Title : query_by_db
Usage :
Function: get gquery object by db name
Returns :
Args : db name (scalar string)
=cut
sub query_by_db {
my $self = shift;
my $db = shift;
$self->throw("db must be specified") unless $db;
return $self->{_query_by_db}->{$db} if $self->{_query_by_db}->{$db};
my $som = $self->result->som;
my $i;
for ($i = 1; my $val = $som->valueof("//eGQueryResult/[$i]/DbName"); $i++) {
last if $val eq $db;
}
my $curidx = $self->{_idx};
my $query;
{
local $self->{_idx} = $i;
$query = $self->next_query;
}
return $query;
}
1;
####
package Bio::DB::SoapEUtilities::GQueryAdaptor::gquery;
use strict;
use warnings;
use base qw(Bio::Root::Root);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my %args = @args;
$self->_set_from_args( \%args,
-methods => [map { /^-?(.*)/ } keys %args],
-create => 1,
-code =>
'my $self = shift;
my $d = shift;
my $k = \'_\'.$method;
$self->{$k} = $d if $d;
return (ref $self->{$k} eq \'ARRAY\') ?
@{$self->{$k}} : $self->{$k};'
);
return $self;
}
1;