Other packages in the module: Bio::DB::SoapEUtilities::GQueryAdaptor

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Summary

Bio::DB::SoapEUtilities::GQueryAdaptor - Handle for Entrez SOAP GlobalQuery items

Package variables

Included modules

Inherit

Bio::Root::Root

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;
 }

Description

This adaptor provides an iterator (next_query()) and other
convenience functions for parsing NCBI Entrez EUtility egquery
SOAP results.

Methods

Methods description

 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    :

 Title   : next_query
 Usage   : 
 Function: return the next global query from the attached Result
 Returns : 
 Args    :

 Title   : found_in_dbs
 Usage   : 
 Function: Return list of db names containing hits for 
           the query term
 Returns : array of scalar strings
 Args    : none

 Title   : query_by_db
 Usage   : 
 Function: get gquery object by db name
 Returns : 
 Args    : db name (scalar string)

Methods code

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 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 rewind {

 shift->{'_idx'} = 1; };

}

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'}};

}

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);

}

General documentation

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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _