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

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Summary

Bio::DB::SoapEUtilities::DocSumAdaptor - Handle for Entrez SOAP DocSums

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

 my $fac = Bio::DB::SoapEUtilities->new();
 # run a query, returning a DocSumAdaptor
 my $docs = $fac->esummary( -db => 'taxonomy',
                            -id => 527031 )->run(-auto_adapt=>1);
 # iterate over docsums
 while (my $d = $docs->next_docsum) {
    @available_items = $docsum->item_names;
    # any available item can be called as an accessor
    # from the docsum object...watch your case...
    $sci_name = $d->ScientificName;
    $taxid = $d->TaxId;
 }

Description

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

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::DB::SoapEUtilities::DocSumAdaptor();
 Function: Builds a new Bio::DB::SoapEUtilities::DocSumAdaptor object
 Returns : an instance of Bio::DB::SoapEUtilities::DocSumAdaptor
 Args    :

 Title   : next_docsum
 Usage   : 
 Function: return the next DocSum from the attached Result
 Returns : 
 Args    :

Methods code

sub new {

    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($result) = $self->_rearrange([qw(RESULT)], @args);
    $self->throw("DocSumAdaptor requires a SoapEUtilities::Result argument")
	unless $result;
    $self->throw("DocSumAdaptor only works with elink results") unless
	$result->util eq 'esummary';
    $self->{'_result'} = $result;
    $self->{'_idx'} = 1;
    return $self;

}

sub next_docsum {

    my $self = shift;
    my $stem = "//Body/".$self->result->result_type."/[".$self->{'_idx'}."]";
    my $som = $self->result->som;
    return unless $som->valueof($stem);
    my ($ret, %params);
    my $get = sub { $som->valueof("$stem/".shift) };
    
    $params{'-id'} = $get->('Id');

    my $names = [];
    for (my $i = 1; my $data = $som->dataof("$stem/[$i]"); $i++) {
	if ( $data->value and $data->value !~ /^\s*$/) {
	    my $name = $data->attr->{'Name'};
	    next unless $name;
	    my $content = $som->valueof("$stem/[$i]/ItemContent");
	    unless (defined $content) {
		next unless $som->dataof("$stem/[$i]/Item");
		my $h = {};
		_traverse_items("$stem/[$i]", $som, $h);
		$content = $h;
	    }
	    push @$names, $name;
	    $params{$name} = $content;
	}
    }
    $params{'_item_names'} = $names;
    my $class = ref($self)."::docsum";
    $ret = $class->new(%params);
    ($self->{'_idx'})++;
    return $ret;

}

sub rewind {

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

}

sub _traverse_items {

    my ($stem, $som, $h) = @_;
    for (my $i = 1; my $data = $som->dataof($stem."/[$i]"); $i++) {
	my $name = $data->attr->{'Name'};
	next unless $name;
	if ($name =~ /Type$/) {
	    # clip out this node
	    _traverse_items("$stem/[$i]", $som, $h);
	}
	else {
	    my $content = $som->valueof("$stem/[$i]/ItemContent");
	    if ($content) {
		$$h{$name} = $content;
	    }
	    else {
		$$h{$name} = {};
		_traverse_items("$stem/[$i]", $som, $$h{$name});
	    }
	}
    }
    return;
}

1; 

####
package Bio::DB::SoapEUtilities::DocSumAdaptor::docsum;
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 _