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

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Summary

Bio::DB::SoapEUtilities::LinkAdaptor - Handle for Entrez SOAP LinkSets

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

 my $fac = Bio::DB::SoapEUtilities->new();
 # run a query, returning a LinkAdaptor
 $fac->elink( -db => 'nucleotide',
              -dbfrom => 'protein',
              -id => [qw(828392 790 470338)]);
 my $links = $fac->elink->run( -auto_adapt => 1);
 # get the linked ids corresponding to the submitted ids
 # (may be arrays if multiple crossrefs, or undef if none)
 my @nucids = $links->id_map(828392);
 # iterate over linksets
 while ( my $ls = $links->next_linkset ) {
    my @from_ids = $ls->submitted_ids;
    my @to_ids = $ls->ids;
    my $from_db = $ls->db_from;
    my $to_db = $ls->db_to;
 }

Description

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

Methods

Methods description

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

 Title   : next_linkset
 Usage   : 
 Function: return the next LinkSet from the attached Result
 Returns : 
 Args    :

 Title   : id_map
 Usage   : $to_id = $adaptor->id_map($from_id)
 Function: Return 'to-database' ids corresponding to
           given specified 'from-database' or
           submitted ids
 Returns : array of scalars (to-database ids or arrayrefs of ids)
 Args    : array of scalars (from-database ids)

Methods code

sub new {

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

}

sub next_linkset {

    my $self = shift;
    my $stem = "//Body/".$self->result->result_type."/[".$self->{'_idx'}."]";
    return unless $self->result->som and $self->result->som->valueof($stem);
    my $som = $self->result->som;
    my ($ret, %params);
    my $get = sub { $som->valueof("$stem/".shift) };
    
    $params{'-db_from'} = $get->('DbFrom');
    $params{'-db_to'} = $get->('LinkSetDb/DbTo');
    $params{'-link_name'} = $get->('LinkSetDb/LinkName');
    $params{'-submitted_ids'} = [$get->('IdList/*')];
    $params{'-ids'} = [$get->('LinkSetDb/Link/*')];
    $params{'-webenv'} = $get->('WebEnv');
    my $class = ref($self)."::linkset";
    $ret = $class->new(%params);
    ($self->{'_idx'})++;
    return $ret;

}

sub rewind {

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

}

sub id_map {

    my $self = shift;
    my @from_ids = @_;
    my $som = $self->result->som;
    my $stem = "//Body/".$self->result->result_type."/";
    if (!defined $self->{'_id_map'}) {
	my $h = {};
	for (my $i=1; $som->valueof($stem."[$i]"); $i++) {
	    # note this assumes that in the elink query, 
	    # ids were provided individually (not as a comma-sep
	    # list). This is the standard behavior for elink 
	    # in SoapEUtilities.
	    my @to_ids = $som->valueof($stem."[$i]/LinkSetDb/Link/*");
	    $$h{$som->valueof($stem."[$i]/IdList/[1]")} =
		(@to_ids == 1 ? $to_ids[0] :\@ to_ids);
	}
	$self->{'_id_map'} = $h;
    }
    return @{$self->{'_id_map'}}{@from_ids};
}

package Bio::DB::SoapEUtilities::LinkAdaptor::linkset;
use strict;
use warnings;

use base qw(Bio::Root::Root);

}

General documentation

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Please direct usage questions or support issues to the mailing list:
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rather than to the module maintainer directly. Many experienced and
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address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _