Bio::DB::SoapEUtilities::LinkAdaptor

NAME

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

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.

SEE ALSO

Bio::DB::SoapEUtilities

FEEDBACK

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 AT bioperl DOT org                  − General discussion
http://bioperl.org/wiki/Mailing_lists  − About the mailing lists

Support
Please direct usage questions or support issues to the mailing list:

bioperl−l AT bioperl DOT 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.

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/

AUTHOR − Mark A. Jensen

Email maj −at− fortinbras −dot− us

APPENDIX

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

new

 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    :

next_linkset()

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

id_map()

 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)