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.IX Title "Bio::DB::SoapEUtilities::LinkAdaptor 3pm"
.TH Bio::DB::SoapEUtilities::LinkAdaptor 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::DB::SoapEUtilities::LinkAdaptor \- Handle for Entrez SOAP LinkSets
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 10
\& my $fac = Bio::DB::SoapEUtilities\->new();
\& # run a query, returning a LinkAdaptor
\& $fac\->elink( \-db => \*(Aqnucleotide\*(Aq,
\&              \-dbfrom => \*(Aqprotein\*(Aq,
\&              \-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;
\& }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This adaptor provides an iterator (\f(CW\*(C`next_linkset()\*(C'\fR) and other
convenience functions for parsing \s-1NCBI\s0 Entrez EUtility \f(CW\*(C`elink\*(C'\fR
\&\s-1SOAP\s0 results.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::DB::SoapEUtilities
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
bioperl\-l@bioperl.org
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Mark A. Jensen"
.IX Header "AUTHOR - Mark A. Jensen"
Email maj \-at\- fortinbras \-dot\- us
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& 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    :
.Ve
.SS "\fBnext_linkset()\fP"
.IX Subsection "next_linkset()"
.Vb 5
\& Title   : next_linkset
\& Usage   : 
\& Function: return the next LinkSet from the attached Result
\& Returns : 
\& Args    :
.Ve
.SS "\fBid_map()\fP"
.IX Subsection "id_map()"
.Vb 7
\& Title   : id_map
\& Usage   : $to_id = $adaptor\->id_map($from_id)
\& Function: Return \*(Aqto\-database\*(Aq ids corresponding to
\&           given specified \*(Aqfrom\-database\*(Aq or
\&           submitted ids
\& Returns : array of scalars (to\-database ids or arrayrefs of ids)
\& Args    : array of scalars (from\-database ids)
.Ve