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.IX Title "Bio::DB::SoapEUtilities::FetchAdaptor 3pm"
.TH Bio::DB::SoapEUtilities::FetchAdaptor 3pm 2024-04-27 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH NAME
Bio::DB::SoapEUtilities::FetchAdaptor \- Conversion of Entrez SOAP messages to BioPerl objects
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 9
\& $fac = Bio::DB::SoapEUtilities\->new();
\& $soap_result = $fac\->efetch( \-db => \*(Aqprotein\*(Aq, \-id => 2597988 );
\& $adp = Bio::DB::SoapEUtilities::FetchAdaptor(
\&         \-result => $soap_result,
\&         \-type => \*(Aqseq\*(Aq
\&        );
\& while ( $gb_seq = $adp\->next_obj ) {
\&    # do stuff
\& }
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
\&\f(CW\*(C`FetchAdaptor\*(C'\fR is the base class of a system, modeled after
Bio::SeqIO, to parse SOAP responses from the NCBI Entrez \f(CW\*(C`efetch\*(C'\fR
utility into germane BioPerl objects.
.PP
The user will rarely need to instantiate a \f(CW\*(C`FetchAdaptor\*(C'\fR with
Bio::DB::SoapEUtilities::Result object as in the "SYNOPSIS". It
usually suffices to use the \f(CW\*(C`\-auto_adapt\*(C'\fR parameter in the factory
\&\f(CWrun()\fR method:
.PP
.Vb 5
\& my $fac = Bio::DB::SoapEUtilities\->new();
\& my $taxio = $fac\->efetch(\-db => \*(Aqtaxonomy\*(Aq, \-id => 1394)\->run(\-auto_adapt=>1);
\& my $sp = $taxio\->next_species; # Bio::Species objects
\& my $seqio = $fac\->efetch(\-db => \*(Aqprotein\*(Aq, \-id => 730439)\->run(\-auto_adapt=>1);
\& my $seq = $seqio\->next_seq; # Bio::Seq::RichSeq objects
.Ve
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::DB::SoapEUtilities, \f(CW\*(C`FetchAdaptor\*(C'\fR subclasses
.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 7
\& Title   : new
\& Usage   : my $obj = new Bio::DB::SoapEUtilities::FetchAdaptor();
\& Function: Builds a new Bio::DB::SoapEUtilities::FetchAdaptor object
\& Returns : an instance of Bio::DB::SoapEUtilities::FetchAdaptor
\& Args    : named arguments
\&           \-som => $soap_som_object (soap message)
\&           \-type => $type ( optional, forces loading of $type adaptor )
.Ve
.SS \fB_initialize()\fP
.IX Subsection "_initialize()"
.Vb 5
\& Title   : _initialize
\& Usage   : 
\& Function: 
\& Returns : 
\& Args    :
.Ve
.SS \fB_load_adaptor()\fP
.IX Subsection "_load_adaptor()"
.Vb 5
\& Title   : _load_adaptor
\& Usage   : 
\& Function: loads a FetchAdaptor subclass
\& Returns : 
\& Args    : adaptor type (subclass name)
.Ve
.SS \fBobj_class()\fP
.IX Subsection "obj_class()"
.Vb 6
\& Title   : obj_class
\& Usage   : $adaptor\->obj_class
\& Function: Returns the fully qualified BioPerl classname
\&           of the objects returned by next_obj()
\& Returns : scalar string (class name)
\& Args    : none
.Ve
.SS \fBnext_obj()\fP
.IX Subsection "next_obj()"
.Vb 6
\& Title   : next_obj
\& Usage   : $obj = $adaptor\->next_obj
\& Function: Returns the next parsed BioPerl object from the 
\&           adaptor
\& Returns : object of class obj_class()
\& Args    : none
.Ve
.SS \fBrewind()\fP
.IX Subsection "rewind()"
.Vb 5
\& Title   : rewind
\& Usage   : 
\& Function: Rewind the adaptor\*(Aqs iterator
\& Returns : 
\& Args    : none
.Ve
.SS \fBresult()\fP
.IX Subsection "result()"
.Vb 5
\& Title   : result
\& Usage   : 
\& Function: contains the SoapEUtilities::Result object
\& Returns : Bio::DB::SoapEUtilities::Result object
\& Args    : none
.Ve
.SS \fBtype()\fP
.IX Subsection "type()"
.Vb 5
\& Title   : type
\& Usage   : 
\& Function: contains the fetch type of this adaptor
\& Returns : 
\& Args    :
.Ve