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.\" ========================================================================
.\"
.IX Title "Bio::DB::Biblio::biofetch 3pm"
.TH Bio::DB::Biblio::biofetch 3pm "2012-03-02" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::DB::Biblio::biofetch \- A BioFetch\-based access to a bibliographic 
  citation retrieval
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Do not use this object directly, only access it through the
\&\fIBio::Biblio\fR module:
.PP
.Vb 3
\&  use Bio::Biblio;
\&  my $biblio = Bio::Biblio\->new(\-access => \*(Aqbiofetch\*(Aq);
\&  my $ref = $biblio\->get_by_id(\*(Aq20063307\*(Aq));
\&
\&  my $ids = [\*(Aq20063307\*(Aq, \*(Aq98276153\*(Aq];
\&  my $refio = $biblio\->get_all($ids);
\&  while ($ref = $refio\->next_bibref) { 
\&    print $ref\->identifier, "\en";
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This class uses BioFetch protocol based service to retrieve Medline
references by their \s-1ID\s0.
.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
\&\fIbioperl\-l@bioperl.org\fR
.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
\&  https://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Heikki Lehvaslaiho (heikki-at-bioperl-dot-org)
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
.PP
This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
.SH "DISCLAIMER"
.IX Header "DISCLAIMER"
This software is provided \*(L"as is\*(R" without warranty of any kind.
.SH "BUGS AND LIMITATIONS"
.IX Header "BUGS AND LIMITATIONS"
.IP "\(bu" 1
Only method \fIget_by_id()\fR is supported.
.SH "APPENDIX"
.IX Header "APPENDIX"
The main documentation details are to be found in
Bio::DB::BiblioI.
.PP
Here is the rest of the object methods.  Internal methods are preceded
with an underscore _.
.SS "get_by_id"
.IX Subsection "get_by_id"
.Vb 5
\& Title   : get_by_id
\& Usage   : $entry = $db\->get_\|_by_id(\*(Aq20063307\*(Aq)
\& Function: Gets a Bio::Biblio::RefI object by its name
\& Returns : a Bio::Biblio::Medline object
\& Args    : the id (as a string) of the reference
.Ve
.SS "get_all"
.IX Subsection "get_all"
.Vb 9
\&  Title   : get_all
\&  Usage   : $seq = $db\->get_all($ref);
\&  Function: Retrieves reference objects from the server \*(Aqen masse\*(Aq, 
\&            rather than one  at a time.  For large numbers of sequences, 
\&            this is far superior than get_by_id().
\&  Example :
\&  Returns : a stream of Bio::Biblio::Medline objects
\&  Args    : $ref : either an array reference, a filename, or a filehandle
\&            from which to get the list of unique ids/accession numbers.
.Ve
.SS "get_seq_stream"
.IX Subsection "get_seq_stream"
.Vb 6
\& Title   : get_seq_stream
\& Usage   : my $seqio = $self\->get_seq_stream(%qualifiers)
\& Function: builds a url and queries a web db
\& Returns : a Bio::SeqIO stream capable of producing sequence
\& Args    : %qualifiers = a hash qualifiers that the implementing class 
\&           will process to make a url suitable for web querying
.Ve
.SS "postprocess_data"
.IX Subsection "postprocess_data"
.Vb 8
\& Title   : postprocess_data
\& Usage   : $self\->postprocess_data ( \*(Aqtype\*(Aq => \*(Aqstring\*(Aq,
\&                                     \*(Aqlocation\*(Aq => \e$datastr);
\& Function: process downloaded data before loading into a Bio::SeqIO
\& Returns : void
\& Args    : hash with two keys \- \*(Aqtype\*(Aq can be \*(Aqstring\*(Aq or \*(Aqfile\*(Aq
\&                              \- \*(Aqlocation\*(Aq either file location or string 
\&                                           reference containing data
.Ve
.SS "\s-1VERSION\s0 and Revision"
.IX Subsection "VERSION and Revision"
.Vb 2
\& Usage   : print $Bio::DB::Biblio::biofetch::VERSION;
\&           print $Bio::DB::Biblio::biofetch::Revision;
.Ve
.SS "Defaults"
.IX Subsection "Defaults"
.Vb 1
\& Usage   : print $Bio::DB::Biblio::biofetch::DEFAULT_SERVICE;
.Ve