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#
#
# BioPerl module for Bio::DB::SwissProt
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code
# Reworked to use Bio::DB::WebDBSeqI 2000-12-11

=head1 NAME

Bio::DB::SwissProt - Database object interface to SwissProt retrieval

=head1 SYNOPSIS

    use Bio::DB::SwissProt;

    $sp = Bio::DB::SwissProt->new();

    $seq = $sp->get_Seq_by_id('KPY1_ECOLI'); # SwissProt ID
    # <4-letter-identifier>_<species 5-letter code>
    # or ...
    $seq = $sp->get_Seq_by_acc('P43780'); # SwissProt AC
    # [OPQ]xxxxx


    # In fact in this implementation
    # these methods call the same webscript so you can use
    # then interchangeably

    # choose a different server to query
    $sp = Bio::DB::SwissProt->new('-servertype' => 'expasy',
				 '-hostlocation' => 'us');

    $seq = $sp->get_Seq_by_id('BOLA_HAEIN'); # SwissProtID

=head1 DESCRIPTION

SwissProt is a curated database of proteins managed by the Swiss
Bioinformatics Institute. Additional tools for
parsing and manipulating swissprot files can be found at
ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/.

Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the
SwissProt database via an Expasy retrieval.

In order to make changes transparent we have host type (currently only
expasy) and location (default to Switzerland) separated out.  This
allows the user to pick the closest Expasy mirror for running their
queries.


=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.


  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support

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

I<bioperl-l@bioperl.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.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Jason Stajich

Email Jason Stajich  E<lt>jason@bioperl.org E<lt>

Thanks go to Alexandre Gattiker E<lt>gattiker@isb-sib.chE<gt> of Swiss
Institute of Bioinformatics for helping point us in the direction of
the correct expasy scripts and for swissknife references.

Also thanks to Heikki Lehvaslaiho E<lt>heikki-at-bioperl-dot-orgE<gt>
for help with adding EBI swall server.

=head1 APPENDIX

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

=cut

# Let the code begin...

package Bio::DB::SwissProt;
use strict;

use HTTP::Request::Common;