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obtained via a query object, and are attached to the correct C<Bio::Seq>
objects when the query is handled by C<Bio::DB::HIV::get_Seq_by_query>
or C<Bio::DB::HIV::get_Stream_by_query>.

=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
the Bioperl mailing list.  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
of the bugs and their resolution. Bug reports can be submitted via
the web:

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

=head1 AUTHOR - Mark A. Jensen

Email maj@fortinbras.us

=head1 CONTRIBUTORS

Mark A. Jensen

=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::HIV;
use strict;
use warnings;
use vars qw( $LANL_BASE $LANL_MAP_DB $LANL_MAKE_SEARCH_IF $LANL_SEARCH );

# Object preamble - inherits from Bio::DB::WebDBSeqI

use Bio::Root::Root;
use HTTP::Request::Common;
use Bio::DB::HIV::HIVAnnotProcessor;

use base qw(Bio::DB::WebDBSeqI);


BEGIN {
    # base change of 01/14/09
    $LANL_BASE = "http://www.hiv.lanl.gov/components/sequence/HIV/asearch";
    $LANL_MAP_DB = "map_db.comp";
    $LANL_MAKE_SEARCH_IF = "make_search_if.comp";
    $LANL_SEARCH = "search.comp";
    @Bio::ResponseProblem::Exception::ISA = qw( Bio::Root::Exception );
    @Bio::HIVSorry::Exception::ISA = qw ( Bio::Root::Exception );
    @Bio::WebError::Exception::ISA = qw( Bio::Root::Exception );
}

=head1 Constructor

=head2 new

 Title   : new
 Usage   : my $obj = new Bio::DB::HIV();
 Function: Builds a new Bio::DB::HIV object
 Returns : an instance of Bio::DB::HIV
 Args    :

=cut

sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($lanl_base, $lanl_map_db, $lanl_make_search_if, $lanl_search) =
      $self->_rearrange([qw(
                           LANL_BASE
                           LANL_MAP_DB
                           LANL_MAKE_SEARCH_IF
                           LANL_SEARCH
                           )], @args);

  $lanl_base                  && $self->lanl_base($lanl_base);
  $lanl_map_db                && $self->map_db($lanl_map_db);
  $lanl_make_search_if        && $self->make_search_if($lanl_make_search_if);
  $lanl_search                && $self->search_($lanl_search);
  # defaults
  $self->lanl_base            || $self->lanl_base($LANL_BASE);
  $self->map_db               || $self->map_db($LANL_MAP_DB);
  $self->make_search_if       || $self->make_search_if($LANL_MAKE_SEARCH_IF);
  $self->search_              || $self->search_($LANL_SEARCH);
  $self->url_base_address     || $self->url_base_address($self->lanl_base);

  $self->request_format("fasta");

  return $self;
}

=head1 WebDBSeqI compliance

=head2 get_request

 Title   : get_request
 Usage   : my $url = $self->get_request
 Function: returns a HTTP::Request object
 Returns :
 Args    : %qualifiers = a hash of qualifiers with keys in
            (-ids, -format, -mode, -query)
 Note    : Several layers of requests are performed to get to the sequence;
           see Bio::DB::Query::HIVQuery.

=cut

sub get_request {
    my $self = shift;
    my %quals = @_;
    my ($resp);
    my (@ids, $mode, @interface, @query_parms, $query);

    # html parsing regexps
    my $tags_re = qr{(?:\s*<[^>]+>\s*)};
    my $session_id_re = qr{<input.*name="id".*value="([0-9a-f]+)"}m;
    my $search_form_re = qr{<form[^>]*action=".*/search.comp"};
    my $seqs_found_re = qr{Displaying$tags_re*(?:\s*[0-9-]*\s*)*$tags_re*of$tags_re*\s*([0-9]+)$tags_re*sequences found};
    my $no_seqs_found_re = qr{Sorry.*no sequences found};
    my $too_many_re = qr{too many records: $tags_re*([0-9]+)};
    # find something like:
    #  <strong>tables without join:</strong><br>SequenceAccessions<br>
    my $tbl_no_join_re = qr{tables without join}i;
#    my $sorry_bud_re = qr{};

    # handle "qualifiers"
    foreach (keys %quals) {
	m/mode/ && do {
	    $mode = $quals{$_};
	    next;
	};
	m/uids/ && do {
	    $self->throw(-class=>"Bio::Root::BadParameter",
			 -text=>"Arrayref required for qualifier \"$_\"",
			 -value=>$quals{$_}) unless ref($quals{$_}) eq 'ARRAY';
	    @ids = @{$quals{$_}};
	    next;
	};
	m/query/ && do {
	    $self->throw(-class=>"Bio::Root::BadParameter",
			 -text=>"Bio::DB::Query::HIVQuery required for qualifier \"$_\"",
			 -value=>$quals{$_}) unless $quals{$_}->isa("Bio::DB::Query::HIVQuery");
	    $query = $quals{$_};
	    next;
	};
	do {
	    1; #else stub
	};
    }
	# what kind of request?
    for my $m ($mode) {
	($m =~ m/single/) && do {
	    @interface = (
		'sequenceentry' => 'se_sequence',
		'sequenceentry' => 'se_id',
		'action' => 'Search Interface'
		);
	    @query_parms = map { ('sequenceentry.se_id' => $_ ) } @ids;
	    push @query_parms, (