NAME

       Bio::DB::Query::WebQuery - Helper class for web-based sequence queryies

SYNOPSIS

         # Do not use this class directly.  See Bio::DB::QueryI and one of
         # the implementor classes (such as Bio::DB::GenBankQuery) for
         # information.

       See Bio::DB::QueryI, Bio::DB::GenBankQuery

DESCRIPTION

       Do not use this class directly.  See Bio::DB::QueryI and one of the implementor classes
       (such as Bio::DB::Query::GenBank) for information.

       Those writing subclasses must define _get_params() and _parse_response(), and possibly
       override _request_method().

FEEDBACK

   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

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

       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.

   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

AUTHOR - Lincoln Stein

       Email lstein@cshl.org

APPENDIX

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

   new
        Title   : new
        Usage   : $db = Bio::DB::WebQuery->new(@args)
        Function: create new query object
        Returns : new query object
        Args    : -db       database (e.g. 'protein')
                  -ids      array ref of ids (overrides query)
                  -verbose  turn on verbose debugging

       This method creates a new query object.  Typically you will specify a -db and a -query
       argument.  The value of -query is a database-specific string.

       If you provide an array reference of IDs in -ids, the query will be ignored and the list
       of IDs will be used when the query is passed to the database.

   ua
        Title   : ua
        Usage   : my $ua = $self->ua or
                  $self->ua($ua)
        Function: Get/Set a LWP::UserAgent for use
        Returns : reference to LWP::UserAgent Object
        Args    : $ua - must be a LWP::UserAgent

   proxy
        Title   : proxy
        Usage   : $httpproxy = $db->proxy('http')  or
                  $db->proxy(['http','ftp'], 'http://myproxy' )
        Function: Get/Set a proxy for use of proxy
        Returns : a string indicating the proxy
        Args    : $protocol : an array ref of the protocol(s) to set/get
                  $proxyurl : url of the proxy to use for the specified protocol
                  $username : username (if proxy requires authentication)
                  $password : password (if proxy requires authentication)

   authentication
        Title   : authentication
        Usage   : $db->authentication($user,$pass)
        Function: Get/Set authentication credentials
        Returns : Array of user/pass
        Args    : Array or user/pass

   ids
        Title   : ids
        Usage   : @ids = $db->ids([@ids])
        Function: get/set matching ids
        Returns : array of sequence ids
        Args    : (optional) array ref with new set of ids

   query
        Title   : query
        Usage   : $query = $db->query([$query])
        Function: get/set query string
        Returns : string
        Args    : (optional) new query string

   delay
        Title   : delay
        Usage   : $secs = $self->delay([$secs])
        Function: get/set number of seconds to delay between fetches
        Returns : number of seconds to delay
        Args    : new value

       NOTE: the default is to use the value specified by delay_policy().  This can be overridden
       by calling this method, or by passing the -delay argument to new().

   delay_policy
        Title   : delay_policy
        Usage   : $secs = $self->delay_policy
        Function: return number of seconds to delay between calls to remote db
        Returns : number of seconds to delay
        Args    : none

       NOTE: The default delay policy is 0s.  Override in subclasses to implement delays.  The
       timer has only second resolution, so the delay will actually be +/- 1s.

   _sleep
        Title   : _sleep
        Usage   : $self->_sleep
        Function: sleep for a number of seconds indicated by the delay policy
        Returns : none
        Args    : none

       NOTE: This method keeps track of the last time it was called and only imposes a sleep if
       it was called more recently than the delay_policy() allows.

   _fetch_ids
        Title   : _fetch_ids
        Usage   : @ids = $db->_fetch_ids
        Function: run query, get ids
        Returns : array of sequence ids
        Args    : none

   _run_query
        Title   : _run_query
        Usage   : $success = $db->_run_query
        Function: run query, parse results
        Returns : true if successful
        Args    : none

   _truncated
        Title   : _truncated
        Usage   : $flag = $db->_truncated([$newflag])
        Function: get/set truncation flag
        Returns : boolean
        Args    : new flag

       Some databases will truncate output unless explicitly asked not to.  This flag allows a
       "two probe" attempt.

   _get_request
        Title   : _get_request
        Usage   : $http_request = $db->_get_request(@params)
        Function: create an HTTP::Request with indicated parameters
        Returns : HTTP::Request object
        Args    : CGI parameter list

   _parse_response
        Title   : _parse_response
        Usage   : $db->_parse_response($content)
        Function: parse out response
        Returns : empty
        Args    : none
        Throws  : 'unparseable output exception'

       NOTE: This method must be implemented by subclass.

   _request_parameters
        Title   : _request_parameters
        Usage   : ($method,$base,@params = $db->_request_parameters
        Function: return information needed to construct the request
        Returns : list of method, url base and key=>value pairs
        Args    : none

       NOTE: This method must be implemented by subclass.

   _generate_id_string
        Title   : _generate_id_string
        Usage   : $string = $db->_generate_id_string
        Function: joins IDs together in string (implementation-dependent)
        Returns : string of concatenated IDs
        Args    : array ref of ids (normally passed into the constructor)

       NOTE: This method must be implemented by subclass.