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Christopher Fields


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


  # 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


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().


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AUTHOR - Lincoln Stein

Email lstein@cshl.org


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


 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.


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


 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)


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


 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


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


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


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


 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.


 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


 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.


 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.


 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.