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::GenBankQuery) for information. Those writing subclasses must define _get_params() and _parse_response(), and possibly override _request_method().

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/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email lstein@cshl.org 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

_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.