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().
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AUTHOR - Lincoln Stein
Email [email protected]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
_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.