| Bio::DB::Query::WebQuery(3pm) | User Contributed Perl Documentation | Bio::DB::Query::WebQuery(3pm) |
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().
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.
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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.
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:
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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
$self->ua($ua)
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 : 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().
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.
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.
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.
| 2021-08-15 | perl v5.32.1 |