Bio::DB::Query::WebQueUser)Contributed Perl DocumenBio::DB::Query::WebQuery(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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
_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.
perl v5.14.1 2011-07-22 Bio::DB::Query::WebQuery(3)
