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:

  https://github.com/bioperl/bioperl-live/issues

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

delay¶

 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().

delay_policy¶

 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.

_sleep¶

 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.

_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.