/ 
BioPerl-1.7.8
River stage two • 60 direct dependents • 65 total dependents
/ Bio::DB::Query::WebQuery

NAME

Bio::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:

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

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

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.