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Bio::DB::Query::WebQuery.3pm

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:

   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.