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.\" ========================================================================
.\"
.IX Title "Bio::DB::Query::WebQuery 3pm"
.TH Bio::DB::Query::WebQuery 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::DB::Query::WebQuery \- Helper class for web\-based sequence queryies
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  # Do not use this class directly.  See Bio::DB::QueryI and one of
\&  # the implementor classes (such as Bio::DB::GenBankQuery) for
\&  # information.
.Ve
.PP
See Bio::DB::QueryI, Bio::DB::GenBankQuery
.SH "DESCRIPTION"
.IX Header "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.
.PP
Those writing subclasses must define \fB_get_params()\fR and
\&\fB_parse_response()\fR, and possibly override \fB_request_method()\fR.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Lincoln Stein"
.IX Header "AUTHOR - Lincoln Stein"
Email lstein@cshl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 7
\& Title   : new
\& Usage   : $db = Bio::DB::WebQuery\->new(@args)
\& Function: create new query object
\& Returns : new query object
\& Args    : \-db       database (e.g. \*(Aqprotein\*(Aq)
\&           \-ids      array ref of ids (overrides query)
\&           \-verbose  turn on verbose debugging
.Ve
.PP
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.
.PP
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.
.SS "ua"
.IX Subsection "ua"
.Vb 6
\& 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
.Ve
.SS "proxy"
.IX Subsection "proxy"
.Vb 9
\& Title   : proxy
\& Usage   : $httpproxy = $db\->proxy(\*(Aqhttp\*(Aq)  or
\&           $db\->proxy([\*(Aqhttp\*(Aq,\*(Aqftp\*(Aq], \*(Aqhttp://myproxy\*(Aq )
\& 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)
.Ve
.SS "authentication"
.IX Subsection "authentication"
.Vb 5
\& Title   : authentication
\& Usage   : $db\->authentication($user,$pass)
\& Function: Get/Set authentication credentials
\& Returns : Array of user/pass
\& Args    : Array or user/pass
.Ve
.SS "ids"
.IX Subsection "ids"
.Vb 5
\& 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
.Ve
.SS "query"
.IX Subsection "query"
.Vb 5
\& Title   : query
\& Usage   : $query = $db\->query([$query])
\& Function: get/set query string
\& Returns : string
\& Args    : (optional) new query string
.Ve
.SS "delay"
.IX Subsection "delay"
.Vb 5
\& 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
.Ve
.PP
\&\s-1NOTE:\s0 the default is to use the value specified by \fBdelay_policy()\fR.
This can be overridden by calling this method, or by passing the
\&\-delay argument to \fBnew()\fR.
.SS "delay_policy"
.IX Subsection "delay_policy"
.Vb 5
\& 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
.Ve
.PP
\&\s-1NOTE:\s0 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.
.SS "_sleep"
.IX Subsection "_sleep"
.Vb 5
\& Title   : _sleep
\& Usage   : $self\->_sleep
\& Function: sleep for a number of seconds indicated by the delay policy
\& Returns : none
\& Args    : none
.Ve
.PP
\&\s-1NOTE:\s0 This method keeps track of the last time it was called and only
imposes a sleep if it was called more recently than the \fBdelay_policy()\fR
allows.
.SS "_fetch_ids"
.IX Subsection "_fetch_ids"
.Vb 5
\& Title   : _fetch_ids
\& Usage   : @ids = $db\->_fetch_ids
\& Function: run query, get ids
\& Returns : array of sequence ids
\& Args    : none
.Ve
.SS "_run_query"
.IX Subsection "_run_query"
.Vb 5
\& Title   : _run_query
\& Usage   : $success = $db\->_run_query
\& Function: run query, parse results
\& Returns : true if successful
\& Args    : none
.Ve
.SS "_truncated"
.IX Subsection "_truncated"
.Vb 5
\& Title   : _truncated
\& Usage   : $flag = $db\->_truncated([$newflag])
\& Function: get/set truncation flag
\& Returns : boolean
\& Args    : new flag
.Ve
.PP
Some databases will truncate output unless explicitly asked
not to.  This flag allows a \*(L"two probe\*(R" attempt.
.SS "_get_request"
.IX Subsection "_get_request"
.Vb 5
\& 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
.Ve
.SS "_parse_response"
.IX Subsection "_parse_response"
.Vb 6
\& Title   : _parse_response
\& Usage   : $db\->_parse_response($content)
\& Function: parse out response
\& Returns : empty
\& Args    : none
\& Throws  : \*(Aqunparseable output exception\*(Aq
.Ve
.PP
\&\s-1NOTE:\s0 This method must be implemented by subclass.
.SS "_request_parameters"
.IX Subsection "_request_parameters"
.Vb 5
\& 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
.Ve
.PP
\&\s-1NOTE:\s0 This method must be implemented by subclass.
.SS "_generate_id_string"
.IX Subsection "_generate_id_string"
.Vb 5
\& 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)
.Ve
.PP
\&\s-1NOTE:\s0 This method must be implemented by subclass.