Bio::DB::GenericWebDBI - abstract interface for parameter-based remote database access
# # grab data from HTTP::Response object using concrete class # $data = $db->get_response->content; # # $data is the raw data output from the HTTP::Response object; # this data may be preparsed using the private method _parse_response
WARNING: Please do NOT spam the web servers with multiple requests.
This class acts as a user agent interface for any generic web database, but is specifically geared towards CGI-based databases which accept parameters.
File and filehandle support to be added
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : url_base_address Usage : my $address = $self->url_base_address or $self->url_base_address($address) Function: Get/Set the base URL for the Web Database Returns : Base URL for the Web Database Args : $address - URL for the WebDatabase
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)
Title : authentication Usage : $db->authentication($user,$pass) Function: Get/Set authentication credentials Returns : Array of user/pass Args : Array or user/pass
Title : db Usage : $db->db Function: Get/Set database parameter Returns : string Args : optional string
Title : id Usage : $agent->id($id) $agent->id(\@id) Function: Get/Set id(s) Returns : reference to id(s) Args : a single id or reference to array of id(s)
Title : retmode Usage : $agent->retmode($mode) Function: Get/Set return mode for query (text, xml, html, asn.1, etc) Returns : string for return mode Args : optional string
Title : get_response Usage : $agent->get_response; Function: get the request based on set object parameters, retrieved using the private method _get_params Returns : HTTP::Response object Args : none This is implemented by the derived class
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().
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.
Title : _submit_request Usage : my $url = $self->get_request Function: builds request object based on set parameters Returns : HTTP::Request Args : optional : Bio::DB::EUtilities cookie
Title : _get_params Usage : my $url = $self->_get_params Function: builds parameter list for web request Returns : hash of parameter-value paris Args : optional : Bio::DB::EUtilities cookie
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.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.