Bio::Tools::Run::AnalysisFactory - A directory of analysis tools # list all available analyses from the default location, # using a default (SOAP) access method use Bio::Tools::Run::AnalysisFactory; my $list = new Bio::Tools::Run::AnalysisFactory ->available_analyses; use Data::Dumper; print Dumper ($list); # ditto, but from a different location use Bio::Tools::Run::AnalysisFactory; my $list = new Bio::Tools::Run::AnalysisFactory (-location => 'http://somewhere/something') ->available_analyses; # ...and using a different access method # (this example is not yet impelmented) use Bio::Tools::Run::AnalysisFactory; my $list = new Bio::Tools::Run::AnalysisFactory (-location => 'http://somewhere/something', -access => 'novella') ->available_analyses; # list available categories of analyses use Bio::Tools::Run::AnalysisFactory; my $categories = new Bio::Tools::Run::AnalysisFactory ->available_categories; use Data::Dumper; print Dumper ($categories); # show all analyses group by categories use Bio::Tools::Run::AnalysisFactory; my $factory = new Bio::Tools::Run::AnalysisFactory; foreach $cat ( @{ $factory->available_categories } ) { my @sublist = @{ $factory->available_analyses ($cat) }; print "$cat:\n\t", join ("\n\t", @{ $factory->available_analyses ($cat) }), "\n"; } # create an analysis object use Bio::Tools::Run::AnalysisFactory; $service = new Bio::Tools::Run::AnalysisFactory ->create_analysis ('edit.seqret'); $service->run ( #... )->results; The module represents a list of available analysis tools from a given location using a given access method. Additionally, for any of the available analyses, it can create an object of type "Bio::Tools::Run::Analysis". The module is a higher-level abstraction whose main job is to load a 'real-work-doing' implementation. Which one is used, it depends on the "-access" parameter. The same design is used here as for "Bio::Tools::Run::Analysis" module. There is available a SOAP access to almost all EMBOSS applications, running at European Bioinformatics Institute. The documentation of all "public" methods are to be found in "Bio::Factory::AnalysisI".

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Martin Senger (martin.senger@gmail.com) Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. This software is provided "as is" without warranty of any kind. http://www.ebi.ac.uk/soaplab/Perl_Client.html Here is the rest of the object methods. Internal methods are preceded with an underscore _.

new
Usage : my $factory = new Bio::Tools::Run::AnalysisFactory (-access => 'soap', -location => 'http://...'); Returns : a new Bio::Tools::Run::AnalysisFactory object representing a list of available analyses Args : There may be additional arguments which are specific to the access method (see methods 'new' or '_initialize' of the access-specific implementations (such as module Bio::Tools::Run::AnalysisFactory::soap for a SOAP-based access). The recognised and used arguments are: -access -location -httpproxy -timeout It builds, populates and returns a new "Bio::Tools::Run::AnalysisFactory" object. This is how it is seen from the outside. But in fact, it builds, populates and returns a more specific lower-level object, for example "Bio::Tools::Run::AnalysisFactory::soap" object - which one it is it depends on the "-access" parameter. It indicates what lower-level module to load. Default is 'soap'. Other (but future) possibilities are: -access => 'novella' -access => 'local' A location of the service. The contents is access-specific (see details in the lower-level implementation modules). Default is "http://www.ebi.ac.uk/soaplab/services" (there are services running at European Bioinformatics Institute on top of most of EMBOSS analyses, and on some others). In addition to the location parameter, you may need to specify also a location/URL of an HTTP proxy server (if your site requires one). The expected format is "http://server:port". There is no default value. It is also an access-specific parameter which may not be used by all access methods. For long(er) running jobs the HTTP connection may be time-outed. In order to avoid it (or, vice-versa, to call timeout sooner) you may specify "timeout" with the number of seconds the connection will be kept alive. Zero means to keep it alive forever. The default value is two minutes.

_load_access_module
Usage : $class->_load_access_module ($access) Returns : 1 on success, undef on failure Args : 'access' should contain the last part of the name of a module who does the real implementation It does (in the run-time) a similar thing as require Bio::Tools::Run::AnalysisFactory::$access It prints an error on STDERR if it fails to find and load the module (for example, because of the compilation errors in the module).

_guess_access
Usage : $class->_guess_access ($rh_params) Returns : string with a guessed access protocol (e.g. 'soap'), or undef if the guessing failed Args : 'rh_params' is a hash reference containing parameters given to the 'new' method. It makes an expert guess what kind of access/transport protocol should be used to access the underlying analysis. The guess is based on the parameters in rh_params. Rememeber that this method is called only if there was no -access parameter which could tell directly what access method to use.

VERSION and Revision
Usage : print $Bio::Tools::Run::AnalysisFactory::VERSION; print $Bio::Tools::Run::AnalysisFactory::Revision;