Bio::Tools::Run::AnalysisFactory(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::AnalysisFactory(3pm) |
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 $list = Bio::Tools::Run::AnalysisFactory->new(); ->available_analyses; use Data::Dumper; print Dumper ($list); # ditto, but from a different location use Bio::Tools::Run::AnalysisFactory; my $list = Bio::Tools::Run::AnalysisFactory->new(-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 = Bio::Tools::Run::AnalysisFactory->new(-location => 'http://somewhere/something', -access => 'novella') ->available_analyses; # list available categories of analyses use Bio::Tools::Run::AnalysisFactory; my $categories = Bio::Tools::Run::AnalysisFactory->new(); ->available_categories; use Data::Dumper; print Dumper ($categories); # show all analyses group by categories use Bio::Tools::Run::AnalysisFactory; my $factory = Bio::Tools::Run::AnalysisFactory->new(); 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 = Bio::Tools::Run::AnalysisFactory->new(); ->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".
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/wiki/Mailing_lists - About the mailing lists
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.
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://redmine.open-bio.org/projects/bioperl/
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.
Here is the rest of the object methods. Internal methods are preceded with an underscore _.
Usage : my $factory = Bio::Tools::Run::AnalysisFactory->new(-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.
-access => 'novella' -access => 'local'
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).
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).
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. Remember that this method is called only if there was no -access parameter which could tell directly what access method to use.
Usage : print $Bio::Tools::Run::AnalysisFactory::VERSION; print $Bio::Tools::Run::AnalysisFactory::Revision;
2020-10-28 | perl v5.30.3 |