oracular (3) Bio::Tools::Run::AnalysisFactory.3pm.gz

NAME

       Bio::Tools::Run::AnalysisFactory - A directory of analysis tools

SYNOPSIS

         # 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;

DESCRIPTION

       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".

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 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

   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 of the bugs and their resolution.
       Bug reports can be submitted via the web:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Martin Senger (martin.senger@gmail.com)

COPYRIGHT

       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.

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

SEE ALSO

       •   http://www.ebi.ac.uk/soaplab/Perl_Client.html

APPENDIX

       Here is the rest of the object methods.  Internal methods are preceded with an underscore _.

   new
        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
           It indicates what lower-level module to load.  Default is 'soap'.  Other (but future) possibilities
           are:

              -access => 'novella'
              -access => 'local'

       -location
           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).

       -httpproxy
           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.

       -timeout
           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. Remember 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;