Bio::Tools::Run::AnalysisFactory man page on Pidora

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Bio::Tools::Run::AnalyUseraContributed PerlBio::Tools::Run::AnalysisFactory(3)

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://bugzilla.open-bio.org/

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
       ยท   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. 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;

perl v5.14.1			  2011-07-2Bio::Tools::Run::AnalysisFactory(3)
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