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Bio::SimpleAnalysisI(3User Contributed Perl DocumentatiBio::SimpleAnalysisI(3)

NAME
       Bio::SimpleAnalysisI - A simple interface to any (local or remote)
       analysis tool

SYNOPSIS
       This is an interface module - you do not instantiate it.	 Use other
       modules instead (those that implement this interface).

DESCRIPTION
       This interface contains public methods for accessing and controlling
       local and remote analysis tools. It is meant to be used on the client
       side. The interface consists only of a necessary set of methods for
       synchronous invocation of analysis tools. For more complex set,
       including an asynchronous access, see interface "Bio::AnalysisI" (which
       inherits from this one, by the way).

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/Tools/webservices/soaplab/guide

APPENDIX
       This is actually the main documentation...

       If you try to call any of these methods directly on this
       "Bio::SimpleAnalysisI" object you will get a not implemented error
       message.

   analysis_name
	Usage	: $tool->analysis_name;
	Returns : a name of this analysis
	Args	: none

   analysis_spec
	Usage	: $tool->analysis_spec;
	Returns : a hash reference describing this analysis
	Args	: none

       The returned hash reference uses the following keys (not all of them
       always present, perhaps others present as well): "name", "type",
       "version", "supplier", "installation", "description".

   input_spec
	Usage	: $tool->input_spec;
	Returns : an array reference with hashes as elements
	Args	: none

       The analysis input data are named, and can be also associated with a
       default value, with allowed values and with few other attributes. The
       names are important for feeding the analysis with the input data (the
       inputs are given to methods "run" and "wait_for" as name/value pairs).

   result_spec
	Usage	: $tool->result_spec;
	Returns : a hash reference with result names as keys
		  and result types as values
	Args	: none

       An analysis can produce several results, or the same result in several
       different formats. All such results are named and can be retrieved
       using their names by metod "result".

       Here is an example of the result specification:

	 $result_spec = {
		 'outseq' => 'String',
		 'report' => 'String',
		 'detailed_status' => 'String'
	       };

   run
	Usage	: $tool->run ( ['sequence=@my.seq', 'osformat=embl'] )
	Returns : $self
	Args	: data and parameters for this execution
		  (in various formats)

       Create a job, start it, and wait for its completion. The method is
       identical to the method "wait_for". Why there are two methods doing the
       same? Because it is expected that the sub-classes may implement them
       differently (an example is an interface "Bio::AnalysisI" which uses
       method "run" for an asynchronous execution and method "wait_for" for a
       synchronous one.

       Usually, after this call, you ask for results of the finished job:

	   $analysis->run (...)->result;

       The input data and prameters for this execution can be specified in
       various ways:

       array reference
	   The array has scalar elements of the form

	      name = [[@]value]

	   where "name" is the name of an input data or input parameter (see
	   method "input_spec" for finding what names are recognized by this
	   analysis) and "value" is a value for this data/parameter. If
	   "value" is missing a 1 is assumed (which is convenient for the
	   boolean options). If "value" starts with "@" it is treated as a
	   local filename, and its contents is used as the data/parameter
	   value.

       hash reference
	   The same as with the array reference but now there is no need to
	   use an equal sign. The hash keys are input names and hash values
	   their data. The values can again start with a "@" sign indicating a
	   local filename.

   wait_for
	Usage	: $tool->wait_for ( { 'sequence' => '@my,file' } )
	Returns : $self
	Args	: the same as for method 'run'

       Create a job, start it and wait for its completion. The method is
       identical to the method "run". See details in the "run" method.

   status
	Usage	: $tool->status
	Returns : string describing a status of the execution
	Args	: none

       It returns one of the following strings (and perhaps more if a server
       implementation extended possible job states):

	  CREATED	       (not run yet)
	  COMPLETED	       (run and finished normally)
	  TERMINATED_BY_ERROR  (run and finished with an error or a signal)

   result
	Usage	: $job->result (...)
	Returns : a result created by running an analysis
	Args	: none (but an implementation may choose
		  to add arguments for instructions how to process
		  the raw result)

       The method returns a scalar representing a result of an executed job.
       If the job was terminated by an error the result may contain an error
       message instead of the real data (or both, depending on the
       implementation).

perl v5.14.1			  2011-07-22	       Bio::SimpleAnalysisI(3)
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