Bio::SimpleAnalysisI - A simple interface to any (local or remote) analysis tool This is an interface module - you do not instantiate it. Use other modules instead (those that implement this interface). 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).

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 email or the web: bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/ Martin Senger (senger@ebi.ac.uk) 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://industry.ebi.ac.uk/soaplab/Perl_Client.html 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: 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. 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).