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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:

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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).