Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Tools::Analysis::SimpleAnalysisBase - abstract superclass for SimpleAnalysis


       # not to be run directly


       This class is a generic implementation of SimpleAnalysisI and should be used as a base
       class for specific implementations.

       Modules implementing SimpleAnalysisBase only need to provide specific _init(), _run() and
       result() methods, plus any get/set methods for parameters to the analysis program.


       Bio::SimpleAnalysisI, Bio::WebAgent


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       Richard Adams,, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Usage   : $job->new(...)
        Returns : a new analysis object,
        Args    : none (but an implementation may choose
                  to add arguments representing parameters for the analysis
                  program. Each key value of must have a method implemented
                  for it in a subclass. A seq () method is provided here as
                  this will probably be needed by all sequence analysis programs

        Usage   : $job->seq()
        Returns : a Bio::PrimarySeqI implementing sequence object, or void
        Args    : None, or a Bio::PrimarySeqI implementing object

           Usage     : $analysis->analysis_name();
           Returns   : The analysis name
           Arguments : none

           Usage    :  $analysis->analysis_spec();
           Returns  :  a hash reference to  a hash of analysis parameters. See
                       Bio::SimpleAnalysisI for a list of recommended key values.
           Arguments:  none

           Usage     : $analysis->clear();
           Returns   : true value on success
           Arguments : none
           Purpose   : to remove raw results from a previous analysis so that
                       an analysis can be repeated with different parameters.

           Usage     : $analysis->input_spec();
           Returns   : a  reference to  an array of  hashes of analysis parameters. See
                       Bio::SimpleAnalysisI for a list of recommended key values.
           Arguments : none

           Usage     : $analysis->result_spec();
           Returns   : a  reference to  a   hashes of resultformats. See
                       Bio::SimpleAnalysisI for a list of recommended key values.
                       The key values can be used as parameters to the result()
                       method, the values provide descriptions.
           Arguments : none

perl v5.26.1                                2017-12-Bio::Tools::Analysis::SimpleAnalysisBase(3pm)