oracular (3) Bio::Tools::Analysis::SimpleAnalysisBase.3pm.gz

NAME

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

SYNOPSIS

       # not to be run directly

DESCRIPTION

       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.

SEE ALSO

       Bio::SimpleAnalysisI, Bio::WebAgent

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 one of the Bioperl mailing lists.  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 the bugs and their resolution.  Bug
       reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHORS

       Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

APPENDIX

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

   new
        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

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

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

   analysis_spec
           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

   clear
           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.

   input_spec
           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

   result_spec
           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