Bio::Tools::Analysis::SimpleAnalysisBase(3pm)		User Contributed Perl Documentation	     Bio::Tools::Analysis::SimpleAnalysisBase(3pm)

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://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02			     Bio::Tools::Analysis::SimpleAnalysisBase(3pm)