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Bio::Tools::Analysis::UserlContributed:Perls::Analysis::SimpleAnalysisBase(3)

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

perl v5.32.1			  2Bio::Tools::Analysis::SimpleAnalysisBase(3)

NAME | SYNOPSIS | DESCRIPTION | SEE ALSO | FEEDBACK | AUTHORS | APPENDIX

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