Bio::Tools::Analysis::SimpleAnalysisBase - abstract superclass for SimpleAnalysis implementations
# 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.
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
Richard Adams, Richard.Adams@ed.ac.uk, 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