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.
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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