Bio::Tools::Analysis::SimpleAnalysisBase - abstact superclass for SimpleAnalysis implementations # no to be run directly This class is a generic implementation of SimpleAnalysisI and should be used as a base class for specific implementations. SimpleAnalysis implementing modules just need to provide a specific _run() result() and _init() methods, plus any get/set methods for parameter to the analysis program. Bio::SimpleAnalysisI, Bio::WebAgent

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki@ebi.ac.uk 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
Useage : $analysis->analysis_name(); Returns : The analysis name Arguments: none

analysis_spec
Useage : $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
Useage : $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
Useage : $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