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BioPerl-1.7.8
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::Analysis::SimpleAnalysisBase

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