Bio::Tools::Analysis::SimpleAnalysisBase(3pm) User Contributed Perl Documentation Bio::Tools::Analysis::SimpleAnalysisBase(3pm)
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://redmine.open-bio.org/projects/bioperl/
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 v5.14.2 2012-03-02 Bio::Tools::Analysis::SimpleAnalysisBase(3pm)