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.
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