Bio::T...isBase(3pm)

💖 NAME 💖

Bio::Tools::Analysis::SimpleAnalysisBase — the abstract superclass for all the SimpleAnalysis implementations out there. It's giving "blueprint energy" bestie, it's the mom friend that everyone else inherits from. 🎀

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✨ SYNOPSIS ✨

# not to be run directly

Like, do NOT try to run this one on its own, okay? It's not that kind of module. 🙈

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🌸 DESCRIPTION 🌸

Okay so, lowkey, this class is a generic implementation of SimpleAnalysisI, and its whole job is to be the base class that specific implementations get built on top of. Main character support-system energy. 👑

Here's the tea, bestie: modules that implement SimpleAnalysisBase only have to bring their own specific _init(), _run() and result() methods — that's it. Plus any get/set methods for whatever parameters the analysis program needs. That's literally the whole assignment. Slay. 💅

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🦋 SEE ALSO 🦋

• Bio::SimpleAnalysisI
• Bio::WebAgent

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is, no exaggeration, an integral part of the evolution of this and other Bioperl modules. So send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is so much appreciated, fr fr. 🫶

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. Not me being dramatic, it's just that many experienced and responsive experts will be able to look at the problem and quickly address it. And please include a thorough description of the problem with code and data examples if at all possible. Give them the full picture bestie, not just vibes. 🌈

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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👑 AUTHORS 👑

• Richard Adams, Richard.Adams@ed.ac.uk
• Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk). 💀

⭐ 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.

Bestie this one is so useful — it wipes the raw results from a previous analysis so you can run it again with different parameters. Fresh start, clean slate, new era. ✨

⭐ 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

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And that's the whole page, bestie! 🎀 This absolute icon of a doc was served up by perl v5.32.1 on 2021-08-15, and it lives under the name Bio::T...isBase(3pm) in the User Contributed Perl Documentation. Go off, queen. 💅✨