[Bioperl-l] BioPerl Deobfuscator updated

Phillip San Miguel pmiguel at purdue.edu
Thu Oct 5 20:42:00 UTC 2006

David Messina wrote:
> I'm pleased to announce a revised version of the BioPerl Deobfuscator  
> is now available. Many thanks to Mauricio Cuadra for updating  
> bioperl.org's installation:
> http://bioperl.org/cgi-bin/deob_interface.cgi
> I've incorporated many of the suggestions you all sent in after the  
> first release, and many of the modules that had non-standard  
> documentation have been updated in the meantime, too, so hopefully  
> you'll find it much improved. There are still some issues with a few  
> modules; please report any problems you see. Also, it's now indexing  
> bioperl-live instead of 1.4, which should make it a little more  
> useful, too. A complete list of changes is below.
> I welcome your bug reports and suggestions for improvements, via  
> email, this list, Bugzilla, or the Wiki page.
> Thanks,
> Dave
Here are some comments:
Would be good to have the column headings for the methods table in the 
fixed part of the page, rather than the scroll box. That way you could 
always see the column headings from anywhere in the list.

Second, I've noticed that there are a fair number of methods that have 
"not documented" for "Returns" and "Usage". But in every case I've 
checked both of these were documented. For example, consider methods for 
Bio::Seq::SeqWithQuality. The method "accession_number" is listed as 
"not documented". But if you click on Bio::Seq:SeqWithQuality link to 
the documentation, usage is defined as: "$unique_biological_key = 
$obj->accession_number;" and returns is defined as "A string".

Finally, it would be good to have the version of bioperl being 
deobfuscated on the deob_interface.cgi page. Just as a quick 
sanity-checking measure. After poking around a bit I found that 
bioperl-live is being indexed in the wiki. But, I can tell, it is just 
the sort of thing I'm going to forget and look for every time come  back 
to the page after a few months...

Overall very nice, though. Just what is needed when I'm trying to 
remember "which was the method that returns subseq string and which one 
returns an object?"

Phillip SanMiguel
Purdue University

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