[Bioperl-l] BioPerl Deobfuscator updated

David Messina dmessina at wustl.edu
Thu Oct 5 18:07:56 UTC 2006

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:


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.



0.0.3  Mon Oct  2 20:01:45 CDT 2006
        FIX: change default $deob_detail_path to be a relative URL  
instead of
             having localhost hardcoded. Thanks to Jason Stajich for  
             this out.
        FIX: Bio::Ontology modules are no longer missing their prefix  
in the
             class list, and their methods are now shown in the lower  
             as expected. Thanks to Hilmar Lapp for reporting this bug.
        FIX: can now handle (and ignore) VERSION POD section.
        FIX: missing SYNOPSIS section now handled properly. In fact, the
             SYNOPSIS and DESCRIPTION sections can be in reverse  
order now,
             although for consistency this is not recommended.
        FIX: Bug #2114: "Obfuscator doesn't show "Bio:Matrix:Generic"  
has been
             fixed. This bug turned out to afflict multiple modules,  
             weren't getting parsed correctly by deob_index.pl.
        NEW: Table cells have been padded out to get rid of that  
             look. Thanks to Sendu Bala for this great suggestion.
        NEW: If the 'Returns' subsection of a method's documentation  
             a POD L<> link, the Deobfuscator assumes this to be a  
             name, and wraps it in an href for display. This feature is
             not robust, but seems to work well enough for now.
        NEW: the list of classes is now sorted alphabetically depth- 
first, so
             that subclasses appear just after their parent class.  
Thanks to
             Amir Karger for noticing the strange sorting behavior.
        NEW: HTML page title now 'BioPerl Deobfuscator' to  
distinguish it from
             other Deobfuscators out there. Thanks to Amir Karger for
             suggesting this.
        NEW: 'No match' search string now more prominent. Yep, kudos  
to Amir
             Karger again -- another great idea!
        NEW: Search box caption now explicitly states that only  
package names
             can be searched. Big ups to Amir Karger for this  
             The ability to search method names is planned for a  
future version.
        NEW: added -x option to deob_index.pl. This allows the use of an
             'excluded modules' file. This feature was added to  
resolve an
             issue with four modules which rely on external modules  
to compile.
             Class::Inspector, used by the Deobfuscator needs to load a
             module to traverse its inheritance tree, and modules  
must compile
             before they can be loaded.
     CHANGE: using short name now when traversing with File::Find to  
             identify excluded modules (deob_index.pl).

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