[Bioperl-l] BioPerl Deobfuscator updated
dmessina at wustl.edu
Thu Oct 5 14:07:56 EDT 2006
I'm pleased to announce a revised version of the BioPerl Deobfuscator
is now available. Many thanks to Mauricio Cuadra for updating
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
having localhost hardcoded. Thanks to Jason Stajich for
FIX: Bio::Ontology modules are no longer missing their prefix
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
although for consistency this is not recommended.
FIX: Bug #2114: "Obfuscator doesn't show "Bio:Matrix:Generic"
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-
that subclasses appear just after their parent class.
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
NEW: 'No match' search string now more prominent. Yep, kudos
Karger again -- another great idea!
NEW: Search box caption now explicitly states that only
can be searched. Big ups to Amir Karger for this
The ability to search method names is planned for a
NEW: added -x option to deob_index.pl. This allows the use of an
'excluded modules' file. This feature was added to
issue with four modules which rely on external modules
Class::Inspector, used by the Deobfuscator needs to load a
module to traverse its inheritance tree, and modules
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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