[Bioperl-l] Deobfuscator interface now available

[David Messina]

Responding to:
>>> Amir Karger
>> Sendu Bala
>  Chris Fields


> The Deobfuscator currently indexes bioperl-1.4, so it's not completely
> up-to-date.  I believe Mauricio and Dave may be working on updating  
> to the
> newer versions and maybe bioperl-live, as well as getting the other  
> bioperl
> packages up and running.

That's correct -- Mauricio is currently working on a version that  
will allow you to search 1.4, 1.5.1, or bioperl-live. The  
Deobfuscator indexes will be updated (daily?) to keep them in sync  
with the CVS repository.


>>> A couple of minor interface thoughts.
>>>
>>> 1)There's quite a lot of methods for many of the classes. As such, I
>>> think I'll often want to browse through what's available in a  
>>> class. But
>>> 60% or so of the screen real estate is used for "Enter a search
>>> string... OR select a class from the list". IMO, it would be  
>>> better to
>>> have two pages, a search page and a result page.   It only takes  
>>> a click
>>> on Back (or a "new search" button) to get to a new search, and  
>>> now you
>>> can use your whole screen for reading your results.
>>
>> As the compromise it must be, I like the way it behaves. I don't like
>> lots of windows. I especially don't like pop up windows. Right now  
>> when
>> I'm using the bioperl docs I tend to have a whole bunch of tabs  
>> open to
>> different class pages at once, so being able to see an overview  
>> all on
>> one page in Deobfuscator is very nice.

I think the current behavior makes sense as the default, but I like  
the idea of being able to view the search results in a separate  
window for easier browsing. Thanks for the suggestion; I'll add it to  
the list.


>> Further to that, I'd love it if clicking on a method name caused an
>> in-place css(&|javascript) reveal (similar to how a well implemented
>> drop down menu works in a website) rather than a new window opened.
>> Alternatively, just have more columns in the results table, ie.  
>> usage,
>> function, returns, args columns. I feel that opening a window for  
>> each
>> method you want to understand is far too slow.
>
> Agreed.

Yeah, the way it currently works is admittedly lame, and was done as  
a placeholder until we figured out a better way to do it. An in-place  
reveal sounds like a good solution.


>>> 2) Please sort the "select a class from the list" alphabetically. I
>>> guess I can enter a search term to get the right classes, but it  
>>> would
>>> be nice to be able to browse.

Agreed. I think we were doing this in an earlier test version, but I  
must have left it out of the release I handed off to Mauricio.


>>> 3) Minimalist is nice, but documentation is even nicer. It wasn't  
>>> clear
>>> to me that the search searches within class names rather than  
>>> function
>>> names. What I really want to know sometimes is which module has,  
>>> say,
>>> the revcom method in it.
>>
>> This would be a great feature to add.

That's a great idea.


>>> 4) When I search for something that's not found, I get a screen that
>>> looks pretty familiar, with the extra text "No match to string  
>>> found"
>>> down at the bottom. It took me a while to even notice it.  
>>> (Studies show
>>> that most users don't read most of the text on a page.) Bold  
>>> might be
>>> nice here. Or put the error at the top of the screen. Or both.

Added to the list.


>>> 5) I'll save my stupidest comment for last - please make the page  
>>> title
>>> "Bioperl Deobfuscator", so that when I bookmark it I'll know what  
>>> the
>>> bookmark stands for.

Added to the list. Not stupid, by the way -- much to my surprise,  
there are at least 2 or 3 other (obviously inferior :) )  
deobfuscators floating around out there.


>> Another minor interface thought:
>> 6) Have a little more cell padding in all the tables. Things are  
>> just a
>> little too cramped and things start to look messy/ run into each  
>> other.

Added to the list.


Thanks to all of you for taking the time to give such detailed  
feedback -- it's really helpful.

There is a wiki page on the BioPerl site for this project (http:// 
www.bioperl.org/wiki/Deobfuscator), so I'll be putting your comments  
there for tracking and further discussion. Please feel free to add to  
it.


Dave


-- 
Dave Messina
WashU Genome Sequencing Center
dmessina at wustl.edu
314-286-1825