[Bioperl-l] Deobfuscator interface now available

[Hilmar Lapp]

I wasn't using the search. It's in the scrollable table for browsing.  
-hilmar

On May 15, 2006, at 3:07 PM, Chris Fields wrote:

> I'll have to give it a try on Mac OS X (we have an ancient G4 in  
> the lab
> which I can try it on).  I'll let you know what I find.
>
> This is what I get when I do a search for 'Bio::Ont*' using Firefox  
> on WinXP
> and this Deobfuscator link (http://bioperl.org/cgi-bin/ 
> deob_interface.cgi?);
> all the classes have links that work (I added newline and tab to  
> make it a
> bit more readable) :
>
> Bio::OntologyIO	
> 	Parser factory for Ontology formats
> Bio::OntologyIO::Handlers::BaseSAXHandler	
> 	no short description available
> Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler
> 	no short description available
> Bio::Ontology::OntologyI
> 	Interface for an ontology implementation
> Bio::Ontology::TermFactory
> 	Instantiates a new Bio::Ontology::TermI (or derived class) through a
> factory
> Bio::Ontology::OntologyStore
> 	A repository of ontologies
> Bio::Ontology::RelationshipFactory
> 	Instantiates a new Bio::Ontology::RelationshipI (or derived class)
> through a factory
> Bio::Ontology::Ontology
> 	standard implementation of an Ontology
>
> So the names seem fine here.
>
> When I click on a class (Bio::Ontology::Ontology) I get in the results
> section:
>
> Method                  Class                                      
> Returns
> Usage
> add_relationship        Bio::Ontology::Ontology	                  Its
> argument.     add_relationship(RelationshipI relationship):  
> RelationshipI
> add_relationship_type   Bio::Ontology::OntologyEngineI            not
> documented    not documented
> add_term                Bio::Ontology::Ontology                   its
> argument.     add_term(TermI term): TermI
>
> ....and so on
>
> Where each method is clickable and opens a new page containing a  
> table:
>
> Bio::Ontology::Ontology::add_relationship
> Usage	add_relationship(RelationshipI relationship): RelationshipI
> Function	Adds a relationship object to the ontology engine.
> Returns	Its argument.
> Args	A RelationshipI object.
>
>
> Each class is also linked to the bioperl-live PDOC.  Clicking on class
> Bio::Ontology::Ontology in the results table gets me this page (no new
> page):
>
> http://doc.bioperl.org/bioperl-live/Bio/Ontology/Ontology.html
>
>
> Chris
>
>> -----Original Message-----
>> From: Hilmar Lapp [mailto:hlapp at gmx.net]
>> Sent: Monday, May 15, 2006 1:09 PM
>> To: Chris Fields
>> Cc: 'Mauricio Herrera Cuadra'; 'bioperl-l'
>> Subject: Re: [Bioperl-l] Deobfuscator interface now available
>>
>> Safari or Firefox on MacOSX don't do this. Note that the appearance
>> in the browsable list is already different (the prefix is missing),
>> and the JavaScript link also lacks the prefix in the module name in
>> contrast to others, e.g., Bio::Ontology::Ontology (which is one of
>> the few Bio::Ontology exceptions that do work and do display  
>> correctly).
>>
>> I suppose there is something peculiar about the code formatting of
>> those modules? Some of the modules under Bio::OntologyIO are also
>> affected BTW.
>>
>> What happens is after you click on the link the page apppears to
>> reload (i.e., gets submitted) but the second table that is supposed
>> open underneath the first doesn't appear. However, the sort-by drop
>> down selector does appear.
>>
>> 	-hilmar
>>
>> On May 15, 2006, at 1:22 PM, Chris Fields wrote:
>>
>>> That's strange.  Clicking on the list gives me the results for that
>>> module.
>>> When I click on the hyperlinks in the results section they open
>>> fine; the
>>> method column links opens a new page containing usage-function-
>>> returns-args
>>> and the class column links opens pdoc (same page) for bioperl-
>>> live.  I'm
>>> using Firefox 1.5 on WinXP.
>>>
>>> Chris
>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>> bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
>>>> Sent: Monday, May 15, 2006 12:01 PM
>>>> To: Mauricio Herrera Cuadra
>>>> Cc: bioperl-l
>>>> Subject: Re: [Bioperl-l] Deobfuscator interface now available
>>>>
>>>> Hey, thanks to Laura & David for this interface.
>>>>
>>>> Any idea why most of the Bio::Ontology::* modules show up without
>>>> their leading Bio::Ontology? And clicking on those hyperlinks  
>>>> doesn't
>>>> go anywhere either ... Anything different with those modules that I
>>>> can fix?
>>>>
>>>> 	-hilmar
>>>>
>>>> On May 14, 2006, at 12:09 AM, Mauricio Herrera Cuadra wrote:
>>>>
>>>>> I'm glad to announce the availability of the Deobfuscator
>>>>> interface at
>>>>> the BioPerl website. You can use it at the following URL:
>>>>>
>>>>> http://bioperl.org/cgi-bin/deob_interface.cgi
>>>>>
>>>>> Many thanks to Laura Kavanaugh and David Messina for this great
>>>>> contribution to the BioPerl project!
>>>>>
>>>>> Mauricio.
>>>>>
>>>>> --
>>>>> MAURICIO HERRERA CUADRA
>>>>> arareko at campus.iztacala.unam.mx
>>>>> Laboratorio de Genética
>>>>> Unidad de Morfofisiología y Función
>>>>> Facultad de Estudios Superiores Iztacala, UNAM
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>> --
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> --
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>
>
>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================