[Bioperl-l] Deobfuscator interface now available
Hilmar Lapp
hlapp at gmx.net
Mon May 15 21:37:56 UTC 2006
It does have the following line though (and a 'use' statement for
OntologyIO);
@ISA = qw( Bio::OntologyIO );
So what is it doing 'wrong' (there aren't any tests or so in which
anything erroneous would show)?
-hilmar
On May 15, 2006, at 4:56 PM, Chris Fields wrote:
> Okay, I see what you mean. Using the search term "Bio::Ont*" also
> explains
> why I didn't see it ;P. Yeah, the bug shows up here too (WinXP and
> Mac OS
> X), and those links are broken like you said. Could be something
> to do with
> indexing.
>
> Using the methods script in the FAQ
> (http://www.bioperl.org/wiki/FAQ#Why_can.
> 27t_I_easily_get_a_list_of_all_the_
> methods_a_object_can_call.3F) I get this:
>
> C:\Perl\Scripts>methods.pl Bio::OntologyIO::simplehierarchy
> Bio::OntologyIO::simplehierarchy::Dumper
> Bio::OntologyIO::simplehierarchy::basename
> Bio::OntologyIO::simplehierarchy::dirname
> Bio::OntologyIO::simplehierarchy::fileparse
> Bio::OntologyIO::simplehierarchy::fileparse_set_fstype
>
> 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 2:24 PM
>> To: Chris Fields
>> Cc: 'Mauricio Herrera Cuadra'; 'bioperl-l'
>> Subject: Re: [Bioperl-l] Deobfuscator interface now available
>>
>> 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 :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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 :
===========================================================
More information about the Bioperl-l
mailing list