[Bioperl-l] Deobfuscator interface now available

[Chris Fields]

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 :
> ===========================================================
> 
> 
>