[Bioperl-l] Deobfuscator interface now available

Mon May 15 19:12:34 UTC 2006

I just tried the same thing (links, search, etc) with Mac OS X v 10.3.9 and
Safari (no Firefox sorry) and it worked fine as well (all links, no missing
Bio::Ontology, etc).  Not sure what it could be...

Chris

> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Monday, May 15, 2006 2:08 PM
> To: 'Hilmar Lapp'
> Cc: 'Mauricio Herrera Cuadra'; 'bioperl-l'
> Subject: RE: [Bioperl-l] Deobfuscator interface now available
> 
> 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 :
> > ===========================================================
> >
> >
> >