[Bioperl-l] Deobfuscator interface now available
Chris Fields
cjfields at uiuc.edu
Mon May 15 22:03:48 UTC 2006
And Bio::OntologyIO works on it's own:
C:\Perl\Scripts>methods.pl Bio::OntologyIO
Bio::OntologyIO::DESTROY
Bio::OntologyIO::new
Bio::OntologyIO::next_ontology
Bio::OntologyIO::term_factory
Bio::OntologyIO::unescape
Bio::Root::IO::catfile
Bio::Root::IO::close
Bio::Root::IO::dup
Bio::Root::IO::exists_exe
Bio::Root::IO::file
Bio::Root::IO::flush
Bio::Root::IO::gensym
Bio::Root::IO::mode
Bio::Root::IO::noclose
Bio::Root::IO::qualify
Bio::Root::IO::qualify_to_ref
Bio::Root::IO::rmtree
Bio::Root::IO::tempdir
Bio::Root::IO::tempfile
Bio::Root::IO::ungensym
Bio::Root::Root::confess
Bio::Root::Root::debug
Bio::Root::Root::throw
Bio::Root::Root::verbose
Bio::Root::RootI::carp
Bio::Root::RootI::deprecated
Bio::Root::RootI::stack_trace
Bio::Root::RootI::stack_trace_dump
Bio::Root::RootI::throw_not_implemented
Bio::Root::RootI::warn
Bio::Root::RootI::warn_not_implemented
But when I try these:
C:\Perl\Scripts>methods.pl Bio::OntologyIO::goflat
C:\Perl\Scripts>methods.pl Bio::OntologyIO::dagflat
I get nada. It could be related to the way the methods are parsed using
Class::Inspector :
print join ("\n", sort
@{Class::Inspector->methods($class,'full','public')}), "\n";
I haven't tried it on all the weird Bio::Ontology-missing modules (don't
have time today). It's not common to all of those modules though:
C:\Perl\Scripts>methods.pl Bio::OntologyIO::InterProParser
Bio::OntologyIO::DESTROY
Bio::OntologyIO::InterProParser::next_ontology
Bio::OntologyIO::InterProParser::parse
Bio::OntologyIO::InterProParser::secondary_accessions_map
Bio::OntologyIO::new
Bio::OntologyIO::term_factory
Bio::OntologyIO::unescape
Bio::Root::IO::catfile
Bio::Root::IO::close
Bio::Root::IO::dup
Bio::Root::IO::exists_exe
Bio::Root::IO::file
Bio::Root::IO::flush
Bio::Root::IO::gensym
Bio::Root::IO::mode
Bio::Root::IO::noclose
Bio::Root::IO::qualify
Bio::Root::IO::qualify_to_ref
Bio::Root::IO::rmtree
Bio::Root::IO::tempdir
Bio::Root::IO::tempfile
Bio::Root::IO::ungensym
Bio::Root::Root::confess
Bio::Root::Root::debug
Bio::Root::Root::throw
Bio::Root::Root::verbose
Bio::Root::RootI::carp
Bio::Root::RootI::deprecated
Bio::Root::RootI::stack_trace
Bio::Root::RootI::stack_trace_dump
Bio::Root::RootI::throw_not_implemented
Bio::Root::RootI::warn
Bio::Root::RootI::warn_not_implemented
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 4:38 PM
> To: Chris Fields
> Cc: 'Mauricio Herrera Cuadra'; 'bioperl-l'
> Subject: Re: [Bioperl-l] Deobfuscator interface now available
>
> 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 :
> ===========================================================
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
More information about the Bioperl-l
mailing list