[Bioperl-l] Deobfuscator interface now available
Chris Fields
cjfields at uiuc.edu
Mon May 15 20:56:29 UTC 2006
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 :
> ===========================================================
>
>
>
>
>
>
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