[BioRuby] newick gsub(' ','_')

[Ben Woodcroft]

Ok, if I come across something I'll tell you. Thanks, ben

2009/7/21 Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp>

> Hi,
>
> On Tue, 21 Jul 2009 11:19:21 +1000
> Ben Woodcroft <donttrustben at gmail.com> wrote:
>
> > OK, thanks - that makes sense. The particular program I'm using, figtree,
> > understands underscores as spaces, and so I never really had any problem
> in
> > the first place.
> >
> > But to be academic I don't actually agree that the specification says
> blanks
> > should be converted underscores in otherwise unquoted strings - I think
> > quoting them is equally valid (and possibly supported by more programs),
> but
> > maybe that's just me. Happy to accept the community judgement on that
> one.
> >
> > Would it make sense to allow quoting to be forced by the user? I don't
> see
> > anything in the specification that is against that, so long as everything
> > inside is properly escaped.
>
> Why unquoted labels are preferred is that naive programs
> that cannot understand quotes might have problems with
> quotes and speces. Providing unquoted labels as many as
> possible may reduce such problems, though it isn't perfect.
>
> Programs that can understand quoted labels should also be
> aware of the underscore rule in unquoted labels, and
> theoretically no problem with unquoted labels.  However,
> if you know any strange programs that can parse quoted labels
> but can not understand underscores in unquoted labels,
> please tell us.
>
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
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> BioRuby at lists.open-bio.org
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>



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