[Biojava-l] Rooted trees in nexus files

[Andreas Prlic]

excellent, thanks for taking this on!
Andreas


2009/11/4 Tiago Antão <tiagoantao at gmail.com>

> Unless anyone with experience in biojava development wants to take on
> this, I would volunteer to do this. I ended up using the PhyloXML
> forester-atv parser (and moving to phyloxml instead of nexus), but as
> I reported this, I might as well sort it out...
>
> 2009/11/4 Richard Holland <holland at eaglegenomics.com>:
> > ah... except a problem! The parser does not know all names in the string
> in
> > advance, so if it auto-assigns one that is then used later in the string,
> we
> > have the same problem with name clashes as before.
> >
> > The names the parser assigns cannot totally avoid all clashes unless it
> has
> > already parsed the string to find out what names were used in the string
> > itself already. So some kind of pre-parse would be necessary.
> >
> > On 4 Nov 2009, at 12:46, Richard Holland wrote:
> >
> >> Sounds good.
> >>
> >> On 4 Nov 2009, at 12:40, Tiago Antão wrote:
> >>
> >>> 2009/11/3 Richard Holland <holland at eaglegenomics.com>:
> >>>>
> >>>> The prefix for the parser currently is hardcoded as p. Two new methods
> -
> >>>> set
> >>>> and getDefaultPrefix which accept a string should be provided (it
> should
> >>>> check that the string is valid, i.e. all alphanumeric and with no
> spaces
> >>>> or
> >>>> other Newick-sensitive characters). The parser should be changed to
> use
> >>>> the
> >>>> output from getDefaultPrefix() instead of the hardcoded p. The default
> >>>> behaviour should be such that it behaves the same as at present unless
> >>>> the
> >>>> user explicitly says otherwise by calling the setDefaultPrefix()
> method.
> >>>
> >>> This default behavior would still raise an exception with nodes called
> >>> p* . I would suggest a minor change: If there is a clash, the parser
> >>> would try the next p* (or whatever defaultPrefix) ...
> >>>
> >>> Example to make it clear: if there is a leaf called p2, internal nodes
> >>> generated would be p1, p3, p4, ....
> >>>
> >>> --
> >>> "The hottest places in hell are reserved for those who, in times of
> >>> moral crisis, maintain a neutrality." - Dante
> >>
> >> --
> >> Richard Holland, BSc MBCS
> >> Operations and Delivery Director, Eagle Genomics Ltd
> >> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> >> http://www.eaglegenomics.com/
> >>
> >>
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > --
> > Richard Holland, BSc MBCS
> > Operations and Delivery Director, Eagle Genomics Ltd
> > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> > http://www.eaglegenomics.com/
> >
> >
>
>
>
> --
> "The hottest places in hell are reserved for those who, in times of
> moral crisis, maintain a neutrality." - Dante
>
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