excellent, thanks for taking this on! Andreas
2009/11/4 Tiago Antão <[email protected]> > 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 <[email protected]>: > > 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 <[email protected]>: > >>>> > >>>> 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: [email protected] > >> http://www.eaglegenomics.com/ > >> > >> > >> _______________________________________________ > >> Biojava-l mailing list - [email protected] > >> 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: [email protected] > > http://www.eaglegenomics.com/ > > > > > > > > -- > "The hottest places in hell are reserved for those who, in times of > moral crisis, maintain a neutrality." - Dante > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
