Hi,
now I am confused :)
I did my fixes on the SVN version from this repository:
svn://code.open-bio.org/biojava/biojava-live/trunk
The revision I was working on is 7269. This is the current HEAD
including the NEW parser, isn't it ? Tiago, you are listed as author
in the javadoc and the last commit comment on the TreesBlock states
that it contains your changes...so I am pretty sure I did my changes
on the right version ?
cheers,
-thasso
On Dec 15, 2009, at 16:02 , Tiago Antão wrote:
Hi Thasso,
I think you are using an old version (even the current stable is "old"
AFAIK)... I have changed TreeBlock quite a lot, as it was somewhat
problematic.
2009/12/15 Thasso Griebel <[email protected]>:
Hi,
I wanted to take a look at the parser anyways, so I took the
opportunity.
As far as i see this, the newline is just a minor part of the
problem. I
think the bigger issue here is parsing inner node labels. I
attached a patch
that fixes the problem, at least for inner nodes with label and
inner nodes
with label and weights. Wikipedia states that Newick allows leaves
without
any labels, but in case of phylogenetic trees I think one can
safely ignore
this, though the parser should maybe throw an exception.
If you are interested I also updated the unit test.
hope it helps, cheers,
-thasso
On Dec 15, 2009, at 12:43 , Tiago Antão wrote:
2009/12/15 Richard Holland <[email protected]>:
Hi there.
I believe the code used to be able to parse this kind of tree,
but TIago
recently rewrote it so I'm no longer certain.
Tiago - your new code doesn't seem to be coping with the
insertion of a
newline at random points in the Tree string. I think you might
need to
modify your tokenize() method to handle this better? Could you
also add a
unit test using this particular tree.
Yep, will take care of this over the weekend. Maybe before, but no
promises.
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