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/
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--
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/
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