#1 Node.pm method fails to read distance in scientific notation

[Mikhail Bezruchko]

Original submission information:

Date: 6/24/03.
Submitted by: Arlin.
Submitted to:
Status (open/fixed): open

Problem is in Bio::NEXUS::Node.pm, though the symptom was that
a NEXUS Trees Block produced by span-export.pl is mis-read by
plottree.pl. The problem is due to the presence of a branch length in
scientific notation. Here is the relevant part of the tree:

...(otu_3:0.00064,otu_4:4e-05):0.00234[1],...

4e-05 is not parsed correctly, but editing the file to read '0.00004'
fixed this problem. The ultimate source of the problem is in Node.pm.
Method parse calls method parse_distance to
retrieve the branch length after the colon, but parse_distance does
not recognize 'e' or 'E' as valid tokens. However, method tree_string
will write out distances in scientific notation if they are sufficiently
small. So the input and the output methods are not compatible with
each other.