biopython/biopython — pull request #156 by bendmorris (2013-02-08 15:12:03+00:00)
Title: Newick parser

In light of three issues with the Newick parser:

https://redmine.open-bio.org/issues/3409
https://redmine.open-bio.org/issues/3386
https://redmine.open-bio.org/issues/3407

this is a rewrite of the parser from scratch. It supports quoted node labels and can handle support values either as they were previously handled or from square-bracketed comments, as requested by Arlin. Additionally, it's consistently quite fast:

![newick_parse_times](https://f.cloud.github.com/assets/544977/139616/fac0df38-71fe-11e2-91a8-a95ba7c6340b.png)

The unit tests still pass with these changes, and I'm now able to parse trees that previously raised exceptions.