Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Contact Us
Online Help
Domain Status
Man Pages

Virtual Servers

Topology Map

Server Agreement
Year 2038

USA Flag



Man Pages
Bio::TreeIO::NewickParser(3) User Contributed Perl Documentation Bio::TreeIO::NewickParser(3)

Module which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification.
Taken largely from the Ensembl Compara file with the same name (Bio::EnsEMBL::Compara::Graph::NewickParser), this module adapts the parser to work with BioPerl's event handler-based parsing scheme.
This module is used by and, and is NOT called directly. Instead, both of those parsing modules extend this module in order to gain access to the main parsing method.

  # From
  use base qw(Bio::TreeIO Bio::TreeIO::NewickParser);
  # in the next_tree method...

This module correctly parses the Newick and NHX formats, sending calls to the BioPerl TreeEventHandler when appropriate in order to build and populate the node objects.

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.                  - General discussion  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

2019-01-01 perl v5.28.1

Search for    or go to Top of page |  Section 3 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.