GSP
Quick Navigator

Search Site

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

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::TREEIO::NEWICKPARSER (3)

.ds Aq ’

NAME

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 nhx.pm and newick.pm, and is NOT called directly. Instead, both of those parsing modules extend this module in order to gain access to the main parsing method.

CONTENTS

SYNOPSIS



  # From newick.pm
  use base qw(Bio::TreeIO Bio::TreeIO::NewickParser);

  # in the next_tree method...
  $self->parse_newick($_);



DESCRIPTION

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.

FEEDBACK

    Mailing Lists

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.



  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists



    Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

    Reporting Bugs

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:



  https://github.com/bioperl/bioperl-live/issues



AUTHOR - Jessica Severin (EnsEMBL implementation), Greg Jordan (BioPerl adaptation)

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


perl v5.20.3 BIO::TREEIO::NEWICKPARSER (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.