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.
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)¶