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.\"
.IX Title "Bio::TreeIO::NewickParser 3pm"
.TH Bio::TreeIO::NewickParser 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::TreeIO::NewickParser \- newick string parser
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  # From newick.pm
\&  use base qw(Bio::TreeIO Bio::TreeIO::NewickParser);
\&
\&  # in the next_tree method...
\&  $self\->parse_newick($_);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module correctly parses the Newick and \s-1NHX\s0 formats, sending calls
to the BioPerl TreeEventHandler when appropriate in order to build and
populate the node objects.
.PP
Module which implements a newick string parser as a finite state
machine which enables it to parse the full Newick specification.
.PP
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.
.PP
This module is used by nhx.pm and newick.pm, and is \s-1NOT\s0 called
directly. Instead, both of those parsing modules extend this module in
order to gain access to the main parsing method.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jessica Severin (EnsEMBL implementation), Greg Jordan (BioPerl adaptation)"
.IX Header "AUTHOR - Jessica Severin (EnsEMBL implementation), Greg Jordan (BioPerl adaptation)"