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Bio::TreeIO::NewickParUser3Contributed Perl DocumeBio::TreeIO::NewickParser(3)

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)
perl v5.24.1			  2017-07-08	  Bio::TreeIO::NewickParser(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jessica Severin (EnsEMBL implementation), Greg Jordan (BioPerl

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