NAME

Bio::TreeIO::NewickParser - newick string parser

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.

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.

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)