Christopher Fields > BioPerl-1.6.924 > Bio::TreeIO::NewickParser



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Module Version: 1.006924   Source  


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


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

  # in the next_tree method...


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.


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

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