class Bio::Newick

   # File lib/bio/db/newick.rb
72 def initialize(str, options = nil)
73   str = str.sub(/\;(.*)/m, ';')
74   @original_string = str
75   @entry_overrun = $1
76   @options = (options or {})
77 end

Creates a new Newick object. options for parsing can be set.

Available options:

:bootstrap_style

:traditional for traditional bootstrap style, :molphy for molphy style, :disabled to ignore bootstrap strings. For details of default actions, please read the notes below.

:parser

:naive for using naive parser, compatible with BioRuby 1.1.0, which ignores quoted strings and do not convert underscores to spaces.

Notes for bootstrap style: Molphy-style bootstrap values may always be parsed, even if the options[:bootstrap_style] is set to :traditional or :disabled.

Note for default or traditional bootstrap style: By default, if all of the internal node’s names are numeric and there are no NHX and no molphy-style boostrap values, the names of internal nodes are regarded as bootstrap values. options[:bootstrap_style] = :disabled or :molphy to disable the feature (or at least one NHX tag exists).

    # File lib/bio/db/newick.rb
102 def reparse
103   if defined?(@tree)
104     remove_instance_variable(:@tree)
105   end
106   self.tree
107   self
108 end

Re-parses the tree from the original string. Returns self. This method is useful after changing parser options.

   # File lib/bio/db/newick.rb
91 def tree
92   if !defined?(@tree)
93     @tree = __parse_newick(@original_string, @options)
94   else
95     @tree
96   end
97 end

Gets the tree. Returns a Bio::Tree object.