Newick standard phylogenetic tree parser class.
This is alpha version. Incompatible changes may be made frequently.
delemiter of the entry
same as Bio::Tree::Edge
same as Bio::Tree::Node
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, line 71 def initialize(str, options = nil) str = str.sub(/\;(.*)/, ';') @original_string = str @entry_overrun = $1 @options = (options or {}) 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, line 101 def reparse if defined?(@tree) remove_instance_variable(:@tree) end self.tree self end
Gets the tree. Returns a Bio::Tree object.
# File lib/bio/db/newick.rb, line 90 def tree if !defined?(@tree) @tree = __parse_newick(@original_string, @options) else @tree end end
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