Class: Bio::Newick

Inherits:
Object show all
Defined in:
lib/bio/db/newick.rb

Overview

Newick standard phylogenetic tree parser class.

This is alpha version. Incompatible changes may be made frequently.

Defined Under Namespace

Classes: ParseError

Constant Summary collapse

DELIMITER =

delemiter of the entry

RS = ";"
Edge =

same as Bio::Tree::Edge

Bio::Tree::Edge
Node =

same as Bio::Tree::Node

Bio::Tree::Node

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(str, options = nil) ⇒ Newick

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).



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# File 'lib/bio/db/newick.rb', line 71

def initialize(str, options = nil)
  str = str.sub(/\;(.*)/m, ';')
  @original_string = str
  @entry_overrun = $1
  @options = (options or {})
end

Instance Attribute Details

#entry_overrun ⇒ Object (readonly)

string after this entry



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# File 'lib/bio/db/newick.rb', line 86

def entry_overrun
  @entry_overrun
end

#options ⇒ Object (readonly)

parser options (in some cases, options can be automatically set by the parser)



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# File 'lib/bio/db/newick.rb', line 80

def options
  @options
end

#original_string ⇒ Object (readonly)

original string before parsing



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# File 'lib/bio/db/newick.rb', line 83

def original_string
  @original_string
end

Instance Method Details

#reparse ⇒ Object

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



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# File 'lib/bio/db/newick.rb', line 101

def reparse
  if defined?(@tree)
    remove_instance_variable(:@tree)
  end
  self.tree
  self
end

#tree ⇒ Object

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



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# File 'lib/bio/db/newick.rb', line 90

def tree
  if !defined?(@tree)
    @tree = __parse_newick(@original_string, @options)
  else
    @tree
  end
end