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.

Note: molphy-style bootstrap values may be parsed, even if the options is set to :traditional or :disabled. Note: 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 = :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 267

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 282

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 276

def options
  @options
end

#original_string ⇒ Object (readonly)

original string before parsing



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# File 'lib/bio/db/newick.rb', line 279

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 297

def reparse
  remove_instance_variable(:tree)
  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 286

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