Class | Bio::Newick |
In: |
lib/bio/db/newick.rb
|
Parent: | Object |
DELIMITER | = | RS = ";" | delemiter of the entry | |
Edge | = | Bio::Tree::Edge | same as Bio::Tree::Edge | |
Node | = | Bio::Tree::Node | same as Bio::Tree::Node |
entry_overrun | [R] | string after this entry |
options | [R] | parser options (in some cases, options can be automatically set by the parser) |
original_string | [R] | original string before parsing |
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 315 315: def initialize(str, options = nil) 316: str = str.sub(/\;(.*)/m, ';') 317: @original_string = str 318: @entry_overrun = $1 319: @options = (options or {}) 320: end