class Bio::Newick
Newick
standard phylogenetic tree parser class.
This is alpha version. Incompatible changes may be made frequently.
Constants
- DELIMITER
delemiter of the entry
- Edge
same as
Bio::Tree::Edge
- Node
same as
Bio::Tree::Node
Attributes
string after this entry
parser options (in some cases, options can be automatically set by the parser)
original string before parsing
Public Class Methods
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 71 def initialize(str, options = nil) 72 str = str.sub(/\;(.*)/m, ';') 73 @original_string = str 74 @entry_overrun = $1 75 @options = (options or {}) 76 end
Public Instance Methods
Re-parses the tree from the original string. Returns self. This method is useful after changing parser options.
# File lib/bio/db/newick.rb 101 def reparse 102 if defined?(@tree) 103 remove_instance_variable(:@tree) 104 end 105 self.tree 106 self 107 end
Gets the tree. Returns a Bio::Tree
object.
# File lib/bio/db/newick.rb 90 def tree 91 if !defined?(@tree) 92 @tree = __parse_newick(@original_string, @options) 93 else 94 @tree 95 end 96 end