Class: Bio::Newick

Inherits:
Object
  • Object
show all
Defined in:
lib/iroki/main/main.rb

Instance Method Summary collapse

Instance Method Details

#__parse_newick_tokenize(str, options) ⇒ Object

splits string to tokens



48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
 
# File 'lib/iroki/main/main.rb', line 48

def __parse_newick_tokenize(str, options)
  str = str.chop if str[-1..-1] == ';'
  # http://evolution.genetics.washington.edu/phylip/newick_doc.html
  # quoted_label ==> ' string_of_printing_characters '
  # single quote in quoted_label is '' (two single quotes)
  #

  if __get_option(:parser, options) == :naive then
    ary = str.split(/([\(\)\,\:\[\]])/)
    ary.collect! { |x| x.strip!; x.empty? ? nil : x }
    ary.compact!
    ary.collect! do |x|
      if /\A([\(\)\,\:\[\]])\z/ =~ x then
        x.intern
      else
        x
      end
    end
    return ary
  end

  tokens = []
  ss = StringScanner.new(str)

  while !(ss.eos?)
    if ss.scan(/\s+/) then
      # do nothing

    elsif ss.scan(/[\(\)\,\:\[\]]/) then
      # '(' or ')' or ',' or ':' or '[' or ']'
      t = ss.matched
      tokens.push t.intern

    elsif ss.scan(/\'/) then
      # quoted_label
      t = ''
      while true
        if ss.scan(/([^\']*)\'/) then
          t.concat ss[1]
          if  ss.scan(/\'/) then
            # single quote in quoted_label
            t.concat ss.matched
          else
            break
          end
        else
          # incomplete quoted_label?
          break
        end
      end #while true
      unless ss.match?(/\s*[\(\)\,\:\[\]]/) or ss.match?(/\s*\z/) then
        # label continues? (illegal, but try to rescue)
        if ss.scan(/[^\(\)\,\:\[\]]+/) then
          t.concat ss.matched.lstrip
        end
      end
      tokens.push t

    elsif ss.scan(/[^\(\)\,\:\[\]]+/) then
      # unquoted_label
      t = ss.matched.strip
      t.gsub!(/[\r\n]/, '')

      unless __get_option(:parser, options) == :iroki then
        # unquoted underscore should be converted to blank
        t.gsub!(/\_/, ' ')
      end
      tokens.push t unless t.empty?

    else
      # unquoted_label in end of string
      t = ss.rest.strip
      t.gsub!(/[\r\n]/, '')

      unless __get_option(:parser, options) == :iroki then
        # unquoted underscore should be converted to blank
        t.gsub!(/\_/, ' ')
      end

      tokens.push t unless t.empty?
      ss.terminate

    end
  end #while !(ss.eos?)

  tokens
end