ambiguity.rb

require 'inline'

module Ambiguity
  def add_ambiguity_macro inline_builder
    # Macro for matching nucleotides including ambiguity codes.
    inline_builder.prefix %{
      #define MATCH(A,B) ((bitmap[A] & bitmap[B]) != 0)
    }

    # Bitmap for matching nucleotides including ambiguity codes.
    # For each value bits are set from the left: bit pos 1 for A,
    # bit pos 2 for T, bit pos 3 for C, and bit pos 4 for G.
    inline_builder.prefix %{
      char bitmap[256] = {
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 1,14, 4,11, 0, 0, 8, 7, 0, 0,10, 0, 5,15, 0,
          0, 0, 9,12, 2, 2,13, 3, 0, 6, 0, 0, 0, 0, 0, 0,
          0, 1,14, 4,11, 0, 0, 8, 7, 0, 0,10, 0, 5,15, 0,
          0, 0, 9,12, 2, 2,13, 3, 0, 6, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
      };
    }
  end
end

error.txt

/Users/maasha/biopieces/code_ruby/lib/maasha/seq/levenshtein.rb:51:in `block in <class:Levenshtein>': undefined method `add_ambiguity_macro' for Levenshtein:Class (NoMethodError)
        from /usr/local/lib/ruby/gems/1.9.1/gems/RubyInline-3.12.1/lib/inline.rb:844:in `inline'
        from /Users/maasha/biopieces/code_ruby/lib/maasha/seq/levenshtein.rb:50:in `<class:Levenshtein>'
        from /Users/maasha/biopieces/code_ruby/lib/maasha/seq/levenshtein.rb:31:in `<top (required)>'
        from /Users/maasha/biopieces/code_ruby/lib/maasha/seq.rb:394:in `edit_distance'
        from ./test.rb:8:in `<main>'

levenshtein.rb

require 'inline'
require 'maasha/seq/ambiguity'

# Class to calculate the Levenshtein distance between two
# given strings.
# http://en.wikipedia.org/wiki/Levenshtein_distance
class Levenshtein
  include Ambiguity

  BYTES_IN_INT = 4

  def self.distance(s, t)
    return 0        if s == t;
    return t.length if s.length == 0;
    return s.length if t.length == 0;

    v0 = "\0" * (t.length + 1) * BYTES_IN_INT
    v1 = "\0" * (t.length + 1) * BYTES_IN_INT

    l = self.new
    l.distance_C(s, t, s.length, t.length, v0, v1)
  end

  # >>>>>>>>>>>>>>> RubyInline C code <<<<<<<<<<<<<<<

  inline do |builder|
    add_ambiguity_macro(builder)

    builder.prefix %{
      unsigned int min(unsigned int a, unsigned int b, unsigned int c)
      {
          unsigned int m = a;

          if (m > b) m = b;
          if (m > c) m = c;

          return m;
      }
    }

    builder.c %{
      VALUE distance_C(
        VALUE _s,       // string
        VALUE _t,       // string
        VALUE _s_len,   // string length
        VALUE _t_len,   // string length
        VALUE _v0,      // score vector
        VALUE _v1       // score vector
      )
      {
        char         *s     = (char *) StringValuePtr(_s);
        char         *t     = (char *) StringValuePtr(_t);
        unsigned int  s_len = FIX2UINT(_s_len);
        unsigned int  t_len = FIX2UINT(_t_len);
        unsigned int  *v0   = (unsigned int *) StringValuePtr(_v0);
        unsigned int  *v1   = (unsigned int *) StringValuePtr(_v1);

        unsigned int i    = 0;
        unsigned int j    = 0;
        unsigned int cost = 0;
       
        for (i = 0; i < t_len + 1; i++)
          v0[i] = i;
       
        for (i = 0; i < s_len; i++)
        {
          v1[0] = i + 1;
       
          for (j = 0; j < t_len; j++)
          {
            cost = (MATCH(s[i], t[j])) ? 0 : 1;
            v1[j + 1] = min(v1[j] + 1, v0[j + 1] + 1, v0[j] + cost);
          }
       
          for (j = 0; j < t_len + 1; j++)
            v0[j] = v1[j];
        }
       
        return UINT2NUM(v1[t_len]);
      }
    }
  end
end