# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
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
+ extend Ambiguity
+
BYTES_IN_INT = 4
def self.distance(s, t)
v1 = "\0" * (t.length + 1) * BYTES_IN_INT
l = self.new
- l.distance_C(s, t, s.length, t.length, v0, v1)
+ l.levenshtein_distance_C(s, t, s.length, t.length, v0, v1)
end
# >>>>>>>>>>>>>>> RubyInline C code <<<<<<<<<<<<<<<
inline do |builder|
- # Macro for matching nucleotides including ambiguity codes.
- 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.
- 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
- };
- }
+ add_ambiguity_macro(builder)
builder.prefix %{
unsigned int min(unsigned int a, unsigned int b, unsigned int c)
}
builder.c %{
- VALUE distance_C(
+ VALUE levenshtein_distance_C(
VALUE _s, // string
VALUE _t, // string
VALUE _s_len, // string length