added levenshtein edit distance calculator

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2180 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/levenshtein.rb b/code_ruby/lib/maasha/levenshtein.rb
new file mode 100644 (file)
index 0000000..1447e17
--- /dev/null
+++ b/code_ruby/lib/maasha/levenshtein.rb
@@ -0,0 +1,107 @@
+# Copyright (C) 2013 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'inline'
+
+class Levenshtein
+  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
+
+  def initialize
+  end
+
+  # >>>>>>>>>>>>>>> RubyInline C code <<<<<<<<<<<<<<<
+
+  inline do |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,
+        VALUE _t,
+        VALUE _s_len,
+        VALUE _t_len,
+        VALUE _v0,
+        VALUE _v1
+      )
+      {
+        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 = (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
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/code_ruby/test/maasha/test_levenshtein.rb b/code_ruby/test/maasha/test_levenshtein.rb
new file mode 100755 (executable)
index 0000000..fca9029
--- /dev/null
+++ b/code_ruby/test/maasha/test_levenshtein.rb
@@ -0,0 +1,53 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# Copyright (C) 2013 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'test/unit'
+require 'test/helper'
+require 'maasha/levenshtein'
+
+class LevenshteinTest < Test::Unit::TestCase
+  test "Levenshtein.distance returns 0 with identical strings" do
+    assert_equal(0, Levenshtein.distance("foo", "foo"))
+  end
+  
+  test "Levenshtein.distance returns s length if t is empty" do
+    assert_equal(3, Levenshtein.distance("foo", ""))
+  end
+
+  test "Levenshtein.distance returns t length if s is empty" do
+    assert_equal(5, Levenshtein.distance("", "fobar"))
+  end
+
+  test "Levenshtein.distance with mismatch only returns correctly" do
+    assert_equal(1, Levenshtein.distance("foo", "fox"))
+  end
+
+  test "Levenshtein.distance returns correctly" do
+    assert_equal(3, Levenshtein.distance("kitten", "sitting"))
+    assert_equal(3, Levenshtein.distance("Saturday", "Sunday"))
+  end
+end