From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 21 Jun 2013 09:35:03 +0000 (+0000)
Subject: added edit_distance method to seq.rb
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=b2ea0b5a51a558478af60e9df4c643dd58552086

added edit_distance method to seq.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2184 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 2788e5d..e4b6bfd 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -27,9 +27,10 @@ require 'maasha/seq/digest'
 require 'maasha/seq/trim'
 require 'narray'
 
-autoload :BackTrack,   'maasha/seq/backtrack.rb'
-autoload :Dynamic,     'maasha/seq/dynamic.rb'
-autoload :Homopolymer, 'maasha/seq/homopolymer.rb'
+autoload :BackTrack,   'maasha/seq/backtrack'
+autoload :Dynamic,     'maasha/seq/dynamic'
+autoload :Homopolymer, 'maasha/seq/homopolymer'
+autoload :Levenshtein, 'maasha/seq/levenshtein'
 
 # Residue alphabets
 DNA     = %w[a t c g]
@@ -68,7 +69,6 @@ TRANS_TAB11 = {
   "GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
 }
 
-
 # Error class for all exceptions to do with Seq.
 class SeqError < StandardError; end
 
@@ -384,8 +384,14 @@ class Seq
 
   # Method to determine the Hamming Distance between
   # two Sequence objects (case insensitive).
-  def hamming_distance(seq)
-    self.seq.upcase.hamming_distance(seq.seq.upcase)
+  def hamming_distance(entry)
+    self.seq.upcase.hamming_distance(entry.seq.upcase)
+  end
+
+  # Method to determine the Edit Distance between
+  # two Sequence objects (case insensitive).
+  def edit_distance(entry)
+    Levenshtein.distance(self.seq, entry.seq)
   end
 
   # Method that generates a random sequence of a given length and type.
diff --git a/code_ruby/test/maasha/seq/test_levenshtein.rb b/code_ruby/test/maasha/seq/test_levenshtein.rb
new file mode 100755
index 0000000..a260829
--- /dev/null
+++ b/code_ruby/test/maasha/seq/test_levenshtein.rb
@@ -0,0 +1,60 @@
+#!/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/seq/levenshtein'
+
+class LevenshteinTest < Test::Unit::TestCase
+  test "Levenshtein.distance returns 0 with identical strings" do
+    assert_equal(0, Levenshtein.distance("atcg", "atcg"))
+  end
+  
+  test "Levenshtein.distance returns s length if t is empty" do
+    assert_equal(4, Levenshtein.distance("atcg", ""))
+  end
+
+  test "Levenshtein.distance returns t length if s is empty" do
+    assert_equal(5, Levenshtein.distance("", "atcgn"))
+  end
+
+  test "Levenshtein.distance with mismatch only returns correctly" do
+    assert_equal(1, Levenshtein.distance("atcg", "atgg"))
+  end
+
+  test "Levenshtein.distance with ambiguity code returns correctly" do
+    assert_equal(0, Levenshtein.distance("atcg", "nnnn"))
+  end
+
+  test "Levenshtein.distance with insertion returns correctly" do
+    assert_equal(1, Levenshtein.distance("atcg", "attcg"))
+  end
+
+  test "Levenshtein.distance returns correctly" do
+    assert_equal(2, Levenshtein.distance("atcg", "tgncg"))
+  end
+end
diff --git a/code_ruby/test/maasha/test_levenshtein.rb b/code_ruby/test/maasha/test_levenshtein.rb
deleted file mode 100755
index fca9029..0000000
--- a/code_ruby/test/maasha/test_levenshtein.rb
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/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
diff --git a/code_ruby/test/maasha/test_seq.rb b/code_ruby/test/maasha/test_seq.rb
index 8eed8d5..5947ee8 100755
--- a/code_ruby/test/maasha/test_seq.rb
+++ b/code_ruby/test/maasha/test_seq.rb
@@ -298,13 +298,18 @@ class TestSeq < Test::Unit::TestCase
     assert_equal("UAGCuagc", @entry.complement!.seq)
   end
 
-
-  test "#hamming distance returns correctly" do
+  test "#hamming_distance returns correctly" do
     seq1 = Seq.new("test1", "ATCG")
     seq2 = Seq.new("test2", "atgg")
     assert_equal(1, seq1.hamming_distance(seq2))
   end
 
+  test "#edit_distance returns correctly" do
+    seq1 = Seq.new("test1", "ATCG")
+    seq2 = Seq.new("test2", "tgncg")
+    assert_equal(2, seq1.edit_distance(seq2))
+  end
+
   test "#generate with length < 1 raises" do
     assert_raise(SeqError) { @entry.generate(-10, :dna) }
     assert_raise(SeqError) { @entry.generate(0, :dna) }