fixing name space collision

[biopieces.git] / code_ruby / test / maasha / seq / test_backtrack.rb

diff --git a/code_ruby/test/maasha/seq/test_backtrack.rb b/code_ruby/test/maasha/seq/test_backtrack.rb
index 02260e89d8dcf869cd0c9fe28751a5fe75bb407d..1af799e07ad2321bb7f627e8c112398f9c43375a 100644 (file)
--- a/code_ruby/test/maasha/seq/test_backtrack.rb
+++ b/code_ruby/test/maasha/seq/test_backtrack.rb
@@ -27,8 +27,11 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
 require 'test/unit'
 require 'maasha/seq'
+require 'maasha/seq/backtrack'
 
-include BackTrack
+class Seq
+  include BackTrack
+end
 
 class BackTrackTest < Test::Unit::TestCase
   def setup
@@ -98,48 +101,48 @@ class BackTrackTest < Test::Unit::TestCase
   end
 
   def test_BackTrack_patscan_perfect_left_is_ok
-    assert_equal("0:7:0:0:0:tacgatg", @seq.patscan("TACGATG").first.to_s)
+    assert_equal("0:7:tacgatg", @seq.patscan("TACGATG").first.to_s)
   end
 
   def test_BackTrack_patscan_perfect_right_is_ok
-    assert_equal("13:7:0:0:0:tgcacgg", @seq.patscan("TGCACGG").first.to_s)
+    assert_equal("13:7:tgcacgg", @seq.patscan("TGCACGG").first.to_s)
   end
 
   def test_BackTrack_patscan_ambiguity_is_ok
-    assert_equal("13:7:0:0:0:tgcacgg", @seq.patscan("TGCACNN").first.to_s)
+    assert_equal("13:7:tgcacgg", @seq.patscan("TGCACNN").first.to_s)
   end
 
   def test_BackTrack_patscan_pos_is_ok
-    assert_equal("10:1:0:0:0:g", @seq.patscan("N", 10).first.to_s)
-    assert_equal("19:1:0:0:0:g", @seq.patscan("N", 10).last.to_s)
+    assert_equal("10:1:g", @seq.patscan("N", 10).first.to_s)
+    assert_equal("19:1:g", @seq.patscan("N", 10).last.to_s)
   end
 
   def test_BackTrack_patscan_mis_left_is_ok
-    assert_equal("0:7:1:0:0:tacgatg", @seq.patscan("Aacgatg", 0, 1).first.to_s)
+    assert_equal("0:7:tacgatg", @seq.patscan("Aacgatg", 0, 1).first.to_s)
   end
 
   def test_BackTrack_patscan_mis_right_is_ok
-    assert_equal("13:7:1:0:0:tgcacgg", @seq.patscan("tgcacgA", 0, 1).first.to_s)
+    assert_equal("13:7:tgcacgg", @seq.patscan("tgcacgA", 0, 1).first.to_s)
   end
 
   def test_BackTrack_patscan_ins_left_is_ok
-    assert_equal("0:7:0:1:0:tacgatg", @seq.patscan("Atacgatg", 0, 0, 1).first.to_s)
+    assert_equal("0:7:tacgatg", @seq.patscan("Atacgatg", 0, 0, 1).first.to_s)
   end
 
   def test_BackTrack_patscan_ins_right_is_ok
-    assert_equal("13:7:0:1:0:tgcacgg", @seq.patscan("tgcacggA", 0, 0, 1).first.to_s)
+    assert_equal("13:7:tgcacgg", @seq.patscan("tgcacggA", 0, 0, 1).first.to_s)
   end
 
   def test_BackTrack_patscan_del_left_is_ok
-    assert_equal("0:7:0:0:1:tacgatg", @seq.patscan("acgatg", 0, 0, 0, 1).first.to_s)
+    assert_equal("0:7:tacgatg", @seq.patscan("acgatg", 0, 0, 0, 1).first.to_s)
   end
 
   def test_BackTrack_patscan_del_right_is_ok
-    assert_equal("12:8:0:0:1:atgcacgg", @seq.patscan("tgcacgg", 0, 0, 0, 1).first.to_s)
+    assert_equal("12:8:atgcacgg", @seq.patscan("tgcacgg", 0, 0, 0, 1).first.to_s)
   end
 
   def test_BackTrack_patscan_ambiguity_mis_ins_del_all_ok
-    assert_equal("0:20:1:1:1:tacgatgctagcatgcacgg", @seq.patscan("tacatgcNagGatgcCacgg", 0, 1, 1, 1).first.to_s)
+    assert_equal("0:20:tacgatgctagcatgcacgg", @seq.patscan("tacatgcNagGatgcCacgg", 0, 1, 1, 1).first.to_s)
   end
 end