fixing name space collision

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

diff --git a/code_ruby/test/maasha/seq/test_patternmatcher.rb b/code_ruby/test/maasha/seq/test_patternmatcher.rb
index d6caf419cd2fdac6a0612267a3b007041c1ae603..8e1121e28fd60ea8c301c83da48d0bee0843e62f 100755 (executable)
--- a/code_ruby/test/maasha/seq/test_patternmatcher.rb
+++ b/code_ruby/test/maasha/seq/test_patternmatcher.rb
@@ -26,114 +26,110 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'maasha/seq'
-require 'maasha/seq/patternmatcher'
+require 'maasha/seq/dynamic'
 require 'test/unit'
 require 'pp'
 
-include PatternMatcher
+class Seq
+  include Dynamic
+end
 
-class TestPatternMatcher < Test::Unit::TestCase
+class TestDynamic < Test::Unit::TestCase
   def setup
     @p = Seq.new("test", "atcg")
   end
 
-  def test_PatternMatcher_no_match_returns_nil
-    assert_nil(@p.match("gggg"))
+  def test_Dynamic_no_match_returns_nil
+    assert_nil(@p.patmatch("gggg"))
+  end
+
+  def test_Dynamic_patmatch_perfect_returns_correctly
+    m = @p.patmatch("atcg")
+    assert_equal(0, m.beg)
+    assert_equal("atcg", m.match)
+    assert_equal(0, m.mis)
+    assert_equal(0, m.ins)
+    assert_equal(0, m.del)
+    assert_equal(4, m.length)
+  end
+
+  def test_Dynamic_patmatch_perfect_with_ambiguity_codes_returns_correctly
+    m = @p.patmatch("nnnn")
+    assert_equal(0, m.beg)
+    assert_equal("atcg", m.match)
+    assert_equal(0, m.mis)
+    assert_equal(0, m.ins)
+    assert_equal(0, m.del)
+    assert_equal(4, m.length)
+  end
+
+  def test_Dynamic_patmatch_with_one_mismatch_and_edit_dist_zero_returns_nil
+    assert_nil(@p.patmatch("aCcg"))
+  end
+
+  def test_Dynamic_patmatch_with_one_mismatch_and_edit_dist_one_returns_correctly
+    m = @p.patmatch("aCcg", 0, 1)
+    assert_equal(0, m.beg)
+    assert_equal("atcg", m.match)
+    assert_equal(1, m.mis)
+    assert_equal(0, m.ins)
+    assert_equal(0, m.del)
+    assert_equal(4, m.length)
+  end
+
+  def test_Dynamic_patmatch_with_two_mismatch_and_edit_dist_one_returns_nil
+    assert_nil(@p.patmatch("aGcA", 0, 1))
+  end
+
+  def test_Dynamic_patmatch_with_one_insertion_and_edit_dist_zero_returns_nil
+    assert_nil(@p.patmatch("atGcg"))
   end
 
-#  def test_PatternMatcher_match_perfect_returns_correctly
-#    m = @p.match("atcg")
-#    assert_equal(0, m.pos)
-#    assert_equal("atcg", m.match)
-#    assert_equal(4, m.matches)
-#    assert_equal(0, m.mismatches)
-#    assert_equal(0, m.insertions)
-#    assert_equal(0, m.deletions)
-#    assert_equal(4, m.length)
-#  end
-#
-#  def test_PatternMatcher_match_perfect_with_ambiguity_codes_returns_correctly
-#    m = @p.match("nnnn")
-#    assert_equal(0, m.pos)
-#    assert_equal("atcg", m.match)
-#    assert_equal(4, m.matches)
-#    assert_equal(0, m.mismatches)
-#    assert_equal(0, m.insertions)
-#    assert_equal(0, m.deletions)
-#    assert_equal(4, m.length)
-#  end
-#
-#  def test_PatternMatcher_match_with_one_mismatch_and_edit_dist_zero_returns_nil
-#    assert_nil(@p.match("aCcg"))
-#  end
-#
-#  def test_PatternMatcher_match_with_one_mismatch_and_edit_dist_one_returns_correctly
-#    m = @p.match("aCcg", 0, 1)
-#    assert_equal(0, m.pos)
-#    assert_equal("atcg", m.match)
-#    assert_equal(3, m.matches)
-#    assert_equal(1, m.mismatches)
-#    assert_equal(0, m.insertions)
-#    assert_equal(0, m.deletions)
-#    assert_equal(4, m.length)
-#  end
-#
-#  def test_PatternMatcher_match_with_two_mismatch_and_edit_dist_one_returns_nil
-#    assert_nil(@p.match("aGcA", 0, 1))
-#  end
-#
-#  def test_PatternMatcher_match_with_one_insertion_and_edit_dist_zero_returns_nil
-#    assert_nil(@p.match("atGcg"))
-#  end
-#
-#  def test_PatternMatcher_match_with_one_insertion_and_edit_dist_one_returns_correctly
-#    m = @p.match("atGcg", 0, 1)
-#    assert_equal(0, m.pos)
-#    assert_equal("atcg", m.match)
-#    assert_equal(4, m.matches)
-#    assert_equal(0, m.mismatches)
-#    assert_equal(1, m.insertions)
-#    assert_equal(0, m.deletions)
-#    assert_equal(4, m.length)
-#  end
-#
-#  def test_PatternMatcher_match_with_two_insertions_and_edit_dist_one_returns_nil
-#    assert_nil(@p.match("atGcTg", 0, 1))
-#  end
-#
-#  def test_PatternMatcher_match_with_two_insertions_and_edit_dist_two_returns_correctly
-#    m = @p.match("atGcTg", 0, 2)
-#    assert_equal(0, m.pos)
-#    assert_equal("atcg", m.match)
-#    assert_equal(4, m.matches)
-#    assert_equal(0, m.mismatches)
-#    assert_equal(2, m.insertions)
-#    assert_equal(0, m.deletions)
-#    assert_equal(4, m.length)
-#  end
-#
-#  def test_PatternMatcher_match_with_one_deletion_and_edit_distance_zero_returns_nil
-#    assert_nil(@p.match("acg"))
-#  end
-#
-#  def test_PatternMatcher_match_with_one_deletion_and_edit_distance_one_returns_correctly
-#    m = @p.match("acg", 0, 1)
-#    assert_equal(0, m.pos)
-#    assert_equal("atcg", m.match)
-#    assert_equal(3, m.matches)
-#    assert_equal(0, m.mismatches)
-#    assert_equal(0, m.insertions)
-#    assert_equal(1, m.deletions)
-#    assert_equal(4, m.length)
-#  end
-#
-#  def test_PatternMatcher_scan_locates_three_patterns_ok
-#    p = Seq.new("test", "ataacgagctagctagctagctgactac")
-#    assert_equal(3, p.scan("tag").count)
-#  end
-#
-#  def test_PatternMatcher_scan_with_pos_locates_two_patterns_ok
-#    p = Seq.new("test", "ataacgagctagctagctagctgactac")
-#    assert_equal(2, p.scan("tag", 10).count)
-#  end
+  def test_Dynamic_patmatch_with_one_insertion_and_edit_dist_one_returns_correctly
+    m = @p.patmatch("atGcg", 0, 1)
+    assert_equal(0, m.beg)
+    assert_equal("atcg", m.match)
+    assert_equal(0, m.mis)
+    assert_equal(1, m.ins)
+    assert_equal(0, m.del)
+    assert_equal(4, m.length)
+  end
+
+  def test_Dynamic_patmatch_with_two_insertions_and_edit_dist_one_returns_nil
+    assert_nil(@p.patmatch("atGcTg", 0, 1))
+  end
+
+  def test_Dynamic_patmatch_with_two_insertions_and_edit_dist_two_returns_correctly
+    m = @p.patmatch("atGcTg", 0, 2)
+    assert_equal(0, m.beg)
+    assert_equal("atcg", m.match)
+    assert_equal(0, m.mis)
+    assert_equal(2, m.ins)
+    assert_equal(0, m.del)
+    assert_equal(4, m.length)
+  end
+
+  def test_Dynamic_patmatch_with_one_deletion_and_edit_distance_zero_returns_nil
+    assert_nil(@p.patmatch("acg"))
+  end
+
+  def test_Dynamic_patmatch_with_one_deletion_and_edit_distance_one_returns_correctly
+    m = @p.patmatch("acg", 0, 1)
+    assert_equal(0, m.beg)
+    assert_equal("atcg", m.match)
+    assert_equal(0, m.mis)
+    assert_equal(0, m.ins)
+    assert_equal(1, m.del)
+    assert_equal(4, m.length)
+  end
+
+  def test_Dynamic_patscan_locates_three_patterns_ok
+    p = Seq.new("test", "ataacgagctagctagctagctgactac")
+    assert_equal(3, p.patscan("tag").count)
+  end
+
+  def test_Dynamic_patscan_with_pos_locates_two_patterns_ok
+    p = Seq.new("test", "ataacgagctagctagctagctgactac")
+    assert_equal(2, p.patscan("tag", 10).count)
+  end
 end