refactorying PatternMatcher to Dynamic

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2032 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/test/maasha/seq/test_patternmatcher.rb b/code_ruby/test/maasha/seq/test_patternmatcher.rb
index 8327117c30529fb81d5839900276ceff0802c51e..8e1121e28fd60ea8c301c83da48d0bee0843e62f 100755 (executable)
--- a/code_ruby/test/maasha/seq/test_patternmatcher.rb
+++ b/code_ruby/test/maasha/seq/test_patternmatcher.rb
@@ -26,25 +26,24 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'maasha/seq'
-require 'maasha/seq/patternmatcher'
+require 'maasha/seq/dynamic'
 require 'test/unit'
 require 'pp'
 
 class Seq
-  include PatternMatcher
+  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
+  def test_Dynamic_no_match_returns_nil
     assert_nil(@p.patmatch("gggg"))
   end
 
-  def test_PatternMatcher_patmatch_perfect_returns_correctly
+  def test_Dynamic_patmatch_perfect_returns_correctly
     m = @p.patmatch("atcg")
     assert_equal(0, m.beg)
     assert_equal("atcg", m.match)
@@ -54,7 +53,7 @@ class TestPatternMatcher < Test::Unit::TestCase
     assert_equal(4, m.length)
   end
 
-  def test_PatternMatcher_patmatch_perfect_with_ambiguity_codes_returns_correctly
+  def test_Dynamic_patmatch_perfect_with_ambiguity_codes_returns_correctly
     m = @p.patmatch("nnnn")
     assert_equal(0, m.beg)
     assert_equal("atcg", m.match)
@@ -64,11 +63,11 @@ class TestPatternMatcher < Test::Unit::TestCase
     assert_equal(4, m.length)
   end
 
-  def test_PatternMatcher_patmatch_with_one_mismatch_and_edit_dist_zero_returns_nil
+  def test_Dynamic_patmatch_with_one_mismatch_and_edit_dist_zero_returns_nil
     assert_nil(@p.patmatch("aCcg"))
   end
 
-  def test_PatternMatcher_patmatch_with_one_mismatch_and_edit_dist_one_returns_correctly
+  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)
@@ -78,15 +77,15 @@ class TestPatternMatcher < Test::Unit::TestCase
     assert_equal(4, m.length)
   end
 
-  def test_PatternMatcher_patmatch_with_two_mismatch_and_edit_dist_one_returns_nil
+  def test_Dynamic_patmatch_with_two_mismatch_and_edit_dist_one_returns_nil
     assert_nil(@p.patmatch("aGcA", 0, 1))
   end
 
-  def test_PatternMatcher_patmatch_with_one_insertion_and_edit_dist_zero_returns_nil
+  def test_Dynamic_patmatch_with_one_insertion_and_edit_dist_zero_returns_nil
     assert_nil(@p.patmatch("atGcg"))
   end
 
-  def test_PatternMatcher_patmatch_with_one_insertion_and_edit_dist_one_returns_correctly
+  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)
@@ -96,11 +95,11 @@ class TestPatternMatcher < Test::Unit::TestCase
     assert_equal(4, m.length)
   end
 
-  def test_PatternMatcher_patmatch_with_two_insertions_and_edit_dist_one_returns_nil
+  def test_Dynamic_patmatch_with_two_insertions_and_edit_dist_one_returns_nil
     assert_nil(@p.patmatch("atGcTg", 0, 1))
   end
 
-  def test_PatternMatcher_patmatch_with_two_insertions_and_edit_dist_two_returns_correctly
+  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)
@@ -110,11 +109,11 @@ class TestPatternMatcher < Test::Unit::TestCase
     assert_equal(4, m.length)
   end
 
-  def test_PatternMatcher_patmatch_with_one_deletion_and_edit_distance_zero_returns_nil
+  def test_Dynamic_patmatch_with_one_deletion_and_edit_distance_zero_returns_nil
     assert_nil(@p.patmatch("acg"))
   end
 
-  def test_PatternMatcher_patmatch_with_one_deletion_and_edit_distance_one_returns_correctly
+  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)
@@ -124,12 +123,12 @@ class TestPatternMatcher < Test::Unit::TestCase
     assert_equal(4, m.length)
   end
 
-  def test_PatternMatcher_patscan_locates_three_patterns_ok
+  def test_Dynamic_patscan_locates_three_patterns_ok
     p = Seq.new("test", "ataacgagctagctagctagctgactac")
     assert_equal(3, p.patscan("tag").count)
   end
 
-  def test_PatternMatcher_patscan_with_pos_locates_two_patterns_ok
+  def test_Dynamic_patscan_with_pos_locates_two_patterns_ok
     p = Seq.new("test", "ataacgagctagctagctagctgactac")
     assert_equal(2, p.patscan("tag", 10).count)
   end