renamed patternmatcher to dynamic

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2034 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/test/maasha/seq/test_dynamic.rb b/code_ruby/test/maasha/seq/test_dynamic.rb
new file mode 100755 (executable)
index 0000000..8e1121e
--- /dev/null
+++ b/code_ruby/test/maasha/seq/test_dynamic.rb
@@ -0,0 +1,135 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 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 'maasha/seq'
+require 'maasha/seq/dynamic'
+require 'test/unit'
+require 'pp'
+
+class Seq
+  include Dynamic
+end
+
+class TestDynamic < Test::Unit::TestCase
+  def setup
+    @p = Seq.new("test", "atcg")
+  end
+
+  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_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

diff --git a/code_ruby/test/maasha/seq/test_patternmatcher.rb b/code_ruby/test/maasha/seq/test_patternmatcher.rb
deleted file mode 100755 (executable)
index 8e1121e..0000000
--- a/code_ruby/test/maasha/seq/test_patternmatcher.rb
+++ /dev/null
@@ -1,135 +0,0 @@
-#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-# Copyright (C) 2007-2010 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 'maasha/seq'
-require 'maasha/seq/dynamic'
-require 'test/unit'
-require 'pp'
-
-class Seq
-  include Dynamic
-end
-
-class TestDynamic < Test::Unit::TestCase
-  def setup
-    @p = Seq.new("test", "atcg")
-  end
-
-  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_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