added test for align dir

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2050 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/test/maasha/align/test_matches.rb b/code_ruby/test/maasha/align/test_matches.rb
new file mode 100755 (executable)
index 0000000..115e85f
--- /dev/null
+++ b/code_ruby/test/maasha/align/test_matches.rb
@@ -0,0 +1,60 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2012 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 'maasha/align/matches'
+require 'pp'
+
+class MatchesTest < Test::Unit::TestCase
+  def test_Matches_find_with_no_match_returns_correctly
+    assert_equal("[]", Matches.find("atcg", "atcg", 0, 0, 3, 3, 8).to_s)
+  end
+
+  def test_Matches_find_with_one_match_returns_correctly
+    assert_equal("[q: 2 3 s: 0 1 l: 2 s: 0.0]", Matches.find("01cg", "cg23", 0, 0, 3, 3, 2).to_s)
+    assert_equal("[q: 0 1 s: 2 3 l: 2 s: 0.0]", Matches.find("cg23", "01cg", 0, 0, 3, 3, 2).to_s)
+  end
+
+  def test_Matches_find_with_two_matches_returns_correctly
+    assert_equal("[q: 0 1 s: 0 1 l: 2 s: 0.0, q: 3 4 s: 3 4 l: 2 s: 0.0]", Matches.find("atXcg", "atYcg", 0, 0, 4, 4, 2).to_s)
+    assert_equal("[q: 0 1 s: 0 1 l: 2 s: 0.0, q: 3 4 s: 3 4 l: 2 s: 0.0]", Matches.find("atYcg", "atXcg", 0, 0, 4, 4, 2).to_s)
+  end
+
+  def test_Matches_find_dont_expand_match_outside_space
+    assert_equal("[q: 1 2 s: 1 2 l: 2 s: 0.0]", Matches.find("atcg", "atcg", 1, 1, 2, 2, 2).to_s)
+  end
+
+  def test_Matches_find_right_expands_correctly
+    assert_equal("[q: 0 3 s: 0 3 l: 4 s: 0.0]", Matches.find("atcg", "atcg", 0, 0, 3, 3, 3).to_s)
+  end
+
+#  def test_Matches_find_left_expands_correctly
+#    flunk
+#    assert_equal("[q: 1 2 s: 1 2 l: 2 s: 0.0]", Matches.find("ccccc", "cccc", 0, 0, 3, 3, 2).to_s)
+#  end
+end
+

diff --git a/code_ruby/test/maasha/align/test_mem.rb b/code_ruby/test/maasha/align/test_mem.rb
new file mode 100755 (executable)
index 0000000..04c6b8f
--- /dev/null
+++ b/code_ruby/test/maasha/align/test_mem.rb
@@ -0,0 +1,36 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# 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 'maasha/align/mem'
+require 'pp'
+
+class MemTest < Test::Unit::TestCase
+  def test_Matches_find_with_no_match_returns_correctly
+    assert_equal("[]", Matches.find("atcg", "atcg", 0, 0, 3, 3, 8).to_s)
+  end
+end