+#!/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