end
def test_PatternMatcher_no_match_returns_nil
end
def test_PatternMatcher_no_match_returns_nil
- assert_nil(@p.match("gggg"))
+ assert_nil(@p.patmatch("gggg"))
- def test_PatternMatcher_match_perfect_returns_correctly
- m = @p.match("atcg")
+ def test_PatternMatcher_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.beg)
assert_equal("atcg", m.match)
assert_equal(0, m.mis)
assert_equal(4, m.length)
end
assert_equal(4, m.length)
end
- def test_PatternMatcher_match_perfect_with_ambiguity_codes_returns_correctly
- m = @p.match("nnnn")
+ def test_PatternMatcher_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.beg)
assert_equal("atcg", m.match)
assert_equal(0, m.mis)
assert_equal(4, m.length)
end
assert_equal(4, m.length)
end
- def test_PatternMatcher_match_with_one_mismatch_and_edit_dist_zero_returns_nil
- assert_nil(@p.match("aCcg"))
+ def test_PatternMatcher_patmatch_with_one_mismatch_and_edit_dist_zero_returns_nil
+ assert_nil(@p.patmatch("aCcg"))
- def test_PatternMatcher_match_with_one_mismatch_and_edit_dist_one_returns_correctly
- m = @p.match("aCcg", 0, 1)
+ def test_PatternMatcher_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.beg)
assert_equal("atcg", m.match)
assert_equal(1, m.mis)
assert_equal(4, m.length)
end
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))
+ def test_PatternMatcher_patmatch_with_two_mismatch_and_edit_dist_one_returns_nil
+ assert_nil(@p.patmatch("aGcA", 0, 1))
- def test_PatternMatcher_match_with_one_insertion_and_edit_dist_zero_returns_nil
- assert_nil(@p.match("atGcg"))
+ def test_PatternMatcher_patmatch_with_one_insertion_and_edit_dist_zero_returns_nil
+ assert_nil(@p.patmatch("atGcg"))
- def test_PatternMatcher_match_with_one_insertion_and_edit_dist_one_returns_correctly
- m = @p.match("atGcg", 0, 1)
+ def test_PatternMatcher_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(0, m.beg)
assert_equal("atcg", m.match)
assert_equal(0, m.mis)
assert_equal(4, m.length)
end
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))
+ def test_PatternMatcher_patmatch_with_two_insertions_and_edit_dist_one_returns_nil
+ assert_nil(@p.patmatch("atGcTg", 0, 1))
- def test_PatternMatcher_match_with_two_insertions_and_edit_dist_two_returns_correctly
- m = @p.match("atGcTg", 0, 2)
+ def test_PatternMatcher_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(0, m.beg)
assert_equal("atcg", m.match)
assert_equal(0, m.mis)
assert_equal(4, m.length)
end
assert_equal(4, m.length)
end
- def test_PatternMatcher_match_with_one_deletion_and_edit_distance_zero_returns_nil
- assert_nil(@p.match("acg"))
+ def test_PatternMatcher_patmatch_with_one_deletion_and_edit_distance_zero_returns_nil
+ assert_nil(@p.patmatch("acg"))
- def test_PatternMatcher_match_with_one_deletion_and_edit_distance_one_returns_correctly
- m = @p.match("acg", 0, 1)
+ def test_PatternMatcher_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.beg)
assert_equal("atcg", m.match)
assert_equal(0, m.mis)
assert_equal(4, m.length)
end
assert_equal(4, m.length)
end
- def test_PatternMatcher_scan_locates_three_patterns_ok
+ def test_PatternMatcher_patscan_locates_three_patterns_ok
p = Seq.new("test", "ataacgagctagctagctagctgactac")
p = Seq.new("test", "ataacgagctagctagctagctgactac")
- assert_equal(3, p.scan("tag").count)
+ assert_equal(3, p.patscan("tag").count)
- def test_PatternMatcher_scan_with_pos_locates_two_patterns_ok
+ def test_PatternMatcher_patscan_with_pos_locates_two_patterns_ok
p = Seq.new("test", "ataacgagctagctagctagctgactac")
p = Seq.new("test", "ataacgagctagctagctagctgactac")
- assert_equal(2, p.scan("tag", 10).count)
+ assert_equal(2, p.patscan("tag", 10).count)