#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+$:.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
# Copyright (C) 2007-2010 Martin A. Hansen.
require 'maasha/seq'
require 'test/unit'
-require 'pp'
+require 'test/helper'
class TestDynamic < Test::Unit::TestCase
def setup
@p.extend(Dynamic)
end
- def test_Dynamic_no_match_returns_nil
+ test "#patmatch with no match returns nil" do
assert_nil(@p.patmatch("gggg"))
end
- def test_Dynamic_patmatch_perfect_returns_correctly
+ test "#patmatch with perfect match returns correctly" do
m = @p.patmatch("atcg")
assert_equal(0, m.beg)
assert_equal("atcg", m.match)
assert_equal(4, m.length)
end
- def test_Dynamic_patmatch_perfect_with_ambiguity_codes_returns_correctly
+ test "#patmatch with perfect match with ambiguity codes returns correctly" do
m = @p.patmatch("nnnn")
assert_equal(0, m.beg)
assert_equal("atcg", m.match)
assert_equal(4, m.length)
end
- def test_Dynamic_patmatch_with_one_mismatch_and_edit_dist_zero_returns_nil
+ test "#patmatch with one mismatch and edit dist zero returns nil" do
assert_nil(@p.patmatch("aCcg"))
end
- def test_Dynamic_patmatch_with_one_mismatch_and_edit_dist_one_returns_correctly
+ test "#patmatch with one mismatch and edit dist one returns correctly" do
m = @p.patmatch("aCcg", 0, 1)
assert_equal(0, m.beg)
assert_equal("atcg", m.match)
assert_equal(4, m.length)
end
- def test_Dynamic_patmatch_with_two_mismatch_and_edit_dist_one_returns_nil
+ test "#patmatch with two mismatch and edit dist one returns nil" do
assert_nil(@p.patmatch("aGcA", 0, 1))
end
- def test_Dynamic_patmatch_with_one_insertion_and_edit_dist_zero_returns_nil
+ test "#patmatch with one insertion and edit dist zero returns nil" do
assert_nil(@p.patmatch("atGcg"))
end
- def test_Dynamic_patmatch_with_one_insertion_and_edit_dist_one_returns_correctly
+ test "#patmatch with one insertion and edit dist one returns correctly" do
m = @p.patmatch("atGcg", 0, 1)
assert_equal(0, m.beg)
assert_equal("atcg", m.match)
assert_equal(4, m.length)
end
- def test_Dynamic_patmatch_with_two_insertions_and_edit_dist_one_returns_nil
+ test "#patmatch with two insertions and edit dist one returns nil" do
assert_nil(@p.patmatch("atGcTg", 0, 1))
end
- def test_Dynamic_patmatch_with_two_insertions_and_edit_dist_two_returns_correctly
+ test "#patmatch with two insertions and edit dist two returns correctly" do
m = @p.patmatch("atGcTg", 0, 2)
assert_equal(0, m.beg)
assert_equal("atcg", m.match)
assert_equal(4, m.length)
end
- def test_Dynamic_patmatch_with_one_deletion_and_edit_distance_zero_returns_nil
+ test "#patmatch with one deletion and edit distance zero returns nil" do
assert_nil(@p.patmatch("acg"))
end
- def test_Dynamic_patmatch_with_one_deletion_and_edit_distance_one_returns_correctly
+ test "#patmatch with one deletion and edit distance one returns correctly" do
m = @p.patmatch("acg", 0, 1)
assert_equal(0, m.beg)
assert_equal("atcg", m.match)
assert_equal(4, m.length)
end
- def test_Dynamic_patscan_locates_three_patterns_ok
+ test "#patscan locates three patterns ok" do
p = Seq.new("test", "ataacgagctagctagctagctgactac")
p.extend(Dynamic)
assert_equal(3, p.patscan("tag").count)
end
- def test_Dynamic_patscan_with_pos_locates_two_patterns_ok
+ test "#patscan with pos locates two patterns ok" do
p = Seq.new("test", "ataacgagctagctagctagctgactac")
p.extend(Dynamic)
assert_equal(2, p.patscan("tag", 10).count)