2 $:.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
4 # Copyright (C) 2013 Martin A. Hansen.
6 # This program is free software; you can redistribute it and/or
7 # modify it under the terms of the GNU General Public License
8 # as published by the Free Software Foundation; either version 2
9 # of the License, or (at your option) any later version.
11 # This program is distributed in the hope that it will be useful,
12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 # GNU General Public License for more details.
16 # You should have received a copy of the GNU General Public License
17 # along with this program; if not, write to the Free Software
18 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
20 # http://www.gnu.org/copyleft/gpl.html
22 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
24 # This software is part of the Biopieces framework (www.biopieces.org).
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
30 require 'maasha/align/match'
32 class MatchTest < Test::Unit::TestCase
34 @match = Match.new(1, 1, 3)
37 test "#q_end returns correctly" do
38 assert_equal(3, @match.q_end)
41 test "#s_end returns correctly" do
42 assert_equal(3, @match.s_end)
45 test "#to_s returns correctly" do
46 assert_equal("q: 1 3 s: 1 3 l: 3 s: 0.0", @match.to_s)
47 assert_equal("q: 1 3 s: 1 3 l: 3 s: 0.0 tcg", @match.to_s("atcg"))
50 test "#expand to left end returns correctly" do
51 assert_equal("q: 0 3 s: 0 3 l: 4 s: 0.0", @match.expand("atcg", "atcg", 0, 0, 3, 3).to_s)
54 test "#expand to left mismatch returns correctly" do
55 assert_equal("q: 1 3 s: 1 3 l: 3 s: 0.0", @match.expand("gtcg", "atcg", 0, 0, 3, 3).to_s)
58 test "#expand to left space beg returns correctly" do
59 assert_equal("q: 1 3 s: 1 3 l: 3 s: 0.0", @match.expand("atcg", "atcg", 1, 1, 3, 3).to_s)
62 test "#expand to right end returns correctly" do
63 assert_equal("q: 0 4 s: 0 4 l: 5 s: 0.0", @match.expand("atcga", "atcga", 0, 0, 4, 4).to_s)
66 test "#expand to right mismatch returns correctly" do
67 assert_equal("q: 1 3 s: 1 3 l: 3 s: 0.0", @match.expand("gtcga", "atcgg", 0, 0, 4, 4).to_s)
70 test "#expand to right space end returns correctly" do
71 assert_equal("q: 1 3 s: 1 3 l: 3 s: 0.0", @match.expand("atcga", "atcga", 1, 1, 3, 3).to_s)