2 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
4 # Copyright (C) 2007-2011 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 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 class BackTrackTest < Test::Unit::TestCase
34 # 01234567890123456789
35 @seq = Seq.new("test", "tacgatgctagcatgcacgg")
38 def test_BackTrack_patscan_with_bad_pattern_raises
39 ["", "X", "1"].each { |pattern|
40 assert_raise(BackTrackError) { @seq.patscan(pattern) }
44 def test_BackTrack_patscan_with_OK_pattern_dont_raise
45 ["N", "atcg"].each { |pattern|
46 assert_nothing_raised { @seq.patscan(pattern) }
50 def test_BackTrack_patscan_with_bad_pos_raises
52 assert_raise(BackTrackError) { @seq.patscan("N", pos) }
56 def test_BackTrack_patscan_with_OK_pos_dont_raise
58 assert_nothing_raised { @seq.patscan("N", pos) }
62 def test_BackTrack_patscan_with_bad_mis_raises
64 assert_raise(BackTrackError) { @seq.patscan("N", 0, mis) }
68 def test_BackTrack_patscan_with_OK_mis_dont_raise
70 assert_nothing_raised { @seq.patscan("N", 0, mis) }
74 def test_BackTrack_patscan_with_bad_ins_raises
76 assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, ins) }
80 def test_BackTrack_patscan_with_OK_ins_dont_raise
82 assert_nothing_raised { @seq.patscan("N", 0, 0, ins) }
86 def test_BackTrack_patscan_with_bad_del_raises
88 assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, 0, del) }
92 def test_BackTrack_patscan_with_OK_del_dont_raise
94 assert_nothing_raised { @seq.patscan("N", 0, 0, 0, del) }
98 def test_BackTrack_patscan_perfect_left_is_ok
99 assert_equal("0:7:tacgatg", @seq.patscan("TACGATG").first.to_s)
102 def test_BackTrack_patscan_perfect_right_is_ok
103 assert_equal("13:7:tgcacgg", @seq.patscan("TGCACGG").first.to_s)
106 def test_BackTrack_patscan_ambiguity_is_ok
107 assert_equal("13:7:tgcacgg", @seq.patscan("TGCACNN").first.to_s)
110 def test_BackTrack_patscan_pos_is_ok
111 assert_equal("10:1:g", @seq.patscan("N", 10).first.to_s)
112 assert_equal("19:1:g", @seq.patscan("N", 10).last.to_s)
115 def test_BackTrack_patscan_mis_left_is_ok
116 assert_equal("0:7:tacgatg", @seq.patscan("Aacgatg", 0, 1).first.to_s)
119 def test_BackTrack_patscan_mis_right_is_ok
120 assert_equal("13:7:tgcacgg", @seq.patscan("tgcacgA", 0, 1).first.to_s)
123 def test_BackTrack_patscan_ins_left_is_ok
124 assert_equal("0:7:tacgatg", @seq.patscan("Atacgatg", 0, 0, 1).first.to_s)
127 def test_BackTrack_patscan_ins_right_is_ok
128 assert_equal("13:7:tgcacgg", @seq.patscan("tgcacggA", 0, 0, 1).first.to_s)
131 def test_BackTrack_patscan_del_left_is_ok
132 assert_equal("0:7:tacgatg", @seq.patscan("acgatg", 0, 0, 0, 1).first.to_s)
135 def test_BackTrack_patscan_del_right_is_ok
136 assert_equal("12:8:atgcacgg", @seq.patscan("tgcacgg", 0, 0, 0, 1).first.to_s)
139 def test_BackTrack_patscan_ambiguity_mis_ins_del_all_ok
140 assert_equal("0:20:tacgatgctagcatgcacgg", @seq.patscan("tacatgcNagGatgcCacgg", 0, 1, 1, 1).first.to_s)