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 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
30 require 'maasha/seq/backtrack'
36 class BackTrackTest < Test::Unit::TestCase
39 # 01234567890123456789
40 @seq = Seq.new("test", "tacgatgctagcatgcacgg")
43 def test_BackTrack_patscan_with_bad_pattern_raises
44 ["", "X", "1"].each { |pattern|
45 assert_raise(BackTrackError) { @seq.patscan(pattern) }
49 def test_BackTrack_patscan_with_OK_pattern_dont_raise
50 ["N", "atcg"].each { |pattern|
51 assert_nothing_raised { @seq.patscan(pattern) }
55 def test_BackTrack_patscan_with_bad_pos_raises
57 assert_raise(BackTrackError) { @seq.patscan("N", pos) }
61 def test_BackTrack_patscan_with_OK_pos_dont_raise
63 assert_nothing_raised { @seq.patscan("N", pos) }
67 def test_BackTrack_patscan_with_bad_mis_raises
69 assert_raise(BackTrackError) { @seq.patscan("N", 0, mis) }
73 def test_BackTrack_patscan_with_OK_mis_dont_raise
75 assert_nothing_raised { @seq.patscan("N", 0, mis) }
79 def test_BackTrack_patscan_with_bad_ins_raises
81 assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, ins) }
85 def test_BackTrack_patscan_with_OK_ins_dont_raise
87 assert_nothing_raised { @seq.patscan("N", 0, 0, ins) }
91 def test_BackTrack_patscan_with_bad_del_raises
93 assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, 0, del) }
97 def test_BackTrack_patscan_with_OK_del_dont_raise
99 assert_nothing_raised { @seq.patscan("N", 0, 0, 0, del) }
103 def test_BackTrack_patscan_perfect_left_is_ok
104 assert_equal("0:7:tacgatg", @seq.patscan("TACGATG").first.to_s)
107 def test_BackTrack_patscan_perfect_right_is_ok
108 assert_equal("13:7:tgcacgg", @seq.patscan("TGCACGG").first.to_s)
111 def test_BackTrack_patscan_ambiguity_is_ok
112 assert_equal("13:7:tgcacgg", @seq.patscan("TGCACNN").first.to_s)
115 def test_BackTrack_patscan_pos_is_ok
116 assert_equal("10:1:g", @seq.patscan("N", 10).first.to_s)
117 assert_equal("19:1:g", @seq.patscan("N", 10).last.to_s)
120 def test_BackTrack_patscan_mis_left_is_ok
121 assert_equal("0:7:tacgatg", @seq.patscan("Aacgatg", 0, 1).first.to_s)
124 def test_BackTrack_patscan_mis_right_is_ok
125 assert_equal("13:7:tgcacgg", @seq.patscan("tgcacgA", 0, 1).first.to_s)
128 def test_BackTrack_patscan_ins_left_is_ok
129 assert_equal("0:7:tacgatg", @seq.patscan("Atacgatg", 0, 0, 1).first.to_s)
132 def test_BackTrack_patscan_ins_right_is_ok
133 assert_equal("13:7:tgcacgg", @seq.patscan("tgcacggA", 0, 0, 1).first.to_s)
136 def test_BackTrack_patscan_del_left_is_ok
137 assert_equal("0:7:tacgatg", @seq.patscan("acgatg", 0, 0, 0, 1).first.to_s)
140 def test_BackTrack_patscan_del_right_is_ok
141 assert_equal("12:8:atgcacgg", @seq.patscan("tgcacgg", 0, 0, 0, 1).first.to_s)
144 def test_BackTrack_patscan_ambiguity_mis_ins_del_all_ok
145 assert_equal("0:20:tacgatgctagcatgcacgg", @seq.patscan("tacatgcNagGatgcCacgg", 0, 1, 1, 1).first.to_s)