2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.datamodel.Sequence;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.JvOptionPane;
31 import org.testng.annotations.BeforeClass;
32 import org.testng.annotations.Test;
34 public class ComparisonTest
37 @BeforeClass(alwaysRun = true)
38 public void setUpJvOptionPane()
40 JvOptionPane.setInteractiveMode(false);
41 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
44 @Test(groups = { "Functional" })
45 public void testIsGap()
47 assertTrue(Comparison.isGap('-'));
48 assertTrue(Comparison.isGap('.'));
49 assertTrue(Comparison.isGap(' '));
50 assertFalse(Comparison.isGap('X'));
51 assertFalse(Comparison.isGap('x'));
52 assertFalse(Comparison.isGap('*'));
53 assertFalse(Comparison.isGap('G'));
57 * Test for isNucleotide is that sequences in a dataset are more than 85%
58 * AGCTU. Test is not case-sensitive and ignores gaps.
60 @Test(groups = { "Functional" })
61 public void testIsNucleotide_sequences()
63 SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
64 assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
66 Comparison.isNucleotide(new SequenceI[][]
67 { new SequenceI[] { seq } }));
69 seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
70 assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
72 seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
73 assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
75 seq = new Sequence("eightyfivepercentgapped",
76 "--agc--tuA--GCPV-a---gct-uA-GC---UV");
77 assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
79 seq = new Sequence("nineypercentgapped",
80 "ag--ct-u-A---GC---g----Vag--c---tuAGCUV");
81 assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
83 seq = new Sequence("allgap", "---------");
84 assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
86 seq = new Sequence("DNA", "ACTugGCCAG");
87 SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
89 * 90% DNA but one protein sequence - expect false
92 Comparison.isNucleotide(new SequenceI[]
93 { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 }));
95 Comparison.isNucleotide(new SequenceI[][]
96 { new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
98 { seq, seq, seq, seq, seq, seq2 } }));
100 * 80% DNA but one protein sequence - Expect false
103 Comparison.isNucleotide(new SequenceI[]
104 { seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 }));
106 Comparison.isNucleotide(new SequenceI[][]
107 { new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
109 { seq, seq, seq, seq, seq2, seq2, null } }));
111 seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
113 assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
115 assertFalse(Comparison.isNucleotide((SequenceI[]) null));
116 assertFalse(Comparison.isNucleotide((SequenceI[][]) null));
120 * Test the percentage identity calculation for two sequences
122 @Test(groups = { "Functional" })
123 public void testPID_includingGaps()
125 String seq1 = "ABCDEFG"; // extra length here is ignored
126 String seq2 = "abcdef";
127 assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
129 // comparison range defaults to length of first sequence
130 seq2 = "abcdefghijklmnopqrstuvwxyz";
131 assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
133 // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
136 int length = seq1.length();
138 // match gap-residue, match gap-gap: 9/10 identical
139 // TODO should gap-gap be included in a PID score? JAL-791
140 assertEquals(90f, Comparison.PID(seq1, seq2, 0, length, true, false),
142 // overloaded version of the method signature above:
143 assertEquals(90f, Comparison.PID(seq1, seq2), 0.001f);
145 // don't match gap-residue, match gap-gap: 7/10 identical
146 // TODO should gap-gap be included in a PID score?
147 assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false),
151 @Test(groups = { "Functional" })
152 public void testIsNucleotide()
154 assertTrue(Comparison.isNucleotide('a'));
155 assertTrue(Comparison.isNucleotide('A'));
156 assertTrue(Comparison.isNucleotide('c'));
157 assertTrue(Comparison.isNucleotide('C'));
158 assertTrue(Comparison.isNucleotide('g'));
159 assertTrue(Comparison.isNucleotide('G'));
160 assertTrue(Comparison.isNucleotide('t'));
161 assertTrue(Comparison.isNucleotide('T'));
162 assertTrue(Comparison.isNucleotide('u'));
163 assertTrue(Comparison.isNucleotide('U'));
164 assertFalse(Comparison.isNucleotide('-'));
165 assertFalse(Comparison.isNucleotide('P'));
169 * Test the percentage identity calculation for two sequences
171 @Test(groups = { "Functional" })
172 public void testPID_ungappedOnly()
174 // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
175 // the extra length of seq1 is ignored
176 String seq1 = "a--b-cdefhr";
177 String seq2 = "a---bcdefg";
178 int length = seq1.length();
181 * As currently coded, 'ungappedOnly' ignores gap-residue but counts
182 * gap-gap. Is this a bug - should gap-gap also be ignored, giving a PID of
185 * Note also there is no variant of the calculation that penalises
186 * gap-residue i.e. counts it as a mismatch. This would give a score of 5/8
187 * (if we ignore gap-gap) or 5/10 (if we count gap-gap as a match).
189 // match gap-residue, match gap-gap: 7/8 identical
190 assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, true, true),
193 // don't match gap-residue with 'ungapped only' - same as above
194 assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, false, true),
198 @Test(groups = { "Functional" })
199 public void testIsNucleotideSequence()
201 assertFalse(Comparison.isNucleotideSequence(null, true));
202 assertTrue(Comparison.isNucleotideSequence("", true));
203 assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", true));
204 assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", false));
205 assertFalse(Comparison.isNucleotideSequence("xAgGcCtTuU", false));
206 assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false));
207 assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true));
208 assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false));
211 @Test(groups = { "Functional" })
212 public void testIsSameResidue()
214 assertTrue(Comparison.isSameResidue('a', 'a', false));
215 assertTrue(Comparison.isSameResidue('a', 'a', true));
216 assertTrue(Comparison.isSameResidue('A', 'a', false));
217 assertTrue(Comparison.isSameResidue('a', 'A', false));
219 assertFalse(Comparison.isSameResidue('a', 'A', true));
220 assertFalse(Comparison.isSameResidue('A', 'a', true));