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.
21 package jalview.analysis;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertNull;
26 import jalview.datamodel.AlignmentAnnotation;
27 import jalview.datamodel.Annotation;
28 import jalview.datamodel.Sequence;
29 import jalview.datamodel.SequenceI;
31 import org.testng.annotations.Test;
33 public class AAFrequencyTest
35 @Test(groups = { "Functional" })
36 public void testCalculate_noProfile()
38 SequenceI seq1 = new Sequence("Seq1", "CAG-T");
39 SequenceI seq2 = new Sequence("Seq2", "CAC-T");
40 SequenceI seq3 = new Sequence("Seq3", "C---G");
41 SequenceI seq4 = new Sequence("Seq4", "CA--t");
42 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
43 Profile[] result = new Profile[seq1.getLength()];
45 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
48 Profile col = result[0];
49 assertEquals(100f, col.getPercentageIdentity(false));
50 assertEquals(100f, col.getPercentageIdentity(true));
51 assertEquals(4, col.getMaxCount());
52 assertEquals("C", col.getModalResidue());
53 assertNull(col.getCounts());
57 assertEquals(75f, col.getPercentageIdentity(false));
58 assertEquals(100f, col.getPercentageIdentity(true));
59 assertEquals(3, col.getMaxCount());
60 assertEquals("A", col.getModalResidue());
62 // col 2 is 50% G 50% C or 25/25 counting gaps
64 assertEquals(25f, col.getPercentageIdentity(false));
65 assertEquals(50f, col.getPercentageIdentity(true));
66 assertEquals(1, col.getMaxCount());
67 assertEquals("CG", col.getModalResidue());
71 assertEquals(0f, col.getPercentageIdentity(false));
72 assertEquals(0f, col.getPercentageIdentity(true));
73 assertEquals(0, col.getMaxCount());
74 assertEquals("", col.getModalResidue());
76 // col 4 is 75% T 25% G
78 assertEquals(75f, col.getPercentageIdentity(false));
79 assertEquals(75f, col.getPercentageIdentity(true));
80 assertEquals(3, col.getMaxCount());
81 assertEquals("T", col.getModalResidue());
84 @Test(groups = { "Functional" })
85 public void testCalculate_withProfile()
87 SequenceI seq1 = new Sequence("Seq1", "CAGT");
88 SequenceI seq2 = new Sequence("Seq2", "CACT");
89 SequenceI seq3 = new Sequence("Seq3", "C--G");
90 SequenceI seq4 = new Sequence("Seq4", "CA-t");
91 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
92 Profile[] result = new Profile[seq1.getLength()];
94 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
95 Profile profile = result[0];
96 assertEquals(4, profile.getCounts().getCount('C'));
97 assertEquals(4, profile.getHeight());
98 assertEquals(4, profile.getNonGapped());
101 assertEquals(3, profile.getCounts().getCount('A'));
102 assertEquals(4, profile.getHeight());
103 assertEquals(3, profile.getNonGapped());
106 assertEquals(1, profile.getCounts().getCount('C'));
107 assertEquals(1, profile.getCounts().getCount('G'));
108 assertEquals(4, profile.getHeight());
109 assertEquals(2, profile.getNonGapped());
112 assertEquals(3, profile.getCounts().getCount('T'));
113 assertEquals(1, profile.getCounts().getCount('G'));
114 assertEquals(4, profile.getHeight());
115 assertEquals(4, profile.getNonGapped());
118 @Test(groups = { "Functional" }, enabled = false)
119 public void testCalculate_withProfileTiming()
121 SequenceI seq1 = new Sequence("Seq1", "CAGT");
122 SequenceI seq2 = new Sequence("Seq2", "CACT");
123 SequenceI seq3 = new Sequence("Seq3", "C--G");
124 SequenceI seq4 = new Sequence("Seq4", "CA-t");
125 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
126 Profile[] result = new Profile[seq1.getLength()];
128 // ensure class loaded and initialized
129 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
131 long start = System.currentTimeMillis();
132 for (int i = 0; i < reps; i++)
134 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
136 System.out.println(System.currentTimeMillis() - start);
140 * Test generation of consensus annotation with options 'include gaps'
141 * (profile percentages are of all sequences, whether gapped or not), and
142 * 'show logo' (the full profile with all residue percentages is reported in
143 * the description for the tooltip)
145 @Test(groups = { "Functional" })
146 public void testCompleteConsensus_includeGaps_showLogo()
149 * first compute the profiles
151 SequenceI seq1 = new Sequence("Seq1", "CAG-T");
152 SequenceI seq2 = new Sequence("Seq2", "CAC-T");
153 SequenceI seq3 = new Sequence("Seq3", "C---G");
154 SequenceI seq4 = new Sequence("Seq4", "CA--t");
155 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
156 Profile[] profiles = new Profile[seq1.getLength()];
157 AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
159 AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
160 "PID", new Annotation[seq1.getLength()]);
162 .completeConsensus(consensus, profiles, 0, 5, false, true, 4);
164 Annotation ann = consensus.annotations[0];
165 assertEquals("C 100%", ann.description);
166 assertEquals("C", ann.displayCharacter);
167 ann = consensus.annotations[1];
168 assertEquals("A 75%", ann.description);
169 assertEquals("A", ann.displayCharacter);
170 ann = consensus.annotations[2];
171 assertEquals("C 25%; G 25%", ann.description);
172 assertEquals("+", ann.displayCharacter);
173 ann = consensus.annotations[3];
174 assertEquals("", ann.description);
175 assertEquals("-", ann.displayCharacter);
176 ann = consensus.annotations[4];
177 assertEquals("T 75%; G 25%", ann.description);
178 assertEquals("T", ann.displayCharacter);
182 * Test generation of consensus annotation with options 'ignore gaps' (profile
183 * percentages are of the non-gapped sequences) and 'no logo' (only the modal
184 * residue[s] percentage is reported in the description for the tooltip)
186 @Test(groups = { "Functional" })
187 public void testCompleteConsensus_ignoreGaps_noLogo()
190 * first compute the profiles
192 SequenceI seq1 = new Sequence("Seq1", "CAG-T");
193 SequenceI seq2 = new Sequence("Seq2", "CAC-T");
194 SequenceI seq3 = new Sequence("Seq3", "C---G");
195 SequenceI seq4 = new Sequence("Seq4", "CA--t");
196 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
197 Profile[] profiles = new Profile[seq1.getLength()];
198 AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
200 AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
201 "PID", new Annotation[seq1.getLength()]);
203 .completeConsensus(consensus, profiles, 0, 5, true, false, 4);
205 Annotation ann = consensus.annotations[0];
206 assertEquals("C 100%", ann.description);
207 assertEquals("C", ann.displayCharacter);
208 ann = consensus.annotations[1];
209 assertEquals("A 100%", ann.description);
210 assertEquals("A", ann.displayCharacter);
211 ann = consensus.annotations[2];
212 assertEquals("[CG] 50%", ann.description);
213 assertEquals("+", ann.displayCharacter);
214 ann = consensus.annotations[3];
215 assertEquals("", ann.description);
216 assertEquals("-", ann.displayCharacter);
217 ann = consensus.annotations[4];
218 assertEquals("T 75%", ann.description);
219 assertEquals("T", ann.displayCharacter);