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.ProfileI;
29 import jalview.datamodel.Sequence;
30 import jalview.datamodel.SequenceI;
32 import org.testng.annotations.Test;
34 public class AAFrequencyTest
36 @Test(groups = { "Functional" })
37 public void testCalculate_noProfile()
39 SequenceI seq1 = new Sequence("Seq1", "CAG-T");
40 SequenceI seq2 = new Sequence("Seq2", "CAC-T");
41 SequenceI seq3 = new Sequence("Seq3", "C---G");
42 SequenceI seq4 = new Sequence("Seq4", "CA--t");
43 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
44 ProfileI[] result = new ProfileI[seq1.getLength()];
46 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
49 ProfileI col = result[0];
50 assertEquals(100f, col.getPercentageIdentity(false));
51 assertEquals(100f, col.getPercentageIdentity(true));
52 assertEquals(4, col.getMaxCount());
53 assertEquals("C", col.getModalResidue());
54 assertNull(col.getCounts());
58 assertEquals(75f, col.getPercentageIdentity(false));
59 assertEquals(100f, col.getPercentageIdentity(true));
60 assertEquals(3, col.getMaxCount());
61 assertEquals("A", col.getModalResidue());
63 // col 2 is 50% G 50% C or 25/25 counting gaps
65 assertEquals(25f, col.getPercentageIdentity(false));
66 assertEquals(50f, col.getPercentageIdentity(true));
67 assertEquals(1, col.getMaxCount());
68 assertEquals("CG", col.getModalResidue());
72 assertEquals(0f, col.getPercentageIdentity(false));
73 assertEquals(0f, col.getPercentageIdentity(true));
74 assertEquals(0, col.getMaxCount());
75 assertEquals("", col.getModalResidue());
77 // col 4 is 75% T 25% G
79 assertEquals(75f, col.getPercentageIdentity(false));
80 assertEquals(75f, col.getPercentageIdentity(true));
81 assertEquals(3, col.getMaxCount());
82 assertEquals("T", col.getModalResidue());
85 @Test(groups = { "Functional" })
86 public void testCalculate_withProfile()
88 SequenceI seq1 = new Sequence("Seq1", "CAGT");
89 SequenceI seq2 = new Sequence("Seq2", "CACT");
90 SequenceI seq3 = new Sequence("Seq3", "C--G");
91 SequenceI seq4 = new Sequence("Seq4", "CA-t");
92 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
93 ProfileI[] result = new ProfileI[seq1.getLength()];
95 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
96 ProfileI profile = result[0];
97 assertEquals(4, profile.getCounts().getCount('C'));
98 assertEquals(4, profile.getHeight());
99 assertEquals(4, profile.getNonGapped());
102 assertEquals(3, profile.getCounts().getCount('A'));
103 assertEquals(4, profile.getHeight());
104 assertEquals(3, profile.getNonGapped());
107 assertEquals(1, profile.getCounts().getCount('C'));
108 assertEquals(1, profile.getCounts().getCount('G'));
109 assertEquals(4, profile.getHeight());
110 assertEquals(2, profile.getNonGapped());
113 assertEquals(3, profile.getCounts().getCount('T'));
114 assertEquals(1, profile.getCounts().getCount('G'));
115 assertEquals(4, profile.getHeight());
116 assertEquals(4, profile.getNonGapped());
119 @Test(groups = { "Functional" }, enabled = false)
120 public void testCalculate_withProfileTiming()
122 SequenceI seq1 = new Sequence("Seq1", "CAGT");
123 SequenceI seq2 = new Sequence("Seq2", "CACT");
124 SequenceI seq3 = new Sequence("Seq3", "C--G");
125 SequenceI seq4 = new Sequence("Seq4", "CA-t");
126 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
127 ProfileI[] result = new ProfileI[seq1.getLength()];
129 // ensure class loaded and initialized
130 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
132 long start = System.currentTimeMillis();
133 for (int i = 0; i < reps; i++)
135 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
137 System.out.println(System.currentTimeMillis() - start);
141 * Test generation of consensus annotation with options 'include gaps'
142 * (profile percentages are of all sequences, whether gapped or not), and
143 * 'show logo' (the full profile with all residue percentages is reported in
144 * the description for the tooltip)
146 @Test(groups = { "Functional" })
147 public void testCompleteConsensus_includeGaps_showLogo()
150 * first compute the profiles
152 SequenceI seq1 = new Sequence("Seq1", "CAG-T");
153 SequenceI seq2 = new Sequence("Seq2", "CAC-T");
154 SequenceI seq3 = new Sequence("Seq3", "C---G");
155 SequenceI seq4 = new Sequence("Seq4", "CA--t");
156 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
157 ProfileI[] profiles = new ProfileI[seq1.getLength()];
158 AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
160 AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
161 "PID", new Annotation[seq1.getLength()]);
163 .completeConsensus(consensus, profiles, 0, 5, false, true, 4);
165 Annotation ann = consensus.annotations[0];
166 assertEquals("C 100%", ann.description);
167 assertEquals("C", ann.displayCharacter);
168 ann = consensus.annotations[1];
169 assertEquals("A 75%", ann.description);
170 assertEquals("A", ann.displayCharacter);
171 ann = consensus.annotations[2];
172 assertEquals("C 25%; G 25%", ann.description);
173 assertEquals("+", ann.displayCharacter);
174 ann = consensus.annotations[3];
175 assertEquals("", ann.description);
176 assertEquals("-", ann.displayCharacter);
177 ann = consensus.annotations[4];
178 assertEquals("T 75%; G 25%", ann.description);
179 assertEquals("T", ann.displayCharacter);
183 * Test generation of consensus annotation with options 'ignore gaps' (profile
184 * percentages are of the non-gapped sequences) and 'no logo' (only the modal
185 * residue[s] percentage is reported in the description for the tooltip)
187 @Test(groups = { "Functional" })
188 public void testCompleteConsensus_ignoreGaps_noLogo()
191 * first compute the profiles
193 SequenceI seq1 = new Sequence("Seq1", "CAG-T");
194 SequenceI seq2 = new Sequence("Seq2", "CAC-T");
195 SequenceI seq3 = new Sequence("Seq3", "C---G");
196 SequenceI seq4 = new Sequence("Seq4", "CA--t");
197 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
198 ProfileI[] profiles = new ProfileI[seq1.getLength()];
199 AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
201 AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
202 "PID", new Annotation[seq1.getLength()]);
204 .completeConsensus(consensus, profiles, 0, 5, true, false, 4);
206 Annotation ann = consensus.annotations[0];
207 assertEquals("C 100%", ann.description);
208 assertEquals("C", ann.displayCharacter);
209 ann = consensus.annotations[1];
210 assertEquals("A 100%", ann.description);
211 assertEquals("A", ann.displayCharacter);
212 ann = consensus.annotations[2];
213 assertEquals("[CG] 50%", ann.description);
214 assertEquals("+", ann.displayCharacter);
215 ann = consensus.annotations[3];
216 assertEquals("", ann.description);
217 assertEquals("-", ann.displayCharacter);
218 ann = consensus.annotations[4];
219 assertEquals("T 75%", ann.description);
220 assertEquals("T", ann.displayCharacter);