1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.analysis

File AAFrequencyTest.java

 

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AAFrequencyTest 41 192 11
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Contributing tests

This file is covered by 8 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.analysis;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24    import static org.testng.AssertJUnit.assertNull;
25   
26    import jalview.datamodel.AlignmentAnnotation;
27    import jalview.datamodel.Annotation;
28    import jalview.datamodel.Profile;
29    import jalview.datamodel.ProfileI;
30    import jalview.datamodel.ProfilesI;
31    import jalview.datamodel.ResidueCount;
32    import jalview.datamodel.Sequence;
33    import jalview.datamodel.SequenceI;
34    import jalview.gui.JvOptionPane;
35   
36    import java.util.Hashtable;
37   
38    import org.testng.annotations.BeforeClass;
39    import org.testng.annotations.Test;
40   
 
41    public class AAFrequencyTest
42    {
43   
 
44  1 toggle @BeforeClass(alwaysRun = true)
45    public void setUpJvOptionPane()
46    {
47  1 JvOptionPane.setInteractiveMode(false);
48  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49    }
50   
 
51  1 toggle @Test(groups = { "Functional" })
52    public void testCalculate_noProfile()
53    {
54  1 SequenceI seq1 = new Sequence("Seq1", "CAG-T");
55  1 SequenceI seq2 = new Sequence("Seq2", "CAC-T");
56  1 SequenceI seq3 = new Sequence("Seq3", "C---G");
57  1 SequenceI seq4 = new Sequence("Seq4", "CA--t");
58  1 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
59  1 int width = seq1.getLength();
60  1 ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, false);
61   
62    // col 0 is 100% C
63  1 ProfileI col = result.get(0);
64  1 assertEquals(100f, col.getPercentageIdentity(false));
65  1 assertEquals(100f, col.getPercentageIdentity(true));
66  1 assertEquals(4, col.getMaxCount());
67  1 assertEquals("C", col.getModalResidue());
68  1 assertNull(col.getCounts());
69   
70    // col 1 is 75% A
71  1 col = result.get(1);
72  1 assertEquals(75f, col.getPercentageIdentity(false));
73  1 assertEquals(100f, col.getPercentageIdentity(true));
74  1 assertEquals(3, col.getMaxCount());
75  1 assertEquals("A", col.getModalResidue());
76   
77    // col 2 is 50% G 50% C or 25/25 counting gaps
78  1 col = result.get(2);
79  1 assertEquals(25f, col.getPercentageIdentity(false));
80  1 assertEquals(50f, col.getPercentageIdentity(true));
81  1 assertEquals(1, col.getMaxCount());
82  1 assertEquals("CG", col.getModalResidue());
83   
84    // col 3 is all gaps
85  1 col = result.get(3);
86  1 assertEquals(0f, col.getPercentageIdentity(false));
87  1 assertEquals(0f, col.getPercentageIdentity(true));
88  1 assertEquals(0, col.getMaxCount());
89  1 assertEquals("", col.getModalResidue());
90   
91    // col 4 is 75% T 25% G
92  1 col = result.get(4);
93  1 assertEquals(75f, col.getPercentageIdentity(false));
94  1 assertEquals(75f, col.getPercentageIdentity(true));
95  1 assertEquals(3, col.getMaxCount());
96  1 assertEquals("T", col.getModalResidue());
97    }
98   
 
99  1 toggle @Test(groups = { "Functional" })
100    public void testCalculate_withProfile()
101    {
102  1 SequenceI seq1 = new Sequence("Seq1", "CAGT");
103  1 SequenceI seq2 = new Sequence("Seq2", "CACT");
104  1 SequenceI seq3 = new Sequence("Seq3", "C--G");
105  1 SequenceI seq4 = new Sequence("Seq4", "CA-t");
106  1 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
107  1 int width = seq1.getLength();
108  1 ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, true);
109   
110  1 ProfileI profile = result.get(0);
111  1 assertEquals(4, profile.getCounts().getCount('C'));
112  1 assertEquals(4, profile.getHeight());
113  1 assertEquals(4, profile.getNonGapped());
114   
115  1 profile = result.get(1);
116  1 assertEquals(3, profile.getCounts().getCount('A'));
117  1 assertEquals(4, profile.getHeight());
118  1 assertEquals(3, profile.getNonGapped());
119   
120  1 profile = result.get(2);
121  1 assertEquals(1, profile.getCounts().getCount('C'));
122  1 assertEquals(1, profile.getCounts().getCount('G'));
123  1 assertEquals(4, profile.getHeight());
124  1 assertEquals(2, profile.getNonGapped());
125   
126  1 profile = result.get(3);
127  1 assertEquals(3, profile.getCounts().getCount('T'));
128  1 assertEquals(1, profile.getCounts().getCount('G'));
129  1 assertEquals(4, profile.getHeight());
130  1 assertEquals(4, profile.getNonGapped());
131    }
132   
 
133  0 toggle @Test(groups = { "Functional" }, enabled = false)
134    public void testCalculate_withProfileTiming()
135    {
136  0 SequenceI seq1 = new Sequence("Seq1", "CAGT");
137  0 SequenceI seq2 = new Sequence("Seq2", "CACT");
138  0 SequenceI seq3 = new Sequence("Seq3", "C--G");
139  0 SequenceI seq4 = new Sequence("Seq4", "CA-t");
140  0 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
141   
142    // ensure class loaded and initialised
143  0 int width = seq1.getLength();
144  0 AAFrequency.calculate(seqs, width, 0, width, true);
145   
146  0 int reps = 100000;
147  0 long start = System.currentTimeMillis();
148  0 for (int i = 0; i < reps; i++)
149    {
150  0 AAFrequency.calculate(seqs, width, 0, width, true);
151    }
152  0 System.out.println(System.currentTimeMillis() - start);
153    }
154   
155    /**
156    * Test generation of consensus annotation with options 'include gaps'
157    * (profile percentages are of all sequences, whether gapped or not), and
158    * 'show logo' (the full profile with all residue percentages is reported in
159    * the description for the tooltip)
160    */
 
161  1 toggle @Test(groups = { "Functional" })
162    public void testCompleteConsensus_includeGaps_showLogo()
163    {
164    /*
165    * first compute the profiles
166    */
167  1 SequenceI seq1 = new Sequence("Seq1", "CAG-T");
168  1 SequenceI seq2 = new Sequence("Seq2", "CAC-T");
169  1 SequenceI seq3 = new Sequence("Seq3", "C---G");
170  1 SequenceI seq4 = new Sequence("Seq4", "CA--t");
171  1 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
172  1 int width = seq1.getLength();
173  1 ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
174   
175  1 AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
176    "PID", new Annotation[width]);
177  1 AAFrequency.completeConsensus(consensus, profiles, 0, 5, false, true,
178    4);
179   
180  1 Annotation ann = consensus.annotations[0];
181  1 assertEquals("C 100%", ann.description);
182  1 assertEquals("C", ann.displayCharacter);
183  1 ann = consensus.annotations[1];
184  1 assertEquals("A 75%", ann.description);
185  1 assertEquals("A", ann.displayCharacter);
186  1 ann = consensus.annotations[2];
187  1 assertEquals("C 25%; G 25%", ann.description);
188  1 assertEquals("+", ann.displayCharacter);
189  1 ann = consensus.annotations[3];
190  1 assertEquals("", ann.description);
191  1 assertEquals("-", ann.displayCharacter);
192  1 ann = consensus.annotations[4];
193  1 assertEquals("T 75%; G 25%", ann.description);
194  1 assertEquals("T", ann.displayCharacter);
195    }
196   
197    /**
198    * Test generation of consensus annotation with options 'ignore gaps' (profile
199    * percentages are of the non-gapped sequences) and 'no logo' (only the modal
200    * residue[s] percentage is reported in the description for the tooltip)
201    */
 
202  1 toggle @Test(groups = { "Functional" })
203    public void testCompleteConsensus_ignoreGaps_noLogo()
204    {
205    /*
206    * first compute the profiles
207    */
208  1 SequenceI seq1 = new Sequence("Seq1", "CAG-T");
209  1 SequenceI seq2 = new Sequence("Seq2", "CAC-T");
210  1 SequenceI seq3 = new Sequence("Seq3", "C---G");
211  1 SequenceI seq4 = new Sequence("Seq4", "CA--t");
212  1 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
213  1 int width = seq1.getLength();
214  1 ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
215   
216  1 AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
217    "PID", new Annotation[width]);
218  1 AAFrequency.completeConsensus(consensus, profiles, 0, 5, true, false,
219    4);
220   
221  1 Annotation ann = consensus.annotations[0];
222  1 assertEquals("C 100%", ann.description);
223  1 assertEquals("C", ann.displayCharacter);
224  1 ann = consensus.annotations[1];
225  1 assertEquals("A 100%", ann.description);
226  1 assertEquals("A", ann.displayCharacter);
227  1 ann = consensus.annotations[2];
228  1 assertEquals("[CG] 50%", ann.description);
229  1 assertEquals("+", ann.displayCharacter);
230  1 ann = consensus.annotations[3];
231  1 assertEquals("", ann.description);
232  1 assertEquals("-", ann.displayCharacter);
233  1 ann = consensus.annotations[4];
234  1 assertEquals("T 75%", ann.description);
235  1 assertEquals("T", ann.displayCharacter);
236    }
237   
238    /**
239    * Test to include rounding down of a non-zero count to 0% (JAL-3202)
240    */
 
241  1 toggle @Test(groups = { "Functional" })
242    public void testExtractProfile()
243    {
244    /*
245    * 200 sequences of which 30 gapped (170 ungapped)
246    * max count 70 for modal residue 'G'
247    */
248  1 ProfileI profile = new Profile(200, 30, 70, "G");
249  1 ResidueCount counts = new ResidueCount();
250  1 counts.put('G', 70);
251  1 counts.put('R', 60);
252  1 counts.put('L', 38);
253  1 counts.put('H', 2);
254  1 profile.setCounts(counts);
255   
256    /*
257    * [0, noOfValues, totalPercent, char1, count1, ...]
258    * G: 70/170 = 41.2 = 41
259    * R: 60/170 = 35.3 = 35
260    * L: 38/170 = 22.3 = 22
261    * H: 2/170 = 1
262    * total (rounded) percentages = 99
263    */
264  1 int[] extracted = AAFrequency.extractProfile(profile, true);
265  1 int[] expected = new int[] { 0, 4, 99, 'G', 41, 'R', 35, 'L', 22, 'H',
266    1 };
267  1 org.testng.Assert.assertEquals(extracted, expected);
268   
269    /*
270    * add some counts of 1; these round down to 0% and should be discarded
271    */
272  1 counts.put('G', 68); // 68/170 = 40% exactly (percentages now total 98)
273  1 counts.put('Q', 1);
274  1 counts.put('K', 1);
275  1 extracted = AAFrequency.extractProfile(profile, true);
276  1 expected = new int[] { 0, 4, 98, 'G', 40, 'R', 35, 'L', 22, 'H', 1 };
277  1 org.testng.Assert.assertEquals(extracted, expected);
278   
279    }
280   
281    /**
282    * Tests for the profile calculation where gaps are included i.e. the
283    * denominator is the total number of sequences in the column
284    */
 
285  1 toggle @Test(groups = { "Functional" })
286    public void testExtractProfile_countGaps()
287    {
288    /*
289    * 200 sequences of which 30 gapped (170 ungapped)
290    * max count 70 for modal residue 'G'
291    */
292  1 ProfileI profile = new Profile(200, 30, 70, "G");
293  1 ResidueCount counts = new ResidueCount();
294  1 counts.put('G', 70);
295  1 counts.put('R', 60);
296  1 counts.put('L', 38);
297  1 counts.put('H', 2);
298  1 profile.setCounts(counts);
299   
300    /*
301    * [0, noOfValues, totalPercent, char1, count1, ...]
302    * G: 70/200 = 35%
303    * R: 60/200 = 30%
304    * L: 38/200 = 19%
305    * H: 2/200 = 1%
306    * total (rounded) percentages = 85
307    */
308  1 int[] extracted = AAFrequency.extractProfile(profile, false);
309  1 int[] expected = new int[] { AlignmentAnnotation.SEQUENCE_PROFILE, 4,
310    85, 'G', 35, 'R', 30, 'L', 19, 'H', 1 };
311  1 org.testng.Assert.assertEquals(extracted, expected);
312   
313    /*
314    * add some counts of 1; these round down to 0% and should be discarded
315    */
316  1 counts.put('G', 68); // 68/200 = 34%
317  1 counts.put('Q', 1);
318  1 counts.put('K', 1);
319  1 extracted = AAFrequency.extractProfile(profile, false);
320  1 expected = new int[] { AlignmentAnnotation.SEQUENCE_PROFILE, 4, 84, 'G',
321    34, 'R', 30, 'L', 19, 'H', 1 };
322  1 org.testng.Assert.assertEquals(extracted, expected);
323   
324    }
325   
 
326  1 toggle @Test(groups = { "Functional" })
327    public void testExtractCdnaProfile()
328    {
329    /*
330    * 200 sequences of which 30 gapped (170 ungapped)
331    * max count 70 for modal residue 'G'
332    */
333  1 Hashtable profile = new Hashtable();
334   
335    /*
336    * cdna profile is {seqCount, ungappedCount, codonCount1, ...codonCount64}
337    * where 1..64 positions correspond to encoded codons
338    * see CodingUtils.encodeCodon()
339    */
340  1 int[] codonCounts = new int[66];
341  1 char[] codon1 = new char[] { 'G', 'C', 'A' };
342  1 char[] codon2 = new char[] { 'c', 'C', 'A' };
343  1 char[] codon3 = new char[] { 't', 'g', 'A' };
344  1 char[] codon4 = new char[] { 'G', 'C', 't' };
345  1 int encoded1 = CodingUtils.encodeCodon(codon1);
346  1 int encoded2 = CodingUtils.encodeCodon(codon2);
347  1 int encoded3 = CodingUtils.encodeCodon(codon3);
348  1 int encoded4 = CodingUtils.encodeCodon(codon4);
349  1 codonCounts[2 + encoded1] = 30;
350  1 codonCounts[2 + encoded2] = 70;
351  1 codonCounts[2 + encoded3] = 9;
352  1 codonCounts[2 + encoded4] = 1;
353  1 codonCounts[0] = 120;
354  1 codonCounts[1] = 110;
355  1 profile.put(AAFrequency.PROFILE, codonCounts);
356   
357    /*
358    * [0, noOfValues, totalPercent, char1, count1, ...]
359    * codon1: 30/110 = 27.2 = 27%
360    * codon2: 70/110 = 63.6% = 63%
361    * codon3: 9/110 = 8.1% = 8%
362    * codon4: 1/110 = 0.9% = 0% should be discarded
363    * total (rounded) percentages = 98
364    */
365  1 int[] extracted = AAFrequency.extractCdnaProfile(profile, true);
366  1 int[] expected = new int[] { AlignmentAnnotation.CDNA_PROFILE, 3, 98,
367    encoded2, 63, encoded1, 27, encoded3, 8 };
368  1 org.testng.Assert.assertEquals(extracted, expected);
369    }
370   
 
371  1 toggle @Test(groups = { "Functional" })
372    public void testExtractCdnaProfile_countGaps()
373    {
374    /*
375    * 200 sequences of which 30 gapped (170 ungapped)
376    * max count 70 for modal residue 'G'
377    */
378  1 Hashtable profile = new Hashtable();
379   
380    /*
381    * cdna profile is {seqCount, ungappedCount, codonCount1, ...codonCount64}
382    * where 1..64 positions correspond to encoded codons
383    * see CodingUtils.encodeCodon()
384    */
385  1 int[] codonCounts = new int[66];
386  1 char[] codon1 = new char[] { 'G', 'C', 'A' };
387  1 char[] codon2 = new char[] { 'c', 'C', 'A' };
388  1 char[] codon3 = new char[] { 't', 'g', 'A' };
389  1 char[] codon4 = new char[] { 'G', 'C', 't' };
390  1 int encoded1 = CodingUtils.encodeCodon(codon1);
391  1 int encoded2 = CodingUtils.encodeCodon(codon2);
392  1 int encoded3 = CodingUtils.encodeCodon(codon3);
393  1 int encoded4 = CodingUtils.encodeCodon(codon4);
394  1 codonCounts[2 + encoded1] = 30;
395  1 codonCounts[2 + encoded2] = 70;
396  1 codonCounts[2 + encoded3] = 9;
397  1 codonCounts[2 + encoded4] = 1;
398  1 codonCounts[0] = 120;
399  1 codonCounts[1] = 110;
400  1 profile.put(AAFrequency.PROFILE, codonCounts);
401   
402    /*
403    * [0, noOfValues, totalPercent, char1, count1, ...]
404    * codon1: 30/120 = 25%
405    * codon2: 70/120 = 58.3 = 58%
406    * codon3: 9/120 = 7.5 = 7%
407    * codon4: 1/120 = 0.8 = 0% should be discarded
408    * total (rounded) percentages = 90
409    */
410  1 int[] extracted = AAFrequency.extractCdnaProfile(profile, false);
411  1 int[] expected = new int[] { AlignmentAnnotation.CDNA_PROFILE, 3, 90,
412    encoded2, 58, encoded1, 25, encoded3, 7 };
413  1 org.testng.Assert.assertEquals(extracted, expected);
414    }
415    }