Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AAFrequencyTest	41	192	11	0.926470692.6%	Show methods

Class AAFrequencyTest

Class AAFrequencyTest	Line # 41	Total Statements 192	Complexity 11	TOTAL Coverage 0.926470692.6%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4444	2.02	1.01	1.0 1.0100%
testCalculate_noProfile() : void   testCalculate_noProfile() : void	5151	33.033	1.01	1.0 1.0100%
testCalculate_withProfile() : void   testCalculate_withProfile() : void	9999	25.025	1.01	1.0 1.0100%
testCalculate_withProfileTiming() : void   testCalculate_withProfileTiming() : void	133133	12.012	2.02	0.0 0.00%
testCompleteConsensus_includeGaps_showLogo() : void   testCompleteConsensus_includeGaps_showLogo() : void	161161	24.024	1.01	1.0 1.0100%
testCompleteConsensus_ignoreGaps_noLogo() : void   testCompleteConsensus_ignoreGaps_noLogo() : void	202202	24.024	1.01	1.0 1.0100%
testExtractProfile() : void   testExtractProfile() : void	241241	16.016	1.01	1.0 1.0100%
testExtractProfile_countGaps() : void   testExtractProfile_countGaps() : void	285285	16.016	1.01	1.0 1.0100%
testExtractCdnaProfile() : void   testExtractCdnaProfile() : void	326326	20.020	1.01	1.0 1.0100%
testExtractCdnaProfile_countGaps() : void   testExtractCdnaProfile_countGaps() : void	371371	20.020	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.16666667	jalview.analysis.AAFrequencyTest.testCalculate_noProfilejalview.analysis.AAFrequencyTest.testCalculate_noProfile	1PASS
	0.12745099	jalview.analysis.AAFrequencyTest.testCalculate_withProfilejalview.analysis.AAFrequencyTest.testCalculate_withProfile	1PASS
	0.12254902	jalview.analysis.AAFrequencyTest.testCompleteConsensus_ignoreGaps_noLogojalview.analysis.AAFrequencyTest.testCompleteConsensus_ignoreGaps_noLogo	1PASS
	0.12254902	jalview.analysis.AAFrequencyTest.testCompleteConsensus_includeGaps_showLogojalview.analysis.AAFrequencyTest.testCompleteConsensus_includeGaps_showLogo	1PASS
	0.10294118	jalview.analysis.AAFrequencyTest.testExtractCdnaProfilejalview.analysis.AAFrequencyTest.testExtractCdnaProfile	1PASS
	0.10294118	jalview.analysis.AAFrequencyTest.testExtractCdnaProfile_countGapsjalview.analysis.AAFrequencyTest.testExtractCdnaProfile_countGaps	1PASS
	0.083333336	jalview.analysis.AAFrequencyTest.testExtractProfilejalview.analysis.AAFrequencyTest.testExtractProfile	1PASS
	0.083333336	jalview.analysis.AAFrequencyTest.testExtractProfile_countGapsjalview.analysis.AAFrequencyTest.testExtractProfile_countGaps	1PASS

 

Source view

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
		92.6% Uncovered Elements: 15 (204) Complexity: 11 Complexity Density: 0.06
41		public class AAFrequencyTest
42		{
43
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
44	1	@BeforeClass(alwaysRun = true)...
45		public void setUpJvOptionPane()
46		{
47	1	JvOptionPane.setInteractiveMode(false);
48	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49		}
50
		100% Uncovered Elements: 0 (33) Complexity: 1 Complexity Density: 0.03 1PASS
51	1	@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
		100% Uncovered Elements: 0 (25) Complexity: 1 Complexity Density: 0.04 1PASS
99	1	@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
		0% Uncovered Elements: 14 (14) Complexity: 2 Complexity Density: 0.17 1PASS
133	0	@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		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
161	1	@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		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
202	1	@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		*/
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
241	1	@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		*/
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
285	1	@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
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
326	1	@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
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
371	1	@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		}