Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResidueCountTest	34	242	22	1.0100%	Show methods

Class ResidueCountTest

Class ResidueCountTest	Line # 34	Total Statements 242	Complexity 22	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3737	2.02	1.01	1.0 1.0100%
test_countNucleotide() : void   test_countNucleotide() : void	4747	20.020	1.01	1.0 1.0100%
testAddGap() : void   testAddGap() : void	8080	11.011	1.01	1.0 1.0100%
testOverflow() : void   testOverflow() : void	9797	26.026	1.01	1.0 1.0100%
test_countPeptide() : void   test_countPeptide() : void	142142	17.017	1.01	1.0 1.0100%
test_unexpectedPeptide() : void   test_unexpectedPeptide() : void	166166	14.014	3.03	1.0 1.0100%
test_unexpectedNucleotide() : void   test_unexpectedNucleotide() : void	191191	11.011	3.03	1.0 1.0100%
testGetModalCount() : void   testGetModalCount() : void	213213	23.023	1.01	1.0 1.0100%
testGetResiduesForCount() : void   testGetResiduesForCount() : void	247247	47.047	1.01	1.0 1.0100%
testGetSymbolCounts_nucleotide() : void   testGetSymbolCounts_nucleotide() : void	309309	16.016	1.01	1.0 1.0100%
testGetSymbolCounts_peptide() : void   testGetSymbolCounts_peptide() : void	335335	15.015	1.01	1.0 1.0100%
testToString() : void   testToString() : void	358358	10.010	1.01	1.0 1.0100%
testGetTooltip() : void   testGetTooltip() : void	377377	15.015	5.05	1.0 1.0100%
testPut() : void   testPut() : void	422422	15.015	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.1764706	jalview.datamodel.ResidueCountTest.testGetResiduesForCountjalview.datamodel.ResidueCountTest.testGetResiduesForCount	1PASS
	0.0992647	jalview.datamodel.ResidueCountTest.testOverflowjalview.datamodel.ResidueCountTest.testOverflow	1PASS
	0.0882353	jalview.datamodel.ResidueCountTest.testGetModalCountjalview.datamodel.ResidueCountTest.testGetModalCount	1PASS
	0.0882353	jalview.datamodel.ResidueCountTest.testGetTooltipjalview.datamodel.ResidueCountTest.testGetTooltip	1PASS
	0.07720588	jalview.datamodel.ResidueCountTest.test_countNucleotidejalview.datamodel.ResidueCountTest.test_countNucleotide	1PASS
	0.06985294	jalview.datamodel.ResidueCountTest.test_unexpectedPeptidejalview.datamodel.ResidueCountTest.test_unexpectedPeptide	1PASS
	0.066176474	jalview.datamodel.ResidueCountTest.test_countPeptidejalview.datamodel.ResidueCountTest.test_countPeptide	1PASS
	0.0625	jalview.datamodel.ResidueCountTest.testGetSymbolCounts_nucleotidejalview.datamodel.ResidueCountTest.testGetSymbolCounts_nucleotide	1PASS
	0.05882353	jalview.datamodel.ResidueCountTest.test_unexpectedNucleotidejalview.datamodel.ResidueCountTest.test_unexpectedNucleotide	1PASS
	0.05882353	jalview.datamodel.ResidueCountTest.testGetSymbolCounts_peptidejalview.datamodel.ResidueCountTest.testGetSymbolCounts_peptide	1PASS
	0.05882353	jalview.datamodel.ResidueCountTest.testPutjalview.datamodel.ResidueCountTest.testPut	1PASS
	0.04411765	jalview.datamodel.ResidueCountTest.testAddGapjalview.datamodel.ResidueCountTest.testAddGap	1PASS
	0.040441178	jalview.datamodel.ResidueCountTest.testToStringjalview.datamodel.ResidueCountTest.testToString	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.datamodel;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertTrue;
26
27		import jalview.datamodel.ResidueCount.SymbolCounts;
28		import jalview.gui.JvOptionPane;
29
30		import org.junit.Assert;
31		import org.testng.annotations.BeforeClass;
32		import org.testng.annotations.Test;
33
		100% Uncovered Elements: 0 (272) Complexity: 22 Complexity Density: 0.09
34		public class ResidueCountTest
35		{
36
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
37	1	@BeforeClass(alwaysRun = true)...
38		public void setUpJvOptionPane()
39		{
40	1	JvOptionPane.setInteractiveMode(false);
41	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
42		}
43
44		/**
45		* Test a mix of add and put for nucleotide counting
46		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
47	1	@Test(groups = "Functional")...
48		public void test_countNucleotide()
49		{
50	1	ResidueCount rc = new ResidueCount(true);
51	1	assertEquals(rc.getCount('A'), 0);
52	1	assertEquals(rc.getGapCount(), 0);
53		// add then add
54	1	assertEquals(rc.add('A'), 1);
55	1	assertEquals(rc.add('a'), 2);
56		// put then add
57	1	rc.put('g', 3);
58	1	assertEquals(rc.add('G'), 4);
59		// add then put
60	1	assertEquals(rc.add('c'), 1);
61	1	rc.put('C', 4);
62	1	assertEquals(rc.add('N'), 1);
63
64	1	assertEquals(rc.getCount('a'), 2);
65	1	assertEquals(rc.getCount('A'), 2);
66	1	assertEquals(rc.getCount('G'), 4);
67	1	assertEquals(rc.getCount('c'), 4);
68	1	assertEquals(rc.getCount('T'), 0); // never seen
69	1	assertEquals(rc.getCount('N'), 1);
70	1	assertEquals(rc.getCount('?'), 0);
71	1	assertEquals(rc.getCount('-'), 0);
72
73	1	assertFalse(rc.isCountingInts());
74	1	assertFalse(rc.isUsingOtherData());
75		}
76
77		/**
78		* Test adding to gap count (either using addGap or add)
79		*/
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
80	1	@Test(groups = "Functional")...
81		public void testAddGap()
82		{
83	1	ResidueCount rc = new ResidueCount(true);
84	1	rc.addGap();
85	1	rc.add('-');
86	1	rc.add('.');
87	1	rc.add(' ');
88
89	1	assertEquals(rc.getGapCount(), 4);
90	1	assertEquals(rc.getCount(' '), 4);
91	1	assertEquals(rc.getCount('-'), 4);
92	1	assertEquals(rc.getCount('.'), 4);
93	1	assertFalse(rc.isUsingOtherData());
94	1	assertFalse(rc.isCountingInts());
95		}
96
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
97	1	@Test(groups = "Functional")...
98		public void testOverflow()
99		{
100		/*
101		* overflow from add
102		*/
103	1	ResidueCount rc = new ResidueCount(true);
104	1	rc.addGap();
105	1	rc.put('A', Short.MAX_VALUE - 1);
106	1	assertFalse(rc.isCountingInts());
107	1	rc.add('A');
108	1	assertFalse(rc.isCountingInts());
109	1	rc.add('A');
110	1	assertTrue(rc.isCountingInts());
111	1	assertEquals(rc.getCount('a'), Short.MAX_VALUE + 1);
112	1	rc.add('A');
113	1	assertTrue(rc.isCountingInts());
114	1	assertEquals(rc.getCount('a'), Short.MAX_VALUE + 2);
115	1	assertEquals(rc.getGapCount(), 1);
116	1	rc.addGap();
117	1	assertEquals(rc.getGapCount(), 2);
118
119		/*
120		* overflow from put
121		*/
122	1	rc = new ResidueCount(true);
123	1	rc.put('G', Short.MAX_VALUE + 1);
124	1	assertTrue(rc.isCountingInts());
125	1	assertEquals(rc.getCount('g'), Short.MAX_VALUE + 1);
126	1	rc.put('G', 1);
127	1	assertTrue(rc.isCountingInts());
128	1	assertEquals(rc.getCount('g'), 1);
129
130		/*
131		* underflow from put
132		*/
133	1	rc = new ResidueCount(true);
134	1	rc.put('G', Short.MIN_VALUE - 1);
135	1	assertTrue(rc.isCountingInts());
136	1	assertEquals(rc.getCount('g'), Short.MIN_VALUE - 1);
137		}
138
139		/**
140		* Test a mix of add and put for peptide counting
141		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
142	1	@Test(groups = "Functional")...
143		public void test_countPeptide()
144		{
145	1	ResidueCount rc = new ResidueCount(false);
146	1	rc.put('q', 4);
147	1	rc.add('Q');
148	1	rc.add('X');
149	1	rc.add('x');
150	1	rc.add('W');
151	1	rc.put('w', 7);
152	1	rc.put('m', 12);
153	1	rc.put('M', 13);
154
155	1	assertEquals(rc.getCount('q'), 5);
156	1	assertEquals(rc.getCount('X'), 2);
157	1	assertEquals(rc.getCount('W'), 7);
158	1	assertEquals(rc.getCount('m'), 13);
159	1	assertEquals(rc.getCount('G'), 0);
160	1	assertEquals(rc.getCount('-'), 0);
161
162	1	assertFalse(rc.isCountingInts());
163	1	assertFalse(rc.isUsingOtherData());
164		}
165
		100% Uncovered Elements: 0 (18) Complexity: 3 Complexity Density: 0.21 1PASS
166	1	@Test(groups = "Functional")...
167		public void test_unexpectedPeptide()
168		{
169	1	ResidueCount rc = new ResidueCount(false);
170		// expected characters (upper or lower case):
171	1	String aas = "ACDEFGHIKLMNPQRSTVWXY";
172	1	String lower = aas.toLowerCase();
173	22	for (int i = 0; i < aas.length(); i++)
174		{
175	21	rc.put(aas.charAt(i), i);
176	21	rc.add(lower.charAt(i));
177		}
178	22	for (int i = 0; i < aas.length(); i++)
179		{
180	21	assertEquals(rc.getCount(aas.charAt(i)), i + 1);
181		}
182	1	assertFalse(rc.isUsingOtherData());
183
184	1	rc.put('J', 4);
185	1	assertTrue(rc.isUsingOtherData());
186	1	assertEquals(rc.getCount('J'), 4);
187	1	rc.add('j');
188	1	assertEquals(rc.getCount('J'), 5);
189		}
190
		100% Uncovered Elements: 0 (15) Complexity: 3 Complexity Density: 0.27 1PASS
191	1	@Test(groups = "Functional")...
192		public void test_unexpectedNucleotide()
193		{
194	1	ResidueCount rc = new ResidueCount(true);
195		// expected characters (upper or lower case):
196	1	String nucs = "ACGTUN";
197	1	String lower = nucs.toLowerCase();
198	7	for (int i = 0; i < nucs.length(); i++)
199		{
200	6	rc.put(nucs.charAt(i), i);
201	6	rc.add(lower.charAt(i));
202		}
203	7	for (int i = 0; i < nucs.length(); i++)
204		{
205	6	assertEquals(rc.getCount(nucs.charAt(i)), i + 1);
206		}
207	1	assertFalse(rc.isUsingOtherData());
208
209	1	rc.add('J');
210	1	assertTrue(rc.isUsingOtherData());
211		}
212
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
213	1	@Test(groups = "Functional")...
214		public void testGetModalCount()
215		{
216	1	ResidueCount rc = new ResidueCount(true);
217	1	rc.add('c');
218	1	rc.add('g');
219	1	rc.add('c');
220	1	assertEquals(rc.getModalCount(), 2);
221
222		// modal count is in the 'short overflow' counts
223	1	rc = new ResidueCount();
224	1	rc.add('c');
225	1	rc.put('g', Short.MAX_VALUE);
226	1	rc.add('G');
227	1	assertEquals(rc.getModalCount(), Short.MAX_VALUE + 1);
228
229		// modal count is in the 'other data' counts
230	1	rc = new ResidueCount(false);
231	1	rc.add('Q');
232	1	rc.add('{');
233	1	rc.add('{');
234	1	assertEquals(rc.getModalCount(), 2);
235
236		// verify modal count excludes gap
237	1	rc = new ResidueCount();
238	1	rc.add('Q');
239	1	rc.add('P');
240	1	rc.add('Q');
241	1	rc.addGap();
242	1	rc.addGap();
243	1	rc.addGap();
244	1	assertEquals(rc.getModalCount(), 2);
245		}
246
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
247	1	@Test(groups = "Functional")...
248		public void testGetResiduesForCount()
249		{
250	1	ResidueCount rc = new ResidueCount(true);
251	1	rc.add('c');
252	1	rc.add('g');
253	1	rc.add('c');
254	1	assertEquals(rc.getResiduesForCount(2), "C");
255	1	assertEquals(rc.getResiduesForCount(1), "G");
256	1	assertEquals(rc.getResiduesForCount(3), "");
257	1	assertEquals(rc.getResiduesForCount(0), "");
258	1	assertEquals(rc.getResiduesForCount(-1), "");
259
260		// modal count is in the 'short overflow' counts
261	1	rc = new ResidueCount(true);
262	1	rc.add('c');
263	1	rc.put('g', Short.MAX_VALUE);
264	1	rc.add('G');
265	1	assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "G");
266	1	assertEquals(rc.getResiduesForCount(1), "C");
267
268		// peptide modal count is in the 'short overflow' counts
269	1	rc = new ResidueCount(false);
270	1	rc.add('c');
271	1	rc.put('p', Short.MAX_VALUE);
272	1	rc.add('P');
273	1	assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "P");
274	1	assertEquals(rc.getResiduesForCount(1), "C");
275
276		// modal count is in the 'other data' counts
277	1	rc = new ResidueCount();
278	1	rc.add('Q');
279	1	rc.add('{');
280	1	rc.add('{');
281	1	assertEquals(rc.getResiduesForCount(1), "Q");
282	1	assertEquals(rc.getResiduesForCount(2), "{");
283
284		// residues share modal count
285	1	rc = new ResidueCount();
286	1	rc.add('G');
287	1	rc.add('G');
288	1	rc.add('c');
289	1	rc.add('C');
290	1	rc.add('U');
291	1	assertEquals(rc.getResiduesForCount(1), "U");
292	1	assertEquals(rc.getResiduesForCount(2), "CG");
293
294		// expected and unexpected symbols share modal count
295	1	rc = new ResidueCount();
296	1	rc.add('G');
297	1	rc.add('t');
298	1	rc.add('[');
299	1	rc.add('[');
300	1	rc.add('t');
301	1	rc.add('G');
302	1	rc.add('c');
303	1	rc.add('C');
304	1	rc.add('U');
305	1	assertEquals(rc.getResiduesForCount(1), "U");
306	1	assertEquals(rc.getResiduesForCount(2), "CGT[");
307		}
308
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
309	1	@Test(groups = "Functional")...
310		public void testGetSymbolCounts_nucleotide()
311		{
312	1	ResidueCount rc = new ResidueCount(true);
313	1	rc.add('g');
314	1	rc.add('c');
315	1	rc.add('G');
316	1	rc.add('J'); // 'otherData'
317	1	rc.add('g');
318	1	rc.add('N');
319	1	rc.put('[', 0); // 'otherdata'
320
321	1	SymbolCounts sc = rc.getSymbolCounts();
322	1	Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'J', '[' },
323		sc.symbols);
324	1	Assert.assertArrayEquals(new int[] { 1, 3, 1, 1, 0 }, sc.values);
325
326		// now with overflow to int counts
327	1	rc.put('U', Short.MAX_VALUE);
328	1	rc.add('u');
329	1	sc = rc.getSymbolCounts();
330	1	Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'U', 'J', '[' },
331		sc.symbols);
332	1	Assert.assertArrayEquals(new int[] { 1, 3, 1, 32768, 1, 0 }, sc.values);
333		}
334
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
335	1	@Test(groups = "Functional")...
336		public void testGetSymbolCounts_peptide()
337		{
338	1	ResidueCount rc = new ResidueCount(false);
339	1	rc.add('W');
340	1	rc.add('q');
341	1	rc.add('W');
342	1	rc.add('Z'); // 'otherData'
343	1	rc.add('w');
344	1	rc.add('L');
345
346	1	SymbolCounts sc = rc.getSymbolCounts();
347	1	Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
348	1	Assert.assertArrayEquals(new int[] { 1, 1, 3, 1 }, sc.values);
349
350		// now with overflow to int counts
351	1	rc.put('W', Short.MAX_VALUE);
352	1	rc.add('W');
353	1	sc = rc.getSymbolCounts();
354	1	Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
355	1	Assert.assertArrayEquals(new int[] { 1, 1, 32768, 1 }, sc.values);
356		}
357
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
358	1	@Test(groups = "Functional")...
359		public void testToString()
360		{
361	1	ResidueCount rc = new ResidueCount();
362	1	rc.add('q');
363	1	rc.add('c');
364	1	rc.add('Q');
365	1	assertEquals(rc.toString(), "[ C:1 Q:2 ]");
366
367		// add 'other data'
368	1	rc.add('{');
369	1	assertEquals(rc.toString(), "[ C:1 Q:2 {:1 ]");
370
371		// switch from short to int counting:
372	1	rc.put('G', Short.MAX_VALUE);
373	1	rc.add('g');
374	1	assertEquals(rc.toString(), "[ C:1 G:32768 Q:2 {:1 ]");
375		}
376
		100% Uncovered Elements: 0 (23) Complexity: 5 Complexity Density: 0.33 1PASS
377	1	@Test(groups = "Functional")...
378		public void testGetTooltip()
379		{
380	1	ResidueCount rc = new ResidueCount();
381
382		// no counts!
383	1	assertEquals(rc.getTooltip(20, 1), "");
384
385		/*
386		* count 7 C, 6 K, 7 Q, 10 P, 9 W, 1 F (total 40)
387		*/
388	8	for (int i = 0; i < 7; i++)
389		{
390	7	rc.add('c');
391	7	rc.add('q');
392		}
393	11	for (int i = 0; i < 10; i++)
394		{
395	10	rc.add('p');
396		}
397	10	for (int i = 0; i < 9; i++)
398		{
399	9	rc.add('W');
400		}
401	7	for (int i = 0; i < 6; i++)
402		{
403	6	rc.add('K');
404		}
405	1	rc.add('F');
406
407		/*
408		* percentages are rounded (0.5 rounded up)
409		* 10/40 9/40 7/40 6/40 1/40
410		*/
411	1	assertEquals(rc.getTooltip(40, 0),
412		"P 25%; W 23%; C 18%; Q 18%; K 15%; F 3%");
413
414	1	rc.add('Q');
415		/*
416		* 10/30 9/30 8/30 7/30 6/30 1/30
417		*/
418	1	assertEquals(rc.getTooltip(30, 1),
419		"P 33.3%; W 30.0%; Q 26.7%; C 23.3%; K 20.0%; F 3.3%");
420		}
421
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
422	1	@Test(groups = "Functional")...
423		public void testPut()
424		{
425	1	ResidueCount rc = new ResidueCount();
426	1	rc.put('q', 3);
427	1	assertEquals(rc.getCount('Q'), 3);
428	1	rc.put(' ', 4);
429	1	assertEquals(rc.getGapCount(), 4);
430	1	rc.put('.', 5);
431	1	assertEquals(rc.getGapCount(), 5);
432	1	rc.put('-', 6);
433	1	assertEquals(rc.getGapCount(), 6);
434
435	1	rc.put('?', 5);
436	1	assertEquals(rc.getCount('?'), 5);
437	1	rc.put('?', 6);
438	1	rc.put('!', 7);
439	1	assertEquals(rc.getCount('?'), 6);
440	1	assertEquals(rc.getCount('!'), 7);
441		}
442		}