Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResidueCountTest	36	253	22	1.0100%	Show methods

Class ResidueCountTest

Class ResidueCountTest	Line # 36	Total Statements 253	Complexity 22	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3939	2.02	1.01	1.0 1.0100%
test_countNucleotide() : void   test_countNucleotide() : void	4949	20.020	1.01	1.0 1.0100%
testAddGap() : void   testAddGap() : void	8282	22.022	1.01	1.0 1.0100%
testOverflow() : void   testOverflow() : void	111111	26.026	1.01	1.0 1.0100%
test_countPeptide() : void   test_countPeptide() : void	156156	17.017	1.01	1.0 1.0100%
test_unexpectedPeptide() : void   test_unexpectedPeptide() : void	180180	14.014	3.03	1.0 1.0100%
test_unexpectedNucleotide() : void   test_unexpectedNucleotide() : void	205205	11.011	3.03	1.0 1.0100%
testGetModalCount() : void   testGetModalCount() : void	227227	23.023	1.01	1.0 1.0100%
testGetResiduesForCount() : void   testGetResiduesForCount() : void	261261	47.047	1.01	1.0 1.0100%
testGetSymbolCounts_nucleotide() : void   testGetSymbolCounts_nucleotide() : void	323323	16.016	1.01	1.0 1.0100%
testGetSymbolCounts_peptide() : void   testGetSymbolCounts_peptide() : void	349349	15.015	1.01	1.0 1.0100%
testToString() : void   testToString() : void	372372	10.010	1.01	1.0 1.0100%
testGetTooltip() : void   testGetTooltip() : void	391391	15.015	5.05	1.0 1.0100%
testPut() : void   testPut() : void	436436	15.015	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.1696113	jalview.datamodel.ResidueCountTest.testGetResiduesForCountjalview.datamodel.ResidueCountTest.testGetResiduesForCount	1PASS
	0.09540636	jalview.datamodel.ResidueCountTest.testOverflowjalview.datamodel.ResidueCountTest.testOverflow	1PASS
	0.08480565	jalview.datamodel.ResidueCountTest.testGetTooltipjalview.datamodel.ResidueCountTest.testGetTooltip	1PASS
	0.08480565	jalview.datamodel.ResidueCountTest.testGetModalCountjalview.datamodel.ResidueCountTest.testGetModalCount	1PASS
	0.08127209	jalview.datamodel.ResidueCountTest.testAddGapjalview.datamodel.ResidueCountTest.testAddGap	1PASS
	0.074204944	jalview.datamodel.ResidueCountTest.test_countNucleotidejalview.datamodel.ResidueCountTest.test_countNucleotide	1PASS
	0.06713781	jalview.datamodel.ResidueCountTest.test_unexpectedPeptidejalview.datamodel.ResidueCountTest.test_unexpectedPeptide	1PASS
	0.06360424	jalview.datamodel.ResidueCountTest.test_countPeptidejalview.datamodel.ResidueCountTest.test_countPeptide	1PASS
	0.06007067	jalview.datamodel.ResidueCountTest.testGetSymbolCounts_nucleotidejalview.datamodel.ResidueCountTest.testGetSymbolCounts_nucleotide	1PASS
	0.056537103	jalview.datamodel.ResidueCountTest.testGetSymbolCounts_peptidejalview.datamodel.ResidueCountTest.testGetSymbolCounts_peptide	1PASS
	0.056537103	jalview.datamodel.ResidueCountTest.testPutjalview.datamodel.ResidueCountTest.testPut	1PASS
	0.056537103	jalview.datamodel.ResidueCountTest.test_unexpectedNucleotidejalview.datamodel.ResidueCountTest.test_unexpectedNucleotide	1PASS
	0.038869258	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 java.util.Locale;
24
25		import static org.testng.Assert.assertEquals;
26		import static org.testng.Assert.assertFalse;
27		import static org.testng.Assert.assertTrue;
28
29		import jalview.datamodel.ResidueCount.SymbolCounts;
30		import jalview.gui.JvOptionPane;
31
32		import org.junit.Assert;
33		import org.testng.annotations.BeforeClass;
34		import org.testng.annotations.Test;
35
		100% Uncovered Elements: 0 (283) Complexity: 22 Complexity Density: 0.09
36		public class ResidueCountTest
37		{
38
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
39	1	@BeforeClass(alwaysRun = true)...
40		public void setUpJvOptionPane()
41		{
42	1	JvOptionPane.setInteractiveMode(false);
43	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
44		}
45
46		/**
47		* Test a mix of add and put for nucleotide counting
48		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
49	1	@Test(groups = "Functional")...
50		public void test_countNucleotide()
51		{
52	1	ResidueCount rc = new ResidueCount(true);
53	1	assertEquals(rc.getCount('A'), 0);
54	1	assertEquals(rc.getGapCount(), 0);
55		// add then add
56	1	assertEquals(rc.add('A'), 1);
57	1	assertEquals(rc.add('a'), 2);
58		// put then add
59	1	rc.put('g', 3);
60	1	assertEquals(rc.add('G'), 4);
61		// add then put
62	1	assertEquals(rc.add('c'), 1);
63	1	rc.put('C', 4);
64	1	assertEquals(rc.add('N'), 1);
65
66	1	assertEquals(rc.getCount('a'), 2);
67	1	assertEquals(rc.getCount('A'), 2);
68	1	assertEquals(rc.getCount('G'), 4);
69	1	assertEquals(rc.getCount('c'), 4);
70	1	assertEquals(rc.getCount('T'), 0); // never seen
71	1	assertEquals(rc.getCount('N'), 1);
72	1	assertEquals(rc.getCount('?'), 0);
73	1	assertEquals(rc.getCount('-'), 0);
74
75	1	assertFalse(rc.isCountingInts());
76	1	assertFalse(rc.isUsingOtherData());
77		}
78
79		/**
80		* Test adding to gap count (either using addGap or add)
81		*/
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
82	1	@Test(groups = "Functional")...
83		public void testAddGap()
84		{
85	1	ResidueCount rc = new ResidueCount(true);
86	1	rc.addGap();
87	1	rc.add('-');
88	1	rc.add('.');
89	1	rc.add(' ');
90
91	1	assertEquals(rc.getGapCount(), 4);
92	1	assertEquals(rc.getCount(' '), 4);
93	1	assertEquals(rc.getCount('-'), 4);
94	1	assertEquals(rc.getCount('.'), 4);
95	1	assertFalse(rc.isUsingOtherData());
96	1	assertFalse(rc.isCountingInts());
97
98	1	rc.set(ResidueCount.GAP_COUNT, Short.MAX_VALUE - 2);
99	1	assertEquals(rc.getGapCount(), Short.MAX_VALUE - 2);
100	1	assertFalse(rc.isCountingInts());
101	1	rc.addGap();
102	1	assertEquals(rc.getGapCount(), Short.MAX_VALUE - 1);
103	1	assertFalse(rc.isCountingInts());
104	1	rc.addGap();
105	1	assertEquals(rc.getGapCount(), Short.MAX_VALUE);
106	1	rc.addGap();
107	1	assertTrue(rc.isCountingInts());
108	1	assertEquals(rc.getGapCount(), Short.MAX_VALUE + 1);
109		}
110
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
111	1	@Test(groups = "Functional")...
112		public void testOverflow()
113		{
114		/*
115		* overflow from add
116		*/
117	1	ResidueCount rc = new ResidueCount(true);
118	1	rc.addGap();
119	1	rc.put('A', Short.MAX_VALUE - 1);
120	1	assertFalse(rc.isCountingInts());
121	1	rc.add('A');
122	1	assertFalse(rc.isCountingInts());
123	1	rc.add('A');
124	1	assertTrue(rc.isCountingInts());
125	1	assertEquals(rc.getCount('a'), Short.MAX_VALUE + 1);
126	1	rc.add('A');
127	1	assertTrue(rc.isCountingInts());
128	1	assertEquals(rc.getCount('a'), Short.MAX_VALUE + 2);
129	1	assertEquals(rc.getGapCount(), 1);
130	1	rc.addGap();
131	1	assertEquals(rc.getGapCount(), 2);
132
133		/*
134		* overflow from put
135		*/
136	1	rc = new ResidueCount(true);
137	1	rc.put('G', Short.MAX_VALUE + 1);
138	1	assertTrue(rc.isCountingInts());
139	1	assertEquals(rc.getCount('g'), Short.MAX_VALUE + 1);
140	1	rc.put('G', 1);
141	1	assertTrue(rc.isCountingInts());
142	1	assertEquals(rc.getCount('g'), 1);
143
144		/*
145		* underflow from put
146		*/
147	1	rc = new ResidueCount(true);
148	1	rc.put('G', Short.MIN_VALUE - 1);
149	1	assertTrue(rc.isCountingInts());
150	1	assertEquals(rc.getCount('g'), Short.MIN_VALUE - 1);
151		}
152
153		/**
154		* Test a mix of add and put for peptide counting
155		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
156	1	@Test(groups = "Functional")...
157		public void test_countPeptide()
158		{
159	1	ResidueCount rc = new ResidueCount(false);
160	1	rc.put('q', 4);
161	1	rc.add('Q');
162	1	rc.add('X');
163	1	rc.add('x');
164	1	rc.add('W');
165	1	rc.put('w', 7);
166	1	rc.put('m', 12);
167	1	rc.put('M', 13);
168
169	1	assertEquals(rc.getCount('q'), 5);
170	1	assertEquals(rc.getCount('X'), 2);
171	1	assertEquals(rc.getCount('W'), 7);
172	1	assertEquals(rc.getCount('m'), 13);
173	1	assertEquals(rc.getCount('G'), 0);
174	1	assertEquals(rc.getCount('-'), 0);
175
176	1	assertFalse(rc.isCountingInts());
177	1	assertFalse(rc.isUsingOtherData());
178		}
179
		100% Uncovered Elements: 0 (18) Complexity: 3 Complexity Density: 0.21 1PASS
180	1	@Test(groups = "Functional")...
181		public void test_unexpectedPeptide()
182		{
183	1	ResidueCount rc = new ResidueCount(false);
184		// expected characters (upper or lower case):
185	1	String aas = "ACDEFGHIKLMNPQRSTVWXY";
186	1	String lower = aas.toLowerCase(Locale.ROOT);
187	22	for (int i = 0; i < aas.length(); i++)
188		{
189	21	rc.put(aas.charAt(i), i);
190	21	rc.add(lower.charAt(i));
191		}
192	22	for (int i = 0; i < aas.length(); i++)
193		{
194	21	assertEquals(rc.getCount(aas.charAt(i)), i + 1);
195		}
196	1	assertFalse(rc.isUsingOtherData());
197
198	1	rc.put('J', 4);
199	1	assertTrue(rc.isUsingOtherData());
200	1	assertEquals(rc.getCount('J'), 4);
201	1	rc.add('j');
202	1	assertEquals(rc.getCount('J'), 5);
203		}
204
		100% Uncovered Elements: 0 (15) Complexity: 3 Complexity Density: 0.27 1PASS
205	1	@Test(groups = "Functional")...
206		public void test_unexpectedNucleotide()
207		{
208	1	ResidueCount rc = new ResidueCount(true);
209		// expected characters (upper or lower case):
210	1	String nucs = "ACGTUN";
211	1	String lower = nucs.toLowerCase(Locale.ROOT);
212	7	for (int i = 0; i < nucs.length(); i++)
213		{
214	6	rc.put(nucs.charAt(i), i);
215	6	rc.add(lower.charAt(i));
216		}
217	7	for (int i = 0; i < nucs.length(); i++)
218		{
219	6	assertEquals(rc.getCount(nucs.charAt(i)), i + 1);
220		}
221	1	assertFalse(rc.isUsingOtherData());
222
223	1	rc.add('J');
224	1	assertTrue(rc.isUsingOtherData());
225		}
226
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
227	1	@Test(groups = "Functional")...
228		public void testGetModalCount()
229		{
230	1	ResidueCount rc = new ResidueCount(true);
231	1	rc.add('c');
232	1	rc.add('g');
233	1	rc.add('c');
234	1	assertEquals(rc.getModalCount(), 2);
235
236		// modal count is in the 'short overflow' counts
237	1	rc = new ResidueCount();
238	1	rc.add('c');
239	1	rc.put('g', Short.MAX_VALUE);
240	1	rc.add('G');
241	1	assertEquals(rc.getModalCount(), Short.MAX_VALUE + 1);
242
243		// modal count is in the 'other data' counts
244	1	rc = new ResidueCount(false);
245	1	rc.add('Q');
246	1	rc.add('{');
247	1	rc.add('{');
248	1	assertEquals(rc.getModalCount(), 2);
249
250		// verify modal count excludes gap
251	1	rc = new ResidueCount();
252	1	rc.add('Q');
253	1	rc.add('P');
254	1	rc.add('Q');
255	1	rc.addGap();
256	1	rc.addGap();
257	1	rc.addGap();
258	1	assertEquals(rc.getModalCount(), 2);
259		}
260
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
261	1	@Test(groups = "Functional")...
262		public void testGetResiduesForCount()
263		{
264	1	ResidueCount rc = new ResidueCount(true);
265	1	rc.add('c');
266	1	rc.add('g');
267	1	rc.add('c');
268	1	assertEquals(rc.getResiduesForCount(2), "C");
269	1	assertEquals(rc.getResiduesForCount(1), "G");
270	1	assertEquals(rc.getResiduesForCount(3), "");
271	1	assertEquals(rc.getResiduesForCount(0), "");
272	1	assertEquals(rc.getResiduesForCount(-1), "");
273
274		// modal count is in the 'short overflow' counts
275	1	rc = new ResidueCount(true);
276	1	rc.add('c');
277	1	rc.put('g', Short.MAX_VALUE);
278	1	rc.add('G');
279	1	assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "G");
280	1	assertEquals(rc.getResiduesForCount(1), "C");
281
282		// peptide modal count is in the 'short overflow' counts
283	1	rc = new ResidueCount(false);
284	1	rc.add('c');
285	1	rc.put('p', Short.MAX_VALUE);
286	1	rc.add('P');
287	1	assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "P");
288	1	assertEquals(rc.getResiduesForCount(1), "C");
289
290		// modal count is in the 'other data' counts
291	1	rc = new ResidueCount();
292	1	rc.add('Q');
293	1	rc.add('{');
294	1	rc.add('{');
295	1	assertEquals(rc.getResiduesForCount(1), "Q");
296	1	assertEquals(rc.getResiduesForCount(2), "{");
297
298		// residues share modal count
299	1	rc = new ResidueCount();
300	1	rc.add('G');
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), "CG");
307
308		// expected and unexpected symbols share modal count
309	1	rc = new ResidueCount();
310	1	rc.add('G');
311	1	rc.add('t');
312	1	rc.add('[');
313	1	rc.add('[');
314	1	rc.add('t');
315	1	rc.add('G');
316	1	rc.add('c');
317	1	rc.add('C');
318	1	rc.add('U');
319	1	assertEquals(rc.getResiduesForCount(1), "U");
320	1	assertEquals(rc.getResiduesForCount(2), "CGT[");
321		}
322
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
323	1	@Test(groups = "Functional")...
324		public void testGetSymbolCounts_nucleotide()
325		{
326	1	ResidueCount rc = new ResidueCount(true);
327	1	rc.add('g');
328	1	rc.add('c');
329	1	rc.add('G');
330	1	rc.add('J'); // 'otherData'
331	1	rc.add('g');
332	1	rc.add('N');
333	1	rc.put('[', 0); // 'otherdata'
334
335	1	SymbolCounts sc = rc.getSymbolCounts();
336	1	Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'J', '[' },
337		sc.symbols);
338	1	Assert.assertArrayEquals(new int[] { 1, 3, 1, 1, 0 }, sc.values);
339
340		// now with overflow to int counts
341	1	rc.put('U', Short.MAX_VALUE);
342	1	rc.add('u');
343	1	sc = rc.getSymbolCounts();
344	1	Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'U', 'J', '[' },
345		sc.symbols);
346	1	Assert.assertArrayEquals(new int[] { 1, 3, 1, 32768, 1, 0 }, sc.values);
347		}
348
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
349	1	@Test(groups = "Functional")...
350		public void testGetSymbolCounts_peptide()
351		{
352	1	ResidueCount rc = new ResidueCount(false);
353	1	rc.add('W');
354	1	rc.add('q');
355	1	rc.add('W');
356	1	rc.add('Z'); // 'otherData'
357	1	rc.add('w');
358	1	rc.add('L');
359
360	1	SymbolCounts sc = rc.getSymbolCounts();
361	1	Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
362	1	Assert.assertArrayEquals(new int[] { 1, 1, 3, 1 }, sc.values);
363
364		// now with overflow to int counts
365	1	rc.put('W', Short.MAX_VALUE);
366	1	rc.add('W');
367	1	sc = rc.getSymbolCounts();
368	1	Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
369	1	Assert.assertArrayEquals(new int[] { 1, 1, 32768, 1 }, sc.values);
370		}
371
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
372	1	@Test(groups = "Functional")...
373		public void testToString()
374		{
375	1	ResidueCount rc = new ResidueCount();
376	1	rc.add('q');
377	1	rc.add('c');
378	1	rc.add('Q');
379	1	assertEquals(rc.toString(), "[ C:1 Q:2 ]");
380
381		// add 'other data'
382	1	rc.add('{');
383	1	assertEquals(rc.toString(), "[ C:1 Q:2 {:1 ]");
384
385		// switch from short to int counting:
386	1	rc.put('G', Short.MAX_VALUE);
387	1	rc.add('g');
388	1	assertEquals(rc.toString(), "[ C:1 G:32768 Q:2 {:1 ]");
389		}
390
		100% Uncovered Elements: 0 (23) Complexity: 5 Complexity Density: 0.33 1PASS
391	1	@Test(groups = "Functional")...
392		public void testGetTooltip()
393		{
394	1	ResidueCount rc = new ResidueCount();
395
396		// no counts!
397	1	assertEquals(rc.getTooltip(20, 1), "");
398
399		/*
400		* count 7 C, 6 K, 7 Q, 10 P, 9 W, 1 F (total 40)
401		*/
402	8	for (int i = 0; i < 7; i++)
403		{
404	7	rc.add('c');
405	7	rc.add('q');
406		}
407	11	for (int i = 0; i < 10; i++)
408		{
409	10	rc.add('p');
410		}
411	10	for (int i = 0; i < 9; i++)
412		{
413	9	rc.add('W');
414		}
415	7	for (int i = 0; i < 6; i++)
416		{
417	6	rc.add('K');
418		}
419	1	rc.add('F');
420
421		/*
422		* percentages are rounded (0.5 rounded up)
423		* 10/40 9/40 7/40 6/40 1/40
424		*/
425	1	assertEquals(rc.getTooltip(40, 0),
426		"P 25%; W 23%; C 18%; Q 18%; K 15%; F 3%");
427
428	1	rc.add('Q');
429		/*
430		* 10/30 9/30 8/30 7/30 6/30 1/30
431		*/
432	1	assertEquals(rc.getTooltip(30, 1),
433		"P 33.3%; W 30.0%; Q 26.7%; C 23.3%; K 20.0%; F 3.3%");
434		}
435
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
436	1	@Test(groups = "Functional")...
437		public void testPut()
438		{
439	1	ResidueCount rc = new ResidueCount();
440	1	rc.put('q', 3);
441	1	assertEquals(rc.getCount('Q'), 3);
442	1	rc.put(' ', 4);
443	1	assertEquals(rc.getGapCount(), 4);
444	1	rc.put('.', 5);
445	1	assertEquals(rc.getGapCount(), 5);
446	1	rc.put('-', 6);
447	1	assertEquals(rc.getGapCount(), 6);
448
449	1	rc.put('?', 5);
450	1	assertEquals(rc.getCount('?'), 5);
451	1	rc.put('?', 6);
452	1	rc.put('!', 7);
453	1	assertEquals(rc.getCount('?'), 6);
454	1	assertEquals(rc.getCount('!'), 7);
455		}
456		}