Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResidueCountTest	38	269	23	1.0100%	Show methods

Class ResidueCountTest

Class ResidueCountTest	Line # 38	Total Statements 269	Complexity 23	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4141	2.02	1.01	1.0 1.0100%
test_countNucleotide() : void   test_countNucleotide() : void	5151	21.021	1.01	1.0 1.0100%
testAddGap() : void   testAddGap() : void	8585	23.023	1.01	1.0 1.0100%
testOverflow() : void   testOverflow() : void	115115	26.026	1.01	1.0 1.0100%
test_countPeptide() : void   test_countPeptide() : void	160160	18.018	1.01	1.0 1.0100%
test_unexpectedPeptide() : void   test_unexpectedPeptide() : void	185185	14.014	3.03	1.0 1.0100%
test_unexpectedNucleotide() : void   test_unexpectedNucleotide() : void	210210	11.011	3.03	1.0 1.0100%
testGetModalCount() : void   testGetModalCount() : void	232232	23.023	1.01	1.0 1.0100%
testGetResiduesForCount() : void   testGetResiduesForCount() : void	266266	47.047	1.01	1.0 1.0100%
testGetSymbolCounts_nucleotide() : void   testGetSymbolCounts_nucleotide() : void	328328	16.016	1.01	1.0 1.0100%
testGetSymbolCounts_peptide() : void   testGetSymbolCounts_peptide() : void	354354	15.015	1.01	1.0 1.0100%
testToString() : void   testToString() : void	377377	10.010	1.01	1.0 1.0100%
testGetTooltip() : void   testGetTooltip() : void	396396	15.015	5.05	1.0 1.0100%
testPut() : void   testPut() : void	441441	15.015	1.01	1.0 1.0100%
testConstructor_forSequences() : void   testConstructor_forSequences() : void	462462	13.013	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.16	jalview.datamodel.ResidueCountTest.testGetResiduesForCountjalview.datamodel.ResidueCountTest.testGetResiduesForCount	1PASS
	0.09	jalview.datamodel.ResidueCountTest.testOverflowjalview.datamodel.ResidueCountTest.testOverflow	1PASS
	0.08	jalview.datamodel.ResidueCountTest.testGetModalCountjalview.datamodel.ResidueCountTest.testGetModalCount	1PASS
	0.08	jalview.datamodel.ResidueCountTest.testGetTooltipjalview.datamodel.ResidueCountTest.testGetTooltip	1PASS
	0.08	jalview.datamodel.ResidueCountTest.testAddGapjalview.datamodel.ResidueCountTest.testAddGap	1PASS
	0.07333333	jalview.datamodel.ResidueCountTest.test_countNucleotidejalview.datamodel.ResidueCountTest.test_countNucleotide	1PASS
	0.06333333	jalview.datamodel.ResidueCountTest.test_unexpectedPeptidejalview.datamodel.ResidueCountTest.test_unexpectedPeptide	1PASS
	0.06333333	jalview.datamodel.ResidueCountTest.test_countPeptidejalview.datamodel.ResidueCountTest.test_countPeptide	1PASS
	0.05666667	jalview.datamodel.ResidueCountTest.testGetSymbolCounts_nucleotidejalview.datamodel.ResidueCountTest.testGetSymbolCounts_nucleotide	1PASS
	0.053333335	jalview.datamodel.ResidueCountTest.testGetSymbolCounts_peptidejalview.datamodel.ResidueCountTest.testGetSymbolCounts_peptide	1PASS
	0.053333335	jalview.datamodel.ResidueCountTest.test_unexpectedNucleotidejalview.datamodel.ResidueCountTest.test_unexpectedNucleotide	1PASS
	0.053333335	jalview.datamodel.ResidueCountTest.testPutjalview.datamodel.ResidueCountTest.testPut	1PASS
	0.046666667	jalview.datamodel.ResidueCountTest.testConstructor_forSequencesjalview.datamodel.ResidueCountTest.testConstructor_forSequences	1PASS
	0.036666665	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 java.util.Arrays;
33
34		import org.junit.Assert;
35		import org.testng.annotations.BeforeClass;
36		import org.testng.annotations.Test;
37
		100% Uncovered Elements: 0 (300) Complexity: 23 Complexity Density: 0.09
38		public class ResidueCountTest
39		{
40
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
41	1	@BeforeClass(alwaysRun = true)...
42		public void setUpJvOptionPane()
43		{
44	1	JvOptionPane.setInteractiveMode(false);
45	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
46		}
47
48		/**
49		* Test a mix of add and put for nucleotide counting
50		*/
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
51	1	@Test(groups = "Functional")...
52		public void test_countNucleotide()
53		{
54	1	ResidueCount rc = new ResidueCount(true);
55	1	assertEquals(rc.getCount('A'), 0);
56	1	assertEquals(rc.getGapCount(), 0);
57		// add then add
58	1	assertEquals(rc.add('A'), 1);
59	1	assertEquals(rc.add('a'), 2);
60		// put then add
61	1	rc.put('g', 3);
62	1	assertEquals(rc.add('G'), 4);
63		// add then put
64	1	assertEquals(rc.add('c'), 1);
65	1	rc.put('C', 4);
66	1	assertEquals(rc.add('N'), 1);
67
68	1	assertEquals(rc.getCount('a'), 2);
69	1	assertEquals(rc.getCount('A'), 2);
70	1	assertEquals(rc.getCount('G'), 4);
71	1	assertEquals(rc.getCount('c'), 4);
72	1	assertEquals(rc.getCount('T'), 0); // never seen
73	1	assertEquals(rc.getCount('N'), 1);
74	1	assertEquals(rc.getCount('?'), 0);
75	1	assertEquals(rc.getCount('-'), 0);
76	1	assertEquals(rc.getTotalResidueCount(), 11);
77
78	1	assertFalse(rc.isCountingInts());
79	1	assertFalse(rc.isUsingOtherData());
80		}
81
82		/**
83		* Test adding to gap count (either using addGap or add)
84		*/
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
85	1	@Test(groups = "Functional")...
86		public void testAddGap()
87		{
88	1	ResidueCount rc = new ResidueCount(true);
89	1	rc.addGap();
90	1	rc.add('-');
91	1	rc.add('.');
92	1	rc.add(' ');
93
94	1	assertEquals(rc.getGapCount(), 4);
95	1	assertEquals(rc.getCount(' '), 4);
96	1	assertEquals(rc.getCount('-'), 4);
97	1	assertEquals(rc.getCount('.'), 4);
98	1	assertEquals(rc.getTotalResidueCount(), 0);
99	1	assertFalse(rc.isUsingOtherData());
100	1	assertFalse(rc.isCountingInts());
101
102	1	rc.set(ResidueCount.GAP_COUNT, Short.MAX_VALUE - 2);
103	1	assertEquals(rc.getGapCount(), Short.MAX_VALUE - 2);
104	1	assertFalse(rc.isCountingInts());
105	1	rc.addGap();
106	1	assertEquals(rc.getGapCount(), Short.MAX_VALUE - 1);
107	1	assertFalse(rc.isCountingInts());
108	1	rc.addGap();
109	1	assertEquals(rc.getGapCount(), Short.MAX_VALUE);
110	1	rc.addGap();
111	1	assertTrue(rc.isCountingInts());
112	1	assertEquals(rc.getGapCount(), Short.MAX_VALUE + 1);
113		}
114
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
115	1	@Test(groups = "Functional")...
116		public void testOverflow()
117		{
118		/*
119		* overflow from add
120		*/
121	1	ResidueCount rc = new ResidueCount(true);
122	1	rc.addGap();
123	1	rc.put('A', Short.MAX_VALUE - 1);
124	1	assertFalse(rc.isCountingInts());
125	1	rc.add('A');
126	1	assertFalse(rc.isCountingInts());
127	1	rc.add('A');
128	1	assertTrue(rc.isCountingInts());
129	1	assertEquals(rc.getCount('a'), Short.MAX_VALUE + 1);
130	1	rc.add('A');
131	1	assertTrue(rc.isCountingInts());
132	1	assertEquals(rc.getCount('a'), Short.MAX_VALUE + 2);
133	1	assertEquals(rc.getGapCount(), 1);
134	1	rc.addGap();
135	1	assertEquals(rc.getGapCount(), 2);
136
137		/*
138		* overflow from put
139		*/
140	1	rc = new ResidueCount(true);
141	1	rc.put('G', Short.MAX_VALUE + 1);
142	1	assertTrue(rc.isCountingInts());
143	1	assertEquals(rc.getCount('g'), Short.MAX_VALUE + 1);
144	1	rc.put('G', 1);
145	1	assertTrue(rc.isCountingInts());
146	1	assertEquals(rc.getCount('g'), 1);
147
148		/*
149		* underflow from put
150		*/
151	1	rc = new ResidueCount(true);
152	1	rc.put('G', Short.MIN_VALUE - 1);
153	1	assertTrue(rc.isCountingInts());
154	1	assertEquals(rc.getCount('g'), Short.MIN_VALUE - 1);
155		}
156
157		/**
158		* Test a mix of add and put for peptide counting
159		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
160	1	@Test(groups = "Functional")...
161		public void test_countPeptide()
162		{
163	1	ResidueCount rc = new ResidueCount(false);
164	1	rc.put('q', 4);
165	1	rc.add('Q');
166	1	rc.add('X');
167	1	rc.add('x');
168	1	rc.add('W');
169	1	rc.put('w', 7);
170	1	rc.put('m', 12);
171	1	rc.put('M', 13);
172
173	1	assertEquals(rc.getCount('q'), 5);
174	1	assertEquals(rc.getCount('X'), 2);
175	1	assertEquals(rc.getCount('W'), 7);
176	1	assertEquals(rc.getCount('m'), 13);
177	1	assertEquals(rc.getCount('G'), 0);
178	1	assertEquals(rc.getCount('-'), 0);
179	1	assertEquals(rc.getTotalResidueCount(), 27);
180
181	1	assertFalse(rc.isCountingInts());
182	1	assertFalse(rc.isUsingOtherData());
183		}
184
		100% Uncovered Elements: 0 (18) Complexity: 3 Complexity Density: 0.21 1PASS
185	1	@Test(groups = "Functional")...
186		public void test_unexpectedPeptide()
187		{
188	1	ResidueCount rc = new ResidueCount(false);
189		// expected characters (upper or lower case):
190	1	String aas = "ACDEFGHIKLMNPQRSTVWXY";
191	1	String lower = aas.toLowerCase(Locale.ROOT);
192	22	for (int i = 0; i < aas.length(); i++)
193		{
194	21	rc.put(aas.charAt(i), i);
195	21	rc.add(lower.charAt(i));
196		}
197	22	for (int i = 0; i < aas.length(); i++)
198		{
199	21	assertEquals(rc.getCount(aas.charAt(i)), i + 1);
200		}
201	1	assertFalse(rc.isUsingOtherData());
202
203	1	rc.put('J', 4);
204	1	assertTrue(rc.isUsingOtherData());
205	1	assertEquals(rc.getCount('J'), 4);
206	1	rc.add('j');
207	1	assertEquals(rc.getCount('J'), 5);
208		}
209
		100% Uncovered Elements: 0 (15) Complexity: 3 Complexity Density: 0.27 1PASS
210	1	@Test(groups = "Functional")...
211		public void test_unexpectedNucleotide()
212		{
213	1	ResidueCount rc = new ResidueCount(true);
214		// expected characters (upper or lower case):
215	1	String nucs = "ACGTUN";
216	1	String lower = nucs.toLowerCase(Locale.ROOT);
217	7	for (int i = 0; i < nucs.length(); i++)
218		{
219	6	rc.put(nucs.charAt(i), i);
220	6	rc.add(lower.charAt(i));
221		}
222	7	for (int i = 0; i < nucs.length(); i++)
223		{
224	6	assertEquals(rc.getCount(nucs.charAt(i)), i + 1);
225		}
226	1	assertFalse(rc.isUsingOtherData());
227
228	1	rc.add('J');
229	1	assertTrue(rc.isUsingOtherData());
230		}
231
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
232	1	@Test(groups = "Functional")...
233		public void testGetModalCount()
234		{
235	1	ResidueCount rc = new ResidueCount(true);
236	1	rc.add('c');
237	1	rc.add('g');
238	1	rc.add('c');
239	1	assertEquals(rc.getModalCount(), 2);
240
241		// modal count is in the 'short overflow' counts
242	1	rc = new ResidueCount();
243	1	rc.add('c');
244	1	rc.put('g', Short.MAX_VALUE);
245	1	rc.add('G');
246	1	assertEquals(rc.getModalCount(), Short.MAX_VALUE + 1);
247
248		// modal count is in the 'other data' counts
249	1	rc = new ResidueCount(false);
250	1	rc.add('Q');
251	1	rc.add('{');
252	1	rc.add('{');
253	1	assertEquals(rc.getModalCount(), 2);
254
255		// verify modal count excludes gap
256	1	rc = new ResidueCount();
257	1	rc.add('Q');
258	1	rc.add('P');
259	1	rc.add('Q');
260	1	rc.addGap();
261	1	rc.addGap();
262	1	rc.addGap();
263	1	assertEquals(rc.getModalCount(), 2);
264		}
265
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
266	1	@Test(groups = "Functional")...
267		public void testGetResiduesForCount()
268		{
269	1	ResidueCount rc = new ResidueCount(true);
270	1	rc.add('c');
271	1	rc.add('g');
272	1	rc.add('c');
273	1	assertEquals(rc.getResiduesForCount(2), "C");
274	1	assertEquals(rc.getResiduesForCount(1), "G");
275	1	assertEquals(rc.getResiduesForCount(3), "");
276	1	assertEquals(rc.getResiduesForCount(0), "");
277	1	assertEquals(rc.getResiduesForCount(-1), "");
278
279		// modal count is in the 'short overflow' counts
280	1	rc = new ResidueCount(true);
281	1	rc.add('c');
282	1	rc.put('g', Short.MAX_VALUE);
283	1	rc.add('G');
284	1	assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "G");
285	1	assertEquals(rc.getResiduesForCount(1), "C");
286
287		// peptide modal count is in the 'short overflow' counts
288	1	rc = new ResidueCount(false);
289	1	rc.add('c');
290	1	rc.put('p', Short.MAX_VALUE);
291	1	rc.add('P');
292	1	assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "P");
293	1	assertEquals(rc.getResiduesForCount(1), "C");
294
295		// modal count is in the 'other data' counts
296	1	rc = new ResidueCount();
297	1	rc.add('Q');
298	1	rc.add('{');
299	1	rc.add('{');
300	1	assertEquals(rc.getResiduesForCount(1), "Q");
301	1	assertEquals(rc.getResiduesForCount(2), "{");
302
303		// residues share modal count
304	1	rc = new ResidueCount();
305	1	rc.add('G');
306	1	rc.add('G');
307	1	rc.add('c');
308	1	rc.add('C');
309	1	rc.add('U');
310	1	assertEquals(rc.getResiduesForCount(1), "U");
311	1	assertEquals(rc.getResiduesForCount(2), "CG");
312
313		// expected and unexpected symbols share modal count
314	1	rc = new ResidueCount();
315	1	rc.add('G');
316	1	rc.add('t');
317	1	rc.add('[');
318	1	rc.add('[');
319	1	rc.add('t');
320	1	rc.add('G');
321	1	rc.add('c');
322	1	rc.add('C');
323	1	rc.add('U');
324	1	assertEquals(rc.getResiduesForCount(1), "U");
325	1	assertEquals(rc.getResiduesForCount(2), "CGT[");
326		}
327
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
328	1	@Test(groups = "Functional")...
329		public void testGetSymbolCounts_nucleotide()
330		{
331	1	ResidueCount rc = new ResidueCount(true);
332	1	rc.add('g');
333	1	rc.add('c');
334	1	rc.add('G');
335	1	rc.add('J'); // 'otherData'
336	1	rc.add('g');
337	1	rc.add('N');
338	1	rc.put('[', 0); // 'otherdata'
339
340	1	SymbolCounts sc = rc.getSymbolCounts();
341	1	Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'J', '[' },
342		sc.symbols);
343	1	Assert.assertArrayEquals(new int[] { 1, 3, 1, 1, 0 }, sc.values);
344
345		// now with overflow to int counts
346	1	rc.put('U', Short.MAX_VALUE);
347	1	rc.add('u');
348	1	sc = rc.getSymbolCounts();
349	1	Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'U', 'J', '[' },
350		sc.symbols);
351	1	Assert.assertArrayEquals(new int[] { 1, 3, 1, 32768, 1, 0 }, sc.values);
352		}
353
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
354	1	@Test(groups = "Functional")...
355		public void testGetSymbolCounts_peptide()
356		{
357	1	ResidueCount rc = new ResidueCount(false);
358	1	rc.add('W');
359	1	rc.add('q');
360	1	rc.add('W');
361	1	rc.add('Z'); // 'otherData'
362	1	rc.add('w');
363	1	rc.add('L');
364
365	1	SymbolCounts sc = rc.getSymbolCounts();
366	1	Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
367	1	Assert.assertArrayEquals(new int[] { 1, 1, 3, 1 }, sc.values);
368
369		// now with overflow to int counts
370	1	rc.put('W', Short.MAX_VALUE);
371	1	rc.add('W');
372	1	sc = rc.getSymbolCounts();
373	1	Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
374	1	Assert.assertArrayEquals(new int[] { 1, 1, 32768, 1 }, sc.values);
375		}
376
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
377	1	@Test(groups = "Functional")...
378		public void testToString()
379		{
380	1	ResidueCount rc = new ResidueCount();
381	1	rc.add('q');
382	1	rc.add('c');
383	1	rc.add('Q');
384	1	assertEquals(rc.toString(), "[ C:1 Q:2 ]");
385
386		// add 'other data'
387	1	rc.add('{');
388	1	assertEquals(rc.toString(), "[ C:1 Q:2 {:1 ]");
389
390		// switch from short to int counting:
391	1	rc.put('G', Short.MAX_VALUE);
392	1	rc.add('g');
393	1	assertEquals(rc.toString(), "[ C:1 G:32768 Q:2 {:1 ]");
394		}
395
		100% Uncovered Elements: 0 (23) Complexity: 5 Complexity Density: 0.33 1PASS
396	1	@Test(groups = "Functional")...
397		public void testGetTooltip()
398		{
399	1	ResidueCount rc = new ResidueCount();
400
401		// no counts!
402	1	assertEquals(rc.getTooltip(20, 1), "");
403
404		/*
405		* count 7 C, 6 K, 7 Q, 10 P, 9 W, 1 F (total 40)
406		*/
407	8	for (int i = 0; i < 7; i++)
408		{
409	7	rc.add('c');
410	7	rc.add('q');
411		}
412	11	for (int i = 0; i < 10; i++)
413		{
414	10	rc.add('p');
415		}
416	10	for (int i = 0; i < 9; i++)
417		{
418	9	rc.add('W');
419		}
420	7	for (int i = 0; i < 6; i++)
421		{
422	6	rc.add('K');
423		}
424	1	rc.add('F');
425
426		/*
427		* percentages are rounded (0.5 rounded up)
428		* 10/40 9/40 7/40 6/40 1/40
429		*/
430	1	assertEquals(rc.getTooltip(40, 0),
431		"P 25%; W 23%; C 18%; Q 18%; K 15%; F 3%");
432
433	1	rc.add('Q');
434		/*
435		* 10/30 9/30 8/30 7/30 6/30 1/30
436		*/
437	1	assertEquals(rc.getTooltip(30, 1),
438		"P 33.3%; W 30.0%; Q 26.7%; C 23.3%; K 20.0%; F 3.3%");
439		}
440
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
441	1	@Test(groups = "Functional")...
442		public void testPut()
443		{
444	1	ResidueCount rc = new ResidueCount();
445	1	rc.put('q', 3);
446	1	assertEquals(rc.getCount('Q'), 3);
447	1	rc.put(' ', 4);
448	1	assertEquals(rc.getGapCount(), 4);
449	1	rc.put('.', 5);
450	1	assertEquals(rc.getGapCount(), 5);
451	1	rc.put('-', 6);
452	1	assertEquals(rc.getGapCount(), 6);
453
454	1	rc.put('?', 5);
455	1	assertEquals(rc.getCount('?'), 5);
456	1	rc.put('?', 6);
457	1	rc.put('!', 7);
458	1	assertEquals(rc.getCount('?'), 6);
459	1	assertEquals(rc.getCount('!'), 7);
460		}
461
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
462	1	@Test(groups = "Functional")...
463		public void testConstructor_forSequences()
464		{
465	1	SequenceI seq1 = new Sequence("seq1", "abcde--. FCD");
466	1	SequenceI seq2 = new Sequence("seq2", "ab.kKqBd-.");
467	1	ResidueCount rc = new ResidueCount(Arrays.asList(seq1, seq2));
468
469	1	assertEquals(rc.getGapCount(), 7);
470	1	assertEquals(rc.getTotalResidueCount(), 15); // excludes gaps
471	1	assertEquals(rc.getCount('a'), 2);
472	1	assertEquals(rc.getCount('A'), 2);
473	1	assertEquals(rc.getCount('B'), 3);
474	1	assertEquals(rc.getCount('c'), 2);
475	1	assertEquals(rc.getCount('D'), 3);
476	1	assertEquals(rc.getCount('f'), 1);
477	1	assertEquals(rc.getCount('K'), 2);
478	1	assertEquals(rc.getCount('Q'), 1);
479		}
480		}