Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResidueCountTest	38	269	23	0.00%	Show methods

Class ResidueCountTest

Class ResidueCountTest	Line # 38	Total Statements 269	Complexity 23	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4141	2.02	1.01	0.0 0.00%
test_countNucleotide() : void   test_countNucleotide() : void	5151	21.021	1.01	0.0 0.00%
testAddGap() : void   testAddGap() : void	8585	23.023	1.01	0.0 0.00%
testOverflow() : void   testOverflow() : void	115115	26.026	1.01	0.0 0.00%
test_countPeptide() : void   test_countPeptide() : void	160160	18.018	1.01	0.0 0.00%
test_unexpectedPeptide() : void   test_unexpectedPeptide() : void	185185	14.014	3.03	0.0 0.00%
test_unexpectedNucleotide() : void   test_unexpectedNucleotide() : void	210210	11.011	3.03	0.0 0.00%
testGetModalCount() : void   testGetModalCount() : void	232232	23.023	1.01	0.0 0.00%
testGetResiduesForCount() : void   testGetResiduesForCount() : void	266266	47.047	1.01	0.0 0.00%
testGetSymbolCounts_nucleotide() : void   testGetSymbolCounts_nucleotide() : void	328328	16.016	1.01	0.0 0.00%
testGetSymbolCounts_peptide() : void   testGetSymbolCounts_peptide() : void	354354	15.015	1.01	0.0 0.00%
testToString() : void   testToString() : void	377377	10.010	1.01	0.0 0.00%
testGetTooltip() : void   testGetTooltip() : void	396396	15.015	5.05	0.0 0.00%
testPut() : void   testPut() : void	441441	15.015	1.01	0.0 0.00%
testConstructor_forSequences() : void   testConstructor_forSequences() : void	462462	13.013	1.01	0.0 0.00%

 

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