Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
FeatureMatcherSetTest	20	191	12	3	0.98598.5%	Show methods

Class FeatureMatcherSetTest

Class FeatureMatcherSetTest	Line # 20	Total Statements 191	Complexity 12	Uncovered Elements 3	TOTAL Coverage 0.98598.5%
testMatches_byAttribute() : void   testMatches_byAttribute() : void	2222	21.021	1.01	0.00	1.0 1.0100%
testAnd() : void   testAnd() : void	5656	31.031	1.01	0.00	1.0 1.0100%
testToString() : void   testToString() : void	114114	20.020	2.02	1.01	0.95 0.9595%
testOr() : void   testOr() : void	158158	21.021	2.02	1.01	0.95238096 0.9523809695.2%
testIsEmpty() : void   testIsEmpty() : void	198198	5.05	1.01	0.00	1.0 1.0100%
testGetMatchers() : void   testGetMatchers() : void	209209	14.014	1.01	0.00	1.0 1.0100%
testMatches_compoundKey() : void   testMatches_compoundKey() : void	246246	28.028	1.01	0.00	1.0 1.0100%
testToStableString() : void   testToStableString() : void	294294	23.023	2.02	1.01	0.95652175 0.9565217595.7%
testFromString() : void   testFromString() : void	355355	28.028	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.16	jalview.datamodel.features.FeatureMatcherSetTest.testAndjalview.datamodel.features.FeatureMatcherSetTest.testAnd	1PASS
	0.145	jalview.datamodel.features.FeatureMatcherSetTest.testMatches_compoundKeyjalview.datamodel.features.FeatureMatcherSetTest.testMatches_compoundKey	1PASS
	0.145	jalview.datamodel.features.FeatureMatcherSetTest.testFromStringjalview.datamodel.features.FeatureMatcherSetTest.testFromString	1PASS
	0.115	jalview.datamodel.features.FeatureMatcherSetTest.testToStableStringjalview.datamodel.features.FeatureMatcherSetTest.testToStableString	1PASS
	0.11	jalview.datamodel.features.FeatureMatcherSetTest.testMatches_byAttributejalview.datamodel.features.FeatureMatcherSetTest.testMatches_byAttribute	1PASS
	0.105	jalview.datamodel.features.FeatureMatcherSetTest.testOrjalview.datamodel.features.FeatureMatcherSetTest.testOr	1PASS
	0.1	jalview.datamodel.features.FeatureMatcherSetTest.testToStringjalview.datamodel.features.FeatureMatcherSetTest.testToString	1PASS
	0.075	jalview.datamodel.features.FeatureMatcherSetTest.testGetMatchersjalview.datamodel.features.FeatureMatcherSetTest.testGetMatchers	1PASS
	0.03	jalview.datamodel.features.FeatureMatcherSetTest.testIsEmptyjalview.datamodel.features.FeatureMatcherSetTest.testIsEmpty	1PASS

 

Source view

1		package jalview.datamodel.features;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertFalse;
5		import static org.testng.Assert.assertNull;
6		import static org.testng.Assert.assertSame;
7		import static org.testng.Assert.assertTrue;
8		import static org.testng.Assert.fail;
9
10		import jalview.datamodel.SequenceFeature;
11		import jalview.util.matcher.Condition;
12
13		import java.util.HashMap;
14		import java.util.Iterator;
15		import java.util.Locale;
16		import java.util.Map;
17
18		import org.testng.annotations.Test;
19
		98.5% Uncovered Elements: 3 (200) Complexity: 12 Complexity Density: 0.06
20		public class FeatureMatcherSetTest
21		{
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
22	1	@Test(groups = "Functional")...
23		public void testMatches_byAttribute()
24		{
25		/*
26		* a numeric matcher - MatcherTest covers more conditions
27		*/
28	1	FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2",
29		"AF");
30	1	FeatureMatcherSetI fms = new FeatureMatcherSet();
31	1	fms.and(fm);
32	1	SequenceFeature sf = new SequenceFeature("Cath", "desc", 11, 12, "grp");
33	1	assertFalse(fms.matches(sf));
34	1	sf.setValue("AF", "foobar");
35	1	assertFalse(fms.matches(sf));
36	1	sf.setValue("AF", "-2");
37	1	assertTrue(fms.matches(sf));
38	1	sf.setValue("AF", "-1");
39	1	assertTrue(fms.matches(sf));
40	1	sf.setValue("AF", "-3");
41	1	assertFalse(fms.matches(sf));
42	1	sf.setValue("AF", "");
43	1	assertFalse(fms.matches(sf));
44
45		/*
46		* a string pattern matcher
47		*/
48	1	fm = FeatureMatcher.byAttribute(Condition.Contains, "Cat", "AF");
49	1	fms = new FeatureMatcherSet();
50	1	fms.and(fm);
51	1	assertFalse(fms.matches(sf));
52	1	sf.setValue("AF", "raining cats and dogs");
53	1	assertTrue(fms.matches(sf));
54		}
55
		100% Uncovered Elements: 0 (31) Complexity: 1 Complexity Density: 0.03 1PASS
56	1	@Test(groups = "Functional")...
57		public void testAnd()
58		{
59		// condition1: AF value contains "dog" (matches)
60	1	FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.Contains,
61		"dog", "AF");
62		// condition 2: CSQ value does not contain "how" (does not match)
63	1	FeatureMatcherI fm2 = FeatureMatcher.byAttribute(Condition.NotContains,
64		"how", "CSQ");
65
66	1	SequenceFeature sf = new SequenceFeature("Cath", "helix domain", 11, 12,
67		6.2f, "grp");
68	1	sf.setValue("AF", "raining cats and dogs");
69	1	sf.setValue("CSQ", "showers");
70
71	1	assertTrue(fm1.matches(sf));
72	1	assertFalse(fm2.matches(sf));
73
74	1	FeatureMatcherSetI fms = new FeatureMatcherSet();
75	1	assertTrue(fms.matches(sf)); // if no conditions, then 'all' pass
76	1	fms.and(fm1);
77	1	assertTrue(fms.matches(sf));
78	1	fms.and(fm2);
79	1	assertFalse(fms.matches(sf));
80
81		/*
82		* OR a failed attribute condition with a matched label condition
83		*/
84	1	fms = new FeatureMatcherSet();
85	1	fms.and(fm2);
86	1	assertFalse(fms.matches(sf));
87	1	FeatureMatcher byLabelPass = FeatureMatcher.byLabel(Condition.Contains,
88		"Helix");
89	1	fms.or(byLabelPass);
90	1	assertTrue(fms.matches(sf));
91
92		/*
93		* OR a failed attribute condition with a failed score condition
94		*/
95	1	fms = new FeatureMatcherSet();
96	1	fms.and(fm2);
97	1	assertFalse(fms.matches(sf));
98	1	FeatureMatcher byScoreFail = FeatureMatcher.byScore(Condition.LT,
99		"5.9");
100	1	fms.or(byScoreFail);
101	1	assertFalse(fms.matches(sf));
102
103		/*
104		* OR failed attribute and score conditions with matched label condition
105		*/
106	1	fms = new FeatureMatcherSet();
107	1	fms.or(fm2);
108	1	fms.or(byScoreFail);
109	1	assertFalse(fms.matches(sf));
110	1	fms.or(byLabelPass);
111	1	assertTrue(fms.matches(sf));
112		}
113
		95% Uncovered Elements: 1 (20) Complexity: 2 Complexity Density: 0.1 1PASS
114	1	@Test(groups = "Functional")...
115		public void testToString()
116		{
117	1	Locale.setDefault(Locale.ENGLISH);
118	1	FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.LT, "1.2",
119		"AF");
120	1	assertEquals(fm1.toString(), "AF < 1.2");
121
122	1	FeatureMatcher fm2 = FeatureMatcher.byAttribute(Condition.NotContains,
123		"path", "CLIN_SIG");
124	1	assertEquals(fm2.toString(), "CLIN_SIG does not contain 'path'");
125
126		/*
127		* AND them
128		*/
129	1	FeatureMatcherSetI fms = new FeatureMatcherSet();
130	1	assertEquals(fms.toString(), "");
131	1	fms.and(fm1);
132	1	assertEquals(fms.toString(), "AF < 1.2");
133	1	fms.and(fm2);
134	1	assertEquals(fms.toString(),
135		"(AF < 1.2) and (CLIN_SIG does not contain 'path')");
136
137		/*
138		* OR them
139		*/
140	1	fms = new FeatureMatcherSet();
141	1	assertEquals(fms.toString(), "");
142	1	fms.or(fm1);
143	1	assertEquals(fms.toString(), "AF < 1.2");
144	1	fms.or(fm2);
145	1	assertEquals(fms.toString(),
146		"(AF < 1.2) or (CLIN_SIG does not contain 'path')");
147
148	1	try
149		{
150	1	fms.and(fm1);
151	0	fail("Expected exception");
152		} catch (IllegalStateException e)
153		{
154		// expected
155		}
156		}
157
		95.2% Uncovered Elements: 1 (21) Complexity: 2 Complexity Density: 0.1 1PASS
158	1	@Test(groups = "Functional")...
159		public void testOr()
160		{
161		// condition1: AF value contains "dog" (matches)
162	1	FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.Contains,
163		"dog", "AF");
164		// condition 2: CSQ value does not contain "how" (does not match)
165	1	FeatureMatcherI fm2 = FeatureMatcher.byAttribute(Condition.NotContains,
166		"how", "CSQ");
167
168	1	SequenceFeature sf = new SequenceFeature("Cath", "desc", 11, 12, "grp");
169	1	sf.setValue("AF", "raining cats and dogs");
170	1	sf.setValue("CSQ", "showers");
171
172	1	assertTrue(fm1.matches(sf));
173	1	assertFalse(fm2.matches(sf));
174
175	1	FeatureMatcherSetI fms = new FeatureMatcherSet();
176	1	assertTrue(fms.matches(sf)); // if no conditions, then 'all' pass
177	1	fms.or(fm1);
178	1	assertTrue(fms.matches(sf));
179	1	fms.or(fm2);
180	1	assertTrue(fms.matches(sf)); // true or false makes true
181
182	1	fms = new FeatureMatcherSet();
183	1	fms.or(fm2);
184	1	assertFalse(fms.matches(sf));
185	1	fms.or(fm1);
186	1	assertTrue(fms.matches(sf)); // false or true makes true
187
188	1	try
189		{
190	1	fms.and(fm2);
191	0	fail("Expected exception");
192		} catch (IllegalStateException e)
193		{
194		// expected
195		}
196		}
197
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
198	1	@Test(groups = "Functional")...
199		public void testIsEmpty()
200		{
201	1	FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2.0",
202		"AF");
203	1	FeatureMatcherSetI fms = new FeatureMatcherSet();
204	1	assertTrue(fms.isEmpty());
205	1	fms.and(fm);
206	1	assertFalse(fms.isEmpty());
207		}
208
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
209	1	@Test(groups = "Functional")...
210		public void testGetMatchers()
211		{
212	1	FeatureMatcherSetI fms = new FeatureMatcherSet();
213
214		/*
215		* empty iterable:
216		*/
217	1	Iterator<FeatureMatcherI> iterator = fms.getMatchers().iterator();
218	1	assertFalse(iterator.hasNext());
219
220		/*
221		* one matcher:
222		*/
223	1	FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.GE, "-2",
224		"AF");
225	1	fms.and(fm1);
226	1	iterator = fms.getMatchers().iterator();
227	1	assertSame(fm1, iterator.next());
228	1	assertFalse(iterator.hasNext());
229
230		/*
231		* two matchers:
232		*/
233	1	FeatureMatcherI fm2 = FeatureMatcher.byAttribute(Condition.LT, "8f",
234		"AF");
235	1	fms.and(fm2);
236	1	iterator = fms.getMatchers().iterator();
237	1	assertSame(fm1, iterator.next());
238	1	assertSame(fm2, iterator.next());
239	1	assertFalse(iterator.hasNext());
240		}
241
242		/**
243		* Tests for the 'compound attribute' key i.e. where first key's value is a map
244		* from which we take the value for the second key, e.g. CSQ : Consequence
245		*/
		100% Uncovered Elements: 0 (28) Complexity: 1 Complexity Density: 0.04 1PASS
246	1	@Test(groups = "Functional")...
247		public void testMatches_compoundKey()
248		{
249		/*
250		* a numeric matcher - MatcherTest covers more conditions
251		*/
252	1	FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2",
253		"CSQ", "Consequence");
254	1	SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 10, "grp");
255	1	FeatureMatcherSetI fms = new FeatureMatcherSet();
256	1	fms.and(fm);
257	1	assertFalse(fms.matches(sf));
258	1	Map<String, String> csq = new HashMap<>();
259	1	sf.setValue("CSQ", csq);
260	1	assertFalse(fms.matches(sf));
261	1	csq.put("Consequence", "-2");
262	1	assertTrue(fms.matches(sf));
263	1	csq.put("Consequence", "-1");
264	1	assertTrue(fms.matches(sf));
265	1	csq.put("Consequence", "-3");
266	1	assertFalse(fms.matches(sf));
267	1	csq.put("Consequence", "");
268	1	assertFalse(fms.matches(sf));
269	1	csq.put("Consequence", "junk");
270	1	assertFalse(fms.matches(sf));
271
272		/*
273		* a string pattern matcher
274		*/
275	1	fm = FeatureMatcher.byAttribute(Condition.Contains, "Cat", "CSQ",
276		"Consequence");
277	1	fms = new FeatureMatcherSet();
278	1	fms.and(fm);
279	1	assertFalse(fms.matches(sf));
280	1	csq.put("PolyPhen", "damaging");
281	1	assertFalse(fms.matches(sf));
282	1	csq.put("Consequence", "damaging");
283	1	assertFalse(fms.matches(sf));
284	1	csq.put("Consequence", "Catastrophic");
285	1	assertTrue(fms.matches(sf));
286		}
287
288		/**
289		* Tests for toStableString which (unlike toString) does not i18n the
290		* conditions
291		*
292		* @see FeatureMatcherTest#testToStableString()
293		*/
		95.7% Uncovered Elements: 1 (23) Complexity: 2 Complexity Density: 0.09 1PASS
294	1	@Test(groups = "Functional")...
295		public void testToStableString()
296		{
297	1	FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.LT, "1.2",
298		"AF");
299	1	assertEquals(fm1.toStableString(), "AF LT 1.2");
300
301	1	FeatureMatcher fm2 = FeatureMatcher.byAttribute(Condition.NotContains,
302		"path", "CLIN_SIG");
303	1	assertEquals(fm2.toStableString(), "CLIN_SIG NotContains path");
304
305		/*
306		* AND them
307		*/
308	1	FeatureMatcherSetI fms = new FeatureMatcherSet();
309	1	assertEquals(fms.toStableString(), "");
310	1	fms.and(fm1);
311		// no brackets needed if a single condition
312	1	assertEquals(fms.toStableString(), "AF LT 1.2");
313		// brackets if more than one condition
314	1	fms.and(fm2);
315	1	assertEquals(fms.toStableString(),
316		"(AF LT 1.2) AND (CLIN_SIG NotContains path)");
317
318		/*
319		* OR them
320		*/
321	1	fms = new FeatureMatcherSet();
322	1	assertEquals(fms.toStableString(), "");
323	1	fms.or(fm1);
324	1	assertEquals(fms.toStableString(), "AF LT 1.2");
325	1	fms.or(fm2);
326	1	assertEquals(fms.toStableString(),
327		"(AF LT 1.2) OR (CLIN_SIG NotContains path)");
328
329		/*
330		* attribute or value including space is quoted
331		*/
332	1	FeatureMatcher fm3 = FeatureMatcher.byAttribute(Condition.NotMatches,
333		"foo bar", "CSQ", "Poly Phen");
334	1	assertEquals(fm3.toStableString(),
335		"'CSQ:Poly Phen' NotMatches 'foo bar'");
336	1	fms.or(fm3);
337	1	assertEquals(fms.toStableString(),
338		"(AF LT 1.2) OR (CLIN_SIG NotContains path) OR ('CSQ:Poly Phen' NotMatches 'foo bar')");
339
340	1	try
341		{
342	1	fms.and(fm1);
343	0	fail("Expected exception");
344		} catch (IllegalStateException e)
345		{
346		// expected
347		}
348		}
349
350		/**
351		* Tests for parsing a string representation of a FeatureMatcherSet
352		*
353		* @see FeatureMatcherSetTest#testToStableString()
354		*/
		100% Uncovered Elements: 0 (28) Complexity: 1 Complexity Density: 0.04 1PASS
355	1	@Test(groups = "Functional")...
356		public void testFromString()
357		{
358	1	String descriptor = "AF LT 1.2";
359	1	FeatureMatcherSetI fms = FeatureMatcherSet.fromString(descriptor);
360
361		/*
362		* shortcut asserts by verifying a 'roundtrip',
363		* which we trust if other tests pass :-)
364		*/
365	1	assertEquals(fms.toStableString(), descriptor);
366
367		// brackets optional, quotes optional, condition case insensitive
368	1	fms = FeatureMatcherSet.fromString("('AF' lt '1.2')");
369	1	assertEquals(fms.toStableString(), descriptor);
370
371	1	descriptor = "(AF LT 1.2) AND (CLIN_SIG NotContains path)";
372	1	fms = FeatureMatcherSet.fromString(descriptor);
373	1	assertEquals(fms.toStableString(), descriptor);
374
375		// AND is not case-sensitive
376	1	fms = FeatureMatcherSet
377		.fromString("(AF LT 1.2) and (CLIN_SIG NotContains path)");
378	1	assertEquals(fms.toStableString(), descriptor);
379
380	1	descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path)";
381	1	fms = FeatureMatcherSet.fromString(descriptor);
382	1	assertEquals(fms.toStableString(), descriptor);
383
384		// OR is not case-sensitive
385	1	fms = FeatureMatcherSet
386		.fromString("(AF LT 1.2) or (CLIN_SIG NotContains path)");
387	1	assertEquals(fms.toStableString(), descriptor);
388
389		// can get away without brackets on last match condition
390	1	fms = FeatureMatcherSet
391		.fromString("(AF LT 1.2) or CLIN_SIG NotContains path");
392	1	assertEquals(fms.toStableString(), descriptor);
393
394	1	descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path) OR ('CSQ:Poly Phen' NotMatches 'foo bar')";
395	1	fms = FeatureMatcherSet.fromString(descriptor);
396	1	assertEquals(fms.toStableString(), descriptor);
397
398		// can't mix OR and AND
399	1	descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path) AND ('CSQ:Poly Phen' NotMatches 'foo bar')";
400	1	assertNull(FeatureMatcherSet.fromString(descriptor));
401
402		// can't mix AND and OR
403	1	descriptor = "(AF LT 1.2) and (CLIN_SIG NotContains path) or ('CSQ:Poly Phen' NotMatches 'foo bar')";
404	1	assertNull(FeatureMatcherSet.fromString(descriptor));
405
406		// brackets missing
407	1	assertNull(FeatureMatcherSet
408		.fromString("AF LT 1.2 or CLIN_SIG NotContains path"));
409
410		// invalid conjunction
411	1	assertNull(FeatureMatcherSet.fromString("(AF LT 1.2) but (AF GT -2)"));
412
413		// unbalanced quote (1)
414	1	assertNull(FeatureMatcherSet.fromString("('AF lt '1.2')"));
415
416		// unbalanced quote (2)
417	1	assertNull(FeatureMatcherSet.fromString("('AF' lt '1.2)"));
418		}
419		}