Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureMatcherTest	20	170	11	1.0100%	Show methods

Class FeatureMatcherTest

Class FeatureMatcherTest	Line # 20	Total Statements 170	Complexity 11	TOTAL Coverage 1.0100%
testMatches_byLabel() : void   testMatches_byLabel() : void	2222	12.012	1.01	1.0 1.0100%
testMatches_byScore() : void   testMatches_byScore() : void	6969	15.015	1.01	1.0 1.0100%
testMatches_byAttribute() : void   testMatches_byAttribute() : void	9595	25.025	1.01	1.0 1.0100%
testToString() : void   testToString() : void	135135	11.011	1.01	1.0 1.0100%
testGetAttribute() : void   testGetAttribute() : void	170170	6.06	1.01	1.0 1.0100%
testIsByAttribute() : void   testIsByAttribute() : void	192192	3.03	1.01	1.0 1.0100%
testIsByLabel() : void   testIsByLabel() : void	202202	3.03	1.01	1.0 1.0100%
testIsByScore() : void   testIsByScore() : void	212212	3.03	1.01	1.0 1.0100%
testGetMatcher() : void   testGetMatcher() : void	222222	4.04	1.01	1.0 1.0100%
testFromString() : void   testFromString() : void	232232	76.076	1.01	1.0 1.0100%
testToStableString() : void   testToStableString() : void	340340	12.012	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.42541435	jalview.datamodel.features.FeatureMatcherTest.testFromStringjalview.datamodel.features.FeatureMatcherTest.testFromString	1PASS
	0.1436464	jalview.datamodel.features.FeatureMatcherTest.testMatches_byAttributejalview.datamodel.features.FeatureMatcherTest.testMatches_byAttribute	1PASS
	0.08839779	jalview.datamodel.features.FeatureMatcherTest.testMatches_byScorejalview.datamodel.features.FeatureMatcherTest.testMatches_byScore	1PASS
	0.0718232	jalview.datamodel.features.FeatureMatcherTest.testMatches_byLabeljalview.datamodel.features.FeatureMatcherTest.testMatches_byLabel	1PASS
	0.0718232	jalview.datamodel.features.FeatureMatcherTest.testToStableStringjalview.datamodel.features.FeatureMatcherTest.testToStableString	1PASS
	0.06629834	jalview.datamodel.features.FeatureMatcherTest.testToStringjalview.datamodel.features.FeatureMatcherTest.testToString	1PASS
	0.038674034	jalview.datamodel.features.FeatureMatcherTest.testGetAttributejalview.datamodel.features.FeatureMatcherTest.testGetAttribute	1PASS
	0.027624309	jalview.datamodel.features.FeatureMatcherTest.testGetMatcherjalview.datamodel.features.FeatureMatcherTest.testGetMatcher	1PASS
	0.022099448	jalview.datamodel.features.FeatureMatcherTest.testIsByAttributejalview.datamodel.features.FeatureMatcherTest.testIsByAttribute	1PASS
	0.022099448	jalview.datamodel.features.FeatureMatcherTest.testIsByLabeljalview.datamodel.features.FeatureMatcherTest.testIsByLabel	1PASS
	0.022099448	jalview.datamodel.features.FeatureMatcherTest.testIsByScorejalview.datamodel.features.FeatureMatcherTest.testIsByScore	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
9		import java.util.Locale;
10
11		import org.testng.annotations.Test;
12
13		import jalview.datamodel.SequenceFeature;
14		import jalview.util.MessageManager;
15		import jalview.util.matcher.Condition;
16		import jalview.util.matcher.Matcher;
17		import jalview.util.matcher.MatcherI;
18		import junit.extensions.PA;
19
		100% Uncovered Elements: 0 (181) Complexity: 11 Complexity Density: 0.06
20		public class FeatureMatcherTest
21		{
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
22	1	@Test(groups = "Functional")...
23		public void testMatches_byLabel()
24		{
25	1	SequenceFeature sf = new SequenceFeature("Cath", "this is my label", 11,
26		12, "grp");
27
28		/*
29		* contains - not case sensitive
30		*/
31	1	assertTrue(
32		FeatureMatcher.byLabel(Condition.Contains, "IS").matches(sf));
33	1	assertTrue(FeatureMatcher.byLabel(Condition.Contains, "").matches(sf));
34	1	assertFalse(
35		FeatureMatcher.byLabel(Condition.Contains, "ISNT").matches(sf));
36
37		/*
38		* does not contain
39		*/
40	1	assertTrue(FeatureMatcher.byLabel(Condition.NotContains, "isnt")
41		.matches(sf));
42	1	assertFalse(FeatureMatcher.byLabel(Condition.NotContains, "is")
43		.matches(sf));
44
45		/*
46		* matches
47		*/
48	1	assertTrue(FeatureMatcher.byLabel(Condition.Matches, "THIS is MY label")
49		.matches(sf));
50	1	assertFalse(FeatureMatcher.byLabel(Condition.Matches, "THIS is MY")
51		.matches(sf));
52
53		/*
54		* does not match
55		*/
56	1	assertFalse(FeatureMatcher
57		.byLabel(Condition.NotMatches, "THIS is MY label").matches(sf));
58	1	assertTrue(FeatureMatcher.byLabel(Condition.NotMatches, "THIS is MY")
59		.matches(sf));
60
61		/*
62		* is present / not present
63		*/
64	1	assertTrue(FeatureMatcher.byLabel(Condition.Present, "").matches(sf));
65	1	assertFalse(
66		FeatureMatcher.byLabel(Condition.NotPresent, "").matches(sf));
67		}
68
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
69	1	@Test(groups = "Functional")...
70		public void testMatches_byScore()
71		{
72	1	SequenceFeature sf = new SequenceFeature("Cath", "this is my label", 11,
73		12, 3.2f, "grp");
74
75	1	assertTrue(FeatureMatcher.byScore(Condition.LT, "3.3").matches(sf));
76	1	assertFalse(FeatureMatcher.byScore(Condition.LT, "3.2").matches(sf));
77	1	assertFalse(FeatureMatcher.byScore(Condition.LT, "2.2").matches(sf));
78
79	1	assertTrue(FeatureMatcher.byScore(Condition.LE, "3.3").matches(sf));
80	1	assertTrue(FeatureMatcher.byScore(Condition.LE, "3.2").matches(sf));
81	1	assertFalse(FeatureMatcher.byScore(Condition.LE, "2.2").matches(sf));
82
83	1	assertFalse(FeatureMatcher.byScore(Condition.EQ, "3.3").matches(sf));
84	1	assertTrue(FeatureMatcher.byScore(Condition.EQ, "3.2").matches(sf));
85
86	1	assertFalse(FeatureMatcher.byScore(Condition.GE, "3.3").matches(sf));
87	1	assertTrue(FeatureMatcher.byScore(Condition.GE, "3.2").matches(sf));
88	1	assertTrue(FeatureMatcher.byScore(Condition.GE, "2.2").matches(sf));
89
90	1	assertFalse(FeatureMatcher.byScore(Condition.GT, "3.3").matches(sf));
91	1	assertFalse(FeatureMatcher.byScore(Condition.GT, "3.2").matches(sf));
92	1	assertTrue(FeatureMatcher.byScore(Condition.GT, "2.2").matches(sf));
93		}
94
		100% Uncovered Elements: 0 (25) Complexity: 1 Complexity Density: 0.04 1PASS
95	1	@Test(groups = "Functional")...
96		public void testMatches_byAttribute()
97		{
98		/*
99		* a numeric matcher - MatcherTest covers more conditions
100		*/
101	1	FeatureMatcherI fm = FeatureMatcher
102		.byAttribute(Condition.GE, "-2", "AF");
103	1	SequenceFeature sf = new SequenceFeature("Cath", "desc", 11, 12, "grp");
104	1	assertFalse(fm.matches(sf));
105	1	sf.setValue("AF", "foobar");
106	1	assertFalse(fm.matches(sf));
107	1	sf.setValue("AF", "-2");
108	1	assertTrue(fm.matches(sf));
109	1	sf.setValue("AF", "-1");
110	1	assertTrue(fm.matches(sf));
111	1	sf.setValue("AF", "-3");
112	1	assertFalse(fm.matches(sf));
113	1	sf.setValue("AF", "");
114	1	assertFalse(fm.matches(sf));
115
116		/*
117		* a string pattern matcher
118		*/
119	1	fm = FeatureMatcher.byAttribute(Condition.Contains, "Cat", "AF");
120	1	assertFalse(fm.matches(sf));
121	1	sf.setValue("AF", "raining cats and dogs");
122	1	assertTrue(fm.matches(sf));
123
124	1	fm = FeatureMatcher.byAttribute(Condition.Present, "", "AC");
125	1	assertFalse(fm.matches(sf));
126	1	sf.setValue("AC", "21");
127	1	assertTrue(fm.matches(sf));
128
129	1	fm = FeatureMatcher.byAttribute(Condition.NotPresent, "", "AC_Females");
130	1	assertTrue(fm.matches(sf));
131	1	sf.setValue("AC_Females", "21");
132	1	assertFalse(fm.matches(sf));
133		}
134
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
135	1	@Test(groups = "Functional")...
136		public void testToString()
137		{
138	1	Locale.setDefault(Locale.ENGLISH);
139
140		/*
141		* toString uses the i18n translation of the enum conditions
142		*/
143	1	FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.LT, "1.2",
144		"AF");
145	1	assertEquals(fm.toString(), "AF < 1.2");
146
147		/*
148		* Present / NotPresent omit the value pattern
149		*/
150	1	fm = FeatureMatcher.byAttribute(Condition.Present, "", "AF");
151	1	assertEquals(fm.toString(), "AF is present");
152	1	fm = FeatureMatcher.byAttribute(Condition.NotPresent, "", "AF");
153	1	assertEquals(fm.toString(), "AF is not present");
154
155		/*
156		* by Label
157		*/
158	1	fm = FeatureMatcher.byLabel(Condition.Matches, "foobar");
159	1	assertEquals(fm.toString(),
160		MessageManager.getString("label.label") + " matches 'foobar'");
161
162		/*
163		* by Score
164		*/
165	1	fm = FeatureMatcher.byScore(Condition.GE, "12.2");
166	1	assertEquals(fm.toString(),
167		MessageManager.getString("label.score") + " >= 12.2");
168		}
169
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
170	1	@Test(groups = "Functional")...
171		public void testGetAttribute()
172		{
173	1	FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2",
174		"AF");
175	1	assertEquals(fm.getAttribute(), new String[] { "AF" });
176
177		/*
178		* compound key (attribute / subattribute)
179		*/
180	1	fm = FeatureMatcher.byAttribute(Condition.GE, "-2F", "CSQ",
181		"Consequence");
182	1	assertEquals(fm.getAttribute(), new String[] { "CSQ", "Consequence" });
183
184		/*
185		* answers null if match is by Label or by Score
186		*/
187	1	assertNull(FeatureMatcher.byLabel(Condition.NotContains, "foo")
188		.getAttribute());
189	1	assertNull(FeatureMatcher.byScore(Condition.LE, "-1").getAttribute());
190		}
191
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
192	1	@Test(groups = "Functional")...
193		public void testIsByAttribute()
194		{
195	1	assertFalse(FeatureMatcher.byLabel(Condition.NotContains, "foo")
196		.isByAttribute());
197	1	assertFalse(FeatureMatcher.byScore(Condition.LE, "-1").isByAttribute());
198	1	assertTrue(FeatureMatcher.byAttribute(Condition.LE, "-1", "AC")
199		.isByAttribute());
200		}
201
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
202	1	@Test(groups = "Functional")...
203		public void testIsByLabel()
204		{
205	1	assertTrue(FeatureMatcher.byLabel(Condition.NotContains, "foo")
206		.isByLabel());
207	1	assertFalse(FeatureMatcher.byScore(Condition.LE, "-1").isByLabel());
208	1	assertFalse(FeatureMatcher.byAttribute(Condition.LE, "-1", "AC")
209		.isByLabel());
210		}
211
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
212	1	@Test(groups = "Functional")...
213		public void testIsByScore()
214		{
215	1	assertFalse(FeatureMatcher.byLabel(Condition.NotContains, "foo")
216		.isByScore());
217	1	assertTrue(FeatureMatcher.byScore(Condition.LE, "-1").isByScore());
218	1	assertFalse(FeatureMatcher.byAttribute(Condition.LE, "-1", "AC")
219		.isByScore());
220		}
221
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
222	1	@Test(groups = "Functional")...
223		public void testGetMatcher()
224		{
225	1	FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2f",
226		"AF");
227	1	assertEquals(fm.getMatcher().getCondition(), Condition.GE);
228	1	assertEquals(PA.getValue(fm.getMatcher(), "floatValue"), -2F);
229	1	assertEquals(fm.getMatcher().getPattern(), "-2.0");
230		}
231
		100% Uncovered Elements: 0 (76) Complexity: 1 Complexity Density: 0.01 1PASS
232	1	@Test(groups = "Functional")...
233		public void testFromString()
234		{
235	1	FeatureMatcherI fm = FeatureMatcher.fromString("'AF' LT 1.2");
236	1	assertFalse(fm.isByLabel());
237	1	assertFalse(fm.isByScore());
238	1	assertEquals(fm.getAttribute(), new String[] { "AF" });
239	1	MatcherI matcher = fm.getMatcher();
240	1	assertSame(Condition.LT, matcher.getCondition());
241	1	assertEquals(PA.getValue(matcher, "floatValue"), 1.2f);
242	1	assertSame(PA.getValue(matcher, "patternType"),
243		Matcher.PatternType.Float);
244	1	assertEquals(matcher.getPattern(), "1.2");
245
246		// quotes are optional, condition is not case sensitive
247	1	fm = FeatureMatcher.fromString("AF lt '1.2'");
248	1	matcher = fm.getMatcher();
249	1	assertFalse(fm.isByLabel());
250	1	assertFalse(fm.isByScore());
251	1	assertEquals(fm.getAttribute(), new String[] { "AF" });
252	1	assertSame(Condition.LT, matcher.getCondition());
253	1	assertEquals(PA.getValue(matcher, "floatValue"), 1.2F);
254	1	assertEquals(matcher.getPattern(), "1.2");
255
256	1	fm = FeatureMatcher.fromString("'AF' Present");
257	1	matcher = fm.getMatcher();
258	1	assertFalse(fm.isByLabel());
259	1	assertFalse(fm.isByScore());
260	1	assertEquals(fm.getAttribute(), new String[] { "AF" });
261	1	assertSame(Condition.Present, matcher.getCondition());
262	1	assertSame(PA.getValue(matcher, "patternType"),
263		Matcher.PatternType.String);
264
265	1	fm = FeatureMatcher.fromString("CSQ:Consequence contains damaging");
266	1	matcher = fm.getMatcher();
267	1	assertFalse(fm.isByLabel());
268	1	assertFalse(fm.isByScore());
269	1	assertEquals(fm.getAttribute(), new String[] { "CSQ", "Consequence" });
270	1	assertSame(Condition.Contains, matcher.getCondition());
271	1	assertEquals(matcher.getPattern(), "damaging");
272
273		// keyword Label is not case sensitive
274	1	fm = FeatureMatcher.fromString("LABEL Matches 'foobar'");
275	1	matcher = fm.getMatcher();
276	1	assertTrue(fm.isByLabel());
277	1	assertFalse(fm.isByScore());
278	1	assertNull(fm.getAttribute());
279	1	assertSame(Condition.Matches, matcher.getCondition());
280	1	assertEquals(matcher.getPattern(), "foobar");
281
282	1	fm = FeatureMatcher.fromString("'Label' matches 'foo bar'");
283	1	matcher = fm.getMatcher();
284	1	assertTrue(fm.isByLabel());
285	1	assertFalse(fm.isByScore());
286	1	assertNull(fm.getAttribute());
287	1	assertSame(Condition.Matches, matcher.getCondition());
288	1	assertEquals(matcher.getPattern(), "foo bar");
289
290		// quotes optional on pattern
291	1	fm = FeatureMatcher.fromString("'Label' matches foo bar");
292	1	matcher = fm.getMatcher();
293	1	assertTrue(fm.isByLabel());
294	1	assertFalse(fm.isByScore());
295	1	assertNull(fm.getAttribute());
296	1	assertSame(Condition.Matches, matcher.getCondition());
297	1	assertEquals(matcher.getPattern(), "foo bar");
298
299		// integer condition
300	1	fm = FeatureMatcher.fromString("Score GE 12");
301	1	matcher = fm.getMatcher();
302	1	assertFalse(fm.isByLabel());
303	1	assertTrue(fm.isByScore());
304	1	assertNull(fm.getAttribute());
305	1	assertSame(Condition.GE, matcher.getCondition());
306	1	assertEquals(matcher.getPattern(), "12");
307	1	assertEquals(PA.getValue(matcher, "floatValue"), 0f);
308	1	assertEquals(PA.getValue(matcher, "longValue"), 12L);
309	1	assertSame(PA.getValue(matcher, "patternType"),
310		Matcher.PatternType.Integer);
311
312		// keyword Score is not case sensitive
313	1	fm = FeatureMatcher.fromString("'SCORE' ge '12.2'");
314	1	matcher = fm.getMatcher();
315	1	assertFalse(fm.isByLabel());
316	1	assertTrue(fm.isByScore());
317	1	assertNull(fm.getAttribute());
318	1	assertSame(Condition.GE, matcher.getCondition());
319	1	assertEquals(matcher.getPattern(), "12.2");
320	1	assertEquals(PA.getValue(matcher, "floatValue"), 12.2F);
321
322		// invalid numeric pattern
323	1	assertNull(FeatureMatcher.fromString("Score eq twelve"));
324		// unbalanced opening quote
325	1	assertNull(FeatureMatcher.fromString("'Score ge 12.2"));
326		// unbalanced pattern quote
327	1	assertNull(FeatureMatcher.fromString("'Score' ge '12.2"));
328		// pattern missing
329	1	assertNull(FeatureMatcher.fromString("Score ge"));
330		// condition and pattern missing
331	1	assertNull(FeatureMatcher.fromString("Score"));
332		// everything missing
333	1	assertNull(FeatureMatcher.fromString(""));
334		}
335
336		/**
337		* Tests for toStableString which (unlike toString) does not i18n the
338		* conditions
339		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
340	1	@Test(groups = "Functional")...
341		public void testToStableString()
342		{
343		// attribute name not quoted unless it contains space
344	1	FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.LT, "1.2",
345		"AF");
346	1	assertEquals(fm.toStableString(), "AF LT 1.2");
347
348		/*
349		* Present / NotPresent omit the value pattern
350		*/
351	1	fm = FeatureMatcher.byAttribute(Condition.Present, "", "AF");
352	1	assertEquals(fm.toStableString(), "AF Present");
353	1	fm = FeatureMatcher.byAttribute(Condition.NotPresent, "", "AF");
354	1	assertEquals(fm.toStableString(), "AF NotPresent");
355
356		/*
357		* by Label
358		* pattern not quoted unless it contains space
359		*/
360	1	fm = FeatureMatcher.byLabel(Condition.Matches, "foobar");
361	1	assertEquals(fm.toStableString(), "Label Matches foobar");
362
363	1	fm = FeatureMatcher.byLabel(Condition.Matches, "foo bar");
364	1	assertEquals(fm.toStableString(), "Label Matches 'foo bar'");
365
366		/*
367		* by Score
368		*/
369	1	fm = FeatureMatcher.byScore(Condition.GE, "12.2");
370	1	assertEquals(fm.toStableString(), "Score GE 12.2");
371		}
372		}