Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
FeatureAttributesTest	20	45	6	0	1.0100%	Show methods

Class FeatureAttributesTest

Class FeatureAttributesTest	Line # 20	Total Statements 45	Complexity 6	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUp() : void   setUp() : void	2626	2.02	1.01	0.00	1.0 1.0100%
tearDown() : void   tearDown() : void	3636	2.02	1.01	0.00	1.0 1.0100%
testAttributeNameComparator() : void   testAttributeNameComparator() : void	4747	7.07	1.01	0.00	1.0 1.0100%
testGetMinMax() : void   testGetMinMax() : void	7070	18.018	1.01	0.00	1.0 1.0100%
testGetDescription() : void   testGetDescription() : void	104104	6.06	1.01	0.00	1.0 1.0100%
testDatatype() : void   testDatatype() : void	118118	10.010	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.37254903	jalview.datamodel.features.FeatureAttributesTest.testGetMinMaxjalview.datamodel.features.FeatureAttributesTest.testGetMinMax	1PASS
	0.21568628	jalview.datamodel.features.FeatureAttributesTest.testDatatypejalview.datamodel.features.FeatureAttributesTest.testDatatype	1PASS
	0.15686275	jalview.datamodel.features.FeatureAttributesTest.testAttributeNameComparatorjalview.datamodel.features.FeatureAttributesTest.testAttributeNameComparator	1PASS
	0.13725491	jalview.datamodel.features.FeatureAttributesTest.testGetDescriptionjalview.datamodel.features.FeatureAttributesTest.testGetDescription	1PASS

 

Source view

1		package jalview.datamodel.features;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertNull;
5		import static org.testng.Assert.assertTrue;
6
7		import jalview.datamodel.SequenceFeature;
8		import jalview.datamodel.features.FeatureAttributes.Datatype;
9
10		import java.util.Comparator;
11		import java.util.HashMap;
12		import java.util.Map;
13
14		import org.testng.annotations.AfterMethod;
15		import org.testng.annotations.BeforeClass;
16		import org.testng.annotations.Test;
17
18		import junit.extensions.PA;
19
		100% Uncovered Elements: 0 (51) Complexity: 6 Complexity Density: 0.13
20		public class FeatureAttributesTest
21		{
22
23		/**
24		* clear down attributes map before tests
25		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
26	1	@BeforeClass(alwaysRun = true)...
27		public void setUp()
28		{
29	1	FeatureAttributes fa = FeatureAttributes.getInstance();
30	1	((Map<?, ?>) PA.getValue(fa, "attributes")).clear();
31		}
32
33		/**
34		* clear down attributes map after tests
35		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
36	4	@AfterMethod(alwaysRun = true)...
37		public void tearDown()
38		{
39	4	FeatureAttributes fa = FeatureAttributes.getInstance();
40	4	((Map<?, ?>) PA.getValue(fa, "attributes")).clear();
41		}
42
43		/**
44		* Test the method that keeps attribute names in non-case-sensitive order,
45		* including handling of 'compound' names
46		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
47	1	@Test(groups="Functional")...
48		public void testAttributeNameComparator()
49		{
50	1	FeatureAttributes fa = FeatureAttributes.getInstance();
51	1	Comparator<String[]> comp = (Comparator<String[]>) PA.getValue(fa,
52		"comparator");
53
54	1	assertEquals(
55		comp.compare(new String[] { "CSQ" }, new String[] { "csq" }), 0);
56
57	1	assertTrue(comp.compare(new String[] { "CSQ", "a" },
58		new String[] { "csq" }) > 0);
59
60	1	assertTrue(comp.compare(new String[] { "CSQ" }, new String[] { "csq",
61		"b" }) < 0);
62
63	1	assertTrue(comp.compare(new String[] { "CSQ", "AF" }, new String[] {
64		"csq", "ac" }) > 0);
65
66	1	assertTrue(comp.compare(new String[] { "CSQ", "ac" }, new String[] {
67		"csq", "AF" }) < 0);
68		}
69
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
70	1	@Test(groups = "Functional")...
71		public void testGetMinMax()
72		{
73	1	SequenceFeature sf = new SequenceFeature("Pfam", "desc", 10, 20,
74		"group");
75	1	FeatureAttributes fa = FeatureAttributes.getInstance();
76	1	assertNull(fa.getMinMax("Pfam", "kd"));
77	1	sf.setValue("domain", "xyz");
78	1	assertNull(fa.getMinMax("Pfam", "kd"));
79	1	sf.setValue("kd", "1.3");
80	1	assertEquals(fa.getMinMax("Pfam", "kd"), new float[] { 1.3f, 1.3f });
81	1	sf.setValue("kd", "-2.6");
82	1	assertEquals(fa.getMinMax("Pfam", "kd"), new float[] { -2.6f, 1.3f });
83		// setting 'mixed' character and numeric values wipes the min/max value
84	1	sf.setValue("kd", "some text");
85	1	assertNull(fa.getMinMax("Pfam", "kd"));
86
87	1	Map<String, String> csq = new HashMap<>();
88	1	csq.put("AF", "-3");
89	1	sf.setValue("CSQ", csq);
90	1	assertEquals(fa.getMinMax("Pfam", "CSQ", "AF"),
91		new float[]
92		{ -3f, -3f });
93	1	csq.put("AF", "4");
94	1	sf.setValue("CSQ", csq);
95	1	assertEquals(fa.getMinMax("Pfam", "CSQ", "AF"),
96		new float[]
97		{ -3f, 4f });
98		}
99
100		/**
101		* Test the method that returns an attribute description, provided it is
102		* recorded and unique
103		*/
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
104	1	@Test(groups = "Functional")...
105		public void testGetDescription()
106		{
107	1	FeatureAttributes fa = FeatureAttributes.getInstance();
108		// with no description returns null
109	1	assertNull(fa.getDescription("Pfam", "kd"));
110		// with a unique description, returns that value
111	1	fa.addDescription("Pfam", "desc1", "kd");
112	1	assertEquals(fa.getDescription("Pfam", "kd"), "desc1");
113		// with ambiguous description, returns null
114	1	fa.addDescription("Pfam", "desc2", "kd");
115	1	assertNull(fa.getDescription("Pfam", "kd"));
116		}
117
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
118	1	@Test(groups = "Functional")...
119		public void testDatatype()
120		{
121	1	FeatureAttributes fa = FeatureAttributes.getInstance();
122	1	assertNull(fa.getDatatype("Pfam", "kd"));
123	1	SequenceFeature sf = new SequenceFeature("Pfam", "desc", 10, 20,
124		"group");
125	1	sf.setValue("kd", "-1");
126	1	sf.setValue("domain", "Metal");
127	1	sf.setValue("phase", "1");
128	1	sf.setValue("phase", "reverse");
129	1	assertEquals(fa.getDatatype("Pfam", "kd"), Datatype.Number);
130	1	assertEquals(fa.getDatatype("Pfam", "domain"), Datatype.Character);
131	1	assertEquals(fa.getDatatype("Pfam", "phase"), Datatype.Mixed);
132		}
133		}