Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureAttributesTest	40	45	6	0.00%	Show methods

Class FeatureAttributesTest

Class FeatureAttributesTest	Line # 40	Total Statements 45	Complexity 6	TOTAL Coverage 0.00%
setUp() : void   setUp() : void	4646	2.02	1.01	0.0 0.00%
tearDown() : void   tearDown() : void	5656	2.02	1.01	0.0 0.00%
testAttributeNameComparator() : void   testAttributeNameComparator() : void	6767	7.07	1.01	0.0 0.00%
testGetMinMax() : void   testGetMinMax() : void	9595	18.018	1.01	0.0 0.00%
testGetDescription() : void   testGetDescription() : void	129129	6.06	1.01	0.0 0.00%
testDatatype() : void   testDatatype() : void	143143	10.010	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.features;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertNull;
25		import static org.testng.Assert.assertTrue;
26
27		import jalview.datamodel.SequenceFeature;
28		import jalview.datamodel.features.FeatureAttributes.Datatype;
29
30		import java.util.Comparator;
31		import java.util.HashMap;
32		import java.util.Map;
33
34		import org.testng.annotations.AfterMethod;
35		import org.testng.annotations.BeforeClass;
36		import org.testng.annotations.Test;
37
38		import junit.extensions.PA;
39
		0% Uncovered Elements: 51 (51) Complexity: 6 Complexity Density: 0.13
40		public class FeatureAttributesTest
41		{
42
43		/**
44		* clear down attributes map before tests
45		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
46	0	@BeforeClass(alwaysRun = true)...
47		public void setUp()
48		{
49	0	FeatureAttributes fa = FeatureAttributes.getInstance();
50	0	((Map<?, ?>) PA.getValue(fa, "attributes")).clear();
51		}
52
53		/**
54		* clear down attributes map after tests
55		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
56	0	@AfterMethod(alwaysRun = true)...
57		public void tearDown()
58		{
59	0	FeatureAttributes fa = FeatureAttributes.getInstance();
60	0	((Map<?, ?>) PA.getValue(fa, "attributes")).clear();
61		}
62
63		/**
64		* Test the method that keeps attribute names in non-case-sensitive order,
65		* including handling of 'compound' names
66		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14 4-
67	0	@Test(groups = "Functional")...
68		public void testAttributeNameComparator()
69		{
70	0	FeatureAttributes fa = FeatureAttributes.getInstance();
71	0	Comparator<String[]> comp = (Comparator<String[]>) PA.getValue(fa,
72		"comparator");
73
74	0	assertEquals(
75		comp.compare(new String[]
76		{ "CSQ" }, new String[] { "csq" }), 0);
77
78	0	assertTrue(
79		comp.compare(new String[]
80		{ "CSQ", "a" }, new String[] { "csq" }) > 0);
81
82	0	assertTrue(
83		comp.compare(new String[]
84		{ "CSQ" }, new String[] { "csq", "b" }) < 0);
85
86	0	assertTrue(
87		comp.compare(new String[]
88		{ "CSQ", "AF" }, new String[] { "csq", "ac" }) > 0);
89
90	0	assertTrue(
91		comp.compare(new String[]
92		{ "CSQ", "ac" }, new String[] { "csq", "AF" }) < 0);
93		}
94
		0% Uncovered Elements: 18 (18) Complexity: 1 Complexity Density: 0.06 4-
95	0	@Test(groups = "Functional")...
96		public void testGetMinMax()
97		{
98	0	SequenceFeature sf = new SequenceFeature("Pfam", "desc", 10, 20,
99		"group");
100	0	FeatureAttributes fa = FeatureAttributes.getInstance();
101	0	assertNull(fa.getMinMax("Pfam", "kd"));
102	0	sf.setValue("domain", "xyz");
103	0	assertNull(fa.getMinMax("Pfam", "kd"));
104	0	sf.setValue("kd", "1.3");
105	0	assertEquals(fa.getMinMax("Pfam", "kd"), new float[] { 1.3f, 1.3f });
106	0	sf.setValue("kd", "-2.6");
107	0	assertEquals(fa.getMinMax("Pfam", "kd"), new float[] { -2.6f, 1.3f });
108		// setting 'mixed' character and numeric values wipes the min/max value
109	0	sf.setValue("kd", "some text");
110	0	assertNull(fa.getMinMax("Pfam", "kd"));
111
112	0	Map<String, String> csq = new HashMap<>();
113	0	csq.put("AF", "-3");
114	0	sf.setValue("CSQ", csq);
115	0	assertEquals(fa.getMinMax("Pfam", "CSQ", "AF"),
116		new float[]
117		{ -3f, -3f });
118	0	csq.put("AF", "4");
119	0	sf.setValue("CSQ", csq);
120	0	assertEquals(fa.getMinMax("Pfam", "CSQ", "AF"),
121		new float[]
122		{ -3f, 4f });
123		}
124
125		/**
126		* Test the method that returns an attribute description, provided it is
127		* recorded and unique
128		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17 4-
129	0	@Test(groups = "Functional")...
130		public void testGetDescription()
131		{
132	0	FeatureAttributes fa = FeatureAttributes.getInstance();
133		// with no description returns null
134	0	assertNull(fa.getDescription("Pfam", "kd"));
135		// with a unique description, returns that value
136	0	fa.addDescription("Pfam", "desc1", "kd");
137	0	assertEquals(fa.getDescription("Pfam", "kd"), "desc1");
138		// with ambiguous description, returns null
139	0	fa.addDescription("Pfam", "desc2", "kd");
140	0	assertNull(fa.getDescription("Pfam", "kd"));
141		}
142
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1 4-
143	0	@Test(groups = "Functional")...
144		public void testDatatype()
145		{
146	0	FeatureAttributes fa = FeatureAttributes.getInstance();
147	0	assertNull(fa.getDatatype("Pfam", "kd"));
148	0	SequenceFeature sf = new SequenceFeature("Pfam", "desc", 10, 20,
149		"group");
150	0	sf.setValue("kd", "-1");
151	0	sf.setValue("domain", "Metal");
152	0	sf.setValue("phase", "1");
153	0	sf.setValue("phase", "reverse");
154	0	assertEquals(fa.getDatatype("Pfam", "kd"), Datatype.Number);
155	0	assertEquals(fa.getDatatype("Pfam", "domain"), Datatype.Character);
156	0	assertEquals(fa.getDatatype("Pfam", "phase"), Datatype.Mixed);
157		}
158		}