Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AnnotationRowFilterTest	20	39	5	3	0.931818293.2%	Show methods

Class AnnotationRowFilterTest

Class AnnotationRowFilterTest	Line # 20	Total Statements 39	Complexity 5	Uncovered Elements 3	TOTAL Coverage 0.931818293.2%
valueChanged(boolean) : void   valueChanged(boolean) : void	3838	0.00	1.01	0.00	-1.0 -1.0 -
updateView() : void   updateView() : void	4343	0.00	1.01	0.00	-1.0 -1.0 -
reset() : void   reset() : void	4848	0.00	1.01	0.00	-1.0 -1.0 -
setUp() : void   setUp() : void	2626	5.05	1.01	0.00	1.0 1.0100%
testGetAnnotationItems() : void   testGetAnnotationItems() : void	5959	34.034	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.79545456	jalview.gui.AnnotationRowFilterTest.testGetAnnotationItemsjalview.gui.AnnotationRowFilterTest.testGetAnnotationItems	1PASS

 

Source view

1		package jalview.gui;
2
3		import static org.testng.Assert.assertEquals;
4
5		import jalview.bin.Cache;
6		import jalview.datamodel.AlignmentAnnotation;
7		import jalview.datamodel.AlignmentI;
8		import jalview.datamodel.SequenceI;
9		import jalview.io.DataSourceType;
10		import jalview.io.FileLoader;
11
12		import java.util.Vector;
13
14		import org.testng.annotations.BeforeClass;
15		import org.testng.annotations.Test;
16
17		/**
18		* Tests for methods of base class of annotation column or colour chooser
19		*/
		93.2% Uncovered Elements: 3 (44) Complexity: 5 Complexity Density: 0.13
20		public class AnnotationRowFilterTest
21		{
22		AlignFrame af;
23
24		private AnnotationRowFilter testee;
25
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
26	1	@BeforeClass(alwaysRun = true)...
27		public void setUp()
28		{
29	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
30	1	Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
31		Boolean.TRUE.toString());
32	1	Cache.applicationProperties.setProperty(
33		Preferences.SHOW_AUTOCALC_ABOVE, Boolean.TRUE.toString());
34	1	af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
35		DataSourceType.FILE);
36	1	testee = new AnnotationRowFilter(af.viewport, af.alignPanel)
37		{
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
38	0	@Override...
39		public void valueChanged(boolean updateAllAnnotation)
40		{
41		}
42
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
43	0	@Override...
44		public void updateView()
45		{
46		}
47
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
48	0	@Override...
49		public void reset()
50		{
51		}
52		};
53		}
54
55		/**
56		* Test the method that builds the drop-down list of annotations to choose
57		* from for colour by annotation or select columns by annotation
58		*/
		100% Uncovered Elements: 0 (34) Complexity: 1 Complexity Density: 0.03 1PASS
59	1	@Test(groups = "Functional")...
60		public void testGetAnnotationItems()
61		{
62	1	AlignmentI al = af.getViewport().getAlignment();
63	1	SequenceI seq1 = al.findSequenceMatch("FER_CAPAA")[0];
64	1	SequenceI seq2 = al.findSequenceMatch("FER_BRANA")[0];
65
66	1	AlignmentAnnotation ann1 = new AlignmentAnnotation("ann1Label", "ann1",
67		null);
68	1	al.addAnnotation(ann1);
69	1	AlignmentAnnotation ann2 = new AlignmentAnnotation("Significance",
70		"ann2", null);
71	1	al.addAnnotation(ann2);
72		/*
73		* a second Significance alignment annotation
74		*/
75	1	AlignmentAnnotation ann2a = new AlignmentAnnotation("Significance",
76		"ann2", null);
77	1	al.addAnnotation(ann2a);
78
79	1	AlignmentAnnotation ann3 = new AlignmentAnnotation("Jronn", "Jronn",
80		null);
81	1	ann3.setSequenceRef(seq1);
82	1	al.addAnnotation(ann3);
83	1	AlignmentAnnotation ann4 = new AlignmentAnnotation("Jronn", "Jronn",
84		null);
85	1	ann4.setSequenceRef(seq2);
86	1	al.addAnnotation(ann4);
87	1	AlignmentAnnotation ann5 = new AlignmentAnnotation("Jnet", "Jnet", null);
88	1	ann5.setSequenceRef(seq2);
89	1	al.addAnnotation(ann5);
90		/*
91		* a second Jnet annotation for FER_BRANA
92		*/
93	1	AlignmentAnnotation ann6 = new AlignmentAnnotation("Jnet", "Jnet", null);
94	1	ann6.setSequenceRef(seq2);
95	1	al.addAnnotation(ann6);
96
97		/*
98		* drop-down items with 'Per-sequence only' not checked
99		*/
100	1	Vector<String> items = testee.getAnnotationItems(false);
101	1	assertEquals(
102		items.toString(),
103		"[Conservation, Quality, Consensus, Occupancy, ann1Label, Significance, Significance_1, Jronn_FER_CAPAA, Jronn_FER_BRANA, Jnet_FER_BRANA, Jnet_FER_BRANA_2]");
104	1	assertEquals(testee.getAnnotationMenuLabel(ann1), "ann1Label");
105	1	assertEquals(testee.getAnnotationMenuLabel(ann2), "Significance");
106	1	assertEquals(testee.getAnnotationMenuLabel(ann2a), "Significance_1");
107	1	assertEquals(testee.getAnnotationMenuLabel(ann3), "Jronn_FER_CAPAA");
108	1	assertEquals(testee.getAnnotationMenuLabel(ann4), "Jronn_FER_BRANA");
109	1	assertEquals(testee.getAnnotationMenuLabel(ann5), "Jnet_FER_BRANA");
110	1	assertEquals(testee.getAnnotationMenuLabel(ann6), "Jnet_FER_BRANA_2");
111
112		/*
113		* drop-down items with 'Per-sequence only' checked
114		*/
115	1	items = testee.getAnnotationItems(true);
116	1	assertEquals(items.toString(), "[Jronn, Jnet]");
117		// the first annotation of the type is associated with the menu item
118	1	assertEquals(testee.getAnnotationMenuLabel(ann3), "Jronn");
119	1	assertEquals(testee.getAnnotationMenuLabel(ann5), "Jnet");
120		}
121		}