Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AnnotationColourGradientTest	18	80	27	0	1.0100%	Show methods

Class AnnotationColourGradientTest

Class AnnotationColourGradientTest	Line # 18	Total Statements 80	Complexity 27	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUp() : void   setUp() : void	3838	10.010	2.02	0.00	1.0 1.0100%
testShadeCalculation_noThreshold() : void   testShadeCalculation_noThreshold() : void	6363	5.05	2.02	0.00	1.0 1.0100%
testShadeCalculation_aboveThreshold() : void   testShadeCalculation_aboveThreshold() : void	8383	15.015	4.04	0.00	1.0 1.0100%
testShadeCalculation_belowThreshold() : void   testShadeCalculation_belowThreshold() : void	132132	14.014	4.04	0.00	1.0 1.0100%
testFindColour_aboveThreshold() : void   testFindColour_aboveThreshold() : void	182182	12.012	5.05	0.00	1.0 1.0100%
testFindColour_belowThreshold() : void   testFindColour_belowThreshold() : void	224224	11.011	5.05	0.00	1.0 1.0100%
testFindColour_noThreshold() : void   testFindColour_noThreshold() : void	257257	6.06	2.02	0.00	1.0 1.0100%
testFindColour_originalColours() : void   testFindColour_originalColours() : void	276276	7.07	3.03	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.17460318	jalview.schemes.AnnotationColourGradientTest.testShadeCalculation_aboveThresholdjalview.schemes.AnnotationColourGradientTest.testShadeCalculation_aboveThreshold	1PASS
	0.16666667	jalview.schemes.AnnotationColourGradientTest.testFindColour_aboveThresholdjalview.schemes.AnnotationColourGradientTest.testFindColour_aboveThreshold	1PASS
	0.16666667	jalview.schemes.AnnotationColourGradientTest.testShadeCalculation_belowThresholdjalview.schemes.AnnotationColourGradientTest.testShadeCalculation_belowThreshold	1PASS
	0.15873016	jalview.schemes.AnnotationColourGradientTest.testFindColour_belowThresholdjalview.schemes.AnnotationColourGradientTest.testFindColour_belowThreshold	1PASS
	0.0952381	jalview.schemes.AnnotationColourGradientTest.testFindColour_originalColoursjalview.schemes.AnnotationColourGradientTest.testFindColour_originalColours	1PASS
	0.071428575	jalview.schemes.AnnotationColourGradientTest.testFindColour_noThresholdjalview.schemes.AnnotationColourGradientTest.testFindColour_noThreshold	1PASS
	0.06349207	jalview.schemes.AnnotationColourGradientTest.testShadeCalculation_noThresholdjalview.schemes.AnnotationColourGradientTest.testShadeCalculation_noThreshold	1PASS

 

Source view

1		package jalview.schemes;
2
3		import static org.testng.Assert.assertEquals;
4
5		import jalview.datamodel.Alignment;
6		import jalview.datamodel.AlignmentAnnotation;
7		import jalview.datamodel.AlignmentI;
8		import jalview.datamodel.Annotation;
9		import jalview.datamodel.GraphLine;
10		import jalview.datamodel.Sequence;
11		import jalview.datamodel.SequenceI;
12
13		import java.awt.Color;
14
15		import org.testng.annotations.BeforeClass;
16		import org.testng.annotations.Test;
17
		100% Uncovered Elements: 0 (126) Complexity: 27 Complexity Density: 0.34
18		public class AnnotationColourGradientTest
19		{
20		final static int WIDTH = 11;
21
22		final static int THRESHOLD_FIVE = 5;
23
24		private AlignmentAnnotation ann;
25
26		private SequenceI seq;
27
28		private AlignmentI al;
29
30		Color minColour = new Color(50, 200, 150);
31
32		Color maxColour = new Color(150, 100, 250);
33
34		/**
35		* Setup creates an annotation over 11 columns with values 0-10 and threshold
36		* 5
37		*/
		100% Uncovered Elements: 0 (12) Complexity: 2 Complexity Density: 0.2
38	1	@BeforeClass(alwaysRun = true)...
39		public void setUp()
40		{
41	1	Annotation[] anns = new Annotation[WIDTH];
42		/*
43		* set annotations with values 0-10, graded colours
44		*/
45	12	for (int col = 0; col < WIDTH; col++)
46		{
47	11	int hue = col * 20;
48	11	Color colour = new Color(hue, hue, hue);
49	11	anns[col] = new Annotation("a", "a", 'a', col, colour);
50		}
51
52	1	seq = new Sequence("Seq", "");
53	1	al = new Alignment(new SequenceI[]{ seq});
54
55		/*
56		* AlignmentAnnotation constructor works out min-max range
57		*/
58	1	ann = new AlignmentAnnotation("", "", anns);
59	1	ann.setThreshold(new GraphLine(THRESHOLD_FIVE, "", Color.RED));
60	1	seq.addAlignmentAnnotation(ann);
61		}
62
		100% Uncovered Elements: 0 (7) Complexity: 2 Complexity Density: 0.4 1PASS
63	1	@Test(groups = "Functional")...
64		public void testShadeCalculation_noThreshold()
65		{
66	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
67		minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
68	12	for (int col = 0; col < WIDTH; col++)
69		{
70	11	Color result = testee.shadeCalculation(ann, col);
71		/*
72		* column <n> is n/10 of the way from minCol to maxCol
73		*/
74	11	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
75		150 + 10 * col);
76	11	assertEquals(result, expected, "for column " + col);
77		}
78		}
79
80		/**
81		* Test the 'colour above threshold' case
82		*/
		100% Uncovered Elements: 0 (21) Complexity: 4 Complexity Density: 0.27 1PASS
83	1	@Test(groups = "Functional")...
84		public void testShadeCalculation_aboveThreshold()
85		{
86	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
87		minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
88	12	for (int col = 0; col < WIDTH; col++)
89		{
90	11	Color result = testee.shadeCalculation(ann, col);
91		/*
92		* colour is derived regardless of the threshold value
93		* (the renderer will suppress colouring if above/below threshold)
94		*/
95	11	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
96		150 + 10 * col);
97	11	assertEquals(result, expected, "for column " + col);
98		}
99
100		/*
101		* now make 6-10 the span of the colour range
102		* (annotation value == column number in this test)
103		*/
104	1	testee.setThresholdIsMinMax(true);
105	6	for (int col = 0; col < THRESHOLD_FIVE; col++)
106		{
107		/*
108		* colours below the threshold are computed as before
109		*/
110	5	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
111		150 + 10 * col);
112	5	Color result = testee.shadeCalculation(ann, col);
113	5	assertEquals(result, expected, "for column " + col);
114		}
115	7	for (int col = THRESHOLD_FIVE; col < WIDTH; col++)
116		{
117		/*
118		* colours for values >= threshold are graduated
119		* range is 6-10 so steps of 100/5 = 20
120		*/
121	6	int factor = col - THRESHOLD_FIVE;
122	6	Color expected = new Color(50 + 20 * factor, 200 - 20 * factor,
123		150 + 20 * factor);
124	6	Color result = testee.shadeCalculation(ann, col);
125	6	assertEquals(result, expected, "for column " + col);
126		}
127		}
128
129		/**
130		* Test the 'colour below threshold' case
131		*/
		100% Uncovered Elements: 0 (20) Complexity: 4 Complexity Density: 0.29 1PASS
132	1	@Test(groups = "Functional")...
133		public void testShadeCalculation_belowThreshold()
134		{
135	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
136		minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
137
138	12	for (int col = 0; col < WIDTH; col++)
139		{
140	11	Color result = testee.shadeCalculation(ann, col);
141		/*
142		* colour is derived regardless of the threshold value
143		* (the renderer will suppress colouring if above/below threshold)
144		*/
145	11	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
146		150 + 10 * col);
147	11	assertEquals(result, expected, "for column " + col);
148		}
149
150		/*
151		* now make 0-5 the span of the colour range
152		* (annotation value == column number in this test)
153		*/
154	1	testee.setThresholdIsMinMax(true);
155	6	for (int col = THRESHOLD_FIVE + 1; col < WIDTH; col++)
156		{
157		/*
158		* colours above the threshold are computed as before
159		*/
160	5	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
161		150 + 10 * col);
162	5	Color result = testee.shadeCalculation(ann, col);
163	5	assertEquals(result, expected, "for column " + col);
164		}
165
166	7	for (int col = 0; col <= THRESHOLD_FIVE; col++)
167		{
168		/*
169		* colours for values <= threshold are graduated
170		* range is 0-5 so steps of 100/5 = 20
171		*/
172	6	Color expected = new Color(50 + 20 * col, 200 - 20 * col,
173		150 + 20 * col);
174	6	Color result = testee.shadeCalculation(ann, col);
175	6	assertEquals(result, expected, "for column " + col);
176		}
177		}
178
179		/**
180		* Test the 'colour above threshold' case
181		*/
		100% Uncovered Elements: 0 (20) Complexity: 5 Complexity Density: 0.42 1PASS
182	1	@Test(groups = "Functional")...
183		public void testFindColour_aboveThreshold()
184		{
185	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
186		minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
187	1	testee = (AnnotationColourGradient) testee.getInstance(al, null);
188
189	12	for (int col = 0; col < WIDTH; col++)
190		{
191	11	Color result = testee.findColour('a', col, seq);
192		/*
193		* expect white below threshold of 5
194		*/
195	11	Color expected = col < 5 ? Color.white : new Color(50 + 10 * col,
196		200 - 10 * col,
197		150 + 10 * col);
198	11	assertEquals(result, expected, "for column " + col);
199		}
200
201		/*
202		* now make 6-10 the span of the colour range
203		* (annotation value == column number in this test)
204		*/
205	1	testee.setThresholdIsMinMax(true);
206	12	for (int col = 0; col < WIDTH; col++)
207		{
208		/*
209		* colours for values >= threshold are graduated
210		* range is 6-10 so steps of 100/5 = 20
211		*/
212	11	int factor = col - THRESHOLD_FIVE;
213	11	Color expected = col < 5 ? Color.white : new Color(50 + 20 * factor,
214		200 - 20 * factor,
215		150 + 20 * factor);
216	11	Color result = testee.findColour('a', col, seq);
217	11	assertEquals(result, expected, "for column " + col);
218		}
219		}
220
221		/**
222		* Test the 'colour below threshold' case
223		*/
		100% Uncovered Elements: 0 (19) Complexity: 5 Complexity Density: 0.45 1PASS
224	1	@Test(groups = "Functional")...
225		public void testFindColour_belowThreshold()
226		{
227	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
228		minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
229	1	testee = (AnnotationColourGradient) testee.getInstance(al, null);
230
231	12	for (int col = 0; col < WIDTH; col++)
232		{
233	11	Color result = testee.findColour('a', col, seq);
234	11	Color expected = col > 5 ? Color.white : new Color(50 + 10 * col,
235		200 - 10 * col, 150 + 10 * col);
236	11	assertEquals(result, expected, "for column " + col);
237		}
238
239		/*
240		* now make 0-5 the span of the colour range
241		* (annotation value == column number in this test)
242		*/
243	1	testee.setThresholdIsMinMax(true);
244	12	for (int col = 0; col < WIDTH; col++)
245		{
246		/*
247		* colours for values <= threshold are graduated
248		* range is 0-5 so steps of 100/5 = 20
249		*/
250	11	Color expected = col > 5 ? Color.white : new Color(50 + 20 * col,
251		200 - 20 * col, 150 + 20 * col);
252	11	Color result = testee.findColour('a', col, seq);
253	11	assertEquals(result, expected, "for column " + col);
254		}
255		}
256
		100% Uncovered Elements: 0 (8) Complexity: 2 Complexity Density: 0.33 1PASS
257	1	@Test(groups = "Functional")...
258		public void testFindColour_noThreshold()
259		{
260	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
261		minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
262	1	testee = (AnnotationColourGradient) testee.getInstance(al, null);
263
264	12	for (int col = 0; col < WIDTH; col++)
265		{
266	11	Color result = testee.findColour('a', col, seq);
267		/*
268		* column <n> is n/10 of the way from minCol to maxCol
269		*/
270	11	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
271		150 + 10 * col);
272	11	assertEquals(result, expected, "for column " + col);
273		}
274		}
275
		100% Uncovered Elements: 0 (11) Complexity: 3 Complexity Density: 0.43 1PASS
276	1	@Test(groups = "Functional")...
277		public void testFindColour_originalColours()
278		{
279	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
280		minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
281	1	testee = (AnnotationColourGradient) testee.getInstance(al, null);
282
283		/*
284		* flag corresponding to 'use original colours' checkbox
285		* - just use the individual annotation colours
286		*/
287	1	testee.setPredefinedColours(true);
288
289		/*
290		* the annotation colour is returned, except for column 0 where it is
291		* black - in this case the colour scheme colour overrides it
292		*/
293	12	for (int col = 0; col < WIDTH; col++)
294		{
295	11	int hue = col * 20;
296	11	Color c = col == 0 ? minColour : new Color(hue, hue, hue);
297	11	assertEquals(testee.findColour('a', col, seq), c, "for column " + col);
298		}
299		}
300		}