Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ResidueShaderTest	26	119	17	15	0.889705989%	Show methods

Class ResidueShaderTest

Class ResidueShaderTest	Line # 26	Total Statements 119	Complexity 17	Uncovered Elements 15	TOTAL Coverage 0.889705989%
testAboveThreshold() : void   testAboveThreshold() : void	2929	27.027	1.01	0.00	1.0 1.0100%
getConsSequence() : SequenceI   getConsSequence() : SequenceI	9999	1.01	1.01	0.00	1.0 1.0100%
testApplyConservation() : void   testApplyConservation() : void	8484	49.049	1.01	0.00	1.0 1.0100%
getConsSequence() : SequenceI   getConsSequence() : SequenceI	200200	1.01	1.01	0.00	1.0 1.0100%
testFindColour_gapColour() : void   testFindColour_gapColour() : void	172172	29.029	1.01	0.00	1.0 1.0100%
setCounts(ResidueCount) : void   setCounts(ResidueCount) : void	270270	0.00	1.01	0.00	-1.0 -1.0 -
getPercentageIdentity(boolean) : float   getPercentageIdentity(boolean) : float	275275	1.01	1.01	0.00	1.0 1.0100%
getCounts() : ResidueCount   getCounts() : ResidueCount	281281	1.01	1.01	1.01	0.0 0.00%
getHeight() : int   getHeight() : int	287287	1.01	1.01	1.01	0.0 0.00%
getGapped() : int   getGapped() : int	293293	1.01	1.01	1.01	0.0 0.00%
getMaxCount() : int   getMaxCount() : int	299299	1.01	1.01	1.01	0.0 0.00%
getModalResidue() : String   getModalResidue() : String	305305	1.01	1.01	0.00	1.0 1.0100%
getNonGapped() : int   getNonGapped() : int	311311	1.01	1.01	1.01	0.0 0.00%
get(int) : ProfileI   get(int) : ProfileI	266266	1.01	1.01	0.00	1.0 1.0100%
getStartColumn() : int   getStartColumn() : int	318318	1.01	1.01	1.01	0.0 0.00%
getEndColumn() : int   getEndColumn() : int	324324	1.01	1.01	1.01	0.0 0.00%
getStubConsensus(String,float) : ProfilesI   getStubConsensus(String,float) : ProfilesI	261261	2.02	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.38235295	jalview.renderer.ResidueShaderTest.testApplyConservationjalview.renderer.ResidueShaderTest.testApplyConservation	1PASS
	0.30147058	jalview.renderer.ResidueShaderTest.testFindColour_gapColourjalview.renderer.ResidueShaderTest.testFindColour_gapColour	1PASS
	0.20588236	jalview.renderer.ResidueShaderTest.testAboveThresholdjalview.renderer.ResidueShaderTest.testAboveThreshold	1PASS

 

Source view

1		package jalview.renderer;
2
3		import static org.testng.AssertJUnit.assertEquals;
4		import static org.testng.AssertJUnit.assertFalse;
5		import static org.testng.AssertJUnit.assertTrue;
6
7		import jalview.analysis.Conservation;
8		import jalview.datamodel.Profile;
9		import jalview.datamodel.ProfileI;
10		import jalview.datamodel.Profiles;
11		import jalview.datamodel.ProfilesI;
12		import jalview.datamodel.ResidueCount;
13		import jalview.datamodel.Sequence;
14		import jalview.datamodel.SequenceI;
15		import jalview.schemes.ColourSchemeI;
16		import jalview.schemes.PIDColourScheme;
17		import jalview.schemes.ResidueProperties;
18		import jalview.schemes.UserColourScheme;
19		import jalview.schemes.ZappoColourScheme;
20
21		import java.awt.Color;
22		import java.util.Collections;
23
24		import org.testng.annotations.Test;
25
		89% Uncovered Elements: 15 (136) Complexity: 17 Complexity Density: 0.14
26		public class ResidueShaderTest
27		{
28
		100% Uncovered Elements: 0 (27) Complexity: 1 Complexity Density: 0.04 1PASS
29	1	@Test(groups = "Functional")...
30		public void testAboveThreshold()
31		{
32		/*
33		* make up profiles for this alignment:
34		* AR-Q
35		* AR--
36		* SR-T
37		* SR-T
38		*/
39	1	ProfileI[] profiles = new ProfileI[4];
40	1	profiles[0] = new Profile(4, 0, 2, "AS");
41	1	profiles[1] = new Profile(4, 0, 4, "R");
42	1	profiles[2] = new Profile(4, 4, 0, "");
43	1	profiles[3] = new Profile(4, 1, 2, "T");
44	1	ResidueShader ccs = new ResidueShader(new PIDColourScheme());
45	1	ccs.setConsensus(new Profiles(profiles));
46
47		/*
48		* no threshold
49		*/
50	1	ccs.setThreshold(0, true);
51	1	assertTrue(ccs.aboveThreshold('a', 0));
52	1	assertTrue(ccs.aboveThreshold('S', 0));
53	1	assertTrue(ccs.aboveThreshold('W', 0));
54	1	assertTrue(ccs.aboveThreshold('R', 1));
55	1	assertTrue(ccs.aboveThreshold('W', 2));
56	1	assertTrue(ccs.aboveThreshold('t', 3));
57	1	assertTrue(ccs.aboveThreshold('Q', 3));
58
59		/*
60		* with threshold, include gaps
61		*/
62	1	ccs.setThreshold(60, false);
63	1	assertFalse(ccs.aboveThreshold('a', 0));
64	1	assertFalse(ccs.aboveThreshold('S', 0));
65	1	assertTrue(ccs.aboveThreshold('R', 1));
66	1	assertFalse(ccs.aboveThreshold('W', 2));
67	1	assertFalse(ccs.aboveThreshold('t', 3)); // 50% < 60%
68
69		/*
70		* with threshold, ignore gaps
71		*/
72	1	ccs.setThreshold(60, true);
73	1	assertFalse(ccs.aboveThreshold('a', 0));
74	1	assertFalse(ccs.aboveThreshold('S', 0));
75	1	assertTrue(ccs.aboveThreshold('R', 1));
76	1	assertFalse(ccs.aboveThreshold('W', 2));
77	1	assertTrue(ccs.aboveThreshold('t', 3)); // 67% > 60%
78		}
79
80		/**
81		* Test colour bleaching based on conservation score and conservation slider.
82		* Scores of 10 or 11 should leave colours unchanged. Gap is always white.
83		*/
		100% Uncovered Elements: 0 (49) Complexity: 1 Complexity Density: 0.02 1PASS
84	1	@Test(groups = "Functional")...
85		public void testApplyConservation()
86		{
87	1	ResidueShader ccs = new ResidueShader(new PIDColourScheme());
88
89		// no conservation present - no fading
90	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 12));
91
92		/*
93		* stub Conservation to return a given consensus string
94		*/
95	1	final String consSequence = "0123456789+*-";
96	1	Conservation cons = new Conservation(null,
97		Collections.<SequenceI> emptyList(), 0, 0)
98		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
99	1	@Override...
100		public SequenceI getConsSequence()
101		{
102	1	return new Sequence("seq", consSequence);
103		}
104		};
105	1	ccs.setConservation(cons);
106
107		// column out of range:
108	1	assertEquals(Color.RED,
109		ccs.applyConservation(Color.RED, consSequence.length()));
110
111		/*
112		* with 100% threshold, 'fade factor' is
113		* (11-score)/10 * 100/20 = (11-score)/2
114		* which is >= 1 for all scores i.e. all fade to white except +, *
115		*/
116	1	ccs.setConservationInc(100);
117	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 0));
118	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 1));
119	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 2));
120	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 3));
121	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 4));
122	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 5));
123	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 6));
124	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 7));
125	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 8));
126	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 9));
127	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 10));
128	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 11));
129	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 12));
130
131		/*
132		* with 0% threshold, there should be no fading
133		*/
134	1	ccs.setConservationInc(0);
135	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 0));
136	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 1));
137	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 2));
138	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 3));
139	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 4));
140	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 5));
141	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 6));
142	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 7));
143	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 8));
144	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 9));
145	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 10));
146	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 11));
147	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 12)); // gap
148
149		/*
150		* with 40% threshold, 'fade factor' is
151		* (11-score)/10 * 40/20 = (11-score)/5
152		* which is {>1, >1, >1, >1, >1, >1, 1, 0.8, 0.6, 0.4} for score 0-9
153		* e.g. score 7 colour fades 80% of the way to white (255, 255, 255)
154		*/
155	1	ccs.setConservationInc(40);
156	1	Color colour = new Color(155, 105, 55);
157	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 0));
158	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 1));
159	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 2));
160	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 3));
161	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 4));
162	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 5));
163	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 6));
164	1	assertEquals(new Color(235, 225, 215), ccs.applyConservation(colour, 7));
165	1	assertEquals(new Color(215, 195, 175), ccs.applyConservation(colour, 8));
166	1	assertEquals(new Color(195, 165, 135), ccs.applyConservation(colour, 9));
167	1	assertEquals(colour, ccs.applyConservation(colour, 10));
168	1	assertEquals(colour, ccs.applyConservation(colour, 11));
169	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 12));
170		}
171
		100% Uncovered Elements: 0 (29) Complexity: 1 Complexity Density: 0.03 1PASS
172	1	@Test(groups = "Functional")...
173		public void testFindColour_gapColour()
174		{
175		/*
176		* normally, a gap is coloured white
177		*/
178	1	ResidueShader rs = new ResidueShader(new ZappoColourScheme());
179	1	assertEquals(Color.white, rs.findColour(' ', 7, null));
180
181		/*
182		* a User Colour Scheme may specify a bespoke gap colour
183		*/
184	1	Color[] colours = new Color[ResidueProperties.maxProteinIndex + 1];
185	1	colours[5] = Color.blue; // Q colour
186	1	colours[23] = Color.red; // gap colour
187	1	ColourSchemeI cs = new UserColourScheme(colours);
188	1	rs = new ResidueShader(cs);
189
190	1	assertEquals(Color.red, rs.findColour(' ', 7, null));
191	1	assertEquals(Color.blue, rs.findColour('Q', 7, null));
192
193		/*
194		* stub Conservation to return a given consensus string
195		*/
196	1	final String consSequence = "0123456789+*-";
197	1	Conservation cons = new Conservation(null,
198		Collections.<SequenceI> emptyList(), 0, 0)
199		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
200	1	@Override...
201		public SequenceI getConsSequence()
202		{
203	1	return new Sequence("seq", consSequence);
204		}
205		};
206	1	rs.setConservation(cons);
207
208		/*
209		* with 0% threshold, there should be no fading
210		*/
211	1	rs.setConservationInc(0);
212	1	assertEquals(Color.red, rs.findColour(' ', 7, null));
213	1	assertEquals(Color.blue, rs.findColour('Q', 7, null));
214
215		/*
216		* with 40% threshold, 'fade factor' is
217		* (11-score)/10 * 40/20 = (11-score)/5
218		* so position 7, score 7 fades 80% of the way to white (255, 255, 255)
219		*/
220	1	rs.setConservationInc(40);
221
222		/*
223		* gap colour is unchanged for Conservation
224		*/
225	1	assertEquals(Color.red, rs.findColour(' ', 7, null));
226	1	assertEquals(Color.red, rs.findColour('-', 7, null));
227	1	assertEquals(Color.red, rs.findColour('.', 7, null));
228
229		/*
230		* residue colour is faded 80% of the way from
231		* blue(0, 0, 255) to white(255, 255, 255)
232		* making (204, 204, 255)
233		*/
234	1	assertEquals(new Color(204, 204, 255), rs.findColour('Q', 7, null));
235
236		/*
237		* turn off By Conservation, apply Above Identity Threshold
238		* providing a stub Consensus that has modal residue "Q" with pid 60%
239		*/
240	1	rs.setConservationApplied(false);
241	1	ProfilesI consensus = getStubConsensus("Q", 60f);
242	1	rs.setConsensus(consensus);
243
244		// with consensus pid (60) above threshold (50), colours are unchanged
245	1	rs.setThreshold(50, false);
246	1	assertEquals(Color.blue, rs.findColour('Q', 7, null));
247	1	assertEquals(Color.red, rs.findColour('-', 7, null));
248
249		// with consensus pid (60) below threshold (70),
250		// residue colour becomes white, gap colour is unchanged
251	1	rs.setThreshold(70, false);
252	1	assertEquals(Color.white, rs.findColour('Q', 7, null));
253	1	assertEquals(Color.red, rs.findColour('-', 7, null));
254		}
255
256		/**
257		* @param modalResidue
258		* @param pid
259		* @return
260		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
261	1	protected ProfilesI getStubConsensus(final String modalResidue,...
262		final float pid)
263		{
264	1	ProfilesI consensus = new ProfilesI() {
265
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
266	6	@Override...
267		public ProfileI get(int i)
268		{
269	6	return new ProfileI() {
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
270	0	@Override...
271		public void setCounts(ResidueCount residueCounts)
272		{
273		}
274
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
275	6	@Override...
276		public float getPercentageIdentity(boolean ignoreGaps)
277		{
278	6	return pid;
279		}
280
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
281	0	@Override...
282		public ResidueCount getCounts()
283		{
284	0	return null;
285		}
286
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
287	0	@Override...
288		public int getHeight()
289		{
290	0	return 0;
291		}
292
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
293	0	@Override...
294		public int getGapped()
295		{
296	0	return 0;
297		}
298
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
299	0	@Override...
300		public int getMaxCount()
301		{
302	0	return 0;
303		}
304
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
305	6	@Override...
306		public String getModalResidue()
307		{
308	6	return modalResidue;
309		}
310
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
311	0	@Override...
312		public int getNonGapped()
313		{
314	0	return 0;
315		}};
316		}
317
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
318	0	@Override...
319		public int getStartColumn()
320		{
321	0	return 0;
322		}
323
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
324	0	@Override...
325		public int getEndColumn()
326		{
327	0	return 0;
328		}
329
330		};
331	1	return consensus;
332		}
333		}