Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResidueShaderTest	47	124	23	0.8231292482.3%	Show methods

Class ResidueShaderTest

Class ResidueShaderTest	Line # 47	Total Statements 124	Complexity 23	TOTAL Coverage 0.8231292482.3%
testAboveThreshold() : void   testAboveThreshold() : void	5050	27.027	1.01	1.0 1.0100%
getConsSequence() : SequenceI   getConsSequence() : SequenceI	120120	1.01	1.01	1.0 1.0100%
testApplyConservation() : void   testApplyConservation() : void	105105	49.049	1.01	1.0 1.0100%
getConsSequence() : SequenceI   getConsSequence() : SequenceI	224224	1.01	1.01	1.0 1.0100%
testFindColour_gapColour() : void   testFindColour_gapColour() : void	196196	29.029	1.01	1.0 1.0100%
setCounts(ResidueCount) : void   setCounts(ResidueCount) : void	296296	0.00	1.01	-1.0 -1.0 -
getPercentageIdentity(boolean) : float   getPercentageIdentity(boolean) : float	301301	1.01	1.01	1.0 1.0100%
getCounts() : ResidueCount   getCounts() : ResidueCount	307307	1.01	1.01	0.0 0.00%
getHeight() : int   getHeight() : int	313313	1.01	1.01	0.0 0.00%
getGapped() : int   getGapped() : int	319319	1.01	1.01	0.0 0.00%
getMaxCount() : int   getMaxCount() : int	325325	1.01	1.01	0.0 0.00%
getModalResidue() : String   getModalResidue() : String	331331	1.01	1.01	1.0 1.0100%
getNonGapped() : int   getNonGapped() : int	337337	1.01	1.01	0.0 0.00%
setSSCounts(SecondaryStructureCount) : void   setSSCounts(SecondaryStructureCount) : void	343343	0.00	1.01	-1.0 -1.0 -
getSSPercentageIdentity(boolean) : float   getSSPercentageIdentity(boolean) : float	351351	1.01	1.01	0.0 0.00%
getMaxSSCount() : int   getMaxSSCount() : int	358358	1.01	1.01	0.0 0.00%
getModalSS() : String   getModalSS() : String	365365	1.01	1.01	0.0 0.00%
getSSCounts() : SecondaryStructureCount   getSSCounts() : SecondaryStructureCount	372372	1.01	1.01	0.0 0.00%
getSeqWithSSCount() : int   getSeqWithSSCount() : int	379379	1.01	1.01	0.0 0.00%
get(int) : ProfileI   get(int) : ProfileI	291291	1.01	1.01	1.0 1.0100%
getStartColumn() : int   getStartColumn() : int	388388	1.01	1.01	0.0 0.00%
getEndColumn() : int   getEndColumn() : int	394394	1.01	1.01	0.0 0.00%
getStubConsensus(String,float) : ProfilesI   getStubConsensus(String,float) : ProfilesI	285285	2.02	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.3537415	jalview.renderer.ResidueShaderTest.testApplyConservationjalview.renderer.ResidueShaderTest.testApplyConservation	1PASS
	0.27891156	jalview.renderer.ResidueShaderTest.testFindColour_gapColourjalview.renderer.ResidueShaderTest.testFindColour_gapColour	1PASS
	0.1904762	jalview.renderer.ResidueShaderTest.testAboveThresholdjalview.renderer.ResidueShaderTest.testAboveThreshold	1PASS

 

Source view

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.renderer;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import jalview.analysis.Conservation;
28		import jalview.datamodel.Profile;
29		import jalview.datamodel.ProfileI;
30		import jalview.datamodel.Profiles;
31		import jalview.datamodel.ProfilesI;
32		import jalview.datamodel.ResidueCount;
33		import jalview.datamodel.SecondaryStructureCount;
34		import jalview.datamodel.Sequence;
35		import jalview.datamodel.SequenceI;
36		import jalview.schemes.ColourSchemeI;
37		import jalview.schemes.PIDColourScheme;
38		import jalview.schemes.ResidueProperties;
39		import jalview.schemes.UserColourScheme;
40		import jalview.schemes.ZappoColourScheme;
41
42		import java.awt.Color;
43		import java.util.Collections;
44
45		import org.testng.annotations.Test;
46
		82.3% Uncovered Elements: 26 (147) Complexity: 23 Complexity Density: 0.19
47		public class ResidueShaderTest
48		{
49
		100% Uncovered Elements: 0 (27) Complexity: 1 Complexity Density: 0.04 1PASS
50	1	@Test(groups = "Functional")...
51		public void testAboveThreshold()
52		{
53		/*
54		* make up profiles for this alignment:
55		* AR-Q
56		* AR--
57		* SR-T
58		* SR-T
59		*/
60	1	ProfileI[] profiles = new ProfileI[4];
61	1	profiles[0] = new Profile(4, 0, 2, "AS");
62	1	profiles[1] = new Profile(4, 0, 4, "R");
63	1	profiles[2] = new Profile(4, 4, 0, "");
64	1	profiles[3] = new Profile(4, 1, 2, "T");
65	1	ResidueShader ccs = new ResidueShader(new PIDColourScheme());
66	1	ccs.setConsensus(new Profiles(profiles));
67
68		/*
69		* no threshold
70		*/
71	1	ccs.setThreshold(0, true);
72	1	assertTrue(ccs.aboveThreshold('a', 0));
73	1	assertTrue(ccs.aboveThreshold('S', 0));
74	1	assertTrue(ccs.aboveThreshold('W', 0));
75	1	assertTrue(ccs.aboveThreshold('R', 1));
76	1	assertTrue(ccs.aboveThreshold('W', 2));
77	1	assertTrue(ccs.aboveThreshold('t', 3));
78	1	assertTrue(ccs.aboveThreshold('Q', 3));
79
80		/*
81		* with threshold, include gaps
82		*/
83	1	ccs.setThreshold(60, false);
84	1	assertFalse(ccs.aboveThreshold('a', 0));
85	1	assertFalse(ccs.aboveThreshold('S', 0));
86	1	assertTrue(ccs.aboveThreshold('R', 1));
87	1	assertFalse(ccs.aboveThreshold('W', 2));
88	1	assertFalse(ccs.aboveThreshold('t', 3)); // 50% < 60%
89
90		/*
91		* with threshold, ignore gaps
92		*/
93	1	ccs.setThreshold(60, true);
94	1	assertFalse(ccs.aboveThreshold('a', 0));
95	1	assertFalse(ccs.aboveThreshold('S', 0));
96	1	assertTrue(ccs.aboveThreshold('R', 1));
97	1	assertFalse(ccs.aboveThreshold('W', 2));
98	1	assertTrue(ccs.aboveThreshold('t', 3)); // 67% > 60%
99		}
100
101		/**
102		* Test colour bleaching based on conservation score and conservation slider.
103		* Scores of 10 or 11 should leave colours unchanged. Gap is always white.
104		*/
		100% Uncovered Elements: 0 (49) Complexity: 1 Complexity Density: 0.02 1PASS
105	1	@Test(groups = "Functional")...
106		public void testApplyConservation()
107		{
108	1	ResidueShader ccs = new ResidueShader(new PIDColourScheme());
109
110		// no conservation present - no fading
111	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 12));
112
113		/*
114		* stub Conservation to return a given consensus string
115		*/
116	1	final String consSequence = "0123456789+*-";
117	1	Conservation cons = new Conservation(null,
118		Collections.<SequenceI> emptyList(), 0, 0)
119		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
120	1	@Override...
121		public SequenceI getConsSequence()
122		{
123	1	return new Sequence("seq", consSequence);
124		}
125		};
126	1	ccs.setConservation(cons);
127
128		// column out of range:
129	1	assertEquals(Color.RED,
130		ccs.applyConservation(Color.RED, consSequence.length()));
131
132		/*
133		* with 100% threshold, 'fade factor' is
134		* (11-score)/10 * 100/20 = (11-score)/2
135		* which is >= 1 for all scores i.e. all fade to white except +, *
136		*/
137	1	ccs.setConservationInc(100);
138	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 0));
139	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 1));
140	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 2));
141	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 3));
142	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 4));
143	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 5));
144	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 6));
145	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 7));
146	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 8));
147	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 9));
148	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 10));
149	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 11));
150	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 12));
151
152		/*
153		* with 0% threshold, there should be no fading
154		*/
155	1	ccs.setConservationInc(0);
156	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 0));
157	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 1));
158	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 2));
159	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 3));
160	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 4));
161	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 5));
162	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 6));
163	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 7));
164	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 8));
165	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 9));
166	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 10));
167	1	assertEquals(Color.RED, ccs.applyConservation(Color.RED, 11));
168	1	assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 12)); // gap
169
170		/*
171		* with 40% threshold, 'fade factor' is
172		* (11-score)/10 * 40/20 = (11-score)/5
173		* which is {>1, >1, >1, >1, >1, >1, 1, 0.8, 0.6, 0.4} for score 0-9
174		* e.g. score 7 colour fades 80% of the way to white (255, 255, 255)
175		*/
176	1	ccs.setConservationInc(40);
177	1	Color colour = new Color(155, 105, 55);
178	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 0));
179	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 1));
180	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 2));
181	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 3));
182	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 4));
183	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 5));
184	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 6));
185	1	assertEquals(new Color(235, 225, 215),
186		ccs.applyConservation(colour, 7));
187	1	assertEquals(new Color(215, 195, 175),
188		ccs.applyConservation(colour, 8));
189	1	assertEquals(new Color(195, 165, 135),
190		ccs.applyConservation(colour, 9));
191	1	assertEquals(colour, ccs.applyConservation(colour, 10));
192	1	assertEquals(colour, ccs.applyConservation(colour, 11));
193	1	assertEquals(Color.WHITE, ccs.applyConservation(colour, 12));
194		}
195
		100% Uncovered Elements: 0 (29) Complexity: 1 Complexity Density: 0.03 1PASS
196	1	@Test(groups = "Functional")...
197		public void testFindColour_gapColour()
198		{
199		/*
200		* normally, a gap is coloured white
201		*/
202	1	ResidueShader rs = new ResidueShader(new ZappoColourScheme());
203	1	assertEquals(Color.white, rs.findColour(' ', 7, null));
204
205		/*
206		* a User Colour Scheme may specify a bespoke gap colour
207		*/
208	1	Color[] colours = new Color[ResidueProperties.maxProteinIndex + 1];
209	1	colours[5] = Color.blue; // Q colour
210	1	colours[23] = Color.red; // gap colour
211	1	ColourSchemeI cs = new UserColourScheme(colours);
212	1	rs = new ResidueShader(cs);
213
214	1	assertEquals(Color.red, rs.findColour(' ', 7, null));
215	1	assertEquals(Color.blue, rs.findColour('Q', 7, null));
216
217		/*
218		* stub Conservation to return a given consensus string
219		*/
220	1	final String consSequence = "0123456789+*-";
221	1	Conservation cons = new Conservation(null,
222		Collections.<SequenceI> emptyList(), 0, 0)
223		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
224	1	@Override...
225		public SequenceI getConsSequence()
226		{
227	1	return new Sequence("seq", consSequence);
228		}
229		};
230	1	rs.setConservation(cons);
231
232		/*
233		* with 0% threshold, there should be no fading
234		*/
235	1	rs.setConservationInc(0);
236	1	assertEquals(Color.red, rs.findColour(' ', 7, null));
237	1	assertEquals(Color.blue, rs.findColour('Q', 7, null));
238
239		/*
240		* with 40% threshold, 'fade factor' is
241		* (11-score)/10 * 40/20 = (11-score)/5
242		* so position 7, score 7 fades 80% of the way to white (255, 255, 255)
243		*/
244	1	rs.setConservationInc(40);
245
246		/*
247		* gap colour is unchanged for Conservation
248		*/
249	1	assertEquals(Color.red, rs.findColour(' ', 7, null));
250	1	assertEquals(Color.red, rs.findColour('-', 7, null));
251	1	assertEquals(Color.red, rs.findColour('.', 7, null));
252
253		/*
254		* residue colour is faded 80% of the way from
255		* blue(0, 0, 255) to white(255, 255, 255)
256		* making (204, 204, 255)
257		*/
258	1	assertEquals(new Color(204, 204, 255), rs.findColour('Q', 7, null));
259
260		/*
261		* turn off By Conservation, apply Above Identity Threshold
262		* providing a stub Consensus that has modal residue "Q" with pid 60%
263		*/
264	1	rs.setConservationApplied(false);
265	1	ProfilesI consensus = getStubConsensus("Q", 60f);
266	1	rs.setConsensus(consensus);
267
268		// with consensus pid (60) above threshold (50), colours are unchanged
269	1	rs.setThreshold(50, false);
270	1	assertEquals(Color.blue, rs.findColour('Q', 7, null));
271	1	assertEquals(Color.red, rs.findColour('-', 7, null));
272
273		// with consensus pid (60) below threshold (70),
274		// residue colour becomes white, gap colour is unchanged
275	1	rs.setThreshold(70, false);
276	1	assertEquals(Color.white, rs.findColour('Q', 7, null));
277	1	assertEquals(Color.red, rs.findColour('-', 7, null));
278		}
279
280		/**
281		* @param modalResidue
282		* @param pid
283		* @return
284		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
285	1	protected ProfilesI getStubConsensus(final String modalResidue,...
286		final float pid)
287		{
288	1	ProfilesI consensus = new ProfilesI()
289		{
290
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
291	6	@Override...
292		public ProfileI get(int i)
293		{
294	6	return new ProfileI()
295		{
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
296	0	@Override...
297		public void setCounts(ResidueCount residueCounts)
298		{
299		}
300
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
301	6	@Override...
302		public float getPercentageIdentity(boolean ignoreGaps)
303		{
304	6	return pid;
305		}
306
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
307	0	@Override...
308		public ResidueCount getCounts()
309		{
310	0	return null;
311		}
312
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
313	0	@Override...
314		public int getHeight()
315		{
316	0	return 0;
317		}
318
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
319	0	@Override...
320		public int getGapped()
321		{
322	0	return 0;
323		}
324
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
325	0	@Override...
326		public int getMaxCount()
327		{
328	0	return 0;
329		}
330
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
331	6	@Override...
332		public String getModalResidue()
333		{
334	6	return modalResidue;
335		}
336
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
337	0	@Override...
338		public int getNonGapped()
339		{
340	0	return 0;
341		}
342
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
343	0	@Override...
344		public void setSSCounts(
345		SecondaryStructureCount secondaryStructureCount)
346		{
347		// TODO Auto-generated method stub
348
349		}
350
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
351	0	@Override...
352		public float getSSPercentageIdentity(boolean ignoreGaps)
353		{
354		// TODO Auto-generated method stub
355	0	return 0;
356		}
357
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
358	0	@Override...
359		public int getMaxSSCount()
360		{
361		// TODO Auto-generated method stub
362	0	return 0;
363		}
364
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
365	0	@Override...
366		public String getModalSS()
367		{
368		// TODO Auto-generated method stub
369	0	return null;
370		}
371
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
372	0	@Override...
373		public SecondaryStructureCount getSSCounts()
374		{
375		// TODO Auto-generated method stub
376	0	return null;
377		}
378
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
379	0	@Override...
380		public int getSeqWithSSCount()
381		{
382		// TODO Auto-generated method stub
383	0	return 0;
384		}
385		};
386		}
387
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
388	0	@Override...
389		public int getStartColumn()
390		{
391	0	return 0;
392		}
393
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
394	0	@Override...
395		public int getEndColumn()
396		{
397	0	return 0;
398		}
399
400		};
401	1	return consensus;
402		}
403		}