Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
FeatureColourTest	43	353	13	1	0.997260399.7%	Show methods

Class FeatureColourTest

Class FeatureColourTest	Line # 43	Total Statements 353	Complexity 13	Uncovered Elements 1	TOTAL Coverage 0.997260399.7%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4646	2.02	1.01	0.00	1.0 1.0100%
testCopyConstructor() : void   testCopyConstructor() : void	5353	68.068	1.01	0.00	1.0 1.0100%
testCopyConstructor_minMax() : void   testCopyConstructor_minMax() : void	149149	55.055	1.01	0.00	1.0 1.0100%
testGetColor_simpleColour() : void   testGetColor_simpleColour() : void	236236	2.02	1.01	0.00	1.0 1.0100%
testGetColor_colourByLabel() : void   testGetColor_colourByLabel() : void	244244	5.05	1.01	0.00	1.0 1.0100%
testGetColor_Graduated() : void   testGetColor_Graduated() : void	255255	7.07	1.01	0.00	1.0 1.0100%
testGetColor_aboveBelowThreshold() : void   testGetColor_aboveBelowThreshold() : void	275275	16.016	1.01	0.00	1.0 1.0100%
testToJalviewFormat() : void   testToJalviewFormat() : void	310310	50.050	1.01	0.00	1.0 1.0100%
testParseJalviewFeatureColour() : void   testParseJalviewFeatureColour() : void	444444	94.094	2.02	1.01	0.9893617 0.989361798.9%
testGetColor_colourByAttributeText() : void   testGetColor_colourByAttributeText() : void	612612	8.08	1.01	0.00	1.0 1.0100%
testGetColor_GraduatedByAttributeValue() : void   testGetColor_GraduatedByAttributeValue() : void	634634	10.010	1.01	0.00	1.0 1.0100%
testGetDescription() : void   testGetDescription() : void	670670	36.036	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.25753424	jalview.schemes.FeatureColourTest.testParseJalviewFeatureColourjalview.schemes.FeatureColourTest.testParseJalviewFeatureColour	1PASS
	0.1890411	jalview.schemes.FeatureColourTest.testCopyConstructorjalview.schemes.FeatureColourTest.testCopyConstructor	1PASS
	0.15342465	jalview.schemes.FeatureColourTest.testCopyConstructor_minMaxjalview.schemes.FeatureColourTest.testCopyConstructor_minMax	1PASS
	0.13972603	jalview.schemes.FeatureColourTest.testToJalviewFormatjalview.schemes.FeatureColourTest.testToJalviewFormat	1PASS
	0.101369865	jalview.schemes.FeatureColourTest.testGetDescriptionjalview.schemes.FeatureColourTest.testGetDescription	1PASS
	0.04657534	jalview.schemes.FeatureColourTest.testGetColor_aboveBelowThresholdjalview.schemes.FeatureColourTest.testGetColor_aboveBelowThreshold	1PASS
	0.030136986	jalview.schemes.FeatureColourTest.testGetColor_GraduatedByAttributeValuejalview.schemes.FeatureColourTest.testGetColor_GraduatedByAttributeValue	1PASS
	0.024657534	jalview.schemes.FeatureColourTest.testGetColor_colourByAttributeTextjalview.schemes.FeatureColourTest.testGetColor_colourByAttributeText	1PASS
	0.021917809	jalview.schemes.FeatureColourTest.testGetColor_Graduatedjalview.schemes.FeatureColourTest.testGetColor_Graduated	1PASS
	0.016438356	jalview.schemes.FeatureColourTest.testGetColor_colourByLabeljalview.schemes.FeatureColourTest.testGetColor_colourByLabel	1PASS
	0.008219178	jalview.schemes.FeatureColourTest.testGetColor_simpleColourjalview.schemes.FeatureColourTest.testGetColor_simpleColour	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.schemes;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25		import static org.testng.AssertJUnit.assertNull;
26		import static org.testng.AssertJUnit.assertTrue;
27		import static org.testng.AssertJUnit.fail;
28		import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
29
30		import jalview.api.FeatureColourI;
31		import jalview.datamodel.SequenceFeature;
32		import jalview.gui.JvOptionPane;
33		import jalview.util.ColorUtils;
34		import jalview.util.Format;
35
36		import java.awt.Color;
37
38		import org.testng.annotations.BeforeClass;
39		import org.testng.annotations.Test;
40
41		import junit.extensions.PA;
42
		99.7% Uncovered Elements: 1 (365) Complexity: 13 Complexity Density: 0.04
43		public class FeatureColourTest
44		{
45
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
46	1	@BeforeClass(alwaysRun = true)...
47		public void setUpJvOptionPane()
48		{
49	1	JvOptionPane.setInteractiveMode(false);
50	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51		}
52
		100% Uncovered Elements: 0 (68) Complexity: 1 Complexity Density: 0.01 1PASS
53	1	@Test(groups = { "Functional" })...
54		public void testCopyConstructor()
55		{
56		/*
57		* plain colour
58		*/
59	1	FeatureColour fc = new FeatureColour(Color.RED);
60	1	FeatureColour fc1 = new FeatureColour(fc);
61	1	assertTrue(fc1.getColour().equals(Color.RED));
62	1	assertFalse(fc1.isGraduatedColour());
63	1	assertFalse(fc1.isColourByLabel());
64	1	assertFalse(fc1.isColourByAttribute());
65	1	assertNull(fc1.getAttributeName());
66
67		/*
68		* min-max colour
69		*/
70	1	fc = new FeatureColour(Color.gray, Color.black, 10f, 20f);
71	1	fc.setAboveThreshold(true);
72	1	fc.setThreshold(12f);
73	1	fc1 = new FeatureColour(fc);
74	1	assertTrue(fc1.isGraduatedColour());
75	1	assertFalse(fc1.isColourByLabel());
76	1	assertTrue(fc1.isAboveThreshold());
77	1	assertFalse(fc1.isColourByAttribute());
78	1	assertNull(fc1.getAttributeName());
79	1	assertEquals(12f, fc1.getThreshold());
80	1	assertEquals(Color.gray, fc1.getMinColour());
81	1	assertEquals(Color.black, fc1.getMaxColour());
82	1	assertEquals(Color.gray, fc1.getNoColour());
83	1	assertEquals(10f, fc1.getMin());
84	1	assertEquals(20f, fc1.getMax());
85
86		/*
87		* min-max-noValue colour
88		*/
89	1	fc = new FeatureColour(Color.gray, Color.black, Color.green, 10f, 20f);
90	1	fc.setAboveThreshold(true);
91	1	fc.setThreshold(12f);
92	1	fc1 = new FeatureColour(fc);
93	1	assertTrue(fc1.isGraduatedColour());
94	1	assertFalse(fc1.isColourByLabel());
95	1	assertFalse(fc1.isColourByAttribute());
96	1	assertNull(fc1.getAttributeName());
97	1	assertTrue(fc1.isAboveThreshold());
98	1	assertEquals(12f, fc1.getThreshold());
99	1	assertEquals(Color.gray, fc1.getMinColour());
100	1	assertEquals(Color.black, fc1.getMaxColour());
101	1	assertEquals(Color.green, fc1.getNoColour());
102	1	assertEquals(10f, fc1.getMin());
103	1	assertEquals(20f, fc1.getMax());
104
105		/*
106		* colour by label
107		*/
108	1	fc = new FeatureColour();
109	1	fc.setColourByLabel(true);
110	1	fc1 = new FeatureColour(fc);
111	1	assertTrue(fc1.isColourByLabel());
112	1	assertFalse(fc1.isGraduatedColour());
113	1	assertFalse(fc1.isColourByAttribute());
114	1	assertNull(fc1.getAttributeName());
115
116		/*
117		* colour by attribute (label)
118		*/
119	1	fc = new FeatureColour();
120	1	fc.setColourByLabel(true);
121	1	fc.setAttributeName("AF");
122	1	fc1 = new FeatureColour(fc);
123	1	assertTrue(fc1.isColourByLabel());
124	1	assertFalse(fc1.isGraduatedColour());
125	1	assertTrue(fc1.isColourByAttribute());
126	1	assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
127
128		/*
129		* colour by attribute (value)
130		*/
131	1	fc = new FeatureColour(Color.gray, Color.black, Color.green, 10f, 20f);
132	1	fc.setAboveThreshold(true);
133	1	fc.setThreshold(12f);
134	1	fc.setAttributeName("AF");
135	1	fc1 = new FeatureColour(fc);
136	1	assertTrue(fc1.isGraduatedColour());
137	1	assertFalse(fc1.isColourByLabel());
138	1	assertTrue(fc1.isColourByAttribute());
139	1	assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
140	1	assertTrue(fc1.isAboveThreshold());
141	1	assertEquals(12f, fc1.getThreshold());
142	1	assertEquals(Color.gray, fc1.getMinColour());
143	1	assertEquals(Color.black, fc1.getMaxColour());
144	1	assertEquals(Color.green, fc1.getNoColour());
145	1	assertEquals(10f, fc1.getMin());
146	1	assertEquals(20f, fc1.getMax());
147		}
148
		100% Uncovered Elements: 0 (55) Complexity: 1 Complexity Density: 0.02 1PASS
149	1	@Test(groups = { "Functional" })...
150		public void testCopyConstructor_minMax()
151		{
152		/*
153		* graduated colour
154		*/
155	1	FeatureColour fc = new FeatureColour(Color.BLUE, Color.RED, 1f, 5f);
156	1	assertTrue(fc.isGraduatedColour());
157	1	assertFalse(fc.isColourByLabel());
158	1	assertFalse(fc.isColourByAttribute());
159	1	assertNull(fc.getAttributeName());
160	1	assertEquals(1f, fc.getMin());
161	1	assertEquals(5f, fc.getMax());
162
163		/*
164		* update min-max bounds
165		*/
166	1	FeatureColour fc1 = new FeatureColour(fc, 2f, 6f);
167	1	assertTrue(fc1.isGraduatedColour());
168	1	assertFalse(fc1.isColourByLabel());
169	1	assertFalse(fc1.isColourByAttribute());
170	1	assertNull(fc1.getAttributeName());
171	1	assertEquals(2f, fc1.getMin());
172	1	assertEquals(6f, fc1.getMax());
173	1	assertFalse((boolean) PA.getValue(fc1, "isHighToLow"));
174
175		/*
176		* update min-max bounds - high to low
177		*/
178	1	fc1 = new FeatureColour(fc, 23f, 16f);
179	1	assertTrue(fc1.isGraduatedColour());
180	1	assertFalse(fc1.isColourByLabel());
181	1	assertFalse(fc1.isColourByAttribute());
182	1	assertNull(fc1.getAttributeName());
183	1	assertEquals(23f, fc1.getMin());
184	1	assertEquals(16f, fc1.getMax());
185	1	assertTrue((boolean) PA.getValue(fc1, "isHighToLow"));
186
187		/*
188		* graduated colour by attribute
189		*/
190	1	fc1.setAttributeName("AF");
191	1	fc1 = new FeatureColour(fc1, 13f, 36f);
192	1	assertTrue(fc1.isGraduatedColour());
193	1	assertFalse(fc1.isColourByLabel());
194	1	assertTrue(fc1.isColourByAttribute());
195	1	assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
196	1	assertEquals(13f, fc1.getMin());
197	1	assertEquals(36f, fc1.getMax());
198	1	assertFalse((boolean) PA.getValue(fc1, "isHighToLow"));
199
200		/*
201		* colour by label
202		*/
203	1	fc = new FeatureColour(Color.BLUE, Color.RED, 1f, 5f);
204	1	fc.setColourByLabel(true);
205	1	assertFalse(fc.isGraduatedColour());
206	1	assertTrue(fc.isColourByLabel());
207	1	assertFalse(fc.isColourByAttribute());
208	1	assertNull(fc.getAttributeName());
209	1	assertEquals(1f, fc.getMin());
210	1	assertEquals(5f, fc.getMax());
211
212		/*
213		* update min-max bounds
214		*/
215	1	fc1 = new FeatureColour(fc, 2f, 6f);
216	1	assertFalse(fc1.isGraduatedColour());
217	1	assertTrue(fc1.isColourByLabel());
218	1	assertFalse(fc1.isColourByAttribute());
219	1	assertNull(fc1.getAttributeName());
220	1	assertEquals(2f, fc1.getMin());
221	1	assertEquals(6f, fc1.getMax());
222
223		/*
224		* colour by attribute text
225		*/
226	1	fc1.setAttributeName("AC");
227	1	fc1 = new FeatureColour(fc1, 13f, 36f);
228	1	assertFalse(fc1.isGraduatedColour());
229	1	assertTrue(fc1.isColourByLabel());
230	1	assertTrue(fc1.isColourByAttribute());
231	1	assertArrayEquals(new String[] { "AC" }, fc1.getAttributeName());
232	1	assertEquals(13f, fc1.getMin());
233	1	assertEquals(36f, fc1.getMax());
234		}
235
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
236	1	@Test(groups = { "Functional" })...
237		public void testGetColor_simpleColour()
238		{
239	1	FeatureColour fc = new FeatureColour(Color.RED);
240	1	assertEquals(Color.RED,
241		fc.getColor(new SequenceFeature("Cath", "", 1, 2, 0f, null)));
242		}
243
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
244	1	@Test(groups = { "Functional" })...
245		public void testGetColor_colourByLabel()
246		{
247	1	FeatureColour fc = new FeatureColour();
248	1	fc.setColourByLabel(true);
249	1	SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
250		null);
251	1	Color expected = ColorUtils.createColourFromName("desc");
252	1	assertEquals(expected, fc.getColor(sf));
253		}
254
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
255	1	@Test(groups = { "Functional" })...
256		public void testGetColor_Graduated()
257		{
258		/*
259		* graduated colour from
260		* score 0 to 100
261		* gray(128, 128, 128) to red(255, 0, 0)
262		*/
263	1	FeatureColour fc = new FeatureColour(Color.GRAY, Color.RED, 0f, 100f);
264		// feature score is 75 which is 3/4 of the way from GRAY to RED
265	1	SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
266		null);
267		// the colour gradient is computed in float values from 0-1 (where 1 == 255)
268	1	float red = 128 / 255f + 3 / 4f * (255 - 128) / 255f;
269	1	float green = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
270	1	float blue = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
271	1	Color expected = new Color(red, green, blue);
272	1	assertEquals(expected, fc.getColor(sf));
273		}
274
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
275	1	@Test(groups = { "Functional" })...
276		public void testGetColor_aboveBelowThreshold()
277		{
278		// gradient from [50, 150] from WHITE(255, 255, 255) to BLACK(0, 0, 0)
279	1	FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 50f,
280		150f);
281	1	SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 70f,
282		null);
283
284		/*
285		* feature with score of Float.NaN is always assigned minimum colour
286		*/
287	1	SequenceFeature sf2 = new SequenceFeature("type", "desc", 0, 20,
288		Float.NaN, null);
289
290	1	fc.setThreshold(100f); // ignore for now
291	1	assertEquals(new Color(204, 204, 204), fc.getColor(sf));
292	1	assertEquals(Color.white, fc.getColor(sf2));
293
294	1	fc.setAboveThreshold(true); // feature lies below threshold
295	1	assertNull(fc.getColor(sf));
296	1	assertEquals(Color.white, fc.getColor(sf2));
297
298	1	fc.setBelowThreshold(true);
299	1	fc.setThreshold(70f);
300	1	assertNull(fc.getColor(sf)); // feature score == threshold - hidden
301	1	assertEquals(Color.white, fc.getColor(sf2));
302	1	fc.setThreshold(69f);
303	1	assertNull(fc.getColor(sf)); // feature score > threshold - hidden
304	1	assertEquals(Color.white, fc.getColor(sf2));
305		}
306
307		/**
308		* Test output of feature colours to Jalview features file format
309		*/
		100% Uncovered Elements: 0 (50) Complexity: 1 Complexity Density: 0.02 1PASS
310	1	@Test(groups = { "Functional" })...
311		public void testToJalviewFormat()
312		{
313		/*
314		* plain colour - to RGB hex code
315		*/
316	1	FeatureColour fc = new FeatureColour(Color.RED);
317	1	String redHex = Format.getHexString(Color.RED);
318	1	String hexColour = redHex;
319	1	assertEquals("domain\t" + hexColour, fc.toJalviewFormat("domain"));
320
321		/*
322		* colour by label (no threshold)
323		*/
324	1	fc = new FeatureColour();
325	1	fc.setColourByLabel(true);
326	1	assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
327
328		/*
329		* colour by attribute text (no threshold)
330		*/
331	1	fc = new FeatureColour();
332	1	fc.setColourByLabel(true);
333	1	fc.setAttributeName("CLIN_SIG");
334	1	assertEquals("domain\tattribute|CLIN_SIG", fc.toJalviewFormat("domain"));
335
336		/*
337		* colour by label (autoscaled) (an odd state you can reach by selecting
338		* 'above threshold', then deselecting 'threshold is min/max' then 'colour
339		* by label')
340		*/
341	1	fc.setAttributeName((String[]) null);
342	1	fc.setAutoScaled(true);
343	1	assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
344
345		/*
346		* colour by label (above threshold)
347		*/
348	1	fc.setAutoScaled(false);
349	1	fc.setThreshold(12.5f);
350	1	fc.setAboveThreshold(true);
351		// min/max values are output though not used by this scheme
352	1	assertEquals("domain\tlabel|||0.0|0.0|above|12.5",
353		fc.toJalviewFormat("domain"));
354
355		/*
356		* colour by label (below threshold)
357		*/
358	1	fc.setBelowThreshold(true);
359	1	assertEquals("domain\tlabel|||0.0|0.0|below|12.5",
360		fc.toJalviewFormat("domain"));
361
362		/*
363		* colour by attributes text (below threshold)
364		*/
365	1	fc.setBelowThreshold(true);
366	1	fc.setAttributeName("CSQ", "Consequence");
367	1	assertEquals("domain\tattribute|CSQ:Consequence|||0.0|0.0|below|12.5",
368		fc.toJalviewFormat("domain"));
369
370		/*
371		* graduated colour by score, no threshold
372		* - default constructor sets noValueColor = minColor
373		*/
374	1	fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f);
375	1	String greenHex = Format.getHexString(Color.GREEN);
376	1	String expected = String.format(
377		"domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
378		redHex);
379	1	assertEquals(expected, fc.toJalviewFormat("domain"));
380
381		/*
382		* graduated colour by score, no threshold, no value gets min colour
383		*/
384	1	fc = new FeatureColour(Color.GREEN, Color.RED, Color.GREEN, 12f, 25f);
385	1	expected = String.format(
386		"domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
387		redHex);
388	1	assertEquals(expected, fc.toJalviewFormat("domain"));
389
390		/*
391		* graduated colour by score, no threshold, no value gets max colour
392		*/
393	1	fc = new FeatureColour(Color.GREEN, Color.RED, Color.RED, 12f, 25f);
394	1	expected = String.format(
395		"domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|none", greenHex,
396		redHex);
397	1	assertEquals(expected, fc.toJalviewFormat("domain"));
398
399		/*
400		* colour ranges over the actual score ranges (not min/max)
401		*/
402	1	fc.setAutoScaled(true);
403	1	expected = String.format(
404		"domain\tscore|%s|%s|noValueMax|12.0|25.0|none", greenHex,
405		redHex);
406	1	assertEquals(expected, fc.toJalviewFormat("domain"));
407
408		/*
409		* graduated colour by score, below threshold
410		*/
411	1	fc.setThreshold(12.5f);
412	1	fc.setBelowThreshold(true);
413	1	expected = String.format(
414		"domain\tscore|%s|%s|noValueMax|12.0|25.0|below|12.5",
415		greenHex, redHex);
416	1	assertEquals(expected, fc.toJalviewFormat("domain"));
417
418		/*
419		* graduated colour by score, above threshold
420		*/
421	1	fc.setThreshold(12.5f);
422	1	fc.setAboveThreshold(true);
423	1	fc.setAutoScaled(false);
424	1	expected = String.format(
425		"domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|above|12.5",
426		greenHex, redHex);
427	1	assertEquals(expected, fc.toJalviewFormat("domain"));
428
429		/*
430		* graduated colour by attribute, above threshold
431		*/
432	1	fc.setAttributeName("CSQ", "AF");
433	1	fc.setAboveThreshold(true);
434	1	fc.setAutoScaled(false);
435	1	expected = String.format(
436		"domain\tattribute|CSQ:AF|%s|%s|noValueMax|abso|12.0|25.0|above|12.5",
437		greenHex, redHex);
438	1	assertEquals(expected, fc.toJalviewFormat("domain"));
439		}
440
441		/**
442		* Test parsing of feature colours from Jalview features file format
443		*/
		98.9% Uncovered Elements: 1 (94) Complexity: 2 Complexity Density: 0.02 1PASS
444	1	@Test(groups = { "Functional" })...
445		public void testParseJalviewFeatureColour()
446		{
447		/*
448		* simple colour by name
449		*/
450	1	FeatureColourI fc = FeatureColour.parseJalviewFeatureColour("red");
451	1	assertTrue(fc.isSimpleColour());
452	1	assertEquals(Color.RED, fc.getColour());
453
454		/*
455		* simple colour by hex code
456		*/
457	1	fc = FeatureColour.parseJalviewFeatureColour(Format
458		.getHexString(Color.RED));
459	1	assertTrue(fc.isSimpleColour());
460	1	assertEquals(Color.RED, fc.getColour());
461
462		/*
463		* simple colour by rgb triplet
464		*/
465	1	fc = FeatureColour.parseJalviewFeatureColour("255,0,0");
466	1	assertTrue(fc.isSimpleColour());
467	1	assertEquals(Color.RED, fc.getColour());
468
469		/*
470		* malformed colour
471		*/
472	1	try
473		{
474	1	fc = FeatureColour.parseJalviewFeatureColour("oops");
475	0	fail("expected exception");
476		} catch (IllegalArgumentException e)
477		{
478	1	assertEquals("Invalid colour descriptor: oops", e.getMessage());
479		}
480
481		/*
482		* colour by label (no threshold)
483		*/
484	1	fc = FeatureColour.parseJalviewFeatureColour("label");
485	1	assertTrue(fc.isColourByLabel());
486	1	assertFalse(fc.hasThreshold());
487
488		/*
489		* colour by label (with threshold)
490		*/
491	1	fc = FeatureColour
492		.parseJalviewFeatureColour("label|||0.0|0.0|above|12.0");
493	1	assertTrue(fc.isColourByLabel());
494	1	assertTrue(fc.isAboveThreshold());
495	1	assertEquals(12.0f, fc.getThreshold());
496
497		/*
498		* colour by attribute text (no threshold)
499		*/
500	1	fc = FeatureColour.parseJalviewFeatureColour("attribute|CLIN_SIG");
501	1	assertTrue(fc.isColourByAttribute());
502	1	assertTrue(fc.isColourByLabel());
503	1	assertFalse(fc.hasThreshold());
504	1	assertArrayEquals(new String[] { "CLIN_SIG" }, fc.getAttributeName());
505
506		/*
507		* colour by attributes text (with score threshold)
508		*/
509	1	fc = FeatureColour.parseJalviewFeatureColour(
510		"attribute|CSQ:Consequence|||0.0|0.0|above|12.0");
511	1	assertTrue(fc.isColourByLabel());
512	1	assertTrue(fc.isColourByAttribute());
513	1	assertArrayEquals(new String[] { "CSQ", "Consequence" },
514		fc.getAttributeName());
515	1	assertTrue(fc.isAboveThreshold());
516	1	assertEquals(12.0f, fc.getThreshold());
517
518		/*
519		* graduated colour by score (with colour names) (no threshold)
520		*/
521	1	fc = FeatureColour.parseJalviewFeatureColour("red|green|10.0|20.0");
522	1	assertTrue(fc.isGraduatedColour());
523	1	assertFalse(fc.hasThreshold());
524	1	assertEquals(Color.RED, fc.getMinColour());
525	1	assertEquals(Color.GREEN, fc.getMaxColour());
526	1	assertEquals(10f, fc.getMin());
527	1	assertEquals(20f, fc.getMax());
528	1	assertTrue(fc.isAutoScaled());
529
530		/*
531		* graduated colour (explicitly by 'score') (no threshold)
532		*/
533	1	fc = FeatureColour
534		.parseJalviewFeatureColour("Score|red|green|10.0|20.0");
535	1	assertTrue(fc.isGraduatedColour());
536	1	assertFalse(fc.hasThreshold());
537	1	assertEquals(Color.RED, fc.getMinColour());
538	1	assertEquals(Color.GREEN, fc.getMaxColour());
539	1	assertEquals(10f, fc.getMin());
540	1	assertEquals(20f, fc.getMax());
541	1	assertTrue(fc.isAutoScaled());
542
543		/*
544		* graduated colour by attribute (no threshold)
545		*/
546	1	fc = FeatureColour
547		.parseJalviewFeatureColour("attribute|AF|red|green|10.0|20.0");
548	1	assertTrue(fc.isGraduatedColour());
549	1	assertTrue(fc.isColourByAttribute());
550	1	assertArrayEquals(new String[] { "AF" }, fc.getAttributeName());
551	1	assertFalse(fc.hasThreshold());
552	1	assertEquals(Color.RED, fc.getMinColour());
553	1	assertEquals(Color.GREEN, fc.getMaxColour());
554	1	assertEquals(10f, fc.getMin());
555	1	assertEquals(20f, fc.getMax());
556	1	assertTrue(fc.isAutoScaled());
557
558		/*
559		* graduated colour by score (colours by hex code) (above threshold)
560		*/
561	1	String descriptor = String.format("%s|%s|10.0|20.0|above|15",
562		Format.getHexString(Color.RED),
563		Format.getHexString(Color.GREEN));
564	1	fc = FeatureColour.parseJalviewFeatureColour(descriptor);
565	1	assertTrue(fc.isGraduatedColour());
566	1	assertTrue(fc.hasThreshold());
567	1	assertTrue(fc.isAboveThreshold());
568	1	assertEquals(15f, fc.getThreshold());
569	1	assertEquals(Color.RED, fc.getMinColour());
570	1	assertEquals(Color.GREEN, fc.getMaxColour());
571	1	assertEquals(10f, fc.getMin());
572	1	assertEquals(20f, fc.getMax());
573	1	assertTrue(fc.isAutoScaled());
574
575		/*
576		* graduated colour by attributes (below threshold)
577		*/
578	1	fc = FeatureColour.parseJalviewFeatureColour(
579		"attribute|CSQ:AF|red|green|10.0|20.0|below|13");
580	1	assertTrue(fc.isGraduatedColour());
581	1	assertTrue(fc.isColourByAttribute());
582	1	assertArrayEquals(new String[] { "CSQ", "AF" }, fc.getAttributeName());
583	1	assertTrue(fc.hasThreshold());
584	1	assertTrue(fc.isBelowThreshold());
585	1	assertEquals(13f, fc.getThreshold());
586	1	assertEquals(Color.RED, fc.getMinColour());
587	1	assertEquals(Color.GREEN, fc.getMaxColour());
588	1	assertEquals(10f, fc.getMin());
589	1	assertEquals(20f, fc.getMax());
590	1	assertTrue(fc.isAutoScaled());
591
592		/*
593		* graduated colour (by RGB triplet) (below threshold), absolute scale
594		*/
595	1	descriptor = "255,0,0|0,255,0|abso|10.0|20.0|below|15";
596	1	fc = FeatureColour.parseJalviewFeatureColour(descriptor);
597	1	assertTrue(fc.isGraduatedColour());
598	1	assertFalse(fc.isAutoScaled());
599	1	assertTrue(fc.hasThreshold());
600	1	assertTrue(fc.isBelowThreshold());
601	1	assertEquals(15f, fc.getThreshold());
602	1	assertEquals(Color.RED, fc.getMinColour());
603	1	assertEquals(Color.GREEN, fc.getMaxColour());
604	1	assertEquals(10f, fc.getMin());
605	1	assertEquals(20f, fc.getMax());
606
607	1	descriptor = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
608	1	fc = FeatureColour.parseJalviewFeatureColour(descriptor);
609	1	assertTrue(fc.isGraduatedColour());
610		}
611
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
612	1	@Test(groups = { "Functional" })...
613		public void testGetColor_colourByAttributeText()
614		{
615	1	FeatureColour fc = new FeatureColour();
616	1	fc.setColourByLabel(true);
617	1	fc.setAttributeName("consequence");
618	1	SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
619		null);
620
621		/*
622		* if feature has no such attribute, use 'no value' colour
623		*/
624	1	assertEquals(FeatureColour.DEFAULT_NO_COLOUR, fc.getColor(sf));
625
626		/*
627		* if feature has attribute, generate colour from value
628		*/
629	1	sf.setValue("consequence", "benign");
630	1	Color expected = ColorUtils.createColourFromName("benign");
631	1	assertEquals(expected, fc.getColor(sf));
632		}
633
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
634	1	@Test(groups = { "Functional" })...
635		public void testGetColor_GraduatedByAttributeValue()
636		{
637		/*
638		* graduated colour based on attribute value for AF
639		* given a min-max range of 0-100
640		*/
641	1	FeatureColour fc = new FeatureColour(new Color(50, 100, 150),
642		new Color(150, 200, 250), Color.yellow, 0f, 100f);
643	1	String attName = "AF";
644	1	fc.setAttributeName(attName);
645
646		/*
647		* first case: feature lacks the attribute - use 'no value' colour
648		*/
649	1	SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
650		null);
651	1	assertEquals(Color.yellow, fc.getColor(sf));
652
653		/*
654		* second case: attribute present but not numeric - treat as if absent
655		*/
656	1	sf.setValue(attName, "twelve");
657	1	assertEquals(Color.yellow, fc.getColor(sf));
658
659		/*
660		* third case: valid attribute value
661		*/
662	1	sf.setValue(attName, "20.0");
663	1	Color expected = new Color(70, 120, 170);
664	1	assertEquals(expected, fc.getColor(sf));
665		}
666
667		/**
668		* Test description of feature colour suitable for a tooltip
669		*/
		100% Uncovered Elements: 0 (36) Complexity: 1 Complexity Density: 0.03 1PASS
670	1	@Test(groups = { "Functional" })...
671		public void testGetDescription()
672		{
673		/*
674		* plain colour
675		*/
676	1	FeatureColour fc = new FeatureColour(Color.RED);
677	1	assertEquals(
678		String.format("r=%d,g=%d,b=%d", Color.RED.getRed(),
679		Color.red.getGreen(), Color.red.getBlue()),
680		fc.getDescription());
681
682		/*
683		* colour by label (no threshold)
684		*/
685	1	fc = new FeatureColour();
686	1	fc.setColourByLabel(true);
687	1	assertEquals("By Label", fc.getDescription());
688
689		/*
690		* colour by attribute text (no threshold)
691		*/
692	1	fc = new FeatureColour();
693	1	fc.setColourByLabel(true);
694	1	fc.setAttributeName("CLIN_SIG");
695	1	assertEquals("By CLIN_SIG", fc.getDescription());
696
697		/*
698		* colour by label (above score threshold)
699		*/
700	1	fc = new FeatureColour();
701	1	fc.setColourByLabel(true);
702	1	fc.setAutoScaled(false);
703	1	fc.setThreshold(12.5f);
704	1	fc.setAboveThreshold(true);
705	1	assertEquals("By Label (Score > 12.5)",
706		fc.getDescription());
707
708		/*
709		* colour by label (below score threshold)
710		*/
711	1	fc.setBelowThreshold(true);
712	1	assertEquals("By Label (Score < 12.5)",
713		fc.getDescription());
714
715		/*
716		* colour by attributes text (below score threshold)
717		*/
718	1	fc.setBelowThreshold(true);
719	1	fc.setAttributeName("CSQ", "Consequence");
720	1	assertEquals(
721		"By CSQ:Consequence (Score < 12.5)",
722		fc.getDescription());
723
724		/*
725		* graduated colour by score, no threshold
726		*/
727	1	fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f);
728	1	assertEquals("By Score", fc.getDescription());
729
730		/*
731		* graduated colour by score, below threshold
732		*/
733	1	fc.setThreshold(12.5f);
734	1	fc.setBelowThreshold(true);
735	1	assertEquals("By Score (< 12.5)",
736		fc.getDescription());
737
738		/*
739		* graduated colour by score, above threshold
740		*/
741	1	fc.setThreshold(12.5f);
742	1	fc.setAboveThreshold(true);
743	1	fc.setAutoScaled(false);
744	1	assertEquals("By Score (> 12.5)",
745		fc.getDescription());
746
747		/*
748		* graduated colour by attribute, no threshold
749		*/
750	1	fc.setAttributeName("CSQ", "AF");
751	1	fc.setAboveThreshold(false);
752	1	fc.setAutoScaled(false);
753	1	assertEquals("By CSQ:AF", fc.getDescription());
754
755		/*
756		* graduated colour by attribute, above threshold
757		*/
758	1	fc.setAboveThreshold(true);
759	1	fc.setAutoScaled(false);
760	1	assertEquals("By CSQ:AF (> 12.5)",
761		fc.getDescription());
762		}
763		}