Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureColourTest	41	366	15	0.9947229699.5%	Show methods

Class FeatureColourTest

Class FeatureColourTest	Line # 41	Total Statements 366	Complexity 15	TOTAL Coverage 0.9947229699.5%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4444	2.02	1.01	1.0 1.0100%
testConstructors() : void   testConstructors() : void	5151	16.016	1.01	1.0 1.0100%
testCopyConstructor() : void   testCopyConstructor() : void	7575	74.074	1.01	1.0 1.0100%
testGetColor_simpleColour() : void   testGetColor_simpleColour() : void	185185	2.02	1.01	1.0 1.0100%
testGetColor_colourByLabel() : void   testGetColor_colourByLabel() : void	193193	5.05	1.01	1.0 1.0100%
testGetColor_Graduated() : void   testGetColor_Graduated() : void	204204	7.07	1.01	1.0 1.0100%
testGetColor_aboveBelowThreshold() : void   testGetColor_aboveBelowThreshold() : void	225225	16.016	1.01	1.0 1.0100%
testToJalviewFormat() : void   testToJalviewFormat() : void	260260	50.050	1.01	1.0 1.0100%
testParseJalviewFeatureColour() : void   testParseJalviewFeatureColour() : void	398398	117.0117	3.03	0.982906 0.98290698.3%
testGetColor_colourByAttributeText() : void   testGetColor_colourByAttributeText() : void	615615	8.08	1.01	1.0 1.0100%
testGetColor_GraduatedByAttributeValue() : void   testGetColor_GraduatedByAttributeValue() : void	637637	10.010	1.01	1.0 1.0100%
testIsOutwithThreshold() : void   testIsOutwithThreshold() : void	671671	23.023	1.01	1.0 1.0100%
testGetDescription() : void   testGetDescription() : void	716716	36.036	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.3060686	jalview.schemes.FeatureColourTest.testParseJalviewFeatureColourjalview.schemes.FeatureColourTest.testParseJalviewFeatureColour	1PASS
	0.19788918	jalview.schemes.FeatureColourTest.testCopyConstructorjalview.schemes.FeatureColourTest.testCopyConstructor	1PASS
	0.13456464	jalview.schemes.FeatureColourTest.testToJalviewFormatjalview.schemes.FeatureColourTest.testToJalviewFormat	1PASS
	0.09762533	jalview.schemes.FeatureColourTest.testGetDescriptionjalview.schemes.FeatureColourTest.testGetDescription	1PASS
	0.06332454	jalview.schemes.FeatureColourTest.testIsOutwithThresholdjalview.schemes.FeatureColourTest.testIsOutwithThreshold	1PASS
	0.044854883	jalview.schemes.FeatureColourTest.testGetColor_aboveBelowThresholdjalview.schemes.FeatureColourTest.testGetColor_aboveBelowThreshold	1PASS
	0.044854883	jalview.schemes.FeatureColourTest.testConstructorsjalview.schemes.FeatureColourTest.testConstructors	1PASS
	0.029023746	jalview.schemes.FeatureColourTest.testGetColor_GraduatedByAttributeValuejalview.schemes.FeatureColourTest.testGetColor_GraduatedByAttributeValue	1PASS
	0.023746701	jalview.schemes.FeatureColourTest.testGetColor_colourByAttributeTextjalview.schemes.FeatureColourTest.testGetColor_colourByAttributeText	1PASS
	0.02110818	jalview.schemes.FeatureColourTest.testGetColor_Graduatedjalview.schemes.FeatureColourTest.testGetColor_Graduated	1PASS
	0.015831135	jalview.schemes.FeatureColourTest.testGetColor_colourByLabeljalview.schemes.FeatureColourTest.testGetColor_colourByLabel	1PASS
	0.007915568	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
		99.5% Uncovered Elements: 2 (379) Complexity: 15 Complexity Density: 0.04
41		public class FeatureColourTest
42		{
43
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
44	1	@BeforeClass(alwaysRun = true)...
45		public void setUpJvOptionPane()
46		{
47	1	JvOptionPane.setInteractiveMode(false);
48	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49		}
50
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
51	1	@Test(groups = { "Functional" })...
52		public void testConstructors()
53		{
54	1	FeatureColourI fc = new FeatureColour();
55	1	assertNull(fc.getColour());
56	1	assertTrue(fc.isSimpleColour());
57	1	assertFalse(fc.isColourByLabel());
58	1	assertFalse(fc.isGraduatedColour());
59	1	assertFalse(fc.isColourByAttribute());
60	1	assertEquals(Color.white, fc.getMinColour());
61	1	assertEquals(Color.black, fc.getMaxColour());
62
63	1	fc = new FeatureColour(Color.RED);
64	1	assertEquals(Color.red, fc.getColour());
65	1	assertTrue(fc.isSimpleColour());
66	1	assertFalse(fc.isColourByLabel());
67	1	assertFalse(fc.isGraduatedColour());
68	1	assertFalse(fc.isColourByAttribute());
69	1	assertEquals(ColorUtils.bleachColour(Color.RED, 0.9f),
70		fc.getMinColour());
71	1	assertEquals(Color.RED, fc.getMaxColour());
72
73		}
74
		100% Uncovered Elements: 0 (74) Complexity: 1 Complexity Density: 0.01 1PASS
75	1	@Test(groups = { "Functional" })...
76		public void testCopyConstructor()
77		{
78		/*
79		* plain colour
80		*/
81	1	FeatureColour fc = new FeatureColour(Color.RED);
82	1	FeatureColour fc1 = new FeatureColour(fc);
83	1	assertTrue(fc1.getColour().equals(Color.RED));
84	1	assertFalse(fc1.isGraduatedColour());
85	1	assertFalse(fc1.isColourByLabel());
86	1	assertFalse(fc1.isColourByAttribute());
87	1	assertNull(fc1.getAttributeName());
88
89		/*
90		* min-max colour
91		*/
92	1	fc = new FeatureColour(null, Color.gray, Color.black, Color.gray, 10f,
93		20f);
94	1	fc.setAboveThreshold(true);
95	1	fc.setThreshold(12f);
96	1	fc1 = new FeatureColour(fc);
97	1	assertTrue(fc1.isGraduatedColour());
98	1	assertFalse(fc1.isColourByLabel());
99	1	assertTrue(fc1.isAboveThreshold());
100	1	assertFalse(fc1.isColourByAttribute());
101	1	assertNull(fc1.getAttributeName());
102	1	assertEquals(12f, fc1.getThreshold());
103	1	assertEquals(Color.gray, fc1.getMinColour());
104	1	assertEquals(Color.black, fc1.getMaxColour());
105	1	assertEquals(Color.gray, fc1.getNoColour());
106	1	assertEquals(10f, fc1.getMin());
107	1	assertEquals(20f, fc1.getMax());
108
109		/*
110		* min-max-noValue colour
111		*/
112	1	fc = new FeatureColour(Color.red, Color.gray, Color.black, Color.green,
113		10f, 20f);
114	1	fc.setAboveThreshold(true);
115	1	fc.setThreshold(12f);
116	1	fc1 = new FeatureColour(fc);
117	1	assertTrue(fc1.isGraduatedColour());
118	1	assertFalse(fc1.isColourByLabel());
119	1	assertFalse(fc1.isSimpleColour());
120	1	assertFalse(fc1.isColourByAttribute());
121	1	assertNull(fc1.getAttributeName());
122	1	assertTrue(fc1.isAboveThreshold());
123	1	assertEquals(12f, fc1.getThreshold());
124	1	assertEquals(Color.gray, fc1.getMinColour());
125	1	assertEquals(Color.black, fc1.getMaxColour());
126	1	assertEquals(Color.green, fc1.getNoColour());
127	1	assertEquals(Color.red, fc1.getColour());
128	1	assertEquals(10f, fc1.getMin());
129	1	assertEquals(20f, fc1.getMax());
130
131		/*
132		* colour by label
133		*/
134	1	fc = new FeatureColour();
135	1	fc.setColourByLabel(true);
136	1	fc1 = new FeatureColour(fc);
137	1	assertTrue(fc1.isColourByLabel());
138	1	assertFalse(fc1.isGraduatedColour());
139	1	assertFalse(fc1.isColourByAttribute());
140	1	assertNull(fc1.getAttributeName());
141
142		/*
143		* colour by attribute (label)
144		*/
145	1	fc = new FeatureColour();
146	1	fc.setColourByLabel(true);
147	1	fc.setAttributeName("AF");
148	1	fc1 = new FeatureColour(fc);
149	1	assertTrue(fc1.isColourByLabel());
150	1	assertFalse(fc1.isGraduatedColour());
151	1	assertTrue(fc1.isColourByAttribute());
152	1	assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
153
154		/*
155		* colour by attribute (value)
156		*/
157	1	fc = new FeatureColour(Color.yellow, Color.gray, Color.black,
158		Color.green, 10f, 20f);
159	1	fc.setAboveThreshold(true);
160	1	fc.setThreshold(12f);
161	1	fc.setAttributeName("AF");
162	1	fc1 = new FeatureColour(fc);
163	1	assertTrue(fc1.isGraduatedColour());
164	1	assertFalse(fc1.isColourByLabel());
165	1	assertTrue(fc1.isColourByAttribute());
166	1	assertFalse(fc1.isSimpleColour());
167	1	assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
168	1	assertTrue(fc1.isAboveThreshold());
169	1	assertEquals(12f, fc1.getThreshold());
170	1	assertEquals(Color.gray, fc1.getMinColour());
171	1	assertEquals(Color.black, fc1.getMaxColour());
172	1	assertEquals(Color.green, fc1.getNoColour());
173	1	assertEquals(Color.yellow, fc1.getColour());
174	1	assertEquals(10f, fc1.getMin());
175	1	assertEquals(20f, fc1.getMax());
176
177		/*
178		* modify original attribute label and check that copy doesn't change
179		*/
180	1	fc.setAttributeName("MAF", "AF");
181	1	assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
182
183		}
184
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
185	1	@Test(groups = { "Functional" })...
186		public void testGetColor_simpleColour()
187		{
188	1	FeatureColour fc = new FeatureColour(Color.RED);
189	1	assertEquals(Color.RED,
190		fc.getColor(new SequenceFeature("Cath", "", 1, 2, 0f, null)));
191		}
192
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
193	1	@Test(groups = { "Functional" })...
194		public void testGetColor_colourByLabel()
195		{
196	1	FeatureColour fc = new FeatureColour();
197	1	fc.setColourByLabel(true);
198	1	SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
199		null);
200	1	Color expected = ColorUtils.createColourFromName("desc");
201	1	assertEquals(expected, fc.getColor(sf));
202		}
203
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
204	1	@Test(groups = { "Functional" })...
205		public void testGetColor_Graduated()
206		{
207		/*
208		* graduated colour from
209		* score 0 to 100
210		* gray(128, 128, 128) to red(255, 0, 0)
211		*/
212	1	FeatureColour fc = new FeatureColour(null, Color.GRAY, Color.RED, null,
213		0f, 100f);
214		// feature score is 75 which is 3/4 of the way from GRAY to RED
215	1	SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
216		null);
217		// the colour gradient is computed in float values from 0-1 (where 1 == 255)
218	1	float red = 128 / 255f + 3 / 4f * (255 - 128) / 255f;
219	1	float green = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
220	1	float blue = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
221	1	Color expected = new Color(red, green, blue);
222	1	assertEquals(expected, fc.getColor(sf));
223		}
224
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
225	1	@Test(groups = { "Functional" })...
226		public void testGetColor_aboveBelowThreshold()
227		{
228		// gradient from [50, 150] from WHITE(255, 255, 255) to BLACK(0, 0, 0)
229	1	FeatureColour fc = new FeatureColour(null, Color.WHITE, Color.BLACK,
230		Color.white, 50f, 150f);
231	1	SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 70f,
232		null);
233
234		/*
235		* feature with score of Float.NaN is always assigned minimum colour
236		*/
237	1	SequenceFeature sf2 = new SequenceFeature("type", "desc", 0, 20,
238		Float.NaN, null);
239
240	1	fc.setThreshold(100f); // ignore for now
241	1	assertEquals(new Color(204, 204, 204), fc.getColor(sf));
242	1	assertEquals(Color.white, fc.getColor(sf2));
243
244	1	fc.setAboveThreshold(true); // feature lies below threshold
245	1	assertNull(fc.getColor(sf));
246	1	assertEquals(Color.white, fc.getColor(sf2));
247
248	1	fc.setBelowThreshold(true);
249	1	fc.setThreshold(70f);
250	1	assertNull(fc.getColor(sf)); // feature score == threshold - hidden
251	1	assertEquals(Color.white, fc.getColor(sf2));
252	1	fc.setThreshold(69f);
253	1	assertNull(fc.getColor(sf)); // feature score > threshold - hidden
254	1	assertEquals(Color.white, fc.getColor(sf2));
255		}
256
257		/**
258		* Test output of feature colours to Jalview features file format
259		*/
		100% Uncovered Elements: 0 (50) Complexity: 1 Complexity Density: 0.02 1PASS
260	1	@Test(groups = { "Functional" })...
261		public void testToJalviewFormat()
262		{
263		/*
264		* plain colour - to RGB hex code
265		*/
266	1	FeatureColour fc = new FeatureColour(Color.RED);
267	1	String redHex = Format.getHexString(Color.RED);
268	1	String hexColour = redHex;
269	1	assertEquals("domain\t" + hexColour, fc.toJalviewFormat("domain"));
270
271		/*
272		* colour by label (no threshold)
273		*/
274	1	fc = new FeatureColour();
275	1	fc.setColourByLabel(true);
276	1	assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
277
278		/*
279		* colour by attribute text (no threshold)
280		*/
281	1	fc = new FeatureColour();
282	1	fc.setColourByLabel(true);
283	1	fc.setAttributeName("CLIN_SIG");
284	1	assertEquals("domain\tattribute|CLIN_SIG",
285		fc.toJalviewFormat("domain"));
286
287		/*
288		* colour by label (autoscaled) (an odd state you can reach by selecting
289		* 'above threshold', then deselecting 'threshold is min/max' then 'colour
290		* by label')
291		*/
292	1	fc.setAttributeName((String[]) null);
293	1	fc.setAutoScaled(true);
294	1	assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
295
296		/*
297		* colour by label (above threshold)
298		*/
299	1	fc.setAutoScaled(false);
300	1	fc.setThreshold(12.5f);
301	1	fc.setAboveThreshold(true);
302		// min/max values are output though not used by this scheme
303	1	assertEquals("domain\tlabel|||0.0|0.0|above|12.5",
304		fc.toJalviewFormat("domain"));
305
306		/*
307		* colour by label (below threshold)
308		*/
309	1	fc.setBelowThreshold(true);
310	1	assertEquals("domain\tlabel|||0.0|0.0|below|12.5",
311		fc.toJalviewFormat("domain"));
312
313		/*
314		* colour by attributes text (below threshold)
315		*/
316	1	fc.setBelowThreshold(true);
317	1	fc.setAttributeName("CSQ", "Consequence");
318	1	assertEquals("domain\tattribute|CSQ:Consequence|||0.0|0.0|below|12.5",
319		fc.toJalviewFormat("domain"));
320
321		/*
322		* graduated colour by score, no threshold
323		* - default constructor sets noValueColor = minColor
324		*/
325	1	fc = new FeatureColour(null, Color.GREEN, Color.RED, Color.GREEN, 12f,
326		25f);
327	1	String greenHex = Format.getHexString(Color.GREEN);
328	1	String expected = String.format(
329		"domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
330		redHex);
331	1	assertEquals(expected, fc.toJalviewFormat("domain"));
332
333		/*
334		* graduated colour by score, no threshold, no value gets min colour
335		*/
336	1	fc = new FeatureColour(Color.RED, Color.GREEN, Color.RED, Color.GREEN,
337		12f, 25f);
338	1	expected = String.format(
339		"domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
340		redHex);
341	1	assertEquals(expected, fc.toJalviewFormat("domain"));
342
343		/*
344		* graduated colour by score, no threshold, no value gets max colour
345		*/
346	1	fc = new FeatureColour(Color.RED, Color.GREEN, Color.RED, Color.RED,
347		12f, 25f);
348	1	expected = String.format(
349		"domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|none", greenHex,
350		redHex);
351	1	assertEquals(expected, fc.toJalviewFormat("domain"));
352
353		/*
354		* colour ranges over the actual score ranges (not min/max)
355		*/
356	1	fc.setAutoScaled(true);
357	1	expected = String.format(
358		"domain\tscore|%s|%s|noValueMax|12.0|25.0|none", greenHex,
359		redHex);
360	1	assertEquals(expected, fc.toJalviewFormat("domain"));
361
362		/*
363		* graduated colour by score, below threshold
364		*/
365	1	fc.setThreshold(12.5f);
366	1	fc.setBelowThreshold(true);
367	1	expected = String.format(
368		"domain\tscore|%s|%s|noValueMax|12.0|25.0|below|12.5", greenHex,
369		redHex);
370	1	assertEquals(expected, fc.toJalviewFormat("domain"));
371
372		/*
373		* graduated colour by score, above threshold
374		*/
375	1	fc.setThreshold(12.5f);
376	1	fc.setAboveThreshold(true);
377	1	fc.setAutoScaled(false);
378	1	expected = String.format(
379		"domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|above|12.5",
380		greenHex, redHex);
381	1	assertEquals(expected, fc.toJalviewFormat("domain"));
382
383		/*
384		* graduated colour by attribute, above threshold
385		*/
386	1	fc.setAttributeName("CSQ", "AF");
387	1	fc.setAboveThreshold(true);
388	1	fc.setAutoScaled(false);
389	1	expected = String.format(
390		"domain\tattribute|CSQ:AF|%s|%s|noValueMax|abso|12.0|25.0|above|12.5",
391		greenHex, redHex);
392	1	assertEquals(expected, fc.toJalviewFormat("domain"));
393		}
394
395		/**
396		* Test parsing of feature colours from Jalview features file format
397		*/
		98.3% Uncovered Elements: 2 (117) Complexity: 3 Complexity Density: 0.03 1PASS
398	1	@Test(groups = { "Functional" })...
399		public void testParseJalviewFeatureColour()
400		{
401		/*
402		* simple colour by name
403		*/
404	1	FeatureColourI fc = FeatureColour.parseJalviewFeatureColour("red");
405	1	assertTrue(fc.isSimpleColour());
406	1	assertEquals(Color.RED, fc.getColour());
407
408		/*
409		* simple colour by hex code
410		*/
411	1	fc = FeatureColour
412		.parseJalviewFeatureColour(Format.getHexString(Color.RED));
413	1	assertTrue(fc.isSimpleColour());
414	1	assertEquals(Color.RED, fc.getColour());
415
416		/*
417		* simple colour by rgb triplet
418		*/
419	1	fc = FeatureColour.parseJalviewFeatureColour("255,0,0");
420	1	assertTrue(fc.isSimpleColour());
421	1	assertEquals(Color.RED, fc.getColour());
422
423		/*
424		* malformed colour
425		*/
426	1	try
427		{
428	1	fc = FeatureColour.parseJalviewFeatureColour("oops");
429	0	fail("expected exception");
430		} catch (IllegalArgumentException e)
431		{
432	1	assertEquals("Invalid colour descriptor: oops", e.getMessage());
433		}
434
435		/*
436		* colour by label (no threshold)
437		*/
438	1	fc = FeatureColour.parseJalviewFeatureColour("label");
439	1	assertTrue(fc.isColourByLabel());
440	1	assertFalse(fc.hasThreshold());
441
442		/*
443		* colour by label (with threshold)
444		*/
445	1	fc = FeatureColour
446		.parseJalviewFeatureColour("label|||0.0|0.0|above|12.0");
447	1	assertTrue(fc.isColourByLabel());
448	1	assertTrue(fc.isAboveThreshold());
449	1	assertEquals(12.0f, fc.getThreshold());
450
451		/*
452		* colour by attribute text (no threshold)
453		*/
454	1	fc = FeatureColour.parseJalviewFeatureColour("attribute|CLIN_SIG");
455	1	assertTrue(fc.isColourByAttribute());
456	1	assertTrue(fc.isColourByLabel());
457	1	assertFalse(fc.hasThreshold());
458	1	assertArrayEquals(new String[] { "CLIN_SIG" }, fc.getAttributeName());
459
460		/*
461		* colour by attributes text (with score threshold)
462		*/
463	1	fc = FeatureColour.parseJalviewFeatureColour(
464		"attribute|CSQ:Consequence|||0.0|0.0|above|12.0");
465	1	assertTrue(fc.isColourByLabel());
466	1	assertTrue(fc.isColourByAttribute());
467	1	assertArrayEquals(new String[] { "CSQ", "Consequence" },
468		fc.getAttributeName());
469	1	assertTrue(fc.isAboveThreshold());
470	1	assertEquals(12.0f, fc.getThreshold());
471
472		/*
473		* graduated colour by score (with colour names) (no threshold)
474		*/
475	1	fc = FeatureColour.parseJalviewFeatureColour("red|green|10.0|20.0");
476	1	assertTrue(fc.isGraduatedColour());
477	1	assertFalse(fc.hasThreshold());
478	1	assertEquals(Color.RED, fc.getMinColour());
479	1	assertEquals(Color.GREEN, fc.getMaxColour());
480	1	assertEquals(Color.RED, fc.getNoColour());
481	1	assertEquals(10f, fc.getMin());
482	1	assertEquals(20f, fc.getMax());
483	1	assertTrue(fc.isAutoScaled());
484
485		/*
486		* the same, with 'no value colour' specified as max
487		*/
488	1	fc = FeatureColour
489		.parseJalviewFeatureColour("red|green|novaluemax|10.0|20.0");
490	1	assertEquals(Color.RED, fc.getMinColour());
491	1	assertEquals(Color.GREEN, fc.getMaxColour());
492	1	assertEquals(Color.GREEN, fc.getNoColour());
493	1	assertEquals(10f, fc.getMin());
494	1	assertEquals(20f, fc.getMax());
495
496		/*
497		* the same, with 'no value colour' specified as min
498		*/
499	1	fc = FeatureColour
500		.parseJalviewFeatureColour("red|green|novalueMin|10.0|20.0");
501	1	assertEquals(Color.RED, fc.getMinColour());
502	1	assertEquals(Color.GREEN, fc.getMaxColour());
503	1	assertEquals(Color.RED, fc.getNoColour());
504	1	assertEquals(10f, fc.getMin());
505	1	assertEquals(20f, fc.getMax());
506
507		/*
508		* the same, with 'no value colour' specified as none
509		*/
510	1	fc = FeatureColour
511		.parseJalviewFeatureColour("red|green|novaluenone|10.0|20.0");
512	1	assertEquals(Color.RED, fc.getMinColour());
513	1	assertEquals(Color.GREEN, fc.getMaxColour());
514	1	assertNull(fc.getNoColour());
515	1	assertEquals(10f, fc.getMin());
516	1	assertEquals(20f, fc.getMax());
517
518		/*
519		* the same, with invalid 'no value colour'
520		*/
521	1	try
522		{
523	1	fc = FeatureColour
524		.parseJalviewFeatureColour("red|green|blue|10.0|20.0");
525	0	fail("expected exception");
526		} catch (IllegalArgumentException e)
527		{
528	1	assertEquals(
529		"Couldn't parse the minimum value for graduated colour ('blue')",
530		e.getMessage());
531		}
532
533		/*
534		* graduated colour (explicitly by 'score') (no threshold)
535		*/
536	1	fc = FeatureColour
537		.parseJalviewFeatureColour("Score|red|green|10.0|20.0");
538	1	assertTrue(fc.isGraduatedColour());
539	1	assertFalse(fc.hasThreshold());
540	1	assertEquals(Color.RED, fc.getMinColour());
541	1	assertEquals(Color.GREEN, fc.getMaxColour());
542	1	assertEquals(10f, fc.getMin());
543	1	assertEquals(20f, fc.getMax());
544	1	assertTrue(fc.isAutoScaled());
545
546		/*
547		* graduated colour by attribute (no threshold)
548		*/
549	1	fc = FeatureColour
550		.parseJalviewFeatureColour("attribute|AF|red|green|10.0|20.0");
551	1	assertTrue(fc.isGraduatedColour());
552	1	assertTrue(fc.isColourByAttribute());
553	1	assertArrayEquals(new String[] { "AF" }, fc.getAttributeName());
554	1	assertFalse(fc.hasThreshold());
555	1	assertEquals(Color.RED, fc.getMinColour());
556	1	assertEquals(Color.GREEN, fc.getMaxColour());
557	1	assertEquals(10f, fc.getMin());
558	1	assertEquals(20f, fc.getMax());
559	1	assertTrue(fc.isAutoScaled());
560
561		/*
562		* graduated colour by score (colours by hex code) (above threshold)
563		*/
564	1	String descriptor = String.format("%s|%s|10.0|20.0|above|15",
565		Format.getHexString(Color.RED),
566		Format.getHexString(Color.GREEN));
567	1	fc = FeatureColour.parseJalviewFeatureColour(descriptor);
568	1	assertTrue(fc.isGraduatedColour());
569	1	assertTrue(fc.hasThreshold());
570	1	assertTrue(fc.isAboveThreshold());
571	1	assertEquals(15f, fc.getThreshold());
572	1	assertEquals(Color.RED, fc.getMinColour());
573	1	assertEquals(Color.GREEN, fc.getMaxColour());
574	1	assertEquals(10f, fc.getMin());
575	1	assertEquals(20f, fc.getMax());
576	1	assertTrue(fc.isAutoScaled());
577
578		/*
579		* graduated colour by attributes (below threshold)
580		*/
581	1	fc = FeatureColour.parseJalviewFeatureColour(
582		"attribute|CSQ:AF|red|green|10.0|20.0|below|13");
583	1	assertTrue(fc.isGraduatedColour());
584	1	assertTrue(fc.isColourByAttribute());
585	1	assertArrayEquals(new String[] { "CSQ", "AF" }, fc.getAttributeName());
586	1	assertTrue(fc.hasThreshold());
587	1	assertTrue(fc.isBelowThreshold());
588	1	assertEquals(13f, fc.getThreshold());
589	1	assertEquals(Color.RED, fc.getMinColour());
590	1	assertEquals(Color.GREEN, fc.getMaxColour());
591	1	assertEquals(10f, fc.getMin());
592	1	assertEquals(20f, fc.getMax());
593	1	assertTrue(fc.isAutoScaled());
594
595		/*
596		* graduated colour (by RGB triplet) (below threshold), absolute scale
597		*/
598	1	descriptor = "255,0,0|0,255,0|abso|10.0|20.0|below|15";
599	1	fc = FeatureColour.parseJalviewFeatureColour(descriptor);
600	1	assertTrue(fc.isGraduatedColour());
601	1	assertFalse(fc.isAutoScaled());
602	1	assertTrue(fc.hasThreshold());
603	1	assertTrue(fc.isBelowThreshold());
604	1	assertEquals(15f, fc.getThreshold());
605	1	assertEquals(Color.RED, fc.getMinColour());
606	1	assertEquals(Color.GREEN, fc.getMaxColour());
607	1	assertEquals(10f, fc.getMin());
608	1	assertEquals(20f, fc.getMax());
609
610	1	descriptor = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
611	1	fc = FeatureColour.parseJalviewFeatureColour(descriptor);
612	1	assertTrue(fc.isGraduatedColour());
613		}
614
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
615	1	@Test(groups = { "Functional" })...
616		public void testGetColor_colourByAttributeText()
617		{
618	1	FeatureColour fc = new FeatureColour();
619	1	fc.setColourByLabel(true);
620	1	fc.setAttributeName("consequence");
621	1	SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
622		null);
623
624		/*
625		* if feature has no such attribute, use 'no value' colour
626		*/
627	1	assertEquals(FeatureColour.DEFAULT_NO_COLOUR, fc.getColor(sf));
628
629		/*
630		* if feature has attribute, generate colour from value
631		*/
632	1	sf.setValue("consequence", "benign");
633	1	Color expected = ColorUtils.createColourFromName("benign");
634	1	assertEquals(expected, fc.getColor(sf));
635		}
636
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
637	1	@Test(groups = { "Functional" })...
638		public void testGetColor_GraduatedByAttributeValue()
639		{
640		/*
641		* graduated colour based on attribute value for AF
642		* given a min-max range of 0-100
643		*/
644	1	FeatureColour fc = new FeatureColour(Color.white,
645		new Color(50, 100, 150), new Color(150, 200, 250), Color.yellow,
646		0f, 100f);
647	1	String attName = "AF";
648	1	fc.setAttributeName(attName);
649
650		/*
651		* first case: feature lacks the attribute - use 'no value' colour
652		*/
653	1	SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
654		null);
655	1	assertEquals(Color.yellow, fc.getColor(sf));
656
657		/*
658		* second case: attribute present but not numeric - treat as if absent
659		*/
660	1	sf.setValue(attName, "twelve");
661	1	assertEquals(Color.yellow, fc.getColor(sf));
662
663		/*
664		* third case: valid attribute value
665		*/
666	1	sf.setValue(attName, "20.0");
667	1	Color expected = new Color(70, 120, 170);
668	1	assertEquals(expected, fc.getColor(sf));
669		}
670
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
671	1	@Test(groups = { "Functional" })...
672		public void testIsOutwithThreshold()
673		{
674	1	FeatureColourI fc = new FeatureColour(Color.red);
675	1	SequenceFeature sf = new SequenceFeature("METAL", "desc", 10, 12, 1.2f,
676		"grp");
677	1	assertFalse(fc.isOutwithThreshold(null));
678	1	assertFalse(fc.isOutwithThreshold(sf));
679
680	1	fc = new FeatureColour(null, Color.white, Color.black, Color.green, 0f,
681		10f);
682	1	assertFalse(fc.isOutwithThreshold(sf)); // no threshold
683
684	1	fc.setAboveThreshold(true);
685	1	fc.setThreshold(1f);
686	1	assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is above 1
687
688	1	fc.setThreshold(2f);
689	1	assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not above 2
690
691	1	fc.setBelowThreshold(true);
692	1	assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is below 2
693
694	1	fc.setThreshold(1f);
695	1	assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not below 1
696
697		/*
698		* with attribute value threshold
699		*/
700	1	fc.setAttributeName("AC");
701	1	assertFalse(fc.isOutwithThreshold(sf)); // missing attribute AC is ignored
702
703	1	sf.setValue("AC", "-1");
704	1	assertFalse(fc.isOutwithThreshold(sf)); // value -1 is below 1
705
706	1	sf.setValue("AC", "1");
707	1	assertTrue(fc.isOutwithThreshold(sf)); // value 1 is not below 1
708
709	1	sf.setValue("AC", "junk");
710	1	assertFalse(fc.isOutwithThreshold(sf)); // bad value is ignored
711		}
712
713		/**
714		* Test description of feature colour suitable for a tooltip
715		*/
		100% Uncovered Elements: 0 (36) Complexity: 1 Complexity Density: 0.03 1PASS
716	1	@Test(groups = { "Functional" })...
717		public void testGetDescription()
718		{
719		/*
720		* plain colour
721		*/
722	1	FeatureColour fc = new FeatureColour(Color.RED);
723	1	assertEquals(
724		String.format("r=%d,g=%d,b=%d", Color.RED.getRed(),
725		Color.red.getGreen(), Color.red.getBlue()),
726		fc.getDescription());
727
728		/*
729		* colour by label (no threshold)
730		*/
731	1	fc = new FeatureColour();
732	1	fc.setColourByLabel(true);
733	1	assertEquals("By Label", fc.getDescription());
734
735		/*
736		* colour by attribute text (no threshold)
737		*/
738	1	fc = new FeatureColour();
739	1	fc.setColourByLabel(true);
740	1	fc.setAttributeName("CLIN_SIG");
741	1	assertEquals("By CLIN_SIG", fc.getDescription());
742
743		/*
744		* colour by label (above score threshold)
745		*/
746	1	fc = new FeatureColour();
747	1	fc.setColourByLabel(true);
748	1	fc.setAutoScaled(false);
749	1	fc.setThreshold(12.5f);
750	1	fc.setAboveThreshold(true);
751	1	assertEquals("By Label (Score > 12.5)", fc.getDescription());
752
753		/*
754		* colour by label (below score threshold)
755		*/
756	1	fc.setBelowThreshold(true);
757	1	assertEquals("By Label (Score < 12.5)", fc.getDescription());
758
759		/*
760		* colour by attributes text (below score threshold)
761		*/
762	1	fc.setBelowThreshold(true);
763	1	fc.setAttributeName("CSQ", "Consequence");
764	1	assertEquals("By CSQ:Consequence (Score < 12.5)", fc.getDescription());
765
766		/*
767		* graduated colour by score, no threshold
768		*/
769	1	fc = new FeatureColour(null, Color.GREEN, Color.RED, null, 12f, 25f);
770	1	assertEquals("By Score", fc.getDescription());
771
772		/*
773		* graduated colour by score, below threshold
774		*/
775	1	fc.setThreshold(12.5f);
776	1	fc.setBelowThreshold(true);
777	1	assertEquals("By Score (< 12.5)", fc.getDescription());
778
779		/*
780		* graduated colour by score, above threshold
781		*/
782	1	fc.setThreshold(12.5f);
783	1	fc.setAboveThreshold(true);
784	1	fc.setAutoScaled(false);
785	1	assertEquals("By Score (> 12.5)", fc.getDescription());
786
787		/*
788		* graduated colour by attribute, no threshold
789		*/
790	1	fc.setAttributeName("CSQ", "AF");
791	1	fc.setAboveThreshold(false);
792	1	fc.setAutoScaled(false);
793	1	assertEquals("By CSQ:AF", fc.getDescription());
794
795		/*
796		* graduated colour by attribute, above threshold
797		*/
798	1	fc.setAboveThreshold(true);
799	1	fc.setAutoScaled(false);
800	1	assertEquals("By CSQ:AF (> 12.5)", fc.getDescription());
801		}
802		}