Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AlignFrameTest	59	271	10	3	0.9893238598.9%	Show methods

Class AlignFrameTest

Class AlignFrameTest	Line # 59	Total Statements 271	Complexity 10	Uncovered Elements 3	TOTAL Coverage 0.9893238598.9%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	6363	2.02	1.01	0.00	1.0 1.0100%
testHideFeatureColumns() : void   testHideFeatureColumns() : void	7070	39.039	1.01	0.00	1.0 1.0100%
setUpBeforeClass() : void   setUpBeforeClass() : void	152152	2.02	1.01	0.00	1.0 1.0100%
tearDown() : void   tearDown() : void	162162	1.01	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	172172	7.07	3.03	3.03	0.6666667 0.666666766.7%
testChangeColour_background_groupsAndThresholds() : void   testChangeColour_background_groupsAndThresholds() : void	208208	66.066	1.01	0.00	1.0 1.0100%
testColourThresholdActions() : void   testColourThresholdActions() : void	339339	91.091	1.01	0.00	1.0 1.0100%
testNewView_colourThresholds() : void   testNewView_colourThresholds() : void	508508	63.063	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.32740214	jalview.gui.AlignFrameTest.testColourThresholdActionsjalview.gui.AlignFrameTest.testColourThresholdActions	1PASS
	0.23843417	jalview.gui.AlignFrameTest.testChangeColour_background_groupsAndThresholdsjalview.gui.AlignFrameTest.testChangeColour_background_groupsAndThresholds	1PASS
	0.227758	jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds	1PASS
	0.14234875	jalview.gui.AlignFrameTest.testHideFeatureColumnsjalview.gui.AlignFrameTest.testHideFeatureColumns	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.gui;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertNotSame;
26		import static org.testng.Assert.assertSame;
27		import static org.testng.Assert.assertTrue;
28
29		import jalview.api.FeatureColourI;
30		import jalview.bin.Cache;
31		import jalview.bin.Jalview;
32		import jalview.datamodel.Alignment;
33		import jalview.datamodel.AlignmentI;
34		import jalview.datamodel.HiddenColumns;
35		import jalview.datamodel.Sequence;
36		import jalview.datamodel.SequenceFeature;
37		import jalview.datamodel.SequenceGroup;
38		import jalview.datamodel.SequenceI;
39		import jalview.io.DataSourceType;
40		import jalview.io.FileLoader;
41		import jalview.io.Jalview2xmlTests;
42		import jalview.renderer.ResidueShaderI;
43		import jalview.schemes.BuriedColourScheme;
44		import jalview.schemes.FeatureColour;
45		import jalview.schemes.HelixColourScheme;
46		import jalview.schemes.JalviewColourScheme;
47		import jalview.schemes.StrandColourScheme;
48		import jalview.schemes.TurnColourScheme;
49		import jalview.util.MessageManager;
50
51		import java.awt.Color;
52		import java.util.Iterator;
53
54		import org.testng.annotations.AfterMethod;
55		import org.testng.annotations.BeforeClass;
56		import org.testng.annotations.BeforeMethod;
57		import org.testng.annotations.Test;
58
		98.9% Uncovered Elements: 3 (281) Complexity: 10 Complexity Density: 0.04
59		public class AlignFrameTest
60		{
61		AlignFrame af;
62
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
63	1	@BeforeClass(alwaysRun = true)...
64		public void setUpJvOptionPane()
65		{
66	1	JvOptionPane.setInteractiveMode(false);
67	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
68		}
69
		100% Uncovered Elements: 0 (39) Complexity: 1 Complexity Density: 0.03 1PASS
70	1	@Test(groups = "Functional")...
71		public void testHideFeatureColumns()
72		{
73	1	SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
74	1	SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
75	1	seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
76	1	seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
77		null));
78	1	seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
79		Float.NaN, null));
80	1	seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
81		Float.NaN, null));
82	1	AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
83	1	AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
84		al.getHeight());
85
86		/*
87		* make all features visible (select feature columns checks visibility)
88		*/
89	1	alignFrame.getFeatureRenderer().findAllFeatures(true);
90
91		/*
92		* hiding a feature not present does nothing
93		*/
94	1	assertFalse(alignFrame.hideFeatureColumns("exon", true));
95	1	assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
96
97	1	assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
98		.getNumberOfRegions(), 0);
99
100	1	assertFalse(alignFrame.hideFeatureColumns("exon", false));
101	1	assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
102
103	1	assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
104		.getNumberOfRegions(), 0);
105
106		/*
107		* hiding a feature in all columns does nothing
108		*/
109	1	assertFalse(alignFrame.hideFeatureColumns("Metal", true));
110	1	assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
111
112	1	assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
113		.getNumberOfRegions(), 0);
114
115
116		/*
117		* threshold Metal to hide features where score < 5
118		* seq1 feature in columns 1-5 is hidden
119		* seq2 feature in columns 6-10 is shown
120		*/
121	1	FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
122	1	fc.setAboveThreshold(true);
123	1	fc.setThreshold(5f);
124	1	alignFrame.getFeatureRenderer().setColour("Metal", fc);
125	1	assertTrue(alignFrame.hideFeatureColumns("Metal", true));
126	1	HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
127	1	assertEquals(hidden.getNumberOfRegions(), 1);
128	1	Iterator<int[]> regions = hidden.iterator();
129	1	int[] next = regions.next();
130	1	assertEquals(next[0], 5);
131	1	assertEquals(next[1], 9);
132
133		/*
134		* hide a feature present in some columns
135		* sequence positions [2-4], [7-9] are column positions
136		* [1-3], [6-8] base zero
137		*/
138	1	alignFrame.getViewport().showAllHiddenColumns();
139	1	assertTrue(alignFrame.hideFeatureColumns("Turn", true));
140	1	regions = alignFrame.getViewport().getAlignment()
141		.getHiddenColumns().iterator();
142	1	assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
143		.getNumberOfRegions(), 2);
144	1	next = regions.next();
145	1	assertEquals(next[0], 1);
146	1	assertEquals(next[1], 3);
147	1	next = regions.next();
148	1	assertEquals(next[0], 6);
149	1	assertEquals(next[1], 8);
150		}
151
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
152	1	@BeforeClass(alwaysRun = true)...
153		public static void setUpBeforeClass() throws Exception
154		{
155		/*
156		* use read-only test properties file
157		*/
158	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
159	1	Jalview.main(new String[] { "-nonews" });
160		}
161
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
162	4	@AfterMethod(alwaysRun = true)...
163		public void tearDown()
164		{
165	4	Desktop.instance.closeAll_actionPerformed(null);
166		}
167
168		/**
169		* configure (read-only) properties for test to ensure Consensus is computed
170		* for colour Above PID testing
171		*/
		66.7% Uncovered Elements: 3 (9) Complexity: 3 Complexity Density: 0.43
172	4	@BeforeMethod(alwaysRun = true)...
173		public void setUp()
174		{
175	4	Cache.loadProperties("test/jalview/io/testProps.jvprops");
176	4	Cache.applicationProperties.setProperty("SHOW_IDENTITY",
177		Boolean.TRUE.toString());
178	4	af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
179		DataSourceType.FILE);
180
181		/*
182		* wait for Consensus thread to complete
183		*/
184	4	synchronized (this)
185		{
186	4	while (af.getViewport().getConsensusSeq() == null)
187		{
188	0	try
189		{
190	0	wait(50);
191		} catch (InterruptedException e)
192		{
193		}
194		}
195		}
196		}
197
198		/**
199		* Test that changing background (alignment) colour scheme
200		* <ul>
201		* <li>with Apply Colour to All Groups not selected, does not change group
202		* colours</li>
203		* <li>with Apply Colour to All Groups selected, does change group colours</li>
204		* <li>in neither case, changes alignment or group colour thresholds (PID or
205		* Conservation)</li>
206		* </ul>
207		*/
		100% Uncovered Elements: 0 (66) Complexity: 1 Complexity Density: 0.02 1PASS
208	1	@Test(groups = "Functional")...
209		public void testChangeColour_background_groupsAndThresholds()
210		{
211	1	AlignViewport av = af.getViewport();
212	1	AlignmentI al = av.getAlignment();
213
214		/*
215		* Colour alignment by Buried Index
216		*/
217	1	af.applyToAllGroups_actionPerformed(false);
218	1	af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
219	1	assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
220	1	assertFalse(av.getResidueShading().conservationApplied());
221	1	assertEquals(av.getResidueShading().getThreshold(), 0);
222
223		/*
224		* Apply Conservation 20%
225		*/
226	1	af.conservationMenuItem_actionPerformed(true);
227	1	SliderPanel sp = SliderPanel.getSliderPanel();
228	1	assertEquals(sp.getTitle(), MessageManager.formatMessage(
229		"label.conservation_colour_increment",
230		new String[] { "Background" }));
231	1	assertTrue(sp.isForConservation());
232	1	sp.valueChanged(20);
233	1	assertTrue(av.getResidueShading().conservationApplied());
234	1	assertEquals(av.getResidueShading().getConservationInc(), 20);
235
236		/*
237		* Apply PID threshold 10% (conservation still applies as well)
238		*/
239	1	af.abovePIDThreshold_actionPerformed(true);
240	1	sp = SliderPanel.getSliderPanel();
241	1	assertFalse(sp.isForConservation());
242	1	assertEquals(sp.getTitle(), MessageManager.formatMessage(
243		"label.percentage_identity_threshold",
244		new String[] { "Background" }));
245	1	sp.valueChanged(10);
246	1	assertEquals(av.getResidueShading().getThreshold(), 10);
247	1	assertTrue(av.getResidueShading().conservationApplied());
248	1	assertEquals(av.getResidueShading().getConservationInc(), 20);
249
250		/*
251		* create a group with Strand colouring, 30% Conservation
252		* and 40% PID threshold
253		*/
254	1	SequenceGroup sg = new SequenceGroup();
255	1	sg.addSequence(al.getSequenceAt(0), false);
256	1	sg.setStartRes(15);
257	1	sg.setEndRes(25);
258	1	av.setSelectionGroup(sg);
259
260		/*
261		* apply 30% Conservation to group
262		*/
263	1	PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
264	1	popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
265		.toString());
266	1	assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
267	1	assertEquals(al.getGroups().size(), 1);
268	1	assertSame(al.getGroups().get(0), sg);
269	1	popupMenu.conservationMenuItem_actionPerformed(true);
270	1	sp = SliderPanel.getSliderPanel();
271	1	assertTrue(sp.isForConservation());
272	1	assertEquals(sp.getTitle(), MessageManager.formatMessage(
273		"label.conservation_colour_increment",
274		new String[] { sg.getName() }));
275	1	sp.valueChanged(30);
276	1	assertTrue(sg.getGroupColourScheme().conservationApplied());
277	1	assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
278
279		/*
280		* apply 40% PID threshold to group
281		*/
282	1	popupMenu.abovePIDColour_actionPerformed(true);
283	1	sp = SliderPanel.getSliderPanel();
284	1	assertFalse(sp.isForConservation());
285	1	assertEquals(sp.getTitle(), MessageManager.formatMessage(
286		"label.percentage_identity_threshold",
287		new String[] { sg.getName() }));
288	1	sp.valueChanged(40);
289	1	assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
290		// conservation threshold is unchanged:
291	1	assertTrue(sg.getGroupColourScheme().conservationApplied());
292	1	assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
293
294		/*
295		* change alignment colour - group colour, and all thresholds,
296		* should be unaffected
297		*/
298	1	af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
299	1	assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
300	1	assertTrue(av.getResidueShading().conservationApplied());
301	1	assertEquals(av.getResidueShading().getConservationInc(), 20);
302	1	assertEquals(av.getResidueShading().getThreshold(), 10);
303	1	assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
304	1	assertTrue(sg.getGroupColourScheme().conservationApplied());
305	1	assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
306	1	assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
307
308		/*
309		* Now change alignment colour with Apply Colour To All Groups
310		* - group colour should change, but not colour thresholds
311		*/
312	1	af.applyToAllGroups_actionPerformed(true);
313	1	af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
314	1	assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
315	1	assertTrue(av.getResidueShading().conservationApplied());
316	1	assertEquals(av.getResidueShading().getConservationInc(), 20);
317	1	assertEquals(av.getResidueShading().getThreshold(), 10);
318	1	assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
319	1	assertTrue(sg.getGroupColourScheme().conservationApplied());
320	1	assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
321	1	assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
322		}
323
324		/**
325		* Test residue colouring with various options
326		* <ol>
327		* <li>no PID or Conservation threshold</li>
328		* <li>colour by Conservation applied</li>
329		* <li>colour by Conservation removed</li>
330		* <li>colour above PID - various values</li>
331		* <li>colour above PID removed</li>
332		* <li>Above PID plus By Conservation combined</li>
333		* <li>remove Above PID to leave just By Conservation</li>
334		* <li>re-add Above PID</li>
335		* <li>remove By Conservation to leave just Above PID</li>
336		* <li>remove Above PID to leave original colours</li>
337		* </ol>
338		*/
		100% Uncovered Elements: 0 (91) Complexity: 1 Complexity Density: 0.01 1PASS
339	1	@Test(groups = "Functional")...
340		public void testColourThresholdActions()
341		{
342	1	AlignViewport av = af.getViewport();
343	1	AlignmentI al = av.getAlignment();
344
345		/*
346		* Colour alignment by Helix Propensity, no thresholds
347		*/
348	1	af.applyToAllGroups_actionPerformed(false);
349	1	af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
350	1	assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
351	1	assertFalse(av.getResidueShading().conservationApplied());
352	1	assertEquals(av.getResidueShading().getThreshold(), 0);
353
354		/*
355		* inspect the colour of
356		* FER_CAPAN.9(I), column 14 (14 base 0)
357		* FER_CAPAN.10(SER), column 16 (15 base 0)
358		*/
359	1	SequenceI ferCapan = al.findName("FER_CAPAN");
360	1	ResidueShaderI rs = av.getResidueShading();
361	1	Color c = rs.findColour('I', 14, ferCapan);
362	1	Color i_original = new Color(138, 117, 138);
363	1	assertEquals(c, i_original);
364	1	c = rs.findColour('S', 15, ferCapan);
365	1	Color s_original = new Color(54, 201, 54);
366	1	assertEquals(c, s_original);
367
368		/*
369		* colour by conservation with increment 10
370		*/
371	1	af.conservationMenuItem_actionPerformed(true);
372	1	SliderPanel sp = SliderPanel.getSliderPanel();
373	1	assertTrue(sp.isForConservation());
374	1	assertEquals(sp.getValue(), 30); // initial slider setting
375	1	sp.valueChanged(10);
376	1	assertSame(rs, av.getResidueShading());
377	1	c = rs.findColour('I', 14, ferCapan);
378	1	Color i_faded = new Color(196, 186, 196);
379	1	assertEquals(c, i_faded);
380	1	c = rs.findColour('S', 15, ferCapan);
381	1	Color s_faded = new Color(144, 225, 144);
382	1	assertEquals(c, s_faded);
383
384		/*
385		* deselect By Conservation - colour should revert
386		*/
387	1	af.conservationMenuItem_actionPerformed(false);
388	1	c = rs.findColour('S', 15, ferCapan);
389	1	assertEquals(c, s_original);
390
391		/*
392		* now Above PID, threshold = 0%
393		* should be no change
394		*/
395	1	af.abovePIDThreshold_actionPerformed(true);
396	1	sp = SliderPanel.getSliderPanel();
397	1	assertFalse(sp.isForConservation());
398	1	assertEquals(sp.getValue(), 0); // initial slider setting
399	1	c = rs.findColour('I', 14, ferCapan);
400	1	assertEquals(c, i_original);
401	1	c = rs.findColour('S', 15, ferCapan);
402	1	assertEquals(c, s_original);
403
404		/*
405		* Above PID, threshold = 1%
406		* 15.I becomes White because no match to consensus (V)
407		* 16.S remains coloured as matches 66.66% consensus
408		*/
409	1	sp.valueChanged(1);
410	1	c = rs.findColour('I', 14, ferCapan);
411	1	assertEquals(c, Color.white);
412	1	c = rs.findColour('S', 15, ferCapan);
413	1	assertEquals(c, s_original);
414
415		/*
416		* threshold 66% - no further change yet...
417		*/
418	1	sp.valueChanged(66);
419	1	c = rs.findColour('I', 14, ferCapan);
420	1	assertEquals(c, Color.white);
421	1	c = rs.findColour('S', 15, ferCapan);
422	1	assertEquals(c, s_original);
423
424		/*
425		* threshold 67% - now both residues are white
426		*/
427	1	sp.valueChanged(67);
428	1	c = rs.findColour('I', 14, ferCapan);
429	1	assertEquals(c, Color.white);
430	1	c = rs.findColour('S', 15, ferCapan);
431	1	assertEquals(c, Color.white);
432
433		/*
434		* deselect Above PID - colours should revert
435		*/
436	1	af.abovePIDThreshold_actionPerformed(false);
437	1	c = rs.findColour('I', 14, ferCapan);
438	1	assertEquals(c, i_original);
439	1	c = rs.findColour('S', 15, ferCapan);
440	1	assertEquals(c, s_original);
441
442		/*
443		* Now combine Above 50% PID and By Conservation 10%
444		* 15.I is White because no match to consensus (V)
445		* 16.S is coloured but faded
446		*/
447	1	af.abovePIDThreshold_actionPerformed(true);
448	1	sp = SliderPanel.getSliderPanel();
449	1	assertFalse(sp.isForConservation());
450	1	sp.valueChanged(50);
451	1	af.conservationMenuItem_actionPerformed(true);
452	1	sp = SliderPanel.getSliderPanel();
453	1	assertTrue(sp.isForConservation());
454	1	sp.valueChanged(10);
455	1	c = rs.findColour('I', 14, ferCapan);
456	1	assertEquals(c, Color.white);
457	1	c = rs.findColour('S', 15, ferCapan);
458	1	assertEquals(c, s_faded);
459
460		/*
461		* turn off Above PID - should just leave Conservation fading as before
462		*/
463	1	af.abovePIDThreshold_actionPerformed(false);
464	1	c = rs.findColour('I', 14, ferCapan);
465	1	assertEquals(c, i_faded);
466	1	c = rs.findColour('S', 15, ferCapan);
467	1	assertEquals(c, s_faded);
468
469		/*
470		* Now add Above 50% PID to conservation colouring
471		* - should give the same as PID followed by conservation (above)
472		*/
473	1	af.abovePIDThreshold_actionPerformed(true);
474	1	SliderPanel.getSliderPanel().valueChanged(50);
475	1	c = rs.findColour('I', 14, ferCapan);
476	1	assertEquals(c, Color.white);
477	1	c = rs.findColour('S', 15, ferCapan);
478	1	assertEquals(c, s_faded);
479
480		/*
481		* turn off By Conservation
482		* should leave I white, S original (unfaded) colour
483		*/
484	1	af.conservationMenuItem_actionPerformed(false);
485	1	c = rs.findColour('I', 14, ferCapan);
486	1	assertEquals(c, Color.white);
487	1	c = rs.findColour('S', 15, ferCapan);
488	1	assertEquals(c, s_original);
489
490		/*
491		* finally turn off Above PID to leave original colours
492		*/
493	1	af.abovePIDThreshold_actionPerformed(false);
494	1	c = rs.findColour('I', 14, ferCapan);
495	1	assertEquals(c, i_original);
496	1	c = rs.findColour('S', 15, ferCapan);
497	1	assertEquals(c, s_original);
498		}
499
500		/**
501		* Verify that making a New View transfers alignment and group colour schemes,
502		* including any thresholds, to the new view. Because New View is performed by
503		* saving and reloading a 'project' file, this is similar to verifying a
504		* project save and reload.
505		*
506		* @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
507		*/
		100% Uncovered Elements: 0 (63) Complexity: 1 Complexity Density: 0.02 1PASS
508	1	@Test(groups = "Functional")...
509		public void testNewView_colourThresholds()
510		{
511	1	AlignViewport av = af.getViewport();
512	1	AlignmentI al = av.getAlignment();
513
514		/*
515		* Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
516		*/
517	1	af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
518	1	assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
519	1	af.abovePIDThreshold_actionPerformed(true);
520	1	SliderPanel sp = SliderPanel.getSliderPanel();
521	1	assertFalse(sp.isForConservation());
522	1	sp.valueChanged(10);
523	1	af.conservationMenuItem_actionPerformed(true);
524	1	sp = SliderPanel.getSliderPanel();
525	1	assertTrue(sp.isForConservation());
526	1	sp.valueChanged(20);
527	1	ResidueShaderI rs = av.getResidueShading();
528	1	assertEquals(rs.getThreshold(), 10);
529	1	assertTrue(rs.conservationApplied());
530	1	assertEquals(rs.getConservationInc(), 20);
531
532		/*
533		* create a group with Strand colouring, 30% Conservation
534		* and 40% PID threshold
535		*/
536	1	SequenceGroup sg = new SequenceGroup();
537	1	sg.addSequence(al.getSequenceAt(0), false);
538	1	sg.setStartRes(15);
539	1	sg.setEndRes(25);
540	1	av.setSelectionGroup(sg);
541	1	PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
542	1	popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
543		.toString());
544	1	assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
545	1	assertEquals(al.getGroups().size(), 1);
546	1	assertSame(al.getGroups().get(0), sg);
547	1	popupMenu.conservationMenuItem_actionPerformed(true);
548	1	sp = SliderPanel.getSliderPanel();
549	1	assertTrue(sp.isForConservation());
550	1	sp.valueChanged(30);
551	1	popupMenu.abovePIDColour_actionPerformed(true);
552	1	sp = SliderPanel.getSliderPanel();
553	1	assertFalse(sp.isForConservation());
554	1	sp.valueChanged(40);
555	1	rs = sg.getGroupColourScheme();
556	1	assertTrue(rs.conservationApplied());
557	1	assertEquals(rs.getConservationInc(), 30);
558	1	assertEquals(rs.getThreshold(), 40);
559
560		/*
561		* set slider panel focus to the background alignment
562		*/
563	1	af.conservationMenuItem_actionPerformed(true);
564	1	sp = SliderPanel.getSliderPanel();
565	1	assertTrue(sp.isForConservation());
566	1	assertEquals(sp.getTitle(), MessageManager.formatMessage(
567		"label.conservation_colour_increment",
568		new String[] { "Background" }));
569
570		/*
571		* make a new View, verify alignment and group colour schemes
572		*/
573	1	af.newView_actionPerformed(null);
574	1	assertEquals(af.alignPanel.getViewName(), "View 1");
575	1	AlignViewport av2 = af.getViewport();
576	1	assertNotSame(av, av2);
577	1	assertSame(av2, af.alignPanel.av);
578	1	rs = av2.getResidueShading();
579	1	assertNotSame(av.getResidueShading(), rs);
580	1	assertEquals(rs.getThreshold(), 10);
581	1	assertTrue(rs.conservationApplied(), rs.toString());
582	1	assertEquals(rs.getConservationInc(), 20);
583	1	assertEquals(av2.getAlignment().getGroups().size(), 1);
584	1	sg = av2.getAlignment().getGroups().get(0);
585	1	rs = sg.getGroupColourScheme();
586	1	assertTrue(rs.conservationApplied());
587	1	assertEquals(rs.getConservationInc(), 30);
588	1	assertEquals(rs.getThreshold(), 40);
589
590		/*
591		* check the Conservation SliderPanel (still open) is linked to
592		* and updates the new view (JAL-2385)
593		*/
594	1	sp = SliderPanel.getSliderPanel();
595	1	assertTrue(sp.isForConservation());
596	1	assertEquals(sp.getTitle(), MessageManager.formatMessage(
597		"label.conservation_colour_increment",
598		new String[] { "View 1" }));
599	1	sp.valueChanged(22);
600	1	assertEquals(av2.getResidueShading().getConservationInc(), 22);
601		}
602		}