2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
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;
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;
51 import java.awt.Color;
52 import java.util.Iterator;
54 import org.testng.annotations.AfterMethod;
55 import org.testng.annotations.BeforeClass;
56 import org.testng.annotations.BeforeMethod;
57 import org.testng.annotations.Test;
59 public class AlignFrameTest
63 @BeforeClass(alwaysRun = true)
64 public void setUpJvOptionPane()
66 JvOptionPane.setInteractiveMode(false);
67 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
70 @Test(groups = "Functional")
71 public void testHideFeatureColumns()
73 SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
74 SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
75 seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
76 seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
78 seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
80 seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
82 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
83 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
87 * make all features visible (select feature columns checks visibility)
89 alignFrame.getFeatureRenderer().findAllFeatures(true);
92 * hiding a feature not present does nothing
94 assertFalse(alignFrame.hideFeatureColumns("exon", true));
95 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
97 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
98 .getNumberOfRegions(), 0);
100 assertFalse(alignFrame.hideFeatureColumns("exon", false));
101 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
103 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
104 .getNumberOfRegions(), 0);
107 * hiding a feature in all columns does nothing
109 assertFalse(alignFrame.hideFeatureColumns("Metal", true));
110 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
112 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
113 .getNumberOfRegions(), 0);
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
121 FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
122 fc.setAboveThreshold(true);
124 alignFrame.getFeatureRenderer().setColour("Metal", fc);
125 assertTrue(alignFrame.hideFeatureColumns("Metal", true));
126 HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
127 assertEquals(hidden.getNumberOfRegions(), 1);
128 Iterator<int[]> regions = hidden.iterator();
129 int[] next = regions.next();
130 assertEquals(next[0], 5);
131 assertEquals(next[1], 9);
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
138 alignFrame.getViewport().showAllHiddenColumns();
139 assertTrue(alignFrame.hideFeatureColumns("Turn", true));
140 regions = alignFrame.getViewport().getAlignment()
141 .getHiddenColumns().iterator();
142 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
143 .getNumberOfRegions(), 2);
144 next = regions.next();
145 assertEquals(next[0], 1);
146 assertEquals(next[1], 3);
147 next = regions.next();
148 assertEquals(next[0], 6);
149 assertEquals(next[1], 8);
152 @BeforeClass(alwaysRun = true)
153 public static void setUpBeforeClass() throws Exception
156 * use read-only test properties file
158 Cache.loadProperties("test/jalview/io/testProps.jvprops");
159 Jalview.main(new String[] { "-nonews" });
162 @AfterMethod(alwaysRun = true)
163 public void tearDown()
165 Desktop.instance.closeAll_actionPerformed(null);
169 * configure (read-only) properties for test to ensure Consensus is computed
170 * for colour Above PID testing
172 @BeforeMethod(alwaysRun = true)
175 Cache.loadProperties("test/jalview/io/testProps.jvprops");
176 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
177 Boolean.TRUE.toString());
178 af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
179 DataSourceType.FILE);
182 * wait for Consensus thread to complete
186 while (af.getViewport().getConsensusSeq() == null)
191 } catch (InterruptedException e)
199 * Test that changing background (alignment) colour scheme
201 * <li>with Apply Colour to All Groups not selected, does not change group
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
208 @Test(groups = "Functional")
209 public void testChangeColour_background_groupsAndThresholds()
211 AlignViewport av = af.getViewport();
212 AlignmentI al = av.getAlignment();
215 * Colour alignment by Buried Index
217 af.applyToAllGroups_actionPerformed(false);
218 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
219 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
220 assertFalse(av.getResidueShading().conservationApplied());
221 assertEquals(av.getResidueShading().getThreshold(), 0);
224 * Apply Conservation 20%
226 af.conservationMenuItem_actionPerformed(true);
227 SliderPanel sp = SliderPanel.getSliderPanel();
228 assertEquals(sp.getTitle(), MessageManager.formatMessage(
229 "label.conservation_colour_increment",
230 new String[] { "Background" }));
231 assertTrue(sp.isForConservation());
233 assertTrue(av.getResidueShading().conservationApplied());
234 assertEquals(av.getResidueShading().getConservationInc(), 20);
237 * Apply PID threshold 10% (conservation still applies as well)
239 af.abovePIDThreshold_actionPerformed(true);
240 sp = SliderPanel.getSliderPanel();
241 assertFalse(sp.isForConservation());
242 assertEquals(sp.getTitle(), MessageManager.formatMessage(
243 "label.percentage_identity_threshold",
244 new String[] { "Background" }));
246 assertEquals(av.getResidueShading().getThreshold(), 10);
247 assertTrue(av.getResidueShading().conservationApplied());
248 assertEquals(av.getResidueShading().getConservationInc(), 20);
251 * create a group with Strand colouring, 30% Conservation
252 * and 40% PID threshold
254 SequenceGroup sg = new SequenceGroup();
255 sg.addSequence(al.getSequenceAt(0), false);
258 av.setSelectionGroup(sg);
261 * apply 30% Conservation to group
263 PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
264 popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
266 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
267 assertEquals(al.getGroups().size(), 1);
268 assertSame(al.getGroups().get(0), sg);
269 popupMenu.conservationMenuItem_actionPerformed(true);
270 sp = SliderPanel.getSliderPanel();
271 assertTrue(sp.isForConservation());
272 assertEquals(sp.getTitle(), MessageManager.formatMessage(
273 "label.conservation_colour_increment",
274 new String[] { sg.getName() }));
276 assertTrue(sg.getGroupColourScheme().conservationApplied());
277 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
280 * apply 40% PID threshold to group
282 popupMenu.abovePIDColour_actionPerformed(true);
283 sp = SliderPanel.getSliderPanel();
284 assertFalse(sp.isForConservation());
285 assertEquals(sp.getTitle(), MessageManager.formatMessage(
286 "label.percentage_identity_threshold",
287 new String[] { sg.getName() }));
289 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
290 // conservation threshold is unchanged:
291 assertTrue(sg.getGroupColourScheme().conservationApplied());
292 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
295 * change alignment colour - group colour, and all thresholds,
296 * should be unaffected
298 af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
299 assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
300 assertTrue(av.getResidueShading().conservationApplied());
301 assertEquals(av.getResidueShading().getConservationInc(), 20);
302 assertEquals(av.getResidueShading().getThreshold(), 10);
303 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
304 assertTrue(sg.getGroupColourScheme().conservationApplied());
305 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
306 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
309 * Now change alignment colour with Apply Colour To All Groups
310 * - group colour should change, but not colour thresholds
312 af.applyToAllGroups_actionPerformed(true);
313 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
314 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
315 assertTrue(av.getResidueShading().conservationApplied());
316 assertEquals(av.getResidueShading().getConservationInc(), 20);
317 assertEquals(av.getResidueShading().getThreshold(), 10);
318 assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
319 assertTrue(sg.getGroupColourScheme().conservationApplied());
320 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
321 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
325 * Test residue colouring with various options
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>
339 @Test(groups = "Functional")
340 public void testColourThresholdActions()
342 AlignViewport av = af.getViewport();
343 AlignmentI al = av.getAlignment();
346 * Colour alignment by Helix Propensity, no thresholds
348 af.applyToAllGroups_actionPerformed(false);
349 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
350 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
351 assertFalse(av.getResidueShading().conservationApplied());
352 assertEquals(av.getResidueShading().getThreshold(), 0);
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)
359 SequenceI ferCapan = al.findName("FER_CAPAN");
360 ResidueShaderI rs = av.getResidueShading();
361 Color c = rs.findColour('I', 14, ferCapan);
362 Color i_original = new Color(138, 117, 138);
363 assertEquals(c, i_original);
364 c = rs.findColour('S', 15, ferCapan);
365 Color s_original = new Color(54, 201, 54);
366 assertEquals(c, s_original);
369 * colour by conservation with increment 10
371 af.conservationMenuItem_actionPerformed(true);
372 SliderPanel sp = SliderPanel.getSliderPanel();
373 assertTrue(sp.isForConservation());
374 assertEquals(sp.getValue(), 30); // initial slider setting
376 assertSame(rs, av.getResidueShading());
377 c = rs.findColour('I', 14, ferCapan);
378 Color i_faded = new Color(196, 186, 196);
379 assertEquals(c, i_faded);
380 c = rs.findColour('S', 15, ferCapan);
381 Color s_faded = new Color(144, 225, 144);
382 assertEquals(c, s_faded);
385 * deselect By Conservation - colour should revert
387 af.conservationMenuItem_actionPerformed(false);
388 c = rs.findColour('S', 15, ferCapan);
389 assertEquals(c, s_original);
392 * now Above PID, threshold = 0%
393 * should be no change
395 af.abovePIDThreshold_actionPerformed(true);
396 sp = SliderPanel.getSliderPanel();
397 assertFalse(sp.isForConservation());
398 assertEquals(sp.getValue(), 0); // initial slider setting
399 c = rs.findColour('I', 14, ferCapan);
400 assertEquals(c, i_original);
401 c = rs.findColour('S', 15, ferCapan);
402 assertEquals(c, s_original);
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
410 c = rs.findColour('I', 14, ferCapan);
411 assertEquals(c, Color.white);
412 c = rs.findColour('S', 15, ferCapan);
413 assertEquals(c, s_original);
416 * threshold 66% - no further change yet...
419 c = rs.findColour('I', 14, ferCapan);
420 assertEquals(c, Color.white);
421 c = rs.findColour('S', 15, ferCapan);
422 assertEquals(c, s_original);
425 * threshold 67% - now both residues are white
428 c = rs.findColour('I', 14, ferCapan);
429 assertEquals(c, Color.white);
430 c = rs.findColour('S', 15, ferCapan);
431 assertEquals(c, Color.white);
434 * deselect Above PID - colours should revert
436 af.abovePIDThreshold_actionPerformed(false);
437 c = rs.findColour('I', 14, ferCapan);
438 assertEquals(c, i_original);
439 c = rs.findColour('S', 15, ferCapan);
440 assertEquals(c, s_original);
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
447 af.abovePIDThreshold_actionPerformed(true);
448 sp = SliderPanel.getSliderPanel();
449 assertFalse(sp.isForConservation());
451 af.conservationMenuItem_actionPerformed(true);
452 sp = SliderPanel.getSliderPanel();
453 assertTrue(sp.isForConservation());
455 c = rs.findColour('I', 14, ferCapan);
456 assertEquals(c, Color.white);
457 c = rs.findColour('S', 15, ferCapan);
458 assertEquals(c, s_faded);
461 * turn off Above PID - should just leave Conservation fading as before
463 af.abovePIDThreshold_actionPerformed(false);
464 c = rs.findColour('I', 14, ferCapan);
465 assertEquals(c, i_faded);
466 c = rs.findColour('S', 15, ferCapan);
467 assertEquals(c, s_faded);
470 * Now add Above 50% PID to conservation colouring
471 * - should give the same as PID followed by conservation (above)
473 af.abovePIDThreshold_actionPerformed(true);
474 SliderPanel.getSliderPanel().valueChanged(50);
475 c = rs.findColour('I', 14, ferCapan);
476 assertEquals(c, Color.white);
477 c = rs.findColour('S', 15, ferCapan);
478 assertEquals(c, s_faded);
481 * turn off By Conservation
482 * should leave I white, S original (unfaded) colour
484 af.conservationMenuItem_actionPerformed(false);
485 c = rs.findColour('I', 14, ferCapan);
486 assertEquals(c, Color.white);
487 c = rs.findColour('S', 15, ferCapan);
488 assertEquals(c, s_original);
491 * finally turn off Above PID to leave original colours
493 af.abovePIDThreshold_actionPerformed(false);
494 c = rs.findColour('I', 14, ferCapan);
495 assertEquals(c, i_original);
496 c = rs.findColour('S', 15, ferCapan);
497 assertEquals(c, s_original);
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.
506 * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
508 @Test(groups = "Functional")
509 public void testNewView_colourThresholds()
511 AlignViewport av = af.getViewport();
512 AlignmentI al = av.getAlignment();
515 * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
517 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
518 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
519 af.abovePIDThreshold_actionPerformed(true);
520 SliderPanel sp = SliderPanel.getSliderPanel();
521 assertFalse(sp.isForConservation());
523 af.conservationMenuItem_actionPerformed(true);
524 sp = SliderPanel.getSliderPanel();
525 assertTrue(sp.isForConservation());
527 ResidueShaderI rs = av.getResidueShading();
528 assertEquals(rs.getThreshold(), 10);
529 assertTrue(rs.conservationApplied());
530 assertEquals(rs.getConservationInc(), 20);
533 * create a group with Strand colouring, 30% Conservation
534 * and 40% PID threshold
536 SequenceGroup sg = new SequenceGroup();
537 sg.addSequence(al.getSequenceAt(0), false);
540 av.setSelectionGroup(sg);
541 PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
542 popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
544 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
545 assertEquals(al.getGroups().size(), 1);
546 assertSame(al.getGroups().get(0), sg);
547 popupMenu.conservationMenuItem_actionPerformed(true);
548 sp = SliderPanel.getSliderPanel();
549 assertTrue(sp.isForConservation());
551 popupMenu.abovePIDColour_actionPerformed(true);
552 sp = SliderPanel.getSliderPanel();
553 assertFalse(sp.isForConservation());
555 rs = sg.getGroupColourScheme();
556 assertTrue(rs.conservationApplied());
557 assertEquals(rs.getConservationInc(), 30);
558 assertEquals(rs.getThreshold(), 40);
561 * set slider panel focus to the background alignment
563 af.conservationMenuItem_actionPerformed(true);
564 sp = SliderPanel.getSliderPanel();
565 assertTrue(sp.isForConservation());
566 assertEquals(sp.getTitle(), MessageManager.formatMessage(
567 "label.conservation_colour_increment",
568 new String[] { "Background" }));
571 * make a new View, verify alignment and group colour schemes
573 af.newView_actionPerformed(null);
574 assertEquals(af.alignPanel.getViewName(), "View 1");
575 AlignViewport av2 = af.getViewport();
576 assertNotSame(av, av2);
577 assertSame(av2, af.alignPanel.av);
578 rs = av2.getResidueShading();
579 assertNotSame(av.getResidueShading(), rs);
580 assertEquals(rs.getThreshold(), 10);
581 assertTrue(rs.conservationApplied(), rs.toString());
582 assertEquals(rs.getConservationInc(), 20);
583 assertEquals(av2.getAlignment().getGroups().size(), 1);
584 sg = av2.getAlignment().getGroups().get(0);
585 rs = sg.getGroupColourScheme();
586 assertTrue(rs.conservationApplied());
587 assertEquals(rs.getConservationInc(), 30);
588 assertEquals(rs.getThreshold(), 40);
591 * check the Conservation SliderPanel (still open) is linked to
592 * and updates the new view (JAL-2385)
594 sp = SliderPanel.getSliderPanel();
595 assertTrue(sp.isForConservation());
596 assertEquals(sp.getTitle(), MessageManager.formatMessage(
597 "label.conservation_colour_increment",
598 new String[] { "View 1" }));
600 assertEquals(av2.getResidueShading().getConservationInc(), 22);