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.AlignCalcManagerI;
30 import jalview.bin.Cache;
31 import jalview.bin.Jalview;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceGroup;
37 import jalview.datamodel.SequenceI;
38 import jalview.io.DataSourceType;
39 import jalview.io.FileLoader;
40 import jalview.io.Jalview2xmlTests;
41 import jalview.renderer.ResidueShaderI;
42 import jalview.schemes.BuriedColourScheme;
43 import jalview.schemes.HelixColourScheme;
44 import jalview.schemes.JalviewColourScheme;
45 import jalview.schemes.StrandColourScheme;
46 import jalview.schemes.TurnColourScheme;
47 import jalview.util.MessageManager;
49 import java.awt.Color;
50 import java.util.List;
52 import org.testng.annotations.AfterMethod;
53 import org.testng.annotations.BeforeClass;
54 import org.testng.annotations.BeforeMethod;
55 import org.testng.annotations.Test;
57 public class AlignFrameTest
61 @BeforeClass(alwaysRun = true)
62 public void setUpJvOptionPane()
64 JvOptionPane.setInteractiveMode(false);
65 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
68 @Test(groups = "Functional")
69 public void testHideFeatureColumns()
71 SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
72 SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
73 seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5,
75 seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10,
77 seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
79 seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
81 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
82 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(), al.getHeight());
85 * hiding a feature not present does nothing
87 assertFalse(alignFrame.hideFeatureColumns("exon", true));
88 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
89 assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
90 .getHiddenColumnsCopy()
92 assertFalse(alignFrame.hideFeatureColumns("exon", false));
93 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
94 assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
95 .getHiddenColumnsCopy()
99 * hiding a feature in all columns does nothing
101 assertFalse(alignFrame.hideFeatureColumns("Metal", true));
102 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
103 List<int[]> hidden = alignFrame.getViewport().getAlignment()
105 .getHiddenColumnsCopy();
106 assertTrue(hidden.isEmpty());
109 * hide a feature present in some columns
110 * sequence positions [2-4], [7-9] are column positions
111 * [1-3], [6-8] base zero
113 assertTrue(alignFrame.hideFeatureColumns("Turn", true));
114 hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
115 .getHiddenColumnsCopy();
116 assertEquals(hidden.size(), 2);
117 assertEquals(hidden.get(0)[0], 1);
118 assertEquals(hidden.get(0)[1], 3);
119 assertEquals(hidden.get(1)[0], 6);
120 assertEquals(hidden.get(1)[1], 8);
123 @BeforeClass(alwaysRun = true)
124 public static void setUpBeforeClass() throws Exception
127 * use read-only test properties file
129 Cache.loadProperties("test/jalview/io/testProps.jvprops");
130 Jalview.main(new String[] { "-nonews" });
133 @AfterMethod(alwaysRun = true)
134 public void tearDown()
136 Desktop.instance.closeAll_actionPerformed(null);
140 * configure (read-only) properties for test to ensure Consensus is computed
141 * for colour Above PID testing
143 @BeforeMethod(alwaysRun = true)
146 Cache.loadProperties("test/jalview/io/testProps.jvprops");
147 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
148 Boolean.TRUE.toString());
149 af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
150 DataSourceType.FILE);
153 * wait for Consensus thread to complete
157 while (af.getViewport().getConsensusSeq() == null)
162 } catch (InterruptedException e)
170 * Test that changing background (alignment) colour scheme
172 * <li>with Apply Colour to All Groups not selected, does not change group
174 * <li>with Apply Colour to All Groups selected, does change group colours</li>
175 * <li>in neither case, changes alignment or group colour thresholds (PID or
179 @Test(groups = "Functional")
180 public void testChangeColour_background_groupsAndThresholds()
182 AlignViewport av = af.getViewport();
183 AlignmentI al = av.getAlignment();
186 * Colour alignment by Buried Index
188 af.applyToAllGroups_actionPerformed(false);
189 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
190 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
191 assertFalse(av.getResidueShading().conservationApplied());
192 assertEquals(av.getResidueShading().getThreshold(), 0);
195 * Apply Conservation 20%
197 af.conservationMenuItem_actionPerformed(true);
198 SliderPanel sp = SliderPanel.getSliderPanel();
199 assertEquals(sp.getTitle(), MessageManager.formatMessage(
200 "label.conservation_colour_increment",
201 new String[] { "Background" }));
202 assertTrue(sp.isForConservation());
204 assertTrue(av.getResidueShading().conservationApplied());
205 assertEquals(av.getResidueShading().getConservationInc(), 20);
208 * Apply PID threshold 10% (conservation still applies as well)
210 af.abovePIDThreshold_actionPerformed(true);
211 sp = SliderPanel.getSliderPanel();
212 assertFalse(sp.isForConservation());
213 assertEquals(sp.getTitle(), MessageManager.formatMessage(
214 "label.percentage_identity_threshold",
215 new String[] { "Background" }));
217 assertEquals(av.getResidueShading().getThreshold(), 10);
218 assertTrue(av.getResidueShading().conservationApplied());
219 assertEquals(av.getResidueShading().getConservationInc(), 20);
222 * create a group with Strand colouring, 30% Conservation
223 * and 40% PID threshold
225 SequenceGroup sg = new SequenceGroup();
226 sg.addSequence(al.getSequenceAt(0), false);
229 av.setSelectionGroup(sg);
232 * apply 30% Conservation to group
234 PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
235 popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
237 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
238 assertEquals(al.getGroups().size(), 1);
239 assertSame(al.getGroups().get(0), sg);
240 popupMenu.conservationMenuItem_actionPerformed(true);
241 sp = SliderPanel.getSliderPanel();
242 assertTrue(sp.isForConservation());
243 assertEquals(sp.getTitle(), MessageManager.formatMessage(
244 "label.conservation_colour_increment",
245 new String[] { sg.getName() }));
247 assertTrue(sg.getGroupColourScheme().conservationApplied());
248 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
251 * apply 40% PID threshold to group
253 popupMenu.abovePIDColour_actionPerformed(true);
254 sp = SliderPanel.getSliderPanel();
255 assertFalse(sp.isForConservation());
256 assertEquals(sp.getTitle(), MessageManager.formatMessage(
257 "label.percentage_identity_threshold",
258 new String[] { sg.getName() }));
260 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
261 // conservation threshold is unchanged:
262 assertTrue(sg.getGroupColourScheme().conservationApplied());
263 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
266 * change alignment colour - group colour, and all thresholds,
267 * should be unaffected
269 af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
270 assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
271 assertTrue(av.getResidueShading().conservationApplied());
272 assertEquals(av.getResidueShading().getConservationInc(), 20);
273 assertEquals(av.getResidueShading().getThreshold(), 10);
274 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
275 assertTrue(sg.getGroupColourScheme().conservationApplied());
276 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
277 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
280 * Now change alignment colour with Apply Colour To All Groups
281 * - group colour should change, but not colour thresholds
283 af.applyToAllGroups_actionPerformed(true);
284 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
285 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
286 assertTrue(av.getResidueShading().conservationApplied());
287 assertEquals(av.getResidueShading().getConservationInc(), 20);
288 assertEquals(av.getResidueShading().getThreshold(), 10);
289 assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
290 assertTrue(sg.getGroupColourScheme().conservationApplied());
291 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
292 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
296 * Test residue colouring with various options
298 * <li>no PID or Conservation threshold</li>
299 * <li>colour by Conservation applied</li>
300 * <li>colour by Conservation removed</li>
301 * <li>colour above PID - various values</li>
302 * <li>colour above PID removed</li>
303 * <li>Above PID plus By Conservation combined</li>
304 * <li>remove Above PID to leave just By Conservation</li>
305 * <li>re-add Above PID</li>
306 * <li>remove By Conservation to leave just Above PID</li>
307 * <li>remove Above PID to leave original colours</li>
310 @Test(groups = "Functional")
311 public void testColourThresholdActions()
313 AlignViewport av = af.getViewport();
314 AlignmentI al = av.getAlignment();
317 * Colour alignment by Helix Propensity, no thresholds
319 af.applyToAllGroups_actionPerformed(false);
320 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
321 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
322 assertFalse(av.getResidueShading().conservationApplied());
323 assertEquals(av.getResidueShading().getThreshold(), 0);
326 * inspect the colour of
327 * FER_CAPAN.9(I), column 14 (14 base 0)
328 * FER_CAPAN.10(SER), column 16 (15 base 0)
330 SequenceI ferCapan = al.findName("FER_CAPAN");
331 ResidueShaderI rs = av.getResidueShading();
332 Color c = rs.findColour('I', 14, ferCapan);
333 Color i_original = new Color(138, 117, 138);
334 assertEquals(c, i_original);
335 c = rs.findColour('S', 15, ferCapan);
336 Color s_original = new Color(54, 201, 54);
337 assertEquals(c, s_original);
340 * colour by conservation with increment 10
342 af.conservationMenuItem_actionPerformed(true);
343 SliderPanel sp = SliderPanel.getSliderPanel();
344 assertTrue(sp.isForConservation());
345 assertEquals(sp.getValue(), 30); // initial slider setting
347 assertSame(rs, av.getResidueShading());
348 c = rs.findColour('I', 14, ferCapan);
349 Color i_faded = new Color(196, 186, 196);
350 assertEquals(c, i_faded);
351 c = rs.findColour('S', 15, ferCapan);
352 Color s_faded = new Color(144, 225, 144);
353 assertEquals(c, s_faded);
356 * deselect By Conservation - colour should revert
358 af.conservationMenuItem_actionPerformed(false);
359 c = rs.findColour('S', 15, ferCapan);
360 assertEquals(c, s_original);
363 * now Above PID, threshold = 0%
364 * should be no change
366 af.abovePIDThreshold_actionPerformed(true);
367 sp = SliderPanel.getSliderPanel();
368 assertFalse(sp.isForConservation());
369 assertEquals(sp.getValue(), 0); // initial slider setting
370 c = rs.findColour('I', 14, ferCapan);
371 assertEquals(c, i_original);
372 c = rs.findColour('S', 15, ferCapan);
373 assertEquals(c, s_original);
376 * Above PID, threshold = 1%
377 * 15.I becomes White because no match to consensus (V)
378 * 16.S remains coloured as matches 66.66% consensus
381 c = rs.findColour('I', 14, ferCapan);
382 assertEquals(c, Color.white);
383 c = rs.findColour('S', 15, ferCapan);
384 assertEquals(c, s_original);
387 * threshold 66% - no further change yet...
390 c = rs.findColour('I', 14, ferCapan);
391 assertEquals(c, Color.white);
392 c = rs.findColour('S', 15, ferCapan);
393 assertEquals(c, s_original);
396 * threshold 67% - now both residues are white
399 c = rs.findColour('I', 14, ferCapan);
400 assertEquals(c, Color.white);
401 c = rs.findColour('S', 15, ferCapan);
402 assertEquals(c, Color.white);
405 * deselect Above PID - colours should revert
407 af.abovePIDThreshold_actionPerformed(false);
408 c = rs.findColour('I', 14, ferCapan);
409 assertEquals(c, i_original);
410 c = rs.findColour('S', 15, ferCapan);
411 assertEquals(c, s_original);
414 * Now combine Above 50% PID and By Conservation 10%
415 * 15.I is White because no match to consensus (V)
416 * 16.S is coloured but faded
418 af.abovePIDThreshold_actionPerformed(true);
419 sp = SliderPanel.getSliderPanel();
420 assertFalse(sp.isForConservation());
422 af.conservationMenuItem_actionPerformed(true);
423 sp = SliderPanel.getSliderPanel();
424 assertTrue(sp.isForConservation());
426 c = rs.findColour('I', 14, ferCapan);
427 assertEquals(c, Color.white);
428 c = rs.findColour('S', 15, ferCapan);
429 assertEquals(c, s_faded);
432 * turn off Above PID - should just leave Conservation fading as before
434 af.abovePIDThreshold_actionPerformed(false);
435 c = rs.findColour('I', 14, ferCapan);
436 assertEquals(c, i_faded);
437 c = rs.findColour('S', 15, ferCapan);
438 assertEquals(c, s_faded);
441 * Now add Above 50% PID to conservation colouring
442 * - should give the same as PID followed by conservation (above)
444 af.abovePIDThreshold_actionPerformed(true);
445 SliderPanel.getSliderPanel().valueChanged(50);
446 c = rs.findColour('I', 14, ferCapan);
447 assertEquals(c, Color.white);
448 c = rs.findColour('S', 15, ferCapan);
449 assertEquals(c, s_faded);
452 * turn off By Conservation
453 * should leave I white, S original (unfaded) colour
455 af.conservationMenuItem_actionPerformed(false);
456 c = rs.findColour('I', 14, ferCapan);
457 assertEquals(c, Color.white);
458 c = rs.findColour('S', 15, ferCapan);
459 assertEquals(c, s_original);
462 * finally turn off Above PID to leave original colours
464 af.abovePIDThreshold_actionPerformed(false);
465 c = rs.findColour('I', 14, ferCapan);
466 assertEquals(c, i_original);
467 c = rs.findColour('S', 15, ferCapan);
468 assertEquals(c, s_original);
472 * Verify that making a New View transfers alignment and group colour schemes,
473 * including any thresholds, to the new view. Because New View is performed by
474 * saving and reloading a 'project' file, this is similar to verifying a
475 * project save and reload.
477 * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
479 @Test(groups = "Functional")
480 public void testNewView_colourThresholds()
482 AlignViewport av = af.getViewport();
483 AlignmentI al = av.getAlignment();
486 * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
488 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
489 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
490 af.abovePIDThreshold_actionPerformed(true);
491 SliderPanel sp = SliderPanel.getSliderPanel();
492 assertFalse(sp.isForConservation());
494 af.conservationMenuItem_actionPerformed(true);
495 sp = SliderPanel.getSliderPanel();
496 assertTrue(sp.isForConservation());
498 ResidueShaderI rs = av.getResidueShading();
499 assertEquals(rs.getThreshold(), 10);
500 assertTrue(rs.conservationApplied());
501 assertEquals(rs.getConservationInc(), 20);
504 * create a group with Strand colouring, 30% Conservation
505 * and 40% PID threshold
507 SequenceGroup sg = new SequenceGroup();
508 sg.addSequence(al.getSequenceAt(0), false);
511 av.setSelectionGroup(sg);
512 PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
513 popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
515 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
516 assertEquals(al.getGroups().size(), 1);
517 assertSame(al.getGroups().get(0), sg);
518 popupMenu.conservationMenuItem_actionPerformed(true);
519 sp = SliderPanel.getSliderPanel();
520 assertTrue(sp.isForConservation());
522 popupMenu.abovePIDColour_actionPerformed(true);
523 sp = SliderPanel.getSliderPanel();
524 assertFalse(sp.isForConservation());
526 rs = sg.getGroupColourScheme();
527 assertTrue(rs.conservationApplied());
528 assertEquals(rs.getConservationInc(), 30);
529 assertEquals(rs.getThreshold(), 40);
532 * set slider panel focus to the background alignment
534 af.conservationMenuItem_actionPerformed(true);
535 sp = SliderPanel.getSliderPanel();
536 assertTrue(sp.isForConservation());
537 assertEquals(sp.getTitle(), MessageManager.formatMessage(
538 "label.conservation_colour_increment",
539 new String[] { "Background" }));
542 * make a new View, wait for Conservation thread to complete,
543 * verify alignment and group colour schemes
545 af.newView_actionPerformed(null);
546 assertEquals(af.alignPanel.getViewName(), "View 1");
547 AlignViewport av2 = af.getViewport();
548 assertNotSame(av, av2);
549 assertSame(av2, af.alignPanel.av);
550 AlignCalcManagerI calcManager = av2.getCalcManager();
556 } catch (InterruptedException x)
559 } while (calcManager.isWorking());
560 rs = av2.getResidueShading();
561 assertNotSame(av.getResidueShading(), rs);
562 assertEquals(rs.getThreshold(), 10);
563 assertTrue(rs.conservationApplied(), rs.toString());
564 assertEquals(rs.getConservationInc(), 20);
565 assertEquals(av2.getAlignment().getGroups().size(), 1);
566 sg = av2.getAlignment().getGroups().get(0);
567 rs = sg.getGroupColourScheme();
568 assertTrue(rs.conservationApplied());
569 assertEquals(rs.getConservationInc(), 30);
570 assertEquals(rs.getThreshold(), 40);
573 * check the Conservation SliderPanel (still open) is linked to
574 * and updates the new view (JAL-2385)
576 sp = SliderPanel.getSliderPanel();
577 assertTrue(sp.isForConservation());
578 assertEquals(sp.getTitle(), MessageManager.formatMessage(
579 "label.conservation_colour_increment",
580 new String[] { "View 1" }));
582 assertEquals(av2.getResidueShading().getConservationInc(), 22);