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.junit.Assert.assertNotEquals;
24 import static org.testng.Assert.assertEquals;
25 import static org.testng.Assert.assertFalse;
26 import static org.testng.Assert.assertNotSame;
27 import static org.testng.Assert.assertSame;
28 import static org.testng.Assert.assertTrue;
30 import jalview.api.FeatureColourI;
31 import jalview.bin.Cache;
32 import jalview.bin.Jalview;
33 import jalview.datamodel.Alignment;
34 import jalview.datamodel.AlignmentI;
35 import jalview.datamodel.HiddenColumns;
36 import jalview.datamodel.Sequence;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.io.DataSourceType;
41 import jalview.io.FileLoader;
42 import jalview.project.Jalview2xmlTests;
43 import jalview.renderer.ResidueShaderI;
44 import jalview.schemes.BuriedColourScheme;
45 import jalview.schemes.FeatureColour;
46 import jalview.schemes.HelixColourScheme;
47 import jalview.schemes.JalviewColourScheme;
48 import jalview.schemes.StrandColourScheme;
49 import jalview.schemes.TurnColourScheme;
50 import jalview.util.MessageManager;
52 import java.awt.Color;
53 import java.util.Iterator;
55 import org.testng.annotations.AfterMethod;
56 import org.testng.annotations.BeforeClass;
57 import org.testng.annotations.BeforeMethod;
58 import org.testng.annotations.Test;
60 public class AlignFrameTest
64 @BeforeClass(alwaysRun = true)
65 public void setUpJvOptionPane()
67 JvOptionPane.setInteractiveMode(false);
68 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
69 Jalview.setSynchronous(true);
72 @Test(groups = "Functional")
73 public void testHideFeatureColumns()
75 SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
76 SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
77 seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
78 seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
80 seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
82 seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
84 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
85 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
89 * make all features visible (select feature columns checks visibility)
91 alignFrame.getFeatureRenderer().findAllFeatures(true);
94 * hiding a feature not present does nothing
96 assertFalse(alignFrame.hideFeatureColumns("exon", true));
97 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
99 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
100 .getNumberOfRegions(), 0);
102 assertFalse(alignFrame.hideFeatureColumns("exon", false));
103 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
105 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
106 .getNumberOfRegions(), 0);
109 * hiding a feature in all columns does nothing
111 assertFalse(alignFrame.hideFeatureColumns("Metal", true));
112 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
114 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
115 .getNumberOfRegions(), 0);
119 * threshold Metal to hide features where score < 5
120 * seq1 feature in columns 1-5 is hidden
121 * seq2 feature in columns 6-10 is shown
123 FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
125 fc.setAboveThreshold(true);
127 alignFrame.getFeatureRenderer().setColour("Metal", fc);
128 assertTrue(alignFrame.hideFeatureColumns("Metal", true));
129 HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
130 assertEquals(hidden.getNumberOfRegions(), 1);
131 Iterator<int[]> regions = hidden.iterator();
132 int[] next = regions.next();
133 assertEquals(next[0], 5);
134 assertEquals(next[1], 9);
137 * hide a feature present in some columns
138 * sequence positions [2-4], [7-9] are column positions
139 * [1-3], [6-8] base zero
141 alignFrame.getViewport().showAllHiddenColumns();
142 assertTrue(alignFrame.hideFeatureColumns("Turn", true));
143 regions = alignFrame.getViewport().getAlignment()
144 .getHiddenColumns().iterator();
145 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
146 .getNumberOfRegions(), 2);
147 next = regions.next();
148 assertEquals(next[0], 1);
149 assertEquals(next[1], 3);
150 next = regions.next();
151 assertEquals(next[0], 6);
152 assertEquals(next[1], 8);
155 @BeforeClass(alwaysRun = true)
156 public static void setUpBeforeClass() throws Exception
159 * use read-only test properties file
161 Cache.loadProperties("test/jalview/io/testProps.jvprops");
162 Jalview.main(new String[] { "-nonews" });
165 @AfterMethod(alwaysRun = true)
166 public void tearDown()
168 Desktop.getInstance().closeAll_actionPerformed(null);
172 * configure (read-only) properties for test to ensure Consensus is computed
173 * for colour Above PID testing
175 @BeforeMethod(alwaysRun = true)
178 Cache.loadProperties("test/jalview/io/testProps.jvprops");
179 Cache.getInstance().applicationProperties.setProperty("SHOW_IDENTITY",
180 Boolean.TRUE.toString());
181 af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
182 DataSourceType.FILE);
185 * wait for Consensus thread to complete
189 while (af.getViewport().getConsensusSeq() == null)
194 } catch (InterruptedException e)
202 * Test that changing background (alignment) colour scheme
204 * <li>with Apply Colour to All Groups not selected, does not change group
206 * <li>with Apply Colour to All Groups selected, does change group colours</li>
207 * <li>in neither case, changes alignment or group colour thresholds (PID or
211 @Test(groups = "Functional")
212 public void testChangeColour_background_groupsAndThresholds()
214 AlignViewport av = af.getViewport();
215 AlignmentI al = av.getAlignment();
218 * Colour alignment by Buried Index
220 af.applyToAllGroups_actionPerformed(false);
221 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
222 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
223 assertFalse(av.getResidueShading().conservationApplied());
224 assertEquals(av.getResidueShading().getThreshold(), 0);
227 * Apply Conservation 20%
229 af.conservationMenuItem_actionPerformed(true);
230 SliderPanel sp = SliderPanel.getSliderPanel();
231 assertEquals(sp.getTitle(), MessageManager.formatMessage(
232 "label.conservation_colour_increment",
233 new String[] { "Background" }));
234 assertTrue(sp.isForConservation());
236 assertTrue(av.getResidueShading().conservationApplied());
237 assertEquals(av.getResidueShading().getConservationInc(), 20);
240 * Apply PID threshold 10% (conservation still applies as well)
242 af.abovePIDThreshold_actionPerformed(true);
243 sp = SliderPanel.getSliderPanel();
244 assertFalse(sp.isForConservation());
245 assertEquals(sp.getTitle(), MessageManager.formatMessage(
246 "label.percentage_identity_threshold",
247 new String[] { "Background" }));
249 assertEquals(av.getResidueShading().getThreshold(), 10);
250 assertTrue(av.getResidueShading().conservationApplied());
251 assertEquals(av.getResidueShading().getConservationInc(), 20);
254 * create a group with Strand colouring, 30% Conservation
255 * and 40% PID threshold
257 SequenceGroup sg = new SequenceGroup();
258 sg.addSequence(al.getSequenceAt(0), false);
261 av.setSelectionGroup(sg);
264 * apply 30% Conservation to group
266 PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
267 popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
269 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
270 assertEquals(al.getGroups().size(), 1);
271 assertSame(al.getGroups().get(0), sg);
272 popupMenu.conservationMenuItem_actionPerformed(true);
273 sp = SliderPanel.getSliderPanel();
274 assertTrue(sp.isForConservation());
275 assertEquals(sp.getTitle(), MessageManager.formatMessage(
276 "label.conservation_colour_increment",
277 new String[] { sg.getName() }));
279 assertTrue(sg.getGroupColourScheme().conservationApplied());
280 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
283 * apply 40% PID threshold to group
285 popupMenu.abovePIDColour_actionPerformed(true);
286 sp = SliderPanel.getSliderPanel();
287 assertFalse(sp.isForConservation());
288 assertEquals(sp.getTitle(), MessageManager.formatMessage(
289 "label.percentage_identity_threshold",
290 new String[] { sg.getName() }));
292 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
293 // conservation threshold is unchanged:
294 assertTrue(sg.getGroupColourScheme().conservationApplied());
295 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
298 * change alignment colour - group colour, and all thresholds,
299 * should be unaffected
301 af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
302 assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
303 assertTrue(av.getResidueShading().conservationApplied());
304 assertEquals(av.getResidueShading().getConservationInc(), 20);
305 assertEquals(av.getResidueShading().getThreshold(), 10);
306 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
307 assertTrue(sg.getGroupColourScheme().conservationApplied());
308 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
309 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
312 * Now change alignment colour with Apply Colour To All Groups
313 * - group colour should change, but not colour thresholds
315 af.applyToAllGroups_actionPerformed(true);
316 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
317 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
318 assertTrue(av.getResidueShading().conservationApplied());
319 assertEquals(av.getResidueShading().getConservationInc(), 20);
320 assertEquals(av.getResidueShading().getThreshold(), 10);
321 assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
322 assertTrue(sg.getGroupColourScheme().conservationApplied());
323 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
324 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
328 * Test residue colouring with various options
330 * <li>no PID or Conservation threshold</li>
331 * <li>colour by Conservation applied</li>
332 * <li>colour by Conservation removed</li>
333 * <li>colour above PID - various values</li>
334 * <li>colour above PID removed</li>
335 * <li>Above PID plus By Conservation combined</li>
336 * <li>remove Above PID to leave just By Conservation</li>
337 * <li>re-add Above PID</li>
338 * <li>remove By Conservation to leave just Above PID</li>
339 * <li>remove Above PID to leave original colours</li>
342 @Test(groups = "Functional")
343 public void testColourThresholdActions()
345 AlignViewport av = af.getViewport();
346 AlignmentI al = av.getAlignment();
349 * Colour alignment by Helix Propensity, no thresholds
351 af.applyToAllGroups_actionPerformed(false);
352 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
353 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
354 assertFalse(av.getResidueShading().conservationApplied());
355 assertEquals(av.getResidueShading().getThreshold(), 0);
358 * inspect the colour of
359 * FER_CAPAN.9(I), column 14 (14 base 0)
360 * FER_CAPAN.10(SER), column 16 (15 base 0)
362 SequenceI ferCapan = al.findName("FER_CAPAN");
363 ResidueShaderI rs = av.getResidueShading();
364 Color c = rs.findColour('I', 14, ferCapan);
365 Color i_original = new Color(138, 117, 138);
366 assertEquals(c, i_original);
367 c = rs.findColour('S', 15, ferCapan);
368 Color s_original = new Color(54, 201, 54);
369 assertEquals(c, s_original);
372 * colour by conservation with increment 10
374 af.conservationMenuItem_actionPerformed(true);
375 SliderPanel sp = SliderPanel.getSliderPanel();
376 assertTrue(sp.isForConservation());
377 assertEquals(sp.getValue(), 30); // initial slider setting
379 assertSame(rs, av.getResidueShading());
380 c = rs.findColour('I', 14, ferCapan);
381 Color i_faded = new Color(196, 186, 196);
382 assertEquals(c, i_faded);
383 c = rs.findColour('S', 15, ferCapan);
384 Color s_faded = new Color(144, 225, 144);
385 assertEquals(c, s_faded);
388 * deselect By Conservation - colour should revert
390 af.conservationMenuItem_actionPerformed(false);
391 c = rs.findColour('S', 15, ferCapan);
392 assertEquals(c, s_original);
395 * now Above PID, threshold = 0%
396 * should be no change
398 af.abovePIDThreshold_actionPerformed(true);
399 sp = SliderPanel.getSliderPanel();
400 assertFalse(sp.isForConservation());
401 assertEquals(sp.getValue(), 0); // initial slider setting
402 c = rs.findColour('I', 14, ferCapan);
403 assertEquals(c, i_original);
404 c = rs.findColour('S', 15, ferCapan);
405 assertEquals(c, s_original);
408 * Above PID, threshold = 1%
409 * 15.I becomes White because no match to consensus (V)
410 * 16.S remains coloured as matches 66.66% consensus
413 c = rs.findColour('I', 14, ferCapan);
414 assertEquals(c, Color.white);
415 c = rs.findColour('S', 15, ferCapan);
416 assertEquals(c, s_original);
419 * threshold 66% - no further change yet...
422 c = rs.findColour('I', 14, ferCapan);
423 assertEquals(c, Color.white);
424 c = rs.findColour('S', 15, ferCapan);
425 assertEquals(c, s_original);
428 * threshold 67% - now both residues are white
431 c = rs.findColour('I', 14, ferCapan);
432 assertEquals(c, Color.white);
433 c = rs.findColour('S', 15, ferCapan);
434 assertEquals(c, Color.white);
437 * deselect Above PID - colours should revert
439 af.abovePIDThreshold_actionPerformed(false);
440 c = rs.findColour('I', 14, ferCapan);
441 assertEquals(c, i_original);
442 c = rs.findColour('S', 15, ferCapan);
443 assertEquals(c, s_original);
446 * Now combine Above 50% PID and By Conservation 10%
447 * 15.I is White because no match to consensus (V)
448 * 16.S is coloured but faded
450 af.abovePIDThreshold_actionPerformed(true);
451 sp = SliderPanel.getSliderPanel();
452 assertFalse(sp.isForConservation());
454 af.conservationMenuItem_actionPerformed(true);
455 sp = SliderPanel.getSliderPanel();
456 assertTrue(sp.isForConservation());
458 c = rs.findColour('I', 14, ferCapan);
459 assertEquals(c, Color.white);
460 c = rs.findColour('S', 15, ferCapan);
461 assertEquals(c, s_faded);
464 * turn off Above PID - should just leave Conservation fading as before
466 af.abovePIDThreshold_actionPerformed(false);
467 c = rs.findColour('I', 14, ferCapan);
468 assertEquals(c, i_faded);
469 c = rs.findColour('S', 15, ferCapan);
470 assertEquals(c, s_faded);
473 * Now add Above 50% PID to conservation colouring
474 * - should give the same as PID followed by conservation (above)
476 af.abovePIDThreshold_actionPerformed(true);
477 SliderPanel.getSliderPanel().valueChanged(50);
478 c = rs.findColour('I', 14, ferCapan);
479 assertEquals(c, Color.white);
480 c = rs.findColour('S', 15, ferCapan);
481 assertEquals(c, s_faded);
484 * turn off By Conservation
485 * should leave I white, S original (unfaded) colour
487 af.conservationMenuItem_actionPerformed(false);
488 c = rs.findColour('I', 14, ferCapan);
489 assertEquals(c, Color.white);
490 c = rs.findColour('S', 15, ferCapan);
491 assertEquals(c, s_original);
494 * finally turn off Above PID to leave original colours
496 af.abovePIDThreshold_actionPerformed(false);
497 c = rs.findColour('I', 14, ferCapan);
498 assertEquals(c, i_original);
499 c = rs.findColour('S', 15, ferCapan);
500 assertEquals(c, s_original);
504 * Verify that making a New View transfers alignment and group colour schemes,
505 * including any thresholds, to the new view. Because New View is performed by
506 * saving and reloading a 'project' file, this is similar to verifying a
507 * project save and reload.
509 * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
511 @Test(groups = "Functional")
512 public void testNewView_colourThresholds()
514 AlignViewport av = af.getViewport();
515 AlignmentI al = av.getAlignment();
518 * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
520 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
521 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
522 af.abovePIDThreshold_actionPerformed(true);
523 SliderPanel sp = SliderPanel.getSliderPanel();
524 assertFalse(sp.isForConservation());
526 af.conservationMenuItem_actionPerformed(true);
527 sp = SliderPanel.getSliderPanel();
528 assertTrue(sp.isForConservation());
530 ResidueShaderI rs = av.getResidueShading();
531 assertEquals(rs.getThreshold(), 10);
532 assertTrue(rs.conservationApplied());
533 assertEquals(rs.getConservationInc(), 20);
536 * create a group with Strand colouring, 30% Conservation
537 * and 40% PID threshold
539 SequenceGroup sg = new SequenceGroup();
540 sg.addSequence(al.getSequenceAt(0), false);
543 av.setSelectionGroup(sg);
544 PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
545 popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
547 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
548 assertEquals(al.getGroups().size(), 1);
549 assertSame(al.getGroups().get(0), sg);
550 popupMenu.conservationMenuItem_actionPerformed(true);
551 sp = SliderPanel.getSliderPanel();
552 assertTrue(sp.isForConservation());
554 popupMenu.abovePIDColour_actionPerformed(true);
555 sp = SliderPanel.getSliderPanel();
556 assertFalse(sp.isForConservation());
558 rs = sg.getGroupColourScheme();
559 assertTrue(rs.conservationApplied());
560 assertEquals(rs.getConservationInc(), 30);
561 assertEquals(rs.getThreshold(), 40);
564 * set slider panel focus to the background alignment
566 af.conservationMenuItem_actionPerformed(true);
567 sp = SliderPanel.getSliderPanel();
568 assertTrue(sp.isForConservation());
569 assertEquals(sp.getTitle(), MessageManager.formatMessage(
570 "label.conservation_colour_increment",
571 new String[] { "Background" }));
574 * make a new View, verify alignment and group colour schemes
576 af.newView_actionPerformed(null);
577 assertEquals(af.alignPanel.getViewName(), "View 1");
578 AlignViewport av2 = af.getViewport();
579 assertNotSame(av, av2);
580 assertSame(av2, af.alignPanel.av);
581 rs = av2.getResidueShading();
582 assertNotSame(av.getResidueShading(), rs);
583 assertEquals(rs.getThreshold(), 10);
584 assertTrue(rs.conservationApplied(), rs.toString());
585 assertEquals(rs.getConservationInc(), 20);
586 assertEquals(av2.getAlignment().getGroups().size(), 1);
587 sg = av2.getAlignment().getGroups().get(0);
588 rs = sg.getGroupColourScheme();
589 assertTrue(rs.conservationApplied());
590 assertEquals(rs.getConservationInc(), 30);
591 assertEquals(rs.getThreshold(), 40);
594 * check the Conservation SliderPanel (still open) is linked to
595 * and updates the new view (JAL-2385)
597 sp = SliderPanel.getSliderPanel();
598 assertTrue(sp.isForConservation());
599 assertEquals(sp.getTitle(), MessageManager.formatMessage(
600 "label.conservation_colour_increment",
601 new String[] { "View 1" }));
603 assertEquals(av2.getResidueShading().getConservationInc(), 22);
607 * Verify that making a New View preserves the dataset reference for the
608 * alignment. Otherwise, see a 'duplicate jar entry' reference when trying to
609 * save alignments with multiple views, and codon mappings will not be shared
610 * across all panels in a split frame.
612 * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
614 @Test(groups = "Functional")
615 public void testNewView_dsRefPreserved()
617 AlignViewport av = af.getViewport();
618 AlignmentI al = av.getAlignment();
619 AlignmentI original_ds = al.getDataset();
620 af.newView_actionPerformed(null);
621 assertNotEquals("New view didn't select the a new panel", av,
623 org.testng.Assert.assertEquals(original_ds,
624 af.getViewport().getAlignment().getDataset(),
625 "Dataset was not preserved in new view");