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 java.awt.Color;
31 import java.util.Iterator;
33 import org.testng.annotations.AfterMethod;
34 import org.testng.annotations.BeforeClass;
35 import org.testng.annotations.BeforeMethod;
36 import org.testng.annotations.Test;
38 import jalview.api.FeatureColourI;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.datamodel.Alignment;
42 import jalview.datamodel.AlignmentI;
43 import jalview.datamodel.HiddenColumns;
44 import jalview.datamodel.Sequence;
45 import jalview.datamodel.SequenceFeature;
46 import jalview.datamodel.SequenceGroup;
47 import jalview.datamodel.SequenceI;
48 import jalview.io.DataSourceType;
49 import jalview.io.FileLoader;
50 import jalview.project.Jalview2xmlTests;
51 import jalview.renderer.ResidueShaderI;
52 import jalview.schemes.BuriedColourScheme;
53 import jalview.schemes.FeatureColour;
54 import jalview.schemes.HelixColourScheme;
55 import jalview.schemes.JalviewColourScheme;
56 import jalview.schemes.StrandColourScheme;
57 import jalview.schemes.TurnColourScheme;
58 import jalview.util.MessageManager;
60 public class AlignFrameTest
64 @BeforeClass(alwaysRun = true)
65 public static void setUpBeforeClass() throws Exception
69 * use read-only test properties file
71 Cache.loadProperties("test/jalview/io/testProps.jvprops");
72 Jalview.main(new String[] { "-nonews" });
75 @AfterMethod(alwaysRun = true)
76 public void tearDown()
78 Desktop.instance.closeAll_actionPerformed(null);
82 * configure (read-only) properties for test to ensure Consensus is computed for
83 * colour Above PID testing
85 @BeforeMethod(alwaysRun = true)
88 Cache.loadProperties("test/jalview/io/testProps.jvprops");
89 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
90 Boolean.TRUE.toString());
91 af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
95 * wait for Consensus thread to complete
102 } catch (InterruptedException x)
105 } while (af.getViewport().getCalcManager().isWorking());
108 public static void setUpJvOptionPane()
110 JvOptionPane.setInteractiveMode(false);
111 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
114 @Test(groups = "Functional")
115 public void testHideFeatureColumns()
117 SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
118 SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
119 seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
120 seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
122 seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
124 seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
126 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
127 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
131 * make all features visible (select feature columns checks visibility)
133 alignFrame.getFeatureRenderer().findAllFeatures(true);
136 * hiding a feature not present does nothing
138 assertFalse(alignFrame.hideFeatureColumns("exon", true));
139 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
141 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
142 .getNumberOfRegions(), 0);
144 assertFalse(alignFrame.hideFeatureColumns("exon", false));
145 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
147 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
148 .getNumberOfRegions(), 0);
151 * hiding a feature in all columns does nothing
153 assertFalse(alignFrame.hideFeatureColumns("Metal", true));
154 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
156 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
157 .getNumberOfRegions(), 0);
161 * threshold Metal to hide features where score < 5
162 * seq1 feature in columns 1-5 is hidden
163 * seq2 feature in columns 6-10 is shown
165 FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
167 fc.setAboveThreshold(true);
169 alignFrame.getFeatureRenderer().setColour("Metal", fc);
170 assertTrue(alignFrame.hideFeatureColumns("Metal", true));
171 HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
172 assertEquals(hidden.getNumberOfRegions(), 1);
173 Iterator<int[]> regions = hidden.iterator();
174 int[] next = regions.next();
175 assertEquals(next[0], 5);
176 assertEquals(next[1], 9);
179 * hide a feature present in some columns
180 * sequence positions [2-4], [7-9] are column positions
181 * [1-3], [6-8] base zero
183 alignFrame.getViewport().showAllHiddenColumns();
184 assertTrue(alignFrame.hideFeatureColumns("Turn", true));
185 regions = alignFrame.getViewport().getAlignment()
186 .getHiddenColumns().iterator();
187 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
188 .getNumberOfRegions(), 2);
189 next = regions.next();
190 assertEquals(next[0], 1);
191 assertEquals(next[1], 3);
192 next = regions.next();
193 assertEquals(next[0], 6);
194 assertEquals(next[1], 8);
198 * Test that changing background (alignment) colour scheme
200 * <li>with Apply Colour to All Groups not selected, does not change group
202 * <li>with Apply Colour to All Groups selected, does change group colours</li>
203 * <li>in neither case, changes alignment or group colour thresholds (PID or
207 @Test(groups = "Functional")
208 public void testChangeColour_background_groupsAndThresholds()
210 AlignViewport av = af.getViewport();
211 AlignmentI al = av.getAlignment();
214 * Colour alignment by Buried Index
216 af.applyToAllGroups_actionPerformed(false);
217 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
218 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
219 assertFalse(av.getResidueShading().conservationApplied());
220 assertEquals(av.getResidueShading().getThreshold(), 0);
223 * Apply Conservation 20%
225 af.conservationMenuItem_actionPerformed(true);
226 SliderPanel sp = SliderPanel.getSliderPanel();
227 assertEquals(sp.getTitle(), MessageManager.formatMessage(
228 "label.conservation_colour_increment",
229 new String[] { "Background" }));
230 assertTrue(sp.isForConservation());
232 assertTrue(av.getResidueShading().conservationApplied());
233 assertEquals(av.getResidueShading().getConservationInc(), 20);
236 * Apply PID threshold 10% (conservation still applies as well)
238 af.abovePIDThreshold_actionPerformed(true);
239 sp = SliderPanel.getSliderPanel();
240 assertFalse(sp.isForConservation());
241 assertEquals(sp.getTitle(), MessageManager.formatMessage(
242 "label.percentage_identity_threshold",
243 new String[] { "Background" }));
245 assertEquals(av.getResidueShading().getThreshold(), 10);
246 assertTrue(av.getResidueShading().conservationApplied());
247 assertEquals(av.getResidueShading().getConservationInc(), 20);
250 * create a group with Strand colouring, 30% Conservation
251 * and 40% PID threshold
253 SequenceGroup sg = new SequenceGroup();
254 sg.addSequence(al.getSequenceAt(0), false);
257 av.setSelectionGroup(sg);
260 * apply 30% Conservation to group
261 * (notice menu action applies to selection group even if mouse click
262 * is at a sequence not in the group)
264 PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2),
266 popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
268 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
269 assertEquals(al.getGroups().size(), 1);
270 assertSame(al.getGroups().get(0), sg);
271 popupMenu.conservationMenuItem_actionPerformed(true);
272 sp = SliderPanel.getSliderPanel();
273 assertTrue(sp.isForConservation());
274 assertEquals(sp.getTitle(), MessageManager.formatMessage(
275 "label.conservation_colour_increment",
276 new String[] { sg.getName() }));
278 assertTrue(sg.getGroupColourScheme().conservationApplied());
279 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
282 * apply 40% PID threshold to group
284 popupMenu.abovePIDColour_actionPerformed(true);
285 sp = SliderPanel.getSliderPanel();
286 assertFalse(sp.isForConservation());
287 assertEquals(sp.getTitle(), MessageManager.formatMessage(
288 "label.percentage_identity_threshold",
289 new String[] { sg.getName() }));
291 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
292 // conservation threshold is unchanged:
293 assertTrue(sg.getGroupColourScheme().conservationApplied());
294 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
297 * change alignment colour - group colour, and all thresholds,
298 * should be unaffected
300 af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
301 assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
302 assertTrue(av.getResidueShading().conservationApplied());
303 assertEquals(av.getResidueShading().getConservationInc(), 20);
304 assertEquals(av.getResidueShading().getThreshold(), 10);
305 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
306 assertTrue(sg.getGroupColourScheme().conservationApplied());
307 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
308 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
311 * Now change alignment colour with Apply Colour To All Groups
312 * - group colour should change, but not colour thresholds
314 af.applyToAllGroups_actionPerformed(true);
315 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
316 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
317 assertTrue(av.getResidueShading().conservationApplied());
318 assertEquals(av.getResidueShading().getConservationInc(), 20);
319 assertEquals(av.getResidueShading().getThreshold(), 10);
320 assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
321 assertTrue(sg.getGroupColourScheme().conservationApplied());
322 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
323 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
327 * Test residue colouring with various options
329 * <li>no PID or Conservation threshold</li>
330 * <li>colour by Conservation applied</li>
331 * <li>colour by Conservation removed</li>
332 * <li>colour above PID - various values</li>
333 * <li>colour above PID removed</li>
334 * <li>Above PID plus By Conservation combined</li>
335 * <li>remove Above PID to leave just By Conservation</li>
336 * <li>re-add Above PID</li>
337 * <li>remove By Conservation to leave just Above PID</li>
338 * <li>remove Above PID to leave original colours</li>
341 @Test(groups = "Functional")
342 public void testColourThresholdActions()
344 AlignViewport av = af.getViewport();
345 AlignmentI al = av.getAlignment();
348 * Colour alignment by Helix Propensity, no thresholds
350 af.applyToAllGroups_actionPerformed(false);
351 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
352 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
353 assertFalse(av.getResidueShading().conservationApplied());
354 assertEquals(av.getResidueShading().getThreshold(), 0);
357 * inspect the colour of
358 * FER_CAPAN.9(I), column 15 (14 base 0)
359 * FER_CAPAN.10(SER), column 16 (15 base 0)
361 SequenceI ferCapan = al.findName("FER_CAPAN");
362 ResidueShaderI rs = av.getResidueShading();
363 Color c = rs.findColour('I', 14, ferCapan);
364 Color i_original = new Color(138, 117, 138);
365 assertEquals(c, i_original);
366 c = rs.findColour('S', 15, ferCapan);
367 Color s_original = new Color(54, 201, 54);
368 assertEquals(c, s_original);
371 * colour by conservation with increment 10
373 af.conservationMenuItem_actionPerformed(true);
374 SliderPanel sp = SliderPanel.getSliderPanel();
375 assertTrue(sp.isForConservation());
376 assertEquals(sp.getValue(), 30); // initial slider setting
377 c = rs.findColour('I', 14, ferCapan);
378 Color i_faded = new Color(255, 255, 255);
379 assertEquals(c, i_faded);
381 assertSame(rs, av.getResidueShading());
382 assertEquals(rs.getConservationInc(), 10);
383 c = rs.findColour('I', 14, ferCapan);
384 i_faded = new Color(196, 186, 196);
385 assertEquals(c, i_faded);
386 c = rs.findColour('S', 15, ferCapan);
387 Color s_faded = new Color(144, 225, 144);
388 assertEquals(c, s_faded);
391 * deselect By Conservation - colour should revert
393 af.conservationMenuItem_actionPerformed(false);
394 c = rs.findColour('S', 15, ferCapan);
395 assertEquals(c, s_original);
398 * now Above PID, threshold = 0%
399 * should be no change
401 af.abovePIDThreshold_actionPerformed(true);
402 sp = SliderPanel.getSliderPanel();
403 assertFalse(sp.isForConservation());
404 assertEquals(sp.getValue(), 0); // initial slider setting
405 c = rs.findColour('I', 14, ferCapan);
406 assertEquals(c, i_original);
407 c = rs.findColour('S', 15, ferCapan);
408 assertEquals(c, s_original);
411 * Above PID, threshold = 1%
412 * 15.I becomes White because no match to consensus (V)
413 * 16.S remains coloured as matches 66.66% consensus
416 c = rs.findColour('I', 14, ferCapan);
417 assertEquals(c, Color.white);
418 c = rs.findColour('S', 15, ferCapan);
419 assertEquals(c, s_original);
422 * threshold 66% - no further change yet...
425 c = rs.findColour('I', 14, ferCapan);
426 assertEquals(c, Color.white);
427 c = rs.findColour('S', 15, ferCapan);
428 assertEquals(c, s_original);
431 * threshold 67% - now both residues are white
434 c = rs.findColour('I', 14, ferCapan);
435 assertEquals(c, Color.white);
436 c = rs.findColour('S', 15, ferCapan);
437 assertEquals(c, Color.white);
440 * deselect Above PID - colours should revert
442 af.abovePIDThreshold_actionPerformed(false);
443 c = rs.findColour('I', 14, ferCapan);
444 assertEquals(c, i_original);
445 c = rs.findColour('S', 15, ferCapan);
446 assertEquals(c, s_original);
449 * Now combine Above 50% PID and By Conservation 10%
450 * 15.I is White because no match to consensus (V)
451 * 16.S is coloured but faded
453 af.abovePIDThreshold_actionPerformed(true);
454 sp = SliderPanel.getSliderPanel();
455 assertFalse(sp.isForConservation());
457 af.conservationMenuItem_actionPerformed(true);
458 sp = SliderPanel.getSliderPanel();
459 assertTrue(sp.isForConservation());
461 c = rs.findColour('I', 14, ferCapan);
462 assertEquals(c, Color.white);
463 c = rs.findColour('S', 15, ferCapan);
464 assertEquals(c, s_faded);
467 * turn off Above PID - should just leave Conservation fading as before
469 af.abovePIDThreshold_actionPerformed(false);
470 c = rs.findColour('I', 14, ferCapan);
471 assertEquals(c, i_faded);
472 c = rs.findColour('S', 15, ferCapan);
473 assertEquals(c, s_faded);
476 * Now add Above 50% PID to conservation colouring
477 * - should give the same as PID followed by conservation (above)
479 af.abovePIDThreshold_actionPerformed(true);
480 SliderPanel.getSliderPanel().valueChanged(50);
481 c = rs.findColour('I', 14, ferCapan);
482 assertEquals(c, Color.white);
483 c = rs.findColour('S', 15, ferCapan);
484 assertEquals(c, s_faded);
487 * turn off By Conservation
488 * should leave I white, S original (unfaded) colour
490 af.conservationMenuItem_actionPerformed(false);
491 c = rs.findColour('I', 14, ferCapan);
492 assertEquals(c, Color.white);
493 c = rs.findColour('S', 15, ferCapan);
494 assertEquals(c, s_original);
497 * finally turn off Above PID to leave original colours
499 af.abovePIDThreshold_actionPerformed(false);
500 c = rs.findColour('I', 14, ferCapan);
501 assertEquals(c, i_original);
502 c = rs.findColour('S', 15, ferCapan);
503 assertEquals(c, s_original);
507 * Verify that making a New View transfers alignment and group colour schemes,
508 * including any thresholds, to the new view. Because New View is performed by
509 * saving and reloading a 'project' file, this is similar to verifying a
510 * project save and reload.
512 * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
514 @Test(groups = "Functional")
515 public void testNewView_colourThresholds()
517 AlignViewport av = af.getViewport();
518 AlignmentI al = av.getAlignment();
521 * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
523 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
524 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
525 af.abovePIDThreshold_actionPerformed(true);
526 SliderPanel sp = SliderPanel.getSliderPanel();
527 assertFalse(sp.isForConservation());
529 af.conservationMenuItem_actionPerformed(true);
530 sp = SliderPanel.getSliderPanel();
531 assertTrue(sp.isForConservation());
533 ResidueShaderI rs = av.getResidueShading();
534 assertEquals(rs.getThreshold(), 10);
535 assertTrue(rs.conservationApplied());
536 assertEquals(rs.getConservationInc(), 20);
539 * create a group with Strand colouring, 30% Conservation
540 * and 40% PID threshold
542 SequenceGroup sg = new SequenceGroup();
543 sg.addSequence(al.getSequenceAt(0), false);
546 av.setSelectionGroup(sg);
547 PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0),
549 popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
551 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
552 assertEquals(al.getGroups().size(), 1);
553 assertSame(al.getGroups().get(0), sg);
554 popupMenu.conservationMenuItem_actionPerformed(true);
555 sp = SliderPanel.getSliderPanel();
556 assertTrue(sp.isForConservation());
558 popupMenu.abovePIDColour_actionPerformed(true);
559 sp = SliderPanel.getSliderPanel();
560 assertFalse(sp.isForConservation());
562 rs = sg.getGroupColourScheme();
563 assertTrue(rs.conservationApplied());
564 assertEquals(rs.getConservationInc(), 30);
565 assertEquals(rs.getThreshold(), 40);
568 * set slider panel focus to the background alignment
570 af.conservationMenuItem_actionPerformed(true);
571 sp = SliderPanel.getSliderPanel();
572 assertTrue(sp.isForConservation());
573 assertEquals(sp.getTitle(), MessageManager.formatMessage(
574 "label.conservation_colour_increment",
575 new String[] { "Background" }));
578 * make a new View, verify alignment and group colour schemes
580 af.newView_actionPerformed(null);
581 assertEquals(af.alignPanel.getViewName(), "View 1");
582 AlignViewport av2 = af.getViewport();
583 assertNotSame(av, av2);
584 assertSame(av2, af.alignPanel.av);
585 rs = av2.getResidueShading();
586 assertNotSame(av.getResidueShading(), rs);
587 assertEquals(rs.getThreshold(), 10);
588 assertTrue(rs.conservationApplied(), rs.toString());
589 assertEquals(rs.getConservationInc(), 20);
590 assertEquals(av2.getAlignment().getGroups().size(), 1);
591 sg = av2.getAlignment().getGroups().get(0);
592 rs = sg.getGroupColourScheme();
593 assertTrue(rs.conservationApplied());
594 assertEquals(rs.getConservationInc(), 30);
595 assertEquals(rs.getThreshold(), 40);
598 * check the Conservation SliderPanel (still open) is linked to
599 * and updates the new view (JAL-2385)
601 sp = SliderPanel.getSliderPanel();
602 assertTrue(sp.isForConservation());
603 assertEquals(sp.getTitle(), MessageManager.formatMessage(
604 "label.conservation_colour_increment",
605 new String[] { "View 1" }));
607 assertEquals(av2.getResidueShading().getConservationInc(), 22);
611 * Verify that making a New View preserves the dataset reference for the
612 * alignment. Otherwise, see a 'duplicate jar entry' reference when trying to
613 * save alignments with multiple views, and codon mappings will not be shared
614 * across all panels in a split frame.
616 * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
618 @Test(groups = "Functional")
619 public void testNewView_dsRefPreserved()
621 AlignViewport av = af.getViewport();
622 AlignmentI al = av.getAlignment();
623 AlignmentI original_ds = al.getDataset();
624 af.newView_actionPerformed(null);
625 assertNotEquals("New view didn't select the a new panel", av,
627 org.testng.Assert.assertEquals(original_ds,
628 af.getViewport().getAlignment().getDataset(),
629 "Dataset was not preserved in new view");