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);
71 @Test(groups = "Functional")
72 public void testHideFeatureColumns()
74 SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
75 SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
76 seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
77 seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
79 seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
81 seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
83 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
84 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
88 * make all features visible (select feature columns checks visibility)
90 alignFrame.getFeatureRenderer().findAllFeatures(true);
93 * hiding a feature not present does nothing
95 assertFalse(alignFrame.hideFeatureColumns("exon", true));
96 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
98 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
99 .getNumberOfRegions(), 0);
101 assertFalse(alignFrame.hideFeatureColumns("exon", false));
102 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
104 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
105 .getNumberOfRegions(), 0);
108 * hiding a feature in all columns does nothing
110 assertFalse(alignFrame.hideFeatureColumns("Metal", true));
111 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
113 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
114 .getNumberOfRegions(), 0);
118 * threshold Metal to hide features where score < 5
119 * seq1 feature in columns 1-5 is hidden
120 * seq2 feature in columns 6-10 is shown
122 FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
124 fc.setAboveThreshold(true);
126 alignFrame.getFeatureRenderer().setColour("Metal", fc);
127 assertTrue(alignFrame.hideFeatureColumns("Metal", true));
128 HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
129 assertEquals(hidden.getNumberOfRegions(), 1);
130 Iterator<int[]> regions = hidden.iterator();
131 int[] next = regions.next();
132 assertEquals(next[0], 5);
133 assertEquals(next[1], 9);
136 * hide a feature present in some columns
137 * sequence positions [2-4], [7-9] are column positions
138 * [1-3], [6-8] base zero
140 alignFrame.getViewport().showAllHiddenColumns();
141 assertTrue(alignFrame.hideFeatureColumns("Turn", true));
142 regions = alignFrame.getViewport().getAlignment()
143 .getHiddenColumns().iterator();
144 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
145 .getNumberOfRegions(), 2);
146 next = regions.next();
147 assertEquals(next[0], 1);
148 assertEquals(next[1], 3);
149 next = regions.next();
150 assertEquals(next[0], 6);
151 assertEquals(next[1], 8);
154 @BeforeClass(alwaysRun = true)
155 public static void setUpBeforeClass() throws Exception
158 * use read-only test properties file
160 Cache.loadProperties("test/jalview/io/testProps.jvprops");
161 Cache.setPropertyNoSave("SHOW_JWS2_SERVICES", Boolean.FALSE.toString());
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.setPropertyNoSave("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()
346 AlignViewport av = af.getViewport();
347 AlignmentI al = av.getAlignment();
350 * Colour alignment by Helix Propensity, no thresholds
352 af.applyToAllGroups_actionPerformed(false);
353 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
354 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
355 assertFalse(av.getResidueShading().conservationApplied());
356 assertEquals(av.getResidueShading().getThreshold(), 0);
359 * inspect the colour of
360 * FER_CAPAN.9(I), column 14 (14 base 0)
361 * FER_CAPAN.10(SER), column 16 (15 base 0)
363 SequenceI ferCapan = al.findName("FER_CAPAN");
364 ResidueShaderI rs = av.getResidueShading();
365 Color c = rs.findColour('I', 14, ferCapan);
366 Color i_original = new Color(138, 117, 138);
367 assertEquals(c, i_original);
368 c = rs.findColour('S', 15, ferCapan);
369 Color s_original = new Color(54, 201, 54);
370 assertEquals(c, s_original);
373 * colour by conservation with increment 10
375 af.conservationMenuItem_actionPerformed(true);
376 SliderPanel sp = SliderPanel.getSliderPanel();
377 assertTrue(sp.isForConservation());
378 assertEquals(sp.getValue(), 30); // initial slider setting
380 // BH 2019.08.28 this was necessary so that rs was updated
381 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
385 assertSame(rs, av.getResidueShading());
386 c = rs.findColour('I', 14, ferCapan);
387 Color i_faded = new Color(196, 186, 196);
388 assertEquals(c, i_faded);
389 c = rs.findColour('S', 15, ferCapan);
390 Color s_faded = new Color(144, 225, 144);
391 assertEquals(c, s_faded);
394 * deselect By Conservation - colour should revert
396 af.conservationMenuItem_actionPerformed(false);
397 c = rs.findColour('S', 15, ferCapan);
398 assertEquals(c, s_original);
401 * now Above PID, threshold = 0%
402 * should be no change
404 af.abovePIDThreshold_actionPerformed(true);
405 sp = SliderPanel.getSliderPanel();
406 assertFalse(sp.isForConservation());
407 assertEquals(sp.getValue(), 0); // initial slider setting
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 * Above PID, threshold = 1%
415 * 15.I becomes White because no match to consensus (V)
416 * 16.S remains coloured as matches 66.66% consensus
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 66% - no further change yet...
428 c = rs.findColour('I', 14, ferCapan);
429 assertEquals(c, Color.white);
430 c = rs.findColour('S', 15, ferCapan);
431 assertEquals(c, s_original);
434 * threshold 67% - now both residues are white
437 c = rs.findColour('I', 14, ferCapan);
438 assertEquals(c, Color.white);
439 c = rs.findColour('S', 15, ferCapan);
440 assertEquals(c, Color.white);
443 * deselect Above PID - colours should revert
445 af.abovePIDThreshold_actionPerformed(false);
446 c = rs.findColour('I', 14, ferCapan);
447 assertEquals(c, i_original);
448 c = rs.findColour('S', 15, ferCapan);
449 assertEquals(c, s_original);
452 * Now combine Above 50% PID and By Conservation 10%
453 * 15.I is White because no match to consensus (V)
454 * 16.S is coloured but faded
456 af.abovePIDThreshold_actionPerformed(true);
457 sp = SliderPanel.getSliderPanel();
458 assertFalse(sp.isForConservation());
460 af.conservationMenuItem_actionPerformed(true);
461 sp = SliderPanel.getSliderPanel();
462 assertTrue(sp.isForConservation());
464 c = rs.findColour('I', 14, ferCapan);
465 assertEquals(c, Color.white);
466 c = rs.findColour('S', 15, ferCapan);
467 assertEquals(c, s_faded);
470 * turn off Above PID - should just leave Conservation fading as before
472 af.abovePIDThreshold_actionPerformed(false);
473 c = rs.findColour('I', 14, ferCapan);
474 assertEquals(c, i_faded);
475 c = rs.findColour('S', 15, ferCapan);
476 assertEquals(c, s_faded);
479 * Now add Above 50% PID to conservation colouring
480 * - should give the same as PID followed by conservation (above)
482 af.abovePIDThreshold_actionPerformed(true);
483 SliderPanel.getSliderPanel().valueChanged(50);
484 c = rs.findColour('I', 14, ferCapan);
485 assertEquals(c, Color.white);
486 c = rs.findColour('S', 15, ferCapan);
487 assertEquals(c, s_faded);
490 * turn off By Conservation
491 * should leave I white, S original (unfaded) colour
493 af.conservationMenuItem_actionPerformed(false);
494 c = rs.findColour('I', 14, ferCapan);
495 assertEquals(c, Color.white);
496 c = rs.findColour('S', 15, ferCapan);
497 assertEquals(c, s_original);
500 * finally turn off Above PID to leave original colours
502 af.abovePIDThreshold_actionPerformed(false);
503 c = rs.findColour('I', 14, ferCapan);
504 assertEquals(c, i_original);
505 c = rs.findColour('S', 15, ferCapan);
506 assertEquals(c, s_original);
509 private void waitSome()
518 } catch (InterruptedException e)
525 * Verify that making a New View transfers alignment and group colour schemes,
526 * including any thresholds, to the new view. Because New View is performed by
527 * saving and reloading a 'project' file, this is similar to verifying a
528 * project save and reload.
530 * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
532 @Test(groups = "Functional")
533 public void testNewView_colourThresholds()
535 AlignViewport av = af.getViewport();
536 AlignmentI al = av.getAlignment();
539 * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
541 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
542 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
543 af.abovePIDThreshold_actionPerformed(true);
544 SliderPanel sp = SliderPanel.getSliderPanel();
545 assertFalse(sp.isForConservation());
547 af.conservationMenuItem_actionPerformed(true);
548 sp = SliderPanel.getSliderPanel();
549 assertTrue(sp.isForConservation());
551 ResidueShaderI rs = av.getResidueShading();
552 assertEquals(rs.getThreshold(), 10);
553 assertTrue(rs.conservationApplied());
554 assertEquals(rs.getConservationInc(), 20);
557 * create a group with Strand colouring, 30% Conservation
558 * and 40% PID threshold
560 SequenceGroup sg = new SequenceGroup();
561 sg.addSequence(al.getSequenceAt(0), false);
564 av.setSelectionGroup(sg);
565 PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
566 popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
568 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
569 assertEquals(al.getGroups().size(), 1);
570 assertSame(al.getGroups().get(0), sg);
571 popupMenu.conservationMenuItem_actionPerformed(true);
572 sp = SliderPanel.getSliderPanel();
573 assertTrue(sp.isForConservation());
575 popupMenu.abovePIDColour_actionPerformed(true);
576 sp = SliderPanel.getSliderPanel();
577 assertFalse(sp.isForConservation());
579 rs = sg.getGroupColourScheme();
580 assertTrue(rs.conservationApplied());
581 assertEquals(rs.getConservationInc(), 30);
582 assertEquals(rs.getThreshold(), 40);
585 * set slider panel focus to the background alignment
587 af.conservationMenuItem_actionPerformed(true);
588 sp = SliderPanel.getSliderPanel();
589 assertTrue(sp.isForConservation());
590 assertEquals(sp.getTitle(), MessageManager.formatMessage(
591 "label.conservation_colour_increment",
592 new String[] { "Background" }));
595 * make a new View, verify alignment and group colour schemes
597 af.newView_actionPerformed(null);
598 assertEquals(af.alignPanel.getViewName(), "View 1");
599 AlignViewport av2 = af.getViewport();
600 assertNotSame(av, av2);
601 assertSame(av2, af.alignPanel.av);
602 rs = av2.getResidueShading();
603 assertNotSame(av.getResidueShading(), rs);
604 assertEquals(rs.getThreshold(), 10);
605 assertTrue(rs.conservationApplied(), rs.toString());
606 assertEquals(rs.getConservationInc(), 20);
607 assertEquals(av2.getAlignment().getGroups().size(), 1);
608 sg = av2.getAlignment().getGroups().get(0);
609 rs = sg.getGroupColourScheme();
610 assertTrue(rs.conservationApplied());
611 assertEquals(rs.getConservationInc(), 30);
612 assertEquals(rs.getThreshold(), 40);
615 * check the Conservation SliderPanel (still open) is linked to
616 * and updates the new view (JAL-2385)
618 sp = SliderPanel.getSliderPanel();
619 assertTrue(sp.isForConservation());
620 assertEquals(sp.getTitle(), MessageManager.formatMessage(
621 "label.conservation_colour_increment",
622 new String[] { "View 1" }));
624 assertEquals(av2.getResidueShading().getConservationInc(), 22);
628 * Verify that making a New View preserves the dataset reference for the
629 * alignment. Otherwise, see a 'duplicate jar entry' reference when trying to
630 * save alignments with multiple views, and codon mappings will not be shared
631 * across all panels in a split frame.
633 * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
635 @Test(groups = "Functional")
636 public void testNewView_dsRefPreserved()
638 AlignViewport av = af.getViewport();
639 AlignmentI al = av.getAlignment();
640 AlignmentI original_ds = al.getDataset();
641 af.newView_actionPerformed(null);
642 assertNotEquals("New view didn't select the a new panel", av,
644 org.testng.Assert.assertEquals(original_ds,
645 af.getViewport().getAlignment().getDataset(),
646 "Dataset was not preserved in new view");