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 if (Desktop.instance != null)
79 Desktop.instance.closeAll_actionPerformed(null);
83 * configure (read-only) properties for test to ensure Consensus is computed
84 * for colour Above PID testing
86 @BeforeMethod(alwaysRun = true)
89 Cache.loadProperties("test/jalview/io/testProps.jvprops");
90 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
91 Boolean.TRUE.toString());
92 af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
96 * wait for Consensus thread to complete
103 } catch (InterruptedException x)
106 } while (af.getViewport().getCalcManager().isWorking());
109 public static void setUpJvOptionPane()
111 JvOptionPane.setInteractiveMode(false);
112 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
115 @Test(groups = "Functional")
116 public void testHideFeatureColumns()
118 SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
119 SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
120 seq1.addSequenceFeature(
121 new SequenceFeature("Metal", "", 1, 5, 0f, null));
122 seq2.addSequenceFeature(
123 new SequenceFeature("Metal", "", 6, 10, 10f, null));
124 seq1.addSequenceFeature(
125 new SequenceFeature("Turn", "", 2, 4, Float.NaN, null));
126 seq2.addSequenceFeature(
127 new SequenceFeature("Turn", "", 7, 9, Float.NaN, null));
128 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
129 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
133 * make all features visible (select feature columns checks visibility)
135 alignFrame.getFeatureRenderer().findAllFeatures(true);
138 * hiding a feature not present does nothing
140 assertFalse(alignFrame.hideFeatureColumns("exon", true));
141 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
143 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
144 .getNumberOfRegions(), 0);
146 assertFalse(alignFrame.hideFeatureColumns("exon", false));
147 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
149 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
150 .getNumberOfRegions(), 0);
153 * hiding a feature in all columns does nothing
155 assertFalse(alignFrame.hideFeatureColumns("Metal", true));
156 assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
158 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
159 .getNumberOfRegions(), 0);
162 * threshold Metal to hide features where score < 5
163 * seq1 feature in columns 1-5 is hidden
164 * seq2 feature in columns 6-10 is shown
166 FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
168 fc.setAboveThreshold(true);
170 alignFrame.getFeatureRenderer().setColour("Metal", fc);
171 assertTrue(alignFrame.hideFeatureColumns("Metal", true));
172 HiddenColumns hidden = alignFrame.getViewport().getAlignment()
174 assertEquals(hidden.getNumberOfRegions(), 1);
175 Iterator<int[]> regions = hidden.iterator();
176 int[] next = regions.next();
177 assertEquals(next[0], 5);
178 assertEquals(next[1], 9);
181 * hide a feature present in some columns
182 * sequence positions [2-4], [7-9] are column positions
183 * [1-3], [6-8] base zero
185 alignFrame.getViewport().showAllHiddenColumns();
186 assertTrue(alignFrame.hideFeatureColumns("Turn", true));
187 regions = alignFrame.getViewport().getAlignment().getHiddenColumns()
189 assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
190 .getNumberOfRegions(), 2);
191 next = regions.next();
192 assertEquals(next[0], 1);
193 assertEquals(next[1], 3);
194 next = regions.next();
195 assertEquals(next[0], 6);
196 assertEquals(next[1], 8);
200 * Test that changing background (alignment) colour scheme
202 * <li>with Apply Colour to All Groups not selected, does not change group
204 * <li>with Apply Colour to All Groups selected, does change group
206 * <li>in neither case, changes alignment or group colour thresholds (PID or
210 @Test(groups = "Functional")
211 public void testChangeColour_background_groupsAndThresholds()
213 AlignViewport av = af.getViewport();
214 AlignmentI al = av.getAlignment();
217 * Colour alignment by Buried Index
219 af.applyToAllGroups_actionPerformed(false);
220 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
221 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
222 assertFalse(av.getResidueShading().conservationApplied());
223 assertEquals(av.getResidueShading().getThreshold(), 0);
226 * Apply Conservation 20%
228 af.conservationMenuItem_actionPerformed(true);
229 SliderPanel sp = SliderPanel.getSliderPanel();
230 assertEquals(sp.getTitle(), MessageManager.formatMessage(
231 "label.conservation_colour_increment", new String[]
233 assertTrue(sp.isForConservation());
235 assertTrue(av.getResidueShading().conservationApplied());
236 assertEquals(av.getResidueShading().getConservationInc(), 20);
239 * Apply PID threshold 10% (conservation still applies as well)
241 af.abovePIDThreshold_actionPerformed(true);
242 sp = SliderPanel.getSliderPanel();
243 assertFalse(sp.isForConservation());
244 assertEquals(sp.getTitle(), MessageManager.formatMessage(
245 "label.percentage_identity_threshold", new String[]
248 assertEquals(av.getResidueShading().getThreshold(), 10);
249 assertTrue(av.getResidueShading().conservationApplied());
250 assertEquals(av.getResidueShading().getConservationInc(), 20);
253 * create a group with Strand colouring, 30% Conservation
254 * and 40% PID threshold
256 SequenceGroup sg = new SequenceGroup();
257 sg.addSequence(al.getSequenceAt(0), false);
260 av.setSelectionGroup(sg);
263 * apply 30% Conservation to group
264 * (notice menu action applies to selection group even if mouse click
265 * is at a sequence not in the group)
267 PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2),
269 popupMenu.changeColour_actionPerformed(
270 JalviewColourScheme.Strand.toString());
271 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
272 assertEquals(al.getGroups().size(), 1);
273 assertSame(al.getGroups().get(0), sg);
274 popupMenu.conservationMenuItem_actionPerformed(true);
275 sp = SliderPanel.getSliderPanel();
276 assertTrue(sp.isForConservation());
277 assertEquals(sp.getTitle(), MessageManager.formatMessage(
278 "label.conservation_colour_increment", new String[]
281 assertTrue(sg.getGroupColourScheme().conservationApplied());
282 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
285 * apply 40% PID threshold to group
287 popupMenu.abovePIDColour_actionPerformed(true);
288 sp = SliderPanel.getSliderPanel();
289 assertFalse(sp.isForConservation());
290 assertEquals(sp.getTitle(), MessageManager.formatMessage(
291 "label.percentage_identity_threshold", new String[]
294 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
295 // conservation threshold is unchanged:
296 assertTrue(sg.getGroupColourScheme().conservationApplied());
297 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
300 * change alignment colour - group colour, and all thresholds,
301 * should be unaffected
303 af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
304 assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
305 assertTrue(av.getResidueShading().conservationApplied());
306 assertEquals(av.getResidueShading().getConservationInc(), 20);
307 assertEquals(av.getResidueShading().getThreshold(), 10);
308 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
309 assertTrue(sg.getGroupColourScheme().conservationApplied());
310 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
311 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
314 * Now change alignment colour with Apply Colour To All Groups
315 * - group colour should change, but not colour thresholds
317 af.applyToAllGroups_actionPerformed(true);
318 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
319 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
320 assertTrue(av.getResidueShading().conservationApplied());
321 assertEquals(av.getResidueShading().getConservationInc(), 20);
322 assertEquals(av.getResidueShading().getThreshold(), 10);
323 assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
324 assertTrue(sg.getGroupColourScheme().conservationApplied());
325 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
326 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
330 * Test residue colouring with various options
332 * <li>no PID or Conservation threshold</li>
333 * <li>colour by Conservation applied</li>
334 * <li>colour by Conservation removed</li>
335 * <li>colour above PID - various values</li>
336 * <li>colour above PID removed</li>
337 * <li>Above PID plus By Conservation combined</li>
338 * <li>remove Above PID to leave just By Conservation</li>
339 * <li>re-add Above PID</li>
340 * <li>remove By Conservation to leave just Above PID</li>
341 * <li>remove Above PID to leave original colours</li>
344 @Test(groups = "Functional")
345 public void testColourThresholdActions()
347 AlignViewport av = af.getViewport();
348 AlignmentI al = av.getAlignment();
351 * Colour alignment by Helix Propensity, no thresholds
353 af.applyToAllGroups_actionPerformed(false);
354 af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
355 assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
356 assertFalse(av.getResidueShading().conservationApplied());
357 assertEquals(av.getResidueShading().getThreshold(), 0);
360 * inspect the colour of
361 * FER_CAPAN.9(I), column 15 (14 base 0)
362 * FER_CAPAN.10(SER), column 16 (15 base 0)
364 SequenceI ferCapan = al.findName("FER_CAPAN");
365 ResidueShaderI rs = av.getResidueShading();
366 Color c = rs.findColour('I', 14, ferCapan);
367 Color i_original = new Color(138, 117, 138);
368 assertEquals(c, i_original);
369 c = rs.findColour('S', 15, ferCapan);
370 Color s_original = new Color(54, 201, 54);
371 assertEquals(c, s_original);
374 * colour by conservation with increment 10
376 af.conservationMenuItem_actionPerformed(true);
377 SliderPanel sp = SliderPanel.getSliderPanel();
378 assertTrue(sp.isForConservation());
379 assertEquals(sp.getValue(), 30); // initial slider setting
380 c = rs.findColour('I', 14, ferCapan);
381 Color i_faded = new Color(255, 255, 255);
382 assertEquals(c, i_faded);
384 assertSame(rs, av.getResidueShading());
385 assertEquals(rs.getConservationInc(), 10);
386 c = rs.findColour('I', 14, ferCapan);
387 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);
510 * Verify that making a New View transfers alignment and group colour schemes,
511 * including any thresholds, to the new view. Because New View is performed by
512 * saving and reloading a 'project' file, this is similar to verifying a
513 * project save and reload.
515 * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
517 @Test(groups = "Functional")
518 public void testNewView_colourThresholds()
520 AlignViewport av = af.getViewport();
521 AlignmentI al = av.getAlignment();
524 * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
526 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
527 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
528 af.abovePIDThreshold_actionPerformed(true);
529 SliderPanel sp = SliderPanel.getSliderPanel();
530 assertFalse(sp.isForConservation());
532 af.conservationMenuItem_actionPerformed(true);
533 sp = SliderPanel.getSliderPanel();
534 assertTrue(sp.isForConservation());
536 ResidueShaderI rs = av.getResidueShading();
537 assertEquals(rs.getThreshold(), 10);
538 assertTrue(rs.conservationApplied());
539 assertEquals(rs.getConservationInc(), 20);
542 * create a group with Strand colouring, 30% Conservation
543 * and 40% PID threshold
545 SequenceGroup sg = new SequenceGroup();
546 sg.addSequence(al.getSequenceAt(0), false);
549 av.setSelectionGroup(sg);
550 PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0),
552 popupMenu.changeColour_actionPerformed(
553 JalviewColourScheme.Strand.toString());
554 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
555 assertEquals(al.getGroups().size(), 1);
556 assertSame(al.getGroups().get(0), sg);
557 popupMenu.conservationMenuItem_actionPerformed(true);
558 sp = SliderPanel.getSliderPanel();
559 assertTrue(sp.isForConservation());
561 popupMenu.abovePIDColour_actionPerformed(true);
562 sp = SliderPanel.getSliderPanel();
563 assertFalse(sp.isForConservation());
565 rs = sg.getGroupColourScheme();
566 assertTrue(rs.conservationApplied());
567 assertEquals(rs.getConservationInc(), 30);
568 assertEquals(rs.getThreshold(), 40);
571 * set slider panel focus to the background alignment
573 af.conservationMenuItem_actionPerformed(true);
574 sp = SliderPanel.getSliderPanel();
575 assertTrue(sp.isForConservation());
576 assertEquals(sp.getTitle(), MessageManager.formatMessage(
577 "label.conservation_colour_increment", new String[]
581 * make a new View, verify alignment and group colour schemes
583 af.newView_actionPerformed(null);
584 assertEquals(af.alignPanel.getViewName(), "View 1");
585 AlignViewport av2 = af.getViewport();
586 assertNotSame(av, av2);
587 assertSame(av2, af.alignPanel.av);
588 rs = av2.getResidueShading();
589 assertNotSame(av.getResidueShading(), rs);
590 assertEquals(rs.getThreshold(), 10);
591 assertTrue(rs.conservationApplied(), rs.toString());
592 assertEquals(rs.getConservationInc(), 20);
593 assertEquals(av2.getAlignment().getGroups().size(), 1);
594 sg = av2.getAlignment().getGroups().get(0);
595 rs = sg.getGroupColourScheme();
596 assertTrue(rs.conservationApplied());
597 assertEquals(rs.getConservationInc(), 30);
598 assertEquals(rs.getThreshold(), 40);
601 * check the Conservation SliderPanel (still open) is linked to
602 * and updates the new view (JAL-2385)
604 sp = SliderPanel.getSliderPanel();
605 assertTrue(sp.isForConservation());
606 assertEquals(sp.getTitle(), MessageManager.formatMessage(
607 "label.conservation_colour_increment", new String[]
610 assertEquals(av2.getResidueShading().getConservationInc(), 22);
614 * Verify that making a New View preserves the dataset reference for the
615 * alignment. Otherwise, see a 'duplicate jar entry' reference when trying to
616 * save alignments with multiple views, and codon mappings will not be shared
617 * across all panels in a split frame.
619 * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
621 @Test(groups = "Functional")
622 public void testNewView_dsRefPreserved()
624 AlignViewport av = af.getViewport();
625 AlignmentI al = av.getAlignment();
626 AlignmentI original_ds = al.getDataset();
627 af.newView_actionPerformed(null);
628 assertNotEquals("New view didn't select the a new panel", av,
630 org.testng.Assert.assertEquals(original_ds,
631 af.getViewport().getAlignment().getDataset(),
632 "Dataset was not preserved in new view");