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.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertNotSame;
27 import static org.testng.AssertJUnit.assertSame;
28 import static org.testng.AssertJUnit.assertTrue;
30 import jalview.api.AlignViewportI;
31 import java.util.ArrayList;
32 import java.util.List;
34 import org.testng.Assert;
35 import org.testng.annotations.BeforeClass;
36 import org.testng.annotations.BeforeMethod;
37 import org.testng.annotations.Test;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.datamodel.AlignedCodonFrame;
42 import jalview.datamodel.Alignment;
43 import jalview.datamodel.AlignmentAnnotation;
44 import jalview.datamodel.AlignmentI;
45 import jalview.datamodel.Annotation;
46 import jalview.datamodel.SearchResults;
47 import jalview.datamodel.SearchResultsI;
48 import jalview.datamodel.Sequence;
49 import jalview.datamodel.SequenceGroup;
50 import jalview.datamodel.SequenceI;
51 import jalview.io.DataSourceType;
52 import jalview.io.FileLoader;
53 import jalview.schemes.ClustalxColourScheme;
54 import jalview.schemes.ColourSchemeI;
55 import jalview.schemes.PIDColourScheme;
56 import jalview.structure.StructureSelectionManager;
57 import jalview.util.MapList;
58 import jalview.viewmodel.AlignmentViewport;
59 import jalview.viewmodel.ViewportRanges;
61 public class AlignViewportTest
64 @BeforeClass(alwaysRun = true)
65 public void setUpJvOptionPane()
67 JvOptionPane.setInteractiveMode(false);
68 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
73 AlignmentViewport testee;
75 @BeforeClass(alwaysRun = true)
76 public static void setUpBeforeClass() throws Exception
78 Jalview.main(new String[] {
81 "test/jalview/testProps.jvprops" });
84 * remove any sequence mappings left lying around by other tests
86 StructureSelectionManager ssm = StructureSelectionManager
87 .getStructureSelectionManager(Desktop.getInstance());
91 @BeforeMethod(alwaysRun = true)
94 SequenceI seq1 = new Sequence("Seq1", "ABC");
95 SequenceI seq2 = new Sequence("Seq2", "ABC");
96 SequenceI seq3 = new Sequence("Seq3", "ABC");
97 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
98 al = new Alignment(seqs);
100 testee = new AlignViewport(al);
104 * Test that a mapping is not deregistered when a second view is closed but
105 * the first still holds a reference to the mapping
107 @Test(groups = { "Functional" })
108 public void testDeregisterMapping_onCloseView()
111 * alignment with reference to mappings
113 AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
114 ">Seq1\nCAGT\n", DataSourceType.PASTE);
116 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
117 AlignedCodonFrame acf1 = new AlignedCodonFrame();
118 acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 },
120 AlignedCodonFrame acf2 = new AlignedCodonFrame();
121 acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
124 List<AlignedCodonFrame> mappings = new ArrayList<>();
127 af1.getViewport().getAlignment().setCodonFrames(mappings);
128 af1.newView_actionPerformed(null);
131 * Verify that creating the alignment for the new View has registered the
134 StructureSelectionManager ssm = StructureSelectionManager
135 .getStructureSelectionManager(Desktop.getInstance());
136 List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
137 assertEquals(2, sequenceMappings.size());
138 assertTrue(sequenceMappings.contains(acf1));
139 assertTrue(sequenceMappings.contains(acf2));
142 * Close the second view. Verify that mappings are not removed as the first
143 * view still holds a reference to them.
145 af1.closeMenuItem_actionPerformed(false);
146 assertEquals(2, sequenceMappings.size());
147 assertTrue(sequenceMappings.contains(acf1));
148 assertTrue(sequenceMappings.contains(acf2));
152 * Test that a mapping is deregistered if no alignment holds a reference to it
154 @Test(groups = { "Functional" })
155 public void testDeregisterMapping_withNoReference()
157 Desktop d = Desktop.getInstance();
159 StructureSelectionManager ssm = StructureSelectionManager
160 .getStructureSelectionManager(Desktop.getInstance());
163 AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
164 ">Seq1\nRSVQ\n", DataSourceType.PASTE);
165 AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
166 ">Seq2\nDGEL\n", DataSourceType.PASTE);
167 SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
168 SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
169 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
170 SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
171 // need to be distinct
172 AlignedCodonFrame acf1 = new AlignedCodonFrame();
173 acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
174 new int[] { 1, 12 }, 1, 3));
175 AlignedCodonFrame acf2 = new AlignedCodonFrame();
176 acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
177 new int[] { 1, 12 }, 1, 3));
178 AlignedCodonFrame acf3 = new AlignedCodonFrame();
179 acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
182 List<AlignedCodonFrame> mappings1 = new ArrayList<>();
184 af1.getViewport().getAlignment().setCodonFrames(mappings1);
186 List<AlignedCodonFrame> mappings2 = new ArrayList<>();
189 af2.getViewport().getAlignment().setCodonFrames(mappings2);
192 * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
195 List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
196 assertEquals(0, ssmMappings.size());
197 ssm.registerMapping(acf1);
198 assertEquals(1, ssmMappings.size());
199 ssm.registerMapping(acf2);
200 assertEquals(2, ssmMappings.size());
201 ssm.registerMapping(acf3);
202 assertEquals(3, ssmMappings.size());
205 * Closing AlignFrame2 should remove its mappings from
206 * StructureSelectionManager, since AlignFrame1 has no reference to them
208 af2.closeMenuItem_actionPerformed(true);
209 assertEquals(1, ssmMappings.size());
210 assertTrue(ssmMappings.contains(acf1));
214 * Test that a mapping is not deregistered if another alignment holds a
217 @Test(groups = { "Functional" })
218 public void testDeregisterMapping_withReference()
220 Desktop d = Desktop.getInstance();
222 StructureSelectionManager ssm = StructureSelectionManager
223 .getStructureSelectionManager(Desktop.getInstance());
226 AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
227 ">Seq1\nRSVQ\n", DataSourceType.PASTE);
228 AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
229 ">Seq2\nDGEL\n", DataSourceType.PASTE);
230 SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
231 SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
232 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
233 SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
234 // need to be distinct
235 AlignedCodonFrame acf1 = new AlignedCodonFrame();
236 acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
237 new int[] { 1, 12 }, 1, 3));
238 AlignedCodonFrame acf2 = new AlignedCodonFrame();
239 acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
240 new int[] { 1, 12 }, 1, 3));
241 AlignedCodonFrame acf3 = new AlignedCodonFrame();
242 acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
245 List<AlignedCodonFrame> mappings1 = new ArrayList<>();
248 af1.getViewport().getAlignment().setCodonFrames(mappings1);
250 List<AlignedCodonFrame> mappings2 = new ArrayList<>();
253 af2.getViewport().getAlignment().setCodonFrames(mappings2);
256 * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
259 List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
260 assertEquals(0, ssmMappings.size());
261 ssm.registerMapping(acf1);
262 assertEquals(1, ssmMappings.size());
263 ssm.registerMapping(acf2);
264 assertEquals(2, ssmMappings.size());
265 ssm.registerMapping(acf3);
266 assertEquals(3, ssmMappings.size());
269 * Closing AlignFrame2 should remove mapping acf3 from
270 * StructureSelectionManager, but not acf2, since AlignFrame1 still has a
273 af2.closeMenuItem_actionPerformed(true);
274 assertEquals(2, ssmMappings.size());
275 assertTrue(ssmMappings.contains(acf1));
276 assertTrue(ssmMappings.contains(acf2));
277 assertFalse(ssmMappings.contains(acf3));
281 * Test for JAL-1306 - conservation thread should run even when only Quality
282 * (and not Conservation) is enabled in Preferences
284 @Test(groups = { "Functional" }, timeOut=2000)
285 public void testUpdateConservation_qualityOnly()
287 Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
288 Boolean.TRUE.toString());
289 Cache.setPropertyNoSave("SHOW_QUALITY",
290 Boolean.TRUE.toString());
291 Cache.setPropertyNoSave("SHOW_CONSERVATION",
292 Boolean.FALSE.toString());
293 Cache.setPropertyNoSave("SHOW_OCCUPANCY",
294 Boolean.FALSE.toString());
295 Cache.setPropertyNoSave("SHOW_IDENTITY",
296 Boolean.FALSE.toString());
297 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
298 "examples/uniref50.fa", DataSourceType.FILE);
301 * wait for Conservation thread to complete
303 AlignViewport viewport = af.getViewport();
304 waitForCalculations(viewport);
305 AlignmentAnnotation[] anns = viewport.getAlignment()
306 .getAlignmentAnnotation();
307 assertNotNull("No annotations found", anns);
308 assertEquals("More than one annotation found", 1, anns.length);
309 assertTrue("Annotation is not Quality",
310 anns[0].description.startsWith("Alignment Quality"));
311 Annotation[] annotations = anns[0].annotations;
312 assertNotNull("Quality annotations are null", annotations);
313 assertNotNull("Quality in column 1 is null", annotations[0]);
314 assertTrue("No quality value in column 1", annotations[0].value > 10f);
318 * Wait for consensus etc calculation threads to complete
322 protected void waitForCalculations(AlignViewport viewport)
326 System.out.print("waiting...");
328 while (--n >= 0 || viewport.getCalcManager().isWorking())
333 } catch (InterruptedException e)
337 System.out.println("...done");
341 @Test(groups = { "Functional" })
342 public void testSetGlobalColourScheme()
345 * test for JAL-2283: don't inadvertently turn on colour by conservation
347 Cache.setPropertyNoSave("DEFAULT_COLOUR_PROT", "None");
348 Cache.setPropertyNoSave("SHOW_CONSERVATION",
349 Boolean.TRUE.toString());
350 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
351 "examples/uniref50.fa", DataSourceType.FILE);
352 ColourSchemeI cs = new PIDColourScheme();
353 AlignViewport viewport = af.getViewport();
354 viewport.setGlobalColourScheme(cs);
355 assertFalse(viewport.getResidueShading()
356 .conservationApplied());
359 * JAL-3201 groups have their own ColourSchemeI instances
361 AlignmentI aln = viewport.getAlignment();
362 SequenceGroup sg1 = new SequenceGroup();
363 sg1.addSequence(aln.getSequenceAt(0), false);
364 sg1.addSequence(aln.getSequenceAt(2), false);
365 SequenceGroup sg2 = new SequenceGroup();
366 sg2.addSequence(aln.getSequenceAt(1), false);
367 sg2.addSequence(aln.getSequenceAt(3), false);
370 viewport.setColourAppliesToAllGroups(true);
371 viewport.setGlobalColourScheme(new ClustalxColourScheme());
372 ColourSchemeI cs0 = viewport.getGlobalColourScheme();
373 ColourSchemeI cs1 = sg1.getColourScheme();
374 ColourSchemeI cs2 = sg2.getColourScheme();
375 assertTrue(cs0 instanceof ClustalxColourScheme);
376 assertTrue(cs1 instanceof ClustalxColourScheme);
377 assertTrue(cs2 instanceof ClustalxColourScheme);
378 assertNotSame(cs0, cs1);
379 assertNotSame(cs0, cs2);
380 assertNotSame(cs1, cs2);
383 @Test(groups = { "Functional" })
384 public void testSetGetHasSearchResults()
386 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
387 "examples/uniref50.fa", DataSourceType.FILE);
388 SearchResultsI sr = new SearchResults();
389 SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);
391 // create arbitrary range on first sequence
392 sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15);
395 af.getViewport().setSearchResults(sr);
397 assertTrue(af.getViewport().hasSearchResults());
399 assertEquals(sr, af.getViewport().getSearchResults());
401 // set(null) results in has -> false
403 af.getViewport().setSearchResults(null);
404 assertFalse(af.getViewport().hasSearchResults());
408 * Verify that setting the selection group has the side-effect of setting the
409 * context on the group, unless it already has one, but does not change
410 * whether the group is defined or not.
412 @Test(groups = { "Functional" })
413 public void testSetSelectionGroup()
415 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
416 "examples/uniref50.fa", DataSourceType.FILE);
417 AlignViewportI av = af.getViewport();
418 SequenceGroup sg1 = new SequenceGroup();
419 SequenceGroup sg2 = new SequenceGroup();
420 SequenceGroup sg3 = new SequenceGroup();
422 av.setSelectionGroup(sg1);
423 assertSame(sg1.getContext(), av.getAlignment()); // context set
424 assertFalse(sg1.isDefined()); // group not defined
426 sg2.setContext(sg1, false);
427 av.setSelectionGroup(sg2);
428 assertFalse(sg2.isDefined()); // unchanged
429 assertSame(sg2.getContext(), sg1); // unchanged
431 // create a defined group
432 sg3.setContext(av.getAlignment(), true);
433 av.setSelectionGroup(sg3);
434 assertTrue(sg3.isDefined()); // unchanged
437 * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits occupancy row from viewport
439 @Test(groups = { "Functional" })
440 public void testShowOrDontShowOccupancy()
443 jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
444 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
445 "examples/uniref50.fa", DataSourceType.FILE);
446 AlignViewportI av = af.getViewport();
447 Assert.assertNull(av.getAlignmentGapAnnotation(),
448 "Preference did not disable occupancy row.");
450 for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
455 Assert.assertEquals(c, 0, "Expected zero occupancy rows.");
458 jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.TRUE.toString());
459 af = new FileLoader().LoadFileWaitTillLoaded(
460 "examples/uniref50.fa", DataSourceType.FILE);
461 av = af.getViewport();
462 Assert.assertNotNull(av.getAlignmentGapAnnotation(),
463 "Preference did not enable occupancy row.");
465 for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
466 null, av.getAlignmentGapAnnotation().label))
471 Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
474 @Test(groups = { "Functional" })
475 public void testGetConsensusSeq()
482 * consensus expected to be A-C
484 String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
485 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
486 DataSourceType.PASTE);
487 AlignViewport testme = af.getViewport();
488 waitForCalculations(testme);
489 SequenceI cons = testme.getConsensusSeq();
490 String s = cons.getSequenceAsString();
491 System.out.println("s is " + s);
493 assertEquals("A-C", s);
496 @Test(groups = { "Functional" })
497 public void testHideRevealSequences()
499 ViewportRanges ranges = testee.getRanges();
500 assertEquals(3, al.getHeight());
501 assertEquals(0, ranges.getStartSeq());
502 assertEquals(2, ranges.getEndSeq());
505 * hide first sequence
507 testee.hideSequence(new SequenceI[] { al.getSequenceAt(0) });
508 assertEquals(2, al.getHeight());
509 assertEquals(0, ranges.getStartSeq());
510 assertEquals(1, ranges.getEndSeq());
513 * reveal hidden sequences above the first
515 testee.showSequence(0);
516 assertEquals(3, al.getHeight());
517 assertEquals(0, ranges.getStartSeq());
518 assertEquals(2, ranges.getEndSeq());
521 * hide first and third sequences
523 testee.hideSequence(new SequenceI[] { al.getSequenceAt(0),
524 al.getSequenceAt(2) });
525 assertEquals(1, al.getHeight());
526 assertEquals(0, ranges.getStartSeq());
527 assertEquals(0, ranges.getEndSeq());
530 * reveal all hidden sequences
532 testee.showAllHiddenSeqs();
533 assertEquals(3, al.getHeight());
534 assertEquals(0, ranges.getStartSeq());
535 assertEquals(2, ranges.getEndSeq());