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 java.util.ArrayList;
31 import java.util.List;
33 import org.testng.Assert;
34 import org.testng.annotations.BeforeClass;
35 import org.testng.annotations.BeforeMethod;
36 import org.testng.annotations.Test;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.datamodel.AlignedCodonFrame;
41 import jalview.datamodel.Alignment;
42 import jalview.datamodel.AlignmentAnnotation;
43 import jalview.datamodel.AlignmentI;
44 import jalview.datamodel.Annotation;
45 import jalview.datamodel.SearchResults;
46 import jalview.datamodel.SearchResultsI;
47 import jalview.datamodel.Sequence;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.io.DataSourceType;
51 import jalview.io.FileLoader;
52 import jalview.schemes.ClustalxColourScheme;
53 import jalview.schemes.ColourSchemeI;
54 import jalview.schemes.PIDColourScheme;
55 import jalview.structure.StructureSelectionManager;
56 import jalview.util.MapList;
57 import jalview.viewmodel.ViewportRanges;
58 import jalview.workers.AlignCalcManager;
60 public class AlignViewportTest
63 @BeforeClass(alwaysRun = true)
64 public void setUpJvOptionPane()
66 JvOptionPane.setInteractiveMode(false);
67 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
74 @BeforeClass(alwaysRun = true)
75 public static void setUpBeforeClass() throws Exception
77 Jalview.main(new String[] {
80 "test/jalview/testProps.jvprops" });
83 * remove any sequence mappings left lying around by other tests
85 StructureSelectionManager ssm = StructureSelectionManager
86 .getStructureSelectionManager(Desktop.getInstance());
90 @BeforeMethod(alwaysRun = true)
93 SequenceI seq1 = new Sequence("Seq1", "ABC");
94 SequenceI seq2 = new Sequence("Seq2", "ABC");
95 SequenceI seq3 = new Sequence("Seq3", "ABC");
96 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
97 al = new Alignment(seqs);
99 testee = new AlignViewport(al);
103 * Test that a mapping is not deregistered when a second view is closed but
104 * the first still holds a reference to the mapping
106 @Test(groups = { "Functional" })
107 public void testDeregisterMapping_onCloseView()
110 * alignment with reference to mappings
112 AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
113 ">Seq1\nCAGT\n", DataSourceType.PASTE);
115 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
116 AlignedCodonFrame acf1 = new AlignedCodonFrame();
117 acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 },
119 AlignedCodonFrame acf2 = new AlignedCodonFrame();
120 acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
123 List<AlignedCodonFrame> mappings = new ArrayList<>();
126 af1.getViewport().getAlignment().setCodonFrames(mappings);
127 af1.newView_actionPerformed(null);
130 * Verify that creating the alignment for the new View has registered the
133 StructureSelectionManager ssm = StructureSelectionManager
134 .getStructureSelectionManager(Desktop.getInstance());
135 List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
136 assertEquals(2, sequenceMappings.size());
137 assertTrue(sequenceMappings.contains(acf1));
138 assertTrue(sequenceMappings.contains(acf2));
141 * Close the second view. Verify that mappings are not removed as the first
142 * view still holds a reference to them.
144 af1.closeMenuItem_actionPerformed(false);
145 assertEquals(2, sequenceMappings.size());
146 assertTrue(sequenceMappings.contains(acf1));
147 assertTrue(sequenceMappings.contains(acf2));
151 * Test that a mapping is deregistered if no alignment holds a reference to it
153 @Test(groups = { "Functional" })
154 public void testDeregisterMapping_withNoReference()
156 Desktop d = Desktop.getInstance();
158 StructureSelectionManager ssm = StructureSelectionManager
159 .getStructureSelectionManager(Desktop.getInstance());
162 AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
163 ">Seq1\nRSVQ\n", DataSourceType.PASTE);
164 AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
165 ">Seq2\nDGEL\n", DataSourceType.PASTE);
166 SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
167 SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
168 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
169 SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
170 // need to be distinct
171 AlignedCodonFrame acf1 = new AlignedCodonFrame();
172 acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
173 new int[] { 1, 12 }, 1, 3));
174 AlignedCodonFrame acf2 = new AlignedCodonFrame();
175 acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
176 new int[] { 1, 12 }, 1, 3));
177 AlignedCodonFrame acf3 = new AlignedCodonFrame();
178 acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
181 List<AlignedCodonFrame> mappings1 = new ArrayList<>();
183 af1.getViewport().getAlignment().setCodonFrames(mappings1);
185 List<AlignedCodonFrame> mappings2 = new ArrayList<>();
188 af2.getViewport().getAlignment().setCodonFrames(mappings2);
191 * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
194 List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
195 assertEquals(0, ssmMappings.size());
196 ssm.registerMapping(acf1);
197 assertEquals(1, ssmMappings.size());
198 ssm.registerMapping(acf2);
199 assertEquals(2, ssmMappings.size());
200 ssm.registerMapping(acf3);
201 assertEquals(3, ssmMappings.size());
204 * Closing AlignFrame2 should remove its mappings from
205 * StructureSelectionManager, since AlignFrame1 has no reference to them
207 af2.closeMenuItem_actionPerformed(true);
208 assertEquals(1, ssmMappings.size());
209 assertTrue(ssmMappings.contains(acf1));
213 * Test that a mapping is not deregistered if another alignment holds a
216 @Test(groups = { "Functional" })
217 public void testDeregisterMapping_withReference()
219 Desktop d = Desktop.getInstance();
221 StructureSelectionManager ssm = StructureSelectionManager
222 .getStructureSelectionManager(Desktop.getInstance());
225 AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
226 ">Seq1\nRSVQ\n", DataSourceType.PASTE);
227 AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
228 ">Seq2\nDGEL\n", DataSourceType.PASTE);
229 SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
230 SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
231 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
232 SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
233 // need to be distinct
234 AlignedCodonFrame acf1 = new AlignedCodonFrame();
235 acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
236 new int[] { 1, 12 }, 1, 3));
237 AlignedCodonFrame acf2 = new AlignedCodonFrame();
238 acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
239 new int[] { 1, 12 }, 1, 3));
240 AlignedCodonFrame acf3 = new AlignedCodonFrame();
241 acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
244 List<AlignedCodonFrame> mappings1 = new ArrayList<>();
247 af1.getViewport().getAlignment().setCodonFrames(mappings1);
249 List<AlignedCodonFrame> mappings2 = new ArrayList<>();
252 af2.getViewport().getAlignment().setCodonFrames(mappings2);
255 * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
258 List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
259 assertEquals(0, ssmMappings.size());
260 ssm.registerMapping(acf1);
261 assertEquals(1, ssmMappings.size());
262 ssm.registerMapping(acf2);
263 assertEquals(2, ssmMappings.size());
264 ssm.registerMapping(acf3);
265 assertEquals(3, ssmMappings.size());
268 * Closing AlignFrame2 should remove mapping acf3 from
269 * StructureSelectionManager, but not acf2, since AlignFrame1 still has a
272 af2.closeMenuItem_actionPerformed(true);
273 assertEquals(2, ssmMappings.size());
274 assertTrue(ssmMappings.contains(acf1));
275 assertTrue(ssmMappings.contains(acf2));
276 assertFalse(ssmMappings.contains(acf3));
280 * Test for JAL-1306 - conservation thread should run even when only Quality
281 * (and not Conservation) is enabled in Preferences
283 @Test(groups = { "Functional" }, timeOut=2000)
284 public void testUpdateConservation_qualityOnly()
286 Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
287 Boolean.TRUE.toString());
288 Cache.setPropertyNoSave("SHOW_QUALITY",
289 Boolean.TRUE.toString());
290 Cache.setPropertyNoSave("SHOW_CONSERVATION",
291 Boolean.FALSE.toString());
292 Cache.setPropertyNoSave("SHOW_OCCUPANCY",
293 Boolean.FALSE.toString());
294 Cache.setPropertyNoSave("SHOW_IDENTITY",
295 Boolean.FALSE.toString());
296 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
297 "examples/uniref50.fa", DataSourceType.FILE);
300 * wait for Conservation thread to complete
302 AlignViewport viewport = af.getViewport();
303 waitForCalculations(viewport);
304 AlignmentAnnotation[] anns = viewport.getAlignment()
305 .getAlignmentAnnotation();
306 assertNotNull("No annotations found", anns);
307 assertEquals("More than one annotation found", 1, anns.length);
308 assertTrue("Annotation is not Quality",
309 anns[0].description.startsWith("Alignment Quality"));
310 Annotation[] annotations = anns[0].annotations;
311 assertNotNull("Quality annotations are null", annotations);
312 assertNotNull("Quality in column 1 is null", annotations[0]);
313 assertTrue("No quality value in column 1", annotations[0].value > 10f);
317 * Wait for consensus etc calculation threads to complete
321 protected void waitForCalculations(AlignViewport viewport)
325 System.out.print("waiting...");
327 while (--n >= 0 || viewport.getCalcManager().isWorking())
331 System.out.print(((AlignCalcManager) viewport.getCalcManager()).getQueueLength());
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 AlignViewport 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 AlignViewport av = af.getViewport();
447 Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
449 for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
454 Assert.assertEquals(c, 0, "Expected zero occupancy rows.");
457 jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.TRUE.toString());
458 af = new FileLoader().LoadFileWaitTillLoaded(
459 "examples/uniref50.fa", DataSourceType.FILE);
460 av = af.getViewport();
461 Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
463 for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
464 null, av.getAlignmentGapAnnotation().label))
469 Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
472 @Test(groups = { "Functional" })
473 public void testGetConsensusSeq()
480 * consensus expected to be A-C
482 String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
483 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
484 DataSourceType.PASTE);
485 AlignViewport testme = af.getViewport();
486 waitForCalculations(testme);
487 SequenceI cons = testme.getConsensusSeq();
488 String s = cons.getSequenceAsString();
489 System.out.println("s is " + s);
491 assertEquals("A-C", s);
494 @Test(groups = { "Functional" })
495 public void testHideRevealSequences()
497 ViewportRanges ranges = testee.getRanges();
498 assertEquals(3, al.getHeight());
499 assertEquals(0, ranges.getStartSeq());
500 assertEquals(2, ranges.getEndSeq());
503 * hide first sequence
505 testee.hideSequence(new SequenceI[] { al.getSequenceAt(0) });
506 assertEquals(2, al.getHeight());
507 assertEquals(0, ranges.getStartSeq());
508 assertEquals(1, ranges.getEndSeq());
511 * reveal hidden sequences above the first
513 testee.showSequence(0);
514 assertEquals(3, al.getHeight());
515 assertEquals(0, ranges.getStartSeq());
516 assertEquals(2, ranges.getEndSeq());
519 * hide first and third sequences
521 testee.hideSequence(new SequenceI[] { al.getSequenceAt(0),
522 al.getSequenceAt(2) });
523 assertEquals(1, al.getHeight());
524 assertEquals(0, ranges.getStartSeq());
525 assertEquals(0, ranges.getEndSeq());
528 * reveal all hidden sequences
530 testee.showAllHiddenSeqs();
531 assertEquals(3, al.getHeight());
532 assertEquals(0, ranges.getStartSeq());
533 assertEquals(2, ranges.getEndSeq());