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  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.gui

File AlignViewportTest.java

 

Code metrics

2
217
14
1
525
359
16
0.07
15.5
14
1.14

Classes

Class Line # Actions
AlignViewportTest 59 217 16
0.982832698.3%
 

Contributing tests

This file is covered by 10 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.gui;
22   
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;
29   
30    import java.util.ArrayList;
31    import java.util.List;
32   
33    import org.testng.Assert;
34    import org.testng.annotations.BeforeClass;
35    import org.testng.annotations.BeforeMethod;
36    import org.testng.annotations.Test;
37   
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   
 
59    public class AlignViewportTest
60    {
61   
 
62  1 toggle @BeforeClass(alwaysRun = true)
63    public void setUpJvOptionPane()
64    {
65  1 JvOptionPane.setInteractiveMode(false);
66  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
67    }
68   
69    AlignmentI al;
70   
71    AlignViewport testee;
72   
 
73  1 toggle @BeforeClass(alwaysRun = true)
74    public static void setUpBeforeClass() throws Exception
75    {
76  1 Jalview.main(new String[] { "-nonews", "-props",
77    "test/jalview/testProps.jvprops" });
78   
79    /*
80    * remove any sequence mappings left lying around by other tests
81    */
82  1 StructureSelectionManager ssm = StructureSelectionManager
83    .getStructureSelectionManager(Desktop.instance);
84  1 ssm.resetAll();
85    }
86   
 
87  10 toggle @BeforeMethod(alwaysRun = true)
88    public void setUp()
89    {
90  10 SequenceI seq1 = new Sequence("Seq1", "ABC");
91  10 SequenceI seq2 = new Sequence("Seq2", "ABC");
92  10 SequenceI seq3 = new Sequence("Seq3", "ABC");
93  10 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
94  10 al = new Alignment(seqs);
95  10 al.setDataset(null);
96  10 testee = new AlignViewport(al);
97    }
98   
99    /**
100    * Test that a mapping is not deregistered when a second view is closed but
101    * the first still holds a reference to the mapping
102    */
 
103  1 toggle @Test(groups = { "Functional" })
104    public void testDeregisterMapping_onCloseView()
105    {
106    /*
107    * alignment with reference to mappings
108    */
109  1 AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
110    ">Seq1\nCAGT\n", DataSourceType.PASTE);
111   
112  1 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
113  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
114  1 acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 },
115    1, 1));
116  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
117  1 acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
118    1, 1));
119   
120  1 List<AlignedCodonFrame> mappings = new ArrayList<>();
121  1 mappings.add(acf1);
122  1 mappings.add(acf2);
123  1 af1.getViewport().getAlignment().setCodonFrames(mappings);
124  1 af1.newView_actionPerformed(null);
125   
126    /*
127    * Verify that creating the alignment for the new View has registered the
128    * mappings
129    */
130  1 StructureSelectionManager ssm = StructureSelectionManager
131    .getStructureSelectionManager(Desktop.instance);
132  1 List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
133  1 assertEquals(2, sequenceMappings.size());
134  1 assertTrue(sequenceMappings.contains(acf1));
135  1 assertTrue(sequenceMappings.contains(acf2));
136   
137    /*
138    * Close the second view. Verify that mappings are not removed as the first
139    * view still holds a reference to them.
140    */
141  1 af1.closeMenuItem_actionPerformed(false);
142  1 assertEquals(2, sequenceMappings.size());
143  1 assertTrue(sequenceMappings.contains(acf1));
144  1 assertTrue(sequenceMappings.contains(acf2));
145    }
146   
147    /**
148    * Test that a mapping is deregistered if no alignment holds a reference to it
149    */
 
150  1 toggle @Test(groups = { "Functional" })
151    public void testDeregisterMapping_withNoReference()
152    {
153  1 Desktop d = Desktop.instance;
154  1 assertNotNull(d);
155  1 StructureSelectionManager ssm = StructureSelectionManager
156    .getStructureSelectionManager(Desktop.instance);
157  1 ssm.resetAll();
158   
159  1 AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
160    ">Seq1\nRSVQ\n", DataSourceType.PASTE);
161  1 AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
162    ">Seq2\nDGEL\n", DataSourceType.PASTE);
163  1 SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
164  1 SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
165  1 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
166  1 SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
167    // need to be distinct
168  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
169  1 acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
170    new int[] { 1, 12 }, 1, 3));
171  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
172  1 acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
173    new int[] { 1, 12 }, 1, 3));
174  1 AlignedCodonFrame acf3 = new AlignedCodonFrame();
175  1 acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
176    12 }, 1, 1));
177   
178  1 List<AlignedCodonFrame> mappings1 = new ArrayList<>();
179  1 mappings1.add(acf1);
180  1 af1.getViewport().getAlignment().setCodonFrames(mappings1);
181   
182  1 List<AlignedCodonFrame> mappings2 = new ArrayList<>();
183  1 mappings2.add(acf2);
184  1 mappings2.add(acf3);
185  1 af2.getViewport().getAlignment().setCodonFrames(mappings2);
186   
187    /*
188    * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
189    */
190   
191  1 List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
192  1 assertEquals(0, ssmMappings.size());
193  1 ssm.registerMapping(acf1);
194  1 assertEquals(1, ssmMappings.size());
195  1 ssm.registerMapping(acf2);
196  1 assertEquals(2, ssmMappings.size());
197  1 ssm.registerMapping(acf3);
198  1 assertEquals(3, ssmMappings.size());
199   
200    /*
201    * Closing AlignFrame2 should remove its mappings from
202    * StructureSelectionManager, since AlignFrame1 has no reference to them
203    */
204  1 af2.closeMenuItem_actionPerformed(true);
205  1 assertEquals(1, ssmMappings.size());
206  1 assertTrue(ssmMappings.contains(acf1));
207    }
208   
209    /**
210    * Test that a mapping is not deregistered if another alignment holds a
211    * reference to it
212    */
 
213  1 toggle @Test(groups = { "Functional" })
214    public void testDeregisterMapping_withReference()
215    {
216  1 Desktop d = Desktop.instance;
217  1 assertNotNull(d);
218  1 StructureSelectionManager ssm = StructureSelectionManager
219    .getStructureSelectionManager(Desktop.instance);
220  1 ssm.resetAll();
221   
222  1 AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
223    ">Seq1\nRSVQ\n", DataSourceType.PASTE);
224  1 AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
225    ">Seq2\nDGEL\n", DataSourceType.PASTE);
226  1 SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
227  1 SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
228  1 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
229  1 SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
230    // need to be distinct
231  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
232  1 acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
233    new int[] { 1, 12 }, 1, 3));
234  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
235  1 acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
236    new int[] { 1, 12 }, 1, 3));
237  1 AlignedCodonFrame acf3 = new AlignedCodonFrame();
238  1 acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
239    12 }, 1, 1));
240   
241  1 List<AlignedCodonFrame> mappings1 = new ArrayList<>();
242  1 mappings1.add(acf1);
243  1 mappings1.add(acf2);
244  1 af1.getViewport().getAlignment().setCodonFrames(mappings1);
245   
246  1 List<AlignedCodonFrame> mappings2 = new ArrayList<>();
247  1 mappings2.add(acf2);
248  1 mappings2.add(acf3);
249  1 af2.getViewport().getAlignment().setCodonFrames(mappings2);
250   
251    /*
252    * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
253    */
254   
255  1 List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
256  1 assertEquals(0, ssmMappings.size());
257  1 ssm.registerMapping(acf1);
258  1 assertEquals(1, ssmMappings.size());
259  1 ssm.registerMapping(acf2);
260  1 assertEquals(2, ssmMappings.size());
261  1 ssm.registerMapping(acf3);
262  1 assertEquals(3, ssmMappings.size());
263   
264    /*
265    * Closing AlignFrame2 should remove mapping acf3 from
266    * StructureSelectionManager, but not acf2, since AlignFrame1 still has a
267    * reference to it
268    */
269  1 af2.closeMenuItem_actionPerformed(true);
270  1 assertEquals(2, ssmMappings.size());
271  1 assertTrue(ssmMappings.contains(acf1));
272  1 assertTrue(ssmMappings.contains(acf2));
273  1 assertFalse(ssmMappings.contains(acf3));
274    }
275   
276    /**
277    * Test for JAL-1306 - conservation thread should run even when only Quality
278    * (and not Conservation) is enabled in Preferences
279    */
 
280  1 toggle @Test(groups = { "Functional" }, timeOut=2000)
281    public void testUpdateConservation_qualityOnly()
282    {
283  1 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
284    Boolean.TRUE.toString());
285  1 Cache.applicationProperties.setProperty("SHOW_QUALITY",
286    Boolean.TRUE.toString());
287  1 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
288    Boolean.FALSE.toString());
289  1 Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
290    Boolean.FALSE.toString());
291  1 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
292    Boolean.FALSE.toString());
293  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
294    "examples/uniref50.fa", DataSourceType.FILE);
295   
296    /*
297    * wait for Conservation thread to complete
298    */
299  1 AlignViewport viewport = af.getViewport();
300  1 waitForCalculations(viewport);
301  1 AlignmentAnnotation[] anns = viewport.getAlignment()
302    .getAlignmentAnnotation();
303  1 assertNotNull("No annotations found", anns);
304  1 assertEquals("More than one annotation found", 1, anns.length);
305  1 assertTrue("Annotation is not Quality",
306    anns[0].description.startsWith("Alignment Quality"));
307  1 Annotation[] annotations = anns[0].annotations;
308  1 assertNotNull("Quality annotations are null", annotations);
309  1 assertNotNull("Quality in column 1 is null", annotations[0]);
310  1 assertTrue("No quality value in column 1", annotations[0].value > 10f);
311    }
312   
313    /**
314    * Wait for consensus etc calculation threads to complete
315    *
316    * @param viewport
317    */
 
318  2 toggle protected void waitForCalculations(AlignViewport viewport)
319    {
320  2 synchronized (this)
321    {
322  2 while (viewport.getCalcManager().isWorking())
323    {
324  0 try
325    {
326  0 wait(50);
327    } catch (InterruptedException e)
328    {
329    }
330    }
331    }
332    }
333   
 
334  1 toggle @Test(groups = { "Functional" })
335    public void testSetGlobalColourScheme()
336    {
337    /*
338    * test for JAL-2283: don't inadvertently turn on colour by conservation
339    */
340  1 Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
341  1 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
342    Boolean.TRUE.toString());
343  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
344    "examples/uniref50.fa", DataSourceType.FILE);
345  1 ColourSchemeI cs = new PIDColourScheme();
346  1 AlignViewport viewport = af.getViewport();
347  1 viewport.setGlobalColourScheme(cs);
348  1 assertFalse(viewport.getResidueShading()
349    .conservationApplied());
350   
351    /*
352    * JAL-3201 groups have their own ColourSchemeI instances
353    */
354  1 AlignmentI aln = viewport.getAlignment();
355  1 SequenceGroup sg1 = new SequenceGroup();
356  1 sg1.addSequence(aln.getSequenceAt(0), false);
357  1 sg1.addSequence(aln.getSequenceAt(2), false);
358  1 SequenceGroup sg2 = new SequenceGroup();
359  1 sg2.addSequence(aln.getSequenceAt(1), false);
360  1 sg2.addSequence(aln.getSequenceAt(3), false);
361  1 aln.addGroup(sg1);
362  1 aln.addGroup(sg2);
363  1 viewport.setColourAppliesToAllGroups(true);
364  1 viewport.setGlobalColourScheme(new ClustalxColourScheme());
365  1 ColourSchemeI cs0 = viewport.getGlobalColourScheme();
366  1 ColourSchemeI cs1 = sg1.getColourScheme();
367  1 ColourSchemeI cs2 = sg2.getColourScheme();
368  1 assertTrue(cs0 instanceof ClustalxColourScheme);
369  1 assertTrue(cs1 instanceof ClustalxColourScheme);
370  1 assertTrue(cs2 instanceof ClustalxColourScheme);
371  1 assertNotSame(cs0, cs1);
372  1 assertNotSame(cs0, cs2);
373  1 assertNotSame(cs1, cs2);
374    }
375   
 
376  1 toggle @Test(groups = { "Functional" })
377    public void testSetGetHasSearchResults()
378    {
379  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
380    "examples/uniref50.fa", DataSourceType.FILE);
381  1 SearchResultsI sr = new SearchResults();
382  1 SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);
383   
384    // create arbitrary range on first sequence
385  1 sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15);
386   
387    // test set
388  1 af.getViewport().setSearchResults(sr);
389    // has -> true
390  1 assertTrue(af.getViewport().hasSearchResults());
391    // get == original
392  1 assertEquals(sr, af.getViewport().getSearchResults());
393   
394    // set(null) results in has -> false
395   
396  1 af.getViewport().setSearchResults(null);
397  1 assertFalse(af.getViewport().hasSearchResults());
398    }
399   
400    /**
401    * Verify that setting the selection group has the side-effect of setting the
402    * context on the group, unless it already has one, but does not change
403    * whether the group is defined or not.
404    */
 
405  1 toggle @Test(groups = { "Functional" })
406    public void testSetSelectionGroup()
407    {
408  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
409    "examples/uniref50.fa", DataSourceType.FILE);
410  1 AlignViewport av = af.getViewport();
411  1 SequenceGroup sg1 = new SequenceGroup();
412  1 SequenceGroup sg2 = new SequenceGroup();
413  1 SequenceGroup sg3 = new SequenceGroup();
414   
415  1 av.setSelectionGroup(sg1);
416  1 assertSame(sg1.getContext(), av.getAlignment()); // context set
417  1 assertFalse(sg1.isDefined()); // group not defined
418   
419  1 sg2.setContext(sg1, false);
420  1 av.setSelectionGroup(sg2);
421  1 assertFalse(sg2.isDefined()); // unchanged
422  1 assertSame(sg2.getContext(), sg1); // unchanged
423   
424    // create a defined group
425  1 sg3.setContext(av.getAlignment(), true);
426  1 av.setSelectionGroup(sg3);
427  1 assertTrue(sg3.isDefined()); // unchanged
428    }
429    /**
430    * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits occupancy row from viewport
431    */
 
432  1 toggle @Test(groups = { "Functional" })
433    public void testShowOrDontShowOccupancy()
434    {
435    // disable occupancy
436  1 jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
437  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
438    "examples/uniref50.fa", DataSourceType.FILE);
439  1 AlignViewport av = af.getViewport();
440  1 Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
441  1 int c = 0;
442  1 for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
443    null, "Occupancy"))
444    {
445  0 c++;
446    }
447  1 Assert.assertEquals(c, 0, "Expected zero occupancy rows.");
448   
449    // enable occupancy
450  1 jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.TRUE.toString());
451  1 af = new FileLoader().LoadFileWaitTillLoaded(
452    "examples/uniref50.fa", DataSourceType.FILE);
453  1 av = af.getViewport();
454  1 Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
455  1 c = 0;
456  1 for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
457    null, av.getAlignmentGapAnnotation().label))
458    {
459  1 c++;
460    }
461  1 ;
462  1 Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
463    }
464   
 
465  1 toggle @Test(groups = { "Functional" })
466    public void testGetConsensusSeq()
467    {
468    /*
469    * A-C
470    * A-C
471    * A-D
472    * --D
473    * consensus expected to be A-C
474    */
475  1 String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
476  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
477    DataSourceType.PASTE);
478  1 AlignViewport testme = af.getViewport();
479  1 waitForCalculations(testme);
480  1 SequenceI cons = testme.getConsensusSeq();
481  1 assertEquals("A-C", cons.getSequenceAsString());
482    }
483   
 
484  1 toggle @Test(groups = { "Functional" })
485    public void testHideRevealSequences()
486    {
487  1 ViewportRanges ranges = testee.getRanges();
488  1 assertEquals(3, al.getHeight());
489  1 assertEquals(0, ranges.getStartSeq());
490  1 assertEquals(2, ranges.getEndSeq());
491   
492    /*
493    * hide first sequence
494    */
495  1 testee.hideSequence(new SequenceI[] { al.getSequenceAt(0) });
496  1 assertEquals(2, al.getHeight());
497  1 assertEquals(0, ranges.getStartSeq());
498  1 assertEquals(1, ranges.getEndSeq());
499   
500    /*
501    * reveal hidden sequences above the first
502    */
503  1 testee.showSequence(0);
504  1 assertEquals(3, al.getHeight());
505  1 assertEquals(0, ranges.getStartSeq());
506  1 assertEquals(2, ranges.getEndSeq());
507   
508    /*
509    * hide first and third sequences
510    */
511  1 testee.hideSequence(new SequenceI[] { al.getSequenceAt(0),
512    al.getSequenceAt(2) });
513  1 assertEquals(1, al.getHeight());
514  1 assertEquals(0, ranges.getStartSeq());
515  1 assertEquals(0, ranges.getEndSeq());
516   
517    /*
518    * reveal all hidden sequences
519    */
520  1 testee.showAllHiddenSeqs();
521  1 assertEquals(3, al.getHeight());
522  1 assertEquals(0, ranges.getStartSeq());
523  1 assertEquals(2, ranges.getEndSeq());
524    }
525    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.