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  1. Project Clover database Tue Nov 18 2025 10:51:49 GMT
  2. Package jalview.gui

File AlignViewportTest.java

 

Code metrics

2
237
15
1
579
404
17
0.07
15.8
15
1.13

Classes

Class Line # Actions
AlignViewportTest 61 237 17
0.99212699.2%
 

Contributing tests

This file is covered by 11 tests. .

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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.ContactMatrixI;
46    import jalview.datamodel.SearchResults;
47    import jalview.datamodel.SearchResultsI;
48    import jalview.datamodel.SeqDistanceContactMatrix;
49    import jalview.datamodel.Sequence;
50    import jalview.datamodel.SequenceGroup;
51    import jalview.datamodel.SequenceI;
52    import jalview.io.DataSourceType;
53    import jalview.io.FileLoader;
54    import jalview.schemes.ClustalxColourScheme;
55    import jalview.schemes.ColourSchemeI;
56    import jalview.schemes.PIDColourScheme;
57    import jalview.structure.StructureSelectionManager;
58    import jalview.util.MapList;
59    import jalview.viewmodel.ViewportRanges;
60   
 
61    public class AlignViewportTest
62    {
63   
 
64  1 toggle @BeforeClass(alwaysRun = true)
65    public void setUpJvOptionPane()
66    {
67  1 JvOptionPane.setInteractiveMode(false);
68  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
69    }
70   
71    AlignmentI al;
72   
73    AlignViewport testee;
74   
 
75  1 toggle @BeforeClass(alwaysRun = true)
76    public static void setUpBeforeClass() throws Exception
77    {
78  1 Jalview.main(
79    new String[]
80    { "--nonews", "--props", "test/jalview/testProps.jvprops" });
81   
82    /*
83    * remove any sequence mappings left lying around by other tests
84    */
85  1 StructureSelectionManager ssm = StructureSelectionManager
86    .getStructureSelectionManager(Desktop.instance);
87  1 ssm.resetAll();
88    }
89   
 
90  11 toggle @BeforeMethod(alwaysRun = true)
91    public void setUp()
92    {
93  11 SequenceI seq1 = new Sequence("Seq1", "ABC");
94  11 SequenceI seq2 = new Sequence("Seq2", "ABC");
95  11 SequenceI seq3 = new Sequence("Seq3", "ABC");
96  11 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
97  11 al = new Alignment(seqs);
98  11 al.setDataset(null);
99  11 testee = new AlignViewport(al);
100    }
101   
102    /**
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
105    */
 
106  1 toggle @Test(groups = { "Functional" })
107    public void testDeregisterMapping_onCloseView()
108    {
109    /*
110    * alignment with reference to mappings
111    */
112  1 AlignFrame af1 = new FileLoader()
113    .LoadFileWaitTillLoaded(">Seq1\nCAGT\n", DataSourceType.PASTE);
114   
115  1 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
116  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
117  1 acf1.addMap(s1, s1,
118    new MapList(new int[]
119    { 1, 4 }, new int[] { 1, 4 }, 1, 1));
120  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
121  1 acf2.addMap(s1, s1,
122    new MapList(new int[]
123    { 1, 4 }, new int[] { 4, 1 }, 1, 1));
124   
125  1 List<AlignedCodonFrame> mappings = new ArrayList<>();
126  1 mappings.add(acf1);
127  1 mappings.add(acf2);
128  1 af1.getViewport().getAlignment().setCodonFrames(mappings);
129  1 af1.newView_actionPerformed(null);
130   
131    /*
132    * Verify that creating the alignment for the new View has registered the
133    * mappings
134    */
135  1 StructureSelectionManager ssm = StructureSelectionManager
136    .getStructureSelectionManager(Desktop.instance);
137  1 List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
138  1 assertEquals(2, sequenceMappings.size());
139  1 assertTrue(sequenceMappings.contains(acf1));
140  1 assertTrue(sequenceMappings.contains(acf2));
141   
142    /*
143    * Close the second view. Verify that mappings are not removed as the first
144    * view still holds a reference to them.
145    */
146  1 af1.closeMenuItem_actionPerformed(false);
147  1 assertEquals(2, sequenceMappings.size());
148  1 assertTrue(sequenceMappings.contains(acf1));
149  1 assertTrue(sequenceMappings.contains(acf2));
150    }
151   
152    /**
153    * Test that a mapping is deregistered if no alignment holds a reference to it
154    */
 
155  1 toggle @Test(groups = { "Functional" })
156    public void testDeregisterMapping_withNoReference()
157    {
158  1 Desktop d = Desktop.instance;
159  1 assertNotNull(d);
160  1 StructureSelectionManager ssm = StructureSelectionManager
161    .getStructureSelectionManager(Desktop.instance);
162  1 ssm.resetAll();
163   
164  1 AlignFrame af1 = new FileLoader()
165    .LoadFileWaitTillLoaded(">Seq1\nRSVQ\n", DataSourceType.PASTE);
166  1 AlignFrame af2 = new FileLoader()
167    .LoadFileWaitTillLoaded(">Seq2\nDGEL\n", DataSourceType.PASTE);
168  1 SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
169  1 SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
170  1 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
171  1 SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
172    // need to be distinct
173  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
174  1 acf1.addMap(cs1, s1,
175    new MapList(new int[]
176    { 1, 4 }, new int[] { 1, 12 }, 1, 3));
177  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
178  1 acf2.addMap(cs2, s2,
179    new MapList(new int[]
180    { 1, 4 }, new int[] { 1, 12 }, 1, 3));
181  1 AlignedCodonFrame acf3 = new AlignedCodonFrame();
182  1 acf3.addMap(cs2, cs2,
183    new MapList(new int[]
184    { 1, 12 }, new int[] { 1, 12 }, 1, 1));
185   
186  1 List<AlignedCodonFrame> mappings1 = new ArrayList<>();
187  1 mappings1.add(acf1);
188  1 af1.getViewport().getAlignment().setCodonFrames(mappings1);
189   
190  1 List<AlignedCodonFrame> mappings2 = new ArrayList<>();
191  1 mappings2.add(acf2);
192  1 mappings2.add(acf3);
193  1 af2.getViewport().getAlignment().setCodonFrames(mappings2);
194   
195    /*
196    * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
197    */
198   
199  1 List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
200  1 assertEquals(0, ssmMappings.size());
201  1 ssm.registerMapping(acf1);
202  1 assertEquals(1, ssmMappings.size());
203  1 ssm.registerMapping(acf2);
204  1 assertEquals(2, ssmMappings.size());
205  1 ssm.registerMapping(acf3);
206  1 assertEquals(3, ssmMappings.size());
207   
208    /*
209    * Closing AlignFrame2 should remove its mappings from
210    * StructureSelectionManager, since AlignFrame1 has no reference to them
211    */
212  1 af2.closeMenuItem_actionPerformed(true);
213  1 assertEquals(1, ssmMappings.size());
214  1 assertTrue(ssmMappings.contains(acf1));
215    }
216   
217    /**
218    * Test that a mapping is not deregistered if another alignment holds a
219    * reference to it
220    */
 
221  1 toggle @Test(groups = { "Functional" })
222    public void testDeregisterMapping_withReference()
223    {
224  1 Desktop d = Desktop.instance;
225  1 assertNotNull(d);
226  1 StructureSelectionManager ssm = StructureSelectionManager
227    .getStructureSelectionManager(Desktop.instance);
228  1 ssm.resetAll();
229   
230  1 AlignFrame af1 = new FileLoader()
231    .LoadFileWaitTillLoaded(">Seq1\nRSVQ\n", DataSourceType.PASTE);
232  1 AlignFrame af2 = new FileLoader()
233    .LoadFileWaitTillLoaded(">Seq2\nDGEL\n", DataSourceType.PASTE);
234  1 SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
235  1 SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
236  1 SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
237  1 SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
238    // need to be distinct
239  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
240  1 acf1.addMap(cs1, s1,
241    new MapList(new int[]
242    { 1, 4 }, new int[] { 1, 12 }, 1, 3));
243  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
244  1 acf2.addMap(cs2, s2,
245    new MapList(new int[]
246    { 1, 4 }, new int[] { 1, 12 }, 1, 3));
247  1 AlignedCodonFrame acf3 = new AlignedCodonFrame();
248  1 acf3.addMap(cs2, cs2,
249    new MapList(new int[]
250    { 1, 12 }, new int[] { 1, 12 }, 1, 1));
251   
252  1 List<AlignedCodonFrame> mappings1 = new ArrayList<>();
253  1 mappings1.add(acf1);
254  1 mappings1.add(acf2);
255  1 af1.getViewport().getAlignment().setCodonFrames(mappings1);
256   
257  1 List<AlignedCodonFrame> mappings2 = new ArrayList<>();
258  1 mappings2.add(acf2);
259  1 mappings2.add(acf3);
260  1 af2.getViewport().getAlignment().setCodonFrames(mappings2);
261   
262    /*
263    * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
264    */
265   
266  1 List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
267  1 assertEquals(0, ssmMappings.size());
268  1 ssm.registerMapping(acf1);
269  1 assertEquals(1, ssmMappings.size());
270  1 ssm.registerMapping(acf2);
271  1 assertEquals(2, ssmMappings.size());
272  1 ssm.registerMapping(acf3);
273  1 assertEquals(3, ssmMappings.size());
274   
275    /*
276    * Closing AlignFrame2 should remove mapping acf3 from
277    * StructureSelectionManager, but not acf2, since AlignFrame1 still has a
278    * reference to it
279    */
280  1 af2.closeMenuItem_actionPerformed(true);
281  1 assertEquals(2, ssmMappings.size());
282  1 assertTrue(ssmMappings.contains(acf1));
283  1 assertTrue(ssmMappings.contains(acf2));
284  1 assertFalse(ssmMappings.contains(acf3));
285    }
286   
287    /**
288    * Test for JAL-1306 - conservation thread should run even when only Quality
289    * (and not Conservation) is enabled in Preferences
290    */
 
291  1 toggle @Test(groups = { "Functional" }, timeOut = 2000)
292    public void testUpdateConservation_qualityOnly()
293    {
294  1 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
295    Boolean.TRUE.toString());
296  1 Cache.applicationProperties.setProperty("SHOW_QUALITY",
297    Boolean.TRUE.toString());
298  1 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
299    Boolean.FALSE.toString());
300  1 Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
301    Boolean.FALSE.toString());
302  1 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
303    Boolean.FALSE.toString());
304  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
305    "examples/uniref50.fa", DataSourceType.FILE);
306   
307    /*
308    * wait for Conservation thread to complete
309    */
310  1 AlignViewport viewport = af.getViewport();
311  1 waitForCalculations(viewport);
312  1 AlignmentAnnotation[] anns = viewport.getAlignment()
313    .getAlignmentAnnotation();
314  1 assertNotNull("No annotations found", anns);
315  1 assertEquals("More than one annotation found", 1, anns.length);
316  1 assertTrue("Annotation is not Quality",
317    anns[0].description.startsWith("Alignment Quality"));
318  1 Annotation[] annotations = anns[0].annotations;
319  1 assertNotNull("Quality annotations are null", annotations);
320  1 assertNotNull("Quality in column 1 is null", annotations[0]);
321  1 assertTrue("No quality value in column 1", annotations[0].value > 10f);
322    }
323   
324    /**
325    * Wait for consensus etc calculation threads to complete
326    *
327    * @param viewport
328    */
 
329  2 toggle protected void waitForCalculations(AlignViewport viewport)
330    {
331  2 synchronized (this)
332    {
333  2 do
334    {
335  2 try
336    {
337  2 wait(50);
338    } catch (InterruptedException e)
339    {
340    }
341  2 } while (viewport.getCalcManager().isWorking());
342    }
343    }
344   
 
345  1 toggle @Test(groups = { "Functional" })
346    public void testSetGlobalColourScheme()
347    {
348    /*
349    * test for JAL-2283: don't inadvertently turn on colour by conservation
350    */
351  1 Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
352  1 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
353    Boolean.TRUE.toString());
354  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
355    "examples/uniref50.fa", DataSourceType.FILE);
356  1 ColourSchemeI cs = new PIDColourScheme();
357  1 AlignViewport viewport = af.getViewport();
358  1 viewport.setGlobalColourScheme(cs);
359  1 assertFalse(viewport.getResidueShading().conservationApplied());
360   
361    /*
362    * JAL-3201 groups have their own ColourSchemeI instances
363    */
364  1 AlignmentI aln = viewport.getAlignment();
365  1 SequenceGroup sg1 = new SequenceGroup();
366  1 sg1.addSequence(aln.getSequenceAt(0), false);
367  1 sg1.addSequence(aln.getSequenceAt(2), false);
368  1 SequenceGroup sg2 = new SequenceGroup();
369  1 sg2.addSequence(aln.getSequenceAt(1), false);
370  1 sg2.addSequence(aln.getSequenceAt(3), false);
371  1 aln.addGroup(sg1);
372  1 aln.addGroup(sg2);
373  1 viewport.setColourAppliesToAllGroups(true);
374  1 viewport.setGlobalColourScheme(new ClustalxColourScheme());
375  1 ColourSchemeI cs0 = viewport.getGlobalColourScheme();
376  1 ColourSchemeI cs1 = sg1.getColourScheme();
377  1 ColourSchemeI cs2 = sg2.getColourScheme();
378  1 assertTrue(cs0 instanceof ClustalxColourScheme);
379  1 assertTrue(cs1 instanceof ClustalxColourScheme);
380  1 assertTrue(cs2 instanceof ClustalxColourScheme);
381  1 assertNotSame(cs0, cs1);
382  1 assertNotSame(cs0, cs2);
383  1 assertNotSame(cs1, cs2);
384    }
385   
 
386  1 toggle @Test(groups = { "Functional" })
387    public void testSetGetHasSearchResults()
388    {
389  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
390    "examples/uniref50.fa", DataSourceType.FILE);
391  1 SearchResultsI sr = new SearchResults();
392  1 SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);
393   
394    // create arbitrary range on first sequence
395  1 sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15);
396   
397    // test set
398  1 af.getViewport().setSearchResults(sr);
399    // has -> true
400  1 assertTrue(af.getViewport().hasSearchResults());
401    // get == original
402  1 assertEquals(sr, af.getViewport().getSearchResults());
403   
404    // set(null) results in has -> false
405   
406  1 af.getViewport().setSearchResults(null);
407  1 assertFalse(af.getViewport().hasSearchResults());
408    }
409   
410    /**
411    * Verify that setting the selection group has the side-effect of setting the
412    * context on the group, unless it already has one, but does not change
413    * whether the group is defined or not.
414    */
 
415  1 toggle @Test(groups = { "Functional" })
416    public void testSetSelectionGroup()
417    {
418  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
419    "examples/uniref50.fa", DataSourceType.FILE);
420  1 AlignViewport av = af.getViewport();
421  1 SequenceGroup sg1 = new SequenceGroup();
422  1 SequenceGroup sg2 = new SequenceGroup();
423  1 SequenceGroup sg3 = new SequenceGroup();
424   
425  1 av.setSelectionGroup(sg1);
426  1 assertSame(sg1.getContext(), av.getAlignment()); // context set
427  1 assertFalse(sg1.isDefined()); // group not defined
428   
429  1 sg2.setContext(sg1, false);
430  1 av.setSelectionGroup(sg2);
431  1 assertFalse(sg2.isDefined()); // unchanged
432  1 assertSame(sg2.getContext(), sg1); // unchanged
433   
434    // create a defined group
435  1 sg3.setContext(av.getAlignment(), true);
436  1 av.setSelectionGroup(sg3);
437  1 assertTrue(sg3.isDefined()); // unchanged
438    }
439   
440    /**
441    * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits
442    * occupancy row from viewport
443    */
 
444  1 toggle @Test(groups = { "Functional" })
445    public void testShowOrDontShowOccupancy()
446    {
447    // disable occupancy
448  1 jalview.bin.Cache.setProperty("SHOW_OCCUPANCY",
449    Boolean.FALSE.toString());
450  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
451    "examples/uniref50.fa", DataSourceType.FILE);
452  1 AlignViewport av = af.getViewport();
453  1 Assert.assertNull(av.getAlignmentGapAnnotation(),
454    "Preference did not disable occupancy row.");
455  1 int c = 0;
456  1 for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
457    null, "Occupancy"))
458    {
459  0 c++;
460    }
461  1 Assert.assertEquals(c, 0, "Expected zero occupancy rows.");
462   
463    // enable occupancy
464  1 jalview.bin.Cache.setProperty("SHOW_OCCUPANCY",
465    Boolean.TRUE.toString());
466  1 af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
467    DataSourceType.FILE);
468  1 av = af.getViewport();
469  1 Assert.assertNotNull(av.getAlignmentGapAnnotation(),
470    "Preference did not enable occupancy row.");
471  1 c = 0;
472  1 for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
473    null, av.getAlignmentGapAnnotation().label))
474    {
475  1 c++;
476  1 Assert.assertNotNull(aa.annotations);
477    // check that an arbitrary column has an occupancy of greater than zero
478  1 Assert.assertNotNull(aa.annotations[5],
479    "Expected occupancy to be non-null in column 5");
480  1 Assert.assertNotEquals(aa.annotations[5].value, 0f,
481    "Expected occupancy to not be zero in column 5");
482   
483    }
484  1 ;
485  1 Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
486    }
487   
 
488  1 toggle @Test(groups = { "Functional" })
489    public void testGetConsensusSeq()
490    {
491    /*
492    * A-C
493    * A-C
494    * A-D
495    * --D
496    * consensus expected to be A-C
497    */
498  1 String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
499  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
500    DataSourceType.PASTE);
501  1 AlignViewport testme = af.getViewport();
502  1 waitForCalculations(testme);
503  1 SequenceI cons = testme.getConsensusSeq();
504  1 assertEquals("A-C", cons.getSequenceAsString());
505    }
506   
 
507  1 toggle @Test(groups = { "Functional" })
508    public void testHideRevealSequences()
509    {
510  1 ViewportRanges ranges = testee.getRanges();
511  1 assertEquals(3, al.getHeight());
512  1 assertEquals(0, ranges.getStartSeq());
513  1 assertEquals(2, ranges.getEndSeq());
514   
515    /*
516    * hide first sequence
517    */
518  1 testee.hideSequence(new SequenceI[] { al.getSequenceAt(0) });
519  1 assertEquals(2, al.getHeight());
520  1 assertEquals(0, ranges.getStartSeq());
521  1 assertEquals(1, ranges.getEndSeq());
522   
523    /*
524    * reveal hidden sequences above the first
525    */
526  1 testee.showSequence(0);
527  1 assertEquals(3, al.getHeight());
528  1 assertEquals(0, ranges.getStartSeq());
529  1 assertEquals(2, ranges.getEndSeq());
530   
531    /*
532    * hide first and third sequences
533    */
534  1 testee.hideSequence(
535    new SequenceI[]
536    { al.getSequenceAt(0), al.getSequenceAt(2) });
537  1 assertEquals(1, al.getHeight());
538  1 assertEquals(0, ranges.getStartSeq());
539  1 assertEquals(0, ranges.getEndSeq());
540   
541    /*
542    * reveal all hidden sequences
543    */
544  1 testee.showAllHiddenSeqs();
545  1 assertEquals(3, al.getHeight());
546  1 assertEquals(0, ranges.getStartSeq());
547  1 assertEquals(2, ranges.getEndSeq());
548    }
549   
 
550  1 toggle @Test(groups = { "Functional" })
551    public void testGetSelectionAsNewSequences_withContactMatrices()
552    {
553  1 SequenceI seq = new Sequence("seq", "ACADA");
554  1 ContactMatrixI cmat = new SeqDistanceContactMatrix(5);
555  1 seq.addContactList(cmat);
556  1 Alignment al = new Alignment(new SequenceI[] { seq.deriveSequence() });
557  1 al.addAnnotation(al.getSequenceAt(0).getAnnotation()[0]);
558  1 AlignFrame af = new AlignFrame(al, 500, 500);
559   
560  1 SequenceI selseqs[] = af.getViewport().getSelectionAsNewSequence();
561  1 assertNotNull(selseqs[0].getAnnotation());
562  1 assertNotNull(selseqs[0].getAnnotation()[0]);
563  1 assertEquals(cmat,
564    selseqs[0].getContactMatrixFor(selseqs[0].getAnnotation()[0]));
565   
566  1 assertNotNull(
567    selseqs[0].getContactListFor(selseqs[0].getAnnotation()[0], 2));
568   
569    // now select everything and test again
570  1 af.selectAllSequenceMenuItem_actionPerformed(null);
571  1 selseqs = af.getViewport().getSelectionAsNewSequence();
572  1 assertNotNull(selseqs[0].getAnnotation());
573  1 assertNotNull(selseqs[0].getAnnotation()[0]);
574  1 assertEquals(cmat,
575    selseqs[0].getContactMatrixFor(selseqs[0].getAnnotation()[0]));
576  1 assertNotNull(
577    selseqs[0].getContactListFor(selseqs[0].getAnnotation()[0], 2));
578    }
579    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 18 2025 11:02:12 GMT using coverage data from Tue Nov 18 2025 11:01:58 GMT.
  • OpenClover is free and open-source software.