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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.gui

File AlignViewportTest.java

 

Code metrics

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Classes

Class Line # Actions
AlignViewportTest 59 189 13 1
0.995049599.5%
 

Contributing tests

This file is covered by 10 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.assertSame;
27    import static org.testng.AssertJUnit.assertTrue;
28   
29    import jalview.bin.Cache;
30    import jalview.bin.Jalview;
31    import jalview.datamodel.AlignedCodonFrame;
32    import jalview.datamodel.Alignment;
33    import jalview.datamodel.AlignmentAnnotation;
34    import jalview.datamodel.AlignmentI;
35    import jalview.datamodel.Annotation;
36    import jalview.datamodel.PDBEntry;
37    import jalview.datamodel.PDBEntry.Type;
38    import jalview.datamodel.SearchResults;
39    import jalview.datamodel.SearchResultsI;
40    import jalview.datamodel.Sequence;
41    import jalview.datamodel.SequenceGroup;
42    import jalview.datamodel.SequenceI;
43    import jalview.io.DataSourceType;
44    import jalview.io.FileLoader;
45    import jalview.schemes.ColourSchemeI;
46    import jalview.schemes.PIDColourScheme;
47    import jalview.structure.StructureSelectionManager;
48    import jalview.util.MapList;
49    import jalview.viewmodel.ViewportRanges;
50   
51    import java.util.ArrayList;
52    import java.util.List;
53   
54    import org.testng.Assert;
55    import org.testng.annotations.BeforeClass;
56    import org.testng.annotations.BeforeMethod;
57    import org.testng.annotations.Test;
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" })
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  1 AlignmentAnnotation[] anns = af.viewport.getAlignment()
296    .getAlignmentAnnotation();
297  1 assertNotNull("No annotations found", anns);
298  1 assertEquals("More than one annotation found", 1, anns.length);
299  1 assertTrue("Annotation is not Quality",
300    anns[0].description.startsWith("Alignment Quality"));
301  1 Annotation[] annotations = anns[0].annotations;
302  1 assertNotNull("Quality annotations are null", annotations);
303  1 assertNotNull("Quality in column 1 is null", annotations[0]);
304  1 assertTrue("No quality value in column 1", annotations[0].value > 10f);
305    }
306   
 
307  1 toggle @Test(groups = { "Functional" })
308    public void testSetGlobalColourScheme()
309    {
310    /*
311    * test for JAL-2283: don't inadvertently turn on colour by conservation
312    */
313  1 Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
314  1 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
315    Boolean.TRUE.toString());
316  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
317    "examples/uniref50.fa", DataSourceType.FILE);
318  1 ColourSchemeI cs = new PIDColourScheme();
319  1 af.getViewport().setGlobalColourScheme(cs);
320  1 assertFalse(af.getViewport().getResidueShading()
321    .conservationApplied());
322    }
323   
 
324  1 toggle @Test(groups = { "Functional" })
325    public void testSetGetHasSearchResults()
326    {
327  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
328    "examples/uniref50.fa", DataSourceType.FILE);
329  1 SearchResultsI sr = new SearchResults();
330  1 SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);
331   
332    // create arbitrary range on first sequence
333  1 sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15);
334   
335    // test set
336  1 af.getViewport().setSearchResults(sr);
337    // has -> true
338  1 assertTrue(af.getViewport().hasSearchResults());
339    // get == original
340  1 assertEquals(sr, af.getViewport().getSearchResults());
341   
342    // set(null) results in has -> false
343   
344  1 af.getViewport().setSearchResults(null);
345  1 assertFalse(af.getViewport().hasSearchResults());
346    }
347   
348    /**
349    * Verify that setting the selection group has the side-effect of setting the
350    * context on the group, unless it already has one, but does not change
351    * whether the group is defined or not.
352    */
 
353  1 toggle @Test(groups = { "Functional" })
354    public void testSetSelectionGroup()
355    {
356  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
357    "examples/uniref50.fa", DataSourceType.FILE);
358  1 AlignViewport av = af.getViewport();
359  1 SequenceGroup sg1 = new SequenceGroup();
360  1 SequenceGroup sg2 = new SequenceGroup();
361  1 SequenceGroup sg3 = new SequenceGroup();
362   
363  1 av.setSelectionGroup(sg1);
364  1 assertSame(sg1.getContext(), av.getAlignment()); // context set
365  1 assertFalse(sg1.isDefined()); // group not defined
366   
367  1 sg2.setContext(sg1, false);
368  1 av.setSelectionGroup(sg2);
369  1 assertFalse(sg2.isDefined()); // unchanged
370  1 assertSame(sg2.getContext(), sg1); // unchanged
371   
372    // create a defined group
373  1 sg3.setContext(av.getAlignment(), true);
374  1 av.setSelectionGroup(sg3);
375  1 assertTrue(sg3.isDefined()); // unchanged
376    }
377    /**
378    * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits occupancy row from viewport
379    */
 
380  1 toggle @Test(groups = { "Functional" })
381    public void testShowOrDontShowOccupancy()
382    {
383    // disable occupancy
384  1 jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
385  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
386    "examples/uniref50.fa", DataSourceType.FILE);
387  1 AlignViewport av = af.getViewport();
388  1 Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
389  1 int c = 0;
390  1 for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
391    null, "Occupancy"))
392    {
393  0 c++;
394    }
395  1 Assert.assertEquals(c, 0, "Expected zero occupancy rows.");
396   
397    // enable occupancy
398  1 jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.TRUE.toString());
399  1 af = new FileLoader().LoadFileWaitTillLoaded(
400    "examples/uniref50.fa", DataSourceType.FILE);
401  1 av = af.getViewport();
402  1 Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
403  1 c = 0;
404  1 for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
405    null, av.getAlignmentGapAnnotation().label))
406    {
407  1 c++;
408    }
409  1 ;
410  1 Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
411    }
412   
 
413  1 toggle @Test(groups = { "Functional" })
414    public void testGetConsensusSeq()
415    {
416    /*
417    * A-C
418    * A-C
419    * A-D
420    * --D
421    * consensus expected to be A-C
422    */
423  1 String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
424  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
425    DataSourceType.PASTE);
426  1 AlignViewport testme = af.getViewport();
427  1 SequenceI cons = testme.getConsensusSeq();
428  1 assertEquals("A-C", cons.getSequenceAsString());
429    }
430   
 
431  1 toggle @Test(groups = { "Functional" })
432    public void testHideRevealSequences()
433    {
434  1 ViewportRanges ranges = testee.getRanges();
435  1 assertEquals(3, al.getHeight());
436  1 assertEquals(0, ranges.getStartSeq());
437  1 assertEquals(2, ranges.getEndSeq());
438   
439    /*
440    * hide first sequence
441    */
442  1 testee.hideSequence(new SequenceI[] { al.getSequenceAt(0) });
443  1 assertEquals(2, al.getHeight());
444  1 assertEquals(0, ranges.getStartSeq());
445  1 assertEquals(1, ranges.getEndSeq());
446   
447    /*
448    * reveal hidden sequences above the first
449    */
450  1 testee.showSequence(0);
451  1 assertEquals(3, al.getHeight());
452  1 assertEquals(0, ranges.getStartSeq());
453  1 assertEquals(2, ranges.getEndSeq());
454   
455    /*
456    * hide first and third sequences
457    */
458  1 testee.hideSequence(new SequenceI[] { al.getSequenceAt(0),
459    al.getSequenceAt(2) });
460  1 assertEquals(1, al.getHeight());
461  1 assertEquals(0, ranges.getStartSeq());
462  1 assertEquals(0, ranges.getEndSeq());
463   
464    /*
465    * reveal all hidden sequences
466    */
467  1 testee.showAllHiddenSeqs();
468  1 assertEquals(3, al.getHeight());
469  1 assertEquals(0, ranges.getStartSeq());
470  1 assertEquals(2, ranges.getEndSeq());
471    }
472    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.