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

File Jalview2xmlTests.java

 

Code metrics

40
560
23
1
1,273
967
54
0.1
24.35
23
2.35

Classes

Class Line # Actions
Jalview2xmlTests 95 560 54
0.9711075497.1%
 

Contributing tests

This file is covered by 18 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.project;
22   
23    import static org.testng.Assert.assertEquals;
24    import static org.testng.Assert.assertFalse;
25    import static org.testng.Assert.assertNotNull;
26    import static org.testng.Assert.assertNull;
27    import static org.testng.Assert.assertSame;
28    import static org.testng.Assert.assertTrue;
29   
30    import java.awt.Color;
31    import java.io.File;
32    import java.io.IOException;
33    import java.util.ArrayList;
34    import java.util.HashMap;
35    import java.util.List;
36    import java.util.Map;
37   
38    import javax.swing.JInternalFrame;
39   
40    import org.testng.Assert;
41    import org.testng.AssertJUnit;
42    import org.testng.annotations.BeforeClass;
43    import org.testng.annotations.Test;
44   
45    import jalview.analysis.scoremodels.SimilarityParams;
46    import jalview.api.AlignViewportI;
47    import jalview.api.AlignmentViewPanel;
48    import jalview.api.FeatureColourI;
49    import jalview.api.ViewStyleI;
50    import jalview.datamodel.AlignmentAnnotation;
51    import jalview.datamodel.AlignmentI;
52    import jalview.datamodel.DBRefEntry;
53    import jalview.datamodel.GeneLocus;
54    import jalview.datamodel.HiddenSequences;
55    import jalview.datamodel.Mapping;
56    import jalview.datamodel.PDBEntry;
57    import jalview.datamodel.PDBEntry.Type;
58    import jalview.datamodel.Sequence.DBModList;
59    import jalview.datamodel.SequenceCollectionI;
60    import jalview.datamodel.SequenceFeature;
61    import jalview.datamodel.SequenceGroup;
62    import jalview.datamodel.SequenceI;
63    import jalview.datamodel.features.FeatureMatcher;
64    import jalview.datamodel.features.FeatureMatcherSet;
65    import jalview.datamodel.features.FeatureMatcherSetI;
66    import jalview.gui.AlignFrame;
67    import jalview.gui.AlignViewport;
68    import jalview.gui.AlignmentPanel;
69    import jalview.gui.Desktop;
70    import jalview.gui.JvOptionPane;
71    import jalview.gui.PCAPanel;
72    import jalview.gui.PopupMenu;
73    import jalview.gui.SliderPanel;
74    import jalview.io.DataSourceType;
75    import jalview.io.FileFormat;
76    import jalview.io.FileLoader;
77    import jalview.io.Jalview2xmlBase;
78    import jalview.renderer.ResidueShaderI;
79    import jalview.schemes.AnnotationColourGradient;
80    import jalview.schemes.BuriedColourScheme;
81    import jalview.schemes.ColourSchemeI;
82    import jalview.schemes.ColourSchemeProperty;
83    import jalview.schemes.FeatureColour;
84    import jalview.schemes.JalviewColourScheme;
85    import jalview.schemes.RNAHelicesColour;
86    import jalview.schemes.StrandColourScheme;
87    import jalview.schemes.TCoffeeColourScheme;
88    import jalview.structure.StructureImportSettings;
89    import jalview.util.MapList;
90    import jalview.util.matcher.Condition;
91    import jalview.viewmodel.AlignmentViewport;
92    import jalview.viewmodel.seqfeatures.FeatureRendererModel;
93   
94    @Test(singleThreaded = true)
 
95    public class Jalview2xmlTests extends Jalview2xmlBase
96    {
97   
 
98  1 toggle @Override
99    @BeforeClass(alwaysRun = true)
100    public void setUpJvOptionPane()
101    {
102  1 JvOptionPane.setInteractiveMode(false);
103  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
104    }
105   
 
106  1 toggle @Test(groups = { "Functional" })
107    public void testRNAStructureRecovery() throws Exception
108    {
109  1 String inFile = "examples/RF00031_folded.stk";
110  1 String tfile = File.createTempFile("JalviewTest", ".jvp")
111    .getAbsolutePath();
112  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
113    DataSourceType.FILE);
114  1 assertNotNull(af, "Didn't read input file " + inFile);
115  1 int olddsann = countDsAnn(af.getViewport());
116  1 assertTrue(olddsann > 0, "Didn't find any dataset annotations");
117  1 af.changeColour_actionPerformed(
118    JalviewColourScheme.RNAHelices.toString());
119  1 assertTrue(
120    af.getViewport()
121    .getGlobalColourScheme() instanceof RNAHelicesColour,
122    "Couldn't apply RNA helices colourscheme");
123  1 af.saveAlignment(tfile, FileFormat.Jalview);
124  1 assertTrue(af.isSaveAlignmentSuccessful(),
125    "Failed to store as a project.");
126  1 af.closeMenuItem_actionPerformed(true);
127  1 af = null;
128  1 af = new FileLoader().LoadFileWaitTillLoaded(tfile,
129    DataSourceType.FILE);
130  1 assertNotNull(af, "Failed to import new project");
131  1 int newdsann = countDsAnn(af.getViewport());
132  1 assertEquals(olddsann, newdsann,
133    "Differing numbers of dataset sequence annotation\nOriginally "
134    + olddsann + " and now " + newdsann);
135  1 System.out.println(
136    "Read in same number of annotations as originally present ("
137    + olddsann + ")");
138  1 assertTrue(
139   
140    af.getViewport()
141    .getGlobalColourScheme() instanceof RNAHelicesColour,
142    "RNA helices colourscheme was not applied on import.");
143    }
144   
 
145  1 toggle @Test(groups = { "Functional" })
146    public void testTCoffeeScores() throws Exception
147    {
148  1 String inFile = "examples/uniref50.fa",
149    inAnnot = "examples/uniref50.score_ascii";
150  1 String tfile = File.createTempFile("JalviewTest", ".jvp")
151    .getAbsolutePath();
152  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
153    DataSourceType.FILE);
154  1 assertNotNull(af, "Didn't read input file " + inFile);
155  1 af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
156  1 AlignViewport viewport = af.getViewport();
157  1 assertSame(viewport.getGlobalColourScheme().getClass(),
158    TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
159  1 assertNotNull(
160    ColourSchemeProperty.getColourScheme(viewport,
161    viewport.getAlignment(),
162    viewport.getGlobalColourScheme()
163    .getSchemeName()),
164    "Recognise T-Coffee score from string");
165   
166  1 af.saveAlignment(tfile, FileFormat.Jalview);
167  1 assertTrue(af.isSaveAlignmentSuccessful(),
168    "Failed to store as a project.");
169  1 af.closeMenuItem_actionPerformed(true);
170  1 af = null;
171  1 af = new FileLoader().LoadFileWaitTillLoaded(tfile,
172    DataSourceType.FILE);
173  1 assertNotNull(af, "Failed to import new project");
174  1 assertSame(af.getViewport().getGlobalColourScheme().getClass(),
175    TCoffeeColourScheme.class,
176    "Didn't set T-coffee colourscheme for imported project.");
177  1 System.out.println(
178    "T-Coffee score shading successfully recovered from project.");
179    }
180   
 
181  1 toggle @Test(groups = { "Functional" })
182    public void testColourByAnnotScores() throws Exception
183    {
184  1 String inFile = "examples/uniref50.fa",
185    inAnnot = "examples/testdata/uniref50_iupred.jva";
186  1 String tfile = File.createTempFile("JalviewTest", ".jvp")
187    .getAbsolutePath();
188  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
189    DataSourceType.FILE);
190  1 assertNotNull(af, "Didn't read input file " + inFile);
191  1 af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
192  1 AlignmentAnnotation[] aa = af.getViewport().getAlignment()
193    .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
194  1 assertTrue(
195   
196    aa != null && aa.length > 0,
197    "Didn't find any IUPred annotation to use to shade alignment.");
198  1 AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
199    AnnotationColourGradient.ABOVE_THRESHOLD);
200  1 AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], null,
201    AnnotationColourGradient.BELOW_THRESHOLD);
202  1 cs.setSeqAssociated(true);
203  1 gcs.setSeqAssociated(true);
204  1 af.changeColour(cs);
205  1 SequenceGroup sg = new SequenceGroup();
206  1 sg.setStartRes(57);
207  1 sg.setEndRes(92);
208  1 sg.cs.setColourScheme(gcs);
209  1 af.getViewport().getAlignment().addGroup(sg);
210  1 sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
211  1 sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
212  1 af.alignPanel.alignmentChanged();
213  1 af.saveAlignment(tfile, FileFormat.Jalview);
214  1 assertTrue(af.isSaveAlignmentSuccessful(),
215    "Failed to store as a project.");
216  1 af.closeMenuItem_actionPerformed(true);
217  1 af = null;
218  1 af = new FileLoader().LoadFileWaitTillLoaded(tfile,
219    DataSourceType.FILE);
220  1 assertNotNull(af, "Failed to import new project");
221   
222    // check for group and alignment colourschemes
223   
224  1 ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
225  1 ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups().get(0)
226    .getColourScheme();
227  1 assertNotNull(_rcs, "Didn't recover global colourscheme");
228  1 assertTrue(_rcs instanceof AnnotationColourGradient,
229    "Didn't recover annotation colour global scheme");
230  1 AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
231  1 assertTrue(__rcs.isSeqAssociated(),
232    "Annotation colourscheme wasn't sequence associated");
233   
234  1 boolean diffseqcols = false, diffgseqcols = false;
235  1 SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
236  1 for (int p = 0, pSize = af.getViewport().getAlignment()
237  158 .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
238    {
239  157 if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
240    .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
241    {
242  20 diffseqcols = true;
243    }
244    }
245  1 assertTrue(diffseqcols, "Got Different sequence colours");
246  1 System.out.println(
247    "Per sequence colourscheme (Background) successfully applied and recovered.");
248   
249  1 assertNotNull(_rgcs, "Didn't recover group colourscheme");
250  1 assertTrue(_rgcs instanceof AnnotationColourGradient,
251    "Didn't recover annotation colour group colourscheme");
252  1 __rcs = (AnnotationColourGradient) _rgcs;
253  1 assertTrue(__rcs.isSeqAssociated(),
254    "Group Annotation colourscheme wasn't sequence associated");
255   
256  1 for (int p = 0, pSize = af.getViewport().getAlignment()
257  14 .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
258    {
259  13 if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
260    0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
261    0f))
262    {
263  1 diffgseqcols = true;
264    }
265    }
266  1 assertTrue(diffgseqcols, "Got Different group sequence colours");
267  1 System.out.println(
268    "Per sequence (Group) colourscheme successfully applied and recovered.");
269    }
270   
 
271  1 toggle @Test(groups = { "Functional" })
272    public void gatherViewsHere() throws Exception
273    {
274  1 int origCount = Desktop.getAlignFrames() == null ? 0
275    : Desktop.getAlignFrames().length;
276  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
277    "examples/exampleFile_2_7.jar", DataSourceType.FILE);
278  1 assertNotNull(af, "Didn't read in the example file correctly.");
279  1 assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
280    "Didn't gather the views in the example file.");
281   
282    }
283   
284    /**
285    * Test for JAL-2223 - multiple mappings in View Mapping report
286    *
287    * @throws Exception
288    */
 
289  1 toggle @Test(groups = { "Functional" })
290    public void noDuplicatePdbMappingsMade() throws Exception
291    {
292  1 StructureImportSettings.setProcessSecondaryStructure(true);
293  1 StructureImportSettings.setVisibleChainAnnotation(true);
294  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
295    "examples/exampleFile_2_7.jar", DataSourceType.FILE);
296  1 assertNotNull(af, "Didn't read in the example file correctly.");
297   
298    // locate Jmol viewer
299    // count number of PDB mappings the structure selection manager holds -
300  1 String pdbFile = af.getCurrentView().getStructureSelectionManager()
301    .findFileForPDBId("1A70");
302  1 assertEquals(
303    af.getCurrentView().getStructureSelectionManager()
304    .getMapping(pdbFile).length,
305    2, "Expected only two mappings for 1A70");
306   
307    }
308   
 
309  1 toggle @Test(groups = { "Functional" })
310    public void viewRefPdbAnnotation() throws Exception
311    {
312  1 StructureImportSettings.setProcessSecondaryStructure(true);
313  1 StructureImportSettings.setVisibleChainAnnotation(true);
314  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
315    "examples/exampleFile_2_7.jar", DataSourceType.FILE);
316  1 assertNotNull(af, "Didn't read in the example file correctly.");
317  1 AlignmentViewPanel sps = null;
318  1 for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
319    {
320  5 if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
321    {
322  1 sps = ap;
323  1 break;
324    }
325    }
326  1 assertNotNull(sps, "Couldn't find the structure view");
327  1 AlignmentAnnotation refan = null;
328  1 for (AlignmentAnnotation ra : sps.getAlignment()
329    .getAlignmentAnnotation())
330    {
331  1 if (ra.graph != 0)
332    {
333  1 refan = ra;
334  1 break;
335    }
336    }
337  1 assertNotNull(refan, "Annotation secondary structure not found.");
338  1 SequenceI sq = sps.getAlignment().findName("1A70|");
339  1 assertNotNull(sq, "Couldn't find 1a70 null chain");
340    // compare the manually added temperature factor annotation
341    // to the track automatically transferred from the pdb structure on load
342  1 assertNotNull(sq.getDatasetSequence().getAnnotation(),
343    "1a70 has no annotation");
344  1 for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
345    {
346  2 AlignmentAnnotation alaa;
347  2 sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
348  2 alaa.adjustForAlignment();
349  2 if (ala.graph == refan.graph)
350    {
351  98 for (int p = 0; p < ala.annotations.length; p++)
352    {
353  97 sq.findPosition(p);
354  97 try
355    {
356  97 assertTrue((alaa.annotations[p] == null
357    && refan.annotations[p] == null)
358    || alaa.annotations[p].value == refan.annotations[p].value,
359    "Mismatch at alignment position " + p);
360    } catch (NullPointerException q)
361    {
362  0 Assert.fail("Mismatch of alignment annotations at position " + p
363    + " Ref seq ann: " + refan.annotations[p]
364    + " alignment " + alaa.annotations[p]);
365    }
366    }
367    }
368    }
369   
370    }
371   
 
372  1 toggle @Test(groups = { "Functional" })
373    public void testCopyViewSettings() throws Exception
374    {
375  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
376    "examples/exampleFile_2_7.jar", DataSourceType.FILE);
377  1 assertNotNull(af, "Didn't read in the example file correctly.");
378  1 AlignmentViewPanel sps = null, groups = null;
379  1 for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
380    {
381  5 if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
382    {
383  1 sps = ap;
384    }
385  5 if (ap.getViewName().contains("MAFFT"))
386    {
387  1 groups = ap;
388    }
389    }
390  1 assertNotNull(sps, "Couldn't find the structure view");
391  1 assertNotNull(groups, "Couldn't find the MAFFT view");
392   
393  1 ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
394  1 ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
395  1 AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
396   
397  1 groups.getAlignViewport().setViewStyle(structureStyle);
398  1 AssertJUnit.assertFalse(
399    groupStyle.sameStyle(groups.getAlignViewport().getViewStyle()));
400  1 Assert.assertTrue(structureStyle
401    .sameStyle(groups.getAlignViewport().getViewStyle()));
402   
403    }
404   
405    /**
406    * test store and recovery of expanded views
407    *
408    * @throws Exception
409    */
 
410  1 toggle @Test(groups = { "Functional" }, enabled = true)
411    public void testStoreAndRecoverExpandedviews() throws Exception
412    {
413  1 Desktop.instance.closeAll_actionPerformed(null);
414   
415  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
416    "examples/exampleFile_2_7.jar", DataSourceType.FILE);
417  1 Assert.assertEquals(Desktop.getAlignFrames().length, 1);
418  1 String afid = af.getViewport().getSequenceSetId();
419   
420    // check FileLoader returned a reference to the one alignFrame that is
421    // actually on the Desktop
422  1 assertSame(af, Desktop.getAlignFrameFor(af.getViewport()),
423    "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
424   
425  1 Desktop.explodeViews(af);
426   
427  1 int oldviews = Desktop.getAlignFrames().length;
428  1 Assert.assertEquals(Desktop.getAlignFrames().length,
429    Desktop.getAlignmentPanels(afid).length);
430  1 File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
431  1 try
432    {
433  1 new Jalview2XML(false).saveState(tfile);
434    } catch (Error e)
435    {
436  0 Assert.fail("Didn't save the expanded view state", e);
437    } catch (Exception e)
438    {
439  0 Assert.fail("Didn't save the expanded view state", e);
440    }
441  1 Desktop.instance.closeAll_actionPerformed(null);
442  1 if (Desktop.getAlignFrames() != null)
443    {
444  0 Assert.assertEquals(Desktop.getAlignFrames().length, 0);
445    }
446  1 af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
447    DataSourceType.FILE);
448  1 Assert.assertNotNull(af);
449  1 Assert.assertEquals(Desktop.getAlignFrames().length,
450    Desktop.getAlignmentPanels(
451    af.getViewport().getSequenceSetId()).length);
452  1 Assert.assertEquals(
453    Desktop.getAlignmentPanels(
454    af.getViewport().getSequenceSetId()).length,
455    oldviews);
456    }
457   
458    /**
459    * Test save and reload of a project with a different representative sequence
460    * in each view.
461    *
462    * @throws Exception
463    */
 
464  1 toggle @Test(groups = { "Functional" })
465    public void testStoreAndRecoverReferenceSeqSettings() throws Exception
466    {
467  1 Desktop.instance.closeAll_actionPerformed(null);
468  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
469    "examples/exampleFile_2_7.jar", DataSourceType.FILE);
470  1 assertNotNull(af, "Didn't read in the example file correctly.");
471  1 String afid = af.getViewport().getSequenceSetId();
472   
473    // remember reference sequence for each panel
474  1 Map<String, SequenceI> refseqs = new HashMap<>();
475   
476    /*
477    * mark sequence 2, 3, 4.. in panels 1, 2, 3...
478    * as reference sequence for itself and the preceding sequence
479    */
480  1 int n = 1;
481  1 for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
482    {
483  5 AlignViewportI av = ap.getAlignViewport();
484  5 AlignmentI alignment = ap.getAlignment();
485  5 int repIndex = n % alignment.getHeight();
486  5 SequenceI rep = alignment.getSequenceAt(repIndex);
487  5 refseqs.put(ap.getViewName(), rep);
488   
489    // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
490    // todo refactor this to an alignment view controller
491  5 av.setDisplayReferenceSeq(true);
492  5 av.setColourByReferenceSeq(true);
493  5 av.getAlignment().setSeqrep(rep);
494   
495  5 n++;
496    }
497  1 File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
498    ".jvp");
499  1 try
500    {
501  1 new Jalview2XML(false).saveState(tfile);
502    } catch (Throwable e)
503    {
504  0 Assert.fail("Didn't save the expanded view state", e);
505    }
506  1 Desktop.instance.closeAll_actionPerformed(null);
507  1 if (Desktop.getAlignFrames() != null)
508    {
509  0 Assert.assertEquals(Desktop.getAlignFrames().length, 0);
510    }
511   
512  1 af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
513    DataSourceType.FILE);
514  1 afid = af.getViewport().getSequenceSetId();
515   
516  1 for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
517    {
518    // check representative
519  5 AlignmentI alignment = ap.getAlignment();
520  5 SequenceI rep = alignment.getSeqrep();
521  5 Assert.assertNotNull(rep,
522    "Couldn't restore sequence representative from project");
523    // can't use a strong equals here, because by definition, the sequence IDs
524    // will be different.
525    // could set vamsas session save/restore flag to preserve IDs across
526    // load/saves.
527  5 Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
528    rep.toString(),
529    "Representative wasn't the same when recovered.");
530  5 Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
531    "Display reference sequence view setting not set.");
532  5 Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
533    "Colour By Reference Seq view setting not set.");
534    }
535    }
536   
 
537  1 toggle @Test(groups = { "Functional" })
538    public void testIsVersionStringLaterThan()
539    {
540    /*
541    * No version / development / test / autobuild is leniently assumed to be
542    * compatible
543    */
544  1 assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
545  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
546  1 assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
547  1 assertTrue(Jalview2XML.isVersionStringLaterThan(null,
548    "Development Build"));
549  1 assertTrue(Jalview2XML.isVersionStringLaterThan(null,
550    "DEVELOPMENT BUILD"));
551  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
552    "Development Build"));
553  1 assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
554  1 assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
555  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
556  1 assertTrue(
557    Jalview2XML.isVersionStringLaterThan(null, "Automated Build"));
558  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
559    "Automated Build"));
560  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
561    "AUTOMATED BUILD"));
562   
563    /*
564    * same version returns true i.e. compatible
565    */
566  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
567  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
568  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
569  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
570  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
571   
572    /*
573    * later version returns true
574    */
575  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
576  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
577  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
578  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
579  1 assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
580   
581    /*
582    * earlier version returns false
583    */
584  1 assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
585  1 assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
586  1 assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
587  1 assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
588  1 assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
589    }
590   
591    /**
592    * Test save and reload of a project with a different sequence group (and
593    * representative sequence) in each view.
594    *
595    * @throws Exception
596    */
 
597  1 toggle @Test(groups = { "Functional" })
598    public void testStoreAndRecoverGroupRepSeqs() throws Exception
599    {
600  1 Desktop.instance.closeAll_actionPerformed(null);
601  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
602    "examples/uniref50.fa", DataSourceType.FILE);
603  1 assertNotNull(af, "Didn't read in the example file correctly.");
604  1 String afid = af.getViewport().getSequenceSetId();
605    // make a second view of the alignment
606  1 af.newView_actionPerformed(null);
607   
608    /*
609    * remember representative and hidden sequences marked
610    * on each panel
611    */
612  1 Map<String, SequenceI> repSeqs = new HashMap<>();
613  1 Map<String, List<String>> hiddenSeqNames = new HashMap<>();
614   
615    /*
616    * mark sequence 2, 3, 4.. in panels 1, 2, 3...
617    * as reference sequence for itself and the preceding sequence
618    */
619  1 int n = 1;
620  1 for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
621    {
622  2 AlignViewportI av = ap.getAlignViewport();
623  2 AlignmentI alignment = ap.getAlignment();
624  2 int repIndex = n % alignment.getHeight();
625    // ensure at least one preceding sequence i.e. index >= 1
626  2 repIndex = Math.max(repIndex, 1);
627  2 SequenceI repSeq = alignment.getSequenceAt(repIndex);
628  2 repSeqs.put(ap.getViewName(), repSeq);
629  2 List<String> hiddenNames = new ArrayList<>();
630  2 hiddenSeqNames.put(ap.getViewName(), hiddenNames);
631   
632    /*
633    * have rep sequence represent itself and the one before it
634    * this hides the group (except for the rep seq)
635    */
636  2 SequenceGroup sg = new SequenceGroup();
637  2 sg.addSequence(repSeq, false);
638  2 SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
639  2 sg.addSequence(precedingSeq, false);
640  2 sg.setSeqrep(repSeq);
641  2 assertTrue(sg.getSequences().contains(repSeq));
642  2 assertTrue(sg.getSequences().contains(precedingSeq));
643  2 av.setSelectionGroup(sg);
644  2 assertSame(repSeq, sg.getSeqrep());
645   
646    /*
647    * represent group with sequence adds to a map of hidden rep sequences
648    * (it does not create a group on the alignment)
649    */
650  2 ((AlignmentViewport) av).hideSequences(repSeq, true);
651  2 assertSame(repSeq, sg.getSeqrep());
652  2 assertTrue(sg.getSequences().contains(repSeq));
653  2 assertTrue(sg.getSequences().contains(precedingSeq));
654  2 assertTrue(alignment.getGroups().isEmpty(), "alignment has groups");
655  2 Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
656    .getHiddenRepSequences();
657  2 assertNotNull(hiddenRepSeqsMap);
658  2 assertEquals(1, hiddenRepSeqsMap.size());
659  2 assertSame(sg, hiddenRepSeqsMap.get(repSeq));
660  2 assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
661  2 assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
662  2 hiddenNames.add(precedingSeq.getName());
663   
664  2 n++;
665    }
666  1 File tfile = File.createTempFile("testStoreAndRecoverGroupReps",
667    ".jvp");
668  1 try
669    {
670  1 new Jalview2XML(false).saveState(tfile);
671    } catch (Throwable e)
672    {
673  0 Assert.fail("Didn't save the expanded view state", e);
674    }
675  1 Desktop.instance.closeAll_actionPerformed(null);
676  1 if (Desktop.getAlignFrames() != null)
677    {
678  0 Assert.assertEquals(Desktop.getAlignFrames().length, 0);
679    }
680   
681  1 af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
682    DataSourceType.FILE);
683  1 afid = af.getViewport().getSequenceSetId();
684   
685  1 for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
686    {
687  2 String viewName = ap.getViewName();
688  2 AlignViewportI av = ap.getAlignViewport();
689  2 AlignmentI alignment = ap.getAlignment();
690  2 List<SequenceGroup> groups = alignment.getGroups();
691  2 assertNotNull(groups);
692  2 assertTrue(groups.isEmpty(), "Alignment has groups");
693  2 Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
694    .getHiddenRepSequences();
695  2 assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences");
696  2 assertEquals(1, hiddenRepSeqsMap.size());
697  2 assertEquals(repSeqs.get(viewName).getDisplayId(true),
698    hiddenRepSeqsMap.keySet().iterator().next()
699    .getDisplayId(true));
700   
701    /*
702    * verify hidden sequences in restored panel
703    */
704  2 List<String> hidden = hiddenSeqNames.get(ap.getViewName());
705  2 HiddenSequences hs = alignment.getHiddenSequences();
706  2 assertEquals(hidden.size(), hs.getSize(),
707    "wrong number of restored hidden sequences in "
708    + ap.getViewName());
709    }
710    }
711   
712    /**
713    * Test save and reload of PDBEntry in Jalview project
714    *
715    * @throws Exception
716    */
 
717  1 toggle @Test(groups = { "Functional" })
718    public void testStoreAndRecoverPDBEntry() throws Exception
719    {
720  1 Desktop.instance.closeAll_actionPerformed(null);
721  1 String exampleFile = "examples/3W5V.pdb";
722  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
723    DataSourceType.FILE);
724  1 assertNotNull(af, "Didn't read in the example file correctly.");
725  1 String afid = af.getViewport().getSequenceSetId();
726   
727  1 AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
728  1 System.out.println();
729  1 AlignmentViewPanel ap = alignPanels[0];
730  1 String tfileBase = new File(".").getAbsolutePath().replace(".", "");
731  1 String testFile = tfileBase + exampleFile;
732  1 AlignmentI alignment = ap.getAlignment();
733  1 System.out.println("blah");
734  1 SequenceI[] seqs = alignment.getSequencesArray();
735  1 Assert.assertNotNull(seqs[0]);
736  1 Assert.assertNotNull(seqs[1]);
737  1 Assert.assertNotNull(seqs[2]);
738  1 Assert.assertNotNull(seqs[3]);
739  1 Assert.assertNotNull(seqs[0].getDatasetSequence());
740  1 Assert.assertNotNull(seqs[1].getDatasetSequence());
741  1 Assert.assertNotNull(seqs[2].getDatasetSequence());
742  1 Assert.assertNotNull(seqs[3].getDatasetSequence());
743  1 PDBEntry[] pdbEntries = new PDBEntry[4];
744  1 pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
745  1 pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
746  1 pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
747  1 pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
748  1 Assert.assertEquals(
749    seqs[0].getDatasetSequence().getAllPDBEntries().get(0),
750    pdbEntries[0]);
751  1 Assert.assertEquals(
752    seqs[1].getDatasetSequence().getAllPDBEntries().get(0),
753    pdbEntries[1]);
754  1 Assert.assertEquals(
755    seqs[2].getDatasetSequence().getAllPDBEntries().get(0),
756    pdbEntries[2]);
757  1 Assert.assertEquals(
758    seqs[3].getDatasetSequence().getAllPDBEntries().get(0),
759    pdbEntries[3]);
760   
761  1 File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
762  1 try
763    {
764  1 new Jalview2XML(false).saveState(tfile);
765    } catch (Throwable e)
766    {
767  0 Assert.fail("Didn't save the state", e);
768    }
769  1 Desktop.instance.closeAll_actionPerformed(null);
770  1 if (Desktop.getAlignFrames() != null)
771    {
772  0 Assert.assertEquals(Desktop.getAlignFrames().length, 0);
773    }
774   
775  1 AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
776    tfile.getAbsolutePath(), DataSourceType.FILE);
777  1 String rfid = restoredFrame.getViewport().getSequenceSetId();
778  1 AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
779  1 AlignmentViewPanel rap = rAlignPanels[0];
780  1 AlignmentI rAlignment = rap.getAlignment();
781  1 System.out.println("blah");
782  1 SequenceI[] rseqs = rAlignment.getSequencesArray();
783  1 Assert.assertNotNull(rseqs[0]);
784  1 Assert.assertNotNull(rseqs[1]);
785  1 Assert.assertNotNull(rseqs[2]);
786  1 Assert.assertNotNull(rseqs[3]);
787  1 Assert.assertNotNull(rseqs[0].getDatasetSequence());
788  1 Assert.assertNotNull(rseqs[1].getDatasetSequence());
789  1 Assert.assertNotNull(rseqs[2].getDatasetSequence());
790  1 Assert.assertNotNull(rseqs[3].getDatasetSequence());
791   
792    // The Asserts below are expected to fail until the PDB chainCode is
793    // recoverable from a Jalview projects
794  5 for (int chain = 0; chain < 4; chain++)
795    {
796  4 PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
797    .get(0);
798  4 PDBEntry expected = pdbEntries[chain];
799  4 Assert.assertEquals(recov.getId(), expected.getId(),
800    "Mismatch PDB ID");
801  4 Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
802    "Mismatch PDB ID");
803  4 Assert.assertEquals(recov.getType(), expected.getType(),
804    "Mismatch PDBEntry 'Type'");
805  4 Assert.assertNotNull(recov.getFile(),
806    "Recovered PDBEntry should have a non-null file entry");
807    }
808    }
809   
810    /**
811    * Configure an alignment and a sub-group each with distinct colour schemes,
812    * Conservation and PID thresholds, and confirm these are restored from the
813    * saved project.
814    *
815    * @throws IOException
816    */
 
817  1 toggle @Test(groups = { "Functional" })
818    public void testStoreAndRecoverColourThresholds() throws IOException
819    {
820  1 Desktop.instance.closeAll_actionPerformed(null);
821  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
822    "examples/uniref50.fa", DataSourceType.FILE);
823   
824  1 AlignViewport av = af.getViewport();
825  1 AlignmentI al = av.getAlignment();
826   
827    /*
828    * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
829    */
830  1 av.setColourAppliesToAllGroups(false);
831  1 af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
832  1 assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
833  1 af.abovePIDThreshold_actionPerformed(true);
834  1 SliderPanel sp = SliderPanel.getSliderPanel();
835  1 assertFalse(sp.isForConservation());
836  1 sp.valueChanged(10);
837  1 af.conservationMenuItem_actionPerformed(true);
838  1 sp = SliderPanel.getSliderPanel();
839  1 assertTrue(sp.isForConservation());
840  1 sp.valueChanged(20);
841  1 ResidueShaderI rs = av.getResidueShading();
842  1 assertEquals(rs.getThreshold(), 10);
843  1 assertTrue(rs.conservationApplied());
844  1 assertEquals(rs.getConservationInc(), 20);
845   
846    /*
847    * create a group with Strand colouring, 30% Conservation
848    * and 40% PID threshold
849    * (notice menu action applies to selection group even if mouse click
850    * is at a sequence not in the group)
851    */
852  1 SequenceGroup sg = new SequenceGroup();
853  1 sg.addSequence(al.getSequenceAt(0), false);
854  1 sg.setStartRes(15);
855  1 sg.setEndRes(25);
856  1 av.setSelectionGroup(sg);
857  1 PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2),
858    null);
859  1 popupMenu.changeColour_actionPerformed(
860    JalviewColourScheme.Strand.toString());
861  1 assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
862  1 assertEquals(al.getGroups().size(), 1);
863  1 assertSame(al.getGroups().get(0), sg);
864  1 popupMenu.conservationMenuItem_actionPerformed(true);
865  1 sp = SliderPanel.getSliderPanel();
866  1 assertTrue(sp.isForConservation());
867  1 sp.valueChanged(30);
868  1 popupMenu.abovePIDColour_actionPerformed(true);
869  1 sp = SliderPanel.getSliderPanel();
870  1 assertFalse(sp.isForConservation());
871  1 sp.valueChanged(40);
872  1 assertTrue(sg.getGroupColourScheme().conservationApplied());
873  1 assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
874  1 assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
875   
876    /*
877    * save project, close windows, reload project, verify
878    */
879  1 File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
880    ".jvp");
881  1 tfile.deleteOnExit();
882  1 new Jalview2XML(false).saveState(tfile);
883  1 Desktop.instance.closeAll_actionPerformed(null);
884  1 af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
885    DataSourceType.FILE);
886  1 Assert.assertNotNull(af, "Failed to reload project");
887   
888    /*
889    * verify alignment (background) colouring
890    */
891  1 rs = af.getViewport().getResidueShading();
892  1 assertTrue(rs.getColourScheme() instanceof BuriedColourScheme);
893  1 assertEquals(rs.getThreshold(), 10);
894  1 assertTrue(rs.conservationApplied());
895  1 assertEquals(rs.getConservationInc(), 20);
896   
897    /*
898    * verify group colouring
899    */
900  1 assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1);
901  1 rs = af.getViewport().getAlignment().getGroups().get(0)
902    .getGroupColourScheme();
903  1 assertTrue(rs.getColourScheme() instanceof StrandColourScheme);
904  1 assertEquals(rs.getThreshold(), 40);
905  1 assertTrue(rs.conservationApplied());
906  1 assertEquals(rs.getConservationInc(), 30);
907    }
908   
909    /**
910    * Test save and reload of feature colour schemes and filter settings
911    *
912    * @throws IOException
913    */
 
914  1 toggle @Test(groups = { "Functional" })
915    public void testSaveLoadFeatureColoursAndFilters() throws IOException
916    {
917  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
918    ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
919  1 SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
920   
921    /*
922    * add some features to the sequence
923    */
924  1 int score = 1;
925  1 addFeatures(seq1, "type1", score++);
926  1 addFeatures(seq1, "type2", score++);
927  1 addFeatures(seq1, "type3", score++);
928  1 addFeatures(seq1, "type4", score++);
929  1 addFeatures(seq1, "type5", score++);
930   
931    /*
932    * set colour schemes for features
933    */
934  1 FeatureRendererModel fr = af.getFeatureRenderer();
935  1 fr.findAllFeatures(true);
936   
937    // type1: red
938  1 fr.setColour("type1", new FeatureColour(Color.red));
939   
940    // type2: by label
941  1 FeatureColourI byLabel = new FeatureColour();
942  1 byLabel.setColourByLabel(true);
943  1 fr.setColour("type2", byLabel);
944   
945    // type3: by score above threshold
946  1 FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
947    Color.BLUE, null, 1, 10);
948  1 byScore.setAboveThreshold(true);
949  1 byScore.setThreshold(2f);
950  1 fr.setColour("type3", byScore);
951   
952    // type4: by attribute AF
953  1 FeatureColourI byAF = new FeatureColour();
954  1 byAF.setColourByLabel(true);
955  1 byAF.setAttributeName("AF");
956  1 fr.setColour("type4", byAF);
957   
958    // type5: by attribute CSQ:PolyPhen below threshold
959  1 FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
960    Color.BLUE, null, 1, 10);
961  1 byPolyPhen.setBelowThreshold(true);
962  1 byPolyPhen.setThreshold(3f);
963  1 byPolyPhen.setAttributeName("CSQ", "PolyPhen");
964  1 fr.setColour("type5", byPolyPhen);
965   
966    /*
967    * set filters for feature types
968    */
969   
970    // filter type1 features by (label contains "x")
971  1 FeatureMatcherSetI filterByX = new FeatureMatcherSet();
972  1 filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
973  1 fr.setFeatureFilter("type1", filterByX);
974   
975    // filter type2 features by (score <= 2.4 and score > 1.1)
976  1 FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
977  1 filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
978  1 filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
979  1 fr.setFeatureFilter("type2", filterByScore);
980   
981    // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
982  1 FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
983  1 filterByXY
984    .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
985  1 filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
986    "PolyPhen"));
987  1 fr.setFeatureFilter("type3", filterByXY);
988   
989    /*
990    * save as Jalview project
991    */
992  1 File tfile = File.createTempFile("JalviewTest", ".jvp");
993  1 tfile.deleteOnExit();
994  1 String filePath = tfile.getAbsolutePath();
995  1 af.saveAlignment(filePath, FileFormat.Jalview);
996  1 assertTrue(af.isSaveAlignmentSuccessful(),
997    "Failed to store as a project.");
998   
999    /*
1000    * close current alignment and load the saved project
1001    */
1002  1 af.closeMenuItem_actionPerformed(true);
1003  1 af = null;
1004  1 af = new FileLoader().LoadFileWaitTillLoaded(filePath,
1005    DataSourceType.FILE);
1006  1 assertNotNull(af, "Failed to import new project");
1007   
1008    /*
1009    * verify restored feature colour schemes and filters
1010    */
1011  1 fr = af.getFeatureRenderer();
1012  1 FeatureColourI fc = fr.getFeatureStyle("type1");
1013  1 assertTrue(fc.isSimpleColour());
1014  1 assertEquals(fc.getColour(), Color.red);
1015  1 fc = fr.getFeatureStyle("type2");
1016  1 assertTrue(fc.isColourByLabel());
1017  1 fc = fr.getFeatureStyle("type3");
1018  1 assertTrue(fc.isGraduatedColour());
1019  1 assertNull(fc.getAttributeName());
1020  1 assertTrue(fc.isAboveThreshold());
1021  1 assertEquals(fc.getThreshold(), 2f);
1022  1 fc = fr.getFeatureStyle("type4");
1023  1 assertTrue(fc.isColourByLabel());
1024  1 assertTrue(fc.isColourByAttribute());
1025  1 assertEquals(fc.getAttributeName(), new String[] { "AF" });
1026  1 fc = fr.getFeatureStyle("type5");
1027  1 assertTrue(fc.isGraduatedColour());
1028  1 assertTrue(fc.isColourByAttribute());
1029  1 assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
1030  1 assertTrue(fc.isBelowThreshold());
1031  1 assertEquals(fc.getThreshold(), 3f);
1032   
1033  1 assertEquals(fr.getFeatureFilter("type1").toStableString(),
1034    "Label Contains x");
1035  1 assertEquals(fr.getFeatureFilter("type2").toStableString(),
1036    "(Score LE 2.4) AND (Score GT 1.1)");
1037  1 assertEquals(fr.getFeatureFilter("type3").toStableString(),
1038    "(AF Contains X) OR (CSQ:PolyPhen NE 0)");
1039    }
1040   
 
1041  10 toggle private void addFeature(SequenceI seq, String featureType, int score)
1042    {
1043  10 SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
1044    score, "grp");
1045  10 sf.setValue("AF", score);
1046  10 sf.setValue("CSQ", new HashMap<String, String>()
1047    {
 
1048  10 toggle {
1049  10 put("PolyPhen", Integer.toString(score));
1050    }
1051    });
1052  10 seq.addSequenceFeature(sf);
1053    }
1054   
1055    /**
1056    * Adds two features of the given type to the given sequence, also setting the
1057    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
1058    *
1059    * @param seq
1060    * @param featureType
1061    * @param score
1062    */
 
1063  5 toggle private void addFeatures(SequenceI seq, String featureType, int score)
1064    {
1065  5 addFeature(seq, featureType, score++);
1066  5 addFeature(seq, featureType, score);
1067    }
1068   
1069    /**
1070    * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
1071    * view (JAL-3171) this test ensures we can import and merge those views
1072    */
 
1073  1 toggle @Test(groups = { "Functional" })
1074    public void testMergeDatasetsforViews() throws IOException
1075    {
1076    // simple project - two views on one alignment
1077  1 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
1078    "examples/testdata/projects/twoViews.jvp", DataSourceType.FILE);
1079  1 assertNotNull(af);
1080  1 assertTrue(af.getAlignPanels().size() > 1);
1081  1 verifyDs(af);
1082    }
1083   
1084    /**
1085    * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
1086    * view (JAL-3171) this test ensures we can import and merge those views This
1087    * is a more complex project
1088    */
 
1089  1 toggle @Test(groups = { "Functional" })
1090    public void testMergeDatasetsforManyViews() throws IOException
1091    {
1092  1 Desktop.instance.closeAll_actionPerformed(null);
1093   
1094    // complex project - one dataset, several views on several alignments
1095  1 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
1096    "examples/testdata/projects/manyViews.jvp",
1097    DataSourceType.FILE);
1098  1 assertNotNull(af);
1099   
1100  1 AlignmentI ds = null;
1101  1 for (AlignFrame alignFrame : Desktop.getAlignFrames())
1102    {
1103  3 if (ds == null)
1104    {
1105  1 ds = verifyDs(alignFrame);
1106    }
1107    else
1108    {
1109    // check that this frame's dataset matches the last
1110  2 assertTrue(ds == verifyDs(alignFrame));
1111    }
1112    }
1113    }
1114   
 
1115  4 toggle private AlignmentI verifyDs(AlignFrame af)
1116    {
1117  4 AlignmentI ds = null;
1118  4 for (AlignmentViewPanel ap : af.getAlignPanels())
1119    {
1120  10 if (ds == null)
1121    {
1122  4 ds = ap.getAlignment().getDataset();
1123    }
1124    else
1125    {
1126  6 assertTrue(ap.getAlignment().getDataset() == ds,
1127    "Dataset was not the same for imported 2.10.5 project with several alignment views");
1128    }
1129    }
1130  4 return ds;
1131    }
1132   
 
1133  1 toggle @Test(groups = "Functional")
1134    public void testPcaViewAssociation() throws IOException
1135    {
1136  1 Desktop.instance.closeAll_actionPerformed(null);
1137  1 final String PCAVIEWNAME = "With PCA";
1138    // create a new tempfile
1139  1 File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
1140   
1141    {
1142  1 String exampleFile = "examples/uniref50.fa";
1143  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
1144    DataSourceType.FILE);
1145  1 assertNotNull(af, "Didn't read in the example file correctly.");
1146  1 AlignmentPanel origView = (AlignmentPanel) af.getAlignPanels().get(0);
1147  1 AlignmentPanel newview = af.newView(PCAVIEWNAME, true);
1148    // create another for good measure
1149  1 af.newView("Not the PCA View", true);
1150  1 PCAPanel pcaPanel = new PCAPanel(origView, "BLOSUM62",
1151    new SimilarityParams(true, true, true, false));
1152    // we're in the test exec thread, so we can just run synchronously here
1153  1 pcaPanel.run();
1154   
1155    // now switch the linked view
1156  1 pcaPanel.selectAssociatedView(newview);
1157   
1158  1 assertTrue(pcaPanel.getAlignViewport() == newview.getAlignViewport(),
1159    "PCA should be associated with 'With PCA' view: test is broken");
1160   
1161    // now save and reload project
1162  1 Jalview2XML jv2xml = new jalview.project.Jalview2XML(false);
1163  1 tempfile.delete();
1164  1 jv2xml.saveState(tempfile);
1165  1 assertTrue(jv2xml.errorMessage == null,
1166    "Failed to save dummy project with PCA: test broken");
1167    }
1168   
1169    // load again.
1170  1 Desktop.instance.closeAll_actionPerformed(null);
1171  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
1172    tempfile.getCanonicalPath(), DataSourceType.FILE);
1173  1 JInternalFrame[] frames = Desktop.instance.getAllFrames();
1174    // PCA and the tabbed alignment view should be the only two windows on the
1175    // desktop
1176  1 assertEquals(frames.length, 2,
1177    "PCA and the tabbed alignment view should be the only two windows on the desktop");
1178  1 PCAPanel pcaPanel = (PCAPanel) frames[frames[0] == af ? 1 : 0];
1179   
1180  1 AlignmentViewPanel restoredNewView = null;
1181  1 for (AlignmentViewPanel alignpanel : Desktop.getAlignmentPanels(null))
1182    {
1183  3 if (alignpanel.getAlignViewport() == pcaPanel.getAlignViewport())
1184    {
1185  1 restoredNewView = alignpanel;
1186    }
1187    }
1188  1 assertEquals(restoredNewView.getViewName(), PCAVIEWNAME);
1189  1 assertTrue(
1190    restoredNewView.getAlignViewport() == pcaPanel
1191    .getAlignViewport(),
1192    "Didn't restore correct view association for the PCA view");
1193    }
1194   
1195    /**
1196    * Test save and reload of DBRefEntry including GeneLocus in project
1197    *
1198    * @throws Exception
1199    */
 
1200  1 toggle @Test(groups = { "Functional" })
1201    public void testStoreAndRecoverGeneLocus() throws Exception
1202    {
1203  1 Desktop.instance.closeAll_actionPerformed(null);
1204  1 String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA";
1205  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
1206    DataSourceType.PASTE);
1207  1 assertNotNull(af, "Didn't read in the example file correctly.");
1208   
1209  1 AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0];
1210  1 SequenceI pep = ap.getAlignment().getSequenceAt(0);
1211  1 SequenceI cds = ap.getAlignment().getSequenceAt(1);
1212   
1213    /*
1214    * give 'protein' a dbref to self, a dbref with map to CDS,
1215    * and a dbref with map to gene 'locus'
1216    */
1217  1 DBRefEntry dbref1 = new DBRefEntry("Uniprot", "1", "P30419", null);
1218  1 pep.addDBRef(dbref1);
1219  1 Mapping cdsmap = new Mapping(cds,
1220    new MapList(new int[]
1221    { 1, 4 }, new int[] { 1, 12 }, 1, 3));
1222  1 DBRefEntry dbref2 = new DBRefEntry("EMBLCDS", "2", "X1235", cdsmap);
1223  1 pep.addDBRef(dbref2);
1224  1 Mapping locusmap = new Mapping(null,
1225    new MapList(new int[]
1226    { 1, 4 }, new int[] { 2674123, 2674135 }, 1, 3));
1227  1 DBRefEntry dbref3 = new GeneLocus("human", "GRCh38", "5", locusmap);
1228  1 pep.addDBRef(dbref3);
1229   
1230  1 File tfile = File.createTempFile("testStoreAndRecoverGeneLocus",
1231    ".jvp");
1232  1 try
1233    {
1234  1 new Jalview2XML(false).saveState(tfile);
1235    } catch (Throwable e)
1236    {
1237  0 Assert.fail("Didn't save the state", e);
1238    }
1239  1 Desktop.instance.closeAll_actionPerformed(null);
1240   
1241  1 new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
1242    DataSourceType.FILE);
1243  1 AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];
1244  1 SequenceI rpep = rap.getAlignment().getSequenceAt(0);
1245  1 DBModList<DBRefEntry> dbrefs = rpep.getDBRefs();
1246  1 assertEquals(rpep.getName(), "P30419");
1247  1 assertEquals(dbrefs.size(), 3);
1248  1 DBRefEntry dbRef = dbrefs.get(0);
1249  1 assertFalse(dbRef instanceof GeneLocus);
1250  1 assertNull(dbRef.getMap());
1251  1 assertEquals(dbRef, dbref1);
1252   
1253    /*
1254    * restored dbrefs with mapping have a different 'map to'
1255    * sequence but otherwise match the original dbrefs
1256    */
1257  1 dbRef = dbrefs.get(1);
1258  1 assertFalse(dbRef instanceof GeneLocus);
1259  1 assertTrue(dbRef.equalRef(dbref2));
1260  1 assertNotNull(dbRef.getMap());
1261  1 SequenceI rcds = rap.getAlignment().getSequenceAt(1);
1262  1 assertSame(dbRef.getMap().getTo(), rcds);
1263    // compare MapList but not map.to
1264  1 assertEquals(dbRef.getMap().getMap(), dbref2.getMap().getMap());
1265   
1266    /*
1267    * GeneLocus map.to is null so can compare Mapping objects
1268    */
1269  1 dbRef = dbrefs.get(2);
1270  1 assertTrue(dbRef instanceof GeneLocus);
1271  1 assertEquals(dbRef, dbref3);
1272    }
1273    }
  • 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.