1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
|
9 |
|
|
10 |
|
|
11 |
|
|
12 |
|
|
13 |
|
|
14 |
|
|
15 |
|
|
16 |
|
|
17 |
|
|
18 |
|
|
19 |
|
|
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.assertNotSame; |
27 |
|
import static org.testng.Assert.assertNull; |
28 |
|
import static org.testng.Assert.assertSame; |
29 |
|
import static org.testng.Assert.assertTrue; |
30 |
|
|
31 |
|
import java.awt.Color; |
32 |
|
import java.awt.Rectangle; |
33 |
|
import java.io.File; |
34 |
|
import java.io.IOException; |
35 |
|
import java.util.ArrayList; |
36 |
|
import java.util.BitSet; |
37 |
|
import java.util.HashMap; |
38 |
|
import java.util.List; |
39 |
|
import java.util.Locale; |
40 |
|
import java.util.Map; |
41 |
|
|
42 |
|
import javax.swing.JInternalFrame; |
43 |
|
|
44 |
|
import org.testng.Assert; |
45 |
|
import org.testng.AssertJUnit; |
46 |
|
import org.testng.annotations.BeforeClass; |
47 |
|
import org.testng.annotations.Test; |
48 |
|
|
49 |
|
import jalview.analysis.AlignmentUtils; |
50 |
|
import jalview.analysis.scoremodels.SimilarityParams; |
51 |
|
import jalview.api.AlignViewportI; |
52 |
|
import jalview.api.AlignmentViewPanel; |
53 |
|
import jalview.api.FeatureColourI; |
54 |
|
import jalview.api.ViewStyleI; |
55 |
|
import jalview.bin.Cache; |
56 |
|
import jalview.datamodel.AlignmentAnnotation; |
57 |
|
import jalview.datamodel.AlignmentI; |
58 |
|
import jalview.datamodel.Annotation; |
59 |
|
import jalview.datamodel.ContactListI; |
60 |
|
import jalview.datamodel.ContactMatrix; |
61 |
|
import jalview.datamodel.ContactMatrixI; |
62 |
|
import jalview.datamodel.DBRefEntry; |
63 |
|
import jalview.datamodel.GeneLocus; |
64 |
|
import jalview.datamodel.GroupSet; |
65 |
|
import jalview.datamodel.HiddenSequences; |
66 |
|
import jalview.datamodel.Mapping; |
67 |
|
import jalview.datamodel.PDBEntry; |
68 |
|
import jalview.datamodel.PDBEntry.Type; |
69 |
|
import jalview.datamodel.Sequence; |
70 |
|
import jalview.datamodel.Sequence.DBModList; |
71 |
|
import jalview.datamodel.SequenceCollectionI; |
72 |
|
import jalview.datamodel.SequenceFeature; |
73 |
|
import jalview.datamodel.SequenceGroup; |
74 |
|
import jalview.datamodel.SequenceI; |
75 |
|
import jalview.datamodel.features.FeatureMatcher; |
76 |
|
import jalview.datamodel.features.FeatureMatcherSet; |
77 |
|
import jalview.datamodel.features.FeatureMatcherSetI; |
78 |
|
import jalview.gui.AlignFrame; |
79 |
|
import jalview.gui.AlignViewport; |
80 |
|
import jalview.gui.AlignmentPanel; |
81 |
|
import jalview.gui.Desktop; |
82 |
|
import jalview.gui.JvOptionPane; |
83 |
|
import jalview.gui.OverviewPanel; |
84 |
|
import jalview.gui.PCAPanel; |
85 |
|
import jalview.gui.PopupMenu; |
86 |
|
import jalview.gui.Preferences; |
87 |
|
import jalview.gui.SliderPanel; |
88 |
|
import jalview.io.DataSourceType; |
89 |
|
import jalview.io.FileFormat; |
90 |
|
import jalview.io.FileLoader; |
91 |
|
import jalview.io.Jalview2xmlBase; |
92 |
|
import jalview.renderer.ResidueShaderI; |
93 |
|
import jalview.schemes.AnnotationColourGradient; |
94 |
|
import jalview.schemes.BuriedColourScheme; |
95 |
|
import jalview.schemes.ColourSchemeI; |
96 |
|
import jalview.schemes.ColourSchemeProperty; |
97 |
|
import jalview.schemes.FeatureColour; |
98 |
|
import jalview.schemes.JalviewColourScheme; |
99 |
|
import jalview.schemes.RNAHelicesColour; |
100 |
|
import jalview.schemes.StrandColourScheme; |
101 |
|
import jalview.schemes.TCoffeeColourScheme; |
102 |
|
import jalview.structure.StructureImportSettings; |
103 |
|
import jalview.util.MapList; |
104 |
|
import jalview.util.matcher.Condition; |
105 |
|
import jalview.viewmodel.AlignmentViewport; |
106 |
|
import jalview.viewmodel.seqfeatures.FeatureRendererModel; |
107 |
|
import jalview.ws.datamodel.MappableContactMatrixI; |
108 |
|
import jalview.ws.datamodel.alphafold.PAEContactMatrix; |
109 |
|
|
110 |
|
@Test(singleThreaded = true) |
|
|
| 96.7% |
Uncovered Elements: 31 (927) |
Complexity: 87 |
Complexity Density: 0.11 |
|
111 |
|
public class Jalview2xmlTests extends Jalview2xmlBase |
112 |
|
{ |
113 |
|
|
|
|
| 83.3% |
Uncovered Elements: 1 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
114 |
1 |
@Override... |
115 |
|
@BeforeClass(alwaysRun = true) |
116 |
|
public void setUpJvOptionPane() |
117 |
|
{ |
118 |
1 |
if (Desktop.instance != null) |
119 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
120 |
1 |
JvOptionPane.setInteractiveMode(false); |
121 |
1 |
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
122 |
|
} |
123 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (18) |
Complexity: 1 |
Complexity Density: 0.06 |
1PASS
|
|
124 |
1 |
@Test(groups = { "Functional" })... |
125 |
|
public void testRNAStructureRecovery() throws Exception |
126 |
|
{ |
127 |
1 |
String inFile = "examples/RF00031_folded.stk"; |
128 |
1 |
String tfile = File.createTempFile("JalviewTest", ".jvp") |
129 |
|
.getAbsolutePath(); |
130 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, |
131 |
|
DataSourceType.FILE); |
132 |
1 |
assertNotNull(af, "Didn't read input file " + inFile); |
133 |
1 |
int olddsann = countDsAnn(af.getViewport()); |
134 |
1 |
assertTrue(olddsann > 0, "Didn't find any dataset annotations"); |
135 |
1 |
af.changeColour_actionPerformed( |
136 |
|
JalviewColourScheme.RNAHelices.toString()); |
137 |
1 |
assertTrue( |
138 |
|
af.getViewport() |
139 |
|
.getGlobalColourScheme() instanceof RNAHelicesColour, |
140 |
|
"Couldn't apply RNA helices colourscheme"); |
141 |
1 |
af.saveAlignment(tfile, FileFormat.Jalview); |
142 |
1 |
assertTrue(af.isSaveAlignmentSuccessful(), |
143 |
|
"Failed to store as a project."); |
144 |
1 |
af.closeMenuItem_actionPerformed(true); |
145 |
1 |
af = null; |
146 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile, |
147 |
|
DataSourceType.FILE); |
148 |
1 |
assertNotNull(af, "Failed to import new project"); |
149 |
1 |
int newdsann = countDsAnn(af.getViewport()); |
150 |
1 |
assertEquals(olddsann, newdsann, |
151 |
|
"Differing numbers of dataset sequence annotation\nOriginally " |
152 |
|
+ olddsann + " and now " + newdsann); |
153 |
1 |
System.out.println( |
154 |
|
"Read in same number of annotations as originally present (" |
155 |
|
+ olddsann + ")"); |
156 |
1 |
assertTrue( |
157 |
|
|
158 |
|
af.getViewport() |
159 |
|
.getGlobalColourScheme() instanceof RNAHelicesColour, |
160 |
|
"RNA helices colourscheme was not applied on import."); |
161 |
|
} |
162 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (16) |
Complexity: 1 |
Complexity Density: 0.06 |
1PASS
|
|
163 |
1 |
@Test(groups = { "Functional" })... |
164 |
|
public void testTCoffeeScores() throws Exception |
165 |
|
{ |
166 |
1 |
String inFile = "examples/uniref50.fa", |
167 |
|
inAnnot = "examples/uniref50.score_ascii"; |
168 |
1 |
String tfile = File.createTempFile("JalviewTest", ".jvp") |
169 |
|
.getAbsolutePath(); |
170 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, |
171 |
|
DataSourceType.FILE); |
172 |
1 |
assertNotNull(af, "Didn't read input file " + inFile); |
173 |
1 |
af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); |
174 |
1 |
AlignViewport viewport = af.getViewport(); |
175 |
1 |
assertSame(viewport.getGlobalColourScheme().getClass(), |
176 |
|
TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme"); |
177 |
1 |
assertNotNull( |
178 |
|
ColourSchemeProperty.getColourScheme(viewport, |
179 |
|
viewport.getAlignment(), |
180 |
|
viewport.getGlobalColourScheme().getSchemeName()), |
181 |
|
"Recognise T-Coffee score from string"); |
182 |
|
|
183 |
1 |
af.saveAlignment(tfile, FileFormat.Jalview); |
184 |
1 |
assertTrue(af.isSaveAlignmentSuccessful(), |
185 |
|
"Failed to store as a project."); |
186 |
1 |
af.closeMenuItem_actionPerformed(true); |
187 |
1 |
af = null; |
188 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile, |
189 |
|
DataSourceType.FILE); |
190 |
1 |
assertNotNull(af, "Failed to import new project"); |
191 |
1 |
assertSame(af.getViewport().getGlobalColourScheme().getClass(), |
192 |
|
TCoffeeColourScheme.class, |
193 |
|
"Didn't set T-coffee colourscheme for imported project."); |
194 |
1 |
System.out.println( |
195 |
|
"T-Coffee score shading successfully recovered from project."); |
196 |
|
} |
197 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (56) |
Complexity: 9 |
Complexity Density: 0.19 |
1PASS
|
|
198 |
1 |
@Test(groups = { "Functional" })... |
199 |
|
public void testColourByAnnotScores() throws Exception |
200 |
|
{ |
201 |
1 |
String inFile = "examples/uniref50.fa", |
202 |
|
inAnnot = "examples/testdata/uniref50_iupred.jva"; |
203 |
1 |
String tfile = File.createTempFile("JalviewTest", ".jvp") |
204 |
|
.getAbsolutePath(); |
205 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, |
206 |
|
DataSourceType.FILE); |
207 |
1 |
assertNotNull(af, "Didn't read input file " + inFile); |
208 |
1 |
af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); |
209 |
1 |
AlignmentAnnotation[] aa = af.getViewport().getAlignment() |
210 |
|
.getSequenceAt(0).getAnnotation("IUPredWS (Short)"); |
211 |
1 |
assertTrue( |
212 |
|
|
213 |
|
aa != null && aa.length > 0, |
214 |
|
"Didn't find any IUPred annotation to use to shade alignment."); |
215 |
1 |
AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null, |
216 |
|
AnnotationColourGradient.ABOVE_THRESHOLD); |
217 |
1 |
AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], null, |
218 |
|
AnnotationColourGradient.BELOW_THRESHOLD); |
219 |
1 |
cs.setSeqAssociated(true); |
220 |
1 |
gcs.setSeqAssociated(true); |
221 |
1 |
af.changeColour(cs); |
222 |
1 |
SequenceGroup sg = new SequenceGroup(); |
223 |
1 |
sg.setStartRes(57); |
224 |
1 |
sg.setEndRes(92); |
225 |
1 |
sg.cs.setColourScheme(gcs); |
226 |
1 |
af.getViewport().getAlignment().addGroup(sg); |
227 |
1 |
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false); |
228 |
1 |
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true); |
229 |
1 |
af.alignPanel.alignmentChanged(); |
230 |
1 |
af.saveAlignment(tfile, FileFormat.Jalview); |
231 |
1 |
assertTrue(af.isSaveAlignmentSuccessful(), |
232 |
|
"Failed to store as a project."); |
233 |
1 |
af.closeMenuItem_actionPerformed(true); |
234 |
1 |
af = null; |
235 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile, |
236 |
|
DataSourceType.FILE); |
237 |
1 |
assertNotNull(af, "Failed to import new project"); |
238 |
|
|
239 |
|
|
240 |
|
|
241 |
1 |
ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme(); |
242 |
1 |
ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups().get(0) |
243 |
|
.getColourScheme(); |
244 |
1 |
assertNotNull(_rcs, "Didn't recover global colourscheme"); |
245 |
1 |
assertTrue(_rcs instanceof AnnotationColourGradient, |
246 |
|
"Didn't recover annotation colour global scheme"); |
247 |
1 |
AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs; |
248 |
1 |
assertTrue(__rcs.isSeqAssociated(), |
249 |
|
"Annotation colourscheme wasn't sequence associated"); |
250 |
|
|
251 |
1 |
boolean diffseqcols = false, diffgseqcols = false; |
252 |
1 |
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); |
253 |
1 |
for (int p = 0, pSize = af.getViewport().getAlignment() |
254 |
158 |
.getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) |
255 |
|
{ |
256 |
157 |
if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs |
257 |
|
.findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f)) |
258 |
|
{ |
259 |
20 |
diffseqcols = true; |
260 |
|
} |
261 |
|
} |
262 |
1 |
assertTrue(diffseqcols, "Got Different sequence colours"); |
263 |
1 |
System.out.println( |
264 |
|
"Per sequence colourscheme (Background) successfully applied and recovered."); |
265 |
|
|
266 |
1 |
assertNotNull(_rgcs, "Didn't recover group colourscheme"); |
267 |
1 |
assertTrue(_rgcs instanceof AnnotationColourGradient, |
268 |
|
"Didn't recover annotation colour group colourscheme"); |
269 |
1 |
__rcs = (AnnotationColourGradient) _rgcs; |
270 |
1 |
assertTrue(__rcs.isSeqAssociated(), |
271 |
|
"Group Annotation colourscheme wasn't sequence associated"); |
272 |
|
|
273 |
1 |
for (int p = 0, pSize = af.getViewport().getAlignment() |
274 |
14 |
.getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) |
275 |
|
{ |
276 |
13 |
if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, |
277 |
|
0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null, |
278 |
|
0f)) |
279 |
|
{ |
280 |
1 |
diffgseqcols = true; |
281 |
|
} |
282 |
|
} |
283 |
1 |
assertTrue(diffgseqcols, "Got Different group sequence colours"); |
284 |
1 |
System.out.println( |
285 |
|
"Per sequence (Group) colourscheme successfully applied and recovered."); |
286 |
|
} |
287 |
|
|
|
|
| 83.3% |
Uncovered Elements: 1 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
1PASS
|
|
288 |
1 |
@Test(groups = { "Functional" })... |
289 |
|
public void gatherViewsHere() throws Exception |
290 |
|
{ |
291 |
1 |
int origCount = Desktop.getDesktopAlignFrames() == null ? 0 |
292 |
|
: Desktop.getDesktopAlignFrames().length; |
293 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
294 |
|
"examples/exampleFile_2_7.jar", DataSourceType.FILE); |
295 |
1 |
assertNotNull(af, "Didn't read in the example file correctly."); |
296 |
1 |
assertTrue(Desktop.getDesktopAlignFrames().length == 1 + origCount, |
297 |
|
"Didn't gather the views in the example file."); |
298 |
|
|
299 |
|
} |
300 |
|
|
301 |
|
|
302 |
|
|
303 |
|
|
304 |
|
@throws |
305 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
1PASS
|
|
306 |
1 |
@Test(groups = { "Functional" })... |
307 |
|
public void noDuplicatePdbMappingsMade() throws Exception |
308 |
|
{ |
309 |
1 |
StructureImportSettings.setProcessSecondaryStructure(true); |
310 |
1 |
StructureImportSettings.setVisibleChainAnnotation(true); |
311 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
312 |
|
"examples/exampleFile_2_7.jar", DataSourceType.FILE); |
313 |
1 |
assertNotNull(af, "Didn't read in the example file correctly."); |
314 |
|
|
315 |
|
|
316 |
|
|
317 |
1 |
String pdbFile = af.getCurrentView().getStructureSelectionManager() |
318 |
|
.findFileForPDBId("1A70"); |
319 |
1 |
assertEquals( |
320 |
|
af.getCurrentView().getStructureSelectionManager() |
321 |
|
.getMapping(pdbFile).length, |
322 |
|
2, "Expected only two mappings for 1A70"); |
323 |
|
|
324 |
|
} |
325 |
|
|
|
|
| 94.6% |
Uncovered Elements: 2 (37) |
Complexity: 6 |
Complexity Density: 0.21 |
1PASS
|
|
326 |
1 |
@Test(groups = { "Functional" })... |
327 |
|
public void viewRefPdbAnnotation() throws Exception |
328 |
|
{ |
329 |
1 |
StructureImportSettings.setProcessSecondaryStructure(true); |
330 |
1 |
StructureImportSettings.setVisibleChainAnnotation(true); |
331 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
332 |
|
"examples/exampleFile_2_7.jar", DataSourceType.FILE); |
333 |
1 |
assertNotNull(af, "Didn't read in the example file correctly."); |
334 |
1 |
AlignmentViewPanel sps = null; |
335 |
1 |
for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) |
336 |
|
{ |
337 |
5 |
if ("Spinach Feredoxin Structure".equals(ap.getViewName())) |
338 |
|
{ |
339 |
1 |
sps = ap; |
340 |
1 |
break; |
341 |
|
} |
342 |
|
} |
343 |
1 |
assertNotNull(sps, "Couldn't find the structure view"); |
344 |
1 |
AlignmentAnnotation refan = null; |
345 |
1 |
for (AlignmentAnnotation ra : sps.getAlignment() |
346 |
|
.getAlignmentAnnotation()) |
347 |
|
{ |
348 |
1 |
if (ra.graph != 0) |
349 |
|
{ |
350 |
1 |
refan = ra; |
351 |
1 |
break; |
352 |
|
} |
353 |
|
} |
354 |
1 |
assertNotNull(refan, "Annotation secondary structure not found."); |
355 |
1 |
SequenceI sq = sps.getAlignment().findName("1A70|"); |
356 |
1 |
assertNotNull(sq, "Couldn't find 1a70 null chain"); |
357 |
|
|
358 |
|
|
359 |
1 |
assertNotNull(sq.getDatasetSequence().getAnnotation(), |
360 |
|
"1a70 has no annotation"); |
361 |
1 |
for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation()) |
362 |
|
{ |
363 |
2 |
AlignmentAnnotation alaa; |
364 |
2 |
sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala)); |
365 |
2 |
alaa.adjustForAlignment(); |
366 |
2 |
if (ala.graph == refan.graph) |
367 |
|
{ |
368 |
98 |
for (int p = 0; p < ala.annotations.length; p++) |
369 |
|
{ |
370 |
97 |
sq.findPosition(p); |
371 |
97 |
try |
372 |
|
{ |
373 |
97 |
assertTrue((alaa.annotations[p] == null |
374 |
|
&& refan.annotations[p] == null) |
375 |
|
|| alaa.annotations[p].value == refan.annotations[p].value, |
376 |
|
"Mismatch at alignment position " + p); |
377 |
|
} catch (NullPointerException q) |
378 |
|
{ |
379 |
0 |
Assert.fail("Mismatch of alignment annotations at position " + p |
380 |
|
+ " Ref seq ann: " + refan.annotations[p] |
381 |
|
+ " alignment " + alaa.annotations[p]); |
382 |
|
} |
383 |
|
} |
384 |
|
} |
385 |
|
} |
386 |
|
|
387 |
|
} |
388 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (20) |
Complexity: 3 |
Complexity Density: 0.19 |
1PASS
|
|
389 |
1 |
@Test(groups = { "Functional" })... |
390 |
|
public void testCopyViewSettings() throws Exception |
391 |
|
{ |
392 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
393 |
|
"examples/exampleFile_2_7.jar", DataSourceType.FILE); |
394 |
1 |
assertNotNull(af, "Didn't read in the example file correctly."); |
395 |
1 |
AlignmentViewPanel sps = null, groups = null; |
396 |
1 |
for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) |
397 |
|
{ |
398 |
5 |
if ("Spinach Feredoxin Structure".equals(ap.getViewName())) |
399 |
|
{ |
400 |
1 |
sps = ap; |
401 |
|
} |
402 |
5 |
if (ap.getViewName().contains("MAFFT")) |
403 |
|
{ |
404 |
1 |
groups = ap; |
405 |
|
} |
406 |
|
} |
407 |
1 |
assertNotNull(sps, "Couldn't find the structure view"); |
408 |
1 |
assertNotNull(groups, "Couldn't find the MAFFT view"); |
409 |
|
|
410 |
1 |
ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle(); |
411 |
1 |
ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle(); |
412 |
1 |
AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle)); |
413 |
|
|
414 |
1 |
groups.getAlignViewport().setViewStyle(structureStyle); |
415 |
1 |
AssertJUnit.assertFalse( |
416 |
|
groupStyle.sameStyle(groups.getAlignViewport().getViewStyle())); |
417 |
1 |
Assert.assertTrue(structureStyle |
418 |
|
.sameStyle(groups.getAlignViewport().getViewStyle())); |
419 |
|
|
420 |
|
} |
421 |
|
|
422 |
|
|
423 |
|
|
424 |
|
|
425 |
|
@throws |
426 |
|
|
|
|
| 81.8% |
Uncovered Elements: 4 (22) |
Complexity: 4 |
Complexity Density: 0.2 |
1PASS
|
|
427 |
1 |
@Test(groups = { "Functional" }, enabled = true)... |
428 |
|
public void testStoreAndRecoverExpandedviews() throws Exception |
429 |
|
{ |
430 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
431 |
|
|
432 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
433 |
|
"examples/exampleFile_2_7.jar", DataSourceType.FILE); |
434 |
1 |
Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 1); |
435 |
1 |
String afid = af.getViewport().getSequenceSetId(); |
436 |
|
|
437 |
|
|
438 |
|
|
439 |
1 |
assertSame(af, Desktop.getAlignFrameFor(af.getViewport()), |
440 |
|
"Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window"); |
441 |
|
|
442 |
1 |
Desktop.explodeViews(af); |
443 |
|
|
444 |
1 |
int oldviews = Desktop.getDesktopAlignFrames().length; |
445 |
1 |
Assert.assertEquals(Desktop.getDesktopAlignFrames().length, |
446 |
|
Desktop.getAlignmentPanels(afid).length); |
447 |
1 |
File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp"); |
448 |
1 |
try |
449 |
|
{ |
450 |
1 |
new Jalview2XML(false).saveState(tfile); |
451 |
|
} catch (Error e) |
452 |
|
{ |
453 |
0 |
Assert.fail("Didn't save the expanded view state", e); |
454 |
|
} catch (Exception e) |
455 |
|
{ |
456 |
0 |
Assert.fail("Didn't save the expanded view state", e); |
457 |
|
} |
458 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
459 |
1 |
if (Desktop.getDesktopAlignFrames() != null) |
460 |
|
{ |
461 |
0 |
Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); |
462 |
|
} |
463 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), |
464 |
|
DataSourceType.FILE); |
465 |
1 |
Assert.assertNotNull(af); |
466 |
1 |
Assert.assertEquals(Desktop.getDesktopAlignFrames().length, |
467 |
|
Desktop.getAlignmentPanels( |
468 |
|
af.getViewport().getSequenceSetId()).length); |
469 |
1 |
Assert.assertEquals(Desktop |
470 |
|
.getAlignmentPanels(af.getViewport().getSequenceSetId()).length, |
471 |
|
oldviews); |
472 |
|
} |
473 |
|
|
474 |
|
|
475 |
|
|
476 |
|
|
477 |
|
|
478 |
|
@throws |
479 |
|
|
|
|
| 91.2% |
Uncovered Elements: 3 (34) |
Complexity: 3 |
Complexity Density: 0.09 |
1PASS
|
|
480 |
1 |
@Test(groups = { "Functional" })... |
481 |
|
public void testStoreAndRecoverReferenceSeqSettings() throws Exception |
482 |
|
{ |
483 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
484 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
485 |
|
"examples/exampleFile_2_7.jar", DataSourceType.FILE); |
486 |
1 |
assertNotNull(af, "Didn't read in the example file correctly."); |
487 |
1 |
String afid = af.getViewport().getSequenceSetId(); |
488 |
|
|
489 |
|
|
490 |
1 |
Map<String, SequenceI> refseqs = new HashMap<>(); |
491 |
|
|
492 |
|
|
493 |
|
|
494 |
|
|
495 |
|
|
496 |
1 |
int n = 1; |
497 |
1 |
for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) |
498 |
|
{ |
499 |
3 |
AlignViewportI av = ap.getAlignViewport(); |
500 |
3 |
AlignmentI alignment = ap.getAlignment(); |
501 |
3 |
int repIndex = n % alignment.getHeight(); |
502 |
3 |
SequenceI rep = alignment.getSequenceAt(repIndex); |
503 |
3 |
refseqs.put(ap.getViewName(), rep); |
504 |
|
|
505 |
|
|
506 |
|
|
507 |
3 |
av.setDisplayReferenceSeq(true); |
508 |
3 |
av.setColourByReferenceSeq(true); |
509 |
3 |
av.getAlignment().setSeqrep(rep); |
510 |
|
|
511 |
3 |
n++; |
512 |
|
} |
513 |
1 |
File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq", |
514 |
|
".jvp"); |
515 |
1 |
try |
516 |
|
{ |
517 |
1 |
new Jalview2XML(false).saveState(tfile); |
518 |
|
} catch (Throwable e) |
519 |
|
{ |
520 |
0 |
Assert.fail("Didn't save the expanded view state", e); |
521 |
|
} |
522 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
523 |
1 |
if (Desktop.getDesktopAlignFrames() != null) |
524 |
|
{ |
525 |
0 |
Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); |
526 |
|
} |
527 |
|
|
528 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), |
529 |
|
DataSourceType.FILE); |
530 |
1 |
afid = af.getViewport().getSequenceSetId(); |
531 |
|
|
532 |
1 |
for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) |
533 |
|
{ |
534 |
|
|
535 |
3 |
AlignmentI alignment = ap.getAlignment(); |
536 |
3 |
SequenceI rep = alignment.getSeqrep(); |
537 |
3 |
Assert.assertNotNull(rep, |
538 |
|
"Couldn't restore sequence representative from project"); |
539 |
|
|
540 |
|
|
541 |
|
|
542 |
|
|
543 |
3 |
Assert.assertEquals(refseqs.get(ap.getViewName()).toString(), |
544 |
|
rep.toString(), |
545 |
|
"Representative wasn't the same when recovered."); |
546 |
3 |
Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(), |
547 |
|
"Display reference sequence view setting not set."); |
548 |
3 |
Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(), |
549 |
|
"Colour By Reference Seq view setting not set."); |
550 |
|
} |
551 |
|
} |
552 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (31) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
553 |
1 |
@Test(groups = { "Functional" })... |
554 |
|
public void testIsVersionStringLaterThan() |
555 |
|
{ |
556 |
|
|
557 |
|
|
558 |
|
|
559 |
|
|
560 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan(null, null)); |
561 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null)); |
562 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3")); |
563 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan(null, |
564 |
|
"Development Build")); |
565 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan(null, |
566 |
|
"DEVELOPMENT BUILD")); |
567 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", |
568 |
|
"Development Build")); |
569 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test")); |
570 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST")); |
571 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test")); |
572 |
1 |
assertTrue( |
573 |
|
Jalview2XML.isVersionStringLaterThan(null, "Automated Build")); |
574 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", |
575 |
|
"Automated Build")); |
576 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", |
577 |
|
"AUTOMATED BUILD")); |
578 |
|
|
579 |
|
|
580 |
|
|
581 |
|
|
582 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8")); |
583 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3")); |
584 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1")); |
585 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1")); |
586 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1")); |
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
|
591 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4")); |
592 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9")); |
593 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2")); |
594 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3")); |
595 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1")); |
596 |
|
|
597 |
|
|
598 |
|
|
599 |
|
|
600 |
1 |
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8")); |
601 |
1 |
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3")); |
602 |
1 |
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3")); |
603 |
1 |
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1")); |
604 |
1 |
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1")); |
605 |
|
|
606 |
|
|
607 |
|
|
608 |
1 |
assertFalse(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.2")); |
609 |
1 |
assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.4")); |
610 |
1 |
assertFalse( |
611 |
|
Jalview2XML.isVersionStringLaterThan("2.12.2.0b1", "2.12.2.0")); |
612 |
1 |
assertFalse( |
613 |
|
Jalview2XML.isVersionStringLaterThan("2.12.2.3", "2.12.2.2")); |
614 |
|
|
615 |
|
} |
616 |
|
|
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
@throws |
622 |
|
|
|
|
| 95.3% |
Uncovered Elements: 3 (64) |
Complexity: 3 |
Complexity Density: 0.05 |
1PASS
|
|
623 |
1 |
@Test(groups = { "Functional" })... |
624 |
|
public void testStoreAndRecoverGroupRepSeqs() throws Exception |
625 |
|
{ |
626 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
627 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
628 |
|
"examples/uniref50.fa", DataSourceType.FILE); |
629 |
1 |
assertNotNull(af, "Didn't read in the example file correctly."); |
630 |
1 |
String afid = af.getViewport().getSequenceSetId(); |
631 |
|
|
632 |
1 |
af.newView_actionPerformed(null); |
633 |
|
|
634 |
|
|
635 |
|
|
636 |
|
|
637 |
|
|
638 |
1 |
Map<String, SequenceI> repSeqs = new HashMap<>(); |
639 |
1 |
Map<String, List<String>> hiddenSeqNames = new HashMap<>(); |
640 |
|
|
641 |
|
|
642 |
|
|
643 |
|
|
644 |
|
|
645 |
1 |
int n = 1; |
646 |
1 |
for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) |
647 |
|
{ |
648 |
2 |
AlignViewportI av = ap.getAlignViewport(); |
649 |
2 |
AlignmentI alignment = ap.getAlignment(); |
650 |
2 |
int repIndex = n % alignment.getHeight(); |
651 |
|
|
652 |
2 |
repIndex = Math.max(repIndex, 1); |
653 |
2 |
SequenceI repSeq = alignment.getSequenceAt(repIndex); |
654 |
2 |
repSeqs.put(ap.getViewName(), repSeq); |
655 |
2 |
List<String> hiddenNames = new ArrayList<>(); |
656 |
2 |
hiddenSeqNames.put(ap.getViewName(), hiddenNames); |
657 |
|
|
658 |
|
|
659 |
|
|
660 |
|
|
661 |
|
|
662 |
2 |
SequenceGroup sg = new SequenceGroup(); |
663 |
2 |
sg.addSequence(repSeq, false); |
664 |
2 |
SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1); |
665 |
2 |
sg.addSequence(precedingSeq, false); |
666 |
2 |
sg.setSeqrep(repSeq); |
667 |
2 |
assertTrue(sg.getSequences().contains(repSeq)); |
668 |
2 |
assertTrue(sg.getSequences().contains(precedingSeq)); |
669 |
2 |
av.setSelectionGroup(sg); |
670 |
2 |
assertSame(repSeq, sg.getSeqrep()); |
671 |
|
|
672 |
|
|
673 |
|
|
674 |
|
|
675 |
|
|
676 |
2 |
((AlignmentViewport) av).hideSequences(repSeq, true); |
677 |
2 |
assertSame(repSeq, sg.getSeqrep()); |
678 |
2 |
assertTrue(sg.getSequences().contains(repSeq)); |
679 |
2 |
assertTrue(sg.getSequences().contains(precedingSeq)); |
680 |
2 |
assertTrue(alignment.getGroups().isEmpty(), "alignment has groups"); |
681 |
2 |
Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av |
682 |
|
.getHiddenRepSequences(); |
683 |
2 |
assertNotNull(hiddenRepSeqsMap); |
684 |
2 |
assertEquals(1, hiddenRepSeqsMap.size()); |
685 |
2 |
assertSame(sg, hiddenRepSeqsMap.get(repSeq)); |
686 |
2 |
assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq)); |
687 |
2 |
assertFalse(alignment.getHiddenSequences().isHidden(repSeq)); |
688 |
2 |
hiddenNames.add(precedingSeq.getName()); |
689 |
|
|
690 |
2 |
n++; |
691 |
|
} |
692 |
1 |
File tfile = File.createTempFile("testStoreAndRecoverGroupReps", |
693 |
|
".jvp"); |
694 |
1 |
try |
695 |
|
{ |
696 |
1 |
new Jalview2XML(false).saveState(tfile); |
697 |
|
} catch (Throwable e) |
698 |
|
{ |
699 |
0 |
Assert.fail("Didn't save the expanded view state", e); |
700 |
|
} |
701 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
702 |
1 |
if (Desktop.getDesktopAlignFrames() != null) |
703 |
|
{ |
704 |
0 |
Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); |
705 |
|
} |
706 |
|
|
707 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), |
708 |
|
DataSourceType.FILE); |
709 |
1 |
afid = af.getViewport().getSequenceSetId(); |
710 |
|
|
711 |
1 |
for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) |
712 |
|
{ |
713 |
2 |
String viewName = ap.getViewName(); |
714 |
2 |
AlignViewportI av = ap.getAlignViewport(); |
715 |
2 |
AlignmentI alignment = ap.getAlignment(); |
716 |
2 |
List<SequenceGroup> groups = alignment.getGroups(); |
717 |
2 |
assertNotNull(groups); |
718 |
2 |
assertTrue(groups.isEmpty(), "Alignment has groups"); |
719 |
2 |
Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av |
720 |
|
.getHiddenRepSequences(); |
721 |
2 |
assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences"); |
722 |
2 |
assertEquals(1, hiddenRepSeqsMap.size()); |
723 |
2 |
assertEquals(repSeqs.get(viewName).getDisplayId(true), |
724 |
|
hiddenRepSeqsMap.keySet().iterator().next() |
725 |
|
.getDisplayId(true)); |
726 |
|
|
727 |
|
|
728 |
|
|
729 |
|
|
730 |
2 |
List<String> hidden = hiddenSeqNames.get(ap.getViewName()); |
731 |
2 |
HiddenSequences hs = alignment.getHiddenSequences(); |
732 |
2 |
assertEquals(hidden.size(), hs.getSize(), |
733 |
|
"wrong number of restored hidden sequences in " |
734 |
|
+ ap.getViewName()); |
735 |
|
} |
736 |
|
} |
737 |
|
|
738 |
|
|
739 |
|
|
740 |
|
|
741 |
|
@throws |
742 |
|
|
|
|
| 95.3% |
Uncovered Elements: 3 (64) |
Complexity: 4 |
Complexity Density: 0.07 |
1PASS
|
|
743 |
1 |
@Test(groups = { "Functional" })... |
744 |
|
public void testStoreAndRecoverPDBEntry() throws Exception |
745 |
|
{ |
746 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
747 |
1 |
String exampleFile = "examples/3W5V.pdb"; |
748 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile, |
749 |
|
DataSourceType.FILE); |
750 |
1 |
assertNotNull(af, "Didn't read in the example file correctly."); |
751 |
1 |
String afid = af.getViewport().getSequenceSetId(); |
752 |
|
|
753 |
1 |
AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid); |
754 |
1 |
System.out.println(); |
755 |
1 |
AlignmentViewPanel ap = alignPanels[0]; |
756 |
1 |
String tfileBase = new File(".").getAbsolutePath().replace(".", ""); |
757 |
1 |
String testFile = tfileBase + exampleFile; |
758 |
1 |
AlignmentI alignment = ap.getAlignment(); |
759 |
1 |
System.out.println("blah"); |
760 |
1 |
SequenceI[] seqs = alignment.getSequencesArray(); |
761 |
1 |
Assert.assertNotNull(seqs[0]); |
762 |
1 |
Assert.assertNotNull(seqs[1]); |
763 |
1 |
Assert.assertNotNull(seqs[2]); |
764 |
1 |
Assert.assertNotNull(seqs[3]); |
765 |
1 |
Assert.assertNotNull(seqs[0].getDatasetSequence()); |
766 |
1 |
Assert.assertNotNull(seqs[1].getDatasetSequence()); |
767 |
1 |
Assert.assertNotNull(seqs[2].getDatasetSequence()); |
768 |
1 |
Assert.assertNotNull(seqs[3].getDatasetSequence()); |
769 |
1 |
PDBEntry[] pdbEntries = new PDBEntry[4]; |
770 |
1 |
pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile); |
771 |
1 |
pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile); |
772 |
1 |
pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile); |
773 |
1 |
pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile); |
774 |
1 |
Assert.assertEquals( |
775 |
|
seqs[0].getDatasetSequence().getAllPDBEntries().get(0), |
776 |
|
pdbEntries[0]); |
777 |
1 |
Assert.assertEquals( |
778 |
|
seqs[1].getDatasetSequence().getAllPDBEntries().get(0), |
779 |
|
pdbEntries[1]); |
780 |
1 |
Assert.assertEquals( |
781 |
|
seqs[2].getDatasetSequence().getAllPDBEntries().get(0), |
782 |
|
pdbEntries[2]); |
783 |
1 |
Assert.assertEquals( |
784 |
|
seqs[3].getDatasetSequence().getAllPDBEntries().get(0), |
785 |
|
pdbEntries[3]); |
786 |
|
|
787 |
1 |
File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp"); |
788 |
1 |
try |
789 |
|
{ |
790 |
1 |
new Jalview2XML(false).saveState(tfile); |
791 |
|
} catch (Throwable e) |
792 |
|
{ |
793 |
0 |
Assert.fail("Didn't save the state", e); |
794 |
|
} |
795 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
796 |
1 |
if (Desktop.getDesktopAlignFrames() != null) |
797 |
|
{ |
798 |
0 |
Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); |
799 |
|
} |
800 |
|
|
801 |
1 |
AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded( |
802 |
|
tfile.getAbsolutePath(), DataSourceType.FILE); |
803 |
1 |
String rfid = restoredFrame.getViewport().getSequenceSetId(); |
804 |
1 |
AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid); |
805 |
1 |
AlignmentViewPanel rap = rAlignPanels[0]; |
806 |
1 |
AlignmentI rAlignment = rap.getAlignment(); |
807 |
1 |
System.out.println("blah"); |
808 |
1 |
SequenceI[] rseqs = rAlignment.getSequencesArray(); |
809 |
1 |
Assert.assertNotNull(rseqs[0]); |
810 |
1 |
Assert.assertNotNull(rseqs[1]); |
811 |
1 |
Assert.assertNotNull(rseqs[2]); |
812 |
1 |
Assert.assertNotNull(rseqs[3]); |
813 |
1 |
Assert.assertNotNull(rseqs[0].getDatasetSequence()); |
814 |
1 |
Assert.assertNotNull(rseqs[1].getDatasetSequence()); |
815 |
1 |
Assert.assertNotNull(rseqs[2].getDatasetSequence()); |
816 |
1 |
Assert.assertNotNull(rseqs[3].getDatasetSequence()); |
817 |
|
|
818 |
|
|
819 |
|
|
820 |
5 |
for (int chain = 0; chain < 4; chain++) |
821 |
|
{ |
822 |
4 |
PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries() |
823 |
|
.get(0); |
824 |
4 |
PDBEntry expected = pdbEntries[chain]; |
825 |
4 |
Assert.assertEquals(recov.getId(), expected.getId(), |
826 |
|
"Mismatch PDB ID"); |
827 |
4 |
Assert.assertEquals(recov.getChainCode(), expected.getChainCode(), |
828 |
|
"Mismatch PDB ID"); |
829 |
4 |
Assert.assertEquals(recov.getType(), expected.getType(), |
830 |
|
"Mismatch PDBEntry 'Type'"); |
831 |
4 |
Assert.assertNotNull(recov.getFile(), |
832 |
|
"Recovered PDBEntry should have a non-null file entry"); |
833 |
4 |
Assert.assertEquals( |
834 |
|
recov.getFile().toLowerCase(Locale.ENGLISH) |
835 |
|
.lastIndexOf("pdb"), |
836 |
|
recov.getFile().length() - 3, |
837 |
|
"Recovered PDBEntry file should have PDB suffix"); |
838 |
|
} |
839 |
|
} |
840 |
|
|
841 |
|
|
842 |
|
|
843 |
|
|
844 |
|
|
845 |
|
|
846 |
|
@throws |
847 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (49) |
Complexity: 3 |
Complexity Density: 0.07 |
1PASS
|
|
848 |
1 |
@Test(groups = { "Functional" })... |
849 |
|
public void testStoreAndRecoverAnnotationRowElementColours() |
850 |
|
throws IOException |
851 |
|
{ |
852 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
853 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded("SEQ\tMNQ", |
854 |
|
DataSourceType.PASTE); |
855 |
|
|
856 |
1 |
AlignViewport av = af.getViewport(); |
857 |
1 |
AlignmentI al = av.getAlignment(); |
858 |
1 |
SequenceI fsq; |
859 |
1 |
fsq = al.getSequenceAt(0); |
860 |
1 |
Annotation annots[] = new Annotation[fsq.getLength()]; |
861 |
1 |
AlignmentAnnotation ala = new AlignmentAnnotation("Colour", "Annots", |
862 |
|
annots); |
863 |
1 |
annots[0] = new Annotation(1.0f); |
864 |
1 |
annots[1] = new Annotation(2.0f); |
865 |
1 |
annots[2] = new Annotation(3.0f); |
866 |
1 |
annots[0].colour = Color.RED; |
867 |
1 |
annots[1].colour = Color.GREEN; |
868 |
1 |
annots[2].colour = Color.BLUE; |
869 |
1 |
ala.validateRangeAndDisplay(); |
870 |
1 |
al.getSequenceAt(0).addAlignmentAnnotation(ala); |
871 |
1 |
al.addAnnotation(ala); |
872 |
|
|
873 |
|
|
874 |
|
|
875 |
1 |
AnnotationColourGradient acg = new AnnotationColourGradient(ala, |
876 |
|
af.alignPanel.av.getGlobalColourScheme(), 0); |
877 |
1 |
acg.setSeqAssociated(true); |
878 |
1 |
acg.setPredefinedColours(true); |
879 |
1 |
af.changeColour(acg); |
880 |
1 |
Color seqcol[] = new Color[3]; |
881 |
4 |
for (int iStart = fsq.findIndex(fsq.getStart()), i = 0; i < 3; i++) |
882 |
|
{ |
883 |
3 |
seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas |
884 |
|
.getSequenceRenderer() |
885 |
|
.getResidueColour(fsq, iStart + i, null); |
886 |
|
} |
887 |
|
|
888 |
|
|
889 |
|
|
890 |
1 |
File tfile = File.createTempFile( |
891 |
|
"testStoreAndRecoverAnnotRowElemColors", ".jvp"); |
892 |
1 |
tfile.deleteOnExit(); |
893 |
1 |
new Jalview2XML(false).saveState(tfile); |
894 |
|
|
895 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), |
896 |
|
DataSourceType.FILE); |
897 |
1 |
Assert.assertNotNull(af, "Failed to reload project"); |
898 |
|
|
899 |
|
|
900 |
|
|
901 |
1 |
av = af.getViewport(); |
902 |
|
|
903 |
1 |
ColourSchemeI loadedCscheme = av.getGlobalColourScheme(); |
904 |
1 |
Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient, |
905 |
|
"Didn't apply Annotation colour gradient"); |
906 |
1 |
acg = (AnnotationColourGradient) loadedCscheme; |
907 |
1 |
assertTrue(acg.isSeqAssociated()); |
908 |
1 |
assertTrue(acg.isPredefinedColours()); |
909 |
|
|
910 |
1 |
al = av.getAlignment(); |
911 |
1 |
fsq = al.getSequenceAt(0); |
912 |
1 |
ala = fsq.getAnnotation()[0]; |
913 |
1 |
Assert.assertNotNull(ala, "No annotation row recovered"); |
914 |
1 |
Assert.assertNotNull(ala.annotations); |
915 |
1 |
for (int iStart = al.getSequenceAt(0) |
916 |
4 |
.findIndex(al.getSequenceAt(0).getStart()), i = 0; i < 3; i++) |
917 |
|
{ |
918 |
3 |
Assert.assertTrue(ala.annotations[i].colour != null); |
919 |
3 |
Assert.assertTrue(ala.annotations[i].colour.equals(annots[i].colour)); |
920 |
3 |
Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas |
921 |
|
.getSequenceRenderer() |
922 |
|
.getResidueColour(fsq, iStart + i, null); |
923 |
3 |
Assert.assertTrue(seqcol[i].equals(newseqcol), |
924 |
|
"Sequence shading is different"); |
925 |
|
|
926 |
|
} |
927 |
|
|
928 |
|
} |
929 |
|
|
930 |
|
|
931 |
|
|
932 |
|
|
933 |
|
|
934 |
|
|
935 |
|
@throws |
936 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (57) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
|
937 |
1 |
@Test(groups = { "Functional" })... |
938 |
|
public void testStoreAndRecoverColourThresholds() throws IOException |
939 |
|
{ |
940 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
941 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
942 |
|
"examples/uniref50.fa", DataSourceType.FILE); |
943 |
|
|
944 |
1 |
AlignViewport av = af.getViewport(); |
945 |
1 |
AlignmentI al = av.getAlignment(); |
946 |
|
|
947 |
|
|
948 |
|
|
949 |
|
|
950 |
1 |
av.setColourAppliesToAllGroups(false); |
951 |
1 |
af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString()); |
952 |
1 |
assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme); |
953 |
1 |
af.abovePIDThreshold_actionPerformed(true); |
954 |
1 |
SliderPanel sp = SliderPanel.getSliderPanel(); |
955 |
1 |
assertFalse(sp.isForConservation()); |
956 |
1 |
sp.valueChanged(10); |
957 |
1 |
af.conservationMenuItem_actionPerformed(true); |
958 |
1 |
sp = SliderPanel.getSliderPanel(); |
959 |
1 |
assertTrue(sp.isForConservation()); |
960 |
1 |
sp.valueChanged(20); |
961 |
1 |
ResidueShaderI rs = av.getResidueShading(); |
962 |
1 |
assertEquals(rs.getThreshold(), 10); |
963 |
1 |
assertTrue(rs.conservationApplied()); |
964 |
1 |
assertEquals(rs.getConservationInc(), 20); |
965 |
|
|
966 |
|
|
967 |
|
|
968 |
|
|
969 |
|
|
970 |
|
|
971 |
|
|
972 |
1 |
SequenceGroup sg = new SequenceGroup(); |
973 |
1 |
sg.addSequence(al.getSequenceAt(0), false); |
974 |
1 |
sg.setStartRes(15); |
975 |
1 |
sg.setEndRes(25); |
976 |
1 |
av.setSelectionGroup(sg); |
977 |
1 |
PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2), |
978 |
|
null); |
979 |
1 |
popupMenu.changeColour_actionPerformed( |
980 |
|
JalviewColourScheme.Strand.toString()); |
981 |
1 |
assertTrue(sg.getColourScheme() instanceof StrandColourScheme); |
982 |
1 |
assertEquals(al.getGroups().size(), 1); |
983 |
1 |
assertSame(al.getGroups().get(0), sg); |
984 |
1 |
popupMenu.conservationMenuItem_actionPerformed(true); |
985 |
1 |
sp = SliderPanel.getSliderPanel(); |
986 |
1 |
assertTrue(sp.isForConservation()); |
987 |
1 |
sp.valueChanged(30); |
988 |
1 |
popupMenu.abovePIDColour_actionPerformed(true); |
989 |
1 |
sp = SliderPanel.getSliderPanel(); |
990 |
1 |
assertFalse(sp.isForConservation()); |
991 |
1 |
sp.valueChanged(40); |
992 |
1 |
assertTrue(sg.getGroupColourScheme().conservationApplied()); |
993 |
1 |
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); |
994 |
1 |
assertEquals(sg.getGroupColourScheme().getThreshold(), 40); |
995 |
|
|
996 |
|
|
997 |
|
|
998 |
|
|
999 |
1 |
File tfile = File.createTempFile("testStoreAndRecoverColourThresholds", |
1000 |
|
".jvp"); |
1001 |
1 |
tfile.deleteOnExit(); |
1002 |
1 |
new Jalview2XML(false).saveState(tfile); |
1003 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1004 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), |
1005 |
|
DataSourceType.FILE); |
1006 |
1 |
Assert.assertNotNull(af, "Failed to reload project"); |
1007 |
|
|
1008 |
|
|
1009 |
|
|
1010 |
|
|
1011 |
1 |
rs = af.getViewport().getResidueShading(); |
1012 |
1 |
assertTrue(rs.getColourScheme() instanceof BuriedColourScheme); |
1013 |
1 |
assertEquals(rs.getThreshold(), 10); |
1014 |
1 |
assertTrue(rs.conservationApplied()); |
1015 |
1 |
assertEquals(rs.getConservationInc(), 20); |
1016 |
|
|
1017 |
|
|
1018 |
|
|
1019 |
|
|
1020 |
1 |
assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1); |
1021 |
1 |
rs = af.getViewport().getAlignment().getGroups().get(0) |
1022 |
|
.getGroupColourScheme(); |
1023 |
1 |
assertTrue(rs.getColourScheme() instanceof StrandColourScheme); |
1024 |
1 |
assertEquals(rs.getThreshold(), 40); |
1025 |
1 |
assertTrue(rs.conservationApplied()); |
1026 |
1 |
assertEquals(rs.getConservationInc(), 30); |
1027 |
|
} |
1028 |
|
|
1029 |
|
|
1030 |
|
|
1031 |
|
|
1032 |
|
@throws |
1033 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (71) |
Complexity: 1 |
Complexity Density: 0.01 |
1PASS
|
|
1034 |
1 |
@Test(groups = { "Functional" })... |
1035 |
|
public void testSaveLoadFeatureColoursAndFilters() throws IOException |
1036 |
|
{ |
1037 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
1038 |
|
">Seq1\nACDEFGHIKLM", DataSourceType.PASTE); |
1039 |
1 |
SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0); |
1040 |
|
|
1041 |
|
|
1042 |
|
|
1043 |
|
|
1044 |
1 |
int score = 1; |
1045 |
1 |
addFeatures(seq1, "type1", score++); |
1046 |
1 |
addFeatures(seq1, "type2", score++); |
1047 |
1 |
addFeatures(seq1, "type3", score++); |
1048 |
1 |
addFeatures(seq1, "type4", score++); |
1049 |
1 |
addFeatures(seq1, "type5", score++); |
1050 |
|
|
1051 |
|
|
1052 |
|
|
1053 |
|
|
1054 |
1 |
FeatureRendererModel fr = af.getFeatureRenderer(); |
1055 |
1 |
fr.findAllFeatures(true); |
1056 |
|
|
1057 |
|
|
1058 |
1 |
fr.setColour("type1", new FeatureColour(Color.red)); |
1059 |
|
|
1060 |
|
|
1061 |
1 |
FeatureColourI byLabel = new FeatureColour(); |
1062 |
1 |
byLabel.setColourByLabel(true); |
1063 |
1 |
fr.setColour("type2", byLabel); |
1064 |
|
|
1065 |
|
|
1066 |
1 |
FeatureColourI byScore = new FeatureColour(null, Color.BLACK, |
1067 |
|
Color.BLUE, null, 1, 10); |
1068 |
1 |
byScore.setAboveThreshold(true); |
1069 |
1 |
byScore.setThreshold(2f); |
1070 |
1 |
fr.setColour("type3", byScore); |
1071 |
|
|
1072 |
|
|
1073 |
1 |
FeatureColourI byAF = new FeatureColour(); |
1074 |
1 |
byAF.setColourByLabel(true); |
1075 |
1 |
byAF.setAttributeName("AF"); |
1076 |
1 |
fr.setColour("type4", byAF); |
1077 |
|
|
1078 |
|
|
1079 |
1 |
FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK, |
1080 |
|
Color.BLUE, null, 1, 10); |
1081 |
1 |
byPolyPhen.setBelowThreshold(true); |
1082 |
1 |
byPolyPhen.setThreshold(3f); |
1083 |
1 |
byPolyPhen.setAttributeName("CSQ", "PolyPhen"); |
1084 |
1 |
fr.setColour("type5", byPolyPhen); |
1085 |
|
|
1086 |
|
|
1087 |
|
|
1088 |
|
|
1089 |
|
|
1090 |
|
|
1091 |
1 |
FeatureMatcherSetI filterByX = new FeatureMatcherSet(); |
1092 |
1 |
filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x")); |
1093 |
1 |
fr.setFeatureFilter("type1", filterByX); |
1094 |
|
|
1095 |
|
|
1096 |
1 |
FeatureMatcherSetI filterByScore = new FeatureMatcherSet(); |
1097 |
1 |
filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4")); |
1098 |
1 |
filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1")); |
1099 |
1 |
fr.setFeatureFilter("type2", filterByScore); |
1100 |
|
|
1101 |
|
|
1102 |
1 |
FeatureMatcherSetI filterByXY = new FeatureMatcherSet(); |
1103 |
1 |
filterByXY |
1104 |
|
.and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF")); |
1105 |
1 |
filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ", |
1106 |
|
"PolyPhen")); |
1107 |
1 |
fr.setFeatureFilter("type3", filterByXY); |
1108 |
|
|
1109 |
|
|
1110 |
|
|
1111 |
|
|
1112 |
1 |
File tfile = File.createTempFile("JalviewTest", ".jvp"); |
1113 |
1 |
tfile.deleteOnExit(); |
1114 |
1 |
String filePath = tfile.getAbsolutePath(); |
1115 |
1 |
af.saveAlignment(filePath, FileFormat.Jalview); |
1116 |
1 |
assertTrue(af.isSaveAlignmentSuccessful(), |
1117 |
|
"Failed to store as a project."); |
1118 |
|
|
1119 |
|
|
1120 |
|
|
1121 |
|
|
1122 |
1 |
af.closeMenuItem_actionPerformed(true); |
1123 |
1 |
af = null; |
1124 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(filePath, |
1125 |
|
DataSourceType.FILE); |
1126 |
1 |
assertNotNull(af, "Failed to import new project"); |
1127 |
|
|
1128 |
|
|
1129 |
|
|
1130 |
|
|
1131 |
1 |
fr = af.getFeatureRenderer(); |
1132 |
1 |
FeatureColourI fc = fr.getFeatureStyle("type1"); |
1133 |
1 |
assertTrue(fc.isSimpleColour()); |
1134 |
1 |
assertEquals(fc.getColour(), Color.red); |
1135 |
1 |
fc = fr.getFeatureStyle("type2"); |
1136 |
1 |
assertTrue(fc.isColourByLabel()); |
1137 |
1 |
fc = fr.getFeatureStyle("type3"); |
1138 |
1 |
assertTrue(fc.isGraduatedColour()); |
1139 |
1 |
assertNull(fc.getAttributeName()); |
1140 |
1 |
assertTrue(fc.isAboveThreshold()); |
1141 |
1 |
assertEquals(fc.getThreshold(), 2f); |
1142 |
1 |
fc = fr.getFeatureStyle("type4"); |
1143 |
1 |
assertTrue(fc.isColourByLabel()); |
1144 |
1 |
assertTrue(fc.isColourByAttribute()); |
1145 |
1 |
assertEquals(fc.getAttributeName(), new String[] { "AF" }); |
1146 |
1 |
fc = fr.getFeatureStyle("type5"); |
1147 |
1 |
assertTrue(fc.isGraduatedColour()); |
1148 |
1 |
assertTrue(fc.isColourByAttribute()); |
1149 |
1 |
assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" }); |
1150 |
1 |
assertTrue(fc.isBelowThreshold()); |
1151 |
1 |
assertEquals(fc.getThreshold(), 3f); |
1152 |
|
|
1153 |
1 |
assertEquals(fr.getFeatureFilter("type1").toStableString(), |
1154 |
|
"Label Contains x"); |
1155 |
1 |
assertEquals(fr.getFeatureFilter("type2").toStableString(), |
1156 |
|
"(Score LE 2.4) AND (Score GT 1.1)"); |
1157 |
1 |
assertEquals(fr.getFeatureFilter("type3").toStableString(), |
1158 |
|
"(AF Contains X) OR (CSQ:PolyPhen NE 0)"); |
1159 |
|
} |
1160 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
1161 |
10 |
private void addFeature(SequenceI seq, String featureType, int score)... |
1162 |
|
{ |
1163 |
10 |
SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2, |
1164 |
|
score, "grp"); |
1165 |
10 |
sf.setValue("AF", score); |
1166 |
10 |
sf.setValue("CSQ", new HashMap<String, String>() |
1167 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1168 |
10 |
{... |
1169 |
10 |
put("PolyPhen", Integer.toString(score)); |
1170 |
|
} |
1171 |
|
}); |
1172 |
10 |
seq.addSequenceFeature(sf); |
1173 |
|
} |
1174 |
|
|
1175 |
|
|
1176 |
|
|
1177 |
|
|
1178 |
|
|
1179 |
|
@param |
1180 |
|
@param |
1181 |
|
@param |
1182 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1183 |
5 |
private void addFeatures(SequenceI seq, String featureType, int score)... |
1184 |
|
{ |
1185 |
5 |
addFeature(seq, featureType, score++); |
1186 |
5 |
addFeature(seq, featureType, score); |
1187 |
|
} |
1188 |
|
|
1189 |
|
|
1190 |
|
|
1191 |
|
|
1192 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
1PASS
|
|
1193 |
1 |
@Test(groups = { "Functional" })... |
1194 |
|
public void testMergeDatasetsforViews() throws IOException |
1195 |
|
{ |
1196 |
|
|
1197 |
1 |
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( |
1198 |
|
"examples/testdata/projects/twoViews.jvp", DataSourceType.FILE); |
1199 |
1 |
assertNotNull(af); |
1200 |
1 |
assertTrue(af.getAlignPanels().size() > 1); |
1201 |
1 |
verifyDs(af); |
1202 |
|
} |
1203 |
|
|
1204 |
|
|
1205 |
|
|
1206 |
|
|
1207 |
|
|
1208 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
1PASS
|
|
1209 |
1 |
@Test(groups = { "Functional" })... |
1210 |
|
public void testMergeDatasetsforManyViews() throws IOException |
1211 |
|
{ |
1212 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1213 |
|
|
1214 |
|
|
1215 |
1 |
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( |
1216 |
|
"examples/testdata/projects/manyViews.jvp", |
1217 |
|
DataSourceType.FILE); |
1218 |
1 |
assertNotNull(af); |
1219 |
|
|
1220 |
1 |
AlignmentI ds = null; |
1221 |
1 |
for (AlignFrame alignFrame : Desktop.getDesktopAlignFrames()) |
1222 |
|
{ |
1223 |
3 |
if (ds == null) |
1224 |
|
{ |
1225 |
1 |
ds = verifyDs(alignFrame); |
1226 |
|
} |
1227 |
|
else |
1228 |
|
{ |
1229 |
|
|
1230 |
2 |
assertTrue(ds == verifyDs(alignFrame)); |
1231 |
|
} |
1232 |
|
} |
1233 |
|
} |
1234 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
1235 |
4 |
private AlignmentI verifyDs(AlignFrame af)... |
1236 |
|
{ |
1237 |
4 |
AlignmentI ds = null; |
1238 |
4 |
for (AlignmentViewPanel ap : af.getAlignPanels()) |
1239 |
|
{ |
1240 |
10 |
if (ds == null) |
1241 |
|
{ |
1242 |
4 |
ds = ap.getAlignment().getDataset(); |
1243 |
|
} |
1244 |
|
else |
1245 |
|
{ |
1246 |
6 |
assertTrue(ap.getAlignment().getDataset() == ds, |
1247 |
|
"Dataset was not the same for imported 2.10.5 project with several alignment views"); |
1248 |
|
} |
1249 |
|
} |
1250 |
4 |
return ds; |
1251 |
|
} |
1252 |
|
|
|
|
| 96.9% |
Uncovered Elements: 1 (32) |
Complexity: 3 |
Complexity Density: 0.11 |
1PASS
|
|
1253 |
1 |
@Test(groups = "Functional")... |
1254 |
|
public void testPcaViewAssociation() throws IOException |
1255 |
|
{ |
1256 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1257 |
1 |
final String PCAVIEWNAME = "With PCA"; |
1258 |
|
|
1259 |
1 |
File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp"); |
1260 |
|
|
1261 |
|
{ |
1262 |
1 |
String exampleFile = "examples/uniref50.fa"; |
1263 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile, |
1264 |
|
DataSourceType.FILE); |
1265 |
1 |
assertNotNull(af, "Didn't read in the example file correctly."); |
1266 |
1 |
AlignmentPanel origView = (AlignmentPanel) af.getAlignPanels().get(0); |
1267 |
1 |
AlignmentPanel newview = af.newView(PCAVIEWNAME, true); |
1268 |
|
|
1269 |
1 |
af.newView("Not the PCA View", true); |
1270 |
1 |
PCAPanel pcaPanel = new PCAPanel(origView, "BLOSUM62", |
1271 |
|
new SimilarityParams(true, true, true, false)); |
1272 |
|
|
1273 |
1 |
pcaPanel.run(); |
1274 |
|
|
1275 |
|
|
1276 |
1 |
pcaPanel.selectAssociatedView(newview); |
1277 |
|
|
1278 |
1 |
assertTrue(pcaPanel.getAlignViewport() == newview.getAlignViewport(), |
1279 |
|
"PCA should be associated with 'With PCA' view: test is broken"); |
1280 |
|
|
1281 |
|
|
1282 |
1 |
Jalview2XML jv2xml = new jalview.project.Jalview2XML(false); |
1283 |
1 |
tempfile.delete(); |
1284 |
1 |
jv2xml.saveState(tempfile); |
1285 |
1 |
assertTrue(jv2xml.errorMessage == null, |
1286 |
|
"Failed to save dummy project with PCA: test broken"); |
1287 |
|
} |
1288 |
|
|
1289 |
|
|
1290 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1291 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
1292 |
|
tempfile.getCanonicalPath(), DataSourceType.FILE); |
1293 |
1 |
JInternalFrame[] frames = Desktop.instance.getAllFrames(); |
1294 |
|
|
1295 |
|
|
1296 |
1 |
assertEquals(frames.length, 2, |
1297 |
|
"PCA and the tabbed alignment view should be the only two windows on the desktop"); |
1298 |
1 |
PCAPanel pcaPanel = (PCAPanel) frames[frames[0] == af ? 1 : 0]; |
1299 |
|
|
1300 |
1 |
AlignmentViewPanel restoredNewView = null; |
1301 |
1 |
for (AlignmentViewPanel alignpanel : Desktop.getAlignmentPanels(null)) |
1302 |
|
{ |
1303 |
3 |
if (alignpanel.getAlignViewport() == pcaPanel.getAlignViewport()) |
1304 |
|
{ |
1305 |
1 |
restoredNewView = alignpanel; |
1306 |
|
} |
1307 |
|
} |
1308 |
1 |
assertEquals(restoredNewView.getViewName(), PCAVIEWNAME); |
1309 |
1 |
assertTrue( |
1310 |
|
restoredNewView.getAlignViewport() == pcaPanel |
1311 |
|
.getAlignViewport(), |
1312 |
|
"Didn't restore correct view association for the PCA view"); |
1313 |
|
} |
1314 |
|
|
1315 |
|
|
1316 |
|
|
1317 |
|
|
1318 |
|
@throws |
1319 |
|
|
|
|
| 97.5% |
Uncovered Elements: 1 (40) |
Complexity: 2 |
Complexity Density: 0.05 |
1PASS
|
|
1320 |
1 |
@Test(groups = { "Functional" })... |
1321 |
|
public void testStoreAndRecoverGeneLocus() throws Exception |
1322 |
|
{ |
1323 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1324 |
1 |
String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA"; |
1325 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, |
1326 |
|
DataSourceType.PASTE); |
1327 |
1 |
assertNotNull(af, "Didn't read in the example file correctly."); |
1328 |
|
|
1329 |
1 |
AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0]; |
1330 |
1 |
SequenceI pep = ap.getAlignment().getSequenceAt(0); |
1331 |
1 |
SequenceI cds = ap.getAlignment().getSequenceAt(1); |
1332 |
|
|
1333 |
|
|
1334 |
|
|
1335 |
|
|
1336 |
|
|
1337 |
1 |
DBRefEntry dbref1 = new DBRefEntry("Uniprot", "1", "P30419", null); |
1338 |
1 |
pep.addDBRef(dbref1); |
1339 |
1 |
Mapping cdsmap = new Mapping(cds, |
1340 |
|
new MapList(new int[] |
1341 |
|
{ 1, 4 }, new int[] { 1, 12 }, 1, 3)); |
1342 |
1 |
DBRefEntry dbref2 = new DBRefEntry("EMBLCDS", "2", "X1235", cdsmap); |
1343 |
1 |
pep.addDBRef(dbref2); |
1344 |
1 |
Mapping locusmap = new Mapping(null, |
1345 |
|
new MapList(new int[] |
1346 |
|
{ 1, 4 }, new int[] { 2674123, 2674135 }, 1, 3)); |
1347 |
1 |
DBRefEntry dbref3 = new GeneLocus("human", "GRCh38", "5", locusmap); |
1348 |
1 |
pep.addDBRef(dbref3); |
1349 |
|
|
1350 |
1 |
File tfile = File.createTempFile("testStoreAndRecoverGeneLocus", |
1351 |
|
".jvp"); |
1352 |
1 |
try |
1353 |
|
{ |
1354 |
1 |
new Jalview2XML(false).saveState(tfile); |
1355 |
|
} catch (Throwable e) |
1356 |
|
{ |
1357 |
0 |
Assert.fail("Didn't save the state", e); |
1358 |
|
} |
1359 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1360 |
|
|
1361 |
1 |
new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), |
1362 |
|
DataSourceType.FILE); |
1363 |
1 |
AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0]; |
1364 |
1 |
SequenceI rpep = rap.getAlignment().getSequenceAt(0); |
1365 |
1 |
DBModList<DBRefEntry> dbrefs = rpep.getDBRefs(); |
1366 |
1 |
assertEquals(rpep.getName(), "P30419"); |
1367 |
1 |
assertEquals(dbrefs.size(), 3); |
1368 |
1 |
DBRefEntry dbRef = dbrefs.get(0); |
1369 |
1 |
assertFalse(dbRef instanceof GeneLocus); |
1370 |
1 |
assertNull(dbRef.getMap()); |
1371 |
1 |
assertEquals(dbRef, dbref1); |
1372 |
|
|
1373 |
|
|
1374 |
|
|
1375 |
|
|
1376 |
|
|
1377 |
1 |
dbRef = dbrefs.get(1); |
1378 |
1 |
assertFalse(dbRef instanceof GeneLocus); |
1379 |
1 |
assertTrue(dbRef.equalRef(dbref2)); |
1380 |
1 |
assertNotNull(dbRef.getMap()); |
1381 |
1 |
SequenceI rcds = rap.getAlignment().getSequenceAt(1); |
1382 |
1 |
assertSame(dbRef.getMap().getTo(), rcds); |
1383 |
|
|
1384 |
1 |
assertEquals(dbRef.getMap().getMap(), dbref2.getMap().getMap()); |
1385 |
|
|
1386 |
|
|
1387 |
|
|
1388 |
|
|
1389 |
1 |
dbRef = dbrefs.get(2); |
1390 |
1 |
assertTrue(dbRef instanceof GeneLocus); |
1391 |
1 |
assertEquals(dbRef, dbref3); |
1392 |
|
} |
1393 |
|
|
1394 |
|
|
1395 |
|
|
1396 |
|
|
1397 |
|
@throws |
1398 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (50) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
|
1399 |
1 |
@Test(groups = { "Functional" }, enabled = true)... |
1400 |
|
public void testStoreAndRecoverOverview() throws Exception |
1401 |
|
{ |
1402 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1403 |
|
|
1404 |
1 |
Cache.setProperty("SHOW_OVERVIEW", "false"); |
1405 |
1 |
Cache.setProperty(Preferences.USE_LEGACY_GAP, "false"); |
1406 |
1 |
Cache.setColourProperty(Preferences.GAP_COLOUR, Color.green); |
1407 |
1 |
Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.yellow); |
1408 |
1 |
Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "true"); |
1409 |
|
|
1410 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
1411 |
|
"examples/uniref50.fa", DataSourceType.FILE); |
1412 |
|
|
1413 |
|
|
1414 |
|
|
1415 |
|
|
1416 |
1 |
af.overviewMenuItem_actionPerformed(null); |
1417 |
1 |
OverviewPanel ov1 = af.alignPanel.getOverviewPanel(); |
1418 |
1 |
assertNotNull(ov1); |
1419 |
1 |
ov1.setFrameBounds(20, 30, 200, 400); |
1420 |
1 |
assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa"); |
1421 |
1 |
assertTrue(ov1.isShowHiddenRegions()); |
1422 |
|
|
1423 |
|
|
1424 |
|
|
1425 |
|
|
1426 |
1 |
af.newView_actionPerformed(null); |
1427 |
1 |
af.overviewMenuItem_actionPerformed(null); |
1428 |
1 |
OverviewPanel ov2 = af.alignPanel.getOverviewPanel(); |
1429 |
1 |
assertNotNull(ov2); |
1430 |
1 |
assertNotSame(ov1, ov2); |
1431 |
1 |
ov2.setFrameBounds(25, 35, 205, 405); |
1432 |
1 |
assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original"); |
1433 |
1 |
assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1"); |
1434 |
|
|
1435 |
1 |
File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp"); |
1436 |
1 |
new Jalview2XML(false).saveState(tfile); |
1437 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1438 |
|
|
1439 |
|
|
1440 |
|
|
1441 |
|
|
1442 |
1 |
Cache.setProperty("SHOW_OVERVIEW", "true"); |
1443 |
1 |
Cache.setProperty(Preferences.USE_LEGACY_GAP, "true"); |
1444 |
1 |
Cache.setColourProperty(Preferences.GAP_COLOUR, Color.blue); |
1445 |
1 |
Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.orange); |
1446 |
1 |
Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "false"); |
1447 |
|
|
1448 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), |
1449 |
|
DataSourceType.FILE); |
1450 |
|
|
1451 |
|
|
1452 |
|
|
1453 |
|
|
1454 |
1 |
af.tabSelectionChanged(1); |
1455 |
|
|
1456 |
|
|
1457 |
|
|
1458 |
|
|
1459 |
1 |
ov2 = af.alignPanel.getOverviewPanel(); |
1460 |
1 |
assertEquals(ov2.getCanvas().getGapColour(), Color.green); |
1461 |
|
|
1462 |
1 |
assertEquals(ov2.getCanvas().getResidueColour(), Color.white); |
1463 |
1 |
assertEquals(ov2.getCanvas().getHiddenColour(), Color.yellow); |
1464 |
1 |
assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1"); |
1465 |
1 |
assertEquals(ov2.getFrameBounds(), new Rectangle(25, 35, 205, 405)); |
1466 |
1 |
assertTrue(ov2.isShowHiddenRegions()); |
1467 |
|
|
1468 |
|
|
1469 |
|
|
1470 |
|
|
1471 |
1 |
af.tabSelectionChanged(0); |
1472 |
1 |
ov1 = af.alignPanel.getOverviewPanel(); |
1473 |
1 |
assertEquals(ov1.getCanvas().getGapColour(), Color.green); |
1474 |
|
|
1475 |
1 |
assertEquals(ov1.getCanvas().getResidueColour(), Color.white); |
1476 |
1 |
assertEquals(ov1.getCanvas().getHiddenColour(), Color.yellow); |
1477 |
1 |
assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original"); |
1478 |
|
|
1479 |
1 |
double scaling = jalview.gui.JvSwingUtilsTest.getScaling(ov1); |
1480 |
|
|
1481 |
|
|
1482 |
1 |
Rectangle ov1Rectangle = ov1.getFrameBounds(); |
1483 |
1 |
assertEquals(ov1Rectangle, |
1484 |
|
new Rectangle(20, 30, ov1Rectangle.width, 400)); |
1485 |
1 |
int width = ov1Rectangle.width; |
1486 |
1 |
assertTrue(width >= 200 && width <= 225, |
1487 |
|
"Rectangle width was not in the range expected (200<=width<=225; width=" |
1488 |
|
+ width + ")"); |
1489 |
1 |
assertTrue(ov1.isShowHiddenRegions()); |
1490 |
|
} |
1491 |
|
|
1492 |
|
|
1493 |
|
|
1494 |
|
|
1495 |
|
|
1496 |
|
@throws |
1497 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
|
|
1498 |
1 |
@Test(groups = { "Functional" }, enabled = true)... |
1499 |
|
public void testStoreAndRecoverNoOverview() throws Exception |
1500 |
|
{ |
1501 |
1 |
Cache.setProperty("SHOW_OVERVIEW", "false"); |
1502 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1503 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
1504 |
|
">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE); |
1505 |
|
|
1506 |
1 |
File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp"); |
1507 |
1 |
new Jalview2XML(false).saveState(tfile); |
1508 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1509 |
|
|
1510 |
1 |
Cache.setProperty("SHOW_OVERVIEW", "true"); |
1511 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), |
1512 |
|
DataSourceType.FILE); |
1513 |
|
|
1514 |
1 |
assertNull(af.alignPanel.getOverviewPanel()); |
1515 |
|
} |
1516 |
|
|
1517 |
|
|
1518 |
|
|
1519 |
|
|
1520 |
|
|
1521 |
|
@throws |
1522 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
1PASS
|
|
1523 |
1 |
@Test(groups = { "Functional" }, enabled = true)... |
1524 |
|
public void testAutoShowOverviewForLegacyProjects() throws Exception |
1525 |
|
{ |
1526 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1527 |
1 |
Cache.setProperty("SHOW_OVERVIEW", "true"); |
1528 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
1529 |
|
"examples/exampleFile.jvp", DataSourceType.FILE); |
1530 |
|
|
1531 |
1 |
Cache.setProperty("SHOW_OVERVIEW", "false"); |
1532 |
1 |
assertNotNull(af.alignPanel.getOverviewPanel()); |
1533 |
|
} |
1534 |
|
|
1535 |
|
|
1536 |
|
|
1537 |
|
|
1538 |
|
|
1539 |
|
|
1540 |
|
|
1541 |
|
|
1542 |
|
@throws |
1543 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
|
|
1544 |
0 |
@Test(groups = { "Functional" }, enabled = false)... |
1545 |
|
public void testReloadActuallyReloads() throws Exception |
1546 |
|
{ |
1547 |
0 |
Desktop.instance.closeAll_actionPerformed(null); |
1548 |
0 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
1549 |
|
"examples/exampleFile.jvp", DataSourceType.FILE); |
1550 |
0 |
af.getViewport().getColumnSelection().addElement(3); |
1551 |
0 |
af.hideSelColumns_actionPerformed(null); |
1552 |
0 |
af.newView("new", true); |
1553 |
0 |
af.reload_actionPerformed(null); |
1554 |
0 |
Thread.sleep(30); |
1555 |
|
|
1556 |
0 |
assertTrue(af.isClosed()); |
1557 |
|
} |
1558 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (31) |
Complexity: 11 |
Complexity Density: 0.58 |
1PASS
|
|
1559 |
1 |
@Test(groups = { "Functional" })... |
1560 |
|
public void testMatrixToFloatsAndBack() |
1561 |
|
{ |
1562 |
1 |
int imax = 2000; |
1563 |
1 |
int i = imax; |
1564 |
1 |
SequenceI sq = new Sequence("dummy", "SEQ"); |
1565 |
1998 |
while (sq.getLength() < i) |
1566 |
|
{ |
1567 |
1997 |
sq.setSequence(sq.getSequenceAsString() + 'Q'); |
1568 |
|
} |
1569 |
1 |
float[][] paevals = new float[i][i]; |
1570 |
2001 |
for (i = imax - 1; i >= 0; i--) |
1571 |
|
{ |
1572 |
2003000 |
for (int j = 0; j <= i; j++) |
1573 |
|
{ |
1574 |
2001000 |
paevals[i][j] = ((i - j < 2) |
1575 |
|
|| ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f; |
1576 |
2001000 |
paevals[j][i] = -paevals[i][j]; |
1577 |
|
} |
1578 |
|
} |
1579 |
1 |
PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals); |
1580 |
1 |
String content = ContactMatrix.contactToFloatString(dummyMat); |
1581 |
1 |
Assert.assertTrue(content.contains("\t1.")); |
1582 |
|
|
1583 |
1 |
float[][] vals = ContactMatrix.fromFloatStringToContacts(content, |
1584 |
|
sq.getLength(), sq.getLength()); |
1585 |
1 |
assertEquals(vals[3][4], paevals[3][4]); |
1586 |
1 |
assertEquals(vals[4][3], paevals[4][3]); |
1587 |
|
|
1588 |
|
|
1589 |
2001 |
for (i = 0; i < imax; i++) |
1590 |
|
{ |
1591 |
4002000 |
for (int j = 0; j < imax; j++) |
1592 |
|
{ |
1593 |
4000000 |
assertEquals(vals[i][j], paevals[i][j]); |
1594 |
|
} |
1595 |
|
} |
1596 |
|
} |
1597 |
|
|
|
|
| 96.8% |
Uncovered Elements: 3 (95) |
Complexity: 13 |
Complexity Density: 0.16 |
1PASS
|
|
1598 |
1 |
@Test(groups = { "Functional" })... |
1599 |
|
public void testPAEsaveRestore() throws Exception |
1600 |
|
{ |
1601 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1602 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
1603 |
|
">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE); |
1604 |
1 |
AlignmentI al = af.getViewport().getAlignment(); |
1605 |
|
|
1606 |
|
|
1607 |
1 |
SequenceI sq = al.getSequenceAt(0).getDatasetSequence(); |
1608 |
1 |
int i = sq.getLength(); |
1609 |
1 |
float[][] paevals = new float[i][i]; |
1610 |
12 |
for (i = i - 1; i >= 0; i--) |
1611 |
|
{ |
1612 |
77 |
for (int j = 0; j <= i; j++) |
1613 |
|
{ |
1614 |
66 |
paevals[i][j] = ((i - j < 2) |
1615 |
|
|| ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f; |
1616 |
66 |
paevals[j][i] = -paevals[i][j]; |
1617 |
|
} |
1618 |
|
} |
1619 |
1 |
PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals); |
1620 |
1 |
String content = ContactMatrix.contactToFloatString(dummyMat); |
1621 |
1 |
Assert.assertTrue(content.contains("\t1.")); |
1622 |
|
|
1623 |
1 |
float[][] vals = ContactMatrix.fromFloatStringToContacts(content, |
1624 |
|
sq.getLength(), sq.getLength()); |
1625 |
1 |
assertEquals(vals[3][4], paevals[3][4]); |
1626 |
1 |
assertEquals(vals[4][3], paevals[4][3]); |
1627 |
1 |
dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false, 0.5f, false)); |
1628 |
1 |
Assert.assertNotSame(dummyMat.getNewick(), ""); |
1629 |
1 |
AlignmentAnnotation paeCm = sq.addContactList(dummyMat); |
1630 |
1 |
al.addAnnotation(paeCm); |
1631 |
|
|
1632 |
1 |
for (BitSet gp : dummyMat.getGroups()) |
1633 |
|
{ |
1634 |
3 |
StringBuilder sb = new StringBuilder(); |
1635 |
3 |
for (long val : gp.toLongArray()) |
1636 |
|
{ |
1637 |
3 |
if (sb.length() > 0) |
1638 |
|
{ |
1639 |
0 |
sb.append(","); |
1640 |
|
} |
1641 |
3 |
sb.append(val); |
1642 |
|
} |
1643 |
3 |
String[] longvals = sb.toString().split(","); |
1644 |
3 |
long[] newlongvals = new long[longvals.length]; |
1645 |
6 |
for (int lv = 0; lv < longvals.length; lv++) |
1646 |
|
{ |
1647 |
3 |
try |
1648 |
|
{ |
1649 |
3 |
newlongvals[lv] = Long.valueOf(longvals[lv]); |
1650 |
|
} catch (Exception x) |
1651 |
|
{ |
1652 |
0 |
Assert.fail("failed to deserialise bitset element "); |
1653 |
|
} |
1654 |
|
} |
1655 |
3 |
BitSet newGp = BitSet.valueOf(newlongvals); |
1656 |
3 |
assertTrue(gp.equals(newGp)); |
1657 |
|
} |
1658 |
1 |
File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix", |
1659 |
|
".jvp"); |
1660 |
1 |
new Jalview2XML(false).saveState(tfile); |
1661 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1662 |
|
|
1663 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), |
1664 |
|
DataSourceType.FILE); |
1665 |
1 |
AlignmentI newAl = af.getViewport().getAlignment(); |
1666 |
1 |
SequenceI newSeq = newAl.getSequenceAt(0).getDatasetSequence(); |
1667 |
|
|
1668 |
1 |
Assert.assertEquals(newSeq.getAnnotation().length, 1); |
1669 |
1 |
Assert.assertEquals(newSeq.getAnnotation()[0].graph, paeCm.graph); |
1670 |
|
|
1671 |
|
|
1672 |
1 |
Assert.assertEquals(newSeq.getContactMaps().size(), 1); |
1673 |
|
|
1674 |
1 |
ContactMatrixI restoredMat = newSeq |
1675 |
|
.getContactMatrixFor(newSeq.getAnnotation()[0]); |
1676 |
1 |
Assert.assertNotNull(restoredMat); |
1677 |
1 |
MapList oldMap = ((MappableContactMatrixI) dummyMat).getMapFor(sq); |
1678 |
1 |
MapList newMap = ((MappableContactMatrixI) restoredMat) |
1679 |
|
.getMapFor(newSeq); |
1680 |
1 |
Assert.assertEquals(oldMap.getFromRanges(), newMap.getFromRanges()); |
1681 |
1 |
Assert.assertEquals(oldMap.getToRanges(), newMap.getToRanges()); |
1682 |
1 |
Assert.assertEquals(oldMap.getFromRatio(), newMap.getFromRatio()); |
1683 |
1 |
Assert.assertEquals(oldMap.getToRatio(), newMap.getToRatio()); |
1684 |
12 |
for (i = sq.getLength() - 1; i >= 0; i--) |
1685 |
|
{ |
1686 |
11 |
ContactListI oldCM = dummyMat.getContactList(i), |
1687 |
|
newCM = restoredMat.getContactList(i); |
1688 |
132 |
for (int j = oldCM.getContactHeight(); j >= 0; j--) |
1689 |
|
{ |
1690 |
121 |
double old_j = oldCM.getContactAt(j); |
1691 |
121 |
double new_j = newCM.getContactAt(j); |
1692 |
121 |
Assert.assertEquals(old_j, new_j); |
1693 |
|
} |
1694 |
|
} |
1695 |
1 |
Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups()); |
1696 |
1 |
Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups()); |
1697 |
1 |
Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree()); |
1698 |
1 |
Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick()); |
1699 |
|
|
1700 |
|
|
1701 |
|
|
1702 |
|
|
1703 |
1 |
AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0), |
1704 |
|
newSeq.getAnnotation()[0], null); |
1705 |
|
|
1706 |
1 |
AlignmentViewPanel newview = af.newView("copy of PAE", true); |
1707 |
|
|
1708 |
|
|
1709 |
1 |
AlignmentI newviewAl = newview.getAlignment(); |
1710 |
1 |
SequenceI newviewSeq = newviewAl.getSequenceAt(0); |
1711 |
|
|
1712 |
1 |
Assert.assertEquals(newviewSeq.getAnnotation().length, 1); |
1713 |
1 |
Assert.assertEquals(newviewSeq.getAnnotation()[0].graph, paeCm.graph); |
1714 |
|
|
1715 |
1 |
Assert.assertEquals(newviewSeq.getContactMaps().size(), 1); |
1716 |
|
|
1717 |
|
|
1718 |
1 |
ContactMatrixI newviewMat = newviewSeq |
1719 |
|
.getContactMatrixFor(newviewSeq.getAnnotation()[0]); |
1720 |
1 |
Assert.assertNotNull(newviewMat); |
1721 |
|
|
1722 |
1 |
Assert.assertTrue(newviewMat == restoredMat); |
1723 |
|
|
1724 |
|
|
1725 |
|
|
1726 |
|
|
1727 |
1 |
tfile = File.createTempFile("testStoreAndRecoverPAEmatrixTwoViews", |
1728 |
|
".jvp"); |
1729 |
1 |
new Jalview2XML(false).saveState(tfile); |
1730 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1731 |
|
|
1732 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), |
1733 |
|
DataSourceType.FILE); |
1734 |
1 |
newAl = af.getAlignPanels().get(0).getAlignment(); |
1735 |
1 |
AlignmentAnnotation view1aa = newAl.getSequenceAt(0).getAnnotation()[0]; |
1736 |
|
|
1737 |
1 |
newviewAl = af.getAlignPanels().get(1).getAlignment(); |
1738 |
1 |
AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0) |
1739 |
|
.getAnnotation()[0]; |
1740 |
|
|
1741 |
|
|
1742 |
|
|
1743 |
1 |
Assert.assertTrue(view1aa == view2aa); |
1744 |
|
|
1745 |
1 |
Assert.assertEquals( |
1746 |
|
newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1); |
1747 |
|
|
1748 |
|
|
1749 |
|
|
1750 |
|
|
1751 |
|
|
1752 |
|
|
1753 |
|
|
1754 |
|
|
1755 |
|
} |
1756 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (40) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
1757 |
1 |
@Test(groups = "Functional")... |
1758 |
|
public void testStoreAndRestoreIDwidthAndAnnotationHeight() |
1759 |
|
throws IOException |
1760 |
|
{ |
1761 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1762 |
1 |
final String SECONDVIEW = "With Diffferent IDwidth"; |
1763 |
|
|
1764 |
1 |
File tempfile = File.createTempFile("jvIdWidthStoreRestore", "jvp"); |
1765 |
|
|
1766 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
1767 |
|
"examples/exampleFile.jvp", DataSourceType.FILE); |
1768 |
1 |
assertNotNull(af, "Didn't read in the example file correctly."); |
1769 |
|
|
1770 |
|
|
1771 |
1 |
int idWidth = af.alignPanel.getAlignViewport().getIdWidth(); |
1772 |
1 |
double scaling = jalview.gui.JvSwingUtilsTest.getScaling(af.alignPanel); |
1773 |
|
|
1774 |
|
|
1775 |
1 |
int minExpectedWidth = 128; |
1776 |
1 |
int maxExpectedWidth = 144; |
1777 |
1 |
assertTrue(minExpectedWidth <= idWidth && maxExpectedWidth >= idWidth, |
1778 |
|
"Legacy project import should have fixed ID width. Not within the expected range (" |
1779 |
|
+ minExpectedWidth + "-" + maxExpectedWidth + ")"); |
1780 |
1 |
assertTrue( |
1781 |
|
af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted()); |
1782 |
|
|
1783 |
1 |
af.alignPanel.getAlignViewport().setIdWidth(100); |
1784 |
1 |
af.alignPanel.updateLayout(); |
1785 |
1 |
assertTrue( |
1786 |
|
af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted()); |
1787 |
|
|
1788 |
1 |
Jalview2XML jv2xml = new jalview.project.Jalview2XML(false); |
1789 |
1 |
tempfile.delete(); |
1790 |
1 |
jv2xml.saveState(tempfile); |
1791 |
1 |
assertTrue(jv2xml.errorMessage == null, |
1792 |
|
"Failed to save dummy project with PCA: test broken"); |
1793 |
1 |
af = null; |
1794 |
|
|
1795 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1796 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded( |
1797 |
|
tempfile.getCanonicalPath(), DataSourceType.FILE); |
1798 |
1 |
assertTrue( |
1799 |
|
af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted()); |
1800 |
1 |
assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), 100, |
1801 |
|
"New project exported and import should have adjusted ID width"); |
1802 |
|
|
1803 |
1 |
af.alignPanel.getAlignViewport().setIdWidth(100); |
1804 |
1 |
af.alignPanel.updateLayout(); |
1805 |
1 |
assertTrue( |
1806 |
|
af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted()); |
1807 |
|
|
1808 |
|
|
1809 |
1 |
af.alignPanel.getAlignViewport().setIdWidth(-1); |
1810 |
1 |
af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false); |
1811 |
1 |
af.alignPanel.updateLayout(); |
1812 |
1 |
assertFalse( |
1813 |
|
af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted()); |
1814 |
1 |
assertTrue(af.alignPanel.getAlignViewport().getIdWidth() > -1, |
1815 |
|
"New project exported and import should have adjusted ID width"); |
1816 |
|
|
1817 |
1 |
jv2xml = new jalview.project.Jalview2XML(false); |
1818 |
1 |
tempfile.delete(); |
1819 |
1 |
jv2xml.saveState(tempfile); |
1820 |
1 |
assertTrue(jv2xml.errorMessage == null, |
1821 |
|
"Failed to save dummy project with PCA: test broken"); |
1822 |
1 |
af = null; |
1823 |
|
|
1824 |
1 |
Desktop.instance.closeAll_actionPerformed(null); |
1825 |
1 |
af = new FileLoader().LoadFileWaitTillLoaded( |
1826 |
|
tempfile.getCanonicalPath(), DataSourceType.FILE); |
1827 |
1 |
assertFalse( |
1828 |
|
af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted()); |
1829 |
1 |
assertTrue(af.alignPanel.getAlignViewport().getIdWidth() > -1, |
1830 |
|
"New project exported and import should have adjusted ID width"); |
1831 |
|
} |
1832 |
|
|
1833 |
|
} |