1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
|
9 |
|
|
10 |
|
|
11 |
|
|
12 |
|
|
13 |
|
|
14 |
|
|
15 |
|
|
16 |
|
|
17 |
|
|
18 |
|
|
19 |
|
|
20 |
|
|
21 |
|
package jalview.commands; |
22 |
|
|
23 |
|
import static org.testng.AssertJUnit.assertEquals; |
24 |
|
import static org.testng.AssertJUnit.assertSame; |
25 |
|
import static org.testng.AssertJUnit.assertTrue; |
26 |
|
|
27 |
|
import jalview.commands.EditCommand.Action; |
28 |
|
import jalview.commands.EditCommand.Edit; |
29 |
|
import jalview.datamodel.Alignment; |
30 |
|
import jalview.datamodel.AlignmentI; |
31 |
|
import jalview.datamodel.Sequence; |
32 |
|
import jalview.datamodel.SequenceFeature; |
33 |
|
import jalview.datamodel.SequenceI; |
34 |
|
import jalview.datamodel.features.SequenceFeatures; |
35 |
|
import jalview.gui.JvOptionPane; |
36 |
|
|
37 |
|
import java.util.Collections; |
38 |
|
import java.util.Comparator; |
39 |
|
import java.util.List; |
40 |
|
import java.util.Map; |
41 |
|
|
42 |
|
import org.testng.Assert; |
43 |
|
import org.testng.annotations.BeforeClass; |
44 |
|
import org.testng.annotations.BeforeMethod; |
45 |
|
import org.testng.annotations.Test; |
46 |
|
|
47 |
|
|
48 |
|
|
49 |
|
|
50 |
|
@author |
51 |
|
|
52 |
|
|
|
|
| 96.9% |
Uncovered Elements: 17 (542) |
Complexity: 52 |
Complexity Density: 0.11 |
|
53 |
|
public class EditCommandTest |
54 |
|
{ |
55 |
|
private static Comparator<SequenceFeature> BY_DESCRIPTION = new Comparator<SequenceFeature>() |
56 |
|
{ |
57 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
58 |
1144 |
@Override... |
59 |
|
public int compare(SequenceFeature o1, SequenceFeature o2) |
60 |
|
{ |
61 |
1144 |
return o1.getDescription().compareTo(o2.getDescription()); |
62 |
|
} |
63 |
|
}; |
64 |
|
|
65 |
|
private EditCommand testee; |
66 |
|
|
67 |
|
private SequenceI[] seqs; |
68 |
|
|
69 |
|
private Alignment al; |
70 |
|
|
71 |
|
|
72 |
|
|
73 |
|
|
74 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
75 |
58 |
private static int func(int i)... |
76 |
|
{ |
77 |
58 |
return i * (i + 1) / 2; |
78 |
|
} |
79 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
80 |
1 |
@BeforeClass(alwaysRun = true)... |
81 |
|
public void setUpJvOptionPane() |
82 |
|
{ |
83 |
1 |
JvOptionPane.setInteractiveMode(false); |
84 |
1 |
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
85 |
|
} |
86 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
|
87 |
25 |
@BeforeMethod(alwaysRun = true)... |
88 |
|
public void setUp() |
89 |
|
{ |
90 |
25 |
testee = new EditCommand(); |
91 |
25 |
seqs = new SequenceI[4]; |
92 |
25 |
seqs[0] = new Sequence("seq0", "abcdefghjk"); |
93 |
25 |
seqs[0].setDatasetSequence(new Sequence("seq0ds", "ABCDEFGHJK")); |
94 |
25 |
seqs[1] = new Sequence("seq1", "fghjklmnopq"); |
95 |
25 |
seqs[1].setDatasetSequence(new Sequence("seq1ds", "FGHJKLMNOPQ")); |
96 |
25 |
seqs[2] = new Sequence("seq2", "qrstuvwxyz"); |
97 |
25 |
seqs[2].setDatasetSequence(new Sequence("seq2ds", "QRSTUVWXYZ")); |
98 |
25 |
seqs[3] = new Sequence("seq3", "1234567890"); |
99 |
25 |
seqs[3].setDatasetSequence(new Sequence("seq3ds", "1234567890")); |
100 |
25 |
al = new Alignment(seqs); |
101 |
25 |
al.setGapCharacter('?'); |
102 |
|
} |
103 |
|
|
104 |
|
|
105 |
|
|
106 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
1PASS
|
|
107 |
1 |
@Test(groups = { "Functional" })... |
108 |
|
public void testAppendEdit_insertGap() |
109 |
|
{ |
110 |
|
|
111 |
1 |
testee.appendEdit(Action.INSERT_GAP, seqs, 4, 3, al, true); |
112 |
1 |
assertEquals("abcd???efghjk", seqs[0].getSequenceAsString()); |
113 |
1 |
assertEquals("fghj???klmnopq", seqs[1].getSequenceAsString()); |
114 |
1 |
assertEquals("qrst???uvwxyz", seqs[2].getSequenceAsString()); |
115 |
1 |
assertEquals("1234???567890", seqs[3].getSequenceAsString()); |
116 |
|
|
117 |
|
|
118 |
|
} |
119 |
|
|
120 |
|
|
121 |
|
|
122 |
|
|
123 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
1PASS
|
|
124 |
1 |
@Test(groups = { "Functional" })... |
125 |
|
public void testAppendEdit_deleteGap() |
126 |
|
{ |
127 |
1 |
testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true); |
128 |
1 |
assertEquals("abcdhjk", seqs[0].getSequenceAsString()); |
129 |
1 |
assertEquals("fghjnopq", seqs[1].getSequenceAsString()); |
130 |
1 |
assertEquals("qrstxyz", seqs[2].getSequenceAsString()); |
131 |
1 |
assertEquals("1234890", seqs[3].getSequenceAsString()); |
132 |
|
} |
133 |
|
|
134 |
|
|
135 |
|
|
136 |
|
|
137 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
1PASS
|
|
138 |
1 |
@Test(groups = { "Functional" })... |
139 |
|
public void testCut() |
140 |
|
{ |
141 |
1 |
Edit ec = testee.new Edit(Action.CUT, seqs, 4, 3, al); |
142 |
1 |
EditCommand.cut(ec, new AlignmentI[] { al }); |
143 |
1 |
assertEquals("abcdhjk", seqs[0].getSequenceAsString()); |
144 |
1 |
assertEquals("fghjnopq", seqs[1].getSequenceAsString()); |
145 |
1 |
assertEquals("qrstxyz", seqs[2].getSequenceAsString()); |
146 |
1 |
assertEquals("1234890", seqs[3].getSequenceAsString()); |
147 |
|
|
148 |
1 |
assertEquals("efg", new String(ec.string[0])); |
149 |
1 |
assertEquals("klm", new String(ec.string[1])); |
150 |
1 |
assertEquals("uvw", new String(ec.string[2])); |
151 |
1 |
assertEquals("567", new String(ec.string[3])); |
152 |
|
|
153 |
|
} |
154 |
|
|
155 |
|
|
156 |
|
|
157 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
|
|
158 |
0 |
@Test(groups = { "Functional" }, enabled = false)... |
159 |
|
public void testPaste_undo_redo() |
160 |
|
{ |
161 |
|
|
162 |
|
|
163 |
|
|
164 |
|
|
165 |
|
|
166 |
|
|
167 |
|
|
168 |
0 |
SequenceI[] newSeqs = new SequenceI[2]; |
169 |
0 |
newSeqs[0] = new Sequence("newseq0", "ACEFKL"); |
170 |
0 |
newSeqs[1] = new Sequence("newseq1", "JWMPDH"); |
171 |
|
|
172 |
0 |
new EditCommand("Paste", Action.PASTE, newSeqs, 0, al.getWidth(), al); |
173 |
0 |
assertEquals(6, al.getSequences().size()); |
174 |
0 |
assertEquals("1234567890", seqs[3].getSequenceAsString()); |
175 |
0 |
assertEquals("ACEFKL", seqs[4].getSequenceAsString()); |
176 |
0 |
assertEquals("JWMPDH", seqs[5].getSequenceAsString()); |
177 |
|
} |
178 |
|
|
179 |
|
|
180 |
|
|
181 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
|
|
182 |
1 |
@Test(groups = { "Functional" })... |
183 |
|
public void testUndo_insertGap() |
184 |
|
{ |
185 |
|
|
186 |
1 |
testee.appendEdit(Action.INSERT_GAP, seqs, 4, 3, al, true); |
187 |
|
|
188 |
1 |
assertEquals("abcd???efghjk", seqs[0].getSequenceAsString()); |
189 |
1 |
testee.undoCommand(new AlignmentI[] { al }); |
190 |
1 |
assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); |
191 |
1 |
assertEquals("fghjklmnopq", seqs[1].getSequenceAsString()); |
192 |
1 |
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString()); |
193 |
1 |
assertEquals("1234567890", seqs[3].getSequenceAsString()); |
194 |
|
} |
195 |
|
|
196 |
|
|
197 |
|
|
198 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
|
|
199 |
1 |
@Test(groups = { "Functional" })... |
200 |
|
public void testUndo_deleteGap() |
201 |
|
{ |
202 |
1 |
testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true); |
203 |
|
|
204 |
1 |
assertEquals("abcdhjk", seqs[0].getSequenceAsString()); |
205 |
1 |
testee.undoCommand(new AlignmentI[] { al }); |
206 |
|
|
207 |
1 |
assertEquals("abcd???hjk", seqs[0].getSequenceAsString()); |
208 |
1 |
assertEquals("fghj???nopq", seqs[1].getSequenceAsString()); |
209 |
1 |
assertEquals("qrst???xyz", seqs[2].getSequenceAsString()); |
210 |
1 |
assertEquals("1234???890", seqs[3].getSequenceAsString()); |
211 |
|
} |
212 |
|
|
213 |
|
|
214 |
|
|
215 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
1PASS
|
|
216 |
1 |
@Test(groups = { "Functional" })... |
217 |
|
public void testUndo_multipleCommands() |
218 |
|
{ |
219 |
|
|
220 |
1 |
testee.appendEdit(Action.DELETE_GAP, seqs, 2, 3, al, true); |
221 |
1 |
assertEquals("abfghjk", seqs[0].getSequenceAsString()); |
222 |
1 |
assertEquals("1267890", seqs[3].getSequenceAsString()); |
223 |
|
|
224 |
|
|
225 |
1 |
testee.appendEdit(Action.INSERT_GAP, seqs, 2, 2, al, true); |
226 |
1 |
assertEquals("ab??fghjk", seqs[0].getSequenceAsString()); |
227 |
1 |
assertEquals("12??67890", seqs[3].getSequenceAsString()); |
228 |
|
|
229 |
|
|
230 |
1 |
testee.appendEdit(Action.DELETE_GAP, seqs, 3, 3, al, true); |
231 |
1 |
assertEquals("ab?hjk", seqs[0].getSequenceAsString()); |
232 |
1 |
assertEquals("12?890", seqs[3].getSequenceAsString()); |
233 |
|
|
234 |
|
|
235 |
1 |
testee.undoCommand(new AlignmentI[] { al }); |
236 |
1 |
assertEquals("ab?????hjk", seqs[0].getSequenceAsString()); |
237 |
1 |
assertEquals("12?????890", seqs[3].getSequenceAsString()); |
238 |
|
} |
239 |
|
|
240 |
|
|
241 |
|
|
242 |
|
|
243 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
1PASS
|
|
244 |
1 |
@Test(groups = { "Functional" })... |
245 |
|
public void testUndo_multipleInsertGaps() |
246 |
|
{ |
247 |
1 |
testee.appendEdit(Action.INSERT_GAP, seqs, 4, 1, al, true); |
248 |
1 |
testee.appendEdit(Action.INSERT_GAP, seqs, 5, 1, al, true); |
249 |
1 |
testee.appendEdit(Action.INSERT_GAP, seqs, 6, 1, al, true); |
250 |
|
|
251 |
|
|
252 |
1 |
testee.undoCommand(new AlignmentI[] { al }); |
253 |
1 |
assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); |
254 |
1 |
assertEquals("1234567890", seqs[3].getSequenceAsString()); |
255 |
|
|
256 |
|
} |
257 |
|
|
258 |
|
|
259 |
|
|
260 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
|
|
261 |
1 |
@Test(groups = { "Functional" })... |
262 |
|
public void testUndo_cut() |
263 |
|
{ |
264 |
1 |
testee.appendEdit(Action.CUT, seqs, 4, 3, al, true); |
265 |
|
|
266 |
1 |
assertEquals("abcdhjk", seqs[0].getSequenceAsString()); |
267 |
1 |
testee.undoCommand(new AlignmentI[] { al }); |
268 |
1 |
assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); |
269 |
1 |
assertEquals("fghjklmnopq", seqs[1].getSequenceAsString()); |
270 |
1 |
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString()); |
271 |
1 |
assertEquals("1234567890", seqs[3].getSequenceAsString()); |
272 |
|
} |
273 |
|
|
274 |
|
|
275 |
|
|
276 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
|
|
277 |
1 |
@Test(groups = { "Functional" })... |
278 |
|
public void testReplace() |
279 |
|
{ |
280 |
|
|
281 |
1 |
seqs[1].createDatasetSequence(); |
282 |
1 |
assertEquals("fghjklmnopq", seqs[1].getSequenceAsString()); |
283 |
|
|
284 |
1 |
new EditCommand("", Action.REPLACE, "Z-xY", new SequenceI[] { seqs[1] }, |
285 |
|
4, 8, al); |
286 |
1 |
assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); |
287 |
1 |
assertEquals("fghjZ-xYopq", seqs[1].getSequenceAsString()); |
288 |
|
|
289 |
1 |
assertEquals("fghjZxYopq".toUpperCase(), |
290 |
|
seqs[1].getDatasetSequence().getSequenceAsString()); |
291 |
1 |
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString()); |
292 |
1 |
assertEquals("1234567890", seqs[3].getSequenceAsString()); |
293 |
|
} |
294 |
|
|
295 |
|
|
296 |
|
|
297 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (24) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
|
|
298 |
1 |
@Test(groups = { "Functional" })... |
299 |
|
public void testReplace_withGaps() |
300 |
|
{ |
301 |
1 |
SequenceI seq = new Sequence("seq", "ABC--DEF"); |
302 |
1 |
seq.createDatasetSequence(); |
303 |
1 |
assertEquals("ABCDEF", seq.getDatasetSequence().getSequenceAsString()); |
304 |
1 |
assertEquals(1, seq.getStart()); |
305 |
1 |
assertEquals(6, seq.getEnd()); |
306 |
|
|
307 |
|
|
308 |
|
|
309 |
|
|
310 |
|
|
311 |
|
|
312 |
1 |
EditCommand edit = new EditCommand("", Action.REPLACE, "xyZ", |
313 |
|
new SequenceI[] |
314 |
|
{ seq }, 2, |
315 |
|
4, al); |
316 |
1 |
assertEquals("ABxyZ-DEF", seq.getSequenceAsString()); |
317 |
1 |
assertEquals(1, seq.getStart()); |
318 |
1 |
assertEquals(8, seq.getEnd()); |
319 |
|
|
320 |
1 |
assertEquals("ABxyZDEF".toUpperCase(), |
321 |
|
seq.getDatasetSequence().getSequenceAsString()); |
322 |
1 |
assertEquals(8, seq.getDatasetSequence().getEnd()); |
323 |
|
|
324 |
|
|
325 |
|
|
326 |
|
|
327 |
1 |
AlignmentI[] views = new AlignmentI[] |
328 |
|
{ new Alignment(new SequenceI[] { seq }) }; |
329 |
1 |
edit.undoCommand(views); |
330 |
|
|
331 |
1 |
assertEquals("ABC--DEF", seq.getSequenceAsString()); |
332 |
1 |
assertEquals("ABCDEF", seq.getDatasetSequence().getSequenceAsString()); |
333 |
1 |
assertEquals(1, seq.getStart()); |
334 |
1 |
assertEquals(6, seq.getEnd()); |
335 |
1 |
assertEquals(6, seq.getDatasetSequence().getEnd()); |
336 |
|
|
337 |
|
|
338 |
|
|
339 |
|
|
340 |
1 |
edit.doCommand(views); |
341 |
|
|
342 |
1 |
assertEquals("ABxyZ-DEF", seq.getSequenceAsString()); |
343 |
1 |
assertEquals(1, seq.getStart()); |
344 |
1 |
assertEquals(8, seq.getEnd()); |
345 |
|
|
346 |
1 |
assertEquals("ABxyZDEF".toUpperCase(), |
347 |
|
seq.getDatasetSequence().getSequenceAsString()); |
348 |
1 |
assertEquals(8, seq.getDatasetSequence().getEnd()); |
349 |
|
|
350 |
|
} |
351 |
|
|
352 |
|
|
353 |
|
|
354 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
|
355 |
1 |
@Test(groups = { "Functional" })... |
356 |
|
public void testReplaceFirstResiduesWithGaps() |
357 |
|
{ |
358 |
|
|
359 |
|
|
360 |
1 |
SequenceI dsseq = seqs[1].getDatasetSequence(); |
361 |
1 |
EditCommand edit = new EditCommand("", Action.REPLACE, "----", |
362 |
|
new SequenceI[] |
363 |
|
{ seqs[1] }, 0, 4, al); |
364 |
|
|
365 |
|
|
366 |
1 |
assertEquals("----klmnopq", seqs[1].getSequenceAsString()); |
367 |
|
|
368 |
1 |
assertTrue(dsseq == seqs[1].getDatasetSequence()); |
369 |
|
|
370 |
1 |
assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString()); |
371 |
|
|
372 |
1 |
assertEquals(5, seqs[1].getStart()); |
373 |
1 |
assertEquals(11, seqs[1].getEnd()); |
374 |
|
|
375 |
1 |
AlignmentI[] views = new AlignmentI[] { new Alignment(seqs) }; |
376 |
|
|
377 |
1 |
edit.undoCommand(views); |
378 |
|
|
379 |
|
|
380 |
1 |
assertTrue(dsseq == seqs[1].getDatasetSequence()); |
381 |
|
|
382 |
1 |
assertEquals("fghjklmnopq", seqs[1].getSequenceAsString()); |
383 |
|
|
384 |
1 |
assertEquals(1, seqs[1].getStart()); |
385 |
1 |
assertEquals(11, seqs[1].getEnd()); |
386 |
|
|
387 |
|
|
388 |
1 |
edit.undoCommand(views); |
389 |
|
|
390 |
|
|
391 |
|
|
392 |
|
|
393 |
1 |
assertEquals("----klmnopq", seqs[1].getSequenceAsString()); |
394 |
|
|
395 |
1 |
assertTrue(dsseq == seqs[1].getDatasetSequence()); |
396 |
|
|
397 |
1 |
assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString()); |
398 |
|
|
399 |
1 |
assertEquals(5, seqs[1].getStart()); |
400 |
1 |
assertEquals(11, seqs[1].getEnd()); |
401 |
|
|
402 |
|
} |
403 |
|
|
404 |
|
|
405 |
|
|
406 |
|
|
407 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (25) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
|
|
408 |
1 |
@Test(groups = { "Functional" })... |
409 |
|
public void testAddEdit_multipleInsertGap() |
410 |
|
{ |
411 |
|
|
412 |
|
|
413 |
|
|
414 |
1 |
Edit e = new EditCommand().new Edit(Action.INSERT_GAP, |
415 |
|
new SequenceI[] { seqs[0] }, 1, 1, al); |
416 |
1 |
testee.addEdit(e); |
417 |
1 |
SequenceI edited = new Sequence("seq0", "a?bcdefghjk"); |
418 |
1 |
edited.setDatasetSequence(seqs[0].getDatasetSequence()); |
419 |
1 |
e = new EditCommand().new Edit(Action.INSERT_GAP, |
420 |
|
new SequenceI[] { edited }, 2, 1, al); |
421 |
1 |
testee.addEdit(e); |
422 |
1 |
edited = new Sequence("seq0", "a??bcdefghjk"); |
423 |
1 |
edited.setDatasetSequence(seqs[0].getDatasetSequence()); |
424 |
1 |
e = new EditCommand().new Edit(Action.INSERT_GAP, |
425 |
|
new SequenceI[] { edited }, 3, 1, al); |
426 |
1 |
testee.addEdit(e); |
427 |
1 |
assertEquals(1, testee.getSize()); |
428 |
1 |
assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction()); |
429 |
1 |
assertEquals(1, testee.getEdit(0).getPosition()); |
430 |
1 |
assertEquals(3, testee.getEdit(0).getNumber()); |
431 |
|
|
432 |
|
|
433 |
|
|
434 |
|
|
435 |
1 |
e = new EditCommand().new Edit(Action.INSERT_GAP, |
436 |
|
new SequenceI[] { edited }, 5, 2, al); |
437 |
1 |
testee.addEdit(e); |
438 |
1 |
assertEquals(2, testee.getSize()); |
439 |
1 |
assertEquals(5, testee.getEdit(1).getPosition()); |
440 |
1 |
assertEquals(2, testee.getEdit(1).getNumber()); |
441 |
|
|
442 |
|
|
443 |
|
|
444 |
|
|
445 |
1 |
e = new EditCommand().new Edit(Action.DELETE_GAP, |
446 |
|
new SequenceI[] { edited }, 6, 2, al); |
447 |
1 |
testee.addEdit(e); |
448 |
1 |
assertEquals(3, testee.getSize()); |
449 |
1 |
assertEquals(Action.DELETE_GAP, testee.getEdit(2).getAction()); |
450 |
1 |
assertEquals(6, testee.getEdit(2).getPosition()); |
451 |
1 |
assertEquals(2, testee.getEdit(2).getNumber()); |
452 |
|
} |
453 |
|
|
454 |
|
|
455 |
|
|
456 |
|
|
457 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (29) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
458 |
1 |
@Test(groups = { "Functional" })... |
459 |
|
public void testAddEdit_multipleDeleteGap() |
460 |
|
{ |
461 |
|
|
462 |
|
|
463 |
|
|
464 |
1 |
seqs[0].setSequence("a???bcdefghjk"); |
465 |
1 |
Edit e = new EditCommand().new Edit(Action.DELETE_GAP, |
466 |
|
new SequenceI[] { seqs[0] }, 4, 1, al); |
467 |
1 |
testee.addEdit(e); |
468 |
1 |
assertEquals(1, testee.getSize()); |
469 |
|
|
470 |
1 |
SequenceI edited = new Sequence("seq0", "a??bcdefghjk"); |
471 |
1 |
edited.setDatasetSequence(seqs[0].getDatasetSequence()); |
472 |
1 |
e = new EditCommand().new Edit(Action.DELETE_GAP, |
473 |
|
new SequenceI[] { edited }, 3, 1, al); |
474 |
1 |
testee.addEdit(e); |
475 |
1 |
assertEquals(1, testee.getSize()); |
476 |
|
|
477 |
1 |
edited = new Sequence("seq0", "a?bcdefghjk"); |
478 |
1 |
edited.setDatasetSequence(seqs[0].getDatasetSequence()); |
479 |
1 |
e = new EditCommand().new Edit(Action.DELETE_GAP, |
480 |
|
new SequenceI[] { edited }, 2, 1, al); |
481 |
1 |
testee.addEdit(e); |
482 |
1 |
assertEquals(1, testee.getSize()); |
483 |
1 |
assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction()); |
484 |
1 |
assertEquals(2, testee.getEdit(0).getPosition()); |
485 |
1 |
assertEquals(3, testee.getEdit(0).getNumber()); |
486 |
|
|
487 |
|
|
488 |
|
|
489 |
|
|
490 |
1 |
e = new EditCommand().new Edit(Action.DELETE_GAP, |
491 |
|
new SequenceI[] { edited }, 2, 1, al); |
492 |
1 |
testee.addEdit(e); |
493 |
1 |
assertEquals(2, testee.getSize()); |
494 |
1 |
assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction()); |
495 |
1 |
assertEquals(2, testee.getEdit(1).getPosition()); |
496 |
1 |
assertEquals(1, testee.getEdit(1).getNumber()); |
497 |
|
|
498 |
|
|
499 |
|
|
500 |
|
|
501 |
1 |
e = new EditCommand().new Edit(Action.INSERT_GAP, |
502 |
|
new SequenceI[] { edited }, 1, 1, al); |
503 |
1 |
testee.addEdit(e); |
504 |
1 |
assertEquals(3, testee.getSize()); |
505 |
1 |
assertEquals(Action.INSERT_GAP, testee.getEdit(2).getAction()); |
506 |
1 |
assertEquals(1, testee.getEdit(2).getPosition()); |
507 |
1 |
assertEquals(1, testee.getEdit(2).getNumber()); |
508 |
|
} |
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
|
513 |
|
|
514 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
|
|
515 |
1 |
@Test(groups = { "Functional" })... |
516 |
|
public void testAddEdit_removeAllGaps() |
517 |
|
{ |
518 |
1 |
seqs[0].setSequence("a???bcdefghjk"); |
519 |
1 |
Edit e = new EditCommand().new Edit(Action.DELETE_GAP, |
520 |
|
new SequenceI[] { seqs[0] }, 4, 1, al); |
521 |
1 |
testee.addEdit(e); |
522 |
|
|
523 |
1 |
seqs[1].setSequence("f??ghjklmnopq"); |
524 |
1 |
Edit e2 = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[] |
525 |
|
{ seqs[1] }, 3, 1, al); |
526 |
1 |
testee.addEdit(e2); |
527 |
1 |
assertEquals(2, testee.getSize()); |
528 |
1 |
assertSame(e, testee.getEdit(0)); |
529 |
1 |
assertSame(e2, testee.getEdit(1)); |
530 |
|
} |
531 |
|
|
532 |
|
|
533 |
|
|
534 |
|
|
535 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (14) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
536 |
1 |
@Test(groups = { "Functional" })... |
537 |
|
public void testAddEdit_groupInsertGaps() |
538 |
|
{ |
539 |
|
|
540 |
|
|
541 |
|
|
542 |
1 |
Edit e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] { |
543 |
|
seqs[0], seqs[1] }, 1, 1, al); |
544 |
1 |
testee.addEdit(e); |
545 |
1 |
SequenceI seq1edited = new Sequence("seq0", "a?bcdefghjk"); |
546 |
1 |
seq1edited.setDatasetSequence(seqs[0].getDatasetSequence()); |
547 |
1 |
SequenceI seq2edited = new Sequence("seq1", "f?ghjklmnopq"); |
548 |
1 |
seq2edited.setDatasetSequence(seqs[1].getDatasetSequence()); |
549 |
1 |
e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] { |
550 |
|
seq1edited, seq2edited }, 2, 1, al); |
551 |
1 |
testee.addEdit(e); |
552 |
|
|
553 |
1 |
assertEquals(1, testee.getSize()); |
554 |
1 |
assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction()); |
555 |
1 |
assertEquals(1, testee.getEdit(0).getPosition()); |
556 |
1 |
assertEquals(2, testee.getEdit(0).getNumber()); |
557 |
1 |
assertEquals(seqs[0].getDatasetSequence(), testee.getEdit(0) |
558 |
|
.getSequences()[0].getDatasetSequence()); |
559 |
1 |
assertEquals(seqs[1].getDatasetSequence(), testee.getEdit(0) |
560 |
|
.getSequences()[1].getDatasetSequence()); |
561 |
|
} |
562 |
|
|
563 |
|
|
564 |
|
|
565 |
|
|
566 |
|
|
567 |
|
|
568 |
|
|
569 |
|
|
570 |
|
|
571 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (13) |
Complexity: 1 |
Complexity Density: 0.08 |
1PASS
|
|
572 |
1 |
@Test(groups = { "Functional" })... |
573 |
|
public void testPriorState_multipleInserts() |
574 |
|
{ |
575 |
1 |
EditCommand command = new EditCommand(); |
576 |
1 |
SequenceI seq = new Sequence("", "--A--B-CDEF"); |
577 |
1 |
SequenceI ds = new Sequence("", "ABCDEF"); |
578 |
1 |
seq.setDatasetSequence(ds); |
579 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
580 |
1 |
Edit e = command.new Edit(Action.INSERT_GAP, sqs, 1, 2, '-'); |
581 |
1 |
command.addEdit(e); |
582 |
1 |
e = command.new Edit(Action.INSERT_GAP, sqs, 4, 1, '-'); |
583 |
1 |
command.addEdit(e); |
584 |
1 |
e = command.new Edit(Action.INSERT_GAP, sqs, 0, 2, '-'); |
585 |
1 |
command.addEdit(e); |
586 |
|
|
587 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
588 |
1 |
assertEquals("ABCDEF", unwound.get(ds).getSequenceAsString()); |
589 |
|
} |
590 |
|
|
591 |
|
|
592 |
|
|
593 |
|
|
594 |
|
|
595 |
|
|
596 |
|
|
597 |
|
|
598 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
1PASS
|
|
599 |
1 |
@Test(groups = { "Functional" })... |
600 |
|
public void testPriorState_removeAllGaps() |
601 |
|
{ |
602 |
1 |
EditCommand command = new EditCommand(); |
603 |
1 |
SequenceI seq = new Sequence("", "ABC"); |
604 |
1 |
SequenceI ds = new Sequence("", "ABC"); |
605 |
1 |
seq.setDatasetSequence(ds); |
606 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
607 |
1 |
Edit e = command.new Edit(Action.DELETE_GAP, sqs, 1, 1, '-'); |
608 |
1 |
command.addEdit(e); |
609 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 2, 1, '-'); |
610 |
1 |
command.addEdit(e); |
611 |
|
|
612 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
613 |
1 |
assertEquals("A-B-C", unwound.get(ds).getSequenceAsString()); |
614 |
|
} |
615 |
|
|
616 |
|
|
617 |
|
|
618 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
|
|
619 |
1 |
@Test(groups = { "Functional" })... |
620 |
|
public void testPriorState_singleDelete() |
621 |
|
{ |
622 |
1 |
EditCommand command = new EditCommand(); |
623 |
1 |
SequenceI seq = new Sequence("", "ABCDEF"); |
624 |
1 |
SequenceI ds = new Sequence("", "ABCDEF"); |
625 |
1 |
seq.setDatasetSequence(ds); |
626 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
627 |
1 |
Edit e = command.new Edit(Action.DELETE_GAP, sqs, 2, 2, '-'); |
628 |
1 |
command.addEdit(e); |
629 |
|
|
630 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
631 |
1 |
assertEquals("AB--CDEF", unwound.get(ds).getSequenceAsString()); |
632 |
|
} |
633 |
|
|
634 |
|
|
635 |
|
|
636 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
1PASS
|
|
637 |
1 |
@Test(groups = { "Functional" })... |
638 |
|
public void testPriorState_singleInsert() |
639 |
|
{ |
640 |
1 |
EditCommand command = new EditCommand(); |
641 |
1 |
SequenceI seq = new Sequence("", "AB---CDEF"); |
642 |
1 |
SequenceI ds = new Sequence("", "ABCDEF"); |
643 |
1 |
seq.setDatasetSequence(ds); |
644 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
645 |
1 |
Edit e = command.new Edit(Action.INSERT_GAP, sqs, 2, 3, '-'); |
646 |
1 |
command.addEdit(e); |
647 |
|
|
648 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
649 |
1 |
SequenceI prior = unwound.get(ds); |
650 |
1 |
assertEquals("ABCDEF", prior.getSequenceAsString()); |
651 |
1 |
assertEquals(1, prior.getStart()); |
652 |
1 |
assertEquals(6, prior.getEnd()); |
653 |
|
} |
654 |
|
|
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
1PASS
|
|
659 |
1 |
@Test(groups = { "Functional" })... |
660 |
|
public void testPriorState_singleInsertWithOffset() |
661 |
|
{ |
662 |
1 |
EditCommand command = new EditCommand(); |
663 |
1 |
SequenceI seq = new Sequence("", "AB---CDEF", 8, 13); |
664 |
|
|
665 |
|
|
666 |
1 |
seq.createDatasetSequence(); |
667 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
668 |
1 |
Edit e = command.new Edit(Action.INSERT_GAP, sqs, 2, 3, '-'); |
669 |
1 |
command.addEdit(e); |
670 |
|
|
671 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
672 |
1 |
SequenceI prior = unwound.get(seq.getDatasetSequence()); |
673 |
1 |
assertEquals("ABCDEF", prior.getSequenceAsString()); |
674 |
1 |
assertEquals(8, prior.getStart()); |
675 |
1 |
assertEquals(13, prior.getEnd()); |
676 |
|
} |
677 |
|
|
678 |
|
|
679 |
|
|
680 |
|
|
681 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (36) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
682 |
1 |
@Test(groups = { "Functional" })... |
683 |
|
public void testPriorState_removeGapsMultipleSeqs() |
684 |
|
{ |
685 |
1 |
EditCommand command = new EditCommand(); |
686 |
1 |
String original1 = "--ABC-DEF"; |
687 |
1 |
String original2 = "FG-HI--J"; |
688 |
1 |
String original3 = "M-NOPQ"; |
689 |
|
|
690 |
|
|
691 |
|
|
692 |
|
|
693 |
1 |
SequenceI seq = new Sequence("", "ABC-DEF"); |
694 |
1 |
SequenceI ds1 = new Sequence("", "ABCDEF"); |
695 |
1 |
seq.setDatasetSequence(ds1); |
696 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
697 |
1 |
Edit e = command.new Edit(Action.DELETE_GAP, sqs, 0, 2, '-'); |
698 |
1 |
command.addEdit(e); |
699 |
1 |
seq = new Sequence("", "ABCDEF"); |
700 |
1 |
seq.setDatasetSequence(ds1); |
701 |
1 |
sqs = new SequenceI[] { seq }; |
702 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 3, 1, '-'); |
703 |
1 |
command.addEdit(e); |
704 |
|
|
705 |
|
|
706 |
|
|
707 |
|
|
708 |
1 |
seq = new Sequence("", "FGHI--J"); |
709 |
1 |
SequenceI ds2 = new Sequence("", "FGHIJ"); |
710 |
1 |
seq.setDatasetSequence(ds2); |
711 |
1 |
sqs = new SequenceI[] { seq }; |
712 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 2, 1, '-'); |
713 |
1 |
command.addEdit(e); |
714 |
1 |
seq = new Sequence("", "FGHIJ"); |
715 |
1 |
seq.setDatasetSequence(ds2); |
716 |
1 |
sqs = new SequenceI[] { seq }; |
717 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 4, 2, '-'); |
718 |
1 |
command.addEdit(e); |
719 |
|
|
720 |
|
|
721 |
|
|
722 |
|
|
723 |
1 |
seq = new Sequence("", "MNOPQ"); |
724 |
1 |
SequenceI ds3 = new Sequence("", "MNOPQ"); |
725 |
1 |
seq.setDatasetSequence(ds3); |
726 |
1 |
sqs = new SequenceI[] { seq }; |
727 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 1, 1, '-'); |
728 |
1 |
command.addEdit(e); |
729 |
|
|
730 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
731 |
1 |
assertEquals(original1, unwound.get(ds1).getSequenceAsString()); |
732 |
1 |
assertEquals(original2, unwound.get(ds2).getSequenceAsString()); |
733 |
1 |
assertEquals(original3, unwound.get(ds3).getSequenceAsString()); |
734 |
|
} |
735 |
|
|
736 |
|
|
737 |
|
|
738 |
|
|
739 |
|
|
740 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (32) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
741 |
1 |
@Test(groups = { "Functional" })... |
742 |
|
public void testPriorState_removeGappedCols() |
743 |
|
{ |
744 |
1 |
EditCommand command = new EditCommand(); |
745 |
1 |
String original1 = "--ABC--DEF"; |
746 |
1 |
String original2 = "-G-HI--J"; |
747 |
1 |
String original3 = "-M-NO--PQ"; |
748 |
|
|
749 |
|
|
750 |
|
|
751 |
|
|
752 |
1 |
SequenceI seq1 = new Sequence("", "-ABC--DEF"); |
753 |
1 |
SequenceI ds1 = new Sequence("", "ABCDEF"); |
754 |
1 |
seq1.setDatasetSequence(ds1); |
755 |
1 |
SequenceI seq2 = new Sequence("", "G-HI--J"); |
756 |
1 |
SequenceI ds2 = new Sequence("", "GHIJ"); |
757 |
1 |
seq2.setDatasetSequence(ds2); |
758 |
1 |
SequenceI seq3 = new Sequence("", "M-NO--PQ"); |
759 |
1 |
SequenceI ds3 = new Sequence("", "MNOPQ"); |
760 |
1 |
seq3.setDatasetSequence(ds3); |
761 |
1 |
SequenceI[] sqs = new SequenceI[] { seq1, seq2, seq3 }; |
762 |
1 |
Edit e = command.new Edit(Action.DELETE_GAP, sqs, 0, 1, '-'); |
763 |
1 |
command.addEdit(e); |
764 |
|
|
765 |
|
|
766 |
|
|
767 |
|
|
768 |
1 |
seq1 = new Sequence("", "-ABCDEF"); |
769 |
1 |
seq1.setDatasetSequence(ds1); |
770 |
1 |
seq2 = new Sequence("", "G-HIJ"); |
771 |
1 |
seq2.setDatasetSequence(ds2); |
772 |
1 |
seq3 = new Sequence("", "M-NOPQ"); |
773 |
1 |
seq3.setDatasetSequence(ds3); |
774 |
1 |
sqs = new SequenceI[] { seq1, seq2, seq3 }; |
775 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 4, 2, '-'); |
776 |
1 |
command.addEdit(e); |
777 |
|
|
778 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
779 |
1 |
assertEquals(original1, unwound.get(ds1).getSequenceAsString()); |
780 |
1 |
assertEquals(original2, unwound.get(ds2).getSequenceAsString()); |
781 |
1 |
assertEquals(original3, unwound.get(ds3).getSequenceAsString()); |
782 |
1 |
assertEquals(ds1, unwound.get(ds1).getDatasetSequence()); |
783 |
1 |
assertEquals(ds2, unwound.get(ds2).getDatasetSequence()); |
784 |
1 |
assertEquals(ds3, unwound.get(ds3).getDatasetSequence()); |
785 |
|
} |
786 |
|
|
787 |
|
|
788 |
|
|
789 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (39) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
790 |
1 |
@Test(groups = { "Functional" })... |
791 |
|
public void testCut_withFeatures() |
792 |
|
{ |
793 |
|
|
794 |
|
|
795 |
|
|
796 |
|
|
797 |
1 |
SequenceI seq0 = seqs[0]; |
798 |
1 |
seq0.addSequenceFeature(new SequenceFeature("before", "", 1, 3, 0f, |
799 |
|
null)); |
800 |
1 |
seq0.addSequenceFeature(new SequenceFeature("overlap left", "", 2, 6, |
801 |
|
0f, null)); |
802 |
1 |
seq0.addSequenceFeature(new SequenceFeature("internal", "", 5, 6, 0f, |
803 |
|
null)); |
804 |
1 |
seq0.addSequenceFeature(new SequenceFeature("overlap right", "", 7, 8, |
805 |
|
0f, null)); |
806 |
1 |
seq0.addSequenceFeature(new SequenceFeature("after", "", 8, 10, 0f, |
807 |
|
null)); |
808 |
|
|
809 |
|
|
810 |
|
|
811 |
|
|
812 |
1 |
SequenceFeature internalContact = new SequenceFeature("disulphide bond", "", 5, |
813 |
|
6, 0f, null); |
814 |
1 |
seq0.addSequenceFeature(internalContact); |
815 |
1 |
SequenceFeature overlapLeftContact = new SequenceFeature( |
816 |
|
"disulphide bond", "", 2, 6, 0f, null); |
817 |
1 |
seq0.addSequenceFeature(overlapLeftContact); |
818 |
1 |
SequenceFeature overlapRightContact = new SequenceFeature( |
819 |
|
"disulphide bond", "", 5, 8, 0f, null); |
820 |
1 |
seq0.addSequenceFeature(overlapRightContact); |
821 |
1 |
SequenceFeature spanningContact = new SequenceFeature( |
822 |
|
"disulphide bond", "", 2, 9, 0f, null); |
823 |
1 |
seq0.addSequenceFeature(spanningContact); |
824 |
|
|
825 |
|
|
826 |
|
|
827 |
|
|
828 |
1 |
Edit ec = testee.new Edit(Action.CUT, seqs, 3, 4, al); |
829 |
1 |
EditCommand.cut(ec, new AlignmentI[] { al }); |
830 |
|
|
831 |
1 |
List<SequenceFeature> sfs = seq0.getSequenceFeatures(); |
832 |
1 |
SequenceFeatures.sortFeatures(sfs, true); |
833 |
|
|
834 |
1 |
assertEquals(5, sfs.size()); |
835 |
1 |
SequenceFeature sf = sfs.get(0); |
836 |
1 |
assertEquals("before", sf.getType()); |
837 |
1 |
assertEquals(1, sf.getBegin()); |
838 |
1 |
assertEquals(3, sf.getEnd()); |
839 |
1 |
sf = sfs.get(1); |
840 |
1 |
assertEquals("disulphide bond", sf.getType()); |
841 |
1 |
assertEquals(2, sf.getBegin()); |
842 |
1 |
assertEquals(5, sf.getEnd()); |
843 |
1 |
sf = sfs.get(2); |
844 |
1 |
assertEquals("overlap left", sf.getType()); |
845 |
1 |
assertEquals(2, sf.getBegin()); |
846 |
1 |
assertEquals(3, sf.getEnd()); |
847 |
1 |
sf = sfs.get(3); |
848 |
1 |
assertEquals("after", sf.getType()); |
849 |
1 |
assertEquals(4, sf.getBegin()); |
850 |
1 |
assertEquals(6, sf.getEnd()); |
851 |
1 |
sf = sfs.get(4); |
852 |
1 |
assertEquals("overlap right", sf.getType()); |
853 |
1 |
assertEquals(4, sf.getBegin()); |
854 |
1 |
assertEquals(4, sf.getEnd()); |
855 |
|
} |
856 |
|
|
857 |
|
|
858 |
|
|
859 |
|
|
860 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (55) |
Complexity: 7 |
Complexity Density: 0.16 |
1PASS
|
|
861 |
1 |
@Test(groups = { "Functional" })... |
862 |
|
public void testCut_withFeatures_exhaustive() |
863 |
|
{ |
864 |
|
|
865 |
|
|
866 |
|
|
867 |
1 |
SequenceI seq0 = new Sequence("seq", "ABCDE"); |
868 |
1 |
int start = 8; |
869 |
1 |
int end = 12; |
870 |
1 |
seq0.setStart(start); |
871 |
1 |
seq0.setEnd(end); |
872 |
1 |
AlignmentI alignment = new Alignment(new SequenceI[] { seq0 }); |
873 |
1 |
alignment.setDataset(null); |
874 |
|
|
875 |
|
|
876 |
|
|
877 |
|
|
878 |
1 |
AlignmentI copy = new Alignment( |
879 |
|
new SequenceI[] |
880 |
|
{ alignment.getDataset().getSequenceAt(0).deriveSequence() }); |
881 |
1 |
SequenceI copySeq0 = copy.getSequenceAt(0); |
882 |
|
|
883 |
6 |
for (int from = start; from <= end; from++) |
884 |
|
{ |
885 |
20 |
for (int to = from; to <= end; to++) |
886 |
|
{ |
887 |
15 |
String desc = String.format("%d-%d", from, to); |
888 |
15 |
SequenceFeature sf = new SequenceFeature("test", desc, from, to, |
889 |
|
0f, null); |
890 |
15 |
sf.setValue("from", Integer.valueOf(from)); |
891 |
15 |
sf.setValue("to", Integer.valueOf(to)); |
892 |
15 |
seq0.addSequenceFeature(sf); |
893 |
|
} |
894 |
|
} |
895 |
|
|
896 |
1 |
List<SequenceFeature> sfs = seq0.getSequenceFeatures(); |
897 |
1 |
assertEquals(func(5), sfs.size()); |
898 |
1 |
assertEquals(sfs, copySeq0.getSequenceFeatures()); |
899 |
1 |
String copySequenceFeatures = copySeq0.getSequenceFeatures().toString(); |
900 |
|
|
901 |
|
|
902 |
|
|
903 |
|
|
904 |
|
|
905 |
1 |
SequenceI[] sqs = new SequenceI[] { seq0 }; |
906 |
|
|
907 |
6 |
for (int from = 0; from < seq0.getLength(); from++) |
908 |
|
{ |
909 |
20 |
for (int to = from; to < seq0.getLength(); to++) |
910 |
|
{ |
911 |
15 |
EditCommand ec = new EditCommand("Cut", Action.CUT, sqs, from, (to |
912 |
|
- from + 1), alignment); |
913 |
15 |
final String msg = String.format("Cut %d-%d ", from + 1, to + 1); |
914 |
15 |
boolean newDatasetSequence = copySeq0.getDatasetSequence() != seq0 |
915 |
|
.getDatasetSequence(); |
916 |
|
|
917 |
15 |
verifyCut(seq0, from, to, msg, start); |
918 |
|
|
919 |
|
|
920 |
|
|
921 |
|
|
922 |
15 |
assertEquals("Original dataset sequence was modified", |
923 |
|
copySequenceFeatures, |
924 |
|
copySeq0.getSequenceFeatures().toString()); |
925 |
|
|
926 |
|
|
927 |
|
|
928 |
|
|
929 |
|
|
930 |
15 |
assertEquals("Wrong Dataset size after " + msg, |
931 |
15 |
newDatasetSequence ? 2 : 1, |
932 |
|
alignment.getDataset().getHeight()); |
933 |
|
|
934 |
|
|
935 |
|
|
936 |
|
|
937 |
15 |
AlignmentI[] views = new AlignmentI[] { alignment }; |
938 |
15 |
ec.undoCommand(views); |
939 |
15 |
sfs = seq0.getSequenceFeatures(); |
940 |
15 |
assertEquals("After undo of " + msg, func(5), sfs.size()); |
941 |
15 |
verifyUndo(from, to, sfs); |
942 |
|
|
943 |
|
|
944 |
|
|
945 |
|
|
946 |
|
|
947 |
15 |
assertEquals("Original dataset sequence was modified", |
948 |
|
copySequenceFeatures, |
949 |
|
copySeq0.getSequenceFeatures().toString()); |
950 |
15 |
assertEquals("Wrong Dataset size after Undo of " + msg, 1, |
951 |
|
alignment.getDataset().getHeight()); |
952 |
|
|
953 |
|
|
954 |
|
|
955 |
|
|
956 |
15 |
ec.doCommand(views); |
957 |
15 |
verifyCut(seq0, from, to, msg, start); |
958 |
|
|
959 |
|
|
960 |
|
|
961 |
|
|
962 |
|
|
963 |
15 |
assertEquals("Original dataset sequence was modified", |
964 |
|
copySequenceFeatures, |
965 |
|
copySeq0.getSequenceFeatures().toString()); |
966 |
15 |
assertEquals("Wrong Dataset size after Redo of " + msg, |
967 |
15 |
newDatasetSequence ? 2 : 1, |
968 |
|
alignment.getDataset().getHeight()); |
969 |
|
|
970 |
|
|
971 |
|
|
972 |
|
|
973 |
15 |
ec.undoCommand(views); |
974 |
|
|
975 |
|
|
976 |
|
|
977 |
|
|
978 |
|
|
979 |
15 |
assertEquals("Original dataset sequence was modified", |
980 |
|
copySequenceFeatures, |
981 |
|
copySeq0.getSequenceFeatures().toString()); |
982 |
15 |
assertEquals("Wrong Dataset size after final Undo of " + msg, 1, |
983 |
|
alignment.getDataset().getHeight()); |
984 |
|
} |
985 |
|
} |
986 |
|
} |
987 |
|
|
988 |
|
|
989 |
|
|
990 |
|
|
991 |
|
|
992 |
|
|
993 |
|
@param |
994 |
|
@param |
995 |
|
@param |
996 |
|
@param |
997 |
|
@param |
998 |
|
|
|
|
| 86.7% |
Uncovered Elements: 2 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
999 |
30 |
protected void verifyCut(SequenceI seq0, int from, int to,... |
1000 |
|
final String msg, int seqStart) |
1001 |
|
{ |
1002 |
30 |
List<SequenceFeature> sfs; |
1003 |
30 |
sfs = seq0.getSequenceFeatures(); |
1004 |
|
|
1005 |
30 |
Collections.sort(sfs, BY_DESCRIPTION); |
1006 |
|
|
1007 |
|
|
1008 |
|
|
1009 |
|
|
1010 |
|
|
1011 |
|
|
1012 |
|
|
1013 |
|
|
1014 |
30 |
boolean datasetRetained = from == 0 || to == 4; |
1015 |
30 |
if (datasetRetained) |
1016 |
|
{ |
1017 |
|
|
1018 |
18 |
assertEquals(msg, func(5), sfs.size()); |
1019 |
|
} |
1020 |
12 |
else if (to - from == 4) |
1021 |
|
{ |
1022 |
|
|
1023 |
0 |
assertTrue(sfs.isEmpty()); |
1024 |
|
} |
1025 |
|
else |
1026 |
|
{ |
1027 |
|
|
1028 |
12 |
assertEquals(msg + "wrong number of features left", func(5) |
1029 |
|
- func(to - from + 1), sfs.size()); |
1030 |
|
} |
1031 |
|
|
1032 |
|
|
1033 |
|
|
1034 |
|
|
1035 |
30 |
for (SequenceFeature sf : sfs) |
1036 |
|
{ |
1037 |
420 |
verifyFeatureRelocation(sf, from + 1, to + 1, !datasetRetained, |
1038 |
|
seqStart); |
1039 |
|
} |
1040 |
|
} |
1041 |
|
|
1042 |
|
|
1043 |
|
|
1044 |
|
|
1045 |
|
|
1046 |
|
@param |
1047 |
|
@param |
1048 |
|
@param |
1049 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
1050 |
15 |
protected void verifyUndo(int from, int to, List<SequenceFeature> sfs)... |
1051 |
|
{ |
1052 |
15 |
for (SequenceFeature sf : sfs) |
1053 |
|
{ |
1054 |
225 |
final int oldFrom = ((Integer) sf.getValue("from")).intValue(); |
1055 |
225 |
final int oldTo = ((Integer) sf.getValue("to")).intValue(); |
1056 |
225 |
String msg = String.format( |
1057 |
|
"Undo cut of [%d-%d], feature at [%d-%d] ", from + 1, to + 1, |
1058 |
|
oldFrom, oldTo); |
1059 |
225 |
assertEquals(msg + "start", oldFrom, sf.getBegin()); |
1060 |
225 |
assertEquals(msg + "end", oldTo, sf.getEnd()); |
1061 |
|
} |
1062 |
|
} |
1063 |
|
|
1064 |
|
|
1065 |
|
|
1066 |
|
|
1067 |
|
@param |
1068 |
|
@param |
1069 |
|
|
1070 |
|
@param |
1071 |
|
|
1072 |
|
@param |
1073 |
|
@param |
1074 |
|
|
|
|
| 86.4% |
Uncovered Elements: 6 (44) |
Complexity: 12 |
Complexity Density: 0.5 |
|
1075 |
420 |
private void verifyFeatureRelocation(SequenceFeature sf, int from, int to,... |
1076 |
|
boolean newDataset, int seqStart) |
1077 |
|
{ |
1078 |
|
|
1079 |
420 |
int cutSize = to - from + 1; |
1080 |
420 |
final int oldFrom = ((Integer) sf.getValue("from")).intValue(); |
1081 |
420 |
final int oldTo = ((Integer) sf.getValue("to")).intValue(); |
1082 |
420 |
final int oldFromPosition = oldFrom - seqStart + 1; |
1083 |
420 |
final int oldToPosition = oldTo - seqStart + 1; |
1084 |
|
|
1085 |
420 |
String msg = String.format( |
1086 |
|
"Feature %s relocated to %d-%d after cut of %d-%d", |
1087 |
|
sf.getDescription(), sf.getBegin(), sf.getEnd(), from, to); |
1088 |
420 |
if (!newDataset) |
1089 |
|
{ |
1090 |
|
|
1091 |
270 |
assertEquals("0: " + msg, oldFrom, sf.getBegin()); |
1092 |
270 |
assertEquals("0: " + msg, oldTo, sf.getEnd()); |
1093 |
|
} |
1094 |
150 |
else if (oldToPosition < from) |
1095 |
|
{ |
1096 |
|
|
1097 |
30 |
assertEquals("1: " + msg, oldFrom, sf.getBegin()); |
1098 |
30 |
assertEquals("2: " + msg, oldTo, sf.getEnd()); |
1099 |
|
} |
1100 |
120 |
else if (oldFromPosition > to) |
1101 |
|
{ |
1102 |
|
|
1103 |
30 |
assertEquals("3: " + msg, newDataset ? oldFrom - cutSize : oldFrom, |
1104 |
|
sf.getBegin()); |
1105 |
30 |
assertEquals("4: " + msg, newDataset ? oldTo - cutSize : oldTo, |
1106 |
|
sf.getEnd()); |
1107 |
|
} |
1108 |
90 |
else if (oldFromPosition < from && oldToPosition > to) |
1109 |
|
{ |
1110 |
|
|
1111 |
30 |
assertEquals("5: " + msg, oldFrom, sf.getBegin()); |
1112 |
30 |
assertEquals("6: " + msg, oldTo - cutSize, sf.getEnd()); |
1113 |
|
} |
1114 |
60 |
else if (oldFromPosition < from) |
1115 |
|
{ |
1116 |
|
|
1117 |
30 |
assertEquals("7: " + msg, from - 1 + seqStart - 1, sf.getEnd()); |
1118 |
|
} |
1119 |
30 |
else if (oldToPosition > to) |
1120 |
|
{ |
1121 |
|
|
1122 |
30 |
assertEquals("8: " + msg, newDataset ? from + seqStart - 1 : to + 1, |
1123 |
|
sf.getBegin()); |
1124 |
30 |
assertEquals("9: " + msg, newDataset ? from + oldTo - to - 1 : oldTo, |
1125 |
|
sf.getEnd()); |
1126 |
|
} |
1127 |
|
else |
1128 |
|
{ |
1129 |
|
|
1130 |
0 |
Assert.fail(msg + " - should have been deleted"); |
1131 |
|
} |
1132 |
|
} |
1133 |
|
|
1134 |
|
|
1135 |
|
|
1136 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
1137 |
1 |
@Test(groups = { "Functional" })... |
1138 |
|
public void testCut_withFeatures5prime() |
1139 |
|
{ |
1140 |
1 |
SequenceI seq0 = new Sequence("seq/8-11", "A-BCC"); |
1141 |
1 |
seq0.createDatasetSequence(); |
1142 |
1 |
assertEquals(8, seq0.getStart()); |
1143 |
1 |
seq0.addSequenceFeature(new SequenceFeature("", "", 10, 11, 0f, |
1144 |
|
null)); |
1145 |
1 |
SequenceI[] seqsArray = new SequenceI[] { seq0 }; |
1146 |
1 |
AlignmentI alignment = new Alignment(seqsArray); |
1147 |
|
|
1148 |
|
|
1149 |
|
|
1150 |
|
|
1151 |
|
|
1152 |
1 |
Edit ec = testee.new Edit(Action.CUT, seqsArray, 0, 3, alignment); |
1153 |
1 |
EditCommand.cut(ec, new AlignmentI[] { alignment }); |
1154 |
|
|
1155 |
|
|
1156 |
|
|
1157 |
|
|
1158 |
1 |
assertSame(seq0, alignment.getSequenceAt(0)); |
1159 |
1 |
assertEquals(10, seq0.getStart()); |
1160 |
1 |
List<SequenceFeature> sfs = seq0.getSequenceFeatures(); |
1161 |
1 |
assertEquals(1, sfs.size()); |
1162 |
1 |
SequenceFeature sf = sfs.get(0); |
1163 |
1 |
assertEquals(10, sf.getBegin()); |
1164 |
1 |
assertEquals(11, sf.getEnd()); |
1165 |
|
} |
1166 |
|
} |