2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 import java.io.IOException;
25 import java.lang.reflect.InvocationTargetException;
26 import java.nio.file.Files;
27 import java.util.Date;
28 import java.util.HashSet;
31 import javax.swing.SwingUtilities;
33 import org.testng.Assert;
34 import org.testng.annotations.AfterClass;
35 import org.testng.annotations.AfterMethod;
36 import org.testng.annotations.BeforeClass;
37 import org.testng.annotations.DataProvider;
38 import org.testng.annotations.Test;
40 import jalview.gui.AlignFrame;
41 import jalview.gui.Desktop;
42 import jalview.gui.JvOptionPane;
43 import jalview.util.ArrayUtils;
45 public class CommandsTest
47 private static final String testfiles = "test/jalview/bin/argparser/testfiles";
49 @BeforeClass(alwaysRun = true)
50 public static void setUpBeforeClass() throws Exception
52 Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
53 Date oneHourFromNow = new Date(
54 System.currentTimeMillis() + 3600 * 1000);
55 Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
58 @AfterClass(alwaysRun = true)
59 public static void resetProps()
61 Cache.loadProperties("test/jalview/testProps.jvprops");
64 @BeforeClass(alwaysRun = true)
65 public void setUpJvOptionPane()
67 JvOptionPane.setInteractiveMode(false);
68 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
71 @AfterMethod(alwaysRun = true)
72 public void tearDown()
76 // occasionally we are blocked by Jmol redraws
77 SwingUtilities.invokeAndWait(new Runnable()
83 Desktop.closeDesktop();
86 } catch (Exception foo)
88 System.err.println("Failed during teardown with exception");
89 foo.printStackTrace();
94 public static void callJalviewMain(String[] args)
96 if (Jalview.getInstance() != null)
98 Jalview.getInstance().doMain(args);
106 /* --setprops is currently disabled so this test won't work
107 @Test(groups = "Functional")
108 public void setpropsTest()
110 final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
111 String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
112 String[] args = cmdLine.split("\\s+");
114 Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
119 @Test(groups = { "Functional", "testTask3" }, dataProvider = "cmdLines")
120 public void commandsOpenTest(String cmdLine, boolean cmdArgs,
121 int numFrames, String[] sequences)
125 String[] args = (cmdLine + " --gui").split("\\s+");
126 callJalviewMain(args);
127 Commands cmds = Jalview.getInstance().getCommands();
128 Assert.assertNotNull(cmds);
129 Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
130 "Commands were not provided in the args");
131 Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
132 "Overall command parse and operation is false");
134 Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
135 "Wrong number of AlignFrames");
137 if (sequences != null)
139 Set<String> openedSequenceNames = new HashSet<>();
140 AlignFrame[] afs = Desktop.getDesktopAlignFrames();
141 for (AlignFrame af : afs)
143 openedSequenceNames.addAll(
144 af.getViewport().getAlignment().getSequenceNames());
146 for (String sequence : sequences)
148 Assert.assertTrue(openedSequenceNames.contains(sequence),
149 "Sequence '" + sequence
150 + "' was not found in opened alignment files: "
151 + cmdLine + ".\nOpened sequence names are:\n"
152 + String.join("\n", openedSequenceNames));
157 lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
158 } catch (Exception x)
160 Assert.fail("Unexpected exception during commandsOpenTest", x);
170 { "Functional", "testTask3" },
171 dataProvider = "structureImageOutputFiles")
172 public void structureImageOutputTest(String cmdLine, String[] filenames)
175 cleanupFiles(filenames);
176 String[] args = (cmdLine + " --gui").split("\\s+");
179 callJalviewMain(args);
180 Commands cmds = Jalview.getInstance().getCommands();
181 Assert.assertNotNull(cmds);
182 File lastFile = null;
183 for (String filename : filenames)
185 File file = new File(filename);
186 Assert.assertTrue(file.exists(), "File '" + filename
187 + "' was not created by '" + cmdLine + "'");
188 Assert.assertTrue(file.isFile(), "File '" + filename
189 + "' is not a file from '" + cmdLine + "'");
190 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
191 + "' has no content from '" + cmdLine + "'");
192 // make sure the successive output files get bigger!
193 if (lastFile != null)
194 Assert.assertTrue(Files.size(file.toPath()) > Files
195 .size(lastFile.toPath()));
197 } catch (Exception x)
199 Assert.fail("Unexpected exception during structureImageOutputTest",
203 cleanupFiles(filenames);
208 @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
209 public void argFilesGlobAndSubstitutionsTest(String cmdLine,
210 String[] filenames) throws IOException
212 cleanupFiles(filenames);
213 String[] args = (cmdLine + " --gui").split("\\s+");
216 callJalviewMain(args);
217 Commands cmds = Jalview.getInstance().getCommands();
218 Assert.assertNotNull(cmds);
219 File lastFile = null;
220 for (String filename : filenames)
222 File file = new File(filename);
223 Assert.assertTrue(file.exists(), "File '" + filename
224 + "' was not created by '" + cmdLine + "'");
225 Assert.assertTrue(file.isFile(), "File '" + filename
226 + "' is not a file from '" + cmdLine + "'");
227 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
228 + "' has no content from '" + cmdLine + "'");
229 // make sure the successive output files get bigger!
230 if (lastFile != null)
231 Assert.assertTrue(Files.size(file.toPath()) > Files
232 .size(lastFile.toPath()));
234 } catch (Exception x)
237 "Unexpected exception during argFilesGlobAndSubstitutions",
241 cleanupFiles(filenames);
246 @DataProvider(name = "structureImageOutputFiles")
247 public Object[][] structureImageOutputFiles()
249 return new Object[][] {
251 { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
252 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
253 + "--structureimage=" + testfiles + "/structureimage1.png "
254 + "--open=./examples/test_fab41.result/sample.a2m "
255 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
256 + "--structureimage=" + testfiles
257 + "/structureimage2.png --scale=1.5 "
258 + "--open=./examples/test_fab41.result/sample.a2m "
259 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
260 + "--structureimage=" + testfiles
261 + "/structureimage3.png --scale=2.0 ",
263 { testfiles + "/structureimage1.png",
264 testfiles + "/structureimage2.png",
265 testfiles + "/structureimage3.png" } },
266 { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
267 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
268 + "--structureimage=" + testfiles + "/structureimage1.png "
269 + "--open=./examples/test_fab41.result/sample.a2m "
270 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
271 + "--structureimage=" + testfiles
272 + "/structureimage2.png --scale=1.5 "
273 + "--open=./examples/test_fab41.result/sample.a2m "
274 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
275 + "--structureimage=" + testfiles
276 + "/structureimage3.png --scale=2.0 ",
278 { testfiles + "/structureimage1.png",
279 testfiles + "/structureimage2.png",
280 testfiles + "/structureimage3.png" } },
288 @DataProvider(name = "argfileOutputFiles")
289 public Object[][] argfileOutputFiles()
291 return new Object[][] {
293 { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
294 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
295 testfiles + "/dir3/subdir/test0.png" } },
296 { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
297 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
298 { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
299 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
300 { "--gui --initsubstitutions --append examples/uniref50.fa --image "
301 + testfiles + "/{basename}.png",
303 { testfiles + "/uniref50.png" } },
304 { "--gui --append examples/uniref50.fa --nosubstitutions --image "
305 + testfiles + "/{basename}.png",
307 { testfiles + "/{basename}.png" } }
313 @DataProvider(name = "cmdLines")
314 public Object[][] cmdLines()
316 String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
317 "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
318 String[] t1 = new String[] { "TEST1" };
319 String[] t2 = new String[] { "TEST2" };
320 String[] t3 = new String[] { "TEST3" };
321 return new Object[][] {
324 { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
325 { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
326 { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
327 // NOTE we cannot use shell expansion in tests, so list all files!
328 { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
330 { "--append=[new]examples/uniref50*.fa", true, 2,
332 { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
333 { "examples/uniref50.fa", true, 1, someUniref50Seqs },
334 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
335 ArrayUtils.concatArrays(someUniref50Seqs, t1) },
336 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
337 { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
338 ArrayUtils.concatArrays(t1, t3) },
339 { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
340 ArrayUtils.concatArrays(t1, t2, t3) },
341 { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
342 ArrayUtils.concatArrays(t1, t2) } };
346 public static boolean lookForSequenceName(String sequenceName)
348 AlignFrame[] afs = Desktop.getDesktopAlignFrames();
349 for (AlignFrame af : afs)
351 for (String name : af.getViewport().getAlignment().getSequenceNames())
353 if (sequenceName.equals(name))
362 public static void cleanupFiles(String[] filenames)
364 for (String filename : filenames)
366 File file = new File(filename);
374 private final String deleteDir = "test/deleteAfter";
377 groups = "Functional",
378 dataProvider = "allLinkedIdsData",
379 singleThreaded = true)
380 public void allLinkedIdsTest(String cmdLine, String[] filenames,
381 String[] nonfilenames)
383 String[] args = (cmdLine + " --gui").split("\\s+");
384 callJalviewMain(args);
385 Commands cmds = Jalview.getInstance().getCommands();
386 Assert.assertNotNull(cmds);
387 for (String filename : filenames)
389 Assert.assertTrue(new File(filename).exists(),
390 "File '" + filename + "' was not created");
392 cleanupFiles(filenames);
393 if (nonfilenames != null)
395 for (String nonfilename : nonfilenames)
397 File nonfile = new File(nonfilename);
398 Assert.assertFalse(nonfile.exists(),
399 "File " + nonfilename + " exists when it shouldn't!");
403 File deleteDirF = new File(deleteDir);
404 if (deleteDirF.exists())
410 @DataProvider(name = "allLinkedIdsData")
411 public Object[][] allLinkedIdsData()
413 return new Object[][] {
415 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
417 { "test/jalview/bin/argparser/testfiles/test1.stk",
418 "test/jalview/bin/argparser/testfiles/test2.stk",
419 "test/jalview/bin/argparser/testfiles/test3.stk", },
421 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
423 { "test/jalview/bin/argparser/testfiles/test1.png",
424 "test/jalview/bin/argparser/testfiles/test2.png",
425 "test/jalview/bin/argparser/testfiles/test3.png", },
427 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
429 { "test/jalview/bin/argparser/testfiles/test1.stk",
430 "test/jalview/bin/argparser/testfiles/test2.stk",
431 "test/jalview/bin/argparser/testfiles/test3.stk", },
433 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
434 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
435 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
436 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
437 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
438 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
439 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
440 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
441 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
442 { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
444 { "test/jalview/bin/argparser/testfiles/test1.stk",
445 "test/jalview/bin/argparser/testfiles/test2.stk",
446 "test/jalview/bin/argparser/testfiles/test3.stk",
447 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
448 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
449 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
450 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
451 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
452 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
453 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
454 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
455 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
457 { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
459 { "test/jalview/bin/argparser/testfiles/test1.stk",
460 "test/jalview/bin/argparser/testfiles/test2.stk",
461 "test/jalview/bin/argparser/testfiles/test3.stk",
462 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
463 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
464 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
465 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
466 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
467 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
468 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
469 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
470 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
472 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
474 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
475 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
476 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
477 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
478 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
480 { "test/jalview/bin/argparser/testfiles/test1.stk",
481 "test/jalview/bin/argparser/testfiles/test2.stk",
482 "test/jalview/bin/argparser/testfiles/test3.stk",
483 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
484 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
485 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
486 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
487 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
489 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
490 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
491 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
493 { "test/jalview/bin/argparser/testfiles/test1.stk",
494 "test/jalview/bin/argparser/testfiles/test2.stk",
495 "test/jalview/bin/argparser/testfiles/test3.stk",
496 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
497 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
498 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
499 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
500 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
502 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
503 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
504 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
506 { "test/jalview/bin/argparser/testfiles/test1.stk",
507 "test/jalview/bin/argparser/testfiles/test2.stk",
508 "test/jalview/bin/argparser/testfiles/test3.stk",
509 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
510 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
511 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
512 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
513 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
514 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
515 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
517 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
518 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
519 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
521 { "test/jalview/bin/argparser/testfiles/test1.stk",
522 "test/jalview/bin/argparser/testfiles/test2.stk",
523 "test/jalview/bin/argparser/testfiles/test3.stk",
524 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
525 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
526 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
527 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
528 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
529 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
530 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output {dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.aln --close",
532 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
533 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
534 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
535 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
536 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
538 { "test/jalview/bin/argparser/testfiles/test1.stk",
539 "test/jalview/bin/argparser/testfiles/test2.stk",
540 "test/jalview/bin/argparser/testfiles/test3.stk",
541 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
542 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
543 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
544 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
545 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
546 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
547 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
548 "test/jalview/bin/argparser/testfiles/test1.aln",
549 "test/jalview/bin/argparser/testfiles/test2.aln",
550 "test/jalview/bin/argparser/testfiles/test3.aln",
551 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
552 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
553 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
554 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
555 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
556 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
558 { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
560 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
562 + "/{dirname}/{basename}.aln --close --all --mkdirs",
565 + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
567 + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
569 + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
571 + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
573 + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
575 { "test/jalview/bin/argparser/testfiles/test1.stk",
576 "test/jalview/bin/argparser/testfiles/test2.stk",
577 "test/jalview/bin/argparser/testfiles/test3.stk",
578 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
579 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
580 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
581 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
582 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
583 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
584 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
585 "test/jalview/bin/argparser/testfiles/test1.aln",
586 "test/jalview/bin/argparser/testfiles/test2.aln",
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